PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1S75DVP
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1S75DVP
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 41 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
Nephrin/Neph1 signaling in the kidney podocyte 230
HIF-1-alpha transcription factor network 158
TCGA08_p53 150
TCR signaling in naïve CD8+ T cells 132
FOXA2 and FOXA3 transcription factor networks 120
TCGA08_retinoblastoma 111
PDGFR-alpha signaling pathway 109
IL12-mediated signaling events 89
Aurora B signaling 89
EGFR-dependent Endothelin signaling events 81
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 506 . 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 ( 506 ).

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
Nephrin/Neph1 signaling in the kidney podocyte 0.4545 230 7830 34 -0.51 0.03 1000 -1000 -0.049 -1000
HIF-1-alpha transcription factor network 0.3123 158 12053 76 -1.1 0.046 1000 -1000 -0.16 -1000
TCGA08_p53 0.2964 150 1053 7 -0.42 0.22 1000 -1000 -0.01 -1000
TCR signaling in naïve CD8+ T cells 0.2609 132 12279 93 -0.44 0.2 1000 -1000 -0.084 -1000
FOXA2 and FOXA3 transcription factor networks 0.2372 120 5530 46 -1.1 0.036 1000 -1000 -0.12 -1000
TCGA08_retinoblastoma 0.2194 111 892 8 -0.57 0.16 1000 -1000 -0.009 -1000
PDGFR-alpha signaling pathway 0.2154 109 4837 44 -0.23 0.037 1000 -1000 -0.055 -1000
IL12-mediated signaling events 0.1759 89 7791 87 -0.44 0.12 1000 -1000 -0.12 -1000
Aurora B signaling 0.1759 89 5979 67 -0.26 0.042 1000 -1000 -0.051 -1000
EGFR-dependent Endothelin signaling events 0.1601 81 1714 21 -0.57 0.043 1000 -1000 -0.062 -1000
Glypican 1 network 0.1581 80 3862 48 -0.4 0.046 1000 -1000 -0.047 -1000
Syndecan-4-mediated signaling events 0.1522 77 5168 67 -0.44 0.089 1000 -1000 -0.07 -1000
amb2 Integrin signaling 0.1383 70 5808 82 -0.46 0.038 1000 -1000 -0.056 -1000
FOXM1 transcription factor network 0.1344 68 3470 51 -0.56 0.031 1000 -1000 -0.13 -1000
Aurora C signaling 0.1324 67 471 7 -0.26 0.027 1000 -1000 -0.019 -1000
BMP receptor signaling 0.1285 65 5319 81 -0.53 0.054 1000 -1000 -0.081 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1206 61 2034 33 -0.57 0.056 1000 -1000 -0.044 -1000
Glypican 2 network 0.1166 59 238 4 -0.04 -1000 1000 -1000 0.002 -1000
IL4-mediated signaling events 0.1146 58 5341 91 -0.79 0.49 1000 -1000 -0.11 -1000
JNK signaling in the CD4+ TCR pathway 0.1087 55 948 17 -0.22 0.03 1000 -1000 -0.042 -1000
Caspase cascade in apoptosis 0.1047 53 3941 74 -0.29 0.09 1000 -1000 -0.059 -1000
Syndecan-1-mediated signaling events 0.0988 50 1705 34 -0.25 0.03 1000 -1000 -0.069 -1000
Fc-epsilon receptor I signaling in mast cells 0.0929 47 4620 97 -0.23 0.041 1000 -1000 -0.089 -1000
HIF-2-alpha transcription factor network 0.0791 40 1762 43 -0.52 0.24 1000 -1000 -0.067 -1000
Reelin signaling pathway 0.0731 37 2109 56 -0.17 0.081 1000 -1000 -0.063 -1000
Effects of Botulinum toxin 0.0731 37 985 26 -0.24 0.04 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 0.0731 37 1172 31 -0.37 0.029 1000 -1000 -0.053 -1000
Signaling events mediated by the Hedgehog family 0.0711 36 1873 52 -0.28 0.068 1000 -1000 -0.056 -1000
Arf6 signaling events 0.0711 36 2266 62 -0.57 0.065 1000 -1000 -0.043 -1000
VEGFR1 specific signals 0.0711 36 2061 56 -0.32 0.03 1000 -1000 -0.065 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0652 33 1835 54 -0.44 0.042 1000 -1000 -0.086 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0652 33 2281 68 -0.33 0.057 1000 -1000 -0.096 -1000
p75(NTR)-mediated signaling 0.0632 32 4037 125 -0.31 0.079 1000 -1000 -0.097 -1000
PLK1 signaling events 0.0632 32 2747 85 -0.2 0.043 1000 -1000 -0.038 -1000
IL27-mediated signaling events 0.0632 32 1633 51 -0.59 0.059 1000 -1000 -0.064 -1000
IL2 signaling events mediated by STAT5 0.0613 31 697 22 -0.3 0.036 1000 -1000 -0.066 -1000
Ephrin A reverse signaling 0.0593 30 212 7 -0.023 0.012 1000 -1000 -0.016 -1000
LPA4-mediated signaling events 0.0573 29 359 12 -0.1 0.011 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 0.0573 29 2212 76 -0.85 0.054 1000 -1000 -0.04 -1000
IL23-mediated signaling events 0.0573 29 1782 60 -0.26 0.03 1000 -1000 -0.11 -1000
S1P1 pathway 0.0534 27 985 36 -0.24 0.03 1000 -1000 -0.058 -1000
IL2 signaling events mediated by PI3K 0.0474 24 1419 58 -0.3 0.047 1000 -1000 -0.06 -1000
BCR signaling pathway 0.0474 24 2403 99 -0.21 0.056 1000 -1000 -0.091 -1000
Glucocorticoid receptor regulatory network 0.0455 23 2657 114 -0.34 0.15 1000 -1000 -0.083 -1000
Wnt signaling 0.0455 23 161 7 -0.045 0.028 1000 -1000 -0.024 -1000
Regulation of Telomerase 0.0455 23 2425 102 -0.57 0.063 1000 -1000 -0.067 -1000
Signaling events mediated by PTP1B 0.0435 22 1712 76 -0.57 0.066 1000 -1000 -0.058 -1000
Ceramide signaling pathway 0.0435 22 1717 76 -0.57 0.21 1000 -1000 -0.058 -1000
FoxO family signaling 0.0435 22 1463 64 -0.55 0.095 1000 -1000 -0.061 -1000
Integrins in angiogenesis 0.0435 22 1891 84 -0.26 0.067 1000 -1000 -0.08 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0435 22 1727 78 -0.24 0.046 1000 -1000 -0.061 -1000
Noncanonical Wnt signaling pathway 0.0415 21 565 26 -0.099 0.029 1000 -1000 -0.05 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0415 21 961 45 -0.36 0.078 1000 -1000 -0.075 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0415 21 1896 88 -0.2 0.044 1000 -1000 -0.082 -1000
Visual signal transduction: Rods 0.0395 20 1064 52 -0.15 0.041 1000 -1000 -0.056 -1000
Syndecan-2-mediated signaling events 0.0356 18 1275 69 -0.46 0.063 1000 -1000 -0.048 -1000
EPO signaling pathway 0.0356 18 998 55 -0.17 0.035 1000 -1000 -0.076 -1000
Endothelins 0.0356 18 1771 96 -0.33 0.048 1000 -1000 -0.075 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0356 18 2207 120 -0.11 0.081 1000 -1000 -0.071 -1000
Regulation of nuclear SMAD2/3 signaling 0.0316 16 2201 136 -0.29 0.099 1000 -1000 -0.056 -1000
Thromboxane A2 receptor signaling 0.0316 16 1768 105 -0.57 0.047 1000 -1000 -0.065 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0316 16 1203 74 -0.57 0.1 1000 -1000 -0.084 -1000
Presenilin action in Notch and Wnt signaling 0.0296 15 915 61 -0.14 0.083 1000 -1000 -0.07 -1000
LPA receptor mediated events 0.0296 15 1592 102 -0.25 0.052 1000 -1000 -0.077 -1000
IL6-mediated signaling events 0.0296 15 1199 75 -0.22 0.059 1000 -1000 -0.063 -1000
Class I PI3K signaling events 0.0296 15 1095 73 -0.3 0.079 1000 -1000 -0.059 -1000
Aurora A signaling 0.0277 14 869 60 -0.15 0.063 1000 -1000 -0.039 -1000
IFN-gamma pathway 0.0277 14 953 68 -0.24 0.042 1000 -1000 -0.091 -1000
S1P5 pathway 0.0257 13 227 17 -0.072 0.029 1000 -1000 -0.033 -1000
Nongenotropic Androgen signaling 0.0257 13 678 52 -0.11 0.045 1000 -1000 -0.049 -1000
Plasma membrane estrogen receptor signaling 0.0257 13 1122 86 -0.15 0.053 1000 -1000 -0.085 -1000
PLK2 and PLK4 events 0.0237 12 38 3 0.005 0.026 1000 -1000 -0.015 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0237 12 467 37 -0.17 0.058 1000 -1000 -0.059 -1000
FAS signaling pathway (CD95) 0.0237 12 581 47 -0.28 0.049 1000 -1000 -0.043 -1000
Canonical Wnt signaling pathway 0.0237 12 646 51 -0.14 0.096 1000 -1000 -0.067 -1000
S1P3 pathway 0.0237 12 527 42 -0.24 0.052 1000 -1000 -0.045 -1000
Regulation of Androgen receptor activity 0.0237 12 889 70 -0.91 0.054 1000 -1000 -0.073 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0217 11 308 28 -0.072 0.05 1000 -1000 -0.04 -1000
Signaling events regulated by Ret tyrosine kinase 0.0217 11 957 82 -0.029 0.03 1000 -1000 -0.098 -1000
Signaling mediated by p38-alpha and p38-beta 0.0217 11 497 44 -0.038 0.055 1000 -1000 -0.042 -1000
TCGA08_rtk_signaling 0.0217 11 295 26 -0.23 0.057 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0198 10 733 69 -0.16 0.095 1000 -1000 -0.064 -1000
S1P4 pathway 0.0198 10 250 25 -0.072 0.039 1000 -1000 -0.046 -1000
E-cadherin signaling events 0.0198 10 54 5 0.007 0.025 1000 -1000 -0.003 -1000
a4b1 and a4b7 Integrin signaling 0.0178 9 45 5 0.01 0.029 1000 -1000 -0.004 -1000
Syndecan-3-mediated signaling events 0.0178 9 345 35 -0.012 0.079 1000 -1000 -0.042 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0178 9 1206 125 -0.24 0.044 1000 -1000 -0.078 -1000
ceramide signaling pathway 0.0158 8 436 49 -0.066 0.045 1000 -1000 -0.062 -1000
Visual signal transduction: Cones 0.0138 7 294 38 -0.013 0.045 1000 -1000 -0.023 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0138 7 671 85 -0.039 0.084 1000 -1000 -0.064 -1000
mTOR signaling pathway 0.0138 7 382 53 -0.063 0.053 1000 -1000 -0.059 -1000
Ephrin B reverse signaling 0.0138 7 355 48 -0.049 0.054 1000 -1000 -0.047 -1000
Canonical NF-kappaB pathway 0.0119 6 259 39 -0.12 0.057 1000 -1000 -0.07 -1000
IL1-mediated signaling events 0.0119 6 398 62 -0.042 0.065 1000 -1000 -0.084 -1000
E-cadherin signaling in the nascent adherens junction 0.0119 6 474 76 -0.033 0.051 1000 -1000 -0.086 -1000
Signaling events mediated by PRL 0.0119 6 212 34 -0.046 0.062 1000 -1000 -0.061 -1000
ErbB2/ErbB3 signaling events 0.0099 5 348 65 -0.13 0.042 1000 -1000 -0.062 -1000
Cellular roles of Anthrax toxin 0.0099 5 204 39 -0.01 0.039 1000 -1000 -0.031 -1000
Insulin-mediated glucose transport 0.0099 5 180 32 -0.043 0.057 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class III 0.0099 5 222 40 -0.054 0.055 1000 -1000 -0.025 -1000
EPHB forward signaling 0.0099 5 467 85 -0.053 0.075 1000 -1000 -0.093 -1000
PDGFR-beta signaling pathway 0.0099 5 493 97 -0.016 0.086 1000 -1000 -0.081 -1000
Class IB PI3K non-lipid kinase events 0.0099 5 15 3 -0.023 0.023 1000 -1000 -0.003 -1000
p38 MAPK signaling pathway 0.0099 5 246 44 -0.065 0.057 1000 -1000 -0.05 -1000
Ras signaling in the CD4+ TCR pathway 0.0099 5 99 17 -0.01 0.054 1000 -1000 -0.036 -1000
Regulation of p38-alpha and p38-beta 0.0079 4 246 54 -0.022 0.067 1000 -1000 -0.067 -1000
Arf6 trafficking events 0.0079 4 301 71 -0.12 0.061 1000 -1000 -0.044 -1000
E-cadherin signaling in keratinocytes 0.0079 4 208 43 -0.22 0.042 1000 -1000 -0.055 -1000
BARD1 signaling events 0.0059 3 220 57 -0.097 0.076 1000 -1000 -0.073 -1000
Hedgehog signaling events mediated by Gli proteins 0.0059 3 218 65 -0.007 0.1 1000 -1000 -0.065 -1000
Class I PI3K signaling events mediated by Akt 0.0059 3 218 68 -0.043 0.056 1000 -1000 -0.053 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0059 3 178 52 -0.014 0.099 1000 -1000 -0.046 -1000
Signaling mediated by p38-gamma and p38-delta 0.0059 3 57 15 0 0.031 1000 -1000 -0.045 -1000
Insulin Pathway 0.0059 3 286 74 -0.032 0.08 1000 -1000 -0.08 -1000
Osteopontin-mediated events 0.0040 2 95 38 0 0.087 1000 -1000 -0.074 -1000
Arf6 downstream pathway 0.0040 2 122 43 -0.048 0.049 1000 -1000 -0.034 -1000
Nectin adhesion pathway 0.0040 2 153 63 0 0.058 1000 -1000 -0.07 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0040 2 223 83 -0.043 0.074 1000 -1000 -0.064 -1000
Retinoic acid receptors-mediated signaling 0.0040 2 123 58 -0.014 0.053 1000 -1000 -0.052 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 72 36 -0.052 0.055 1000 -1000 -0.072 -1000
IGF1 pathway 0.0040 2 136 57 -0.048 0.078 1000 -1000 -0.089 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0020 1 23 23 -0.027 0.056 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class II 0.0020 1 110 75 -0.041 0.063 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class I 0.0020 1 177 104 -0.057 0.075 1000 -1000 -0.053 -1000
Atypical NF-kappaB pathway 0.0020 1 60 31 0 0.037 1000 -1000 -0.047 -1000
Arf1 pathway 0.0020 1 73 54 0 0.05 1000 -1000 -0.032 -1000
Circadian rhythm pathway 0.0000 0 21 22 -0.014 0.069 1000 -1000 -0.04 -1000
TRAIL signaling pathway 0.0000 0 33 48 0 0.072 1000 -1000 -0.053 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 2 27 0 0.07 1000 -1000 -0.056 -1000
Rapid glucocorticoid signaling 0.0000 0 8 20 -0.007 0.036 1000 -1000 -0.009 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 0 0.062 1000 -1000 -0.007 -1000
Total NA 3559 192991 7203 -30 -990 131000 -131000 -7.6 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.39 0.23 0.53 369 -10000 0 369
KIRREL -0.058 0.081 -10000 0 -0.62 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.4 0.23 -10000 0 -0.53 369 369
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARRB2 0.028 0.033 -10000 0 -0.7 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.42 0.28 -10000 0 -0.54 390 390
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.34 0.24 -10000 0 -0.57 216 216
FYN -0.4 0.26 0.26 1 -0.51 394 395
mol:Ca2+ -0.41 0.28 -10000 0 -0.53 388 388
mol:DAG -0.41 0.28 -10000 0 -0.54 388 388
NPHS2 -0.34 0.33 -10000 0 -0.69 231 231
mol:IP3 -0.41 0.28 -10000 0 -0.54 388 388
regulation of endocytosis -0.37 0.25 -10000 0 -0.5 347 347
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.28 -10000 0 -0.54 394 394
establishment of cell polarity -0.39 0.23 -10000 0 -0.53 369 369
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.27 -10000 0 -0.65 204 204
Nephrin/NEPH1/beta Arrestin2 -0.38 0.26 -10000 0 -0.51 347 347
NPHS1 -0.51 0.29 -10000 0 -0.67 382 382
Nephrin/NEPH1/podocin -0.4 0.26 -10000 0 -0.51 394 394
TJP1 0.03 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.031 -10000 0 -0.64 1 1
NCK2 0.029 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.41 0.28 -10000 0 -0.54 388 388
CD2AP 0.029 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.28 -10000 0 -0.54 388 388
GRB2 0.029 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.39 0.26 0.28 1 -0.5 388 389
cytoskeleton organization -0.43 0.29 -10000 0 -0.58 349 349
Nephrin/NEPH1 -0.29 0.17 -10000 0 -0.38 369 369
Nephrin/NEPH1/ZO-1 -0.32 0.2 -10000 0 -0.43 367 367
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.85 0.49 -10000 0 -1.3 241 241
HDAC7 0.027 0.01 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.62 0.32 -10000 0 -0.92 192 192
SMAD4 0.031 0.005 -10000 0 -10000 0 0
ID2 -0.85 0.48 -10000 0 -1.3 240 240
AP1 0.029 0.079 -10000 0 -0.46 12 12
ABCG2 -0.85 0.49 -10000 0 -1.3 241 241
HIF1A -0.11 0.075 -10000 0 -0.77 2 2
TFF3 -0.86 0.49 -10000 0 -1.3 241 241
GATA2 0.014 0.095 -10000 0 -0.61 11 11
AKT1 -0.099 0.062 -10000 0 -0.31 1 1
response to hypoxia -0.12 0.062 -10000 0 -0.39 5 5
MCL1 -0.85 0.49 -10000 0 -1.3 241 241
NDRG1 -0.85 0.48 -10000 0 -1.3 232 232
SERPINE1 -0.87 0.52 -10000 0 -1.3 244 244
FECH -0.85 0.48 -10000 0 -1.3 242 242
FURIN -0.85 0.49 -10000 0 -1.3 241 241
NCOA2 0.015 0.079 -10000 0 -0.64 7 7
EP300 -0.1 0.078 -10000 0 -0.36 11 11
HMOX1 -0.86 0.5 -10000 0 -1.3 235 235
BHLHE40 -0.85 0.49 -10000 0 -1.3 239 239
BHLHE41 -0.91 0.52 -10000 0 -1.3 258 258
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.097 0.085 -10000 0 -0.54 2 2
ENG -0.082 0.088 0.43 1 -0.49 2 3
JUN 0.029 0.007 -10000 0 -10000 0 0
RORA -0.85 0.49 -10000 0 -1.3 240 240
ABCB1 -0.27 0.39 -10000 0 -1.3 63 63
TFRC -0.85 0.49 -10000 0 -1.3 239 239
CXCR4 -0.92 0.53 -10000 0 -1.3 273 273
TF -0.9 0.53 -10000 0 -1.3 247 247
CITED2 -0.85 0.48 -10000 0 -1.3 243 243
HIF1A/ARNT -1 0.72 -10000 0 -1.5 277 277
LDHA -0.08 0.12 -10000 0 -0.78 12 12
ETS1 -0.85 0.49 -10000 0 -1.3 240 240
PGK1 -0.85 0.49 -10000 0 -1.3 240 240
NOS2 -0.85 0.49 -10000 0 -1.3 241 241
ITGB2 -0.89 0.52 -10000 0 -1.3 256 256
ALDOA -0.85 0.48 -10000 0 -1.3 233 233
Cbp/p300/CITED2 -0.85 0.48 -10000 0 -1.3 245 245
FOS 0.012 0.1 -10000 0 -0.63 12 12
HK2 -1 0.53 -10000 0 -1.4 306 306
SP1 0.023 0.043 -10000 0 -10000 0 0
GCK -0.17 0.16 -10000 0 -0.96 9 9
HK1 -0.85 0.49 -10000 0 -1.3 234 234
NPM1 -0.82 0.49 -10000 0 -1.3 229 229
EGLN1 -0.85 0.49 -10000 0 -1.3 240 240
CREB1 0.036 0.01 -10000 0 -10000 0 0
PGM1 -0.85 0.48 -10000 0 -1.3 234 234
SMAD3 0.031 0.003 -10000 0 -10000 0 0
EDN1 -0.11 0.14 -10000 0 -0.62 16 16
IGFBP1 -0.89 0.53 -10000 0 -1.3 242 242
VEGFA -0.66 0.34 -10000 0 -1 200 200
HIF1A/JAB1 -0.062 0.058 -10000 0 -0.58 2 2
CP -1 0.53 -10000 0 -1.4 309 309
CXCL12 -0.86 0.49 -10000 0 -1.3 243 243
COPS5 0.025 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.046 0.009 -10000 0 -10000 0 0
BNIP3 -0.85 0.48 -10000 0 -1.3 239 239
EGLN3 -1.1 0.49 -10000 0 -1.4 328 328
CA9 -1.1 0.47 -10000 0 -1.4 336 336
TERT -0.87 0.5 -10000 0 -1.3 249 249
ENO1 -0.85 0.48 -10000 0 -1.3 243 243
PFKL -0.85 0.49 -10000 0 -1.3 243 243
NCOA1 0.029 0.006 -10000 0 -10000 0 0
ADM -0.9 0.52 -10000 0 -1.3 252 252
ARNT -0.11 0.056 -10000 0 -10000 0 0
HNF4A -0.018 0.18 -10000 0 -0.64 37 37
ADFP -0.86 0.48 -10000 0 -1.2 258 258
SLC2A1 -0.57 0.3 -10000 0 -0.92 132 132
LEP -0.86 0.5 -10000 0 -1.3 250 250
HIF1A/ARNT/Cbp/p300 -0.64 0.32 -10000 0 -0.94 192 192
EPO -0.53 0.32 -10000 0 -0.89 173 173
CREBBP -0.1 0.078 -10000 0 -0.36 9 9
HIF1A/ARNT/Cbp/p300/HDAC7 -0.66 0.35 -10000 0 -1 180 180
PFKFB3 -0.85 0.49 -10000 0 -1.3 235 235
NT5E -0.85 0.49 -10000 0 -1.3 231 231
TCGA08_p53

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
CDKN2A -0.42 0.099 0.18 3 -0.44 477 480
TP53 -0.12 0.075 -10000 0 -0.37 32 32
Senescence -0.12 0.074 -10000 0 -0.36 32 32
Apoptosis -0.12 0.074 -10000 0 -0.36 32 32
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.22 0.092 0.23 477 -10000 0 477
MDM4 0.029 0.006 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.24 0.3 0.3 5 -0.58 198 203
FYN -0.3 0.39 0.44 12 -0.72 205 217
LAT/GRAP2/SLP76 -0.29 0.34 0.38 3 -0.66 203 206
IKBKB 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.2 0.29 0.45 20 -0.49 209 229
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.055 0.086 0.17 9 -0.18 58 67
MAP3K8 0.027 0.039 -10000 0 -0.59 2 2
mol:Ca2+ -0.088 0.054 0.071 11 -0.13 271 282
integrin-mediated signaling pathway 0.026 0.07 -10000 0 -0.37 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.31 0.41 0.5 15 -0.73 221 236
TRPV6 -0.44 0.42 0.7 43 -0.64 385 428
CD28 -0.019 0.16 -10000 0 -0.59 37 37
SHC1 -0.32 0.39 0.42 6 -0.73 220 226
receptor internalization -0.35 0.41 0.47 1 -0.77 225 226
PRF1 -0.33 0.43 -10000 0 -0.88 159 159
KRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.15 0.23 0.42 18 -0.39 191 209
LAT -0.38 0.44 0.5 6 -0.81 227 233
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.59 222 222
CD3E -0.22 0.31 -10000 0 -0.6 200 200
CD3G -0.22 0.3 -10000 0 -0.59 197 197
RASGRP2 -0.014 0.029 0.1 3 -0.12 3 6
RASGRP1 -0.17 0.29 0.48 23 -0.47 195 218
HLA-A 0.024 0.029 -10000 0 -0.6 1 1
RASSF5 0.01 0.1 -10000 0 -0.59 15 15
RAP1A/GTP/RAPL 0.026 0.07 -10000 0 -0.37 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.007 0.14 0.25 56 -0.14 4 60
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.12 0.12 -10000 0 -0.28 135 135
PRKCA -0.11 0.17 0.19 29 -0.3 162 191
GRAP2 -0.012 0.16 -10000 0 -0.59 34 34
mol:IP3 -0.14 0.3 0.25 136 -0.46 191 327
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.3 0.37 0.26 1 -0.7 218 219
ORAI1 0.2 0.26 0.67 6 -0.56 43 49
CSK -0.34 0.39 0.37 5 -0.74 221 226
B7 family/CD28 -0.36 0.45 0.32 2 -0.82 212 214
CHUK 0.029 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.39 0.45 -10000 0 -0.85 224 224
PTPN6 -0.32 0.39 0.28 2 -0.74 210 212
VAV1 -0.37 0.44 0.53 4 -0.8 225 229
Monovalent TCR/CD3 -0.26 0.32 -10000 0 -0.61 216 216
CBL 0.028 0.03 -10000 0 -0.64 1 1
LCK -0.31 0.41 0.44 11 -0.75 207 218
PAG1 -0.34 0.39 0.3 3 -0.74 222 225
RAP1A 0.029 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.36 0.44 -10000 0 -0.82 223 223
CD80 -0.11 0.26 -10000 0 -0.59 112 112
CD86 -0.073 0.23 -10000 0 -0.59 80 80
PDK1/CARD11/BCL10/MALT1 -0.14 0.16 0.17 1 -0.33 158 159
HRAS 0.029 0.028 -10000 0 -0.59 1 1
GO:0035030 -0.29 0.34 0.42 3 -0.65 212 215
CD8A -0.25 0.31 -10000 0 -0.59 226 226
CD8B -0.2 0.3 -10000 0 -0.6 179 179
PTPRC -0.039 0.19 -10000 0 -0.59 53 53
PDK1/PKC theta -0.24 0.36 0.56 21 -0.61 209 230
CSK/PAG1 -0.32 0.38 0.41 5 -0.72 217 222
SOS1 0.029 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.034 0.027 -10000 0 -0.45 1 1
GRAP2/SLP76 -0.31 0.38 0.34 1 -0.72 210 211
STIM1 0.11 0.11 0.95 1 -0.6 3 4
RAS family/GTP -0.037 0.14 0.33 28 -0.18 27 55
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.38 0.44 0.47 1 -0.83 225 226
mol:DAG -0.18 0.22 0.14 2 -0.42 204 206
RAP1A/GDP 0.002 0.084 0.2 32 -10000 0 32
PLCG1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.17 0.29 -10000 0 -0.59 160 160
cytotoxic T cell degranulation -0.31 0.41 0.41 1 -0.82 165 166
RAP1A/GTP -0.005 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.24 0.33 0.49 15 -0.58 219 234
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.21 0.39 0.28 81 -0.63 201 282
NRAS 0.029 0.005 -10000 0 -10000 0 0
ZAP70 -0.3 0.31 -10000 0 -0.59 265 265
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.3 0.33 0.31 1 -0.65 209 210
MALT1 0.029 0.005 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
CD8 heterodimer -0.3 0.39 -10000 0 -0.7 232 232
CARD11 -0.093 0.24 -10000 0 -0.59 97 97
PRKCB -0.12 0.16 0.18 27 -0.3 166 193
PRKCE -0.11 0.16 0.18 28 -0.3 164 192
PRKCQ -0.3 0.4 0.5 19 -0.7 216 235
LCP2 -0.014 0.14 -10000 0 -0.59 30 30
BCL10 0.029 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.16 0.25 0.44 20 -0.41 207 227
IKK complex -0.003 0.15 0.28 62 -0.13 5 67
RAS family/GDP -0.012 0.013 -10000 0 -10000 0 0
MAP3K14 -0.11 0.18 0.37 17 -0.3 162 179
PDPK1 -0.18 0.28 0.49 21 -0.46 204 225
TCR/CD3/MHC I/CD8/Fyn -0.36 0.44 0.43 1 -0.83 220 221
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.44 0.42 -10000 0 -1 129 129
PCK1 -0.91 0.67 -10000 0 -1.4 271 271
HNF4A -0.53 0.49 -10000 0 -1.2 119 119
KCNJ11 -0.45 0.45 -10000 0 -1.1 124 124
AKT1 -0.2 0.2 -10000 0 -0.6 33 33
response to starvation -0.015 0.027 -10000 0 -10000 0 0
DLK1 -0.54 0.52 -10000 0 -1.1 167 167
NKX2-1 -0.079 0.19 0.45 1 -0.65 10 11
ACADM -0.44 0.42 -10000 0 -1 127 127
TAT -0.48 0.31 -10000 0 -0.79 194 194
CEBPB -0.023 0.094 -10000 0 -0.64 9 9
CEBPA -0.023 0.095 -10000 0 -0.62 10 10
TTR -0.84 0.46 -10000 0 -1.1 325 325
PKLR -0.48 0.49 -10000 0 -1.2 130 130
APOA1 -0.54 0.49 -10000 0 -1.3 113 113
CPT1C -0.44 0.42 -10000 0 -1 128 128
ALAS1 -0.22 0.21 -10000 0 -0.7 18 18
TFRC -0.63 0.4 -10000 0 -0.94 258 258
FOXF1 0.019 0.077 -10000 0 -0.57 8 8
NF1 0.036 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.011 0.084 -10000 0 -0.6 5 5
CPT1A -0.44 0.42 -10000 0 -1 123 123
HMGCS1 -0.43 0.42 -10000 0 -1 122 122
NR3C1 0.006 0.058 -10000 0 -0.67 1 1
CPT1B -0.45 0.43 -10000 0 -1 131 131
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.03 0.007 -10000 0 -10000 0 0
GCK -0.43 0.43 -10000 0 -1 120 120
CREB1 -0.038 0.08 -10000 0 -0.31 2 2
IGFBP1 -0.25 0.32 -10000 0 -0.77 102 102
PDX1 -0.19 0.2 -10000 0 -0.82 10 10
UCP2 -0.44 0.42 -10000 0 -1 126 126
ALDOB -0.88 0.57 -10000 0 -1.2 362 362
AFP -0.64 0.44 -10000 0 -0.86 312 312
BDH1 -0.57 0.51 -10000 0 -1.1 193 193
HADH -0.44 0.43 -10000 0 -1.1 120 120
F2 -0.59 0.51 -10000 0 -1.2 146 146
HNF1A -0.011 0.084 -10000 0 -0.6 5 5
G6PC -0.77 0.63 -10000 0 -1.4 234 234
SLC2A2 -0.31 0.44 -10000 0 -1.5 46 46
INS 0.001 0.062 -10000 0 -10000 0 0
FOXA1 -0.32 0.28 -10000 0 -0.68 151 151
FOXA3 -0.56 0.31 -10000 0 -0.7 365 365
FOXA2 -0.51 0.5 -10000 0 -1.2 130 130
ABCC8 -0.45 0.44 -10000 0 -1.1 117 117
ALB -1.1 0.44 -10000 0 -1.2 433 433
TCGA08_retinoblastoma

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
CDKN2B 0.025 0.069 -10000 0 -0.59 6 6
CDKN2C 0.078 0.023 -10000 0 -10000 0 0
CDKN2A -0.57 0.13 -10000 0 -0.6 477 477
CCND2 0.14 0.055 0.22 89 -10000 0 89
RB1 -0.15 0.064 0.28 1 -0.24 89 90
CDK4 0.16 0.064 0.3 53 -10000 0 53
CDK6 0.15 0.066 0.25 85 -0.16 1 86
G1/S progression 0.15 0.064 0.24 90 -0.28 1 91
PDGFR-alpha signaling pathway

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
PDGFRA -0.23 0.32 -10000 0 -0.63 193 193
PDGF/PDGFRA/CRKL -0.15 0.24 -10000 0 -0.46 187 187
positive regulation of JUN kinase activity -0.084 0.2 -10000 0 -0.35 168 168
CRKL 0.03 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.24 -10000 0 -0.46 193 193
AP1 -0.12 0.22 0.47 1 -1.1 11 12
mol:IP3 -0.16 0.24 -10000 0 -0.47 184 184
PLCG1 -0.16 0.24 -10000 0 -0.47 184 184
PDGF/PDGFRA/alphaV Integrin -0.15 0.24 -10000 0 -0.46 182 182
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.47 184 184
CAV3 0.012 0.051 -10000 0 -0.63 3 3
CAV1 -0.009 0.14 -10000 0 -0.59 29 29
SHC/Grb2/SOS1 -0.083 0.2 -10000 0 -0.35 168 168
PDGF/PDGFRA/Shf -0.15 0.24 -10000 0 -0.46 189 189
FOS -0.13 0.22 -10000 0 -1 12 12
JUN -0.024 0.023 -10000 0 -10000 0 0
oligodendrocyte development -0.15 0.24 -10000 0 -0.46 182 182
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:DAG -0.16 0.24 -10000 0 -0.47 184 184
PDGF/PDGFRA -0.23 0.32 -10000 0 -0.63 193 193
actin cytoskeleton reorganization -0.15 0.24 -10000 0 -0.46 189 189
SRF 0.025 0.01 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
PI3K -0.11 0.21 -10000 0 -0.39 164 164
PDGF/PDGFRA/Crk/C3G -0.11 0.22 -10000 0 -0.39 187 187
JAK1 -0.16 0.23 -10000 0 -0.46 189 189
ELK1/SRF -0.11 0.18 -10000 0 -0.36 170 170
SHB 0.029 0.006 -10000 0 -10000 0 0
SHF 0.029 0.03 -10000 0 -0.64 1 1
CSNK2A1 0.037 0.017 -10000 0 -10000 0 0
GO:0007205 -0.17 0.24 -10000 0 -0.48 190 190
SOS1 0.029 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.084 0.2 -10000 0 -0.35 168 168
PDGF/PDGFRA/SHB -0.15 0.24 -10000 0 -0.46 189 189
PDGF/PDGFRA/Caveolin-1 -0.17 0.25 -10000 0 -0.47 193 193
ITGAV 0.029 0.007 -10000 0 -10000 0 0
ELK1 -0.15 0.21 -10000 0 -0.42 182 182
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
PDGF/PDGFRA/Crk -0.15 0.24 -10000 0 -0.46 188 188
JAK-STAT cascade -0.16 0.23 -10000 0 -0.46 189 189
cell proliferation -0.15 0.24 -10000 0 -0.46 189 189
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.18 -10000 0 -0.44 68 68
TBX21 -0.4 0.53 0.79 1 -1.1 153 154
B2M 0.023 0.015 -10000 0 -10000 0 0
TYK2 0.004 0.038 -10000 0 -10000 0 0
IL12RB1 -0.18 0.3 -10000 0 -0.63 155 155
GADD45B -0.22 0.34 0.61 1 -0.7 88 89
IL12RB2 -0.085 0.22 -10000 0 -0.6 73 73
GADD45G -0.23 0.34 0.61 1 -0.75 68 69
natural killer cell activation -0.01 0.026 -10000 0 -10000 0 0
RELB 0.03 0.004 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
IL18 0.022 0.062 -10000 0 -0.58 5 5
IL2RA -0.092 0.24 -10000 0 -0.59 98 98
IFNG -0.25 0.3 -10000 0 -0.59 223 223
STAT3 (dimer) -0.3 0.38 -10000 0 -0.76 160 160
HLA-DRB5 -0.009 0.15 -10000 0 -0.58 31 31
FASLG -0.44 0.54 0.79 1 -1.1 183 184
NF kappa B2 p52/RelB -0.34 0.47 -10000 0 -0.95 151 151
CD4 0.019 0.078 -10000 0 -0.59 8 8
SOCS1 0.021 0.067 -10000 0 -0.59 6 6
EntrezGene:6955 -0.003 0.009 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.6 222 222
CD3E -0.22 0.3 -10000 0 -0.6 200 200
CD3G -0.22 0.31 -10000 0 -0.6 197 197
IL12Rbeta2/JAK2 -0.061 0.17 -10000 0 -0.45 73 73
CCL3 -0.37 0.5 0.79 1 -1 145 146
CCL4 -0.38 0.52 0.79 1 -1 156 157
HLA-A 0.021 0.031 -10000 0 -0.59 1 1
IL18/IL18R -0.066 0.21 -10000 0 -0.39 133 133
NOS2 -0.28 0.37 -10000 0 -0.79 124 124
IL12/IL12R/TYK2/JAK2/SPHK2 -0.11 0.18 -10000 0 -0.43 70 70
IL1R1 -0.34 0.47 0.79 1 -0.96 142 143
IL4 0.017 0.038 -10000 0 -10000 0 0
JAK2 0.003 0.037 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.4 0.48 -10000 0 -0.86 234 234
RAB7A -0.18 0.31 0.55 5 -0.67 35 40
lysosomal transport -0.17 0.3 0.55 5 -0.64 35 40
FOS -0.29 0.39 -10000 0 -0.75 165 165
STAT4 (dimer) -0.3 0.43 0.58 5 -0.83 150 155
STAT5A (dimer) -0.44 0.54 -10000 0 -1 202 202
GZMA -0.41 0.54 0.52 1 -1 183 184
GZMB -0.4 0.52 -10000 0 -1.1 152 152
HLX -0.039 0.19 -10000 0 -0.59 55 55
LCK -0.39 0.52 0.56 1 -1.1 154 155
TCR/CD3/MHC II/CD4 -0.22 0.28 -10000 0 -0.53 209 209
IL2/IL2R -0.24 0.3 -10000 0 -0.45 294 294
MAPK14 -0.22 0.35 0.62 1 -0.72 89 90
CCR5 -0.4 0.45 0.61 1 -0.9 185 186
IL1B -0.005 0.076 -10000 0 -0.61 6 6
STAT6 -0.073 0.12 -10000 0 -10000 0 0
STAT4 -0.007 0.14 -10000 0 -0.59 29 29
STAT3 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.028 -10000 0 -0.59 1 1
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
NFKB2 0.029 0.006 -10000 0 -10000 0 0
IL12B -0.062 0.19 -10000 0 -0.62 52 52
CD8A -0.26 0.31 -10000 0 -0.6 226 226
CD8B -0.2 0.3 -10000 0 -0.6 179 179
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.12 0.18 0.44 68 -10000 0 68
IL2RB -0.3 0.31 -10000 0 -0.59 265 265
proteasomal ubiquitin-dependent protein catabolic process -0.27 0.4 0.55 6 -0.76 147 153
IL2RG -0.012 0.16 -10000 0 -0.59 34 34
IL12 -0.045 0.15 -10000 0 -0.47 52 52
STAT5A 0.029 0.005 -10000 0 -10000 0 0
CD247 -0.18 0.29 -10000 0 -0.6 160 160
IL2 0.013 0.086 -10000 0 -0.59 10 10
SPHK2 0.027 0.042 -10000 0 -0.64 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.037 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.42 0.53 -10000 0 -1.1 164 164
MAP2K3 -0.23 0.35 0.61 1 -0.73 91 92
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
MAP2K6 -0.23 0.35 0.61 1 -0.73 90 91
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.024 0.056 -10000 0 -0.58 4 4
IL18RAP -0.13 0.27 -10000 0 -0.59 128 128
IL12Rbeta1/TYK2 -0.13 0.24 -10000 0 -0.48 155 155
EOMES -0.32 0.33 -10000 0 -0.54 298 298
STAT1 (dimer) -0.34 0.41 -10000 0 -0.79 190 190
T cell proliferation -0.21 0.31 0.48 4 -0.6 126 130
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.076 -10000 0 -0.61 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.28 0.3 -10000 0 -0.69 108 108
ATF2 -0.2 0.34 0.56 6 -0.69 78 84
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.13 0.2 -10000 0 -0.4 153 153
STMN1 -0.19 0.22 -10000 0 -0.42 236 236
Aurora B/RasGAP/Survivin -0.22 0.31 -10000 0 -0.54 226 226
Chromosomal passenger complex/Cul3 protein complex -0.094 0.16 -10000 0 -0.46 35 35
BIRC5 -0.16 0.29 -10000 0 -0.6 147 147
DES -0.26 0.31 -10000 0 -0.66 152 152
Aurora C/Aurora B/INCENP -0.12 0.2 -10000 0 -0.33 232 232
Aurora B/TACC1 -0.15 0.2 -10000 0 -0.36 235 235
Aurora B/PP2A -0.18 0.23 -10000 0 -0.42 235 235
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.037 0.06 -10000 0 -0.22 3 3
mitotic metaphase/anaphase transition 0.001 0.006 -10000 0 -10000 0 0
NDC80 -0.26 0.32 -10000 0 -0.57 239 239
Cul3 protein complex 0.042 0.079 -10000 0 -0.4 14 14
KIF2C -0.084 0.15 -10000 0 -0.3 107 107
PEBP1 0.023 0.011 -10000 0 -10000 0 0
KIF20A -0.2 0.29 -10000 0 -0.59 177 177
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.17 0.23 -10000 0 -0.42 214 214
SEPT1 -0.05 0.21 -10000 0 -0.59 64 64
SMC2 0.029 0.006 -10000 0 -10000 0 0
SMC4 0.029 0.007 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.06 0.17 0.28 2 -0.7 12 14
PSMA3 0.028 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -10000 0 -10000 0 0
H3F3B -0.1 0.13 -10000 0 -0.24 231 231
AURKB -0.26 0.31 -10000 0 -0.59 236 236
AURKC 0.027 0.039 -10000 0 -0.59 2 2
CDCA8 -0.006 0.12 -10000 0 -0.61 19 19
cytokinesis -0.17 0.22 -10000 0 -0.48 132 132
Aurora B/Septin1 -0.18 0.28 -10000 0 -0.57 133 133
AURKA 0.024 0.062 -10000 0 -0.59 5 5
INCENP 0.017 0.02 -10000 0 -10000 0 0
KLHL13 0.01 0.11 -10000 0 -0.62 15 15
BUB1 -0.24 0.31 -10000 0 -0.59 218 218
hSgo1/Aurora B/Survivin -0.23 0.31 -10000 0 -0.52 240 240
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.14 0.22 -10000 0 -0.47 110 110
SGOL1 -0.001 0.12 -10000 0 -0.61 18 18
CENPA -0.16 0.2 0.19 1 -0.38 187 188
NCAPG -0.18 0.29 -10000 0 -0.59 171 171
Aurora B/HC8 Proteasome -0.18 0.23 -10000 0 -0.42 235 235
NCAPD2 0.029 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.17 0.23 -10000 0 -0.42 227 227
RHOA 0.021 0.014 -10000 0 -10000 0 0
NCAPH -0.075 0.23 -10000 0 -0.59 84 84
NPM1 -0.1 0.14 -10000 0 -0.62 6 6
RASA1 0.025 0.031 -10000 0 -0.64 1 1
KLHL9 0.029 0.006 -10000 0 -10000 0 0
mitotic prometaphase -0.006 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.23 -10000 0 -0.42 235 235
PPP1CC 0.029 0.006 -10000 0 -10000 0 0
Centraspindlin -0.15 0.24 -10000 0 -0.47 148 148
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
NSUN2 -0.1 0.14 -10000 0 -0.61 6 6
MYLK -0.11 0.14 -10000 0 -0.25 235 235
KIF23 0.017 0.079 -10000 0 -0.6 8 8
VIM -0.22 0.26 -10000 0 -0.47 247 247
RACGAP1 0.025 0.029 -10000 0 -0.6 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.12 0.17 -10000 0 -0.64 18 18
Chromosomal passenger complex -0.17 0.24 -10000 0 -0.45 184 184
Chromosomal passenger complex/EVI5 -0.19 0.32 -10000 0 -0.63 143 143
TACC1 0.027 0.009 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
CUL3 0.029 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.029 0.028 -9999 0 -0.59 1 1
EGFR 0.019 0.068 -9999 0 -0.59 6 6
EGF/EGFR -0.3 0.13 -9999 0 -0.35 402 402
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.28 0.14 -9999 0 -0.65 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.029 0.028 -9999 0 -0.59 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.57 0.2 -9999 0 -0.63 450 450
EGF/EGFR dimer/SHC -0.34 0.15 -9999 0 -0.41 389 389
mol:GDP -0.28 0.14 -9999 0 -0.64 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.11 -9999 0 -0.59 17 17
GRB2/SOS1 0.043 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.26 0.12 -9999 0 -0.6 6 6
SHC1 0.029 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.26 0.13 -9999 0 -0.61 6 6
FRAP1 -0.27 0.12 -9999 0 -0.62 5 5
EGF/EGFR dimer -0.41 0.16 -9999 0 -0.48 403 403
SOS1 0.029 0.005 -9999 0 -10000 0 0
GRB2 0.029 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.026 0.089 -9999 0 -0.43 18 18
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.054 -10000 0 -0.4 6 6
fibroblast growth factor receptor signaling pathway 0.046 0.054 -10000 0 -0.4 6 6
LAMA1 0.013 0.1 -10000 0 -0.57 14 14
PRNP 0.029 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.064 0.2 -10000 0 -0.47 98 98
SMAD2 0.021 0.027 -10000 0 -0.37 1 1
GPC1/PrPc/Cu2+ 0.036 0.023 -10000 0 -0.41 1 1
GPC1/Laminin alpha1 0.028 0.079 -10000 0 -0.47 11 11
TDGF1 -0.4 0.27 -10000 0 -0.54 375 375
CRIPTO/GPC1 -0.29 0.21 -10000 0 -0.48 256 256
APP/GPC1 0.04 0.026 -10000 0 -0.47 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.24 0.18 -10000 0 -0.4 253 253
FLT1 0.023 0.062 -10000 0 -0.59 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.041 0.035 -10000 0 -0.41 1 1
SERPINC1 -0.031 0.19 -10000 0 -0.63 44 44
FYN -0.24 0.18 -10000 0 -0.4 255 255
FGR -0.24 0.18 -10000 0 -0.41 256 256
positive regulation of MAPKKK cascade -0.29 0.2 0.38 3 -0.44 262 265
SLIT2 -0.11 0.27 -10000 0 -0.62 105 105
GPC1/NRG 0.024 0.085 -10000 0 -0.47 13 13
NRG1 0.009 0.11 -10000 0 -0.56 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.13 0.22 -10000 0 -0.37 216 216
LYN -0.24 0.18 -10000 0 -0.4 247 247
mol:Spermine 0.01 0.022 -10000 0 -0.48 1 1
cell growth 0.046 0.054 -10000 0 -0.4 6 6
BMP signaling pathway -0.027 0.031 0.64 1 -10000 0 1
SRC -0.24 0.18 -10000 0 -0.41 248 248
TGFBR1 0.029 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.028 0.17 -10000 0 -0.59 43 43
GPC1 0.027 0.031 -10000 0 -0.64 1 1
TGFBR1 (dimer) 0.029 0.006 -10000 0 -10000 0 0
VEGFA -0.24 0.3 -10000 0 -0.59 220 220
BLK -0.26 0.21 -10000 0 -0.44 260 260
HCK -0.26 0.19 -10000 0 -0.42 260 260
FGF2 0.023 0.066 -10000 0 -0.63 5 5
FGFR1 0.027 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer 0.023 0.061 -10000 0 -0.58 5 5
TGFBR2 0.022 0.014 -10000 0 -10000 0 0
cell death 0.04 0.026 -10000 0 -0.47 1 1
ATIII/GPC1 -0.006 0.15 -10000 0 -0.47 45 45
PLA2G2A/GPC1 -0.003 0.13 -10000 0 -0.43 44 44
LCK -0.26 0.19 -10000 0 -0.42 264 264
neuron differentiation 0.024 0.085 -10000 0 -0.47 13 13
PrPc/Cu2+ 0.022 0.004 -10000 0 -10000 0 0
APP 0.029 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.022 0.014 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 -0.11 0.17 -10000 0 -0.52 31 31
Syndecan-4/Syndesmos -0.32 0.26 -10000 0 -0.67 115 115
positive regulation of JNK cascade -0.37 0.29 -10000 0 -0.68 187 187
Syndecan-4/ADAM12 -0.39 0.33 -10000 0 -0.75 180 180
CCL5 -0.23 0.3 -10000 0 -0.59 211 211
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DNM2 0.03 0.003 -10000 0 -10000 0 0
ITGA5 -0.011 0.15 -10000 0 -0.59 33 33
SDCBP 0.028 0.008 -10000 0 -10000 0 0
PLG -0.3 0.32 -10000 0 -0.59 261 261
ADAM12 -0.14 0.28 -10000 0 -0.59 136 136
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.029 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.086 0.064 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.33 0.27 -10000 0 -0.68 123 123
Syndecan-4/CXCL12/CXCR4 -0.4 0.31 -10000 0 -0.73 187 187
Syndecan-4/Laminin alpha3 -0.32 0.26 -10000 0 -0.67 125 125
MDK -0.015 0.16 -10000 0 -0.59 36 36
Syndecan-4/FZD7 -0.32 0.26 -10000 0 -0.67 118 118
Syndecan-4/Midkine -0.34 0.28 -10000 0 -0.69 138 138
FZD7 0.027 0.031 -10000 0 -0.64 1 1
Syndecan-4/FGFR1/FGF -0.3 0.25 -10000 0 -0.64 106 106
THBS1 0.026 0.052 -10000 0 -0.64 3 3
integrin-mediated signaling pathway -0.31 0.25 -10000 0 -0.64 126 126
positive regulation of MAPKKK cascade -0.37 0.29 -10000 0 -0.68 187 187
Syndecan-4/TACI -0.35 0.29 -10000 0 -0.7 144 144
CXCR4 -0.18 0.29 -10000 0 -0.59 166 166
cell adhesion 0.016 0.077 0.22 4 -0.3 13 17
Syndecan-4/Dynamin -0.32 0.26 -10000 0 -0.67 120 120
Syndecan-4/TSP1 -0.32 0.26 -10000 0 -0.67 122 122
Syndecan-4/GIPC -0.32 0.26 -10000 0 -0.66 123 123
Syndecan-4/RANTES -0.44 0.31 -10000 0 -0.72 227 227
ITGB1 0.03 0.004 -10000 0 -10000 0 0
LAMA1 0.013 0.1 -10000 0 -0.57 14 14
LAMA3 0.022 0.067 -10000 0 -0.59 6 6
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.089 0.13 0.99 8 -10000 0 8
Syndecan-4/alpha-Actinin -0.32 0.26 -10000 0 -0.67 121 121
TFPI 0.02 0.071 -10000 0 -0.56 7 7
F2 -0.2 0.3 -10000 0 -0.58 188 188
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 33 33
positive regulation of cell adhesion -0.32 0.26 -10000 0 -0.66 124 124
ACTN1 0.027 0.031 -10000 0 -0.64 1 1
TNC 0.016 0.094 -10000 0 -0.64 10 10
Syndecan-4/CXCL12 -0.33 0.27 -10000 0 -0.68 124 124
FGF6 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
CXCL12 0.018 0.083 -10000 0 -0.55 10 10
TNFRSF13B -0.033 0.18 -10000 0 -0.59 49 49
FGF2 0.023 0.066 -10000 0 -0.63 5 5
FGFR1 0.027 0.009 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.33 0.26 -10000 0 -0.6 179 179
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.001 0.16 -10000 0 -0.57 37 37
cell migration -0.028 0.021 -10000 0 -10000 0 0
PRKCD 0.03 0.036 -10000 0 -0.57 1 1
vasculogenesis -0.31 0.25 -10000 0 -0.64 122 122
SDC4 -0.34 0.28 -10000 0 -0.63 183 183
Syndecan-4/Tenascin C -0.33 0.26 -10000 0 -0.67 126 126
Syndecan-4/PI-4-5-P2/PKC alpha -0.068 0.05 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.32 0.26 -10000 0 -0.67 115 115
MMP9 -0.25 0.3 -10000 0 -0.58 227 227
Rac1/GTP 0.016 0.078 0.22 4 -0.3 13 17
cytoskeleton organization -0.3 0.25 -10000 0 -0.64 115 115
GIPC1 0.029 0.03 -10000 0 -0.64 1 1
Syndecan-4/TFPI -0.32 0.26 -10000 0 -0.67 122 122
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.045 0.2 -10000 0 -0.43 96 96
alphaM/beta2 Integrin/GPIbA -0.043 0.2 -10000 0 -0.42 94 94
alphaM/beta2 Integrin/proMMP-9 -0.22 0.29 -10000 0 -0.48 246 246
PLAUR 0 0.13 -10000 0 -0.59 24 24
HMGB1 0.025 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.044 0.19 -10000 0 -0.42 93 93
AGER -0.085 0.24 -10000 0 -0.59 88 88
RAP1A 0.029 0.005 -10000 0 -10000 0 0
SELPLG -0.009 0.15 -10000 0 -0.59 31 31
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.25 -10000 0 -0.61 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 227 227
CYR61 0.023 0.059 -10000 0 -0.48 6 6
TLN1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.19 0.16 -10000 0 -0.44 104 104
RHOA 0.021 0.014 -10000 0 -10000 0 0
P-selectin oligomer 0.002 0.13 -10000 0 -0.64 20 20
MYH2 -0.29 0.2 -10000 0 -0.51 172 172
MST1R 0.013 0.073 -10000 0 -0.58 7 7
leukocyte activation during inflammatory response -0.15 0.24 -10000 0 -0.54 81 81
APOB -0.17 0.29 -10000 0 -0.59 164 164
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.023 0.063 -10000 0 -0.6 5 5
JAM3 0.03 0.003 -10000 0 -10000 0 0
GP1BA 0.028 0.03 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/CTGF -0.05 0.2 -10000 0 -0.43 98 98
alphaM/beta2 Integrin -0.23 0.18 -10000 0 -0.4 206 206
JAM3 homodimer 0.03 0.003 -10000 0 -10000 0 0
ICAM2 0.029 0.005 -10000 0 -10000 0 0
ICAM1 0.016 0.091 -10000 0 -0.59 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.23 0.18 -10000 0 -0.4 206 206
cell adhesion -0.043 0.19 -10000 0 -0.42 94 94
NFKB1 -0.11 0.25 0.4 4 -0.63 60 64
THY1 0.028 0.03 -10000 0 -0.64 1 1
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
Lipoprotein(a) -0.1 0.2 -10000 0 -0.38 164 164
alphaM/beta2 Integrin/LRP/tPA -0.029 0.19 -10000 0 -0.51 35 35
IL6 -0.14 0.3 0.39 2 -0.72 73 75
ITGB2 -0.091 0.24 -10000 0 -0.59 93 93
elevation of cytosolic calcium ion concentration -0.044 0.21 -10000 0 -0.55 40 40
alphaM/beta2 Integrin/JAM2/JAM3 -0.021 0.19 -10000 0 -0.52 29 29
JAM2 0.029 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.043 0.19 -10000 0 -0.56 32 32
alphaM/beta2 Integrin/uPA/Plg -0.23 0.27 -10000 0 -0.46 242 242
RhoA/GTP -0.29 0.21 -10000 0 -0.52 181 181
positive regulation of phagocytosis -0.19 0.2 -10000 0 -0.54 80 80
Ron/MSP 0.018 0.083 -10000 0 -0.45 14 14
alphaM/beta2 Integrin/uPAR/uPA -0.043 0.21 -10000 0 -0.56 40 40
alphaM/beta2 Integrin/uPAR -0.058 0.22 -10000 0 -0.45 106 106
PLAU 0.02 0.076 -10000 0 -0.56 8 8
PLAT 0.016 0.085 -10000 0 -0.6 9 9
actin filament polymerization -0.28 0.19 -10000 0 -0.48 171 171
MST1 0.011 0.08 -10000 0 -0.61 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.15 0.24 -10000 0 -0.55 81 81
TNF -0.11 0.24 0.39 3 -0.6 61 64
RAP1B 0.029 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.048 0.2 -10000 0 -0.42 99 99
fibrinolysis -0.23 0.27 -10000 0 -0.46 243 243
HCK -0.003 0.14 -10000 0 -0.59 26 26
dendritic cell antigen processing and presentation -0.23 0.18 -10000 0 -0.4 206 206
VTN -0.069 0.24 -10000 0 -0.63 75 75
alphaM/beta2 Integrin/CYR61 -0.046 0.2 -10000 0 -0.42 96 96
LPA 0.018 0.051 -10000 0 -0.63 3 3
LRP1 0.029 0.005 -10000 0 -10000 0 0
cell migration -0.2 0.28 -10000 0 -0.61 99 99
FN1 -0.018 0.16 -10000 0 -0.59 37 37
alphaM/beta2 Integrin/Thy1 -0.043 0.2 -10000 0 -0.42 94 94
MPO 0.009 0.11 -10000 0 -0.59 16 16
KNG1 -0.46 0.29 -10000 0 -0.63 363 363
RAP1/GDP 0.038 0.01 -10000 0 -10000 0 0
ROCK1 -0.28 0.2 -10000 0 -0.5 164 164
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.31 0.32 -10000 0 -0.61 261 261
CTGF 0.018 0.079 -10000 0 -0.64 7 7
alphaM/beta2 Integrin/Hck -0.059 0.24 -10000 0 -0.5 96 96
ITGAM 0.002 0.12 -10000 0 -0.59 18 18
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.054 0.24 -10000 0 -0.58 57 57
HP -0.12 0.26 -10000 0 -0.59 122 122
leukocyte adhesion -0.072 0.2 -10000 0 -0.54 39 39
SELP 0.002 0.13 -10000 0 -0.64 20 20
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.14 0.54 0.8 1 -1.1 82 83
PLK1 -0.054 0.27 -10000 0 -0.5 84 84
BIRC5 -0.08 0.28 -10000 0 -0.84 7 7
HSPA1B -0.15 0.54 0.79 2 -1.1 77 79
MAP2K1 0.027 0.055 -10000 0 -10000 0 0
BRCA2 -0.15 0.55 -10000 0 -1.1 80 80
FOXM1 -0.22 0.69 -10000 0 -1.5 87 87
XRCC1 -0.15 0.54 -10000 0 -1.1 76 76
FOXM1B/p19 -0.29 0.48 -10000 0 -1.2 75 75
Cyclin D1/CDK4 -0.14 0.5 -10000 0 -1 64 64
CDC2 -0.16 0.57 -10000 0 -1.1 89 89
TGFA -0.13 0.49 -10000 0 -1 66 66
SKP2 -0.13 0.54 0.8 1 -1.1 75 76
CCNE1 0.024 0.069 -10000 0 -0.6 6 6
CKS1B -0.14 0.54 0.71 1 -1.1 78 79
RB1 -0.034 0.3 -10000 0 -0.96 12 12
FOXM1C/SP1 -0.18 0.61 -10000 0 -1.3 85 85
AURKB -0.16 0.32 -10000 0 -1.2 9 9
CENPF -0.16 0.58 -10000 0 -1.2 77 77
CDK4 0.026 0.025 -10000 0 -10000 0 0
MYC -0.12 0.48 -10000 0 -0.97 79 79
CHEK2 0.026 0.062 -10000 0 -0.64 1 1
ONECUT1 -0.15 0.53 -10000 0 -1.1 76 76
CDKN2A -0.56 0.13 -10000 0 -0.59 477 477
LAMA4 -0.2 0.55 0.8 1 -1.1 85 86
FOXM1B/HNF6 -0.19 0.61 -10000 0 -1.3 79 79
FOS -0.16 0.55 -10000 0 -1.1 80 80
SP1 0.029 0.009 -10000 0 -10000 0 0
CDC25B -0.14 0.54 -10000 0 -1.1 74 74
response to radiation 0.006 0.037 -10000 0 -10000 0 0
CENPB -0.14 0.54 -10000 0 -1.1 74 74
CENPA -0.21 0.61 -10000 0 -1.2 100 100
NEK2 -0.18 0.6 0.71 1 -1.2 95 96
HIST1H2BA -0.15 0.54 0.8 1 -1.1 80 81
CCNA2 -0.093 0.25 -10000 0 -0.6 99 99
EP300 0.028 0.03 -10000 0 -0.64 1 1
CCNB1/CDK1 -0.19 0.62 -10000 0 -1.3 82 82
CCNB2 -0.19 0.6 0.79 1 -1.2 101 102
CCNB1 -0.16 0.57 -10000 0 -1.2 82 82
ETV5 -0.14 0.54 -10000 0 -1.1 81 81
ESR1 -0.15 0.54 0.8 1 -1.1 84 85
CCND1 -0.14 0.51 -10000 0 -1.1 69 69
GSK3A 0.027 0.047 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.023 0.2 -10000 0 -0.41 95 95
CDK2 0.031 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.006 0.045 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.17 0.57 -10000 0 -1.2 85 85
GAS1 -0.19 0.58 -10000 0 -1.1 92 92
MMP2 -0.14 0.54 0.8 1 -1.1 76 77
RB1/FOXM1C -0.16 0.54 -10000 0 -1.1 83 83
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.03 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.2 -9999 0 -0.34 232 232
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.031 0.059 -9999 0 -0.62 1 1
AURKB -0.26 0.31 -9999 0 -0.59 236 236
AURKC 0.027 0.039 -9999 0 -0.59 2 2
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.46 0.28 -10000 0 -0.69 257 257
SMAD6-7/SMURF1 0.053 0.021 -10000 0 -10000 0 0
NOG -0.072 0.23 -10000 0 -0.6 80 80
SMAD9 -0.068 0.17 -10000 0 -0.61 39 39
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD5 -0.15 0.16 -10000 0 -0.48 32 32
BMP7/USAG1 -0.53 0.31 -10000 0 -0.65 405 405
SMAD5/SKI -0.15 0.16 0.32 3 -0.48 27 30
SMAD1 -0.024 0.057 -10000 0 -10000 0 0
BMP2 0.025 0.052 -10000 0 -0.64 3 3
SMAD1/SMAD1/SMAD4 0.011 0.056 -10000 0 -10000 0 0
BMPR1A 0.029 0.006 -10000 0 -10000 0 0
BMPR1B -0.42 0.31 -10000 0 -0.63 341 341
BMPR1A-1B/BAMBI -0.26 0.22 -10000 0 -0.41 335 335
AHSG 0.01 0.088 -10000 0 -0.6 10 10
CER1 0.02 0.006 -10000 0 -10000 0 0
BMP2-4/CER1 0.044 0.048 -10000 0 -0.42 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.12 -10000 0 -0.46 9 9
BMP2-4 (homodimer) 0.035 0.051 -10000 0 -0.47 4 4
RGMB 0.023 0.04 -10000 0 -0.59 2 2
BMP6/BMPR2/BMPR1A-1B -0.23 0.2 -10000 0 -0.37 324 324
RGMA 0.023 0.067 -10000 0 -0.64 5 5
SMURF1 0.027 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.12 0.14 -10000 0 -0.4 34 34
BMP2-4/USAG1 -0.22 0.22 -10000 0 -0.41 286 286
SMAD6/SMURF1/SMAD5 -0.14 0.16 0.31 1 -0.48 25 26
SOSTDC1 -0.36 0.33 -10000 0 -0.64 287 287
BMP7/BMPR2/BMPR1A-1B -0.46 0.27 -10000 0 -0.57 407 407
SKI 0.029 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.019 0.08 -10000 0 -0.6 8 8
HFE2 0.004 0.12 -10000 0 -0.59 18 18
ZFYVE16 0.027 0.009 -10000 0 -10000 0 0
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.043 0.074 -10000 0 -0.43 10 10
SMAD5/SMAD5/SMAD4 -0.15 0.16 0.29 2 -0.48 28 30
MAPK1 0.03 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.38 15 15
BMP7 (homodimer) -0.4 0.31 -10000 0 -0.64 322 322
NUP214 0.029 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.021 0.085 -10000 0 -0.45 14 14
SMAD1/SKI -0.019 0.068 0.34 1 -0.42 1 2
SMAD6 0.03 0.003 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.038 0.074 -10000 0 -0.38 13 13
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.13 0.28 -10000 0 -0.63 120 120
BMPR2 (homodimer) 0.029 0.007 -10000 0 -10000 0 0
GADD34/PP1CA 0.054 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.31 0.24 -10000 0 -0.47 335 335
CHRDL1 -0.32 0.33 -10000 0 -0.64 257 257
ENDOFIN/SMAD1 -0.016 0.065 0.34 1 -0.44 1 2
SMAD6-7/SMURF1/SMAD1 0.014 0.068 -10000 0 -0.41 1 1
SMAD6/SMURF1 0.027 0.009 -10000 0 -10000 0 0
BAMBI 0.022 0.068 -10000 0 -0.59 6 6
SMURF2 0.028 0.03 -10000 0 -0.64 1 1
BMP2-4/CHRDL1 -0.18 0.23 -10000 0 -0.41 250 250
BMP2-4/GREM1 -0.057 0.2 -10000 0 -0.41 117 117
SMAD7 0.029 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.063 0.17 -10000 0 -0.56 45 45
SMAD1/SMAD6 -0.019 0.063 -10000 0 -0.44 1 1
TAK1/SMAD6 0.038 0.016 -10000 0 -10000 0 0
BMP7 -0.4 0.32 -10000 0 -0.64 322 322
BMP6 0.019 0.08 -10000 0 -0.6 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.11 -10000 0 -0.35 27 27
PPM1A 0.028 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.021 0.069 0.34 1 -0.44 1 2
SMAD7/SMURF1 0.039 0.015 -10000 0 -10000 0 0
CTDSPL 0.021 0.014 -10000 0 -10000 0 0
PPP1CA 0.03 0.003 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
CTDSP1 0.029 0.007 -10000 0 -10000 0 0
PPP1R15A 0.03 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.18 -10000 0 -0.5 64 64
CHRD 0.017 0.087 -10000 0 -0.62 9 9
BMPR2 0.029 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.14 0.14 -10000 0 -0.41 34 34
BMP4 0.024 0.052 -10000 0 -0.64 3 3
FST -0.04 0.2 -10000 0 -0.63 51 51
BMP2-4/NOG -0.017 0.16 -10000 0 -0.38 79 79
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.42 0.26 -10000 0 -0.66 233 233
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.013 0.1 -10000 0 -0.62 13 13
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.049 -10000 0 -0.6 3 3
TCEB1 0.028 0.007 -10000 0 -10000 0 0
HIF1A/p53 -0.07 0.082 0.26 1 -0.46 15 16
HIF1A -0.077 0.083 -10000 0 -0.49 15 15
COPS5 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.052 -10000 0 -10000 0 0
FIH (dimer) 0.029 0.006 -10000 0 -10000 0 0
CDKN2A -0.57 0.13 -10000 0 -0.59 477 477
ARNT/IPAS 0.029 0.081 -10000 0 -0.46 13 13
HIF1AN 0.029 0.006 -10000 0 -10000 0 0
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
HIF1A/ARNT -0.068 0.084 0.26 1 -0.47 15 16
CUL2 0.03 0.004 -10000 0 -10000 0 0
OS9 0.029 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.043 -10000 0 -0.38 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.067 0.082 -10000 0 -0.47 15 15
PHD1-3/OS9 -0.28 0.13 -10000 0 -0.34 415 415
HIF1A/RACK1/Elongin B/Elongin C -0.047 0.084 -10000 0 -0.45 14 14
VHL 0.021 0.014 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.068 0.083 -10000 0 -0.46 15 15
EGLN3 -0.52 0.2 -10000 0 -0.59 439 439
EGLN2 0.03 0.004 -10000 0 -10000 0 0
EGLN1 0.029 0.006 -10000 0 -10000 0 0
TP53 0.029 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.13 0.26 -10000 0 -0.52 137 137
ARNT 0.029 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.35 0.1 -10000 0 -0.38 443 443
Glypican 2 network

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
MDK -0.015 0.16 -9999 0 -0.59 36 36
GPC2 -0.037 0.19 -9999 0 -0.59 52 52
GPC2/Midkine -0.04 0.19 -9999 0 -0.48 75 75
neuron projection morphogenesis -0.04 0.19 -9999 0 -0.48 75 75
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.44 0.42 -10000 0 -1.1 81 81
STAT6 (cleaved dimer) -0.48 0.44 -10000 0 -1.1 121 121
IGHG1 -0.15 0.16 -10000 0 -0.52 6 6
IGHG3 -0.43 0.4 -10000 0 -1 113 113
AKT1 -0.24 0.27 -10000 0 -0.72 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.18 0.22 -10000 0 -0.65 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.26 -10000 0 -0.75 43 43
THY1 -0.44 0.42 -10000 0 -1.1 77 77
MYB -0.14 0.28 -10000 0 -0.59 139 139
HMGA1 0.028 0.028 -10000 0 -0.59 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.31 -10000 0 -0.78 102 102
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.26 -10000 0 -0.74 45 45
SP1 0.025 0.033 -10000 0 -10000 0 0
INPP5D 0.023 0.055 -10000 0 -0.59 4 4
SOCS5 0.039 0.021 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.47 0.45 -10000 0 -1.1 118 118
SOCS1 -0.31 0.3 -10000 0 -0.76 73 73
SOCS3 -0.26 0.27 -10000 0 -0.77 46 46
FCER2 -0.37 0.37 -10000 0 -0.96 84 84
PARP14 0.029 0.009 -10000 0 -10000 0 0
CCL17 -0.45 0.43 -10000 0 -1.1 81 81
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.66 46 46
T cell proliferation -0.45 0.44 -10000 0 -1.1 102 102
IL4R/JAK1 -0.44 0.42 -10000 0 -1.1 86 86
EGR2 -0.45 0.44 -10000 0 -1.1 87 87
JAK2 -0.02 0.039 -10000 0 -10000 0 0
JAK3 -0.096 0.25 -10000 0 -0.59 102 102
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
JAK1 0.01 0.02 -10000 0 -10000 0 0
COL1A2 -0.17 0.21 -10000 0 -0.65 45 45
CCL26 -0.43 0.43 -10000 0 -1.1 77 77
IL4R -0.46 0.44 -10000 0 -1.2 84 84
PTPN6 0.04 0.015 -10000 0 -10000 0 0
IL13RA2 -0.51 0.5 -10000 0 -1.3 107 107
IL13RA1 -0.019 0.041 -10000 0 -10000 0 0
IRF4 -0.2 0.28 -10000 0 -0.69 89 89
ARG1 -0.15 0.19 -10000 0 -0.75 13 13
CBL -0.3 0.3 -10000 0 -0.79 81 81
GTF3A -0.001 0.049 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
IL13RA1/JAK2 -0.024 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.27 -10000 0 -0.66 77 77
CD40LG -0.046 0.2 -10000 0 -0.64 51 51
MAPK14 -0.3 0.3 -10000 0 -0.79 77 77
mitosis -0.23 0.26 -10000 0 -0.68 50 50
STAT6 -0.5 0.48 -10000 0 -1.2 106 106
SPI1 -0.052 0.21 -10000 0 -0.58 68 68
RPS6KB1 -0.22 0.25 -10000 0 -0.67 43 43
STAT6 (dimer) -0.5 0.48 -10000 0 -1.2 106 106
STAT6 (dimer)/PARP14 -0.46 0.45 -10000 0 -1.1 107 107
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.27 -10000 0 -0.71 68 68
FRAP1 -0.24 0.27 -10000 0 -0.72 51 51
LTA -0.51 0.46 -10000 0 -1.2 109 109
FES 0.027 0.042 -10000 0 -0.64 2 2
T-helper 1 cell differentiation 0.49 0.47 1.2 106 -10000 0 106
CCL11 -0.65 0.57 -10000 0 -1.3 202 202
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.23 0.25 -10000 0 -0.69 55 55
IL2RG -0.009 0.16 -10000 0 -0.59 34 34
IL10 -0.45 0.43 -10000 0 -1.1 94 94
IRS1 0.025 0.052 -10000 0 -0.64 3 3
IRS2 0.02 0.079 -10000 0 -0.6 8 8
IL4 -0.11 0.13 -10000 0 -1.1 3 3
IL5 -0.41 0.43 -10000 0 -1.1 79 79
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.87 83 83
COL1A1 -0.3 0.31 -10000 0 -0.71 121 121
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.43 -10000 0 -1.1 78 78
IL2R gamma/JAK3 -0.083 0.25 -10000 0 -0.55 106 106
TFF3 -0.46 0.44 -10000 0 -1.1 94 94
ALOX15 -0.45 0.42 -10000 0 -1.1 94 94
MYBL1 -0.009 0.15 -10000 0 -0.59 30 30
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.94 95 95
SHC1 0.029 0.007 -10000 0 -10000 0 0
CEBPB 0.02 0.085 -10000 0 -0.6 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.25 -10000 0 -0.7 48 48
mol:PI-3-4-5-P3 -0.24 0.27 -10000 0 -0.72 51 51
PI3K -0.25 0.28 -10000 0 -0.77 51 51
DOK2 -0.011 0.15 -10000 0 -0.59 31 31
ETS1 0.04 0.02 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.23 -10000 0 -0.64 47 47
ITGB3 -0.44 0.43 -10000 0 -1.1 81 81
PIGR -0.79 0.67 -10000 0 -1.4 242 242
IGHE 0.03 0.077 0.3 5 -0.43 2 7
MAPKKK cascade -0.19 0.22 -10000 0 -0.63 47 47
BCL6 0.028 0.007 -10000 0 -10000 0 0
OPRM1 -0.45 0.42 -10000 0 -1.1 82 82
RETNLB -0.45 0.42 -10000 0 -1.1 91 91
SELP -0.46 0.47 -10000 0 -1.3 78 78
AICDA -0.51 0.44 -10000 0 -1.1 128 128
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.22 0.36 -10000 0 -0.58 206 206
MAP4K1 -0.21 0.3 -10000 0 -0.59 197 197
MAP3K8 0.027 0.039 -10000 0 -0.59 2 2
PRKCB 0.022 0.064 -10000 0 -0.61 5 5
DBNL 0.027 0.009 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
MAP3K1 -0.08 0.16 -10000 0 -0.51 38 38
JUN 0.015 0.11 0.33 2 -0.56 13 15
MAP3K7 -0.082 0.16 -10000 0 -0.5 40 40
GRAP2 -0.012 0.16 -10000 0 -0.59 34 34
CRK 0.029 0.005 -10000 0 -10000 0 0
MAP2K4 -0.043 0.19 0.29 28 -0.47 40 68
LAT -0.14 0.28 -10000 0 -0.59 140 140
LCP2 -0.014 0.14 -10000 0 -0.59 30 30
MAPK8 0.011 0.12 0.3 1 -0.58 14 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.088 0.17 -10000 0 -0.51 43 43
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.2 0.34 -10000 0 -0.73 115 115
Caspase cascade in apoptosis

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
TOP1 -0.075 0.18 -10000 0 -0.37 103 103
ACTA1 -0.12 0.22 -10000 0 -0.49 105 105
NUMA1 -0.076 0.18 0.24 1 -0.38 104 105
SPTAN1 -0.12 0.21 -10000 0 -0.49 101 101
LIMK1 -0.1 0.22 0.41 1 -0.47 102 103
BIRC3 -0.065 0.22 -10000 0 -0.58 77 77
BIRC2 0.029 0.004 -10000 0 -10000 0 0
BAX 0.03 0.003 -10000 0 -10000 0 0
CASP10 -0.18 0.28 -10000 0 -0.55 176 176
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
PTK2 -0.079 0.18 0.24 1 -0.37 103 104
DIABLO 0.029 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.12 0.21 -10000 0 -0.48 101 101
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
GSN -0.12 0.22 -10000 0 -0.49 101 101
MADD 0.03 0.003 -10000 0 -10000 0 0
TFAP2A -0.29 0.3 -10000 0 -0.53 277 277
BID -0.072 0.12 -10000 0 -0.28 101 101
MAP3K1 -0.029 0.078 -10000 0 -0.23 2 2
TRADD 0.029 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.042 0.013 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.11 0.22 0.34 2 -0.49 101 103
CASP9 0.029 0.006 -10000 0 -10000 0 0
DNA repair 0.016 0.084 0.3 13 -0.19 3 16
neuron apoptosis 0.006 0.11 -10000 0 -0.63 13 13
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.1 0.21 -10000 0 -0.46 103 103
APAF1 0.029 0.006 -10000 0 -10000 0 0
CASP6 -0.029 0.16 0.36 2 -0.9 7 9
TRAF2 0.029 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.11 0.21 0.43 1 -0.47 101 102
CASP7 0.031 0.11 0.27 42 -0.32 9 51
KRT18 0.012 0.041 -10000 0 -0.31 1 1
apoptosis -0.11 0.21 0.41 2 -0.48 87 89
DFFA -0.12 0.21 -10000 0 -0.49 101 101
DFFB -0.12 0.21 -10000 0 -0.49 101 101
PARP1 -0.016 0.085 0.19 3 -0.3 13 16
actin filament polymerization 0.09 0.21 0.45 94 -0.41 2 96
TNF 0.019 0.081 -10000 0 -0.61 8 8
CYCS -0.046 0.11 0.19 5 -0.22 93 98
SATB1 -0.026 0.14 0.44 2 -0.83 7 9
SLK -0.12 0.22 0.34 1 -0.49 102 103
p15 BID/BAX -0.05 0.12 -10000 0 -0.29 1 1
CASP2 0.027 0.082 -10000 0 -0.47 2 2
JNK cascade 0.028 0.077 0.22 2 -10000 0 2
CASP3 -0.13 0.22 -10000 0 -0.52 101 101
LMNB2 0.025 0.12 0.36 11 -0.54 6 17
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CASP4 0.03 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.012 0.14 -10000 0 -0.33 73 73
negative regulation of DNA binding -0.28 0.29 -10000 0 -0.52 277 277
stress fiber formation -0.12 0.21 0.34 1 -0.48 102 103
GZMB -0.21 0.33 -10000 0 -0.62 178 178
CASP1 0.021 0.003 -10000 0 -10000 0 0
LMNB1 0.019 0.1 0.35 10 -0.42 6 16
APP 0.006 0.12 -10000 0 -0.64 13 13
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.003 -10000 0 -10000 0 0
VIM -0.11 0.2 0.28 1 -0.47 87 88
LMNA 0.022 0.11 0.36 11 -0.4 8 19
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.013 0.066 -10000 0 -0.49 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.12 0.22 0.3 1 -0.49 101 102
APAF-1/Caspase 9 -0.015 0.13 -10000 0 -0.59 22 22
nuclear fragmentation during apoptosis -0.075 0.18 0.24 1 -0.37 104 105
CFL2 -0.094 0.21 0.41 2 -0.46 94 96
GAS2 -0.13 0.22 0.41 1 -0.49 105 106
positive regulation of apoptosis 0.027 0.11 0.36 11 -0.49 6 17
PRF1 -0.13 0.27 -10000 0 -0.58 126 126
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.055 -10000 0 -0.59 4 4
CCL5 -0.23 0.3 -10000 0 -0.59 211 211
SDCBP 0.028 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.17 0.27 2 -0.4 83 85
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 -0.12 0.16 -10000 0 -0.45 48 48
Syndecan-1/Syntenin -0.12 0.16 0.33 2 -0.46 42 44
MAPK3 -0.11 0.15 -10000 0 -0.5 22 22
HGF/MET 0.019 0.1 -10000 0 -0.47 20 20
TGFB1/TGF beta receptor Type II 0.025 0.055 -10000 0 -0.58 4 4
BSG 0.029 0.028 -10000 0 -0.59 1 1
keratinocyte migration -0.12 0.16 -10000 0 -0.44 48 48
Syndecan-1/RANTES -0.25 0.22 0.35 3 -0.49 180 183
Syndecan-1/CD147 -0.11 0.17 -10000 0 -0.53 22 22
Syndecan-1/Syntenin/PIP2 -0.12 0.16 0.26 1 -0.45 42 43
LAMA5 0.028 0.03 -10000 0 -0.64 1 1
positive regulation of cell-cell adhesion -0.12 0.15 -10000 0 -0.44 42 42
MMP7 -0.085 0.25 -10000 0 -0.64 86 86
HGF 0.002 0.12 -10000 0 -0.6 20 20
Syndecan-1/CASK -0.13 0.15 -10000 0 -0.39 83 83
Syndecan-1/HGF/MET -0.12 0.18 -10000 0 -0.53 35 35
regulation of cell adhesion -0.1 0.15 0.52 1 -0.53 14 15
HPSE 0.027 0.042 -10000 0 -0.64 2 2
positive regulation of cell migration -0.13 0.17 0.27 2 -0.4 83 85
SDC1 -0.14 0.17 0.25 1 -0.41 83 84
Syndecan-1/Collagen -0.13 0.17 0.27 2 -0.4 83 85
PPIB 0.03 0.003 -10000 0 -10000 0 0
MET 0.024 0.04 -10000 0 -0.59 2 2
PRKACA 0.03 0.002 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 227 227
MAPK1 -0.1 0.15 -10000 0 -0.5 22 22
homophilic cell adhesion -0.13 0.17 0.27 2 -0.4 83 85
MMP1 -0.092 0.25 -10000 0 -0.6 96 96
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.009 -10000 0 -10000 0 0
LAT2 -0.078 0.15 -10000 0 -0.44 49 49
AP1 -0.046 0.17 -10000 0 -0.47 18 18
mol:PIP3 -0.1 0.3 0.44 38 -0.59 87 125
IKBKB -0.017 0.19 0.34 61 -0.3 49 110
AKT1 -0.072 0.2 0.43 13 -0.52 21 34
IKBKG -0.019 0.19 0.34 58 -0.31 43 101
MS4A2 -0.11 0.26 -10000 0 -0.59 110 110
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
MAP3K1 -0.049 0.2 0.34 40 -0.39 66 106
mol:Ca2+ -0.064 0.24 0.38 45 -0.42 85 130
LYN 0.025 0.012 -10000 0 -10000 0 0
CBLB -0.052 0.11 -10000 0 -0.34 20 20
SHC1 0.029 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.041 0.036 -10000 0 -0.35 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.023 0.055 -10000 0 -0.59 4 4
PLD2 -0.1 0.2 0.35 15 -0.6 20 35
PTPN13 -0.025 0.14 0.39 3 -0.66 9 12
PTPN11 0.026 0.015 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.006 0.17 0.43 31 -0.37 1 32
SYK 0.024 0.036 -10000 0 -0.49 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.17 0.25 -10000 0 -0.58 108 108
LAT -0.13 0.19 -10000 0 -0.46 92 92
PAK2 -0.072 0.2 0.35 21 -0.43 71 92
NFATC2 -0.034 0.069 -10000 0 -0.48 2 2
HRAS -0.09 0.2 0.32 8 -0.46 78 86
GAB2 0.03 0.003 -10000 0 -10000 0 0
PLA2G1B -0.2 0.38 -10000 0 -0.8 143 143
Fc epsilon R1 -0.13 0.24 -10000 0 -0.41 199 199
Antigen/IgE/Fc epsilon R1 -0.12 0.22 -10000 0 -0.38 199 199
mol:GDP -0.11 0.21 0.26 1 -0.47 106 107
JUN 0.029 0.006 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
FOS 0.012 0.1 -10000 0 -0.63 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.055 0.12 -10000 0 -0.35 23 23
CHUK -0.019 0.19 0.34 59 -0.3 51 110
KLRG1 -0.056 0.12 -10000 0 -0.35 21 21
VAV1 -0.12 0.19 -10000 0 -0.46 91 91
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.052 0.11 -10000 0 -0.38 11 11
negative regulation of mast cell degranulation -0.045 0.12 -10000 0 -0.45 9 9
BTK -0.069 0.15 -10000 0 -0.43 18 18
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.072 0.16 -10000 0 -0.36 81 81
GAB2/PI3K/SHP2 -0.11 0.17 -10000 0 -0.57 21 21
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.053 0.12 -10000 0 -0.36 26 26
RAF1 -0.23 0.42 -10000 0 -0.9 143 143
Fc epsilon R1/FcgammaRIIB/SHIP -0.15 0.28 -10000 0 -0.66 81 81
FCER1G -0.083 0.24 -10000 0 -0.59 91 91
FCER1A -0.001 0.13 -10000 0 -0.63 19 19
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.21 -10000 0 -0.39 102 102
MAPK3 -0.21 0.39 -10000 0 -0.81 143 143
MAPK1 -0.21 0.39 -10000 0 -0.81 143 143
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.007 0.14 -10000 0 -0.67 15 15
DUSP1 0.022 0.03 -10000 0 -0.59 1 1
NF-kappa-B/RelA -0.031 0.085 -10000 0 -0.28 1 1
actin cytoskeleton reorganization -0.023 0.14 0.4 3 -0.68 8 11
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.1 0.21 -10000 0 -0.51 71 71
FER -0.052 0.11 -10000 0 -0.36 20 20
RELA 0.03 0.003 -10000 0 -10000 0 0
ITK -0.057 0.11 -10000 0 -0.26 80 80
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG1 -0.089 0.24 0.39 13 -0.5 91 104
cytokine secretion -0.03 0.053 -10000 0 -10000 0 0
SPHK1 -0.071 0.14 -10000 0 -0.44 35 35
PTK2 -0.024 0.15 0.4 3 -0.72 8 11
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.13 0.22 -10000 0 -0.56 83 83
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.061 0.28 0.4 55 -0.53 75 130
MAP2K2 -0.22 0.39 -10000 0 -0.83 143 143
MAP2K1 -0.22 0.39 -10000 0 -0.83 143 143
MAP2K7 0.03 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.052 0.12 0.29 2 -0.35 17 19
MAP2K4 0.017 0.14 -10000 0 -0.81 12 12
Fc epsilon R1/FcgammaRIIB -0.16 0.29 -10000 0 -0.47 210 210
mol:Choline -0.1 0.2 0.35 15 -0.59 20 35
SHC/Grb2/SOS1 -0.022 0.13 -10000 0 -0.39 2 2
FYN 0.028 0.008 -10000 0 -10000 0 0
DOK1 0.029 0.005 -10000 0 -10000 0 0
PXN -0.014 0.15 0.42 10 -0.68 7 17
HCLS1 -0.059 0.13 -10000 0 -0.43 25 25
PRKCB -0.044 0.24 0.37 59 -0.4 79 138
FCGR2B -0.079 0.23 -10000 0 -0.59 87 87
IGHE -0.003 0.011 -10000 0 -10000 0 0
KLRG1/SHIP -0.045 0.12 -10000 0 -0.46 9 9
LCP2 -0.015 0.15 -10000 0 -0.59 30 30
PLA2G4A -0.053 0.11 -10000 0 -0.35 23 23
RASA1 0.025 0.031 -10000 0 -0.64 1 1
mol:Phosphatidic acid -0.1 0.2 0.35 15 -0.59 20 35
IKK complex 0.003 0.17 0.33 60 -0.25 3 63
WIPF1 0.029 0.006 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.016 0.15 -10000 0 -0.72 18 18
oxygen homeostasis -0.003 0.014 -10000 0 -10000 0 0
TCEB2 0.025 0.049 -10000 0 -0.6 3 3
TCEB1 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.14 0.12 -10000 0 -0.44 10 10
EPO -0.28 0.3 -10000 0 -0.69 125 125
FIH (dimer) 0.022 0.023 -10000 0 -10000 0 0
APEX1 0.024 0.019 -10000 0 -10000 0 0
SERPINE1 -0.24 0.3 -10000 0 -0.81 61 61
FLT1 0.001 0.12 -10000 0 -0.75 9 9
ADORA2A -0.23 0.27 0.53 2 -0.75 39 41
germ cell development -0.29 0.33 -10000 0 -0.73 132 132
SLC11A2 -0.22 0.27 -10000 0 -0.75 37 37
BHLHE40 -0.22 0.26 -10000 0 -0.75 38 38
HIF1AN 0.022 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.2 0.2 -10000 0 -0.48 83 83
ETS1 0.045 0.012 -10000 0 -10000 0 0
CITED2 -0.033 0.17 -10000 0 -0.7 24 24
KDR 0.01 0.1 -10000 0 -0.86 5 5
PGK1 -0.22 0.27 -10000 0 -0.75 39 39
SIRT1 0.028 0.006 -10000 0 -10000 0 0
response to hypoxia -0.002 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.25 0.32 -10000 0 -0.89 43 43
EPAS1 -0.18 0.14 0.33 1 -0.36 98 99
SP1 0.036 0.014 -10000 0 -10000 0 0
ABCG2 -0.22 0.27 -10000 0 -0.75 40 40
EFNA1 -0.22 0.27 -10000 0 -0.75 40 40
FXN -0.23 0.27 0.56 1 -0.74 39 40
POU5F1 -0.3 0.35 -10000 0 -0.77 132 132
neuron apoptosis 0.24 0.31 0.85 43 -10000 0 43
EP300 0.028 0.03 -10000 0 -0.64 1 1
EGLN3 -0.52 0.2 -10000 0 -0.6 439 439
EGLN2 0.026 0.018 -10000 0 -10000 0 0
EGLN1 0.022 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.038 0.044 -10000 0 -0.38 3 3
VHL 0.021 0.014 -10000 0 -10000 0 0
ARNT 0.021 0.022 -10000 0 -10000 0 0
SLC2A1 -0.24 0.29 0.5 1 -0.82 46 47
TWIST1 -0.22 0.26 0.56 1 -0.73 41 42
ELK1 0.037 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.17 0.18 -10000 0 -0.5 26 26
VEGFA -0.33 0.36 -10000 0 -0.77 142 142
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.039 0.015 -10000 0 -10000 0 0
VLDLR 0.029 0.007 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
LRPAP1 0.03 0.004 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ITGA3 0.028 0.028 -10000 0 -0.59 1 1
RELN/VLDLR/Fyn -0.086 0.21 -10000 0 -0.4 148 148
MAPK8IP1/MKK7/MAP3K11/JNK1 0.081 0.044 -10000 0 -0.68 1 1
AKT1 -0.063 0.13 -10000 0 -0.38 13 13
MAP2K7 0.03 0.003 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
DAB1 0.01 0.094 -10000 0 -0.59 12 12
RELN/LRP8/DAB1 -0.087 0.2 -10000 0 -0.37 158 158
LRPAP1/LRP8 0.042 0.023 -10000 0 -0.43 1 1
RELN/LRP8/DAB1/Fyn -0.073 0.19 -10000 0 -0.35 157 157
DAB1/alpha3/beta1 Integrin -0.063 0.18 -10000 0 -0.6 1 1
long-term memory -0.11 0.21 -10000 0 -0.62 19 19
DAB1/LIS1 -0.058 0.19 -10000 0 -0.62 1 1
DAB1/CRLK/C3G -0.064 0.18 -10000 0 -0.6 1 1
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
DAB1/NCK2 -0.058 0.19 -10000 0 -0.62 1 1
ARHGEF2 0.029 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.056 0.21 -10000 0 -0.6 67 67
CDK5R1 0.029 0.005 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.64 148 148
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RELN/LRP8/Fyn -0.086 0.21 -10000 0 -0.4 149 149
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.22 -10000 0 -0.39 137 137
MAPK8 0.029 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.087 0.2 -10000 0 -0.37 157 157
ITGB1 0.03 0.004 -10000 0 -10000 0 0
MAP1B -0.085 0.18 -10000 0 -0.35 130 130
RELN/LRP8 -0.086 0.21 -10000 0 -0.4 149 149
GRIN2B/RELN/LRP8/DAB1/Fyn -0.064 0.2 -10000 0 -0.36 125 125
PI3K 0.037 0.036 -10000 0 -0.47 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.042 0.023 -10000 0 -0.43 1 1
RAP1A -0.055 0.18 0.44 5 -0.57 1 6
PAFAH1B1 0.029 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.042 -10000 0 -0.64 2 2
CRLK/C3G 0.042 0.01 -10000 0 -10000 0 0
GRIN2B 0.023 0.039 -10000 0 -0.59 2 2
NCK2 0.029 0.005 -10000 0 -10000 0 0
neuron differentiation -0.032 0.13 -10000 0 -0.37 28 28
neuron adhesion -0.047 0.17 0.4 8 -0.54 1 9
LRP8 0.028 0.028 -10000 0 -0.59 1 1
GSK3B -0.057 0.12 -10000 0 -0.46 3 3
RELN/VLDLR/DAB1/Fyn -0.073 0.19 -10000 0 -0.35 156 156
MAP3K11 0.029 0.03 -10000 0 -0.64 1 1
RELN/VLDLR/DAB1/P13K -0.067 0.14 -10000 0 -0.29 133 133
CDK5 0.027 0.009 -10000 0 -10000 0 0
MAPT 0.011 0.099 0.71 5 -0.59 6 11
neuron migration -0.064 0.18 0.46 4 -0.52 2 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.032 0.13 -10000 0 -0.38 28 28
RELN/VLDLR -0.067 0.2 -10000 0 -0.37 142 142
Effects of Botulinum toxin

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
STX1A 0.008 0.042 0.18 2 -0.44 4 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.024 0.087 -10000 0 -0.46 15 15
STXBP1 0.028 0.03 -10000 0 -0.64 1 1
ACh/CHRNA1 -0.16 0.2 -10000 0 -0.39 215 215
RAB3GAP2/RIMS1/UNC13B 0.04 0.078 -10000 0 -0.39 15 15
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 0.007 0.11 -10000 0 -0.63 15 15
mol:ACh 0.003 0.046 0.1 42 -0.15 3 45
RAB3GAP2 0.029 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.018 0.088 -10000 0 -0.41 7 7
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.16 0.2 -10000 0 -0.39 215 215
UNC13B 0.029 0.006 -10000 0 -10000 0 0
CHRNA1 -0.24 0.3 -10000 0 -0.59 215 215
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.17 -10000 0 -0.43 78 78
SNAP25 -0.02 0.076 -10000 0 -0.21 68 68
VAMP2 0.007 0.001 -10000 0 -10000 0 0
SYT1 -0.075 0.24 -10000 0 -0.63 78 78
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.043 -10000 0 -0.38 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.088 -10000 0 -0.41 7 7
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.024 0.046 -10000 0 -10000 0 0
NFATC2 -0.024 0.053 -10000 0 -0.44 2 2
NFATC3 -0.023 0.046 -10000 0 -10000 0 0
CD40LG -0.27 0.34 -10000 0 -0.78 100 100
PTGS2 -0.26 0.31 -10000 0 -0.71 101 101
JUNB 0.027 0.042 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.033 -10000 0 -10000 0 0
CaM/Ca2+ -0.013 0.033 -10000 0 -10000 0 0
CALM1 0.004 0.027 -10000 0 -10000 0 0
JUN 0.003 0.029 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.016 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.015 -10000 0 -10000 0 0
FOSL1 0.002 0.13 -10000 0 -0.59 23 23
CREM 0.029 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.14 0.2 -10000 0 -0.55 33 33
FOS -0.013 0.1 -10000 0 -0.64 12 12
IFNG -0.36 0.4 -10000 0 -0.77 214 214
AP-1/NFAT1-c-4 -0.3 0.37 -10000 0 -0.86 96 96
FASLG -0.37 0.4 -10000 0 -0.76 220 220
NFAT1-c-4/ICER1 -0.062 0.11 -10000 0 -0.44 2 2
IL2RA -0.3 0.35 0.42 1 -0.81 110 111
FKBP12/FK506 0.022 0.004 -10000 0 -10000 0 0
CSF2 -0.25 0.3 -10000 0 -0.72 91 91
JunB/Fra1/NFAT1-c-4 -0.068 0.12 -10000 0 -0.44 10 10
IL4 -0.24 0.29 -10000 0 -0.69 93 93
IL2 -0.008 0.12 -10000 0 -0.62 17 17
IL3 -0.015 0.075 -10000 0 -0.69 1 1
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
BATF3 -0.026 0.17 -10000 0 -0.59 44 44
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.029 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.18 0.19 -10000 0 -0.58 32 32
IHH -0.081 0.2 -10000 0 -0.69 43 43
SHH Np/Cholesterol/GAS1 0.003 0.1 -10000 0 -0.37 29 29
LRPAP1 0.03 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.003 0.099 0.37 29 -10000 0 29
SMO/beta Arrestin2 -0.087 0.15 -10000 0 -0.52 26 26
SMO -0.098 0.15 -10000 0 -0.53 26 26
AKT1 -0.036 0.11 -10000 0 -0.52 13 13
ARRB2 0.028 0.033 -10000 0 -0.7 1 1
BOC 0.028 0.008 -10000 0 -10000 0 0
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
heart looping -0.097 0.15 -10000 0 -0.53 26 26
STIL -0.071 0.13 -10000 0 -0.43 27 27
DHH N/PTCH2 0.007 0.12 -10000 0 -0.44 35 35
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.49 35 35
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
DHH 0.014 0.098 -10000 0 -0.64 11 11
PTHLH -0.28 0.27 -10000 0 -0.79 39 39
determination of left/right symmetry -0.097 0.15 -10000 0 -0.53 26 26
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
skeletal system development -0.28 0.27 -10000 0 -0.78 39 39
IHH N/Hhip -0.16 0.25 -10000 0 -0.54 146 146
DHH N/Hhip -0.092 0.23 -10000 0 -0.48 126 126
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.097 0.15 -10000 0 -0.53 26 26
pancreas development -0.13 0.28 -10000 0 -0.63 119 119
HHAT 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.036 -10000 0 -0.47 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.15 -10000 0 -0.59 31 31
somite specification -0.097 0.15 -10000 0 -0.53 26 26
SHH Np/Cholesterol/PTCH1 -0.084 0.13 -10000 0 -0.44 28 28
SHH Np/Cholesterol/PTCH2 0.006 0.093 -10000 0 -0.34 31 31
SHH Np/Cholesterol/Megalin -0.004 0.12 -10000 0 -0.41 34 34
SHH 0.011 0.07 -10000 0 -0.47 10 10
catabolic process -0.12 0.16 -10000 0 -0.48 42 42
SMO/Vitamin D3 -0.086 0.14 -10000 0 -0.49 27 27
SHH Np/Cholesterol/Hhip -0.068 0.18 -10000 0 -0.38 109 109
LRP2 -0.022 0.17 -10000 0 -0.59 41 41
receptor-mediated endocytosis -0.099 0.16 -10000 0 -0.54 34 34
SHH Np/Cholesterol/BOC 0.021 0.057 -10000 0 -0.37 10 10
SHH Np/Cholesterol/CDO -0.016 0.12 -10000 0 -0.34 59 59
mesenchymal cell differentiation 0.068 0.17 0.38 109 -10000 0 109
mol:Vitamin D3 -0.078 0.14 -10000 0 -0.44 28 28
IHH N/PTCH2 -0.059 0.16 -10000 0 -0.47 66 66
CDON -0.041 0.2 -10000 0 -0.59 57 57
IHH N/PTCH1 -0.12 0.16 -10000 0 -0.48 44 44
Megalin/LRPAP1 0.004 0.13 -10000 0 -0.47 33 33
PTCH2 -0.002 0.13 -10000 0 -0.59 25 25
SHH Np/Cholesterol 0.011 0.055 -10000 0 -0.37 10 10
PTCH1 -0.12 0.16 -10000 0 -0.48 42 42
HHIP -0.13 0.28 -10000 0 -0.63 119 119
Arf6 signaling events

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
CENTA1/KIF3B 0.03 0.042 -10000 0 -0.4 4 4
ARNO/beta Arrestin1-2 0.023 0.066 -10000 0 -0.78 1 1
EGFR 0.019 0.068 -10000 0 -0.6 6 6
EPHA2 0.027 0.03 -10000 0 -0.64 1 1
USP6 0.028 0.028 -10000 0 -0.59 1 1
IQSEC1 0.021 0.014 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.41 0.16 -10000 0 -0.48 403 403
ARRB2 -0.003 0.072 -10000 0 -0.26 34 34
mol:GTP 0.002 0.046 0.19 6 -0.18 4 10
ARRB1 0.03 0.003 -10000 0 -10000 0 0
FBXO8 0.03 0.004 -10000 0 -10000 0 0
TSHR -0.043 0.2 -10000 0 -0.59 57 57
EGF -0.57 0.2 -10000 0 -0.63 450 450
somatostatin receptor activity 0 0 0.001 12 -0.001 23 35
ARAP2 0.027 0.042 -10000 0 -0.64 2 2
mol:GDP -0.045 0.099 0.23 7 -0.32 25 32
mol:PI-3-4-5-P3 0 0 0.001 7 -0.001 9 16
ITGA2B 0.007 0.12 -10000 0 -0.59 18 18
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.065 0.042 -10000 0 -0.36 3 3
ADAP1 0.021 0.06 -10000 0 -0.64 4 4
KIF13B 0.027 0.009 -10000 0 -10000 0 0
HGF/MET 0.018 0.1 -10000 0 -0.47 20 20
PXN 0.029 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.065 0.11 0.29 11 -0.33 25 36
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.34 0.14 -10000 0 -0.4 400 400
ADRB2 0.02 0.044 -10000 0 -0.64 2 2
receptor agonist activity 0 0 0 18 0 13 31
actin filament binding 0 0 0.001 17 -0.001 24 41
SRC 0.029 0.006 -10000 0 -10000 0 0
ITGB3 0.027 0.042 -10000 0 -0.64 2 2
GNAQ 0.029 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 24 -0.001 12 36
ARF6/GDP -0.048 0.11 0.27 5 -0.41 14 19
ARF6/GDP/GULP/ACAP1 -0.14 0.19 0.27 1 -0.43 85 86
alphaIIb/beta3 Integrin/paxillin/GIT1 0.057 0.081 -10000 0 -0.37 3 3
ACAP1 -0.2 0.3 -10000 0 -0.59 187 187
ACAP2 0.029 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.003 0.098 -10000 0 -0.36 34 34
EFNA1 0.027 0.028 -10000 0 -0.59 1 1
HGF 0.002 0.12 -10000 0 -0.6 20 20
CYTH3 0.011 0.004 -10000 0 -10000 0 0
CYTH2 0.018 0.045 -10000 0 -0.99 1 1
NCK1 0.027 0.031 -10000 0 -0.64 1 1
fibronectin binding 0 0 0.001 29 -0.001 13 42
endosomal lumen acidification 0 0 0.001 3 -0.001 21 24
microtubule-based process 0 0 -10000 0 -0.001 1 1
GULP1 0.007 0.12 -10000 0 -0.62 17 17
GNAQ/ARNO 0.034 0.044 -10000 0 -0.92 1 1
mol:Phosphatidic acid 0 0 0 4 -10000 0 4
PIP3-E 0 0 0.001 2 -10000 0 2
MET 0.024 0.04 -10000 0 -0.59 2 2
GNA14 0.021 0.073 -10000 0 -0.64 6 6
GNA15 0.013 0.1 -10000 0 -0.59 14 14
GIT1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 22 -0.001 15 37
GNA11 0.027 0.042 -10000 0 -0.64 2 2
LHCGR -0.027 0.15 -10000 0 -0.59 33 33
AGTR1 -0.003 0.14 -10000 0 -0.62 24 24
desensitization of G-protein coupled receptor protein signaling pathway -0.003 0.098 -10000 0 -0.36 34 34
IPCEF1/ARNO -0.26 0.12 -10000 0 -0.64 6 6
alphaIIb/beta3 Integrin 0.024 0.095 -10000 0 -0.44 20 20
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.035 0.057 -10000 0 -0.42 7 7
VEGFR1 homodimer/NRP1 0.015 0.053 -10000 0 -0.43 7 7
mol:DAG -0.17 0.18 -10000 0 -0.49 18 18
VEGFR1 homodimer/NRP1/VEGFR 121 -0.13 0.19 -10000 0 -0.34 205 205
CaM/Ca2+ -0.15 0.18 -10000 0 -0.66 6 6
HIF1A 0.03 0.05 -10000 0 -0.62 2 2
GAB1 0.03 0.004 -10000 0 -10000 0 0
AKT1 -0.12 0.16 -10000 0 -0.67 6 6
PLCG1 -0.17 0.18 -10000 0 -0.5 18 18
NOS3 -0.1 0.15 -10000 0 -0.53 11 11
CBL 0.028 0.03 -10000 0 -0.64 1 1
mol:NO -0.096 0.15 0.72 1 -0.5 11 12
FLT1 0.021 0.063 -10000 0 -0.5 7 7
PGF -0.32 0.31 -10000 0 -0.59 276 276
VEGFR1 homodimer/NRP2/VEGFR121 -0.12 0.2 -10000 0 -0.59 9 9
CALM1 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
eNOS/Hsp90 -0.083 0.16 0.56 1 -0.54 6 7
endothelial cell proliferation -0.12 0.16 0.59 1 -0.48 17 18
mol:Ca2+ -0.17 0.18 -10000 0 -0.49 18 18
MAPK3 -0.15 0.16 0.46 2 -0.59 6 8
MAPK1 -0.15 0.16 0.46 2 -0.62 6 8
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
PLGF homodimer -0.32 0.31 -10000 0 -0.59 276 276
PRKACA 0.03 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.009 0.14 -10000 0 -0.59 29 29
VEGFA homodimer -0.24 0.3 -10000 0 -0.59 220 220
VEGFR1 homodimer/VEGFA homodimer -0.14 0.2 -10000 0 -0.37 205 205
platelet activating factor biosynthetic process -0.14 0.16 0.44 2 -0.57 6 8
PI3K -0.14 0.19 -10000 0 -0.72 6 6
PRKCA -0.16 0.17 0.58 1 -0.47 16 17
PRKCB -0.16 0.17 0.58 1 -0.5 15 16
VEGFR1 homodimer/PLGF homodimer -0.19 0.21 -10000 0 -0.37 275 275
VEGFA -0.24 0.3 -10000 0 -0.59 220 220
VEGFB 0.03 0.003 -10000 0 -10000 0 0
mol:IP3 -0.17 0.18 -10000 0 -0.49 18 18
RASA1 0.022 0.056 -10000 0 -0.46 5 5
NRP2 0.02 0.073 -10000 0 -0.59 7 7
VEGFR1 homodimer 0.021 0.062 -10000 0 -0.5 7 7
VEGFB homodimer 0.03 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.031 -10000 0 -0.64 1 1
eNOS/Caveolin-1 -0.11 0.16 -10000 0 -0.52 26 26
PTPN11 0.029 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.14 0.19 -10000 0 -0.71 6 6
mol:L-citrulline -0.096 0.15 0.72 1 -0.5 11 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.1 0.19 -10000 0 -0.68 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.12 0.2 -10000 0 -0.59 8 8
CD2AP 0.029 0.006 -10000 0 -10000 0 0
PI3K/GAB1 -0.13 0.18 -10000 0 -0.69 6 6
PDPK1 -0.13 0.18 0.35 1 -0.7 6 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.12 0.19 -10000 0 -0.58 7 7
mol:NADP -0.096 0.15 0.72 1 -0.5 11 12
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.1 0.19 -10000 0 -0.66 5 5
VEGFR1 homodimer/NRP2 0.029 0.071 -10000 0 -0.4 11 11
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.008 -10000 0 -10000 0 0
VLDLR 0.029 0.007 -10000 0 -10000 0 0
LRPAP1 0.03 0.004 -10000 0 -10000 0 0
NUDC 0.029 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.086 0.21 -10000 0 -0.4 149 149
CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
KATNA1 0.028 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.079 0.19 -10000 0 -0.36 148 148
IQGAP1/CaM 0.041 0.012 -10000 0 -10000 0 0
DAB1 0.01 0.094 -10000 0 -0.59 12 12
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
PLA2G7 -0.44 0.26 -10000 0 -0.59 378 378
CALM1 0.028 0.008 -10000 0 -10000 0 0
DYNLT1 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.042 0.023 -10000 0 -0.43 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.005 -10000 0 -10000 0 0
CDK5R1 0.029 0.005 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.016 0.004 -10000 0 -10000 0 0
CDK5R2 -0.054 0.21 -10000 0 -0.59 64 64
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.097 0.21 -10000 0 -0.41 157 157
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.054 0.19 0.33 18 -0.48 13 31
MAP1B 0.008 0.008 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
p35/CDK5 -0.07 0.16 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.64 148 148
PAFAH/LIS1 -0.27 0.17 -10000 0 -0.37 365 365
LIS1/CLIP170 0.037 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.052 0.13 -10000 0 -0.42 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.06 0.14 -10000 0 -0.44 12 12
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.086 0.16 -10000 0 -0.5 14 14
LIS1/IQGAP1 0.037 0.01 -10000 0 -10000 0 0
RHOA 0.016 0.011 -10000 0 -10000 0 0
PAFAH1B1 0.022 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.028 0.03 -10000 0 -0.64 1 1
PAFAH1B2 0.028 0.03 -10000 0 -0.64 1 1
MAP1B/LIS1/Dynein heavy chain 0.038 0.023 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.05 0.18 0.34 13 -0.46 12 25
LRP8 0.028 0.028 -10000 0 -0.59 1 1
NDEL1/Katanin 60 -0.056 0.18 0.32 23 -0.47 13 36
P39/CDK5 -0.1 0.19 -10000 0 -0.59 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.037 0.011 -10000 0 -10000 0 0
CDK5 -0.086 0.16 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.032 0.009 -10000 0 -10000 0 0
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.071 0.19 -10000 0 -0.35 130 130
RELN/VLDLR -0.067 0.2 -10000 0 -0.37 142 142
CDC42 0.022 0.007 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.14 0.25 -10000 0 -0.67 77 77
NFATC2 -0.074 0.21 -10000 0 -0.72 10 10
NFATC3 -0.019 0.066 -10000 0 -0.32 2 2
CD40LG -0.19 0.34 -10000 0 -0.92 50 50
ITCH 0.04 0.047 -10000 0 -10000 0 0
CBLB 0.038 0.048 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.44 -10000 0 -0.95 119 119
JUNB 0.027 0.042 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.057 -10000 0 -10000 0 0
T cell anergy 0.025 0.074 -10000 0 -0.41 10 10
TLE4 -0.037 0.14 -10000 0 -0.58 6 6
Jun/NFAT1-c-4/p21SNFT -0.13 0.27 -10000 0 -0.86 16 16
AP-1/NFAT1-c-4 -0.18 0.35 -10000 0 -1 25 25
IKZF1 -0.095 0.25 -10000 0 -0.62 85 85
T-helper 2 cell differentiation -0.28 0.25 0.5 2 -0.62 100 102
AP-1/NFAT1 -0.052 0.17 -10000 0 -0.59 10 10
CALM1 0.037 0.035 -10000 0 -10000 0 0
EGR2 -0.089 0.23 -10000 0 -1.3 7 7
EGR3 -0.09 0.23 -10000 0 -1.3 7 7
NFAT1/FOXP3 -0.18 0.32 -10000 0 -0.68 111 111
EGR1 0.014 0.084 -10000 0 -0.64 8 8
JUN 0.011 0.032 -10000 0 -10000 0 0
EGR4 0.021 0.056 -10000 0 -0.58 4 4
mol:Ca2+ -0.001 0.04 -10000 0 -0.33 3 3
GBP3 -0.04 0.15 -10000 0 -0.63 8 8
FOSL1 0.002 0.13 -10000 0 -0.59 23 23
NFAT1-c-4/MAF/IRF4 -0.14 0.31 -10000 0 -0.78 29 29
DGKA -0.038 0.16 -10000 0 -0.72 8 8
CREM 0.029 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.1 0.21 -10000 0 -0.88 8 8
CTLA4 -0.29 0.4 -10000 0 -0.7 224 224
NFAT1-c-4 (dimer)/EGR1 -0.083 0.23 -10000 0 -0.94 9 9
NFAT1-c-4 (dimer)/EGR4 -0.088 0.23 -10000 0 -0.92 8 8
FOS -0.006 0.1 -10000 0 -0.64 12 12
IFNG -0.28 0.35 -10000 0 -0.74 135 135
T cell activation -0.045 0.18 0.47 1 -0.65 11 12
MAF 0.029 0.006 -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 0.057 0.16 0.82 4 -10000 0 4
TNF -0.065 0.23 -10000 0 -1 7 7
FASLG -0.21 0.33 -10000 0 -1.2 10 10
TBX21 -0.2 0.3 -10000 0 -0.64 158 158
BATF3 -0.026 0.17 -10000 0 -0.59 44 44
PRKCQ -0.026 0.1 -10000 0 -0.57 14 14
PTPN1 -0.036 0.15 -10000 0 -0.57 7 7
NFAT1-c-4/ICER1 -0.086 0.23 -10000 0 -0.88 8 8
GATA3 -0.29 0.33 -10000 0 -0.63 238 238
T-helper 1 cell differentiation -0.27 0.34 -10000 0 -0.73 136 136
IL2RA -0.23 0.36 -10000 0 -0.84 91 91
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.037 0.14 -10000 0 -0.58 6 6
E2F1 -0.029 0.19 -10000 0 -0.58 52 52
PPARG 0.022 0.014 -10000 0 -10000 0 0
SLC3A2 -0.036 0.15 -10000 0 -0.58 6 6
IRF4 -0.12 0.26 -10000 0 -0.59 116 116
PTGS2 -0.18 0.32 -10000 0 -0.92 30 30
CSF2 -0.17 0.3 -10000 0 -0.96 26 26
JunB/Fra1/NFAT1-c-4 -0.085 0.23 -10000 0 -0.88 7 7
IL4 -0.28 0.26 0.5 2 -0.65 96 98
IL5 -0.16 0.28 -10000 0 -0.9 22 22
IL2 -0.045 0.18 0.47 1 -0.66 11 12
IL3 -0.029 0.058 -10000 0 -0.9 1 1
RNF128 0.027 0.12 -10000 0 -0.63 16 16
NFATC1 -0.058 0.16 -10000 0 -0.83 4 4
CDK4 0.04 0.13 -10000 0 -10000 0 0
PTPRK -0.04 0.14 -10000 0 -0.6 5 5
IL8 -0.18 0.33 -10000 0 -0.96 33 33
POU2F1 0.029 0.007 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.042 0.025 -10000 0 -0.47 1 1
Necdin/E2F1 -0.008 0.15 -10000 0 -0.43 54 54
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.025 0.15 -10000 0 -0.52 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.17 0.26 -10000 0 -0.43 233 233
NT-4/5 (dimer)/p75(NTR) 0.005 0.12 -10000 0 -0.45 34 34
IKBKB 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.008 0.15 0.41 4 -0.55 11 15
IKBKG 0.03 0.004 -10000 0 -10000 0 0
BDNF -0.052 0.21 -10000 0 -0.59 66 66
MGDIs/NGR/p75(NTR)/LINGO1 0.01 0.14 -10000 0 -0.4 53 53
FURIN 0.03 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.024 0.18 -10000 0 -0.39 90 90
LINGO1 0.005 0.12 -10000 0 -0.59 20 20
Sortilin/TRAF6/NRIF 0.036 0.022 -10000 0 -10000 0 0
proBDNF (dimer) -0.052 0.21 -10000 0 -0.59 66 66
NTRK1 -0.017 0.16 -10000 0 -0.61 35 35
RTN4R 0.022 0.068 -10000 0 -0.59 6 6
neuron apoptosis -0.026 0.16 0.45 6 -0.56 11 17
IRAK1 0.03 0.004 -10000 0 -10000 0 0
SHC1 -0.032 0.15 -10000 0 -0.4 68 68
ARHGDIA 0.028 0.03 -10000 0 -0.64 1 1
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
Gamma Secretase 0.079 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.012 0.16 -10000 0 -0.37 69 69
MAGEH1 0.03 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.01 0.16 -10000 0 -0.52 13 13
Mammalian IAPs/DIABLO 0.012 0.14 -10000 0 -0.33 73 73
proNGF (dimer) -0.026 0.18 -10000 0 -0.58 45 45
MAGED1 0.03 0.003 -10000 0 -10000 0 0
APP 0.029 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.018 0.051 -10000 0 -0.62 3 3
ZNF274 0.03 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.018 0.14 -10000 0 -0.34 69 69
NGF -0.026 0.18 -10000 0 -0.59 45 45
cell cycle arrest 0.014 0.17 0.36 10 -0.38 53 63
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.005 0.098 -10000 0 -0.39 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.024 0.11 -10000 0 -0.38 34 34
NCSTN 0.029 0.007 -10000 0 -10000 0 0
mol:GTP -0.005 0.16 -10000 0 -0.4 68 68
PSENEN 0.03 0.003 -10000 0 -10000 0 0
mol:ceramide -0.025 0.14 -10000 0 -0.36 68 68
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.009 0.068 -10000 0 -0.45 3 3
p75(NTR)/beta APP 0.013 0.12 -10000 0 -0.44 30 30
BEX1 -0.22 0.32 -10000 0 -0.64 185 185
mol:GDP -0.044 0.15 -10000 0 -0.4 68 68
NGF (dimer) -0.25 0.26 -10000 0 -0.44 281 281
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.028 0.14 -10000 0 -0.37 53 53
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RAC1/GTP -0.006 0.14 -10000 0 -0.35 62 62
MYD88 0.021 0.014 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.005 0.16 -10000 0 -0.4 68 68
RHOB 0.029 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.007 0.14 -10000 0 -0.43 52 52
NT3 (dimer) 0.023 0.065 -10000 0 -0.62 5 5
TP53 -0.028 0.14 0.36 2 -0.59 6 8
PRDM4 -0.024 0.14 -10000 0 -0.36 67 67
BDNF (dimer) -0.3 0.29 -10000 0 -0.49 290 290
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
SORT1 0.028 0.03 -10000 0 -0.64 1 1
activation of caspase activity 0.019 0.15 -10000 0 -0.51 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.012 0.16 -10000 0 -0.37 69 69
RHOC 0.029 0.006 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
MAPK10 -0.013 0.15 0.46 7 -0.44 12 19
DIABLO 0.029 0.005 -10000 0 -10000 0 0
SMPD2 -0.025 0.14 -10000 0 -0.36 68 68
APH1B 0.03 0.003 -10000 0 -10000 0 0
APH1A 0.029 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.006 0.16 -10000 0 -0.4 69 69
PSEN1 0.028 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.008 0.13 -10000 0 -0.45 35 35
MAPK8 -0.012 0.14 0.43 7 -0.43 11 18
MAPK9 -0.017 0.13 0.45 6 -0.46 5 11
APAF1 0.029 0.006 -10000 0 -10000 0 0
NTF3 0.023 0.065 -10000 0 -0.62 5 5
NTF4 0.018 0.051 -10000 0 -0.63 3 3
NDN 0.027 0.042 -10000 0 -0.64 2 2
RAC1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.004 0.14 -10000 0 -0.57 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.071 0.028 -10000 0 -0.37 1 1
RhoA-B-C/GTP -0.006 0.16 -10000 0 -0.4 68 68
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.008 0.17 -10000 0 -0.54 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.004 0.17 -10000 0 -0.55 10 10
PRKACB 0.029 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.02 0.16 -10000 0 -0.43 65 65
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.065 0.22 -10000 0 -0.59 77 77
BIRC2 0.03 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.033 0.16 0.33 5 -0.52 7 12
BAD 0.005 0.15 0.48 10 -0.47 5 15
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
NGFR -0.009 0.15 -10000 0 -0.6 31 31
CYCS -0.02 0.14 0.43 2 -0.61 8 10
ADAM17 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.01 0.16 -10000 0 -0.37 68 68
BCL2L11 0.006 0.15 0.46 10 -0.48 5 15
BDNF (dimer)/p75(NTR) -0.047 0.2 -10000 0 -0.45 91 91
PI3K 0.006 0.16 -10000 0 -0.37 64 64
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.012 0.16 -10000 0 -0.55 11 11
NDNL2 0.03 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.029 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.028 0.18 -10000 0 -0.47 69 69
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.012 0.16 -10000 0 -0.55 11 11
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
PLG -0.31 0.32 -10000 0 -0.61 261 261
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.047 0.16 -10000 0 -0.51 23 23
SQSTM1 0.023 0.013 -10000 0 -10000 0 0
NGFRAP1 0.03 0.003 -10000 0 -10000 0 0
CASP3 0.009 0.14 0.46 10 -0.44 5 15
E2F1 -0.035 0.19 -10000 0 -0.59 52 52
CASP9 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.021 0.13 -10000 0 -0.52 1 1
NGF (dimer)/TRKA -0.035 0.18 -10000 0 -0.45 76 76
MMP7 -0.085 0.25 -10000 0 -0.64 86 86
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.025 0.15 -10000 0 -0.54 10 10
MMP3 -0.031 0.18 -10000 0 -0.59 45 45
APAF-1/Caspase 9 -0.054 0.13 -10000 0 -0.48 9 9
PLK1 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
regulation of centriole-centriole cohesion 0.038 0.07 0.14 150 -0.14 2 152
BUB1B -0.008 0.086 0.2 8 -0.3 27 35
PLK1 -0.005 0.047 0.15 10 -0.15 9 19
PLK1S1 0.007 0.032 0.14 10 -0.2 1 11
KIF2A 0.012 0.085 0.25 37 -0.33 4 41
regulation of mitotic centrosome separation -0.005 0.047 0.15 10 -0.15 9 19
GOLGA2 0.029 0.006 -10000 0 -10000 0 0
Hec1/SPC24 -0.074 0.22 -10000 0 -0.44 117 117
WEE1 0.011 0.059 0.23 4 -0.84 1 5
cytokinesis -0.059 0.17 0.26 12 -0.3 106 118
PP2A-alpha B56 -0.026 0.12 -10000 0 -0.6 7 7
AURKA 0.004 0.034 0.14 6 -0.16 5 11
PICH/PLK1 -0.015 0.11 -10000 0 -0.53 17 17
CENPE -0.042 0.13 0.27 3 -0.39 60 63
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.012 0.085 0.25 37 -0.32 4 41
PPP2CA 0.023 0.013 -10000 0 -10000 0 0
FZR1 0.029 0.03 -10000 0 -0.64 1 1
TPX2 -0.019 0.074 0.16 11 -0.16 91 102
PAK1 0.03 0.003 -10000 0 -10000 0 0
SPC24 -0.031 0.18 -10000 0 -0.59 49 49
FBXW11 0.023 0.013 -10000 0 -10000 0 0
CLSPN -0.017 0.077 0.14 3 -0.2 58 61
GORASP1 0.021 0.014 -10000 0 -10000 0 0
metaphase -0.002 0.006 0.017 20 -0.011 100 120
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.004 0.026 0.085 11 -0.077 10 21
G2 phase of mitotic cell cycle 0 0.003 0.017 4 -0.01 3 7
STAG2 0.03 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.11 0.22 -10000 0 -0.46 140 140
spindle elongation -0.005 0.047 0.15 10 -0.15 9 19
ODF2 0.029 0.007 -10000 0 -10000 0 0
BUB1 -0.056 0.12 -10000 0 -0.66 7 7
TPT1 0.002 0.041 0.16 3 -0.2 11 14
CDC25C -0.033 0.11 0.17 10 -0.19 96 106
CDC25B 0.025 0.056 -10000 0 -0.6 4 4
SGOL1 -0.039 0.07 0.14 2 -0.14 150 152
RHOA 0.021 0.014 -10000 0 -10000 0 0
CCNB1/CDK1 0.017 0.072 -10000 0 -0.42 8 8
CDC14B 0.011 0.003 -10000 0 -10000 0 0
CDC20 -0.023 0.17 -10000 0 -0.59 42 42
PLK1/PBIP1 -0.013 0.079 0.14 3 -0.37 17 20
mitosis -0.002 0.003 0.021 4 -0.018 1 5
FBXO5 -0.002 0.047 0.19 7 -0.2 4 11
CDC2 0 0.003 -10000 0 -0.016 9 9
NDC80 -0.1 0.25 -10000 0 -0.59 105 105
metaphase plate congression -0.006 0.064 0.16 1 -0.26 22 23
ERCC6L -0.002 0.11 -10000 0 -0.5 17 17
NLP/gamma Tubulin -0.001 0.032 0.12 7 -0.11 9 16
microtubule cytoskeleton organization 0.002 0.041 0.16 3 -0.2 11 14
G2/M transition DNA damage checkpoint 0 0.002 0.012 2 -10000 0 2
PPP1R12A 0.03 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 -0.095 0.2 -10000 0 -0.35 176 176
GRASP65/GM130/RAB1/GTP/PLK1 0.019 0.046 -10000 0 -10000 0 0
RAB1A 0.029 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.001 0.034 0.12 13 -0.12 8 21
mitotic prometaphase -0.002 0.005 0.017 15 -0.012 1 16
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.059 -10000 0 -0.49 3 3
microtubule-based process -0.12 0.18 0.21 1 -0.36 177 178
Golgi organization -0.005 0.047 0.15 10 -0.15 9 19
Cohesin/SA2 0.007 0.047 0.19 1 -10000 0 1
PPP1CB/MYPT1 0.043 0.011 -10000 0 -10000 0 0
KIF20A -0.2 0.29 -10000 0 -0.59 177 177
APC/C/CDC20 -0.018 0.12 0.19 3 -0.39 42 45
PPP2R1A 0.03 0.003 -10000 0 -10000 0 0
chromosome segregation -0.013 0.077 0.14 3 -0.36 17 20
PRC1 0.024 0.061 -10000 0 -0.59 5 5
ECT2 0.004 0.057 0.24 14 -10000 0 14
C13orf34 -0.001 0.036 0.12 11 -0.13 7 18
NUDC -0.006 0.064 0.16 1 -0.26 22 23
regulation of attachment of spindle microtubules to kinetochore -0.007 0.085 0.2 8 -0.3 27 35
spindle assembly -0.003 0.041 0.14 10 -0.13 8 18
spindle stabilization 0.007 0.032 0.14 10 -0.2 1 11
APC/C/HCDH1 0.029 0.021 -10000 0 -0.41 1 1
MKLP2/PLK1 -0.12 0.18 0.21 1 -0.36 177 178
CCNB1 0.018 0.078 -10000 0 -0.59 8 8
PPP1CB 0.03 0.006 -10000 0 -10000 0 0
BTRC 0.029 0.006 -10000 0 -10000 0 0
ROCK2 -0.022 0.072 0.18 3 -0.32 9 12
TUBG1 0.004 0.037 0.15 4 -0.23 6 10
G2/M transition of mitotic cell cycle -0.01 0.061 -10000 0 -0.41 8 8
MLF1IP -0.006 0.084 -10000 0 -0.45 17 17
INCENP 0.029 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.026 0.055 -10000 0 -0.59 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.059 0.15 0.44 27 -0.35 1 28
IL27/IL27R/JAK1 -0.027 0.27 0.67 3 -0.68 30 33
TBX21 -0.13 0.34 0.57 9 -0.63 106 115
IL12B -0.047 0.19 -10000 0 -0.59 52 52
IL12A 0.007 0.01 0.17 1 -10000 0 1
IL6ST -0.002 0.11 -10000 0 -0.63 15 15
IL27RA/JAK1 0.013 0.064 -10000 0 -10000 0 0
IL27 -0.024 0.15 -10000 0 -0.6 32 32
TYK2 0.011 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.011 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.059 0.15 0.44 27 -0.35 1 28
T cell proliferation during immune response 0.059 0.15 0.44 27 -0.35 1 28
MAPKKK cascade -0.059 0.15 0.35 1 -0.44 27 28
STAT3 0.029 0.005 -10000 0 -10000 0 0
STAT2 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.029 -10000 0 -0.59 1 1
IL12RB1 -0.16 0.29 -10000 0 -0.59 155 155
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.3 0.56 9 -0.62 58 67
IL27/IL27R/JAK2/TYK2 -0.06 0.15 0.35 1 -0.44 27 28
positive regulation of T cell mediated cytotoxicity -0.059 0.15 0.35 1 -0.44 27 28
STAT1 (dimer) 0.019 0.42 0.54 101 -0.74 53 154
JAK2 0.015 0.022 -10000 0 -10000 0 0
JAK1 0.031 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.039 0.15 0.39 2 -0.47 9 11
T cell proliferation -0.088 0.17 -10000 0 -0.55 23 23
IL12/IL12R/TYK2/JAK2 -0.1 0.17 -10000 0 -0.87 2 2
IL17A -0.011 0.11 -10000 0 -10000 0 0
mast cell activation 0.059 0.15 0.44 27 -0.35 1 28
IFNG -0.027 0.056 0.12 7 -0.096 72 79
T cell differentiation -0.008 0.01 0.019 4 -0.023 120 124
STAT3 (dimer) -0.04 0.15 0.39 2 -0.46 10 12
STAT5A (dimer) -0.04 0.15 0.39 2 -0.52 5 7
STAT4 (dimer) -0.058 0.18 0.39 2 -0.55 28 30
STAT4 -0.007 0.14 -10000 0 -0.59 29 29
T cell activation -0.009 0.006 0.07 1 -10000 0 1
IL27R/JAK2/TYK2 -0.011 0.11 -10000 0 -0.49 2 2
GATA3 -0.59 0.65 0.5 1 -1.3 238 239
IL18 0.007 0.045 -10000 0 -0.43 5 5
positive regulation of mast cell cytokine production -0.04 0.15 0.38 2 -0.46 10 12
IL27/EBI3 -0.068 0.23 -10000 0 -0.55 83 83
IL27RA -0.003 0.05 -10000 0 -0.47 1 1
IL6 -0.046 0.2 -10000 0 -0.6 58 58
STAT5A 0.029 0.005 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 -0.011 0.057 -10000 0 -0.39 3 3
IL1B 0.005 0.049 -10000 0 -0.44 6 6
EBI3 -0.069 0.22 -10000 0 -0.6 73 73
TNF 0.003 0.059 -10000 0 -0.46 8 8
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.003 -10000 0 -10000 0 0
ELF1 -0.025 0.12 -10000 0 -0.48 5 5
CCNA2 -0.093 0.25 -10000 0 -0.59 99 99
PIK3CA 0.028 0.031 -10000 0 -0.64 1 1
JAK3 -0.095 0.25 -10000 0 -0.58 102 102
PIK3R1 0.027 0.031 -10000 0 -0.64 1 1
JAK1 0.03 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.056 0.16 -10000 0 -0.48 34 34
SHC1 0.029 0.007 -10000 0 -10000 0 0
SP1 0.036 0.02 -10000 0 -10000 0 0
IL2RA -0.077 0.21 -10000 0 -0.5 99 99
IL2RB -0.3 0.31 -10000 0 -0.58 265 265
SOS1 0.03 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.16 -10000 0 -0.59 34 34
G1/S transition of mitotic cell cycle -0.003 0.13 0.44 6 -0.53 4 10
PTPN11 0.03 0.006 -10000 0 -10000 0 0
CCND2 0.028 0.034 -10000 0 -0.51 2 2
LCK 0.002 0.13 -10000 0 -0.59 22 22
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.013 0.086 -10000 0 -0.58 10 10
CDK6 0.025 0.031 -10000 0 -0.64 1 1
CCND3 -0.039 0.15 0.42 2 -0.49 10 12
Ephrin A reverse 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
MAPKKK cascade -0.01 0.13 -9999 0 -0.42 42 42
EFNA5 -0.023 0.17 -9999 0 -0.63 36 36
FYN 0.008 0.13 -9999 0 -0.38 42 42
neuron projection morphogenesis -0.01 0.13 -9999 0 -0.42 42 42
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.01 0.13 -9999 0 -0.42 42 42
EPHA5 0.012 0.079 -9999 0 -0.6 8 8
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.01 0.019 -10000 0 -0.41 1 1
ADCY5 -0.007 0.083 -10000 0 -0.41 20 20
ADCY6 0.01 0.035 -10000 0 -0.77 1 1
ADCY7 -0.001 0.067 -10000 0 -0.37 16 16
ADCY1 0.002 0.061 -10000 0 -0.4 11 11
ADCY2 -0.064 0.16 -10000 0 -0.37 105 105
ADCY3 0.011 0.019 -10000 0 -0.41 1 1
ADCY8 -0.1 0.18 -10000 0 -0.37 148 148
PRKCE 0.011 0.022 -10000 0 -0.48 1 1
ADCY9 0.01 0.019 -10000 0 -0.41 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.041 0.13 0.29 19 -0.33 35 54
Coregulation of Androgen receptor activity

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
NRIP1 0.028 0.011 -9999 0 -10000 0 0
SVIL 0.029 0.01 -9999 0 -10000 0 0
ZNF318 0.03 0.013 -9999 0 -10000 0 0
JMJD2C 0 0.016 -9999 0 -0.086 16 16
T-DHT/AR/Ubc9 -0.081 0.092 -9999 0 -0.47 21 21
CARM1 0.03 0.003 -9999 0 -10000 0 0
PRDX1 0.029 0.006 -9999 0 -10000 0 0
PELP1 0.03 0.005 -9999 0 -10000 0 0
CTNNB1 0.02 0.016 -9999 0 -10000 0 0
AKT1 0.028 0.009 -9999 0 -10000 0 0
PTK2B 0.027 0.011 -9999 0 -10000 0 0
MED1 0.03 0.006 -9999 0 -10000 0 0
MAK 0.029 0.03 -9999 0 -0.59 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.022 0.054 -9999 0 -0.66 3 3
GSN 0.027 0.013 -9999 0 -10000 0 0
NCOA2 0.019 0.079 -9999 0 -0.64 7 7
NCOA6 0.028 0.011 -9999 0 -10000 0 0
DNA-PK 0.054 0.023 -9999 0 -10000 0 0
NCOA4 0.029 0.005 -9999 0 -10000 0 0
PIAS3 0.029 0.009 -9999 0 -10000 0 0
cell proliferation -0.043 0.1 -9999 0 -0.54 18 18
XRCC5 0.029 0.007 -9999 0 -10000 0 0
UBE3A 0.028 0.015 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.096 0.12 -9999 0 -0.49 36 36
FHL2 -0.049 0.11 -9999 0 -0.74 9 9
RANBP9 0.028 0.01 -9999 0 -10000 0 0
JMJD1A -0.12 0.053 -9999 0 -0.14 425 425
CDK6 0.026 0.031 -9999 0 -0.64 1 1
TGFB1I1 0.026 0.029 -9999 0 -0.59 1 1
T-DHT/AR/CyclinD1 -0.095 0.11 -9999 0 -0.45 39 39
XRCC6 0.03 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.11 -9999 0 -0.5 23 23
CTDSP1 0.028 0.007 -9999 0 -10000 0 0
CTDSP2 0.031 0.012 -9999 0 -10000 0 0
BRCA1 0.029 0.01 -9999 0 -10000 0 0
TCF4 0.03 0.009 -9999 0 -10000 0 0
CDKN2A -0.57 0.13 -9999 0 -0.59 477 477
SRF 0.036 0.016 -9999 0 -10000 0 0
NKX3-1 -0.21 0.12 -9999 0 -0.51 45 45
KLK3 0.02 0.087 -9999 0 -0.44 12 12
TMF1 0.023 0.012 -9999 0 -10000 0 0
HNRNPA1 0.03 0.007 -9999 0 -10000 0 0
AOF2 -0.001 0.006 -9999 0 -10000 0 0
APPL1 0.017 0.014 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.081 0.092 -9999 0 -0.46 22 22
AR -0.08 0.14 -9999 0 -0.66 24 24
UBA3 0.023 0.012 -9999 0 -10000 0 0
PATZ1 0.03 0.007 -9999 0 -10000 0 0
PAWR 0.028 0.03 -9999 0 -0.64 1 1
PRKDC 0.028 0.008 -9999 0 -10000 0 0
PA2G4 0.03 0.007 -9999 0 -10000 0 0
UBE2I 0.029 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.073 0.085 -9999 0 -0.42 23 23
RPS6KA3 0.027 0.033 -9999 0 -0.66 1 1
T-DHT/AR/ARA70 -0.083 0.092 -9999 0 -0.46 22 22
LATS2 0.03 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.073 0.085 -9999 0 -0.42 23 23
Cyclin D3/CDK11 p58 0.021 0.005 -9999 0 -10000 0 0
VAV3 0.01 0.11 -9999 0 -0.64 14 14
KLK2 -0.074 0.093 -9999 0 -0.52 17 17
CASP8 0.029 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.073 0.1 -9999 0 -0.47 23 23
TMPRSS2 -0.85 0.33 -9999 0 -0.97 434 434
CCND1 0.009 0.11 -9999 0 -0.59 17 17
PIAS1 0.028 0.015 -9999 0 -10000 0 0
mol:T-DHT -0.057 0.025 -9999 0 -0.067 410 410
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.027 0.02 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.076 0.095 -9999 0 -0.47 20 20
CMTM2 0.015 0.09 -9999 0 -0.58 11 11
SNURF 0.008 0.12 -9999 0 -0.64 16 16
ZMIZ1 -0.047 0.033 -9999 0 -10000 0 0
CCND3 0.029 0.006 -9999 0 -10000 0 0
TGIF1 0.03 0.007 -9999 0 -10000 0 0
FKBP4 0.028 0.011 -9999 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.36 -10000 0 -1 23 23
IL23A -0.16 0.36 -10000 0 -1.1 12 12
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.36 -10000 0 -0.95 29 29
positive regulation of T cell mediated cytotoxicity -0.2 0.38 -10000 0 -1 35 35
ITGA3 -0.17 0.35 -10000 0 -1 14 14
IL17F -0.11 0.28 0.58 4 -0.73 11 15
IL12B -0.059 0.19 -10000 0 -0.61 52 52
STAT1 (dimer) -0.18 0.37 -10000 0 -0.99 33 33
CD4 -0.17 0.36 -10000 0 -0.94 30 30
IL23 -0.2 0.34 -10000 0 -1 21 21
IL23R -0.022 0.16 -10000 0 -0.8 9 9
IL1B -0.17 0.37 -10000 0 -1 21 21
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.36 -10000 0 -0.97 24 24
TYK2 0.014 0.035 -10000 0 -10000 0 0
STAT4 -0.007 0.14 -10000 0 -0.59 29 29
STAT3 0.03 0.005 -10000 0 -10000 0 0
IL18RAP -0.14 0.27 -10000 0 -0.6 128 128
IL12RB1 -0.17 0.3 -10000 0 -0.61 155 155
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
IL12Rbeta1/TYK2 -0.12 0.24 -10000 0 -0.46 155 155
IL23R/JAK2 -0.026 0.16 -10000 0 -0.78 7 7
positive regulation of chronic inflammatory response -0.2 0.38 -10000 0 -1 35 35
natural killer cell activation 0.002 0.01 0.049 10 -10000 0 10
JAK2 0.009 0.042 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
NFKB1 0.028 0.03 -10000 0 -0.63 1 1
RELA 0.029 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.33 -10000 0 -0.97 23 23
ALOX12B -0.21 0.37 -10000 0 -1 27 27
CXCL1 -0.21 0.41 -10000 0 -1.1 40 40
T cell proliferation -0.2 0.38 -10000 0 -1 35 35
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
IL17A -0.082 0.23 -10000 0 -0.58 6 6
PI3K -0.17 0.36 -10000 0 -0.98 28 28
IFNG -0.04 0.059 0.12 7 -0.11 71 78
STAT3 (dimer) -0.16 0.34 -10000 0 -0.96 23 23
IL18R1 0.012 0.076 -10000 0 -0.61 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.28 -10000 0 -0.72 20 20
IL18/IL18R -0.094 0.2 -10000 0 -0.4 136 136
macrophage activation -0.014 0.015 -10000 0 -0.045 4 4
TNF -0.18 0.37 -10000 0 -1.1 23 23
STAT3/STAT4 -0.19 0.38 -10000 0 -0.97 40 40
STAT4 (dimer) -0.2 0.39 -10000 0 -0.99 44 44
IL18 0.016 0.062 -10000 0 -0.58 5 5
IL19 -0.18 0.35 -10000 0 -0.97 21 21
STAT5A (dimer) -0.18 0.37 -10000 0 -0.98 33 33
STAT1 0.028 0.028 -10000 0 -0.59 1 1
SOCS3 0.027 0.039 -10000 0 -0.59 2 2
CXCL9 -0.26 0.42 -10000 0 -0.97 63 63
MPO -0.18 0.36 -10000 0 -0.97 25 25
positive regulation of humoral immune response -0.2 0.38 -10000 0 -1 35 35
IL23/IL23R/JAK2/TYK2 -0.21 0.39 -10000 0 -1.1 34 34
IL6 -0.2 0.43 -10000 0 -1.1 44 44
STAT5A 0.029 0.005 -10000 0 -10000 0 0
IL2 -0.011 0.087 -10000 0 -0.59 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.01 0.049 10 -10000 0 10
CD3E -0.26 0.43 -10000 0 -0.96 64 64
keratinocyte proliferation -0.2 0.38 -10000 0 -1 35 35
NOS2 -0.17 0.36 -10000 0 -0.95 26 26
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.43 220 220
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
SPHK1 -0.01 0.082 -10000 0 -0.59 6 6
mol:S1P -0.004 0.076 -10000 0 -0.5 6 6
S1P1/S1P/Gi -0.051 0.13 0.32 1 -0.49 16 17
GNAO1 0.026 0.057 -10000 0 -0.59 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.027 0.1 0.33 1 -0.45 9 10
PLCG1 -0.04 0.12 0.32 2 -0.46 15 17
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
GNAI2 0.022 0.016 -10000 0 -10000 0 0
GNAI3 0.03 0.008 -10000 0 -10000 0 0
GNAI1 0.026 0.032 -10000 0 -0.65 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.15 0.19 -10000 0 -0.36 220 220
S1P1/S1P -0.094 0.15 0.25 1 -0.37 24 25
negative regulation of cAMP metabolic process -0.049 0.12 0.32 1 -0.47 16 17
MAPK3 -0.05 0.15 0.42 2 -0.59 21 23
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
KDR 0.029 0.03 -10000 0 -0.64 1 1
PLCB2 -0.1 0.18 0.32 9 -0.44 48 57
RAC1 0.027 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.089 0.12 -10000 0 -0.34 13 13
receptor internalization -0.091 0.14 -10000 0 -0.34 25 25
PTGS2 -0.048 0.23 0.47 7 -0.91 24 31
Rac1/GTP -0.082 0.12 -10000 0 -0.33 14 14
RHOA 0.021 0.014 -10000 0 -10000 0 0
VEGFA -0.24 0.3 -10000 0 -0.58 220 220
negative regulation of T cell proliferation -0.049 0.12 0.32 1 -0.47 16 17
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
MAPK1 -0.052 0.15 0.32 1 -0.59 23 24
S1P1/S1P/PDGFB-D/PDGFRB -0.085 0.14 0.3 1 -0.39 13 14
ABCC1 0.029 0.007 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.067 0.15 -10000 0 -0.53 17 17
UGCG -0.014 0.12 -10000 0 -0.57 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT -0.037 0.16 0.35 3 -0.43 25 28
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.013 0.12 -10000 0 -0.56 19 19
mol:DAG -0.014 0.13 -10000 0 -0.84 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.15 0.29 1 -0.44 17 18
FRAP1 -0.04 0.16 0.36 3 -0.48 23 26
FOXO3 -0.037 0.16 0.36 4 -0.49 17 21
AKT1 -0.045 0.16 0.31 1 -0.48 28 29
GAB2 0.03 0.003 -10000 0 -10000 0 0
SMPD1 0.007 0.046 -10000 0 -0.74 1 1
SGMS1 -0.008 0.12 -10000 0 -0.7 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 0.013 0.027 -10000 0 -0.4 2 2
CALM1 0.028 0.008 -10000 0 -10000 0 0
cell proliferation -0.016 0.12 0.3 4 -0.5 16 20
EIF3A 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.041 0.037 -10000 0 -0.47 2 2
RPS6KB1 -0.019 0.12 -10000 0 -0.91 6 6
mol:sphingomyelin -0.014 0.13 -10000 0 -0.84 12 12
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.094 0.25 -10000 0 -0.58 102 102
PIK3R1 0.028 0.031 -10000 0 -0.64 1 1
JAK1 0.031 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MYC -0.032 0.16 0.43 4 -0.57 7 11
MYB -0.1 0.22 -10000 0 -0.57 24 24
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.058 0.17 0.26 1 -0.49 36 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.006 0.12 -10000 0 -0.86 6 6
mol:PI-3-4-5-P3 -0.056 0.16 0.26 1 -0.48 36 37
Rac1/GDP 0.027 0.029 -10000 0 -0.36 2 2
T cell proliferation -0.048 0.16 0.31 1 -0.46 31 32
SHC1 0.029 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.007 0.021 -10000 0 -0.04 139 139
PRKCZ -0.048 0.16 -10000 0 -0.48 31 31
NF kappa B1 p50/RelA -0.016 0.16 -10000 0 -0.44 16 16
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.085 0.16 -10000 0 -0.48 45 45
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
IL2RA -0.092 0.24 -10000 0 -0.59 98 98
IL2RB -0.3 0.31 -10000 0 -0.58 265 265
TERT -0.049 0.2 -10000 0 -0.59 58 58
E2F1 -0.051 0.14 -10000 0 -0.4 26 26
SOS1 0.03 0.006 -10000 0 -10000 0 0
RPS6 0.026 0.039 -10000 0 -0.59 2 2
mol:cAMP 0.003 0.01 0.019 137 -10000 0 137
PTPN11 0.03 0.006 -10000 0 -10000 0 0
IL2RG -0.01 0.16 -10000 0 -0.59 34 34
actin cytoskeleton organization -0.048 0.16 0.31 1 -0.46 31 32
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.015 0.086 -10000 0 -0.58 10 10
PIK3CA 0.029 0.031 -10000 0 -0.64 1 1
Rac1/GTP 0.047 0.037 -10000 0 -0.35 2 2
LCK 0.004 0.13 -10000 0 -0.59 22 22
BCL2 -0.023 0.14 0.45 2 -0.49 2 4
BCR signaling pathway

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
JUN -0.021 0.15 0.37 13 -0.42 14 27
IKBKB 0.005 0.12 0.34 17 -0.31 2 19
AKT1 0 0.14 0.4 25 -0.29 4 29
IKBKG 0.02 0.11 0.31 16 -10000 0 16
CALM1 -0.002 0.09 0.36 1 -10000 0 1
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
MAP3K1 -0.046 0.2 0.41 16 -0.46 33 49
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.095 0.28 1 -0.32 6 7
DOK1 0.029 0.005 -10000 0 -10000 0 0
AP-1 0.014 0.11 0.31 19 -0.28 6 25
LYN 0.028 0.008 -10000 0 -10000 0 0
BLNK 0.028 0.03 -10000 0 -0.64 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
BCR complex -0.075 0.21 -10000 0 -0.44 121 121
CD22 -0.066 0.16 -10000 0 -0.49 28 28
CAMK2G 0.003 0.088 0.35 1 -10000 0 1
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
INPP5D 0.023 0.055 -10000 0 -0.59 4 4
SHC/GRB2/SOS1 -0.042 0.14 -10000 0 -0.55 3 3
GO:0007205 -0.004 0.095 0.28 1 -0.33 6 7
SYK 0.027 0.034 -10000 0 -0.48 2 2
ELK1 0.001 0.095 0.3 1 -10000 0 1
NFATC1 -0.04 0.15 0.37 7 -0.38 32 39
B-cell antigen/BCR complex -0.075 0.21 -10000 0 -0.44 121 121
PAG1/CSK 0.042 0.011 -10000 0 -10000 0 0
NFKBIB 0.021 0.054 0.15 23 -0.13 5 28
HRAS -0.002 0.094 0.31 2 -0.33 3 5
NFKBIA 0.021 0.053 0.16 19 -0.13 4 23
NF-kappa-B/RelA/I kappa B beta 0.027 0.049 0.16 18 -0.17 1 19
RasGAP/Csk -0.081 0.23 -10000 0 -0.62 43 43
mol:GDP -0.002 0.091 0.3 1 -0.33 4 5
PTEN 0.029 0.006 -10000 0 -10000 0 0
CD79B 0.026 0.048 -10000 0 -0.58 3 3
NF-kappa-B/RelA/I kappa B alpha 0.027 0.049 0.16 18 -0.17 1 19
GRB2 0.029 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.015 0.18 0.4 14 -0.46 12 26
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 -0.006 0.094 0.28 1 -0.33 6 7
CSK 0.03 0.003 -10000 0 -10000 0 0
FOS -0.004 0.11 0.35 3 -0.52 3 6
CHUK 0.011 0.12 0.32 16 -0.32 8 24
IBTK 0.028 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.028 0.16 0.39 1 -0.48 4 5
PTPN6 -0.06 0.15 -10000 0 -0.48 26 26
RELA 0.03 0.003 -10000 0 -10000 0 0
BCL2A1 0.004 0.06 0.16 11 -0.15 1 12
VAV2 -0.076 0.19 -10000 0 -0.5 60 60
ubiquitin-dependent protein catabolic process 0.025 0.052 0.15 25 -0.12 5 30
BTK -0.04 0.14 -10000 0 -0.88 10 10
CD19 -0.093 0.21 -10000 0 -0.56 64 64
MAP4K1 -0.21 0.3 -10000 0 -0.59 197 197
CD72 -0.12 0.26 -10000 0 -0.59 118 118
PAG1 0.028 0.007 -10000 0 -10000 0 0
MAPK14 -0.033 0.18 0.37 21 -0.41 19 40
SH3BP5 0.02 0.032 -10000 0 -0.64 1 1
PIK3AP1 0.001 0.095 0.3 1 -0.45 3 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.061 0.14 -10000 0 -0.46 12 12
RAF1 0.001 0.091 0.31 3 -10000 0 3
RasGAP/p62DOK/SHIP -0.08 0.23 -10000 0 -0.61 44 44
CD79A -0.12 0.27 -10000 0 -0.59 123 123
re-entry into mitotic cell cycle 0.014 0.11 0.3 19 -0.28 6 25
RASA1 0.025 0.031 -10000 0 -0.64 1 1
MAPK3 0.018 0.1 0.39 9 -10000 0 9
MAPK1 0.014 0.092 0.38 5 -10000 0 5
CD72/SHP1 -0.11 0.23 0.34 1 -0.54 82 83
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 -0.034 0.18 0.37 22 -0.4 28 50
actin cytoskeleton organization -0.05 0.18 0.36 5 -0.47 38 43
NF-kappa-B/RelA 0.056 0.089 0.29 19 -10000 0 19
Calcineurin 0.022 0.088 -10000 0 -10000 0 0
PI3K -0.077 0.16 -10000 0 -0.48 38 38
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.007 0.091 0.31 1 -0.38 6 7
SOS1 0.029 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.13 0.23 -10000 0 -0.58 40 40
DAPP1 -0.043 0.15 -10000 0 -0.71 10 10
cytokine secretion -0.037 0.14 0.37 7 -0.36 31 38
mol:DAG -0.006 0.094 0.28 1 -0.33 6 7
PLCG2 0.02 0.075 -10000 0 -0.61 7 7
MAP2K1 0.009 0.093 0.37 4 -10000 0 4
B-cell antigen/BCR complex/FcgammaRIIB -0.11 0.26 -10000 0 -0.46 160 160
mol:PI-3-4-5-P3 -0.059 0.12 -10000 0 -0.35 28 28
ETS1 0.008 0.089 0.43 2 -10000 0 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.022 0.17 -10000 0 -0.61 3 3
B-cell antigen/BCR complex/LYN -0.064 0.14 -10000 0 -0.4 33 33
MALT1 0.029 0.005 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 -0.056 0.19 0.33 2 -0.5 38 40
B-cell antigen/BCR complex/LYN/SYK -0.06 0.18 -10000 0 -0.53 26 26
CARD11 -0.043 0.18 0.36 8 -0.42 54 62
FCGR2B -0.079 0.23 -10000 0 -0.59 87 87
PPP3CA 0.03 0.004 -10000 0 -10000 0 0
BCL10 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.02 0.072 0.21 30 -10000 0 30
PTPRC -0.037 0.19 -10000 0 -0.59 53 53
PDPK1 -0.022 0.11 0.3 12 -0.28 9 21
PPP3CB 0.029 0.006 -10000 0 -10000 0 0
PPP3CC 0.027 0.009 -10000 0 -10000 0 0
POU2F2 0.012 0.054 0.15 11 -10000 0 11
Glucocorticoid receptor regulatory network

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
PCK2 0.036 0.089 -10000 0 -1.2 1 1
SMARCC2 0.031 0.005 -10000 0 -10000 0 0
SMARCC1 0.023 0.015 -10000 0 -10000 0 0
TBX21 -0.18 0.27 0.57 1 -0.55 159 160
SUMO2 0.024 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.035 0.038 -10000 0 -0.8 1 1
FKBP4 0.029 0.006 -10000 0 -10000 0 0
FKBP5 0.02 0.073 -10000 0 -0.59 7 7
GR alpha/HSP90/FKBP51/HSP90 0.064 0.1 0.35 7 -0.42 2 9
PRL -0.028 0.11 -10000 0 -0.62 5 5
cortisol/GR alpha (dimer)/TIF2 0.13 0.22 0.54 51 -0.44 2 53
RELA 0.01 0.081 -10000 0 -0.31 1 1
FGG -0.047 0.29 0.52 11 -0.51 69 80
GR beta/TIF2 0.052 0.11 0.36 6 -0.42 6 12
IFNG -0.29 0.29 -10000 0 -0.67 123 123
apoptosis -0.081 0.21 -10000 0 -0.59 28 28
CREB1 -0.004 0.11 -10000 0 -0.35 40 40
histone acetylation -0.005 0.1 0.3 1 -0.39 7 8
BGLAP -0.019 0.098 -10000 0 -0.57 3 3
GR/PKAc 0.075 0.093 0.38 3 -0.36 1 4
NF kappa B1 p50/RelA 0.016 0.15 -10000 0 -0.46 21 21
SMARCD1 0.031 0.005 -10000 0 -10000 0 0
MDM2 0.039 0.08 0.28 10 -10000 0 10
GATA3 -0.28 0.33 -10000 0 -0.63 238 238
AKT1 0.021 0.008 -10000 0 -10000 0 0
CSF2 -0.026 0.11 -10000 0 -0.65 4 4
GSK3B 0.023 0.012 -10000 0 -10000 0 0
NR1I3 -0.045 0.23 -10000 0 -0.73 15 15
CSN2 0.062 0.15 0.41 12 -0.38 1 13
BRG1/BAF155/BAF170/BAF60A 0.06 0.04 -10000 0 -10000 0 0
NFATC1 0.031 0.007 -10000 0 -10000 0 0
POU2F1 0.032 0.008 -10000 0 -10000 0 0
CDKN1A 0.033 0.059 0.85 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.043 0.2 -10000 0 -0.59 58 58
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.031 0.15 0.35 4 -0.38 20 24
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.019 0.24 -10000 0 -0.72 15 15
JUN -0.18 0.21 -10000 0 -0.56 74 74
IL4 -0.029 0.092 -10000 0 -0.43 4 4
CDK5R1 0.028 0.006 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.22 0.27 7 -0.54 77 84
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.075 0.1 0.36 5 -0.39 2 7
cortisol/GR alpha (monomer) 0.14 0.26 0.61 57 -0.48 1 58
NCOA2 0.019 0.079 -10000 0 -0.64 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.046 0.12 -10000 0 -0.69 12 12
AP-1/NFAT1-c-4 -0.26 0.27 -10000 0 -0.7 74 74
AFP -0.34 0.53 -10000 0 -1.3 103 103
SUV420H1 0.03 0.003 -10000 0 -10000 0 0
IRF1 0.067 0.11 0.44 8 -10000 0 8
TP53 0.05 0.018 -10000 0 -10000 0 0
PPP5C 0.03 0.003 -10000 0 -10000 0 0
KRT17 -0.22 0.34 -10000 0 -1.1 51 51
KRT14 -0.11 0.19 -10000 0 -0.62 34 34
TBP 0.036 0.014 -10000 0 -10000 0 0
CREBBP 0.05 0.054 -10000 0 -10000 0 0
HDAC1 0.027 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.011 -10000 0 -10000 0 0
AP-1 -0.26 0.27 -10000 0 -0.71 74 74
MAPK14 0.025 0.01 -10000 0 -10000 0 0
MAPK10 0.019 0.068 -10000 0 -0.65 5 5
MAPK11 0.024 0.03 -10000 0 -0.6 1 1
KRT5 -0.21 0.26 -10000 0 -0.68 77 77
interleukin-1 receptor activity 0 0.008 -10000 0 -10000 0 0
NCOA1 0.032 0.007 -10000 0 -10000 0 0
STAT1 0.036 0.038 -10000 0 -0.8 1 1
CGA -0.13 0.33 -10000 0 -1.1 47 47
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.076 0.12 0.43 14 -10000 0 14
MAPK3 0.025 0.01 -10000 0 -10000 0 0
MAPK1 0.026 0.009 -10000 0 -10000 0 0
ICAM1 -0.054 0.18 -10000 0 -0.62 26 26
NFKB1 0.009 0.089 -10000 0 -0.55 2 2
MAPK8 -0.12 0.16 -10000 0 -0.43 41 41
MAPK9 0.02 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.086 0.22 -10000 0 -0.62 29 29
BAX 0.036 0.033 -10000 0 -10000 0 0
POMC -0.05 0.14 0.49 1 -0.76 6 7
EP300 0.051 0.061 -10000 0 -0.54 1 1
cortisol/GR alpha (dimer)/p53 0.15 0.22 0.55 55 -10000 0 55
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.061 0.24 3 -10000 0 3
SGK1 0.071 0.088 -10000 0 -10000 0 0
IL13 -0.29 0.25 -10000 0 -0.72 69 69
IL6 -0.1 0.3 -10000 0 -0.84 56 56
PRKACG 0.02 0.006 -10000 0 -10000 0 0
IL5 -0.23 0.2 -10000 0 -0.62 44 44
IL2 -0.16 0.2 -10000 0 -0.64 33 33
CDK5 0.025 0.009 -10000 0 -10000 0 0
PRKACB 0.029 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
IL8 -0.074 0.24 -10000 0 -0.71 43 43
CDK5R1/CDK5 0.036 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.05 0.13 -10000 0 -0.54 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.21 0.52 51 -10000 0 51
SMARCA4 0.032 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.069 0.12 0.39 18 -10000 0 18
NF kappa B1 p50/RelA/Cbp 0.069 0.14 -10000 0 -0.67 2 2
JUN (dimer) -0.18 0.21 -10000 0 -0.56 74 74
YWHAH 0.03 0.004 -10000 0 -10000 0 0
VIPR1 -0.053 0.16 -10000 0 -0.77 15 15
NR3C1 0.065 0.15 0.44 22 -0.62 1 23
NR4A1 0.017 0.11 -10000 0 -0.62 15 15
TIF2/SUV420H1 0.035 0.062 -10000 0 -0.47 7 7
MAPKKK cascade -0.081 0.21 -10000 0 -0.59 28 28
cortisol/GR alpha (dimer)/Src-1 0.14 0.22 0.54 58 -0.5 1 59
PBX1 0.011 0.11 -10000 0 -0.64 15 15
POU1F1 0.021 0.011 -10000 0 -10000 0 0
SELE -0.097 0.32 -10000 0 -1.1 40 40
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.069 0.12 0.4 17 -10000 0 17
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.21 0.52 51 -10000 0 51
mol:cortisol 0.046 0.16 0.34 55 -0.29 25 80
MMP1 -0.17 0.32 -10000 0 -0.78 82 82
Wnt signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.042 0.15 -9999 0 -0.42 48 48
FZD6 0.028 0.007 -9999 0 -10000 0 0
WNT6 0.007 0.11 -9999 0 -0.59 17 17
WNT4 -0.045 0.21 -9999 0 -0.62 56 56
FZD3 0.027 0.009 -9999 0 -10000 0 0
WNT5A 0.019 0.039 -9999 0 -0.43 3 3
WNT11 -0.019 0.17 -9999 0 -0.63 37 37
Regulation of Telomerase

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
Telomerase catalytic core complex -0.17 0.21 0.49 1 -0.65 51 52
RAD9A 0.03 0.003 -10000 0 -10000 0 0
AP1 0.027 0.079 -10000 0 -0.47 12 12
IFNAR2 0.028 0.009 -10000 0 -10000 0 0
AKT1 0.013 0.05 -10000 0 -0.27 12 12
ER alpha/Oestrogen 0.017 0.04 -10000 0 -0.4 4 4
NFX1/SIN3/HDAC complex 0.029 0.068 -10000 0 -0.37 6 6
EGF -0.57 0.2 -10000 0 -0.63 450 450
SMG5 0.029 0.007 -10000 0 -10000 0 0
SMG6 0.029 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.018 -10000 0 -10000 0 0
TERT/c-Abl -0.16 0.2 -10000 0 -0.62 47 47
SAP18 0.029 0.005 -10000 0 -10000 0 0
MRN complex 0.045 0.027 -10000 0 -10000 0 0
WT1 -0.28 0.33 -10000 0 -0.64 231 231
WRN 0.027 0.009 -10000 0 -10000 0 0
SP1 0.026 0.014 -10000 0 -10000 0 0
SP3 0.028 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.18 -10000 0 -0.6 32 32
Mad/Max 0.039 0.015 -10000 0 -10000 0 0
TERT -0.18 0.22 0.5 1 -0.66 51 52
CCND1 -0.16 0.21 0.65 1 -0.72 24 25
MAX 0.027 0.008 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
TERF2 0.026 0.007 -10000 0 -10000 0 0
PTGES3 0.029 0.005 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
Telomerase/911 0.027 0.042 -10000 0 -10000 0 0
CDKN1B -0.13 0.18 -10000 0 -0.35 184 184
RAD1 0.027 0.009 -10000 0 -10000 0 0
XRCC5 0.029 0.007 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
SAP30 0.008 0.11 -10000 0 -0.59 17 17
TRF2/PARP2 0.04 0.013 -10000 0 -10000 0 0
UBE3A 0.029 0.004 -10000 0 -10000 0 0
JUN 0.029 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.009 -10000 0 -10000 0 0
FOS 0.011 0.1 -10000 0 -0.63 12 12
IFN-gamma/IRF1 -0.15 0.22 -10000 0 -0.42 186 186
PARP2 0.029 0.007 -10000 0 -10000 0 0
BLM 0.017 0.086 -10000 0 -0.59 10 10
Telomerase -0.021 0.12 -10000 0 -0.44 8 8
IRF1 0.025 0.031 -10000 0 -0.58 1 1
ESR1 0.023 0.053 -10000 0 -0.55 4 4
KU/TER 0.042 0.011 -10000 0 -10000 0 0
ATM/TRF2 0.043 0.023 -10000 0 -0.43 1 1
ubiquitin-dependent protein catabolic process 0.04 0.055 -10000 0 -0.43 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.04 0.055 -10000 0 -0.44 1 1
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.014 -10000 0 -10000 0 0
ATM 0.01 0.022 -10000 0 -0.46 1 1
SMAD3 0.02 0.041 -10000 0 -0.42 4 4
ABL1 0.029 0.006 -10000 0 -10000 0 0
MXD1 0.029 0.006 -10000 0 -10000 0 0
MRE11A 0.03 0.004 -10000 0 -10000 0 0
HUS1 0.027 0.009 -10000 0 -10000 0 0
RPS6KB1 0.029 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.2 -10000 0 -0.64 31 31
NR2F2 0.031 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.064 -10000 0 -0.43 10 10
MAPK1 0.007 0.064 -10000 0 -0.43 10 10
TGFB1/TGF beta receptor Type II 0.025 0.055 -10000 0 -0.58 4 4
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
HNRNPC 0.029 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.022 -10000 0 -0.46 1 1
NBN 0.028 0.007 -10000 0 -10000 0 0
EGFR 0.019 0.068 -10000 0 -0.59 6 6
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.41 0.16 -10000 0 -0.48 403 403
MYC 0.008 0.11 -10000 0 -0.59 16 16
IL2 0.008 0.087 -10000 0 -0.59 10 10
KU 0.042 0.011 -10000 0 -10000 0 0
RAD50 0.023 0.013 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
TGFB1 0.025 0.055 -10000 0 -0.58 4 4
TRF2/BLM 0.032 0.063 -10000 0 -0.4 10 10
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.15 0.2 -10000 0 -0.63 43 43
SP1/HDAC2 0.035 0.025 -10000 0 -10000 0 0
PINX1 0.027 0.009 -10000 0 -10000 0 0
Telomerase/EST1A -0.14 0.19 -10000 0 -0.6 32 32
Smad3/Myc 0.022 0.082 -10000 0 -0.38 19 19
911 complex 0.051 0.023 -10000 0 -10000 0 0
IFNG -0.24 0.3 -10000 0 -0.57 223 223
Telomerase/PinX1 -0.14 0.18 -10000 0 -0.59 34 34
Telomerase/AKT1/mTOR/p70S6K -0.019 0.097 -10000 0 -0.43 7 7
SIN3B 0.03 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Telomerase/EST1B -0.14 0.18 -10000 0 -0.59 35 35
response to DNA damage stimulus 0.005 0.012 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.063 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.038 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.19 -10000 0 -0.6 32 32
E2F1 -0.037 0.19 -10000 0 -0.59 52 52
ZNFX1 0.029 0.006 -10000 0 -10000 0 0
PIF1 -0.079 0.24 -10000 0 -0.59 88 88
NCL 0.028 0.007 -10000 0 -10000 0 0
DKC1 0.03 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.062 0.13 -10000 0 -0.44 27 27
PTP1B/AKT1 -0.051 0.073 0.21 1 -0.32 6 7
FYN 0.028 0.008 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.066 0.076 0.28 2 -0.31 11 13
EGFR -0.011 0.068 -10000 0 -0.61 6 6
EGF/EGFR -0.3 0.13 -10000 0 -0.36 375 375
CSF1 0.028 0.03 -10000 0 -0.64 1 1
AKT1 0.028 0.008 -10000 0 -10000 0 0
INSR 0.03 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.067 0.087 -10000 0 -0.38 14 14
Insulin Receptor/Insulin -0.02 0.085 0.3 1 -10000 0 1
HCK -0.003 0.14 -10000 0 -0.59 26 26
CRK 0.029 0.005 -10000 0 -10000 0 0
TYK2 -0.06 0.074 0.28 2 -0.35 5 7
EGF -0.57 0.2 -10000 0 -0.64 450 450
YES1 0.03 0.004 -10000 0 -10000 0 0
CAV1 -0.14 0.11 0.32 5 -0.32 46 51
TXN 0.023 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.053 0.079 0.34 1 -0.38 6 7
cell migration 0.066 0.076 0.31 11 -0.28 2 13
STAT3 0.029 0.005 -10000 0 -10000 0 0
PRLR -0.05 0.21 -10000 0 -0.64 57 57
ITGA2B 0.006 0.12 -10000 0 -0.59 18 18
CSF1R 0.017 0.062 -10000 0 -0.59 5 5
Prolactin Receptor/Prolactin -0.027 0.16 -10000 0 -0.48 57 57
FGR 0.025 0.048 -10000 0 -0.59 3 3
PTP1B/p130 Cas -0.059 0.073 -10000 0 -0.34 6 6
Crk/p130 Cas -0.053 0.073 -10000 0 -0.37 2 2
DOK1 -0.027 0.082 0.28 5 -0.32 4 9
JAK2 -0.068 0.14 0.32 1 -0.4 49 50
Jak2/Leptin Receptor/Leptin -0.039 0.12 -10000 0 -0.44 3 3
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
PTPN1 -0.066 0.077 0.28 2 -0.31 11 13
LYN 0.028 0.008 -10000 0 -10000 0 0
CDH2 0.013 0.1 -10000 0 -0.61 13 13
SRC 0.002 0.044 0.34 1 -0.66 1 2
ITGB3 0.026 0.043 -10000 0 -0.64 2 2
CAT1/PTP1B -0.22 0.16 0.4 5 -0.45 72 77
CAPN1 0.028 0.003 -10000 0 -10000 0 0
CSK 0.03 0.003 -10000 0 -10000 0 0
PI3K 0.001 0.085 -10000 0 -0.56 1 1
mol:H2O2 -0.006 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.032 0.11 -10000 0 -0.46 2 2
negative regulation of transcription -0.067 0.14 0.32 1 -0.39 49 50
FCGR2A 0.001 0.13 -10000 0 -0.59 22 22
FER 0.017 0.043 -10000 0 -0.65 2 2
alphaIIb/beta3 Integrin 0.022 0.094 -10000 0 -0.44 20 20
BLK -0.013 0.15 -10000 0 -0.59 32 32
Insulin Receptor/Insulin/Shc 0.05 0.013 -10000 0 -10000 0 0
RHOA 0.02 0.013 -10000 0 -10000 0 0
LEPR 0.029 0.006 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
p210 bcr-abl/Grb2 0.029 0.005 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.19 0.16 0.36 4 -0.43 97 101
PRL 0.003 0.022 -10000 0 -10000 0 0
SOCS3 0.026 0.12 -10000 0 -0.98 6 6
SPRY2 0.025 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.047 0.039 -10000 0 -0.42 3 3
CSF1/CSF1R -0.048 0.076 0.34 1 -0.38 8 9
Ras protein signal transduction 0.033 0.067 0.49 9 -10000 0 9
IRS1 0.025 0.052 -10000 0 -0.64 3 3
INS 0.006 0.019 -10000 0 -10000 0 0
LEP -0.036 0.18 -10000 0 -0.59 46 46
STAT5B -0.059 0.094 0.37 1 -0.34 23 24
STAT5A -0.059 0.094 0.37 1 -0.34 23 24
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.048 0.069 0.34 1 -0.35 4 5
CSN2 0.004 0.071 -10000 0 -0.62 1 1
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
LAT -0.057 0.11 -10000 0 -0.45 8 8
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.002 0.13 -10000 0 -0.59 22 22
SHC1 0.029 0.007 -10000 0 -10000 0 0
NOX4 0.021 0.054 -10000 0 -0.57 4 4
Ceramide signaling pathway

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
SPHK2 0.018 0.039 -10000 0 -0.48 3 3
MAP4K4 0.012 0.067 -10000 0 -0.5 2 2
BAG4 0.026 0.031 -10000 0 -0.64 1 1
PKC zeta/ceramide -0.1 0.085 -10000 0 -0.31 50 50
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
BIRC3 -0.065 0.22 -10000 0 -0.59 77 77
BAX -0.036 0.036 -10000 0 -0.3 4 4
RIPK1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.029 0.069 0.89 3 -10000 0 3
BAD -0.1 0.08 -10000 0 -0.3 47 47
SMPD1 0.022 0.055 0.28 9 -10000 0 9
RB1 -0.1 0.079 -10000 0 -0.3 46 46
FADD/Caspase 8 0.024 0.079 -10000 0 -0.48 3 3
MAP2K4 -0.081 0.077 -10000 0 -0.28 34 34
NSMAF 0.028 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.078 0.088 -10000 0 -0.28 50 50
EGF -0.57 0.2 -10000 0 -0.63 450 450
mol:ceramide -0.11 0.084 0.18 2 -0.3 55 57
MADD 0.03 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.018 0.024 -10000 0 -0.47 1 1
ASAH1 0.027 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.1 0.078 -10000 0 -0.3 46 46
cell proliferation -0.059 0.074 -10000 0 -0.4 8 8
BID -0.004 0.074 -10000 0 -0.56 4 4
MAP3K1 -0.093 0.073 -10000 0 -0.3 37 37
EIF2A -0.076 0.084 0.32 4 -0.6 3 7
TRADD 0.029 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.079 0.073 -10000 0 -0.41 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.079 0.074 -10000 0 -0.46 7 7
Cathepsin D/ceramide -0.1 0.081 -10000 0 -0.3 46 46
FADD 0.013 0.067 -10000 0 -0.5 2 2
KSR1 -0.1 0.084 0.19 1 -0.31 50 51
MAPK8 -0.082 0.086 -10000 0 -0.42 13 13
PRKRA -0.1 0.081 -10000 0 -0.3 45 45
PDGFA 0.025 0.031 -10000 0 -0.64 1 1
TRAF2 0.029 0.006 -10000 0 -10000 0 0
IGF1 0.023 0.062 -10000 0 -0.59 5 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.083 0.18 2 -0.3 55 57
CTSD 0.029 0.03 -10000 0 -0.64 1 1
regulation of nitric oxide biosynthetic process 0.043 0.024 -10000 0 -0.47 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.062 0.08 -10000 0 -0.44 8 8
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.018 0.024 -10000 0 -0.47 1 1
RelA/NF kappa B1 0.043 0.024 -10000 0 -0.47 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.03 -10000 0 -0.64 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.013 0.072 -10000 0 -0.53 2 2
TNFR1A/BAG4/TNF-alpha 0.045 0.063 -10000 0 -0.39 9 9
mol:Sphingosine-1-phosphate 0.018 0.039 -10000 0 -0.47 3 3
MAP2K1 -0.084 0.077 -10000 0 -0.48 7 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
CYCS -0.055 0.036 -10000 0 -0.31 4 4
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
TNFR1A/BAG4 0.039 0.027 -10000 0 -0.47 1 1
EIF2AK2 -0.088 0.088 0.27 6 -0.29 43 49
TNF-alpha/TNFR1A/FAN 0.047 0.059 -10000 0 -0.39 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.074 -10000 0 -0.4 7 7
MAP2K2 -0.085 0.074 -10000 0 -0.46 7 7
SMPD3 0.017 0.054 0.21 2 -0.41 2 4
TNF 0.019 0.081 -10000 0 -0.61 8 8
PKC zeta/PAR4 0.037 0.047 -10000 0 -0.47 4 4
mol:PHOSPHOCHOLINE 0.21 0.087 0.24 404 -10000 0 404
NF kappa B1/RelA/I kappa B alpha 0.075 0.047 -10000 0 -0.35 3 3
AIFM1 -0.062 0.05 -10000 0 -0.35 4 4
BCL2 0.029 0.005 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.55 0.64 -10000 0 -1.2 231 231
PLK1 -0.13 0.25 0.48 1 -0.68 30 31
CDKN1B -0.013 0.15 0.54 1 -0.37 2 3
FOXO3 -0.071 0.18 -10000 0 -0.59 16 16
KAT2B 0.012 0.04 -10000 0 -0.67 1 1
FOXO1/SIRT1 -0.13 0.22 -10000 0 -0.38 207 207
CAT -0.086 0.19 0.48 1 -0.82 7 8
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
AKT1 -0.01 0.05 -10000 0 -0.29 1 1
FOXO1 -0.16 0.23 0.3 1 -0.42 213 214
MAPK10 0.037 0.07 0.34 3 -0.36 4 7
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.094 0.086 0.36 18 -10000 0 18
response to oxidative stress -0.029 0.042 -10000 0 -0.29 1 1
FOXO3A/SIRT1 -0.027 0.19 -10000 0 -0.56 15 15
XPO1 0.03 0.005 -10000 0 -10000 0 0
EP300 -0.01 0.055 -10000 0 -0.48 2 2
BCL2L11 0.004 0.086 -10000 0 -0.72 6 6
FOXO1/SKP2 -0.14 0.22 -10000 0 -0.39 189 189
mol:GDP -0.029 0.042 -10000 0 -0.29 1 1
RAN 0.031 0.006 -10000 0 -10000 0 0
GADD45A 0.058 0.15 -10000 0 -0.63 13 13
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.03 0.11 0.25 1 -0.56 8 9
MST1 0.003 0.083 -10000 0 -0.62 8 8
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.03 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.026 0.11 -10000 0 -0.61 7 7
YWHAB 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.04 0.058 0.34 2 -10000 0 2
MAPK9 0.025 0.048 0.35 2 -10000 0 2
YWHAG 0.027 0.009 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
SIRT1 0.044 0.018 -10000 0 -10000 0 0
SOD2 -0.052 0.18 0.47 1 -0.54 14 15
RBL2 -0.023 0.16 -10000 0 -0.96 6 6
RAL/GDP 0.018 0.034 -10000 0 -10000 0 0
CHUK 0.02 0.026 -10000 0 -10000 0 0
Ran/GTP 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.028 0.03 -10000 0 -0.64 1 1
RAL/GTP 0.027 0.033 -10000 0 -10000 0 0
CSNK1G1 0.03 0.003 -10000 0 -10000 0 0
FASLG -0.22 0.24 -10000 0 -0.47 144 144
SKP2 0.027 0.009 -10000 0 -10000 0 0
USP7 0.03 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.026 -10000 0 -10000 0 0
CCNB1 -0.074 0.19 -10000 0 -0.73 10 10
FOXO1-3a-4/beta catenin -0.041 0.15 0.4 4 -0.43 1 5
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -10000 0 -0.38 189 189
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
SGK1 0.02 0.026 -10000 0 -10000 0 0
CSNK1G3 0.024 0.012 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.012 -10000 0 -10000 0 0
ZFAND5 0.095 0.086 0.4 15 -10000 0 15
SFN -0.043 0.2 -10000 0 -0.59 58 58
CDK2 -0.019 0.059 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.005 0.11 -10000 0 -0.54 11 11
CREBBP -0.018 0.057 -10000 0 -10000 0 0
FBXO32 -0.079 0.18 0.48 1 -0.66 8 9
BCL6 -0.028 0.17 -10000 0 -0.79 8 8
RALB 0.031 0.006 -10000 0 -10000 0 0
RALA 0.028 0.01 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.43 220 220
alphaV beta3 Integrin 0.05 0.061 -10000 0 -0.46 6 6
PTK2 -0.091 0.17 0.57 4 -0.54 8 12
IGF1R 0.03 0.003 -10000 0 -10000 0 0
PI4KB 0.029 0.007 -10000 0 -10000 0 0
MFGE8 0.029 0.028 -10000 0 -0.59 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
CDKN1B -0.041 0.18 -10000 0 -0.48 68 68
VEGFA -0.24 0.3 -10000 0 -0.59 220 220
ILK -0.043 0.18 -10000 0 -0.48 70 70
ROCK1 0.03 0.004 -10000 0 -10000 0 0
AKT1 -0.04 0.17 -10000 0 -0.45 67 67
PTK2B -0.11 0.17 0.36 2 -0.5 2 4
alphaV/beta3 Integrin/JAM-A 0.004 0.15 -10000 0 -0.68 1 1
CBL 0.028 0.03 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.14 0.22 -10000 0 -0.41 205 205
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.064 0.056 -10000 0 -0.35 5 5
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.094 0.16 -10000 0 -0.43 56 56
alphaV/beta3 Integrin/Syndecan-1 0.049 0.06 -10000 0 -0.41 8 8
PI4KA 0.03 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.11 -10000 0 -0.61 3 3
PI4 Kinase 0.042 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
alphaV/beta3 Integrin/Osteopontin 0.052 0.046 -10000 0 -0.41 4 4
RPS6KB1 0.019 0.12 0.48 11 -0.57 3 14
TLN1 0.029 0.006 -10000 0 -10000 0 0
MAPK3 0.003 0.1 -10000 0 -0.64 6 6
GPR124 0.026 0.029 -10000 0 -0.59 1 1
MAPK1 0.003 0.11 -10000 0 -0.64 6 6
PXN 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
alphaV/beta3 Integrin/Tumstatin 0.004 0.15 -10000 0 -0.41 53 53
cell adhesion -0.11 0.18 -10000 0 -0.38 21 21
ANGPTL3 -0.26 0.33 -10000 0 -0.62 225 225
VEGFR2 homodimer/VEGFA homodimer/Src -0.13 0.21 -10000 0 -0.37 216 216
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
TGFBR2 0.022 0.014 -10000 0 -10000 0 0
ITGB3 0.027 0.042 -10000 0 -0.64 2 2
IGF1 0.023 0.062 -10000 0 -0.59 5 5
RAC1 0.027 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.05 0.037 -10000 0 -0.4 2 2
apoptosis 0.029 0.007 -10000 0 -10000 0 0
CD47 0.028 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.051 0.036 -10000 0 -0.41 2 2
VCL 0.029 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.039 0.08 -10000 0 -0.41 13 13
CSF1 0.028 0.03 -10000 0 -0.64 1 1
PIK3C2A -0.044 0.19 -10000 0 -0.49 71 71
PI4 Kinase/Pyk2 -0.14 0.19 -10000 0 -0.56 39 39
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.2 -10000 0 -0.46 4 4
FAK1/Vinculin -0.066 0.15 0.59 3 -0.47 4 7
alphaV beta3/Integrin/ppsTEM5 0.051 0.037 -10000 0 -0.41 2 2
RHOA 0.021 0.014 -10000 0 -10000 0 0
VTN -0.069 0.24 -10000 0 -0.63 75 75
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
FGF2 0.023 0.066 -10000 0 -0.63 5 5
F11R 0.018 0.046 -10000 0 -0.47 4 4
alphaV/beta3 Integrin/Lactadherin 0.054 0.038 -10000 0 -0.39 3 3
alphaV/beta3 Integrin/TGFBR2 0.04 0.04 -10000 0 -0.41 2 2
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.067 0.047 -10000 0 -0.54 2 2
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.051 0.032 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.018 0.16 -10000 0 -0.59 37 37
alphaV/beta3 Integrin/Pyk2 -0.1 0.18 -10000 0 -0.5 2 2
SDC1 0.021 0.073 -10000 0 -0.64 6 6
VAV3 0.029 0.086 0.36 7 -0.67 1 8
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IRS1 0.025 0.052 -10000 0 -0.64 3 3
FAK1/Paxillin -0.067 0.14 0.53 2 -0.5 3 5
cell migration -0.061 0.13 0.52 2 -0.45 3 5
ITGAV 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.013 0.14 -10000 0 -0.92 1 1
SPP1 0.026 0.052 -10000 0 -0.64 3 3
KDR 0.028 0.03 -10000 0 -0.64 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.007 -10000 0 -10000 0 0
COL4A3 -0.044 0.21 -10000 0 -0.61 57 57
angiogenesis -0.006 0.13 0.32 4 -0.66 6 10
Rac1/GTP 0.034 0.067 -10000 0 -0.62 1 1
EDIL3 0.011 0.1 -10000 0 -0.59 13 13
cell proliferation 0.04 0.04 -10000 0 -0.4 2 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.1 0.18 -10000 0 -0.57 22 22
CRKL 0.008 0.11 -10000 0 -0.46 19 19
HRAS -0.012 0.14 -10000 0 -0.55 8 8
mol:PIP3 0.013 0.11 -10000 0 -0.45 18 18
SPRED1 0.03 0.003 -10000 0 -10000 0 0
SPRED2 0.028 0.03 -10000 0 -0.64 1 1
GAB1 0.007 0.12 -10000 0 -0.5 20 20
FOXO3 0.015 0.14 0.46 1 -0.5 18 19
AKT1 0.012 0.15 0.3 3 -0.5 25 28
BAD 0.015 0.14 0.34 4 -0.48 21 25
megakaryocyte differentiation -0.051 0.17 -10000 0 -0.44 52 52
GSK3B 0.017 0.14 0.34 3 -0.57 13 16
RAF1 -0.019 0.11 0.31 2 -0.43 8 10
SHC1 0.029 0.007 -10000 0 -10000 0 0
STAT3 0.006 0.12 -10000 0 -0.48 21 21
STAT1 -0.011 0.24 -10000 0 -1.1 20 20
HRAS/SPRED1 0.005 0.12 -10000 0 -0.43 8 8
cell proliferation 0.006 0.12 -10000 0 -0.48 21 21
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
TEC 0.03 0.004 -10000 0 -10000 0 0
RPS6KB1 0.013 0.13 -10000 0 -0.5 23 23
HRAS/SPRED2 0.003 0.12 -10000 0 -0.42 9 9
LYN/TEC/p62DOK 0.045 0.12 -10000 0 -0.47 16 16
MAPK3 0.012 0.097 0.31 9 -0.34 3 12
STAP1 -0.24 0.18 -10000 0 -0.35 314 314
GRAP2 -0.012 0.16 -10000 0 -0.59 34 34
JAK2 -0.012 0.22 -10000 0 -1 20 20
STAT1 (dimer) -0.007 0.23 -10000 0 -1.1 20 20
mol:Gleevec -0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.036 0.18 -10000 0 -0.55 18 18
actin filament polymerization 0.001 0.11 -10000 0 -0.49 19 19
LYN 0.028 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.21 0.2 -10000 0 -0.74 29 29
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
CBL/CRKL/GRB2 0.039 0.11 -10000 0 -0.48 9 9
PI3K 0.034 0.13 -10000 0 -0.49 18 18
PTEN 0.029 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.055 0.28 -10000 0 -1.2 20 20
MAPK8 0.005 0.12 -10000 0 -0.49 21 21
STAT3 (dimer) 0.006 0.11 -10000 0 -0.47 21 21
positive regulation of transcription 0.015 0.087 0.3 10 -0.29 2 12
mol:GDP -0.028 0.16 -10000 0 -0.5 16 16
PIK3C2B 0.005 0.12 -10000 0 -0.48 21 21
CBL/CRKL 0.025 0.11 -10000 0 -0.46 15 15
FER 0 0.12 -10000 0 -0.49 21 21
SH2B3 0.007 0.12 -10000 0 -0.49 20 20
PDPK1 0.022 0.11 0.34 6 -0.41 17 23
SNAI2 0.005 0.12 -10000 0 -0.5 20 20
positive regulation of cell proliferation 0.011 0.18 -10000 0 -0.81 20 20
KITLG 0.018 0.092 -10000 0 -0.65 9 9
cell motility 0.011 0.18 -10000 0 -0.81 20 20
PTPN6 0.028 0.008 -10000 0 -10000 0 0
EPOR 0.042 0.096 -10000 0 -1.1 2 2
STAT5A (dimer) 0.022 0.17 -10000 0 -0.64 23 23
SOCS1 0.021 0.067 -10000 0 -0.59 6 6
cell migration 0.023 0.15 0.48 31 -10000 0 31
SOS1 0.029 0.005 -10000 0 -10000 0 0
EPO -0.17 0.28 -10000 0 -0.58 160 160
VAV1 -0.12 0.26 -10000 0 -0.59 118 118
GRB10 0.003 0.11 -10000 0 -0.5 19 19
PTPN11 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT 0.005 0.13 -10000 0 -0.48 25 25
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.011 0.092 0.31 3 -0.37 4 7
CBL 0.028 0.03 -10000 0 -0.64 1 1
KIT -0.003 0.27 -10000 0 -1.3 20 20
MAP2K2 -0.011 0.092 0.35 3 -0.37 4 7
SHC/Grb2/SOS1 0.046 0.12 -10000 0 -0.48 13 13
STAT5A 0.021 0.17 -10000 0 -0.66 23 23
GRB2 0.029 0.005 -10000 0 -10000 0 0
response to radiation 0.006 0.12 0.28 1 -0.49 20 21
SHC/GRAP2 0.01 0.12 -10000 0 -0.43 33 33
PTPRO -0.052 0.18 -10000 0 -0.44 56 56
SH2B2 0 0.12 -10000 0 -0.5 19 19
DOK1 0.029 0.005 -10000 0 -10000 0 0
MATK -0.024 0.15 -10000 0 -0.49 31 31
CREBBP 0.046 0.031 -10000 0 -10000 0 0
BCL2 0.042 0.096 -10000 0 -0.88 2 2
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.026 0.041 -9999 0 -0.61 2 2
GNB1/GNG2 -0.027 0.15 -9999 0 -0.45 27 27
mol:DAG -0.034 0.13 -9999 0 -0.43 23 23
PLCG1 -0.035 0.14 -9999 0 -0.44 23 23
YES1 -0.039 0.14 -9999 0 -0.41 43 43
FZD3 0.027 0.009 -9999 0 -10000 0 0
FZD6 0.028 0.007 -9999 0 -10000 0 0
G protein -0.024 0.14 -9999 0 -0.45 22 22
MAP3K7 -0.09 0.17 -9999 0 -0.47 43 43
mol:Ca2+ -0.033 0.13 -9999 0 -0.41 23 23
mol:IP3 -0.034 0.13 -9999 0 -0.43 23 23
NLK -0.001 0.091 -9999 0 -0.81 6 6
GNB1 0.029 0.006 -9999 0 -10000 0 0
CAMK2A -0.099 0.19 -9999 0 -0.46 65 65
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.042 0.15 -9999 0 -0.42 48 48
CSNK1A1 0.023 0.013 -9999 0 -10000 0 0
GNAS -0.04 0.14 -9999 0 -0.41 44 44
GO:0007205 -0.037 0.13 -9999 0 -0.42 23 23
WNT6 0.007 0.11 -9999 0 -0.59 17 17
WNT4 -0.045 0.21 -9999 0 -0.62 56 56
NFAT1/CK1 alpha -0.015 0.13 -9999 0 -0.47 12 12
GNG2 0.028 0.008 -9999 0 -10000 0 0
WNT5A 0.019 0.039 -9999 0 -0.43 3 3
WNT11 -0.019 0.17 -9999 0 -0.63 37 37
CDC42 -0.034 0.14 -9999 0 -0.45 25 25
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.026 0.031 -10000 0 -0.64 1 1
Caspase 8 (4 units) -0.063 0.11 -10000 0 -0.38 1 1
NEF -0.057 0.077 -10000 0 -0.45 5 5
NFKBIA 0.012 0.046 -10000 0 -10000 0 0
BIRC3 -0.052 0.21 -10000 0 -0.54 77 77
CYCS -0.074 0.11 -10000 0 -0.4 2 2
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.25 0.34 -10000 0 -0.73 160 160
MAP2K7 -0.045 0.14 0.38 2 -0.58 15 17
protein ubiquitination 0.032 0.1 0.37 10 -0.51 4 14
CRADD 0.029 0.005 -10000 0 -10000 0 0
DAXX 0.029 0.006 -10000 0 -10000 0 0
FAS 0.029 0.006 -10000 0 -10000 0 0
BID -0.083 0.12 -10000 0 -0.36 2 2
NF-kappa-B/RelA/I kappa B alpha 0.013 0.13 -10000 0 -0.47 2 2
TRADD 0.029 0.006 -10000 0 -10000 0 0
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
CFLAR 0.029 0.006 -10000 0 -10000 0 0
FADD 0.03 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.013 0.13 -10000 0 -0.47 2 2
MAPK8 -0.038 0.13 0.43 3 -0.55 14 17
APAF1 0.029 0.006 -10000 0 -10000 0 0
TRAF1 0.028 0.028 -10000 0 -0.59 1 1
TRAF2 0.029 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.09 0.12 -10000 0 -0.33 6 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.098 -10000 0 -0.56 6 6
CHUK 0.03 0.095 0.29 8 -0.57 4 12
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.078 0.031 -10000 0 -10000 0 0
TCRz/NEF -0.26 0.31 -10000 0 -0.51 266 266
TNF 0.019 0.081 -10000 0 -0.61 8 8
FASLG -0.36 0.4 -10000 0 -0.72 263 263
NFKB1 0.011 0.056 -10000 0 -0.63 1 1
TNFR1A/BAG4/TNF-alpha 0.045 0.063 -10000 0 -0.39 9 9
CASP6 -0.023 0.12 -10000 0 -0.55 12 12
CASP7 -0.067 0.16 0.38 1 -0.49 4 5
RELA 0.013 0.048 -10000 0 -10000 0 0
CASP2 0.027 0.009 -10000 0 -10000 0 0
CASP3 -0.064 0.16 0.38 1 -0.49 4 5
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.027 -10000 0 -0.47 1 1
CASP8 0.029 0.006 -10000 0 -10000 0 0
CASP9 0.029 0.006 -10000 0 -10000 0 0
MAP3K14 0.021 0.098 -10000 0 -0.6 5 5
APAF-1/Caspase 9 -0.089 0.16 -10000 0 -0.45 46 46
BCL2 -0.031 0.13 0.47 3 -0.52 12 15
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.072 0.26 -10000 0 -0.89 28 28
NCK1/PAK1/Dok-R -0.063 0.1 -10000 0 -0.42 26 26
NCK1/Dok-R 0.004 0.28 -10000 0 -1 29 29
PIK3CA 0.026 0.03 -10000 0 -0.64 1 1
mol:beta2-estradiol -0.002 0.036 0.27 8 -10000 0 8
RELA 0.03 0.003 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -10000 0 -10000 0 0
F2 -0.2 0.29 0.27 2 -0.58 184 186
TNIP2 0.03 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.044 0.26 -10000 0 -0.96 29 29
FN1 -0.018 0.16 -10000 0 -0.59 37 37
PLD2 0.002 0.28 -10000 0 -1.1 29 29
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GRB14 -0.007 0.15 -10000 0 -0.64 27 27
ELK1 0.018 0.25 -10000 0 -0.94 29 29
GRB7 0.021 0.073 -10000 0 -0.64 6 6
PAK1 0.03 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.003 0.29 -10000 0 -1 28 28
CDKN1A -0.078 0.24 -10000 0 -0.64 23 23
ITGA5 -0.011 0.15 -10000 0 -0.59 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.001 0.28 -10000 0 -1 29 29
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:NO -0.029 0.22 0.45 5 -0.63 28 33
PLG -0.17 0.31 -10000 0 -1.2 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.047 0.23 -10000 0 -0.83 28 28
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.64 1 1
ANGPT2 -0.13 0.26 -10000 0 -0.63 29 29
BMX -0.043 0.29 -10000 0 -1.1 29 29
ANGPT1 0.044 0.18 -10000 0 -1.2 8 8
tube development -0.097 0.25 -10000 0 -0.71 26 26
ANGPT4 0.004 0.11 -10000 0 -0.59 15 15
response to hypoxia -0.005 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.007 0.31 -10000 0 -1.1 29 29
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 33 33
FGF2 0.028 0.066 -10000 0 -0.62 5 5
STAT5A (dimer) -0.098 0.28 -10000 0 -0.8 26 26
mol:L-citrulline -0.029 0.22 0.45 5 -0.63 28 33
AGTR1 -0.024 0.14 -10000 0 -0.63 24 24
MAPK14 -0.03 0.3 -10000 0 -1.1 30 30
Tie2/SHP2 -0.004 0.27 -10000 0 -1.1 27 27
TEK -0.008 0.29 -10000 0 -1.2 27 27
RPS6KB1 -0.044 0.25 -10000 0 -0.83 29 29
Angiotensin II/AT1 -0.027 0.1 -10000 0 -0.47 24 24
Tie2/Ang1/GRB2 0.013 0.29 -10000 0 -1.1 29 29
MAPK3 0.009 0.25 -10000 0 -0.96 28 28
MAPK1 0.007 0.25 -10000 0 -0.96 29 29
Tie2/Ang1/GRB7 0.01 0.3 -10000 0 -1.1 29 29
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.001 0.28 -10000 0 -1.1 29 29
PI3K -0.063 0.29 -10000 0 -1 29 29
FES -0.025 0.29 -10000 0 -1.1 29 29
Crk/Dok-R 0.006 0.28 -10000 0 -1 28 28
Tie2/Ang1/ABIN2 0.013 0.29 -10000 0 -1.1 29 29
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.06 0.24 0.44 1 -0.78 29 30
STAT5A 0.03 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.041 0.25 0.46 4 -0.84 28 32
Tie2/Ang2 -0.13 0.31 -10000 0 -0.99 26 26
Tie2/Ang1 -0.001 0.31 -10000 0 -1.2 29 29
FOXO1 -0.08 0.25 0.46 1 -0.81 27 28
ELF1 0.031 0.043 -10000 0 -0.63 1 1
ELF2 0.001 0.28 -10000 0 -1.1 29 29
mol:Choline 0.005 0.26 -10000 0 -1 29 29
cell migration -0.042 0.064 -10000 0 -0.23 25 25
FYN -0.11 0.27 -10000 0 -0.82 26 26
DOK2 -0.011 0.15 -10000 0 -0.59 31 31
negative regulation of cell cycle -0.069 0.22 -10000 0 -0.58 23 23
ETS1 0.035 0.041 -10000 0 -0.29 4 4
PXN -0.023 0.22 0.5 7 -0.69 28 35
ITGB1 0.03 0.004 -10000 0 -10000 0 0
NOS3 -0.039 0.23 0.49 3 -0.73 27 30
RAC1 0.027 0.009 -10000 0 -10000 0 0
TNF 0.019 0.09 -10000 0 -0.58 9 9
MAPKKK cascade 0.005 0.26 -10000 0 -1 29 29
RASA1 0.025 0.031 -10000 0 -0.64 1 1
Tie2/Ang1/Shc 0.005 0.29 -10000 0 -1.1 29 29
NCK1 0.027 0.031 -10000 0 -0.64 1 1
vasculogenesis -0.023 0.2 0.41 9 -0.57 28 37
mol:Phosphatidic acid 0.005 0.26 -10000 0 -1 29 29
mol:Angiotensin II -0.011 0.015 -10000 0 -10000 0 0
mol:NADP -0.029 0.22 0.45 5 -0.63 28 33
Rac1/GTP -0.043 0.23 -10000 0 -0.78 28 28
MMP2 -0.002 0.28 -10000 0 -1.1 29 29
Visual signal transduction: Rods

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
mol:K + 0.03 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.005 0.058 -10000 0 -0.48 7 7
Metarhodopsin II/Arrestin 0.015 0.07 -10000 0 -0.37 15 15
PDE6G/GNAT1/GTP 0.014 0.068 -10000 0 -0.4 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.007 0.078 -10000 0 -0.64 7 7
GRK1 0.02 0.005 -10000 0 -10000 0 0
CNG Channel -0.045 0.16 -10000 0 -0.62 10 10
mol:Na + -0.044 0.17 -10000 0 -0.56 18 18
mol:ADP 0.02 0.005 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.029 0.11 -10000 0 -0.4 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.038 0.18 -10000 0 -0.57 18 18
CNGB1 0.013 0.082 -10000 0 -0.59 9 9
RDH5 0.022 0.069 -10000 0 -0.6 6 6
SAG 0.018 0.028 -10000 0 -0.59 1 1
mol:Ca2+ -0.065 0.16 0.41 2 -0.56 16 18
Na + (4 Units) -0.044 0.16 -10000 0 -0.54 16 16
RGS9 0.013 0.098 -10000 0 -0.58 13 13
GNB1/GNGT1 -0.099 0.21 -10000 0 -0.43 144 144
GNAT1/GDP 0.015 0.11 -10000 0 -0.37 26 26
GUCY2D -0.002 0.13 -10000 0 -0.59 23 23
GNGT1 -0.15 0.28 -10000 0 -0.59 144 144
GUCY2F 0.02 0.005 -10000 0 -10000 0 0
GNB5 0.03 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.001 0.094 -10000 0 -0.37 26 26
mol:11-cis-retinal 0.022 0.069 -10000 0 -0.6 6 6
mol:cGMP 0.019 0.1 -10000 0 -0.45 3 3
GNB1 0.029 0.006 -10000 0 -10000 0 0
Rhodopsin 0.018 0.096 -10000 0 -0.44 21 21
SLC24A1 0.03 0.003 -10000 0 -10000 0 0
CNGA1 -0.09 0.26 -10000 0 -0.63 91 91
Metarhodopsin II 0.016 0.064 -10000 0 -0.34 15 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.028 0.11 -10000 0 -0.35 36 36
RGS9BP 0.001 0.13 -10000 0 -0.64 21 21
Metarhodopsin II/Transducin -0.061 0.13 -10000 0 -0.37 47 47
GCAP Family/Ca ++ 0.031 0.071 -10000 0 -0.37 14 14
PDE6A/B 0.016 0.094 -10000 0 -0.46 17 17
mol:Pi 0.028 0.11 -10000 0 -0.39 31 31
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.078 0.18 -10000 0 -0.34 146 146
PDE6B 0.023 0.067 -10000 0 -0.64 5 5
PDE6A 0.006 0.098 -10000 0 -0.59 13 13
PDE6G 0.023 0.066 -10000 0 -0.63 5 5
RHO 0.006 0.1 -10000 0 -0.59 15 15
PDE6 0.027 0.13 -10000 0 -0.65 5 5
GUCA1A 0.012 0.077 -10000 0 -0.59 8 8
GC2/GCAP Family 0.041 0.074 -10000 0 -0.37 14 14
GUCA1C 0.017 0.042 -10000 0 -0.64 2 2
GUCA1B 0.023 0.062 -10000 0 -0.59 5 5
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.006 0.1 -10000 0 -0.37 33 33
EPHB2 0.019 0.076 -10000 0 -0.52 9 9
Syndecan-2/TACI -0.005 0.12 -10000 0 -0.36 48 48
LAMA1 0.013 0.1 -10000 0 -0.57 14 14
Syndecan-2/alpha2 ITGB1 0.055 0.053 -10000 0 -0.34 2 2
HRAS 0.029 0.028 -10000 0 -0.59 1 1
Syndecan-2/CASK 0.015 0.004 -10000 0 -10000 0 0
ITGA5 -0.011 0.15 -10000 0 -0.59 33 33
BAX 0.022 0.007 -10000 0 -10000 0 0
EPB41 0.029 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.032 0.009 -10000 0 -10000 0 0
LAMA3 0.022 0.067 -10000 0 -0.59 6 6
EZR 0.028 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.062 -10000 0 -0.59 5 5
Syndecan-2/MMP2 0.031 0.039 -10000 0 -0.37 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.037 0.044 -10000 0 -0.47 3 3
dendrite morphogenesis 0.029 0.045 -10000 0 -0.4 4 4
Syndecan-2/GM-CSF 0.013 0.066 -10000 0 -0.36 14 14
determination of left/right symmetry 0.02 0.005 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.025 -10000 0 -0.36 1 1
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
MAPK3 0.011 0.063 -10000 0 -0.32 14 14
MAPK1 0.012 0.064 -10000 0 -0.32 14 14
Syndecan-2/RACK1 0.037 0.028 -10000 0 -0.31 1 1
NF1 0.029 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.02 0.005 -10000 0 -10000 0 0
ITGA2 0.023 0.054 -10000 0 -0.56 4 4
MAPK8 0.025 0.007 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.05 0.068 -10000 0 -0.34 8 8
Syndecan-2/Kininogen -0.28 0.19 -10000 0 -0.4 344 344
ITGB1 0.03 0.004 -10000 0 -10000 0 0
SRC 0.063 0.066 0.35 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.032 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.032 0.036 -10000 0 -0.36 4 4
actin cytoskeleton reorganization 0.006 0.1 -10000 0 -0.36 33 33
Syndecan-2/Caveolin-2/Ras 0.043 0.043 -10000 0 -0.33 5 5
Syndecan-2/Laminin alpha3 0.031 0.042 -10000 0 -0.36 5 5
Syndecan-2/RasGAP 0.046 0.042 -10000 0 -0.62 1 1
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 33 33
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
Syndecan-2 dimer 0.029 0.045 -10000 0 -0.4 4 4
GO:0007205 0.004 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.06 0.059 -10000 0 -0.6 1 1
RHOA 0.021 0.014 -10000 0 -10000 0 0
SDCBP 0.028 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.033 0.18 -10000 0 -0.59 49 49
RASA1 0.025 0.031 -10000 0 -0.64 1 1
alpha2/beta1 Integrin 0.037 0.044 -10000 0 -0.47 3 3
Syndecan-2/Synbindin 0.035 0.009 -10000 0 -10000 0 0
TGFB1 0.025 0.055 -10000 0 -0.59 4 4
CASP3 0.025 0.035 -10000 0 -0.32 1 1
FN1 -0.018 0.16 -10000 0 -0.59 37 37
Syndecan-2/IL8 0.009 0.1 -10000 0 -0.37 31 31
SDC2 0.02 0.005 -10000 0 -10000 0 0
KNG1 -0.46 0.29 -10000 0 -0.63 363 363
Syndecan-2/Neurofibromin 0.035 0.01 -10000 0 -10000 0 0
TRAPPC4 0.03 0.004 -10000 0 -10000 0 0
CSF2 0 0.1 -10000 0 -0.59 15 15
Syndecan-2/TGFB1 0.032 0.037 -10000 0 -0.36 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.032 0.009 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.036 0.026 -10000 0 -10000 0 0
PRKACA 0.034 0.031 -10000 0 -10000 0 0
angiogenesis 0.009 0.099 -10000 0 -0.37 31 31
MMP2 0.023 0.063 -10000 0 -0.6 5 5
IL8 -0.012 0.16 -10000 0 -0.6 33 33
calcineurin-NFAT signaling pathway -0.005 0.12 -10000 0 -0.36 48 48
EPO signaling pathway

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
BCL2L1 0.02 0.11 0.46 3 -10000 0 3
CRKL -0.031 0.16 0.38 14 -10000 0 14
mol:DAG -0.025 0.12 -10000 0 -10000 0 0
HRAS -0.008 0.16 0.43 14 -0.45 1 15
MAPK8 -0.058 0.17 0.36 1 -10000 0 1
RAP1A -0.032 0.16 0.38 15 -10000 0 15
GAB1 -0.032 0.16 0.36 13 -10000 0 13
MAPK14 -0.059 0.17 0.36 1 -10000 0 1
EPO -0.17 0.28 -10000 0 -0.58 160 160
PLCG1 -0.025 0.12 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.032 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.075 0.19 -10000 0 -0.35 158 158
GAB1/SHC/GRB2/SOS1 -0.013 0.14 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.42 160 160
IRS2 -0.037 0.16 0.37 13 -0.47 2 15
STAT1 -0.017 0.12 -10000 0 -10000 0 0
STAT5B -0.022 0.12 -10000 0 -10000 0 0
cell proliferation -0.052 0.16 0.38 6 -10000 0 6
GAB1/SHIP/PIK3R1/SHP2/SHC -0.034 0.12 -10000 0 -0.47 1 1
TEC -0.032 0.16 0.36 13 -10000 0 13
SOCS3 0.027 0.039 -10000 0 -0.59 2 2
STAT1 (dimer) -0.016 0.12 -10000 0 -10000 0 0
JAK2 0.014 0.031 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
EPO/EPOR (dimer)/JAK2 -0.026 0.16 -10000 0 -10000 0 0
EPO/EPOR -0.11 0.22 -10000 0 -0.42 160 160
LYN 0.03 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.025 0.15 0.3 1 -10000 0 1
elevation of cytosolic calcium ion concentration 0.016 0.032 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.065 0.19 -10000 0 -0.34 156 156
mol:IP3 -0.025 0.12 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.022 0.15 0.41 2 -0.5 2 4
SH2B3 0.013 0.03 -10000 0 -10000 0 0
NFKB1 -0.059 0.17 0.36 1 -0.66 1 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.047 0.099 -10000 0 -0.34 5 5
PTPN6 -0.043 0.15 0.3 4 -10000 0 4
TEC/VAV2/GRB2 -0.016 0.15 -10000 0 -10000 0 0
EPOR 0.016 0.032 -10000 0 -10000 0 0
INPP5D 0.023 0.055 -10000 0 -0.59 4 4
mol:GDP -0.014 0.15 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG2 0.02 0.075 -10000 0 -0.61 7 7
CRKL/CBL/C3G -0.016 0.15 -10000 0 -0.54 1 1
VAV2 -0.031 0.16 0.37 14 -10000 0 14
CBL -0.033 0.16 0.36 12 -0.58 1 13
SHC/Grb2/SOS1 -0.042 0.13 -10000 0 -10000 0 0
STAT5A -0.022 0.12 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.002 0.13 -10000 0 -10000 0 0
LYN/PLCgamma2 0.035 0.056 -10000 0 -0.44 6 6
PTPN11 0.029 0.005 -10000 0 -10000 0 0
BTK -0.097 0.2 0.38 13 -0.54 26 39
BCL2 0.023 0.12 0.42 4 -10000 0 4
Endothelins

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
AKT1 -0.002 0.16 0.38 2 -0.51 5 7
PTK2B 0.028 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.047 0.14 0.48 2 -0.67 6 8
EDN1 -0.001 0.16 0.42 1 -0.5 21 22
EDN3 0.01 0.094 -10000 0 -0.59 12 12
EDN2 -0.045 0.2 -10000 0 -0.57 61 61
HRAS/GDP 0.031 0.15 0.32 5 -0.6 11 16
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.018 0.12 0.25 2 -0.54 10 12
ADCY4 0.003 0.13 0.34 1 -0.44 4 5
ADCY5 -0.012 0.16 0.35 2 -0.52 15 17
ADCY6 0.002 0.13 0.34 1 -0.44 6 7
ADCY7 -0.009 0.14 0.34 1 -0.47 9 10
ADCY1 -0.007 0.14 0.34 1 -0.48 6 7
ADCY2 -0.067 0.18 0.36 1 -0.46 28 29
ADCY3 0.004 0.13 0.35 2 -0.44 6 8
ADCY8 -0.094 0.19 0.34 1 -0.5 32 33
ADCY9 0.002 0.13 0.35 2 -0.46 5 7
arachidonic acid secretion 0.042 0.15 0.38 7 -0.56 12 19
ETB receptor/Endothelin-1/Gq/GTP 0.027 0.087 -10000 0 -0.52 5 5
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
HRAS 0.029 0.028 -10000 0 -0.58 1 1
ETA receptor/Endothelin-1/G12/GTP 0.035 0.18 0.4 20 -0.53 4 24
ETA receptor/Endothelin-1/Gs/GTP 0.036 0.18 0.38 23 -0.47 6 29
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.028 0.24 0.38 2 -0.65 48 50
EDNRB 0.018 0.058 -10000 0 -0.51 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.03 0.22 0.6 1 -0.56 38 39
CYSLTR1 0.001 0.17 0.41 1 -0.53 7 8
SLC9A1 0.012 0.098 0.28 2 -0.32 4 6
mol:GDP 0.022 0.16 0.33 7 -0.65 11 18
SLC9A3 -0.33 0.29 0.36 1 -0.54 266 267
RAF1 0.012 0.15 0.34 4 -0.62 12 16
JUN 0.048 0.14 -10000 0 -0.67 5 5
JAK2 0 0.17 0.38 2 -0.55 5 7
mol:IP3 0.013 0.13 0.26 1 -0.6 10 11
ETA receptor/Endothelin-1 0.023 0.23 0.47 24 -0.44 39 63
PLCB1 0.02 0.079 -10000 0 -0.64 7 7
PLCB2 -0.039 0.2 -10000 0 -0.59 56 56
ETA receptor/Endothelin-3 0.02 0.11 -10000 0 -0.43 12 12
FOS 0.026 0.19 0.39 4 -0.84 15 19
Gai/GDP -0.1 0.26 -10000 0 -0.55 87 87
CRK 0.03 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.002 0.18 0.33 1 -0.59 14 15
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
PRKCB1 0.014 0.12 -10000 0 -0.57 10 10
GNAQ 0.032 0.007 -10000 0 -10000 0 0
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
GNAL 0.029 0.005 -10000 0 -10000 0 0
Gs family/GDP 0.027 0.14 0.3 5 -0.59 10 15
ETA receptor/Endothelin-1/Gq/GTP 0.034 0.11 0.26 1 -0.59 3 4
MAPK14 0.014 0.1 0.35 1 -0.53 8 9
TRPC6 0.047 0.15 0.49 2 -0.71 6 8
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.012 0.11 -10000 0 -0.52 11 11
ETB receptor/Endothelin-2 -0.024 0.16 -10000 0 -0.44 57 57
ETB receptor/Endothelin-3 0.018 0.083 -10000 0 -0.44 14 14
ETB receptor/Endothelin-1 0.013 0.14 -10000 0 -0.41 18 18
MAPK3 0.029 0.18 0.39 5 -0.73 16 21
MAPK1 0.029 0.18 0.4 5 -0.72 17 22
Rac1/GDP 0.022 0.14 0.31 2 -0.6 10 12
cAMP biosynthetic process -0.025 0.15 0.4 7 -0.48 11 18
MAPK8 0.044 0.16 0.4 1 -0.68 11 12
SRC 0.029 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.011 0.077 -10000 0 -0.46 5 5
p130Cas/CRK/Src/PYK2 0.038 0.16 0.42 9 -0.63 10 19
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.022 0.14 0.34 1 -0.6 10 11
COL1A2 -0.028 0.24 0.64 1 -0.6 60 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.021 0.17 0.29 1 -0.44 56 57
mol:DAG 0.013 0.13 0.26 1 -0.6 10 11
MAP2K2 0.026 0.16 0.46 3 -0.63 15 18
MAP2K1 0.028 0.16 0.37 5 -0.65 13 18
EDNRA 0.021 0.12 0.41 1 -0.44 2 3
positive regulation of muscle contraction 0.019 0.15 0.42 7 -0.46 4 11
Gq family/GDP 0.036 0.15 -10000 0 -0.64 10 10
HRAS/GTP 0.017 0.15 0.32 5 -0.64 11 16
PRKCH 0.013 0.12 -10000 0 -0.57 9 9
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.018 0.13 -10000 0 -0.59 9 9
PRKCB 0.017 0.14 0.33 5 -0.61 12 17
PRKCE 0.017 0.13 -10000 0 -0.56 10 10
PRKCD -0.002 0.12 -10000 0 -0.59 9 9
PRKCG -0.001 0.15 -10000 0 -0.57 17 17
regulation of vascular smooth muscle contraction 0.025 0.21 0.44 3 -0.96 15 18
PRKCQ 0.008 0.14 0.29 1 -0.64 11 12
PLA2G4A 0.04 0.16 0.38 7 -0.62 12 19
GNA14 0.024 0.073 -10000 0 -0.64 6 6
GNA15 0.015 0.1 -10000 0 -0.58 14 14
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA11 0.029 0.043 -10000 0 -0.64 2 2
Rac1/GTP 0.036 0.18 0.4 20 -0.53 4 24
MMP1 -0.1 0.28 0.7 1 -0.62 96 97
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.03 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.025 0.054 -10000 0 -0.36 2 2
NT3 (dimer)/TRKC 0.012 0.13 -10000 0 -0.5 26 26
NT3 (dimer)/TRKB -0.048 0.2 -10000 0 -0.42 100 100
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0.032 -10000 0 -0.45 1 1
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
BDNF -0.052 0.21 -10000 0 -0.59 66 66
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
DYNLT1 0.028 0.008 -10000 0 -10000 0 0
NTRK1 -0.017 0.16 -10000 0 -0.61 35 35
NTRK2 -0.09 0.25 -10000 0 -0.62 92 92
NTRK3 -0.006 0.15 -10000 0 -0.64 27 27
NT-4/5 (dimer)/TRKB -0.055 0.2 -10000 0 -0.42 106 106
neuron apoptosis 0.08 0.18 0.52 41 -10000 0 41
SHC 2-3/Grb2 -0.087 0.2 -10000 0 -0.57 41 41
SHC1 0.029 0.007 -10000 0 -10000 0 0
SHC2 -0.044 0.14 -10000 0 -0.48 27 27
SHC3 -0.11 0.23 -10000 0 -0.6 78 78
STAT3 (dimer) 0.027 0.053 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.006 0.16 -10000 0 -0.4 64 64
RIN/GDP 0.048 0.086 0.3 15 -0.32 4 19
GIPC1 0.029 0.03 -10000 0 -0.64 1 1
KRAS 0.029 0.005 -10000 0 -10000 0 0
DNAJA3 -0.029 0.11 -10000 0 -0.42 16 16
RIN/GTP 0.014 0.021 -10000 0 -0.43 1 1
CCND1 0.012 0.097 -10000 0 -0.51 17 17
MAGED1 0.03 0.003 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.018 0.051 -10000 0 -0.62 3 3
SHC/GRB2/SOS1 0.056 0.017 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.051 0.2 -10000 0 -0.4 114 114
TRKA/NEDD4-2 0.006 0.13 -10000 0 -0.47 32 32
ELMO1 0.026 0.029 -10000 0 -0.59 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.03 -10000 0 -0.39 2 2
NGF -0.026 0.18 -10000 0 -0.59 45 45
HRAS 0.029 0.028 -10000 0 -0.59 1 1
DOCK1 0.028 0.03 -10000 0 -0.64 1 1
GAB2 0.03 0.003 -10000 0 -10000 0 0
RIT2 0.019 0.028 -10000 0 -0.59 1 1
RIT1 0.029 0.007 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
DNM1 0.018 0.084 -10000 0 -0.6 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.013 0.11 -10000 0 -0.42 15 15
mol:GDP 0.056 0.12 0.4 15 -0.44 8 23
NGF (dimer) -0.026 0.18 -10000 0 -0.58 45 45
RhoG/GDP 0.019 0.021 -10000 0 -0.43 1 1
RIT1/GDP 0.05 0.08 0.31 11 -0.31 4 15
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
BDNF (dimer)/TRKB -0.077 0.22 -10000 0 -0.41 139 139
KIDINS220/CRKL/C3G 0.042 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.028 -10000 0 -0.47 1 1
FRS2 family/SHP2 0.057 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.071 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.023 0.065 -10000 0 -0.62 5 5
RAP1/GDP 0.034 0.057 -10000 0 -0.26 4 4
KIDINS220/CRKL 0.03 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.052 0.21 -10000 0 -0.59 66 66
ubiquitin-dependent protein catabolic process -0.014 0.16 -10000 0 -0.38 75 75
Schwann cell development -0.019 0.027 -10000 0 -10000 0 0
EHD4 0.03 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.07 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.041 0.025 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.064 0.2 -10000 0 -0.62 24 24
ABL1 0.029 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.46 10 10
STAT3 0.027 0.053 -10000 0 -10000 0 0
axon guidance -0.071 0.18 -10000 0 -0.59 24 24
MAPK3 -0.06 0.17 -10000 0 -0.45 34 34
MAPK1 -0.059 0.18 -10000 0 -0.43 41 41
CDC42/GDP 0.057 0.088 0.33 16 -0.31 4 20
NTF3 0.023 0.065 -10000 0 -0.62 5 5
NTF4 0.018 0.051 -10000 0 -0.63 3 3
NGF (dimer)/TRKA/FAIM -0.014 0.16 -10000 0 -0.38 75 75
PI3K 0.037 0.036 -10000 0 -0.47 2 2
FRS3 0.029 0.006 -10000 0 -10000 0 0
FAIM 0.029 0.007 -10000 0 -10000 0 0
GAB1 0.03 0.004 -10000 0 -10000 0 0
RASGRF1 -0.034 0.12 -10000 0 -0.44 18 18
SOS1 0.029 0.005 -10000 0 -10000 0 0
MCF2L 0.002 0.1 -10000 0 -0.43 26 26
RGS19 0.029 0.006 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.05 0.095 0.3 5 -0.57 6 11
Rac1/GDP 0.045 0.075 0.28 7 -0.32 4 11
NGF (dimer)/TRKA/GRIT -0.028 0.15 -10000 0 -0.39 76 76
neuron projection morphogenesis 0.002 0.16 0.41 1 -0.98 7 8
NGF (dimer)/TRKA/NEDD4-2 -0.013 0.16 -10000 0 -0.38 75 75
MAP2K1 0.041 0.048 0.43 3 -10000 0 3
NGFR -0.009 0.15 -10000 0 -0.6 31 31
NGF (dimer)/TRKA/GIPC/GAIP -0.006 0.11 -10000 0 -0.42 11 11
RAS family/GTP/PI3K 0.03 0.034 -10000 0 -0.45 2 2
FRS2 family/SHP2/GRB2/SOS1 0.081 0.028 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
PRKCI 0.029 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
MAPKKK cascade -0.064 0.2 -10000 0 -0.6 53 53
RASA1 0.025 0.031 -10000 0 -0.64 1 1
TRKA/c-Abl 0.006 0.13 -10000 0 -0.47 32 32
SQSTM1 0.023 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.058 0.2 -10000 0 -0.38 139 139
NGF (dimer)/TRKA/p62/Atypical PKCs 0.008 0.13 -10000 0 -0.36 18 18
MATK -0.03 0.18 -10000 0 -0.59 48 48
NEDD4L 0.028 0.03 -10000 0 -0.64 1 1
RAS family/GDP -0.009 0.035 -10000 0 -0.26 1 1
NGF (dimer)/TRKA -0.031 0.12 -10000 0 -0.35 36 36
Rac1/GTP -0.029 0.067 -10000 0 -0.35 5 5
FRS2 family/SHP2/CRK family 0.081 0.027 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.034 -10000 0 -0.63 1 1
HSPA8 0.03 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.078 0.072 0.36 1 -0.4 3 4
AKT1 0.03 0.011 -10000 0 -10000 0 0
GSC -0.028 0.16 -10000 0 -0.55 14 14
NKX2-5 -0.009 0.13 -10000 0 -0.59 23 23
muscle cell differentiation -0.028 0.093 0.52 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.093 0.091 -10000 0 -10000 0 0
SMAD4 0.041 0.036 -10000 0 -10000 0 0
CBFB 0.029 0.006 -10000 0 -10000 0 0
SAP18 0.03 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.047 0.045 -10000 0 -0.37 3 3
SMAD3/SMAD4/VDR 0.091 0.062 -10000 0 -10000 0 0
MYC 0.006 0.11 -10000 0 -0.59 16 16
CDKN2B 0.02 0.12 -10000 0 -0.68 2 2
AP1 0.062 0.069 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.054 0.065 -10000 0 -0.49 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.045 0.044 -10000 0 -0.34 1 1
SP3 0.032 0.007 -10000 0 -10000 0 0
CREB1 0.029 0.006 -10000 0 -10000 0 0
FOXH1 -0.019 0.17 -10000 0 -0.6 37 37
SMAD3/SMAD4/GR 0.064 0.057 -10000 0 -0.38 1 1
GATA3 -0.29 0.33 -10000 0 -0.63 238 238
SKI/SIN3/HDAC complex/NCoR1 0.042 0.037 -10000 0 -0.36 1 1
MEF2C/TIF2 0.026 0.14 -10000 0 -0.57 9 9
endothelial cell migration 0.053 0.17 0.53 13 -10000 0 13
MAX 0.03 0.014 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
RUNX2 0.012 0.1 -10000 0 -0.59 14 14
RUNX3 -0.24 0.3 -10000 0 -0.59 213 213
RUNX1 -0.013 0.16 -10000 0 -0.59 34 34
CTBP1 0.03 0.004 -10000 0 -10000 0 0
NR3C1 0.024 0.033 -10000 0 -0.59 1 1
VDR 0.025 0.052 -10000 0 -0.64 3 3
CDKN1A 0.049 0.083 -10000 0 -10000 0 0
KAT2B 0.019 0.032 -10000 0 -0.63 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.039 0.13 -10000 0 -0.41 26 26
DCP1A 0.022 0.014 -10000 0 -10000 0 0
SKI 0.029 0.007 -10000 0 -10000 0 0
SERPINE1 -0.053 0.17 -10000 0 -0.53 13 13
SMAD3/SMAD4/ATF2 0.074 0.051 -10000 0 -0.41 1 1
SMAD3/SMAD4/ATF3 0.072 0.059 -10000 0 -0.42 3 3
SAP30 0.009 0.11 -10000 0 -0.58 17 17
Cbp/p300/PIAS3 0.048 0.042 -10000 0 -0.39 1 1
JUN 0.05 0.065 -10000 0 -0.38 1 1
SMAD3/SMAD4/IRF7 0.064 0.09 -10000 0 -0.38 7 7
TFE3 0.029 0.021 -10000 0 -10000 0 0
COL1A2 -0.031 0.16 -10000 0 -0.46 61 61
mesenchymal cell differentiation -0.062 0.086 0.38 13 -10000 0 13
DLX1 -0.29 0.31 -10000 0 -0.59 258 258
TCF3 0.03 0.003 -10000 0 -10000 0 0
FOS 0.02 0.1 -10000 0 -0.63 12 12
SMAD3/SMAD4/Max 0.079 0.05 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.053 0.028 -10000 0 -0.39 1 1
ZBTB17 0.024 0.041 -10000 0 -0.61 2 2
LAMC1 0.053 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.076 0.044 -10000 0 -10000 0 0
IRF7 0.01 0.11 -10000 0 -0.58 17 17
ESR1 0.025 0.054 -10000 0 -0.54 4 4
HNF4A -0.021 0.18 -10000 0 -0.64 37 37
MEF2C 0.028 0.15 0.48 7 -0.57 7 14
SMAD2-3/SMAD4 0.083 0.05 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.051 0.032 -10000 0 -0.39 1 1
IGHV3OR16-13 -0.023 0.066 -10000 0 -0.49 5 5
TGIF2/HDAC complex 0.029 0.006 -10000 0 -10000 0 0
CREBBP 0.027 0.011 -10000 0 -10000 0 0
SKIL 0.029 0.007 -10000 0 -10000 0 0
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
SNIP1 0.029 0.006 -10000 0 -10000 0 0
GCN5L2 -0.002 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.079 0.054 -10000 0 -10000 0 0
MSG1/HSC70 0.043 0.031 -10000 0 -0.43 2 2
SMAD2 0.031 0.024 -10000 0 -10000 0 0
SMAD3 0.042 0.034 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.052 0.033 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.015 0.068 -10000 0 -0.45 4 4
NCOR1 0.03 0.005 -10000 0 -10000 0 0
NCOA2 0.019 0.079 -10000 0 -0.64 7 7
NCOA1 0.029 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.013 0.11 -10000 0 -0.43 27 27
SMAD2-3/SMAD4/SP1/MIZ-1 0.099 0.096 -10000 0 -10000 0 0
IFNB1 0.031 0.076 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.049 0.15 -10000 0 -0.53 7 7
CITED1 0.027 0.039 -10000 0 -0.59 2 2
SMAD2-3/SMAD4/ARC105 0.098 0.047 -10000 0 -10000 0 0
RBL1 0.029 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.055 0.053 -10000 0 -0.6 1 1
RUNX1-3/PEBPB2 -0.15 0.22 -10000 0 -0.38 225 225
SMAD7 0.08 0.067 -10000 0 -10000 0 0
MYC/MIZ-1 0.019 0.089 -10000 0 -0.44 18 18
SMAD3/SMAD4 0.015 0.095 -10000 0 -0.48 1 1
IL10 -0.16 0.24 -10000 0 -0.64 37 37
PIASy/HDAC complex 0.031 0.009 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.028 0.01 -10000 0 -10000 0 0
IL5 -0.13 0.19 -10000 0 -0.56 17 17
CDK4 0.026 0.014 -10000 0 -10000 0 0
PIAS4 0.032 0.009 -10000 0 -10000 0 0
ATF3 0.024 0.054 -10000 0 -0.56 4 4
SMAD3/SMAD4/SP1 0.069 0.089 -10000 0 -0.38 1 1
FOXG1 -0.011 0.11 -10000 0 -0.59 18 18
FOXO3 0.024 0.012 -10000 0 -10000 0 0
FOXO1 0.025 0.011 -10000 0 -10000 0 0
FOXO4 0.026 0.011 -10000 0 -10000 0 0
heart looping 0.028 0.15 0.48 7 -0.56 7 14
CEBPB 0.019 0.083 -10000 0 -0.59 9 9
SMAD3/SMAD4/DLX1 -0.16 0.22 -10000 0 -0.37 252 252
MYOD1 -0.011 0.14 -10000 0 -0.59 27 27
SMAD3/SMAD4/HNF4 0.039 0.14 -10000 0 -0.42 37 37
SMAD3/SMAD4/GATA3 -0.15 0.25 -10000 0 -0.41 217 217
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.097 0.21 -10000 0 -0.5 27 27
SMAD3/SMAD4/SP1-3 0.086 0.086 -10000 0 -10000 0 0
MED15 0.03 0.004 -10000 0 -10000 0 0
SP1 0.023 0.05 -10000 0 -10000 0 0
SIN3B 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.024 0.15 -10000 0 -0.54 15 15
ITGB5 0.057 0.077 0.43 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP 0.039 0.051 -10000 0 -0.47 3 3
SMAD3/SMAD4/AR 0.056 0.11 -10000 0 -0.42 23 23
AR -0.001 0.14 -10000 0 -0.62 24 24
negative regulation of cell growth 0.055 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.049 0.11 -10000 0 -0.38 27 27
E2F5 0.027 0.031 -10000 0 -0.64 1 1
E2F4 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.04 0.12 -10000 0 -0.44 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 0.054 0.035 -10000 0 -10000 0 0
TFDP1 0.029 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.082 0.073 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX2 0.063 0.086 -10000 0 -0.38 13 13
TGIF2 0.029 0.006 -10000 0 -10000 0 0
TGIF1 0.029 0.005 -10000 0 -10000 0 0
ATF2 0.028 0.03 -10000 0 -0.64 1 1
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.023 0.062 -10000 0 -0.58 5 5
GNB1/GNG2 -0.027 0.054 -10000 0 -0.2 19 19
AKT1 0.026 0.11 0.29 7 -0.34 13 20
EGF -0.57 0.2 -10000 0 -0.63 450 450
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.013 0.076 0.34 3 -0.39 2 5
mol:Ca2+ 0.038 0.12 0.32 7 -0.32 21 28
LYN 0.012 0.069 0.37 2 -10000 0 2
RhoA/GTP 0.008 0.047 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.034 0.13 0.32 8 -0.35 23 31
GNG2 0.028 0.008 -10000 0 -10000 0 0
ARRB2 0.028 0.033 -10000 0 -0.7 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.016 0.077 0.31 2 -0.5 4 6
G beta5/gamma2 -0.035 0.071 -10000 0 -0.27 19 19
PRKCH 0.031 0.13 0.38 3 -0.37 17 20
DNM1 0.018 0.084 -10000 0 -0.6 9 9
TXA2/TP beta/beta Arrestin3 0.004 0.035 -10000 0 -0.42 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.063 0.22 -10000 0 -0.59 73 73
G12 family/GTP 0.009 0.1 -10000 0 -0.32 15 15
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
ADRBK2 0.03 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.029 0.019 -10000 0 -10000 0 0
mol:GDP -0.031 0.092 0.42 4 -0.31 3 7
mol:NADP 0.027 0.009 -10000 0 -10000 0 0
RAB11A 0.03 0.003 -10000 0 -10000 0 0
PRKG1 0.015 0.098 -10000 0 -0.64 11 11
mol:IP3 0.036 0.14 0.39 4 -0.38 30 34
cell morphogenesis 0.029 0.019 -10000 0 -10000 0 0
PLCB2 0.029 0.18 0.45 3 -0.51 32 35
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.007 0.1 0.37 2 -0.39 15 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.095 0.39 1 -0.39 9 10
RHOA 0.021 0.014 -10000 0 -10000 0 0
PTGIR 0.027 0.041 -10000 0 -0.61 2 2
PRKCB1 0.033 0.14 0.37 4 -0.37 35 39
GNAQ 0.029 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.009 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.029 0.18 0.46 3 -0.52 36 39
LCK 0.003 0.098 0.34 3 -0.4 11 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.007 0.08 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.013 0.084 -10000 0 -0.42 15 15
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.081 -10000 0 -10000 0 0
MAPK14 0.035 0.097 0.28 9 -0.25 3 12
TGM2/GTP 0.035 0.16 0.36 3 -0.44 20 23
MAPK11 0.037 0.097 0.28 10 -0.28 4 14
ARHGEF1 0.02 0.069 -10000 0 -0.22 1 1
GNAI2 0.021 0.014 -10000 0 -10000 0 0
JNK cascade 0.035 0.14 0.34 7 -0.38 36 43
RAB11/GDP 0.029 0.003 -10000 0 -10000 0 0
ICAM1 0.035 0.12 0.32 5 -0.31 20 25
cAMP biosynthetic process 0.032 0.14 0.35 6 -0.37 20 26
Gq family/GTP/EBP50 0.018 0.051 0.23 3 -0.25 2 5
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -10000 0 0
SRC 0.012 0.068 0.39 1 -10000 0 1
GNB5 0.03 0.003 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.087 0.27 2 -0.33 15 17
VCAM1 0.034 0.12 0.3 7 -0.31 32 39
TP beta/Gq family/GDP/G beta5/gamma2 0.016 0.077 0.31 2 -0.5 4 6
platelet activation 0.047 0.13 0.35 11 -0.32 12 23
PGI2/IP 0.02 0.03 -10000 0 -0.46 2 2
PRKACA -0.009 0.084 -10000 0 -0.32 2 2
Gq family/GDP/G beta5/gamma2 0.013 0.074 0.26 1 -0.45 4 5
TXA2/TP beta/beta Arrestin2 0.002 0.05 -10000 0 -0.38 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.078 -10000 0 -0.31 1 1
mol:DAG 0.035 0.16 0.39 4 -0.42 33 37
EGFR 0.019 0.068 -10000 0 -0.59 6 6
TXA2/TP alpha 0.032 0.18 0.47 3 -0.5 22 25
Gq family/GTP 0.013 0.049 0.22 1 -0.3 6 7
YES1 0.014 0.071 0.37 2 -10000 0 2
GNAI2/GTP 0 0.067 -10000 0 -10000 0 0
PGD2/DP -0.046 0.16 -10000 0 -0.43 73 73
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
FYN 0.013 0.07 0.34 3 -10000 0 3
mol:NO 0.027 0.009 -10000 0 -10000 0 0
GNA15 0.013 0.1 -10000 0 -0.59 14 14
PGK/cGMP 0.027 0.063 -10000 0 -0.41 9 9
RhoA/GDP 0.021 0.013 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.024 0.092 -10000 0 -0.45 1 1
NOS3 0.027 0.01 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.036 0.14 0.37 6 -0.35 27 33
PRKCB 0.037 0.14 0.35 12 -0.37 29 41
PRKCE 0.036 0.14 0.34 5 -0.36 26 31
PRKCD 0.011 0.13 0.41 3 -0.38 32 35
PRKCG 0.028 0.15 0.42 3 -0.41 34 37
muscle contraction 0.033 0.17 0.39 6 -0.48 35 41
PRKCZ 0.034 0.13 0.34 6 -0.34 30 36
ARR3 0.021 0.005 -10000 0 -10000 0 0
TXA2/TP beta 0.018 0.082 -10000 0 -10000 0 0
PRKCQ 0.03 0.14 0.37 5 -0.38 27 32
MAPKKK cascade 0.03 0.16 0.4 4 -0.45 34 38
SELE 0.028 0.14 0.3 7 -0.4 36 43
TP beta/GNAI2/GDP/G beta/gamma 0.014 0.082 -10000 0 -10000 0 0
ROCK1 0.03 0.004 -10000 0 -10000 0 0
GNA14 0.021 0.073 -10000 0 -0.64 6 6
chemotaxis 0.027 0.2 0.52 2 -0.59 38 40
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.027 0.042 -10000 0 -0.64 2 2
Rac1/GTP 0.02 0.007 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.057 -10000 0 -0.29 13 13
epithelial cell differentiation 0.028 0.071 -10000 0 -0.34 13 13
CYFIP2 0.014 0.079 -10000 0 -0.64 7 7
ENAH 0.062 0.1 0.39 17 -10000 0 17
EGFR 0.019 0.068 -10000 0 -0.59 6 6
EPHA2 0.027 0.03 -10000 0 -0.64 1 1
MYO6 0.057 0.11 0.38 13 -0.49 2 15
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.059 -10000 0 -0.4 7 7
AQP5 -0.11 0.24 -10000 0 -0.51 111 111
CTNND1 0.03 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.061 0.11 0.4 13 -10000 0 13
regulation of calcium-dependent cell-cell adhesion 0.05 0.12 0.4 11 -0.34 13 24
EGF -0.57 0.2 -10000 0 -0.63 450 450
NCKAP1 0.029 0.006 -10000 0 -10000 0 0
AQP3 0.007 0.16 -10000 0 -0.54 28 28
cortical microtubule organization 0.028 0.071 -10000 0 -0.34 13 13
GO:0000145 0.051 0.11 0.39 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.073 -10000 0 -0.35 13 13
MLLT4 0.028 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.046 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.065 0.042 -10000 0 -0.36 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.041 0.084 0.38 2 -10000 0 2
PVRL2 0.03 0.004 -10000 0 -10000 0 0
ZYX 0.047 0.093 0.36 5 -0.33 11 16
ARF6/GTP 0.069 0.045 -10000 0 -0.34 2 2
CDH1 0.007 0.12 -10000 0 -0.62 17 17
EGFR/EGFR/EGF/EGF -0.24 0.14 -10000 0 -0.59 18 18
RhoA/GDP 0.029 0.068 -10000 0 -0.33 11 11
actin cytoskeleton organization 0.05 0.1 0.35 12 -0.46 2 14
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
GIT1 0.029 0.005 -10000 0 -10000 0 0
IGF1R 0.03 0.003 -10000 0 -10000 0 0
IGF1 0.023 0.062 -10000 0 -0.59 5 5
DIAPH1 0.032 0.11 -10000 0 -0.67 7 7
Wnt receptor signaling pathway -0.028 0.071 0.34 13 -10000 0 13
RHOA 0.021 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.009 0.048 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
VCL 0.05 0.1 0.35 12 -0.47 2 14
EFNA1 0.027 0.028 -10000 0 -0.59 1 1
LPP 0.046 0.094 0.39 6 -10000 0 6
Ephrin A1/EPHA2 0.023 0.065 -10000 0 -10000 0 0
SEC6/SEC8 0.001 0.05 -10000 0 -10000 0 0
MGAT3 0.051 0.12 0.41 11 -0.34 13 24
HGF/MET 0.012 0.093 -10000 0 -0.59 3 3
HGF 0.002 0.12 -10000 0 -0.6 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.058 -10000 0 -0.3 13 13
actin cable formation 0.1 0.13 0.33 72 -10000 0 72
KIAA1543 0.048 0.11 0.36 10 -0.54 2 12
KIFC3 0.049 0.093 -10000 0 -0.33 12 12
NCK1 0.027 0.031 -10000 0 -0.64 1 1
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ACTN1 0.052 0.1 0.43 7 -10000 0 7
NCK1/GIT1 0.041 0.026 -10000 0 -0.47 1 1
mol:GDP 0.028 0.071 -10000 0 -0.34 13 13
EXOC4 0.027 0.009 -10000 0 -10000 0 0
STX4 0.049 0.091 -10000 0 -10000 0 0
PIP5K1C 0.061 0.11 0.4 13 -10000 0 13
LIMA1 0.029 0.005 -10000 0 -10000 0 0
ABI1 0.03 0.004 -10000 0 -10000 0 0
ROCK1 0.075 0.11 0.41 19 -10000 0 19
adherens junction assembly 0.071 0.14 0.5 17 -0.72 2 19
IGF-1R heterotetramer/IGF1 0.022 0.07 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
MET 0.024 0.04 -10000 0 -0.59 2 2
PLEKHA7 0.057 0.11 0.36 10 -0.57 2 12
mol:GTP 0.063 0.041 -10000 0 -0.35 3 3
establishment of epithelial cell apical/basal polarity 0.081 0.12 0.38 44 -10000 0 44
cortical actin cytoskeleton stabilization 0.013 0.057 -10000 0 -0.29 13 13
regulation of cell-cell adhesion 0.05 0.1 0.35 12 -0.46 2 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.058 -10000 0 -0.3 13 13
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.081 -10000 0 -0.63 1 1
HDAC1 0.026 0.008 -10000 0 -10000 0 0
AES 0.029 0.004 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
DTX1 -0.03 0.19 -10000 0 -0.63 45 45
LRP6/FZD1 0.039 0.015 -10000 0 -10000 0 0
TLE1 0.028 0.006 -10000 0 -10000 0 0
AP1 -0.064 0.16 -10000 0 -0.32 125 125
NCSTN 0.029 0.007 -10000 0 -10000 0 0
ADAM10 0.029 0.03 -10000 0 -0.64 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.062 -10000 0 -0.75 1 1
NICD/RBPSUH 0.038 0.081 -10000 0 -0.61 1 1
WIF1 0.016 0.066 -10000 0 -0.63 5 5
NOTCH1 0.022 0.082 -10000 0 -0.65 1 1
PSENEN 0.03 0.003 -10000 0 -10000 0 0
KREMEN2 -0.042 0.2 -10000 0 -0.59 57 57
DKK1 0.004 0.12 -10000 0 -0.61 20 20
beta catenin/beta TrCP1 0.035 0.093 0.31 3 -0.42 1 4
APH1B 0.03 0.003 -10000 0 -10000 0 0
APH1A 0.029 0.007 -10000 0 -10000 0 0
AXIN1 0.011 0.067 0.28 4 -0.32 1 5
CtBP/CBP/TCF1/TLE1/AES 0.027 0.038 -10000 0 -0.36 2 2
PSEN1 0.028 0.008 -10000 0 -10000 0 0
FOS 0.012 0.1 -10000 0 -0.63 12 12
JUN 0.029 0.006 -10000 0 -10000 0 0
MAP3K7 0.027 0.008 -10000 0 -10000 0 0
CTNNB1 0.034 0.11 0.3 10 -0.36 4 14
MAPK3 0.029 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.007 0.15 -10000 0 -0.37 70 70
HNF1A 0.023 0.06 -10000 0 -0.64 4 4
CTBP1 0.029 0.004 -10000 0 -10000 0 0
MYC 0.01 0.13 -10000 0 -0.7 9 9
NKD1 -0.14 0.29 -10000 0 -0.63 124 124
FZD1 0.027 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.006 0.13 -10000 0 -0.61 4 4
apoptosis -0.064 0.16 -10000 0 -0.32 125 125
Delta 1/NOTCHprecursor 0.035 0.081 -10000 0 -0.61 1 1
DLL1 0.028 0.008 -10000 0 -10000 0 0
PPARD 0.009 0.15 -10000 0 -0.75 18 18
Gamma Secretase 0.079 0.03 -10000 0 -10000 0 0
APC 0.01 0.073 0.3 3 -0.4 3 6
DVL1 0.02 0.036 -10000 0 -0.43 2 2
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.007 0.16 -10000 0 -0.4 64 64
LRP6 0.029 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
NLK 0.017 0.008 -10000 0 -10000 0 0
CCND1 0.02 0.098 -10000 0 -0.72 2 2
WNT1 -0.001 0.13 -10000 0 -0.58 24 24
Axin1/APC/beta catenin 0.079 0.1 0.4 16 -10000 0 16
DKK2 0.002 0.13 -10000 0 -0.6 22 22
NOTCH1 precursor/DVL1 0.045 0.084 -10000 0 -0.55 1 1
GSK3B 0.028 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.006 0.13 -10000 0 -0.61 4 4
PPP2R5D 0.083 0.15 0.34 110 -0.45 5 115
MAPK1 0.03 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.041 0.098 -10000 0 -0.35 10 10
RBPJ 0.03 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.009 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.038 0.09 -10000 0 -0.36 21 21
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.079 -10000 0 -10000 0 0
AP1 0.019 0.098 -10000 0 -0.44 2 2
mol:PIP3 -0.003 0.068 -10000 0 -0.49 1 1
AKT1 0.009 0.11 0.42 1 -0.4 1 2
PTK2B 0.005 0.087 0.23 2 -0.38 9 11
RHOA -0.04 0.12 -10000 0 -0.38 19 19
PIK3CB 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.059 0.42 2 -0.39 2 4
MAGI3 0.026 0.042 -10000 0 -0.64 2 2
RELA 0.03 0.003 -10000 0 -10000 0 0
apoptosis 0.009 0.08 -10000 0 -0.33 22 22
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
positive regulation of microtubule depolymerization 0.009 0.09 0.27 6 -0.35 9 15
NF kappa B1 p50/RelA 0.027 0.079 -10000 0 -0.4 1 1
endothelial cell migration 0.006 0.1 -10000 0 -0.42 26 26
ADCY4 0.004 0.1 -10000 0 -0.45 21 21
ADCY5 -0.001 0.11 -10000 0 -0.44 26 26
ADCY6 0.004 0.1 -10000 0 -0.45 21 21
ADCY7 0.001 0.1 -10000 0 -0.45 21 21
ADCY1 0.001 0.1 -10000 0 -0.44 21 21
ADCY2 -0.024 0.12 -10000 0 -0.44 26 26
ADCY3 0.004 0.1 -10000 0 -0.44 22 22
ADCY8 -0.032 0.12 -10000 0 -0.44 27 27
ADCY9 0.003 0.1 -10000 0 -0.45 21 21
GSK3B 0.008 0.084 0.28 4 -0.38 7 11
arachidonic acid secretion 0.006 0.1 -10000 0 -0.44 21 21
GNG2 0.028 0.008 -10000 0 -10000 0 0
TRIP6 0.029 0.012 -10000 0 -10000 0 0
GNAO1 0.006 0.095 -10000 0 -0.38 25 25
HRAS 0.029 0.028 -10000 0 -0.59 1 1
NFKBIA 0.032 0.077 0.36 4 -0.38 2 6
GAB1 0.03 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.02 0.16 -10000 0 -0.82 16 16
JUN 0.029 0.006 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.04 0.025 -10000 0 -0.4 1 1
TIAM1 0.003 0.19 -10000 0 -0.97 17 17
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 0.028 0.059 0.42 2 -0.4 2 4
PLCB3 0.035 0.039 -10000 0 -0.36 1 1
FOS 0.012 0.1 -10000 0 -0.63 12 12
positive regulation of mitosis 0.006 0.1 -10000 0 -0.44 21 21
LPA/LPA1-2-3 0.035 0.095 -10000 0 -0.36 24 24
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
stress fiber formation 0.019 0.087 0.31 2 -0.36 7 9
GNAZ 0.007 0.096 -10000 0 -0.4 24 24
EGFR/PI3K-beta/Gab1 0.01 0.074 -10000 0 -0.51 1 1
positive regulation of dendritic cell cytokine production 0.033 0.094 -10000 0 -0.36 24 24
LPA/LPA2/MAGI-3 0.038 0.033 -10000 0 -0.4 2 2
ARHGEF1 0.032 0.093 0.37 6 -10000 0 6
GNAI2 0.003 0.085 -10000 0 -0.37 22 22
GNAI3 0.009 0.09 -10000 0 -0.4 21 21
GNAI1 0.009 0.084 -10000 0 -0.39 18 18
LPA/LPA3 0.017 0.039 -10000 0 -0.43 3 3
LPA/LPA2 0.024 0.015 -10000 0 -10000 0 0
LPA/LPA1 0.005 0.1 -10000 0 -0.43 26 26
HB-EGF/EGFR -0.13 0.19 -10000 0 -0.37 179 179
HBEGF -0.17 0.21 -10000 0 -0.43 185 185
mol:DAG 0.028 0.059 0.42 2 -0.4 2 4
cAMP biosynthetic process 0.011 0.12 0.36 10 -0.43 16 26
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
LYN 0.034 0.082 0.33 7 -0.38 3 10
GNAQ 0.022 0.026 -10000 0 -10000 0 0
LPAR2 0.03 0.003 -10000 0 -10000 0 0
LPAR3 0.02 0.048 -10000 0 -0.59 3 3
LPAR1 0.003 0.13 -10000 0 -0.58 23 23
IL8 -0.034 0.15 0.3 1 -0.5 7 8
PTK2 0.013 0.083 -10000 0 -0.35 12 12
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
CASP3 0.009 0.08 -10000 0 -0.33 22 22
EGFR 0.02 0.068 -10000 0 -0.6 6 6
PLCG1 0.02 0.04 -10000 0 -0.36 2 2
PLD2 0.014 0.084 -10000 0 -0.34 19 19
G12/G13 0.038 0.082 -10000 0 -0.36 15 15
PI3K-beta -0.024 0.1 -10000 0 -0.43 11 11
cell migration 0.03 0.063 -10000 0 -0.26 7 7
SLC9A3R2 0.027 0.031 -10000 0 -0.64 1 1
PXN 0.019 0.088 0.31 2 -0.37 7 9
HRAS/GTP 0.005 0.1 -10000 0 -0.45 21 21
RAC1 0.027 0.009 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 227 227
PRKCE 0.028 0.03 -10000 0 -0.64 1 1
PRKCD 0.025 0.063 0.36 4 -0.38 2 6
Gi(beta/gamma) 0.009 0.1 -10000 0 -0.42 21 21
mol:LPA 0 0.021 -10000 0 -0.28 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.036 0.089 -10000 0 -10000 0 0
MAPKKK cascade 0.006 0.1 -10000 0 -0.44 21 21
contractile ring contraction involved in cytokinesis -0.044 0.12 -10000 0 -0.38 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.018 0.05 -10000 0 -0.34 8 8
GNA15 0.015 0.053 -10000 0 -0.26 15 15
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
MAPT 0.009 0.092 0.27 5 -0.36 9 14
GNA11 0.022 0.034 -10000 0 -0.33 2 2
Rac1/GTP 0.02 0.17 -10000 0 -0.87 16 16
MMP2 0.006 0.1 -10000 0 -0.42 26 26
IL6-mediated signaling events

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
BCL2L1 -0.091 0.24 0.55 4 -0.66 15 19
CRP -0.13 0.29 0.55 1 -0.7 56 57
cell cycle arrest -0.12 0.26 0.48 1 -0.67 39 40
TIMP1 -0.094 0.26 -10000 0 -0.66 35 35
IL6ST 0.006 0.11 -10000 0 -0.62 15 15
Rac1/GDP -0.084 0.18 -10000 0 -0.49 26 26
AP1 0.029 0.13 0.46 1 -0.75 4 5
GAB2 0.03 0.003 -10000 0 -10000 0 0
TNFSF11 -0.13 0.28 0.61 1 -0.74 34 35
HSP90B1 0.026 0.065 -10000 0 -10000 0 0
GAB1 0.03 0.004 -10000 0 -10000 0 0
MAPK14 0.008 0.099 -10000 0 -0.6 3 3
AKT1 0.045 0.042 -10000 0 -0.51 1 1
FOXO1 0.053 0.046 -10000 0 -0.48 1 1
MAP2K6 -0.014 0.1 -10000 0 -0.61 4 4
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.098 0.19 -10000 0 -0.5 36 36
MITF -0.024 0.1 -10000 0 -0.62 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.03 0.003 -10000 0 -10000 0 0
A2M 0.032 0.051 -10000 0 -1.1 1 1
CEBPB 0.022 0.083 -10000 0 -0.58 9 9
GRB2/SOS1/GAB family/SHP2 0.015 0.082 -10000 0 -0.76 3 3
STAT3 -0.14 0.26 0.49 1 -0.71 38 39
STAT1 0.001 0.1 -10000 0 -0.82 7 7
CEBPD -0.094 0.24 0.54 2 -0.68 11 13
PIK3CA 0.029 0.031 -10000 0 -0.64 1 1
PI3K 0.04 0.036 -10000 0 -0.47 2 2
JUN 0.028 0.006 -10000 0 -10000 0 0
PIAS3/MITF -0.01 0.11 -10000 0 -0.59 3 3
MAPK11 0.008 0.1 -10000 0 -0.58 4 4
STAT3 (dimer)/FOXO1 -0.061 0.21 0.43 1 -0.61 7 8
GRB2/SOS1/GAB family 0.031 0.12 -10000 0 -0.72 1 1
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.016 0.12 -10000 0 -0.44 13 13
GRB2 0.029 0.005 -10000 0 -10000 0 0
JAK2 0.029 0.007 -10000 0 -10000 0 0
LBP -0.22 0.4 0.53 5 -0.8 131 136
PIK3R1 0.027 0.031 -10000 0 -0.64 1 1
JAK1 0.028 0.011 -10000 0 -10000 0 0
MYC -0.099 0.25 0.54 3 -0.67 22 25
FGG -0.18 0.31 0.52 1 -0.71 65 66
macrophage differentiation -0.12 0.26 0.48 1 -0.67 39 40
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.009 0.15 -10000 0 -0.68 2 2
JUNB -0.096 0.24 -10000 0 -0.66 21 21
FOS 0.011 0.1 -10000 0 -0.63 12 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.024 0.11 -10000 0 -0.51 6 6
STAT1/PIAS1 -0.028 0.13 -10000 0 -0.58 4 4
GRB2/SOS1/GAB family/SHP2/PI3K 0.042 0.045 -10000 0 -0.54 1 1
STAT3 (dimer) -0.12 0.27 -10000 0 -0.7 39 39
PRKCD -0.11 0.21 0.44 8 -0.56 31 39
IL6R 0.028 0.009 -10000 0 -10000 0 0
SOCS3 0.035 0.11 0.45 1 -0.68 2 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.036 0.082 -10000 0 -0.4 14 14
Rac1/GTP -0.092 0.18 -10000 0 -0.48 37 37
HCK -0.004 0.14 -10000 0 -0.59 26 26
MAPKKK cascade 0.033 0.098 -10000 0 -0.78 3 3
bone resorption -0.12 0.27 0.61 1 -0.7 34 35
IRF1 -0.064 0.26 0.56 6 -0.65 17 23
mol:GDP -0.099 0.17 -10000 0 -0.44 49 49
SOS1 0.029 0.005 -10000 0 -10000 0 0
VAV1 -0.1 0.17 -10000 0 -0.45 49 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.01 0.11 -10000 0 -0.62 5 5
PTPN11 0.012 0.039 -10000 0 -0.71 1 1
IL6/IL6RA -0.021 0.16 -10000 0 -0.45 57 57
gp130 (dimer)/TYK2/TYK2/LMO4 0.038 0.079 -10000 0 -0.4 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.035 0.08 -10000 0 -0.4 14 14
IL6 -0.05 0.2 -10000 0 -0.61 58 58
PIAS3 0.029 0.006 -10000 0 -10000 0 0
PTPRE 0.031 0.018 -10000 0 -10000 0 0
PIAS1 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.017 0.1 -10000 0 -0.47 6 6
LMO4 0.025 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.25 -10000 0 -0.7 27 27
MCL1 0.059 0.058 0.38 1 -0.45 1 2
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.024 0.029 0.3 1 -10000 0 1
DAPP1 0.008 0.11 0.39 5 -0.41 13 18
Src family/SYK family/BLNK-LAT/BTK-ITK -0.079 0.19 0.35 2 -0.51 43 45
mol:DAG -0.02 0.16 0.29 54 -0.26 39 93
HRAS 0.033 0.029 -10000 0 -0.58 1 1
RAP1A 0.033 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.031 0.075 0.24 1 -0.39 3 4
PLCG2 0.02 0.075 -10000 0 -0.61 7 7
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARF5 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.009 0.03 0.3 2 -10000 0 2
ARF1/GTP 0.036 0.056 0.31 3 -10000 0 3
RHOA 0.021 0.014 -10000 0 -10000 0 0
YES1 0.03 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.028 0.3 1 -10000 0 1
ADAP1 0.033 0.07 0.29 3 -10000 0 3
ARAP3 0.009 0.03 0.3 2 -10000 0 2
INPPL1 0.03 0.003 -10000 0 -10000 0 0
PREX1 0.029 0.006 -10000 0 -10000 0 0
ARHGEF6 0.03 0.003 -10000 0 -10000 0 0
ARHGEF7 0.03 0.004 -10000 0 -10000 0 0
ARF1 0.029 0.006 -10000 0 -10000 0 0
NRAS 0.033 0.009 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
FGR 0.025 0.048 -10000 0 -0.59 3 3
mol:Ca2+ 0.001 0.098 0.32 18 -10000 0 18
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.006 -10000 0 -10000 0 0
ZAP70 -0.3 0.31 -10000 0 -0.59 265 265
mol:IP3 -0.008 0.12 0.34 20 -10000 0 20
LYN 0.028 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.042 0.08 0.25 6 -0.38 3 9
RhoA/GDP 0.018 0.048 0.38 1 -10000 0 1
PDK1/Src/Hsp90 0.052 0.029 -10000 0 -0.41 1 1
BLNK 0.028 0.03 -10000 0 -0.64 1 1
actin cytoskeleton reorganization 0.039 0.098 0.36 12 -10000 0 12
SRC 0.029 0.006 -10000 0 -10000 0 0
PLEKHA2 0.012 0.034 -10000 0 -0.36 4 4
RAC1 0.027 0.009 -10000 0 -10000 0 0
PTEN 0.021 0.013 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.024 0.027 0.3 1 -10000 0 1
RhoA/GTP 0.019 0.031 0.3 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.1 0.17 -10000 0 -0.43 57 57
BLK -0.013 0.15 -10000 0 -0.59 32 32
PDPK1 0.027 0.031 -10000 0 -0.64 1 1
CYTH1 0.047 0.073 0.29 11 -10000 0 11
HCK -0.003 0.14 -10000 0 -0.59 26 26
CYTH3 0.036 0.062 0.29 3 -10000 0 3
CYTH2 0.046 0.072 0.29 10 -10000 0 10
KRAS 0.033 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.042 0.056 -10000 0 -0.42 1 1
SGK1 0.037 0.071 -10000 0 -0.45 1 1
INPP5D 0.023 0.055 -10000 0 -0.59 4 4
mol:GDP 0.03 0.082 0.24 10 -0.41 3 13
SOS1 0.029 0.005 -10000 0 -10000 0 0
SYK 0.027 0.034 -10000 0 -0.48 2 2
ARF6/GDP 0.018 0.046 0.39 1 -10000 0 1
mol:PI-3-4-5-P3 0.038 0.061 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.021 0.028 0.3 1 -10000 0 1
VAV1 -0.12 0.26 -10000 0 -0.59 118 118
mol:PI-3-4-P2 0.018 0.041 -10000 0 -0.43 4 4
RAS family/GTP/PI3K Class I 0.079 0.065 0.34 1 -10000 0 1
PLEKHA1 0.013 0.034 -10000 0 -0.36 4 4
Rac1/GDP 0.031 0.074 0.24 1 -0.39 3 4
LAT -0.14 0.28 -10000 0 -0.59 140 140
Rac1/GTP 0.017 0.071 -10000 0 -10000 0 0
ITK -0.057 0.15 0.28 25 -10000 0 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.046 0.18 0.3 47 -0.38 39 86
LCK 0.002 0.13 -10000 0 -0.59 22 22
BTK -0.017 0.15 0.29 11 -10000 0 11
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.038 0.04 -10000 0 -10000 0 0
BIRC5 -0.15 0.28 -10000 0 -0.59 147 147
NFKBIA 0.024 0.027 0.26 1 -10000 0 1
CPEB1 -0.099 0.26 -10000 0 -0.63 96 96
AKT1 0.023 0.025 -10000 0 -10000 0 0
NDEL1 0.029 0.005 -10000 0 -10000 0 0
Aurora A/BRCA1 0.031 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.048 0.053 -10000 0 -0.45 3 3
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.031 0.013 -10000 0 -10000 0 0
PAK1/Aurora A 0.039 0.042 -10000 0 -10000 0 0
MDM2 0.029 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.074 0.19 -10000 0 -0.43 108 108
TP53 0.033 0.026 -10000 0 -0.34 1 1
DLG7 0.021 0.025 -10000 0 -10000 0 0
AURKAIP1 0.025 0.051 -10000 0 -0.62 3 3
ARHGEF7 0.03 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.051 0.056 -10000 0 -0.48 3 3
G2/M transition of mitotic cell cycle 0.031 0.034 -10000 0 -10000 0 0
AURKA 0.031 0.033 -10000 0 -10000 0 0
AURKB -0.067 0.093 -10000 0 -0.18 151 151
CDC25B 0.029 0.032 -10000 0 -0.34 1 1
G2/M transition checkpoint 0.013 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.16 -10000 0 -0.36 95 95
Aurora A/CPEB -0.044 0.16 -10000 0 -0.36 95 95
Aurora A/TACC1/TRAP/chTOG 0.063 0.045 -10000 0 -10000 0 0
BRCA1 0.029 0.005 -10000 0 -10000 0 0
centrosome duplication 0.039 0.041 -10000 0 -10000 0 0
regulation of centrosome cycle 0.046 0.053 -10000 0 -0.45 3 3
spindle assembly 0.061 0.044 -10000 0 -10000 0 0
TDRD7 0.029 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.039 0.16 -10000 0 -0.4 13 13
CENPA -0.05 0.084 -10000 0 -0.25 14 14
Aurora A/PP2A 0.038 0.039 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.03 0.031 0.19 1 -10000 0 1
negative regulation of DNA binding 0.033 0.027 -10000 0 -0.34 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.008 -10000 0 -10000 0 0
RASA1 0.025 0.031 -10000 0 -0.64 1 1
Ajuba/Aurora A 0.013 0.03 -10000 0 -10000 0 0
mitotic prometaphase 0.023 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.033 -10000 0 -10000 0 0
TACC1 0.027 0.009 -10000 0 -10000 0 0
TACC3 0.025 0.055 -10000 0 -0.59 4 4
Aurora A/Antizyme1 0.049 0.052 -10000 0 -0.34 3 3
Aurora A/RasGAP 0.035 0.044 -10000 0 -0.4 1 1
OAZ1 0.029 0.028 -10000 0 -0.59 1 1
RAN 0.029 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.01 -10000 0 -10000 0 0
GIT1 0.029 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.012 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.074 0.19 -10000 0 -0.43 108 108
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 -0.046 0.15 -10000 0 -0.39 15 15
PAK1 0.03 0.003 -10000 0 -10000 0 0
CKAP5 0.03 0.003 -10000 0 -10000 0 0
IFN-gamma pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.082 0.17 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.052 0.15 -10000 0 -0.78 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.006 0.062 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.06 0.086 -10000 0 -0.34 1 1
CaM/Ca2+ -0.075 0.16 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.085 0.15 -10000 0 -0.65 1 1
AKT1 -0.058 0.16 0.4 8 -10000 0 8
MAP2K1 -0.078 0.14 0.31 4 -10000 0 4
MAP3K11 -0.087 0.15 0.31 7 -0.58 1 8
IFNGR1 0.004 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.17 0.25 -10000 0 -0.54 131 131
Rap1/GTP -0.074 0.11 -10000 0 -10000 0 0
CRKL/C3G 0.042 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.088 0.19 -10000 0 -10000 0 0
CEBPB -0.009 0.15 0.51 10 -10000 0 10
STAT3 0.029 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.065 0.17 -10000 0 -0.61 3 3
STAT1 -0.084 0.16 0.32 8 -0.66 1 9
CALM1 0.028 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.24 0.3 -10000 0 -0.58 223 223
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
STAT1 (dimer)/PIAS1 -0.069 0.15 0.32 2 -0.62 1 3
CEBPB/PTGES2/Cbp/p300 -0.011 0.084 -10000 0 -0.4 1 1
mol:Ca2+ -0.083 0.16 -10000 0 -10000 0 0
MAPK3 -0.039 0.13 0.42 3 -0.62 1 4
STAT1 (dimer) -0.076 0.12 -10000 0 -0.49 1 1
MAPK1 -0.039 0.14 0.45 4 -0.59 2 6
JAK2 0.005 0.031 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
JAK1 0.005 0.032 -10000 0 -10000 0 0
CAMK2D 0.03 0.004 -10000 0 -10000 0 0
DAPK1 0.006 0.13 0.45 12 -0.61 3 15
SMAD7 -0.013 0.075 0.24 16 -10000 0 16
CBL/CRKL/C3G -0.063 0.16 -10000 0 -10000 0 0
PI3K -0.072 0.15 -10000 0 -10000 0 0
IFNG -0.24 0.3 -10000 0 -0.58 223 223
apoptosis -0.002 0.12 0.41 13 -0.43 7 20
CAMK2G 0.029 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.005 -10000 0 -10000 0 0
CAMK2A -0.14 0.28 -10000 0 -0.64 119 119
CAMK2B -0.065 0.23 -10000 0 -0.63 69 69
FRAP1 -0.059 0.14 0.36 11 -10000 0 11
PRKCD -0.07 0.14 0.38 5 -10000 0 5
RAP1B 0.029 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.06 0.086 -10000 0 -0.34 1 1
PTPN2 0.03 0.005 -10000 0 -10000 0 0
EP300 0.029 0.03 -10000 0 -0.64 1 1
IRF1 -0.039 0.12 0.42 5 -0.74 1 6
STAT1 (dimer)/PIASy -0.072 0.16 0.37 2 -0.62 1 3
SOCS1 0.028 0.07 -10000 0 -0.98 1 1
mol:GDP -0.062 0.15 -10000 0 -10000 0 0
CASP1 -0.013 0.074 0.24 16 -10000 0 16
PTGES2 0.026 0.043 -10000 0 -0.64 2 2
IRF9 0.022 0.071 0.26 16 -10000 0 16
mol:PI-3-4-5-P3 -0.078 0.14 -10000 0 -10000 0 0
RAP1/GDP -0.062 0.12 -10000 0 -10000 0 0
CBL -0.088 0.15 0.31 6 -10000 0 6
MAP3K1 -0.085 0.15 0.32 6 -10000 0 6
PIAS1 0.03 0.003 -10000 0 -10000 0 0
PIAS4 0.03 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.06 0.086 -10000 0 -0.34 1 1
PTPN11 -0.097 0.15 -10000 0 -10000 0 0
CREBBP 0.029 0.007 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.093 0.31 15 -10000 0 15
GNAI2 0.021 0.014 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.027 0.14 -10000 0 -0.37 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
RhoA/GTP -0.003 0.095 -10000 0 -0.32 15 15
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.36 17 17
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNA12 0.027 0.009 -10000 0 -10000 0 0
S1PR5 -0.072 0.23 -10000 0 -0.59 82 82
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.36 17 17
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
Nongenotropic Androgen 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
PTK2 0.011 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.033 0.089 -10000 0 -0.36 23 23
regulation of S phase of mitotic cell cycle 0.019 0.07 -10000 0 -0.38 6 6
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
HRAS 0.029 0.028 -10000 0 -0.58 1 1
SHBG/T-DHT -0.025 0.13 -10000 0 -0.41 52 52
PELP1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.011 0.003 -10000 0 -10000 0 0
MAP2K1 0.009 0.073 0.35 1 -0.4 3 4
T-DHT/AR -0.001 0.1 -10000 0 -0.47 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.009 13 13
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
mol:GDP -0.006 0.1 -10000 0 -0.46 22 22
cell proliferation 0.005 0.11 0.31 4 -0.57 6 10
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
FOS 0.009 0.14 -10000 0 -0.76 13 13
mol:Ca2+ 0.003 0.016 -10000 0 -0.08 10 10
MAPK3 0.01 0.091 0.31 5 -0.48 5 10
MAPK1 0.012 0.065 -10000 0 -0.5 3 3
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 0 0.001 -10000 0 -0.005 12 12
cAMP biosynthetic process -0.04 0.12 0.24 2 -0.39 51 53
GNG2 0.028 0.008 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 12 12
HRAS/GTP 0.041 0.079 -10000 0 -0.34 18 18
actin cytoskeleton reorganization 0.036 0.03 -10000 0 -0.32 2 2
SRC 0.029 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 12 12
PI3K 0.034 0.031 -10000 0 -0.41 2 2
apoptosis -0.013 0.1 0.5 12 -0.26 2 14
T-DHT/AR/PELP1 0.02 0.093 -10000 0 -0.4 22 22
HRAS/GDP 0.011 0.1 -10000 0 -0.45 22 22
CREB1 0.014 0.11 0.28 1 -0.54 12 13
RAC1-CDC42/GTP 0.045 0.034 -10000 0 -0.33 2 2
AR -0.001 0.14 -10000 0 -0.62 24 24
GNB1 0.029 0.006 -10000 0 -10000 0 0
RAF1 0.011 0.075 0.35 1 -0.39 3 4
RAC1-CDC42/GDP 0.031 0.1 -10000 0 -0.46 16 16
T-DHT/AR/PELP1/Src 0.039 0.084 -10000 0 -0.37 18 18
MAP2K2 0.009 0.072 0.35 1 -0.4 3 4
T-DHT/AR/PELP1/Src/PI3K 0.019 0.07 -10000 0 -0.38 6 6
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
SHBG -0.04 0.2 -10000 0 -0.63 52 52
Gi family/GNB1/GNG2/GDP -0.009 0.12 -10000 0 -0.48 16 16
mol:T-DHT 0 0.001 -10000 0 -0.007 9 9
RAC1 0.027 0.009 -10000 0 -10000 0 0
GNRH1 -0.11 0.2 -10000 0 -0.44 136 136
Gi family/GTP 0.008 0.059 -10000 0 -0.34 8 8
CDC42 0.029 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.053 0.059 -10000 0 -0.32 9 9
ER alpha/Gai/GDP/Gbeta gamma -0.03 0.17 -10000 0 -0.52 38 38
AKT1 -0.03 0.23 -10000 0 -0.73 43 43
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.03 0.23 -10000 0 -0.75 44 44
mol:Ca2+ -0.016 0.12 -10000 0 -0.46 15 15
IGF1R 0.03 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.031 0.054 -10000 0 -0.47 5 5
SHC1 0.029 0.007 -10000 0 -10000 0 0
apoptosis 0.027 0.22 0.69 44 -10000 0 44
RhoA/GTP 0.018 0.031 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.006 0.14 -10000 0 -0.58 12 12
regulation of stress fiber formation -0.034 0.051 -10000 0 -0.38 3 3
E2/ERA-ERB (dimer) 0.027 0.059 -10000 0 -0.38 9 9
KRAS 0.029 0.005 -10000 0 -10000 0 0
G13/GTP 0.032 0.034 -10000 0 -0.36 3 3
pseudopodium formation 0.034 0.051 0.38 3 -10000 0 3
E2/ER alpha (dimer)/PELP1 0.034 0.037 -10000 0 -0.4 3 3
GRB2 0.029 0.005 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
HRAS 0.029 0.028 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.004 0.18 0.3 6 -0.52 41 47
E2/ER beta (dimer) 0.015 0.052 -10000 0 -0.41 7 7
mol:GDP 0.021 0.051 -10000 0 -0.41 3 3
mol:NADP -0.004 0.18 0.3 6 -0.52 41 47
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 -0.017 0.13 -10000 0 -0.48 15 15
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
PLCB1 0.017 0.086 -10000 0 -0.49 9 9
PLCB2 -0.013 0.12 -10000 0 -0.46 14 14
IGF1 0.023 0.062 -10000 0 -0.59 5 5
mol:L-citrulline -0.004 0.18 0.3 6 -0.52 41 47
RHOA 0.021 0.014 -10000 0 -10000 0 0
Gai/GDP -0.11 0.26 -10000 0 -0.53 120 120
JNK cascade 0.014 0.052 -10000 0 -0.41 7 7
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
ESR2 0.02 0.07 -10000 0 -0.56 7 7
GNAQ 0.029 0.006 -10000 0 -10000 0 0
ESR1 0.023 0.053 -10000 0 -0.55 4 4
Gq family/GDP/Gbeta gamma 0.022 0.12 -10000 0 -0.74 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.03 0.14 -10000 0 -0.91 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.007 0.14 -10000 0 -0.6 11 11
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
E2/ER alpha (dimer) 0.017 0.039 -10000 0 -0.4 4 4
STRN 0.025 0.052 -10000 0 -0.64 3 3
GNAL 0.029 0.005 -10000 0 -10000 0 0
PELP1 0.029 0.005 -10000 0 -10000 0 0
MAPK11 0.014 0.048 -10000 0 -0.37 7 7
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
HBEGF -0.081 0.18 0.41 10 -0.55 29 39
cAMP biosynthetic process 0.023 0.048 -10000 0 -0.31 9 9
SRC -0.024 0.16 -10000 0 -0.5 35 35
PI3K 0.037 0.036 -10000 0 -0.47 2 2
GNB1 0.029 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.043 0.063 -10000 0 -0.38 2 2
SOS1 0.029 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.037 0.097 -10000 0 -0.48 13 13
Gs family/GTP 0.031 0.051 -10000 0 -0.31 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.023 -10000 0 -0.33 1 1
vasodilation -0.002 0.17 0.3 6 -0.5 41 47
mol:DAG -0.017 0.13 -10000 0 -0.48 15 15
Gs family/GDP/Gbeta gamma 0.022 0.054 -10000 0 -0.36 2 2
MSN 0.035 0.053 0.38 3 -10000 0 3
Gq family/GTP 0.024 0.075 -10000 0 -0.47 8 8
mol:PI-3-4-5-P3 -0.027 0.22 -10000 0 -0.71 45 45
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.002 0.17 0.5 41 -0.3 6 47
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.062 -10000 0 -0.38 3 3
NOS3 -0.006 0.18 0.32 5 -0.55 41 46
GNA11 0.027 0.042 -10000 0 -0.64 2 2
MAPKKK cascade 0.007 0.18 0.38 4 -0.55 42 46
E2/ER alpha (dimer)/PELP1/Src 0.003 0.15 0.27 1 -0.55 16 17
ruffle organization 0.034 0.051 0.38 3 -10000 0 3
ROCK2 0.04 0.056 0.4 3 -10000 0 3
GNA14 0.021 0.073 -10000 0 -0.64 6 6
GNA15 0.013 0.1 -10000 0 -0.59 14 14
GNA13 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.15 0.2 0.38 7 -0.5 60 67
MMP2 -0.019 0.16 0.33 2 -0.57 20 22
PLK2 and PLK4 events

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
PLK2 0.008 0.11 -9999 0 -0.59 16 16
PLK4 0.026 0.048 -9999 0 -0.59 3 3
regulation of centriole replication 0.005 0.087 -9999 0 -0.43 19 19
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.059 -10000 0 -0.3 15 15
CRKL 0.03 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DOCK1 0.028 0.03 -10000 0 -0.64 1 1
ITGA4 0.01 0.1 -10000 0 -0.59 15 15
alpha4/beta7 Integrin/MAdCAM1 0.03 0.093 -10000 0 -0.37 3 3
EPO -0.17 0.28 -10000 0 -0.59 160 160
alpha4/beta7 Integrin 0.027 0.081 -10000 0 -0.43 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.081 -10000 0 -0.43 15 15
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.43 160 160
lamellipodium assembly 0.022 0.091 0.31 1 -0.54 6 7
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
PI3K 0.037 0.036 -10000 0 -0.47 2 2
ARF6 0.028 0.008 -10000 0 -10000 0 0
JAK2 -0.044 0.12 -10000 0 -0.39 8 8
PXN 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
MADCAM1 0.014 0.092 -10000 0 -0.6 11 11
cell adhesion 0.029 0.091 -10000 0 -0.36 3 3
CRKL/CBL 0.043 0.024 -10000 0 -0.47 1 1
ITGB1 0.03 0.004 -10000 0 -10000 0 0
SRC 0.014 0.084 -10000 0 -0.35 1 1
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.034 0.095 -10000 0 -0.37 25 25
p130Cas/Crk/Dock1 0.037 0.084 -10000 0 -0.59 1 1
VCAM1 0.015 0.091 -10000 0 -0.53 13 13
RHOA 0.021 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.072 -10000 0 -10000 0 0
BCAR1 0.007 0.082 -10000 0 -0.64 1 1
EPOR 0.03 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.028 0.03 -10000 0 -0.64 1 1
GIT1 0.029 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.022 0.094 0.32 1 -0.56 6 7
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.027 0.21 1 -10000 0 1
RFC1 0.008 0.025 -10000 0 -10000 0 0
PRKDC 0.011 0.036 0.23 7 -10000 0 7
RIPK1 0.03 0.007 -10000 0 -10000 0 0
CASP7 -0.011 0.11 -10000 0 -0.63 12 12
FASLG/FAS/FADD/FAF1 -0.072 0.11 0.24 6 -0.27 10 16
MAP2K4 -0.053 0.15 0.31 5 -0.55 19 24
mol:ceramide -0.083 0.13 -10000 0 -0.38 12 12
GSN 0.008 0.027 0.21 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 8 -0.084 0.12 -10000 0 -0.36 9 9
FAS 0.027 0.011 -10000 0 -10000 0 0
BID 0.002 0.041 -10000 0 -10000 0 0
MAP3K1 -0.019 0.13 0.32 5 -0.5 16 21
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
RB1 0.009 0.03 0.22 3 -10000 0 3
CFLAR 0.029 0.007 -10000 0 -10000 0 0
HGF/MET 0.029 0.11 -10000 0 -0.42 25 25
ARHGDIB 0.011 0.036 -10000 0 -10000 0 0
FADD 0.028 0.011 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.027 -10000 0 -0.21 1 1
NFKB1 -0.027 0.089 -10000 0 -0.59 6 6
MAPK8 -0.059 0.17 0.38 4 -0.53 29 33
DFFA 0.008 0.025 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.008 0.025 -10000 0 -10000 0 0
FAS/FADD/MET 0.049 0.035 -10000 0 -0.36 2 2
CFLAR/RIP1 0.043 0.013 -10000 0 -10000 0 0
FAIM3 -0.014 0.16 -10000 0 -0.58 35 35
FAF1 0.026 0.014 -10000 0 -10000 0 0
PARP1 0.008 0.025 -10000 0 -10000 0 0
DFFB 0.008 0.025 -10000 0 -10000 0 0
CHUK -0.021 0.079 -10000 0 -0.55 5 5
FASLG -0.28 0.3 -10000 0 -0.59 247 247
FAS/FADD 0.04 0.017 -10000 0 -10000 0 0
HGF 0.002 0.12 -10000 0 -0.6 20 20
LMNA 0.007 0.033 0.29 1 -0.32 1 2
CASP6 0.008 0.025 -10000 0 -10000 0 0
CASP10 0.027 0.011 -10000 0 -10000 0 0
CASP3 0.006 0.032 -10000 0 -10000 0 0
PTPN13 0.018 0.089 -10000 0 -0.64 9 9
CASP8 0.005 0.07 0.26 35 -10000 0 35
IL6 -0.085 0.3 -10000 0 -1.1 31 31
MET 0.024 0.04 -10000 0 -0.59 2 2
ICAD/CAD 0.01 0.023 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.084 0.13 -10000 0 -0.38 12 12
activation of caspase activity by cytochrome c 0.002 0.041 -10000 0 -10000 0 0
PAK2 0.012 0.038 0.22 10 -10000 0 10
BCL2 0.029 0.005 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.013 -10000 0 -10000 0 0
AES 0.027 0.01 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.015 -10000 0 -10000 0 0
SMAD4 0.029 0.005 -10000 0 -10000 0 0
DKK2 0.002 0.13 -10000 0 -0.6 22 22
TLE1 0.027 0.012 -10000 0 -10000 0 0
MACF1 0.03 0.007 -10000 0 -10000 0 0
CTNNB1 0.036 0.12 0.38 12 -0.41 1 13
WIF1 0.003 0.068 -10000 0 -0.63 5 5
beta catenin/RanBP3 -0.011 0.088 0.35 6 -10000 0 6
KREMEN2 -0.043 0.2 -10000 0 -0.58 57 57
DKK1 0.004 0.12 -10000 0 -0.61 20 20
beta catenin/beta TrCP1 0.018 0.088 0.38 1 -10000 0 1
FZD1 0.028 0.01 -10000 0 -10000 0 0
AXIN2 -0.001 0.12 0.55 7 -1.4 2 9
AXIN1 0.03 0.007 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.12 -10000 0 -0.52 18 18
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.061 0.089 0.34 1 -0.75 1 2
Axin1/APC/GSK3 0.073 0.086 0.3 22 -10000 0 22
Axin1/APC/GSK3/beta catenin/Macf1 0.049 0.1 0.38 6 -10000 0 6
HNF1A 0.021 0.061 -10000 0 -0.64 4 4
CTBP1 0.027 0.011 -10000 0 -10000 0 0
MYC 0 0.13 0.59 12 -0.52 3 15
RANBP3 0.03 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.007 0.15 -10000 0 -0.37 70 70
NKD1 -0.14 0.28 -10000 0 -0.63 124 124
TCF4 0.027 0.012 -10000 0 -10000 0 0
TCF3 0.027 0.011 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.089 -10000 0 -10000 0 0
Ran/GTP 0.021 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.092 0.42 7 -0.52 2 9
LEF1 0.009 0.11 -10000 0 -0.59 15 15
DVL1 0.021 0.031 -10000 0 -0.3 2 2
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.09 0.35 1 -0.6 2 3
DKK1/LRP6/Kremen 2 -0.006 0.16 -10000 0 -0.4 64 64
LRP6 0.03 0.006 -10000 0 -10000 0 0
CSNK1A1 0.021 0.016 -10000 0 -10000 0 0
NLK 0.03 0.005 -10000 0 -10000 0 0
CCND1 -0.015 0.1 0.7 1 -0.57 1 2
WNT1 0 0.13 -10000 0 -0.58 24 24
GSK3A 0.031 0.005 -10000 0 -10000 0 0
GSK3B 0.029 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
PPP2R5D 0.096 0.14 0.34 115 -0.37 6 121
APC 0.027 0.098 0.38 9 -10000 0 9
WNT1/LRP6/FZD1 0.035 0.053 0.26 3 -10000 0 3
CREBBP 0.026 0.012 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.023 0.013 -9999 0 -10000 0 0
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.049 -9999 0 -0.29 3 3
GNAO1 0.026 0.056 -9999 0 -0.6 4 4
S1P/S1P3/G12/G13 0.052 0.022 -9999 0 -10000 0 0
AKT1 0.027 0.039 -9999 0 -0.32 3 3
AKT3 -0.016 0.092 -9999 0 -0.54 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -9999 0 -10000 0 0
GNAI2 0.023 0.015 -9999 0 -10000 0 0
GNAI3 0.031 0.006 -9999 0 -10000 0 0
GNAI1 0.027 0.031 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.031 0.006 -9999 0 -10000 0 0
S1PR2 0.03 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.032 0.042 -9999 0 -0.33 1 1
MAPK3 0.029 0.039 -9999 0 -10000 0 0
MAPK1 0.03 0.04 -9999 0 -10000 0 0
JAK2 -0.026 0.097 -9999 0 -0.46 4 4
CXCR4 -0.078 0.15 -9999 0 -0.36 33 33
FLT1 0.026 0.062 -9999 0 -0.58 5 5
RhoA/GDP 0.016 0.01 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.007 -9999 0 -10000 0 0
SRC 0.029 0.039 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.032 0.042 -9999 0 -0.33 1 1
RAC1 0.027 0.009 -9999 0 -10000 0 0
RhoA/GTP 0.038 0.049 -9999 0 -10000 0 0
VEGFA -0.24 0.31 -9999 0 -0.58 220 220
S1P/S1P2/Gi 0.03 0.043 -9999 0 -0.32 2 2
VEGFR1 homodimer/VEGFA homodimer -0.16 0.24 -9999 0 -0.43 220 220
RHOA 0.021 0.014 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.054 -9999 0 -0.38 2 2
GNAQ 0.029 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.052 -9999 0 -0.64 3 3
G12/G13 0.039 0.015 -9999 0 -10000 0 0
GNA14 0.021 0.073 -9999 0 -0.64 6 6
GNA15 0.013 0.1 -9999 0 -0.59 14 14
GNA12 0.027 0.009 -9999 0 -10000 0 0
GNA13 0.029 0.005 -9999 0 -10000 0 0
GNA11 0.027 0.042 -9999 0 -0.64 2 2
Rac1/GTP 0.028 0.054 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.006 -10000 0 -10000 0 0
SMARCC1 0.009 0.046 -10000 0 -0.66 2 2
REL 0.026 0.045 -10000 0 -0.53 3 3
HDAC7 -0.12 0.095 -10000 0 -0.66 3 3
JUN 0.029 0.006 -10000 0 -10000 0 0
EP300 0.028 0.03 -10000 0 -0.64 1 1
KAT2B 0.02 0.033 -10000 0 -0.64 1 1
KAT5 0.03 0.003 -10000 0 -10000 0 0
MAPK14 -0.017 0.042 -10000 0 -0.51 3 3
FOXO1 0.029 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.14 0.1 -10000 0 -0.7 3 3
MAP2K6 0.014 0.053 -10000 0 -0.66 3 3
BRM/BAF57 0.042 0.012 -10000 0 -10000 0 0
MAP2K4 0.018 0.01 -10000 0 -10000 0 0
SMARCA2 0.029 0.007 -10000 0 -10000 0 0
PDE9A -0.12 0.14 -10000 0 -0.83 13 13
NCOA2 0.019 0.079 -10000 0 -0.64 7 7
CEBPA 0.018 0.086 -10000 0 -0.58 10 10
EHMT2 0.029 0.006 -10000 0 -10000 0 0
cell proliferation -0.12 0.13 0.51 4 -0.5 10 14
NR0B1 -0.016 0.15 -10000 0 -0.59 30 30
EGR1 0.012 0.084 -10000 0 -0.64 8 8
RXRs/9cRA 0.048 0.038 -10000 0 -0.36 3 3
AR/RACK1/Src -0.036 0.065 -10000 0 -0.48 3 3
AR/GR -0.018 0.09 -10000 0 -0.43 15 15
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
PKN1 0.03 0.002 -10000 0 -10000 0 0
RCHY1 0.03 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.017 1 1
MAPK8 -0.014 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.045 0.083 -10000 0 -0.59 4 4
SRC -0.036 0.036 -10000 0 -0.4 2 2
NR3C1 0.022 0.03 -10000 0 -0.59 1 1
KLK3 -0.027 0.14 -10000 0 -0.62 16 16
APPBP2 0 0.019 -10000 0 -10000 0 0
TRIM24 0.027 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.049 0.067 -10000 0 -0.52 4 4
TMPRSS2 -0.91 0.36 -10000 0 -1 433 433
RXRG 0.022 0.058 -10000 0 -0.62 4 4
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.029 0.006 -10000 0 -10000 0 0
RXRB 0.029 0.006 -10000 0 -10000 0 0
CARM1 0.03 0.003 -10000 0 -10000 0 0
NR2C2 0.02 0.033 -10000 0 -0.64 1 1
KLK2 -0.034 0.1 -10000 0 -0.57 11 11
AR -0.022 0.074 -10000 0 -0.36 19 19
SENP1 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
MDM2 0.03 0.007 -10000 0 -10000 0 0
SRY 0 0.004 0.019 17 -10000 0 17
GATA2 0.014 0.095 -10000 0 -0.61 11 11
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.099 0.24 -10000 0 -0.58 100 100
T-DHT/AR/RACK1/Src -0.036 0.065 -10000 0 -0.48 3 3
positive regulation of transcription 0.014 0.095 -10000 0 -0.61 11 11
DNAJA1 -0.001 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.009 -10000 0 -10000 0 0
NCOA1 0.054 0.032 -10000 0 -10000 0 0
SPDEF -0.11 0.26 -10000 0 -0.59 109 109
T-DHT/AR/TIF2 -0.028 0.089 -10000 0 -0.55 6 6
T-DHT/AR/Hsp90 -0.047 0.065 -10000 0 -0.52 3 3
GSK3B 0.024 0.008 -10000 0 -10000 0 0
NR2C1 0.029 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.042 0.043 -10000 0 -0.43 3 3
SIRT1 0.029 0.006 -10000 0 -10000 0 0
ZMIZ2 0.027 0.01 -10000 0 -10000 0 0
POU2F1 -0.071 0.047 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.073 0.1 -10000 0 -0.59 8 8
CREBBP 0.029 0.006 -10000 0 -10000 0 0
SMARCE1 0.029 0.005 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.042 -10000 0 -0.64 2 2
SPHK1 -0.018 0.16 -10000 0 -0.59 38 38
GNAI2 0.021 0.014 -10000 0 -10000 0 0
mol:S1P 0.007 0.061 -10000 0 -0.31 3 3
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
mol:Sphinganine-1-P -0.013 0.12 -10000 0 -0.43 39 39
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.06 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.039 0.015 -10000 0 -10000 0 0
S1PR3 0.029 0.006 -10000 0 -10000 0 0
S1PR2 0.03 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.051 -10000 0 -0.27 3 3
S1PR5 -0.072 0.23 -10000 0 -0.59 82 82
S1PR4 0 0.13 -10000 0 -0.59 24 24
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
S1P/S1P5/G12 -0.02 0.14 -10000 0 -0.33 73 73
S1P/S1P3/Gq 0.022 0.089 -10000 0 -0.38 7 7
S1P/S1P4/Gi 0.015 0.074 0.29 1 -0.34 6 7
GNAQ 0.029 0.006 -10000 0 -10000 0 0
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
GNA14 0.021 0.073 -10000 0 -0.64 6 6
GNA15 0.013 0.1 -10000 0 -0.59 14 14
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.027 0.042 -10000 0 -0.64 2 2
ABCC1 0.029 0.006 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0 0.1 -10000 0 -0.54 15 15
Crk/p130 Cas/Paxillin -0.029 0.082 -10000 0 -0.44 3 3
JUN 0.008 0.09 -10000 0 -0.45 7 7
HRAS 0.029 0.028 -10000 0 -0.59 1 1
RET51/GFRalpha1/GDNF/GRB10 0.021 0.13 -10000 0 -0.39 37 37
RAP1A 0.029 0.005 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.021 0.13 -10000 0 -0.4 36 36
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.011 0.099 -10000 0 -0.36 27 27
RHOA 0.021 0.014 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.12 -10000 0 -0.38 22 22
GRB7 0.021 0.073 -10000 0 -0.64 6 6
RET51/GFRalpha1/GDNF 0.022 0.13 -10000 0 -0.4 34 34
MAPKKK cascade 0.011 0.11 -10000 0 -0.53 4 4
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/IRS1 0.015 0.11 -10000 0 -0.37 34 34
lamellipodium assembly 0.004 0.089 -10000 0 -0.35 6 6
RET51/GFRalpha1/GDNF/SHC 0.021 0.13 -10000 0 -0.4 37 37
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC 0.018 0.1 -10000 0 -0.37 29 29
RET9/GFRalpha1/GDNF/Shank3 0.018 0.1 -10000 0 -0.37 31 31
MAPK3 0.005 0.11 0.52 1 -0.59 3 4
DOK1 0.029 0.005 -10000 0 -10000 0 0
DOK6 0.015 0.095 -10000 0 -0.61 11 11
PXN 0.029 0.006 -10000 0 -10000 0 0
neurite development 0.005 0.11 -10000 0 -0.48 6 6
DOK5 0.017 0.088 -10000 0 -0.63 9 9
GFRA1 -0.014 0.16 -10000 0 -0.58 35 35
MAPK8 0.003 0.093 -10000 0 -0.44 10 10
HRAS/GTP 0.019 0.12 -10000 0 -0.49 8 8
tube development 0.022 0.1 -10000 0 -0.35 25 25
MAPK1 0.011 0.12 0.43 6 -0.59 3 9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.01 0.072 -10000 0 -0.35 1 1
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
PDLIM7 0.019 0.049 -10000 0 -0.59 3 3
RET51/GFRalpha1/GDNF/Dok6 0.026 0.15 -10000 0 -0.63 9 9
SHC1 0.029 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.021 0.13 -10000 0 -0.4 38 38
RET51/GFRalpha1/GDNF/Dok5 0.016 0.15 -10000 0 -0.43 40 40
PRKCA 0.029 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
CREB1 0.008 0.096 -10000 0 -0.44 9 9
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.008 0.08 -10000 0 -0.3 26 26
RET51/GFRalpha1/GDNF/Grb7 0.017 0.15 -10000 0 -0.43 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.006 0.12 -10000 0 -0.61 18 18
DOK4 0.029 0.006 -10000 0 -10000 0 0
JNK cascade 0.008 0.089 -10000 0 -0.44 7 7
RET9/GFRalpha1/GDNF/FRS2 0.019 0.1 -10000 0 -0.37 27 27
SHANK3 0.03 0.004 -10000 0 -10000 0 0
RASA1 0.025 0.031 -10000 0 -0.64 1 1
NCK1 0.027 0.031 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.083 -10000 0 -0.4 7 7
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.006 0.095 -10000 0 -0.38 9 9
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.002 0.11 -10000 0 -0.42 16 16
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.005 0.1 -10000 0 -0.45 11 11
PI3K 0.006 0.14 -10000 0 -0.5 11 11
SOS1 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.03 0.1 -10000 0 -0.35 25 25
GRB10 0.027 0.009 -10000 0 -10000 0 0
activation of MAPKK activity 0.006 0.084 -10000 0 -0.41 3 3
RET51/GFRalpha1/GDNF/FRS2 0.023 0.13 -10000 0 -0.4 31 31
GAB1 0.03 0.004 -10000 0 -10000 0 0
IRS1 0.025 0.052 -10000 0 -0.64 3 3
IRS2 0.02 0.079 -10000 0 -0.6 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.003 0.11 -10000 0 -0.42 15 15
RET51/GFRalpha1/GDNF/PKC alpha 0.021 0.13 -10000 0 -0.39 39 39
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GDNF 0.017 0.048 -10000 0 -0.59 3 3
RAC1 0.027 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.017 0.14 -10000 0 -0.4 38 38
Rac1/GTP 0.011 0.11 -10000 0 -0.44 5 5
RET9/GFRalpha1/GDNF 0.002 0.11 -10000 0 -0.41 31 31
GFRalpha1/GDNF 0 0.13 -10000 0 -0.47 31 31
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.005 0.22 -10000 0 -1.1 18 18
MKNK1 0.029 0.006 -10000 0 -10000 0 0
MAPK14 0.032 0.073 -10000 0 -0.45 1 1
ATF2/c-Jun 0.028 0.06 -10000 0 -0.43 1 1
MAPK11 0.031 0.08 -10000 0 -0.46 3 3
MITF 0.022 0.091 -10000 0 -0.38 19 19
MAPKAPK5 0.032 0.083 -10000 0 -0.35 18 18
KRT8 0.032 0.086 -10000 0 -0.36 19 19
MAPKAPK3 0.021 0.014 -10000 0 -10000 0 0
MAPKAPK2 0.029 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.11 -10000 0 -0.46 19 19
CEBPB 0.028 0.093 -10000 0 -0.5 3 3
SLC9A1 0.031 0.088 -10000 0 -0.56 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.088 -10000 0 -0.53 3 3
p38alpha-beta/MNK1 0.055 0.096 -10000 0 -0.58 2 2
JUN 0.03 0.061 -10000 0 -0.42 1 1
PPARGC1A -0.004 0.14 -10000 0 -0.35 63 63
USF1 0.032 0.08 -10000 0 -0.34 18 18
RAB5/GDP/GDI1 0.022 0.063 -10000 0 -0.39 2 2
NOS2 0.033 0.093 -10000 0 -0.51 2 2
DDIT3 0.03 0.089 -10000 0 -0.49 4 4
RAB5A 0.022 0.014 -10000 0 -10000 0 0
HSPB1 0.045 0.1 0.3 40 -0.44 4 44
p38alpha-beta/HBP1 0.05 0.094 -10000 0 -0.59 2 2
CREB1 0.033 0.091 -10000 0 -0.39 18 18
RAB5/GDP 0.016 0.01 -10000 0 -10000 0 0
EIF4E 0.029 0.077 -10000 0 -0.63 1 1
RPS6KA4 0.034 0.085 -10000 0 -0.58 2 2
PLA2G4A 0.023 0.085 -10000 0 -0.54 2 2
GDI1 0.033 0.085 -10000 0 -0.51 2 2
TP53 0.023 0.1 -10000 0 -0.45 19 19
RPS6KA5 0.03 0.089 -10000 0 -0.38 18 18
ESR1 0.028 0.094 -10000 0 -0.37 21 21
HBP1 0.027 0.009 -10000 0 -10000 0 0
MEF2C 0.031 0.08 -10000 0 -0.37 15 15
MEF2A 0.034 0.084 -10000 0 -0.58 2 2
EIF4EBP1 0.026 0.099 -10000 0 -0.41 18 18
KRT19 -0.038 0.18 -10000 0 -0.38 92 92
ELK4 0.032 0.082 -10000 0 -0.48 2 2
ATF6 0.032 0.08 -10000 0 -0.34 18 18
ATF1 0.033 0.091 -10000 0 -0.39 18 18
p38alpha-beta/MAPKAPK2 0.055 0.094 -10000 0 -0.5 2 2
p38alpha-beta/MAPKAPK3 0.038 0.096 -10000 0 -0.59 2 2
TCGA08_rtk_signaling

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
PDGFRA -0.23 0.32 -10000 0 -0.63 193 193
HRAS 0.029 0.028 -10000 0 -0.59 1 1
EGFR 0.019 0.068 -10000 0 -0.59 6 6
AKT 0.032 0.089 0.28 24 -10000 0 24
FOXO3 0.028 0.008 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
FOXO1 0.029 0.005 -10000 0 -10000 0 0
AKT3 0.029 0.006 -10000 0 -10000 0 0
FOXO4 0.03 0.001 -10000 0 -10000 0 0
MET 0.024 0.04 -10000 0 -0.59 2 2
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
PIK3CB 0.029 0.007 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
PIK3CG 0.023 0.048 -10000 0 -0.59 3 3
PIK3R3 0.029 0.006 -10000 0 -10000 0 0
PIK3R2 0.03 0.003 -10000 0 -10000 0 0
NF1 0.029 0.005 -10000 0 -10000 0 0
RAS -0.029 0.083 -10000 0 -0.27 3 3
ERBB2 0.027 0.042 -10000 0 -0.64 2 2
proliferation/survival/translation -0.044 0.06 0.26 7 -0.23 1 8
PI3K 0 0.1 0.3 24 -0.26 5 29
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
KRAS 0.029 0.005 -10000 0 -10000 0 0
FOXO 0.057 0.072 0.27 22 -10000 0 22
AKT2 0.03 0.004 -10000 0 -10000 0 0
PTEN 0.029 0.006 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.078 0.082 -10000 0 -0.38 1 1
epithelial cell differentiation -0.049 0.1 -10000 0 -0.46 3 3
ITCH 0.063 0.02 -10000 0 -10000 0 0
WWP1 -0.091 0.065 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
EGFR 0.019 0.068 -10000 0 -0.59 6 6
PRL 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.047 0.079 0.38 2 -0.52 1 3
PTPRZ1 -0.045 0.2 -10000 0 -0.63 52 52
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.079 -10000 0 -0.45 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.079 0.083 -10000 0 -0.46 10 10
ADAM17 0.064 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.084 -10000 0 -0.43 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.091 -10000 0 -0.46 9 9
NCOR1 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.069 0.081 -10000 0 -0.46 8 8
GRIN2B -0.067 0.077 -10000 0 -0.44 8 8
ErbB4/ErbB2/betacellulin -0.11 0.14 -10000 0 -0.44 56 56
STAT1 0.028 0.028 -10000 0 -0.59 1 1
HBEGF 0.023 0.013 -10000 0 -10000 0 0
PRLR -0.049 0.21 -10000 0 -0.64 57 57
E4ICDs/ETO2 -0.1 0.08 -10000 0 -0.45 3 3
axon guidance -0.044 0.081 -10000 0 -10000 0 0
NEDD4 0.062 0.047 -10000 0 -0.62 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.025 0.16 -10000 0 -0.48 57 57
CBFA2T3 0.027 0.039 -10000 0 -0.59 2 2
ErbB4/ErbB2/HBEGF -0.047 0.064 -10000 0 -0.44 1 1
MAPK3 -0.051 0.079 0.45 1 -0.54 1 2
STAT1 (dimer) -0.1 0.076 -10000 0 -0.38 1 1
MAPK1 -0.051 0.081 0.38 2 -0.54 1 3
JAK2 0.029 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.075 0.079 -10000 0 -0.46 9 9
NRG1 0.026 0.082 -10000 0 -0.46 12 12
NRG3 0.018 0.084 -10000 0 -0.6 9 9
NRG2 0.012 0.083 -10000 0 -0.59 9 9
NRG4 -0.028 0.18 -10000 0 -0.63 43 43
heart development -0.044 0.081 -10000 0 -10000 0 0
neural crest cell migration -0.075 0.079 -10000 0 -0.45 9 9
ERBB2 0.041 0.035 -10000 0 -0.47 2 2
WWOX/E4ICDs -0.1 0.077 -10000 0 -0.41 2 2
SHC1 0.029 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.13 -10000 0 -0.47 34 34
apoptosis 0.089 0.078 0.43 3 -10000 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.084 0.09 -10000 0 -0.44 5 5
ErbB4/ErbB2/epiregulin -0.084 0.098 -10000 0 -0.41 22 22
ErbB4/ErbB4/betacellulin/betacellulin -0.16 0.15 -10000 0 -0.49 68 68
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.093 0.13 -10000 0 -0.45 30 30
MDM2 -0.1 0.072 -10000 0 -0.38 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.052 0.071 -10000 0 -0.42 10 10
STAT5A -0.038 0.076 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.072 0.086 -10000 0 -0.44 13 13
DLG4 0.029 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.042 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.095 0.068 -10000 0 -0.35 1 1
STAT5A (dimer) -0.048 0.12 -10000 0 -0.51 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.036 0.084 0.35 1 -10000 0 1
LRIG1 0.023 0.013 -10000 0 -10000 0 0
EREG -0.009 0.15 -10000 0 -0.59 31 31
BTC -0.065 0.23 -10000 0 -0.62 72 72
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.045 0.08 -10000 0 -10000 0 0
ERBB4 -0.12 0.085 -10000 0 -0.43 1 1
STAT5B 0.029 0.005 -10000 0 -10000 0 0
YAP1 -0.021 0.04 -10000 0 -0.53 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.095 0.12 -10000 0 -0.44 35 35
glial cell differentiation 0.095 0.068 0.35 1 -10000 0 1
WWOX 0.028 0.028 -10000 0 -0.59 1 1
cell proliferation -0.078 0.15 0.35 1 -0.58 14 15
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.024 0.056 -10000 0 -0.6 4 4
CDC42/GTP 0.014 0.068 -10000 0 -0.33 3 3
PLCG1 0.013 0.057 -10000 0 -0.34 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.005 -10000 0 -10000 0 0
G12/G13 0.039 0.015 -10000 0 -10000 0 0
cell migration 0.013 0.067 -10000 0 -0.32 3 3
S1PR5 -0.072 0.23 -10000 0 -0.59 82 82
S1PR4 0 0.13 -10000 0 -0.59 24 24
MAPK3 0.013 0.057 -10000 0 -0.34 3 3
MAPK1 0.014 0.057 -10000 0 -0.34 3 3
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.36 17 17
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
CDC42/GDP 0.021 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.027 0.14 -10000 0 -0.37 73 73
RHOA 0.015 0.087 0.36 4 -10000 0 4
S1P/S1P4/Gi 0.015 0.061 -10000 0 -0.35 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
S1P/S1P4/G12/G13 0.032 0.083 -10000 0 -0.33 23 23
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.024 0.093 -9999 0 -0.42 18 18
E-cadherin/beta catenin 0.014 0.092 -9999 0 -0.47 16 16
CTNNB1 0.021 0.014 -9999 0 -10000 0 0
JUP 0.025 0.052 -9999 0 -0.64 3 3
CDH1 0.007 0.12 -9999 0 -0.62 17 17
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.03 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ITGA4 0.01 0.1 -9999 0 -0.59 15 15
alpha4/beta7 Integrin 0.027 0.081 -9999 0 -0.43 15 15
alpha4/beta1 Integrin 0.028 0.081 -9999 0 -0.43 15 15
Syndecan-3-mediated signaling events

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.03 0.003 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.043 0.093 -9999 0 -0.64 1 1
Syndecan-3/Neurocan 0.015 0.089 -9999 0 -0.33 29 29
POMC 0.026 0.045 -9999 0 -0.67 2 2
EGFR 0.019 0.068 -9999 0 -0.59 6 6
Syndecan-3/EGFR 0.018 0.079 -9999 0 -0.35 18 18
AGRP 0.022 0.043 -9999 0 -0.64 2 2
NCSTN 0.029 0.007 -9999 0 -10000 0 0
PSENEN 0.03 0.003 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.03 0.003 -9999 0 -10000 0 0
APH1A 0.029 0.007 -9999 0 -10000 0 0
NCAN 0.013 0.09 -9999 0 -0.59 11 11
long-term memory 0.04 0.073 -9999 0 -0.32 11 11
Syndecan-3/IL8 0.002 0.11 -9999 0 -0.32 49 49
PSEN1 0.028 0.008 -9999 0 -10000 0 0
Src/Cortactin 0.043 0.009 -9999 0 -10000 0 0
FYN 0.028 0.008 -9999 0 -10000 0 0
limb bud formation 0.012 0.057 -9999 0 -0.36 11 11
MC4R 0.011 0.077 -9999 0 -0.59 8 8
SRC 0.029 0.006 -9999 0 -10000 0 0
PTN 0.01 0.11 -9999 0 -0.63 13 13
FGFR/FGF/Syndecan-3 0.012 0.058 -9999 0 -0.36 11 11
neuron projection morphogenesis 0.023 0.1 -9999 0 -0.6 2 2
Syndecan-3/AgRP 0.019 0.076 -9999 0 -0.34 21 21
Syndecan-3/AgRP/MC4R 0.027 0.088 -9999 0 -0.33 17 17
Fyn/Cortactin 0.041 0.012 -9999 0 -10000 0 0
SDC3 0.012 0.058 -9999 0 -0.37 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.002 0.11 -9999 0 -0.31 49 49
IL8 -0.012 0.16 -9999 0 -0.6 33 33
Syndecan-3/Fyn/Cortactin 0.042 0.075 -9999 0 -0.33 11 11
Syndecan-3/CASK 0.004 0.069 -9999 0 -0.34 19 19
alpha-MSH/MC4R 0.027 0.069 -9999 0 -0.45 10 10
Gamma Secretase 0.079 0.03 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.04 0.034 -10000 0 -0.47 2 2
AKT1 -0.016 0.14 0.44 7 -0.57 3 10
PTK2B -0.095 0.16 0.36 2 -0.89 1 3
VEGFR2 homodimer/Frs2 0.043 0.043 -10000 0 -0.76 1 1
CAV1 -0.009 0.14 -10000 0 -0.59 29 29
CALM1 0.028 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.1 0.19 -10000 0 -0.7 2 2
endothelial cell proliferation 0.004 0.16 0.49 18 -0.47 2 20
mol:Ca2+ -0.098 0.17 -10000 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.082 0.18 -10000 0 -0.8 1 1
RP11-342D11.1 -0.11 0.16 -10000 0 -0.89 1 1
CDH5 0.028 0.028 -10000 0 -0.59 1 1
VEGFA homodimer -0.11 0.19 -10000 0 -0.37 4 4
SHC1 0.029 0.007 -10000 0 -10000 0 0
SHC2 0.023 0.064 -10000 0 -0.61 5 5
HRAS/GDP -0.076 0.15 -10000 0 -0.6 2 2
SH2D2A -0.16 0.28 -10000 0 -0.59 154 154
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.14 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.21 0.24 -10000 0 -0.62 63 63
VEGFR1 homodimer 0.023 0.061 -10000 0 -0.58 5 5
SHC/GRB2/SOS1 -0.067 0.18 -10000 0 -0.73 1 1
GRB10 -0.093 0.16 -10000 0 -0.75 1 1
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
PAK1 0.03 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.08 0.18 -10000 0 -0.75 2 2
HRAS 0.029 0.028 -10000 0 -0.59 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.047 0.11 -10000 0 -0.4 13 13
HIF1A 0.025 0.043 -10000 0 -0.64 2 2
FRS2 0.029 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.083 0.18 -10000 0 -0.79 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.023 0.013 -10000 0 -10000 0 0
Nck/Pak 0.041 0.025 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.1 0.19 -10000 0 -1 1 1
mol:GDP -0.074 0.16 -10000 0 -0.7 1 1
mol:NADP -0.019 0.13 0.47 5 -0.49 1 6
eNOS/Hsp90 -0.013 0.12 0.37 2 -0.45 1 3
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 -0.099 0.17 -10000 0 -0.76 1 1
HIF1A/ARNT 0.038 0.036 -10000 0 -0.47 2 2
SHB 0.029 0.006 -10000 0 -10000 0 0
VEGFA -0.24 0.3 -10000 0 -0.58 220 220
VEGFC 0.028 0.028 -10000 0 -0.59 1 1
FAK1/Vinculin -0.063 0.15 0.45 2 -0.68 2 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.086 0.19 -10000 0 -0.96 1 1
PTPN6 0.029 0.006 -10000 0 -10000 0 0
EPAS1 0.037 0.035 -10000 0 -0.49 2 2
mol:L-citrulline -0.019 0.13 0.47 5 -0.49 1 6
ITGAV 0.029 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.088 0.19 -10000 0 -0.96 1 1
VEGFR2 homodimer/VEGFA homodimer -0.1 0.19 -10000 0 -0.99 1 1
VEGFR2/3 heterodimer 0.033 0.04 -10000 0 -0.49 2 2
VEGFB 0.03 0.003 -10000 0 -10000 0 0
MAPK11 -0.094 0.16 0.35 1 -0.66 2 3
VEGFR2 homodimer 0.032 0.046 -10000 0 -0.65 2 2
FLT1 0.023 0.062 -10000 0 -0.59 5 5
NEDD4 0.029 0.042 -10000 0 -0.63 2 2
MAPK3 -0.094 0.15 0.35 2 -0.72 1 3
MAPK1 -0.091 0.16 0.35 2 -0.66 1 3
VEGFA145/NRP2 -0.17 0.23 -10000 0 -0.43 218 218
VEGFR1/2 heterodimer 0.04 0.058 -10000 0 -0.56 2 2
KDR 0.032 0.046 -10000 0 -0.65 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.086 0.18 -10000 0 -0.88 2 2
SRC 0.029 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.082 0.17 0.43 5 -0.7 1 6
PI3K -0.05 0.14 -10000 0 -0.58 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.19 -10000 0 -0.62 2 2
FES -0.1 0.17 -10000 0 -0.78 2 2
GAB1 -0.057 0.14 -10000 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.1 0.19 -10000 0 -0.62 2 2
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
ARNT 0.029 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.032 0.12 0.33 1 -0.44 3 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.1 0.19 -10000 0 -0.7 2 2
PI3K/GAB1 -0.015 0.12 -10000 0 -0.5 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.078 0.18 -10000 0 -0.77 1 1
PRKACA 0.03 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.044 0.046 -10000 0 -0.55 1 1
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
CDC42 -0.1 0.17 -10000 0 -0.92 1 1
actin cytoskeleton reorganization -0.21 0.23 -10000 0 -0.62 63 63
PTK2 -0.074 0.14 -10000 0 -0.74 2 2
EDG1 -0.11 0.16 -10000 0 -0.89 1 1
mol:DAG -0.099 0.17 -10000 0 -0.76 1 1
CaM/Ca2+ -0.084 0.16 -10000 0 -0.69 1 1
MAP2K3 -0.096 0.16 0.39 1 -0.74 1 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.075 0.19 -10000 0 -0.79 1 1
PLCG1 -0.1 0.17 -10000 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.088 0.18 -10000 0 -0.8 1 1
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
YES1 0.03 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.1 0.19 -10000 0 -0.7 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.1 0.19 -10000 0 -0.7 2 2
cell migration -0.031 0.13 0.43 3 -0.53 3 6
mol:PI-3-4-5-P3 -0.047 0.13 -10000 0 -0.53 3 3
FYN 0.028 0.008 -10000 0 -10000 0 0
VEGFB/NRP1 -0.09 0.16 -10000 0 -0.84 1 1
mol:NO -0.019 0.13 0.47 5 -0.49 1 6
PXN 0.029 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.087 0.14 -10000 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.088 0.17 -10000 0 -0.79 1 1
VHL 0.021 0.014 -10000 0 -10000 0 0
ITGB3 0.027 0.042 -10000 0 -0.64 2 2
NOS3 -0.023 0.14 0.48 5 -0.56 1 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.19 -10000 0 -0.61 4 4
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA -0.095 0.16 -10000 0 -0.71 1 1
PRKCB -0.096 0.15 -10000 0 -0.64 2 2
VCL 0.029 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.1 0.18 -10000 0 -0.93 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.2 -10000 0 -0.65 6 6
VEGFA165/NRP2 -0.17 0.23 -10000 0 -0.43 218 218
MAPKKK cascade -0.061 0.15 0.4 1 -0.53 2 3
NRP2 0.02 0.073 -10000 0 -0.59 7 7
VEGFC homodimer 0.028 0.028 -10000 0 -0.58 1 1
NCK1 0.027 0.031 -10000 0 -0.64 1 1
ROCK1 0.03 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.061 0.15 0.45 2 -0.68 2 4
MAP3K13 -0.1 0.17 -10000 0 -0.78 1 1
PDPK1 -0.045 0.12 0.29 1 -0.56 3 4
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.017 0.088 -10000 0 -0.56 3 3
BAG4 0.026 0.031 -10000 0 -0.64 1 1
BAD 0.02 0.057 0.38 5 -0.29 2 7
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
BIRC3 -0.066 0.22 -10000 0 -0.59 77 77
BAX 0.021 0.049 0.26 10 -10000 0 10
EnzymeConsortium:3.1.4.12 0.01 0.032 0.13 10 -0.12 3 13
IKBKB 0.024 0.087 0.33 3 -0.52 3 6
MAP2K2 0.028 0.06 0.32 8 -0.29 1 9
MAP2K1 0.029 0.061 0.36 7 -10000 0 7
SMPD1 0.016 0.036 0.21 6 -0.15 2 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.024 0.093 0.35 1 -0.53 4 5
MAP2K4 0.036 0.072 0.23 42 -10000 0 42
protein ubiquitination 0.029 0.1 0.42 7 -0.54 3 10
EnzymeConsortium:2.7.1.37 0.035 0.07 0.38 8 -10000 0 8
response to UV 0 0.001 0.004 15 -0.003 1 16
RAF1 0.017 0.058 0.31 8 -0.25 3 11
CRADD 0.029 0.006 -10000 0 -10000 0 0
mol:ceramide 0.018 0.047 0.21 9 -0.18 3 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0.038 0.011 -10000 0 -10000 0 0
MADD 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.033 0.071 0.23 40 -0.2 1 41
TRADD 0.029 0.006 -10000 0 -10000 0 0
RELA/p50 0.03 0.003 -10000 0 -10000 0 0
MAPK3 0.032 0.06 0.34 7 -10000 0 7
MAPK1 0.032 0.061 0.34 7 -10000 0 7
p50/RELA/I-kappa-B-alpha 0.042 0.012 -10000 0 -10000 0 0
FADD 0.013 0.088 0.35 1 -0.55 3 4
KSR1 0.021 0.057 0.27 9 -0.25 5 14
MAPK8 0.037 0.074 0.32 14 -10000 0 14
TRAF2 0.029 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 6 -10000 0 6
CHUK 0.024 0.089 0.3 2 -0.52 3 5
TNF R/SODD 0.039 0.027 -10000 0 -0.47 1 1
TNF 0.019 0.081 -10000 0 -0.61 8 8
CYCS 0.026 0.061 0.26 14 -0.19 1 15
IKBKG 0.025 0.092 0.33 2 -0.52 3 5
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.012 0.092 -10000 0 -0.51 5 5
RELA 0.03 0.003 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
AIFM1 0.02 0.053 0.25 11 -0.19 1 12
TNF/TNF R/SODD 0.045 0.062 -10000 0 -0.39 9 9
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 6 -10000 0 6
CASP8 0.024 0.099 -10000 0 -0.61 11 11
NSMAF 0.016 0.091 0.31 2 -0.55 3 5
response to hydrogen peroxide 0 0.001 0.004 15 -0.003 1 16
BCL2 0.029 0.005 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.081 -9999 0 -0.32 25 25
RGS9BP 0.001 0.13 -9999 0 -0.64 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.02 0.005 -9999 0 -10000 0 0
mol:Na + 0.021 0.053 -9999 0 -0.38 8 8
mol:ADP 0.003 0.035 -9999 0 -0.49 2 2
GNAT2 0.028 0.007 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.029 0.11 -9999 0 -0.4 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.032 0.01 -9999 0 -10000 0 0
GRK7 0.023 0.043 -9999 0 -0.64 2 2
CNGB3 0.014 0.069 -9999 0 -0.61 6 6
Cone Metarhodopsin II/X-Arrestin 0.016 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.079 -9999 0 -0.43 12 12
Cone PDE6 0.045 0.1 -9999 0 -10000 0 0
Cone Metarhodopsin II 0.027 0.028 -9999 0 -0.39 2 2
Na + (4 Units) 0.025 0.077 -9999 0 -0.43 12 12
GNAT2/GDP 0.04 0.1 -9999 0 -0.35 23 23
GNB5 0.03 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.04 -9999 0 -0.33 2 2
Cone Transducin 0.033 0.086 -9999 0 -0.34 25 25
SLC24A2 0.011 0.076 -9999 0 -0.62 7 7
GNB3/GNGT2 0.018 0.1 -9999 0 -0.43 25 25
GNB3 -0.001 0.13 -9999 0 -0.59 24 24
GNAT2/GTP 0.021 0.005 -9999 0 -10000 0 0
CNGA3 0.018 0.047 -9999 0 -0.59 3 3
ARR3 0.021 0.005 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.021 0.053 -9999 0 -0.38 8 8
mol:Pi 0.028 0.11 -9999 0 -0.39 31 31
Cone CNG Channel 0.044 0.055 -9999 0 -0.39 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.011 0.076 -9999 0 -0.62 7 7
RGS9 0.013 0.098 -9999 0 -0.58 13 13
PDE6C 0.02 0.039 -9999 0 -0.59 2 2
GNGT2 0.028 0.028 -9999 0 -0.59 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.021 0.007 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.034 -10000 0 -0.43 2 2
CRKL 0.049 0.1 0.41 9 -0.44 7 16
mol:PIP3 -0.009 0.031 -10000 0 -0.67 1 1
AKT1 0.003 0.05 -10000 0 -0.47 2 2
PTK2B 0.027 0.009 -10000 0 -10000 0 0
RAPGEF1 0.052 0.1 0.38 12 -0.42 6 18
RANBP10 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
HGF/MET/SHIP2 0.035 0.093 -10000 0 -0.4 20 20
MAP3K5 0.018 0.12 0.44 11 -0.46 4 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.049 0.095 -10000 0 -0.43 10 10
AP1 0.029 0.075 -10000 0 -0.4 12 12
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
apoptosis -0.039 0.24 -10000 0 -0.7 54 54
STAT3 (dimer) 0.029 0.067 -10000 0 -0.41 5 5
GAB1/CRKL/SHP2/PI3K 0.065 0.089 0.43 1 -0.51 3 4
INPP5D 0.023 0.055 -10000 0 -0.59 4 4
CBL/CRK 0.064 0.099 0.35 10 -0.51 4 14
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.029 0.006 -10000 0 -10000 0 0
PTEN 0.029 0.006 -10000 0 -10000 0 0
ELK1 0.023 0.11 0.34 50 -0.24 2 52
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.023 0.043 -10000 0 -0.27 4 4
PAK1 0.005 0.05 0.38 1 -0.55 1 2
HGF/MET/RANBP10 0.035 0.091 -10000 0 -0.4 19 19
HRAS 0.019 0.1 -10000 0 -0.55 6 6
DOCK1 0.052 0.1 0.39 13 -0.51 4 17
GAB1 0.033 0.086 0.25 3 -0.46 7 10
CRK 0.046 0.094 0.32 8 -0.43 7 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.1 -10000 0 -0.56 10 10
JUN 0.029 0.006 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.042 -10000 0 -0.23 10 10
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
cell morphogenesis 0.084 0.15 0.5 31 -0.55 3 34
GRB2/SHC 0.039 0.046 -10000 0 -0.29 1 1
FOS 0.012 0.1 -10000 0 -0.63 12 12
GLMN 0.005 0.001 -10000 0 -10000 0 0
cell motility 0.023 0.11 0.33 50 -0.24 2 52
HGF/MET/MUC20 0.018 0.089 -10000 0 -0.4 20 20
cell migration 0.038 0.045 -10000 0 -0.29 1 1
GRB2 0.029 0.005 -10000 0 -10000 0 0
CBL 0.028 0.03 -10000 0 -0.64 1 1
MET/RANBP10 0.037 0.033 -10000 0 -0.43 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.023 0.063 -10000 0 -0.42 4 4
MET/MUC20 0.018 0.029 -10000 0 -0.43 2 2
RAP1B 0.06 0.11 0.45 16 -0.46 3 19
RAP1A 0.055 0.098 0.4 12 -0.44 3 15
HGF/MET/RANBP9 0.034 0.092 -10000 0 -0.4 20 20
RAF1 0.018 0.097 -10000 0 -0.54 5 5
STAT3 0.029 0.068 -10000 0 -0.41 5 5
cell proliferation 0.042 0.087 0.31 6 -0.48 3 9
RPS6KB1 0.013 0.038 -10000 0 -0.42 3 3
MAPK3 0.011 0.1 0.5 6 -10000 0 6
MAPK1 0.013 0.11 0.56 8 -10000 0 8
RANBP9 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.04 0.12 0.46 14 -0.43 4 18
SRC 0.019 0.058 -10000 0 -0.44 3 3
PI3K 0.036 0.056 -10000 0 -0.44 3 3
MET/Glomulin 0.018 0.033 -10000 0 -0.38 2 2
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K1 0.043 0.1 -10000 0 -0.52 4 4
MET 0.024 0.04 -10000 0 -0.59 2 2
MAP4K1 0.016 0.12 0.44 11 -0.43 8 19
PTK2 0.029 0.007 -10000 0 -10000 0 0
MAP2K2 0.044 0.1 0.42 2 -0.52 4 6
BAD 0.004 0.058 0.38 1 -0.59 2 3
MAP2K4 0.023 0.12 0.42 14 -0.44 3 17
SHP2/GRB2/SOS1/GAB1 0.044 0.069 -10000 0 -0.62 1 1
INPPL1 0.03 0.003 -10000 0 -10000 0 0
PXN 0.029 0.006 -10000 0 -10000 0 0
SH3KBP1 0.03 0.003 -10000 0 -10000 0 0
HGS 0.009 0.039 -10000 0 -0.3 1 1
PLCgamma1/PKC 0.022 0.004 -10000 0 -10000 0 0
HGF 0.002 0.12 -10000 0 -0.6 20 20
RASA1 0.025 0.031 -10000 0 -0.64 1 1
NCK1 0.027 0.031 -10000 0 -0.64 1 1
PTPRJ 0.03 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.04 0.055 -10000 0 -0.42 2 2
PDPK1 0 0.052 -10000 0 -0.5 2 2
HGF/MET/SHIP 0.03 0.1 -10000 0 -0.41 23 23
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.006 -10000 0 -10000 0 0
mol:PIP3 0.007 0.045 -10000 0 -0.35 5 5
FRAP1 0.025 0.042 -10000 0 -10000 0 0
AKT1 0.022 0.064 0.26 3 -0.47 2 5
INSR 0.03 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0.044 0.061 0.3 1 -0.39 2 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.025 -10000 0 -0.26 1 1
TSC2 0.029 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.021 0.04 -10000 0 -0.36 2 2
TSC1 0.029 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.051 -10000 0 -0.36 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.033 -10000 0 -0.3 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.006 -10000 0 -10000 0 0
RPS6KB1 0.038 0.072 0.33 6 -0.55 1 7
MAP3K5 -0.004 0.051 0.17 1 -0.18 39 40
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
apoptosis -0.004 0.051 0.17 1 -0.18 39 40
mol:LY294002 0 0 -10000 0 -0.001 20 20
EIF4B 0.043 0.077 0.33 13 -0.47 1 14
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.053 0.063 0.28 4 -0.61 1 5
eIF4E/eIF4G1/eIF4A1 0.02 0.018 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.034 0.057 -10000 0 -0.36 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.048 0.23 8 -0.22 1 9
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.041 0.052 -10000 0 -0.35 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 20 20
FKBP12/Rapamycin 0.022 0.005 -10000 0 -10000 0 0
PDPK1 0.007 0.051 -10000 0 -0.41 4 4
EIF4E 0.03 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.001 0.16 -10000 0 -0.54 39 39
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0.031 -10000 0 -10000 0 0
TSC1/TSC2 0.049 0.066 0.32 1 -0.42 2 3
tumor necrosis factor receptor activity 0 0 0.001 20 -10000 0 20
RPS6 0.026 0.039 -10000 0 -0.59 2 2
PPP5C 0.03 0.003 -10000 0 -10000 0 0
EIF4G1 0.029 0.007 -10000 0 -10000 0 0
IRS1 0.003 0.051 -10000 0 -0.22 22 22
INS 0.018 0.002 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
PDK2 0.01 0.049 0.21 4 -0.34 4 8
EIF4EBP1 -0.063 0.28 -10000 0 -1 39 39
PIK3CA 0.028 0.031 -10000 0 -0.64 1 1
PPP2R5D 0.029 0.049 0.35 4 -10000 0 4
peptide biosynthetic process 0.018 0.013 -10000 0 -10000 0 0
RHEB 0.027 0.01 -10000 0 -10000 0 0
EIF4A1 0.029 0.005 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.005 17 -0.003 1 18
EEF2 0.018 0.013 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.043 0.26 -10000 0 -0.92 39 39
Ephrin B reverse signaling

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
EFNB2 0.03 0.004 -10000 0 -10000 0 0
EPHB2 0.019 0.076 -10000 0 -0.52 9 9
EFNB1 0.014 0.062 -10000 0 -0.43 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.054 0.074 -10000 0 -0.55 2 2
Ephrin B2/EPHB1-2 0.045 0.06 -10000 0 -0.44 6 6
neuron projection morphogenesis 0.035 0.065 -10000 0 -0.52 2 2
Ephrin B1/EPHB1-2/Tiam1 0.05 0.076 -10000 0 -0.47 4 4
DNM1 0.017 0.083 -10000 0 -0.59 9 9
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.002 0.09 -10000 0 -0.5 14 14
YES1 0 0.13 -10000 0 -0.74 14 14
Ephrin B1/EPHB1-2/NCK2 0.05 0.076 -10000 0 -0.44 5 5
PI3K 0.029 0.1 -10000 0 -0.52 14 14
mol:GDP 0.048 0.075 -10000 0 -0.46 4 4
ITGA2B 0.007 0.12 -10000 0 -0.59 18 18
endothelial cell proliferation 0.035 0.013 -10000 0 -10000 0 0
FYN -0.001 0.13 -10000 0 -0.75 14 14
MAP3K7 -0.003 0.093 -10000 0 -0.56 13 13
FGR 0 0.13 -10000 0 -0.74 14 14
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
RGS3 0.029 0.006 -10000 0 -10000 0 0
cell adhesion 0.015 0.12 -10000 0 -0.6 10 10
LYN 0 0.13 -10000 0 -0.74 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.006 0.12 -10000 0 -0.69 14 14
Ephrin B1/EPHB1-2 -0.006 0.1 -10000 0 -0.6 14 14
SRC 0.002 0.12 -10000 0 -0.72 14 14
ITGB3 0.027 0.042 -10000 0 -0.64 2 2
EPHB1 0.024 0.051 -10000 0 -0.62 3 3
EPHB4 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.036 0.013 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.024 0.095 -10000 0 -0.44 20 20
BLK -0.004 0.13 -10000 0 -0.74 14 14
HCK -0.003 0.13 -10000 0 -0.73 14 14
regulation of stress fiber formation -0.048 0.075 0.43 5 -10000 0 5
MAPK8 0.007 0.088 0.4 1 -0.5 12 13
Ephrin B1/EPHB1-2/RGS3 0.051 0.077 -10000 0 -0.47 4 4
endothelial cell migration 0.017 0.099 0.4 3 -0.5 10 13
NCK2 0.029 0.005 -10000 0 -10000 0 0
PTPN13 0.016 0.1 -10000 0 -0.74 9 9
regulation of focal adhesion formation -0.048 0.075 0.43 5 -10000 0 5
chemotaxis -0.049 0.076 0.46 4 -10000 0 4
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
Rac1/GTP 0.045 0.07 -10000 0 -0.54 2 2
angiogenesis -0.006 0.1 -10000 0 -0.6 14 14
LCK -0.003 0.13 -10000 0 -0.75 14 14
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.026 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.041 0.074 0.31 9 -10000 0 9
ERC1 0.029 0.006 -10000 0 -10000 0 0
RIP2/NOD2 -0.068 0.2 -10000 0 -0.43 112 112
NFKBIA 0.025 0.023 -10000 0 -10000 0 0
BIRC2 0.03 0.004 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
IKBKG 0.008 0.067 -10000 0 -10000 0 0
IKK complex/A20 0.035 0.097 -10000 0 -0.49 1 1
NEMO/A20/RIP2 0.027 0.028 -10000 0 -0.58 1 1
XPO1 0.029 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.085 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.038 0.01 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.076 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.057 0.015 -10000 0 -10000 0 0
NOD2 -0.12 0.26 -10000 0 -0.59 116 116
NFKB1 0.032 0.03 -10000 0 -0.63 1 1
RELA 0.034 0.003 -10000 0 -10000 0 0
MALT1 0.029 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.044 0.007 -10000 0 -10000 0 0
ATM 0.029 0.03 -10000 0 -0.64 1 1
TNF/TNFR1A 0.034 0.063 -10000 0 -0.45 8 8
TRAF6 0.03 0.003 -10000 0 -10000 0 0
PRKCA 0.029 0.005 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
UBE2D3 0.03 0.004 -10000 0 -10000 0 0
TNF 0.019 0.081 -10000 0 -0.61 8 8
NF kappa B1 p50/RelA 0.054 0.037 -10000 0 -0.39 1 1
BCL10 0.029 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.023 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.032 0.086 -10000 0 -10000 0 0
CYLD 0.029 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.039 0.088 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.038 0.01 -10000 0 -10000 0 0
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.02 0.096 -10000 0 -0.39 2 2
IRAK/TOLLIP 0.038 0.012 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
IKBKG 0.03 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.024 0.17 -10000 0 -0.46 65 65
IL1A 0.013 0.094 -10000 0 -0.59 12 12
IL1B 0.017 0.051 -10000 0 -0.44 6 6
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.046 -10000 0 -10000 0 0
IL1R2 -0.042 0.2 -10000 0 -0.61 56 56
IL1R1 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.047 -10000 0 -10000 0 0
TOLLIP 0.03 0.003 -10000 0 -10000 0 0
TICAM2 0.024 0.012 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.059 0.063 0.38 1 -10000 0 1
JUN 0.024 0.056 0.35 9 -10000 0 9
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.065 0.066 -10000 0 -0.66 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 0.04 0.075 -10000 0 -0.33 15 15
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.076 -10000 0 -0.36 1 1
IL1 beta fragment/IL1R1/IL1RAP 0.044 0.055 -10000 0 -0.34 9 9
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.028 0.058 0.36 9 -10000 0 9
IRAK1 0.022 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.027 0.087 -10000 0 -0.44 17 17
IRAK4 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.029 0.007 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
PI3K 0.037 0.036 -10000 0 -0.47 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.077 -10000 0 -0.4 1 1
CHUK 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.044 0.055 -10000 0 -0.34 9 9
IL1 beta/IL1R2 -0.009 0.14 -10000 0 -0.39 59 59
IRAK/TRAF6/TAK1/TAB1/TAB2 0.043 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.049 0.065 -10000 0 -0.89 1 1
IRAK3 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.056 0.061 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.023 0.044 -10000 0 -0.34 1 1
IL1 alpha/IL1R1/IL1RAP 0.042 0.075 -10000 0 -0.37 15 15
RELA 0.03 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.023 0.013 -10000 0 -10000 0 0
MYD88 0.021 0.014 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.055 0.022 -10000 0 -10000 0 0
IL1RAP 0.024 0.056 -10000 0 -0.6 4 4
UBE2N 0.029 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 0.03 0.043 -10000 0 -10000 0 0
CASP1 0.03 0.004 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.027 0.18 -10000 0 -0.46 69 69
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.042 0.06 -10000 0 -0.35 2 2
TMEM189-UBE2V1 0.023 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.016 0.099 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
IL1RN 0.008 0.11 -10000 0 -0.59 17 17
TRAF6/TAK1/TAB1/TAB2 0.05 0.018 -10000 0 -10000 0 0
MAP2K6 0.033 0.06 0.37 9 -10000 0 9
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.023 0.12 -10000 0 -0.48 16 16
KLHL20 0.021 0.077 0.21 2 -0.32 3 5
CYFIP2 0.014 0.079 -10000 0 -0.64 7 7
Rac1/GDP 0.023 0.088 0.3 4 -10000 0 4
ENAH -0.021 0.12 -10000 0 -0.48 17 17
AP1M1 0.03 0.003 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.054 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.035 -10000 0 -0.2 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.083 -10000 0 -0.37 16 16
RAPGEF1 -0.012 0.12 -10000 0 -0.43 12 12
CTNND1 0.03 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.024 0.13 -10000 0 -0.49 17 17
CRK -0.012 0.12 -10000 0 -0.46 14 14
E-cadherin/gamma catenin/alpha catenin 0.029 0.089 -10000 0 -0.43 15 15
alphaE/beta7 Integrin 0.042 0.01 -10000 0 -10000 0 0
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
NCKAP1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.02 -10000 0 -10000 0 0
DLG1 -0.018 0.12 -10000 0 -0.48 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.03 -10000 0 -10000 0 0
MLLT4 0.028 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.019 -10000 0 -10000 0 0
PI3K -0.007 0.038 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.022 0.1 -10000 0 -0.5 18 18
TIAM1 0.029 0.006 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.031 0.074 -10000 0 -0.35 13 13
AKT1 0.022 0.032 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
CDH1 0.007 0.12 -10000 0 -0.62 17 17
RhoA/GDP 0.04 0.086 0.36 7 -10000 0 7
actin cytoskeleton organization 0.022 0.063 0.18 13 -0.22 3 16
CDC42/GDP 0.031 0.11 0.42 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.06 -10000 0 -0.3 15 15
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.034 0.078 -10000 0 -0.37 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin 0.021 0.068 -10000 0 -0.35 13 13
mol:GDP 0.019 0.12 0.44 10 -0.41 2 12
CDC42/GTP/IQGAP1 0.039 0.009 -10000 0 -10000 0 0
JUP 0.025 0.052 -10000 0 -0.64 3 3
p120 catenin/RhoA/GDP 0.018 0.082 0.31 3 -10000 0 3
RAC1/GTP/IQGAP1 0.036 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.044 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.02 0.063 0.18 12 -0.22 17 29
NME1 0.029 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.48 16 16
regulation of cell-cell adhesion 0.014 0.042 -10000 0 -10000 0 0
WASF2 0.014 0.031 -10000 0 -10000 0 0
Rap1/GTP 0.034 0.066 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.088 -10000 0 -0.37 15 15
CCND1 0.02 0.073 0.2 8 -0.27 17 25
VAV2 -0.021 0.17 -10000 0 -0.56 20 20
RAP1/GDP 0.042 0.078 0.29 2 -10000 0 2
adherens junction assembly -0.022 0.12 -10000 0 -0.46 16 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.03 0.004 -10000 0 -10000 0 0
PIP5K1C 0.03 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.047 0.091 -10000 0 -0.66 1 1
E-cadherin/beta catenin -0.001 0.078 -10000 0 -0.41 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.022 0.12 -10000 0 -0.48 15 15
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
Rac1/GTP -0.033 0.081 -10000 0 -0.44 5 5
E-cadherin/beta catenin/alpha catenin 0.024 0.079 -10000 0 -0.4 13 13
ITGAE 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.024 0.13 -10000 0 -0.5 17 17
Signaling events mediated by PRL

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
CCNE1 0.023 0.067 -10000 0 -0.59 6 6
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 0.028 0.008 -10000 0 -10000 0 0
CDKN1A 0.019 0.048 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.028 0.079 -10000 0 -0.43 14 14
mol:Ca2+ -0.024 0.096 0.26 14 -0.44 19 33
AGT 0.003 0.12 -10000 0 -0.56 22 22
CCNA2 -0.046 0.13 -10000 0 -0.63 5 5
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
EGR1 0.012 0.061 -10000 0 -0.46 8 8
CDK2/Cyclin E1 0.06 0.1 -10000 0 -0.58 4 4
MAPK3 0.009 0.075 -10000 0 -0.43 14 14
PRL-2 /Rab GGTase beta 0.043 0.009 -10000 0 -10000 0 0
MAPK1 0.01 0.075 -10000 0 -0.43 14 14
PTP4A1 0.011 0.044 -10000 0 -10000 0 0
PTP4A3 0.011 0.1 -10000 0 -0.59 14 14
PTP4A2 0.029 0.006 -10000 0 -10000 0 0
ITGB1 0.01 0.075 -10000 0 -0.43 14 14
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.018 0.037 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.039 0.035 -10000 0 -0.47 2 2
PRL-1/ATF-5 0.061 0.085 -10000 0 -10000 0 0
RABGGTA 0.026 0.043 -10000 0 -0.64 2 2
BCAR1 -0.007 0.051 0.26 14 -0.49 1 15
RHOC 0.015 0.053 -10000 0 -0.58 1 1
RHOA -0.026 0.12 -10000 0 -0.57 3 3
cell motility 0.02 0.09 0.29 7 -0.34 6 13
PRL-1/alpha Tubulin 0.062 0.08 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.079 -10000 0 -0.43 14 14
ROCK1 0.02 0.084 0.27 6 -0.32 5 11
RABGGTB 0.029 0.006 -10000 0 -10000 0 0
CDK2 0.029 0.005 -10000 0 -10000 0 0
mitosis 0.011 0.044 -10000 0 -10000 0 0
ATF5 0.026 0.048 -10000 0 -0.59 3 3
ErbB2/ErbB3 signaling events

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
USP8 0.011 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.095 -10000 0 -0.53 6 6
NFATC4 0.01 0.067 0.27 8 -0.48 1 9
ERBB2IP 0.028 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.028 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis 0.013 0.074 -10000 0 -10000 0 0
JUN 0.018 0.065 0.27 3 -0.31 2 5
HRAS 0.028 0.028 -10000 0 -0.59 1 1
DOCK7 0.005 0.07 -10000 0 -0.57 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.083 -10000 0 -0.35 20 20
AKT1 0.011 0.005 -10000 0 -10000 0 0
BAD 0.009 0.026 -10000 0 -0.39 2 2
MAPK10 0.018 0.057 0.2 7 -0.31 2 9
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.015 0.079 -10000 0 -10000 0 0
RAF1 -0.007 0.089 0.29 2 -0.51 6 8
ErbB2/ErbB3/neuregulin 2 0.015 0.073 -10000 0 -0.36 16 16
STAT3 0.027 0.1 -10000 0 -0.89 6 6
cell migration 0.038 0.083 0.29 22 -0.26 2 24
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.12 0.19 -10000 0 -0.53 12 12
FOS -0.071 0.14 0.3 2 -0.49 12 14
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.013 0.074 -10000 0 -10000 0 0
MAPK3 -0.094 0.16 0.35 1 -0.56 6 7
MAPK1 -0.094 0.17 0.38 1 -0.58 8 9
JAK2 0.006 0.067 -10000 0 -10000 0 0
NF2 0.018 0.038 -10000 0 -0.79 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.009 0.087 -10000 0 -0.4 17 17
NRG1 0.008 0.11 -10000 0 -0.56 16 16
GRB2/SOS1 0.042 0.01 -10000 0 -10000 0 0
MAPK8 0.012 0.075 -10000 0 -0.34 5 5
MAPK9 0.011 0.045 0.2 5 -0.27 1 6
ERBB2 -0.015 0.031 -10000 0 -0.49 2 2
ERBB3 0.018 0.084 -10000 0 -0.64 8 8
SHC1 0.028 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
apoptosis -0.006 0.022 0.28 2 -10000 0 2
STAT3 (dimer) 0.028 0.1 -10000 0 -0.87 6 6
RNF41 0.009 0.006 -10000 0 -10000 0 0
FRAP1 0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.009 0.049 -10000 0 -0.39 1 1
ErbB2/ErbB2/HSP90 (dimer) 0.016 0.029 -10000 0 -0.42 2 2
CHRNA1 -0.13 0.19 0.34 1 -0.42 59 60
myelination 0.006 0.079 0.36 10 -0.43 1 11
PPP3CB 0.007 0.064 -10000 0 -10000 0 0
KRAS 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.035 0.086 -10000 0 -0.53 5 5
NRG2 0.012 0.083 -10000 0 -0.59 9 9
mol:GDP 0.009 0.086 -10000 0 -0.39 17 17
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K2 -0.017 0.092 0.29 2 -0.48 6 8
SRC 0.029 0.006 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.008 0.068 -10000 0 -10000 0 0
MAP2K1 -0.11 0.18 -10000 0 -0.55 13 13
heart morphogenesis 0.013 0.074 -10000 0 -10000 0 0
RAS family/GDP 0.041 0.092 -10000 0 -0.53 6 6
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.016 0.039 -10000 0 -0.83 1 1
CHRNE 0.013 0.022 0.2 1 -0.19 2 3
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
activation of caspase activity -0.011 0.005 -10000 0 -10000 0 0
nervous system development 0.013 0.074 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.029 0.017 -10000 0 -0.33 1 1
ANTXR2 0.03 0.004 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0.002 0.002 -10000 0 -10000 0 0
monocyte activation 0.005 0.091 -10000 0 -0.36 23 23
MAP2K2 0.014 0.062 -10000 0 -0.59 5 5
MAP2K1 0.004 0.002 -10000 0 -10000 0 0
MAP2K7 0.004 0.002 -10000 0 -10000 0 0
MAP2K6 0.002 0.027 -10000 0 -0.34 3 3
CYAA 0.006 0.007 -10000 0 -10000 0 0
MAP2K4 0.004 0.001 -10000 0 -10000 0 0
IL1B 0.006 0.046 0.24 6 -0.29 7 13
Channel 0.037 0.012 -10000 0 -10000 0 0
NLRP1 0.001 0.034 -10000 0 -0.34 5 5
CALM1 0.028 0.008 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.094 -10000 0 -0.37 31 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation -0.002 0.002 -10000 0 -10000 0 0
MAPK3 0.004 0.002 -10000 0 -10000 0 0
MAPK1 0.004 0.002 -10000 0 -10000 0 0
PGR -0.007 0.062 -10000 0 -0.35 16 16
PA/Cellular Receptors 0.039 0.013 -10000 0 -10000 0 0
apoptosis 0.002 0.002 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.036 0.012 -10000 0 -10000 0 0
macrophage activation 0.005 0.003 -10000 0 -10000 0 0
TNF 0.019 0.081 -10000 0 -0.61 8 8
VCAM1 0.005 0.092 -10000 0 -0.37 23 23
platelet activation -0.007 0.094 -10000 0 -0.37 31 31
MAPKKK cascade -0.01 0.018 -10000 0 -0.14 4 4
IL18 0.004 0.036 -10000 0 -0.31 5 5
negative regulation of macrophage activation 0.002 0.002 -10000 0 -10000 0 0
LEF 0.002 0.002 -10000 0 -10000 0 0
CASP1 0.005 0.017 -10000 0 -0.16 5 5
mol:cAMP -0.007 0.095 -10000 0 -0.37 31 31
necrosis 0.002 0.002 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.036 0.011 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.048 0.12 0.35 2 -0.57 7 9
CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
AKT2 0.03 0.004 -10000 0 -10000 0 0
STXBP4 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.04 0.13 0.28 30 -0.52 13 43
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.021 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
YWHAB 0.029 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.057 0.017 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
ASIP -0.024 0.17 -10000 0 -0.59 41 41
PRKCI 0.029 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
RHOQ 0.029 0.005 -10000 0 -10000 0 0
GYS1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
TRIP10 0.03 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.02 0.064 -10000 0 -0.35 2 2
VAMP2 0.029 0.005 -10000 0 -10000 0 0
SLC2A4 0.039 0.14 0.34 10 -0.6 13 23
STX4 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.028 0.011 -10000 0 -10000 0 0
SFN -0.043 0.2 -10000 0 -0.59 58 58
LNPEP 0.025 0.031 -10000 0 -0.64 1 1
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.028 0.03 -10000 0 -0.64 1 1
HDAC4 0.028 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.018 0.028 0.41 2 -10000 0 2
CDKN1A -0.004 0.025 -10000 0 -0.4 2 2
KAT2B 0.02 0.033 -10000 0 -0.64 1 1
BAX 0.03 0.003 -10000 0 -10000 0 0
FOXO3 -0.007 0.022 0.47 1 -10000 0 1
FOXO1 0.029 0.005 -10000 0 -10000 0 0
FOXO4 0.023 0.016 -10000 0 -0.3 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
TAT 0.017 0.077 -10000 0 -0.59 8 8
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.013 0.1 -10000 0 -0.43 28 28
PPARGC1A -0.035 0.2 -10000 0 -0.63 49 49
FHL2 0.024 0.059 -10000 0 -0.62 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.011 -10000 0 -10000 0 0
HIST2H4A 0.018 0.028 -10000 0 -0.41 2 2
SIRT1/FOXO3a 0.01 0.029 0.31 1 -10000 0 1
SIRT1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.051 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.034 0.031 -10000 0 -0.27 1 1
apoptosis -0.054 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.008 0.13 -10000 0 -0.41 48 48
p53/SIRT1 0.029 0.018 0.3 2 -10000 0 2
SIRT1/FOXO4 0.038 0.024 -10000 0 -0.26 1 1
FOXO1/FHL2/SIRT1 0.048 0.039 -10000 0 -0.36 4 4
HIST1H1E 0.021 0.019 -10000 0 -0.31 1 1
SIRT1/p300 0.038 0.025 -10000 0 -0.48 1 1
muscle cell differentiation -0.004 0.092 0.36 28 -10000 0 28
TP53 0.025 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.055 0.015 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
MEF2D 0.029 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.06 -10000 0 -0.43 8 8
ACSS2 0.02 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.004 0.092 -10000 0 -0.36 28 28
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.006 0.12 -10000 0 -0.4 41 41
cell-cell adhesion -0.004 0.05 0.47 2 -10000 0 2
Ephrin B/EPHB2/RasGAP 0.065 0.068 -10000 0 -0.35 8 8
ITSN1 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.066 -10000 0 -0.41 11 11
Ephrin B1/EPHB1 0.036 0.035 -10000 0 -0.4 3 3
HRAS/GDP 0.034 0.057 -10000 0 -0.48 1 1
Ephrin B/EPHB1/GRB7 0.071 0.071 -10000 0 -0.35 10 10
Endophilin/SYNJ1 0.022 0.054 -10000 0 -10000 0 0
KRAS 0.029 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.073 0.06 -10000 0 -0.34 7 7
endothelial cell migration 0.05 0.036 -10000 0 -0.34 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.073 -10000 0 -0.64 6 6
PAK1 0.029 0.053 -10000 0 -10000 0 0
HRAS 0.029 0.028 -10000 0 -0.59 1 1
RRAS 0.023 0.053 -10000 0 -10000 0 0
DNM1 0.018 0.084 -10000 0 -0.6 9 9
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.027 0.051 -10000 0 -0.33 6 6
lamellipodium assembly 0.004 0.05 -10000 0 -0.47 2 2
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.039 0.045 -10000 0 -0.43 1 1
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
EPHB2 0.019 0.076 -10000 0 -0.52 9 9
EPHB3 0.014 0.098 -10000 0 -0.64 11 11
EPHB1 0.025 0.051 -10000 0 -0.62 3 3
EPHB4 0.027 0.009 -10000 0 -10000 0 0
mol:GDP 0.023 0.054 0.36 2 -0.47 1 3
Ephrin B/EPHB2 0.059 0.058 -10000 0 -0.35 8 8
Ephrin B/EPHB3 0.053 0.079 -10000 0 -0.37 15 15
JNK cascade 0.026 0.066 0.36 5 -0.43 5 10
Ephrin B/EPHB1 0.059 0.055 -10000 0 -0.34 8 8
RAP1/GDP 0.066 0.077 0.35 5 -0.4 1 6
EFNB2 0.03 0.004 -10000 0 -10000 0 0
EFNB3 0.022 0.068 -10000 0 -0.59 6 6
EFNB1 0.03 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.045 0.06 -10000 0 -0.44 6 6
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.046 0.071 -10000 0 -0.54 2 2
Rap1/GTP 0.023 0.056 -10000 0 -0.57 1 1
axon guidance -0.006 0.12 -10000 0 -0.4 41 41
MAPK3 0.033 0.042 -10000 0 -0.39 1 1
MAPK1 0.034 0.042 -10000 0 -0.39 1 1
Rac1/GDP 0.039 0.061 0.36 2 -0.43 1 3
actin cytoskeleton reorganization -0.007 0.043 -10000 0 -0.4 3 3
CDC42/GDP 0.057 0.079 0.36 5 -0.42 1 6
PI3K 0.056 0.039 -10000 0 -0.35 2 2
EFNA5 -0.023 0.17 -10000 0 -0.63 36 36
Ephrin B2/EPHB4 0.036 0.013 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.032 0.048 -10000 0 -0.38 1 1
CDC42 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.018 0.057 -10000 0 -0.54 2 2
PTK2 0.022 0.088 0.53 14 -10000 0 14
MAP4K4 0.026 0.066 0.36 5 -0.44 5 10
SRC 0.029 0.006 -10000 0 -10000 0 0
KALRN 0.028 0.007 -10000 0 -10000 0 0
Intersectin/N-WASP 0.039 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis 0.075 0.12 0.4 39 -0.45 1 40
MAP2K1 0.035 0.043 -10000 0 -0.41 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.062 0.068 -10000 0 -0.43 7 7
cell migration 0.048 0.078 0.43 6 -0.43 1 7
NRAS 0.029 0.005 -10000 0 -10000 0 0
SYNJ1 0.022 0.054 -10000 0 -10000 0 0
PXN 0.029 0.006 -10000 0 -10000 0 0
TF -0.053 0.14 -10000 0 -0.6 2 2
HRAS/GTP 0.046 0.071 -10000 0 -0.53 3 3
Ephrin B1/EPHB1-2 0.045 0.063 -10000 0 -0.42 7 7
cell adhesion mediated by integrin -0.005 0.057 0.37 5 -0.37 3 8
RAC1 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.05 0.071 -10000 0 -0.54 2 2
RAC1-CDC42/GTP 0.005 0.071 -10000 0 -0.68 2 2
RASA1 0.025 0.031 -10000 0 -0.64 1 1
RAC1-CDC42/GDP 0.05 0.061 0.36 2 -0.4 1 3
ruffle organization 0.074 0.13 0.4 46 -0.57 1 47
NCK1 0.027 0.031 -10000 0 -0.64 1 1
receptor internalization 0.012 0.064 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.071 0.064 -10000 0 -10000 0 0
ROCK1 0.02 0.063 -10000 0 -0.37 11 11
RAS family/GDP -0.007 0.043 -10000 0 -0.4 2 2
Rac1/GTP 0.012 0.055 -10000 0 -0.51 2 2
Ephrin B/EPHB1/Src/Paxillin 0.036 0.041 -10000 0 -0.34 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.014 0.08 -10000 0 -0.34 1 1
PDGFB-D/PDGFRB/SLAP 0.011 0.1 -10000 0 -0.43 23 23
PDGFB-D/PDGFRB/APS/CBL 0.041 0.044 -10000 0 -0.38 3 3
AKT1 0.086 0.13 0.39 52 -10000 0 52
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.042 0.1 0.34 6 -10000 0 6
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
FGR 0.036 0.1 0.33 5 -0.62 2 7
mol:Ca2+ 0.049 0.065 0.34 8 -10000 0 8
MYC 0.063 0.13 0.46 18 -0.42 3 21
SHC1 0.029 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.052 0.056 -10000 0 -0.63 1 1
LRP1/PDGFRB/PDGFB 0.046 0.027 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GO:0007205 0.049 0.065 0.33 8 -10000 0 8
PTEN 0.029 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.073 -10000 0 -0.64 6 6
PDGFB-D/PDGFRB/SHP2 0.034 0.02 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.032 0.02 -10000 0 -10000 0 0
cell cycle arrest 0.011 0.1 -10000 0 -0.43 23 23
HRAS 0.029 0.028 -10000 0 -0.59 1 1
HIF1A 0.077 0.12 0.38 50 -0.53 1 51
GAB1 0.046 0.083 0.35 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.046 0.087 0.35 12 -10000 0 12
PDGFB-D/PDGFRB 0.045 0.028 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.02 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.012 0.082 -10000 0 -0.4 1 1
positive regulation of MAPKKK cascade 0.034 0.019 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
mol:IP3 0.049 0.066 0.34 8 -10000 0 8
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.057 -10000 0 -0.48 5 5
SHB 0.029 0.006 -10000 0 -10000 0 0
BLK 0.01 0.13 0.32 3 -0.47 9 12
PTPN2 0.031 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.019 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
VAV2 0.048 0.091 0.38 8 -10000 0 8
CBL 0.028 0.03 -10000 0 -0.64 1 1
PDGFB-D/PDGFRB/DEP1 0.034 0.019 -10000 0 -10000 0 0
LCK 0.028 0.12 0.33 5 -0.57 4 9
PDGFRB 0.024 0.013 -10000 0 -10000 0 0
ACP1 0.029 0.005 -10000 0 -10000 0 0
HCK 0.042 0.081 0.35 4 -10000 0 4
ABL1 0.048 0.09 0.34 10 -0.44 2 12
PDGFB-D/PDGFRB/CBL 0.041 0.076 0.35 3 -0.4 2 5
PTPN1 0.03 0.007 -10000 0 -10000 0 0
SNX15 0.03 0.003 -10000 0 -10000 0 0
STAT3 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.028 -10000 0 -0.59 1 1
cell proliferation 0.063 0.13 0.44 20 -0.37 5 25
SLA -0.001 0.13 -10000 0 -0.59 24 24
actin cytoskeleton reorganization 0.041 0.047 0.36 2 -10000 0 2
SRC 0.049 0.063 0.32 3 -10000 0 3
PI3K 0.011 0.026 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.04 0.052 -10000 0 -0.41 4 4
SH2B2 0.023 0.048 -10000 0 -0.59 3 3
PLCgamma1/SPHK1 0.043 0.1 0.34 6 -10000 0 6
LYN 0.039 0.092 0.32 3 -0.54 3 6
LRP1 0.029 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
STAT5B 0.029 0.005 -10000 0 -10000 0 0
STAT5A 0.029 0.005 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.062 0.05 -10000 0 -10000 0 0
SPHK1 -0.016 0.16 -10000 0 -0.58 38 38
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.049 0.066 0.34 8 -10000 0 8
PLCG1 0.049 0.066 0.34 8 -10000 0 8
NHERF/PDGFRB 0.045 0.034 -10000 0 -0.41 1 1
YES1 0.047 0.077 0.32 2 -0.53 3 5
cell migration 0.044 0.034 -10000 0 -0.4 1 1
SHC/Grb2/SOS1 0.064 0.044 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.031 -10000 0 -0.64 1 1
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.054 0.04 -10000 0 -0.37 1 1
FYN 0.027 0.11 0.32 3 -0.46 7 10
DOK1 0.06 0.063 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.02 -10000 0 -0.43 1 1
PDGFB 0.03 0.004 -10000 0 -10000 0 0
RAC1 0.066 0.12 0.46 13 -0.48 1 14
PRKCD 0.038 0.056 -10000 0 -0.34 1 1
FER 0.036 0.052 -10000 0 -0.38 2 2
MAPKKK cascade 0.043 0.081 0.38 14 -10000 0 14
RASA1 0.046 0.058 -10000 0 -0.38 1 1
NCK1 0.027 0.031 -10000 0 -0.64 1 1
NCK2 0.029 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.074 0.059 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.033 0.02 -10000 0 -10000 0 0
chemotaxis 0.047 0.089 0.34 11 -0.43 2 13
STAT1-3-5/STAT1-3-5 0.053 0.039 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.017 0.01 -10000 0 -10000 0 0
PTPRJ 0.03 0.003 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.023 0.064 0.62 5 -10000 0 5
PI3K Class IB/PDE3B 0.023 0.064 -10000 0 -0.62 5 5
PDE3B 0.023 0.065 -10000 0 -0.62 5 5
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.024 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.037 0.013 -10000 0 -10000 0 0
ATM 0.029 0.03 -10000 0 -0.64 1 1
MAP2K3 0.034 0.07 0.47 3 -0.32 1 4
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.035 0.073 0.41 3 -0.36 3 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.018 0.083 -10000 0 -0.59 9 9
TXN 0.01 0.002 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GADD45B 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.028 0.008 -10000 0 -10000 0 0
MAP3K6 0.028 0.03 -10000 0 -0.64 1 1
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
MAP3K4 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.039 0.027 -10000 0 -0.47 1 1
TAK1/TAB family -0.004 0.014 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.051 0.02 -10000 0 -10000 0 0
TRAF2 0.029 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.039 0.051 -10000 0 -10000 0 0
TRAF6 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.065 0.23 -10000 0 -0.63 69 69
CCM2 0.027 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.027 0.15 -10000 0 -0.4 69 69
MAPK11 0.029 0.028 -10000 0 -0.59 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.01 0.14 -10000 0 -0.36 69 69
OSM/MEKK3 0.039 0.015 -10000 0 -10000 0 0
TAOK1 0.016 0.043 -10000 0 -0.34 7 7
TAOK2 0.02 0.018 -10000 0 -0.37 1 1
TAOK3 0.02 0.018 -10000 0 -0.37 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
MAP3K10 0.028 0.03 -10000 0 -0.64 1 1
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.019 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.057 0.053 -10000 0 -0.3 6 6
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.044 0.12 0.38 2 -0.57 9 11
MAP3K8 0.027 0.039 -10000 0 -0.58 2 2
FOS 0.031 0.1 0.36 4 -0.53 8 12
PRKCA 0.03 0.008 -10000 0 -10000 0 0
PTPN7 -0.01 0.15 -10000 0 -0.59 32 32
HRAS 0.029 0.028 -10000 0 -0.58 1 1
PRKCB 0.023 0.065 -10000 0 -0.62 5 5
NRAS 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.024 -10000 0 -0.33 1 1
MAPK3 0.019 0.089 -10000 0 -0.55 7 7
MAP2K1 0.029 0.054 -10000 0 -0.43 3 3
ELK1 0.03 0.009 -10000 0 -10000 0 0
BRAF 0.029 0.04 -10000 0 -0.45 2 2
mol:GTP 0 0.002 -10000 0 -0.007 13 13
MAPK1 0.018 0.091 -10000 0 -0.51 8 8
RAF1 0.021 0.041 -10000 0 -0.45 2 2
KRAS 0.029 0.006 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.039 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.052 -10000 0 -0.64 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.021 0.03 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.03 0.004 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
MAP3K12 0.028 0.03 -10000 0 -0.64 1 1
FGR 0.025 0.048 -10000 0 -0.59 3 3
p38 alpha/TAB1 -0.022 0.081 -10000 0 -0.61 7 7
PRKG1 0.015 0.098 -10000 0 -0.64 11 11
DUSP8 0.029 0.03 -10000 0 -0.64 1 1
PGK/cGMP/p38 alpha 0.028 0.11 -10000 0 -0.52 10 10
apoptosis -0.021 0.076 -10000 0 -0.57 7 7
RAL/GTP 0.036 0.014 -10000 0 -10000 0 0
LYN 0.028 0.008 -10000 0 -10000 0 0
DUSP1 0.022 0.03 -10000 0 -0.59 1 1
PAK1 0.03 0.003 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.067 0.027 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -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 0.027 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.014 -10000 0 -10000 0 0
MAPK11 0.044 0.12 0.39 12 -0.47 6 18
BLK -0.013 0.15 -10000 0 -0.59 32 32
HCK -0.003 0.14 -10000 0 -0.59 26 26
MAP2K3 0.029 0.005 -10000 0 -10000 0 0
DUSP16 0.029 0.005 -10000 0 -10000 0 0
DUSP10 0.025 0.051 -10000 0 -0.63 3 3
TRAF6/MEKK3 0.037 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.12 0.31 13 -0.66 7 20
positive regulation of innate immune response 0.051 0.14 0.42 12 -0.62 7 19
LCK 0.002 0.13 -10000 0 -0.59 22 22
p38alpha-beta/MKP7 0.055 0.12 0.37 6 -0.62 6 12
p38alpha-beta/MKP5 0.057 0.14 0.45 9 -0.61 7 16
PGK/cGMP 0.011 0.073 -10000 0 -0.48 11 11
PAK2 0.029 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.035 0.12 0.43 4 -0.62 6 10
CDC42 0.029 0.006 -10000 0 -10000 0 0
RALB 0.029 0.005 -10000 0 -10000 0 0
RALA 0.027 0.009 -10000 0 -10000 0 0
PAK3 0.013 0.1 -10000 0 -0.6 13 13
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 0.015 0.099 -10000 0 -0.64 11 11
CLTC 0.019 0.087 -10000 0 -0.34 21 21
calcium ion-dependent exocytosis 0.027 0.028 0.2 1 -10000 0 1
Dynamin 2/GTP 0.033 0.011 -10000 0 -10000 0 0
EXOC4 0.027 0.009 -10000 0 -10000 0 0
CD59 0.015 0.066 -10000 0 -0.3 4 4
CPE 0.004 0.078 -10000 0 -0.37 21 21
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
membrane fusion 0.02 0.015 -10000 0 -10000 0 0
CTNND1 0.026 0.021 -10000 0 -10000 0 0
DNM2 0.03 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.05 0.26 1 -0.44 1 2
TSHR -0.024 0.12 -10000 0 -0.37 57 57
INS 0.017 0.039 -10000 0 -0.77 1 1
BIN1 0.029 0.005 -10000 0 -10000 0 0
mol:Choline 0.02 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.007 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.032 0.011 -10000 0 -10000 0 0
JUP 0.013 0.07 -10000 0 -0.32 5 5
ASAP2/amphiphysin II 0.052 0.018 -10000 0 -10000 0 0
ARF6/GTP 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.009 0.079 -10000 0 -0.37 7 7
clathrin-independent pinocytosis 0.021 0.006 -10000 0 -10000 0 0
MAPK8IP3 -0.013 0.16 -10000 0 -0.59 34 34
positive regulation of endocytosis 0.021 0.006 -10000 0 -10000 0 0
EXOC2 0.029 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.022 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.078 0.42 3 -10000 0 3
positive regulation of phagocytosis 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.009 0.1 -10000 0 -0.36 34 34
ACAP1 0.013 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.008 0.063 -10000 0 -0.29 18 18
clathrin heavy chain/ACAP1 0.022 0.07 -10000 0 -0.47 1 1
JIP4/KLC1 0.052 0.018 -10000 0 -10000 0 0
EXOC1 0.03 0.004 -10000 0 -10000 0 0
exocyst 0.036 0.022 -10000 0 -10000 0 0
RALA/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.037 0.012 -10000 0 -10000 0 0
receptor recycling 0.021 0.006 -10000 0 -10000 0 0
CTNNA1 0.021 0.023 -10000 0 -10000 0 0
NME1 0.02 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0.018 0.09 -10000 0 -0.33 21 21
IL2RA -0.019 0.094 -10000 0 -0.37 7 7
VAMP3 0.02 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.021 0.082 -10000 0 -0.44 4 4
EXOC6 0.029 0.006 -10000 0 -10000 0 0
PLD1 0.021 0.01 -10000 0 -10000 0 0
PLD2 0.021 0.009 -10000 0 -10000 0 0
EXOC5 0.028 0.008 -10000 0 -10000 0 0
PIP5K1C 0.023 0.047 -10000 0 -0.45 1 1
SDC1 0.012 0.076 -10000 0 -0.37 6 6
ARF6/GDP 0.028 0.009 -10000 0 -10000 0 0
EXOC7 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.023 0.081 -10000 0 -0.43 3 3
mol:Phosphatidic acid 0.02 0.015 -10000 0 -10000 0 0
endocytosis -0.05 0.017 -10000 0 -10000 0 0
SCAMP2 0.03 0.003 -10000 0 -10000 0 0
ADRB2 0.061 0.11 0.33 6 -0.37 5 11
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ASAP2 0.029 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.036 0.012 -10000 0 -10000 0 0
KLC1 0.028 0.008 -10000 0 -10000 0 0
AVPR2 -0.12 0.2 0.3 1 -0.57 26 27
RALA 0.027 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.038 0.081 -10000 0 -0.49 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.038 0.068 0.37 1 -0.38 1 2
adherens junction organization 0.001 0.091 0.25 5 -0.44 4 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.042 0.077 0.34 2 -10000 0 2
FMN1 -0.015 0.1 -10000 0 -0.44 11 11
mol:IP3 0.024 0.053 -10000 0 -0.35 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.001 0.078 -10000 0 -0.47 3 3
CTNNB1 0.022 0.014 -10000 0 -10000 0 0
AKT1 0.027 0.06 0.26 1 -0.36 1 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.051 0.14 -10000 0 -0.55 21 21
CTNND1 0.032 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.073 -10000 0 -0.39 4 4
VASP -0.001 0.075 -10000 0 -0.45 3 3
ZYX -0.001 0.073 -10000 0 -0.45 3 3
JUB -0.002 0.075 -10000 0 -0.45 3 3
EGFR(dimer) 0.006 0.085 -10000 0 -0.44 4 4
E-cadherin/beta catenin-gamma catenin 0.023 0.088 -10000 0 -0.4 18 18
mol:PI-3-4-5-P3 0.034 0.069 0.27 2 -0.37 2 4
PIK3CA 0.03 0.031 -10000 0 -0.64 1 1
PI3K 0.034 0.07 0.27 2 -0.37 2 4
FYN -0.2 0.14 -10000 0 -0.44 33 33
mol:Ca2+ 0.024 0.052 -10000 0 -0.34 1 1
JUP 0.028 0.052 -10000 0 -0.63 3 3
PIK3R1 0.028 0.031 -10000 0 -0.64 1 1
mol:DAG 0.024 0.053 -10000 0 -0.35 1 1
CDH1 0.008 0.12 -10000 0 -0.62 17 17
RhoA/GDP 0.04 0.076 0.33 3 -10000 0 3
establishment of polarity of embryonic epithelium 0 0.074 -10000 0 -0.44 3 3
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
EGFR 0.019 0.068 -10000 0 -0.59 6 6
CASR -0.22 0.15 -10000 0 -0.46 16 16
RhoA/GTP 0.03 0.051 -10000 0 -10000 0 0
AKT2 0.028 0.064 0.26 2 -10000 0 2
actin cable formation -0.014 0.1 -10000 0 -0.43 10 10
apoptosis -0.028 0.071 0.37 1 -0.35 6 7
CTNNA1 0.024 0.013 -10000 0 -10000 0 0
mol:GDP 0.017 0.061 0.29 1 -10000 0 1
PIP5K1A 0 0.074 -10000 0 -0.4 4 4
PLCG1 0.024 0.054 -10000 0 -0.35 1 1
Rac1/GTP 0.018 0.085 -10000 0 -0.4 4 4
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.039 0.037 -10000 0 -0.47 2 2
ATM 0.029 0.03 -10000 0 -0.64 1 1
UBE2D3 0.03 0.004 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
ATR 0.028 0.007 -10000 0 -10000 0 0
UBE2L3 0.03 0.004 -10000 0 -10000 0 0
FANCD2 0.021 0.023 -10000 0 -0.36 1 1
protein ubiquitination 0.068 0.059 -10000 0 -0.64 1 1
XRCC5 0.029 0.007 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.045 0.027 -10000 0 -10000 0 0
MRE11A 0.03 0.004 -10000 0 -10000 0 0
DNA-PK 0.054 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.005 0.11 -10000 0 -0.57 13 13
FANCF 0.03 0.004 -10000 0 -10000 0 0
BRCA1 0.029 0.005 -10000 0 -10000 0 0
CCNE1 0.023 0.067 -10000 0 -0.59 6 6
CDK2/Cyclin E1 0.038 0.052 -10000 0 -0.43 6 6
FANCG 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.038 -10000 0 -0.47 2 2
FANCE 0.028 0.028 -10000 0 -0.59 1 1
FANCC 0.029 0.006 -10000 0 -10000 0 0
NBN 0.028 0.007 -10000 0 -10000 0 0
FANCA -0.097 0.25 -10000 0 -0.59 102 102
DNA repair 0.014 0.11 0.37 6 -0.62 4 10
BRCA1/BARD1/ubiquitin 0.039 0.038 -10000 0 -0.47 2 2
BARD1/DNA-PK 0.066 0.04 -10000 0 -0.37 2 2
FANCL 0.029 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.038 0.037 0.47 2 -10000 0 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.028 0.047 -10000 0 -0.69 1 1
BRCA1/BACH1/BARD1/TopBP1 0.052 0.037 -10000 0 -0.41 2 2
BRCA1/BARD1/P53 0.066 0.039 -10000 0 -0.37 2 2
BARD1/CSTF1/BRCA1 0.054 0.035 -10000 0 -0.41 2 2
BRCA1/BACH1 0.029 0.005 -10000 0 -10000 0 0
BARD1 0.025 0.048 -10000 0 -0.48 4 4
PCNA 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.036 -10000 0 -0.41 2 2
BRCA1/BARD1/UbcH7 0.054 0.036 -10000 0 -0.41 2 2
BRCA1/BARD1/RAD51/PCNA 0.057 0.076 -10000 0 -0.34 15 15
BARD1/DNA-PK/P53 0.076 0.042 -10000 0 -0.35 2 2
BRCA1/BARD1/Ubiquitin 0.039 0.038 -10000 0 -0.47 2 2
BRCA1/BARD1/CTIP 0.048 0.048 -10000 0 -0.49 3 3
FA complex -0.002 0.094 -10000 0 -0.43 6 6
BARD1/EWS 0.039 0.038 -10000 0 -0.47 2 2
RBBP8 0.021 0.04 -10000 0 -0.86 1 1
TP53 0.029 0.005 -10000 0 -10000 0 0
TOPBP1 0.028 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.064 0.039 0.37 2 -10000 0 2
BRCA1/BARD1 0.075 0.061 -10000 0 -0.65 1 1
CSTF1 0.029 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.018 0.035 -10000 0 -0.35 4 4
CDK2 0.029 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0.1 -10000 0 -0.59 14 14
RAD50 0.023 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.038 -10000 0 -0.47 2 2
EWSR1 0.03 0.004 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.05 0.032 -10000 0 -0.4 1 1
forebrain development 0.046 0.11 0.45 5 -0.46 6 11
GNAO1 0.024 0.057 -10000 0 -0.6 4 4
SMO/beta Arrestin2 0.039 0.038 -10000 0 -0.5 2 2
SMO 0.026 0.031 -10000 0 -0.64 1 1
ARRB2 0.029 0.033 -10000 0 -0.7 1 1
GLI3/SPOP 0.056 0.092 -10000 0 -0.5 8 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.008 -10000 0 -10000 0 0
GNAI2 0.022 0.014 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.075 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.64 1 1
XPO1 0.03 0.011 -10000 0 -10000 0 0
GLI1/Su(fu) 0.039 0.095 -10000 0 -0.61 4 4
SAP30 0.008 0.11 -10000 0 -0.59 17 17
mol:GDP 0.026 0.031 -10000 0 -0.64 1 1
MIM/GLI2A 0.027 0.031 -10000 0 -10000 0 0
IFT88 0.028 0.03 -10000 0 -0.64 1 1
GNAI3 0.03 0.006 -10000 0 -10000 0 0
GLI2 0.071 0.082 0.31 12 -0.5 1 13
GLI3 0.042 0.098 0.3 3 -0.56 8 11
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.03 0.004 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.028 0.03 -10000 0 -0.64 1 1
GNG2 0.028 0.008 -10000 0 -10000 0 0
Gi family/GTP 0.024 0.045 -10000 0 -0.36 4 4
SIN3B 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.045 0.11 -10000 0 -0.62 8 8
GLI2/Su(fu) 0.071 0.07 0.27 2 -0.5 2 4
FOXA2 -0.007 0.21 -10000 0 -1 14 14
neural tube patterning 0.046 0.11 0.45 5 -0.46 6 11
SPOP 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.045 0.05 -10000 0 -0.54 1 1
GNB1 0.029 0.006 -10000 0 -10000 0 0
CSNK1G2 0.028 0.03 -10000 0 -0.64 1 1
CSNK1G3 0.024 0.012 -10000 0 -10000 0 0
MTSS1 0.027 0.031 -10000 0 -10000 0 0
embryonic limb morphogenesis 0.046 0.11 0.45 5 -0.46 6 11
SUFU 0.029 0.033 -10000 0 -0.58 1 1
LGALS3 0.015 0.088 -10000 0 -0.6 10 10
catabolic process 0.1 0.12 0.38 10 -0.6 5 15
GLI3A/CBP 0.031 0.043 -10000 0 -0.36 2 2
KIF3A 0.023 0.013 -10000 0 -10000 0 0
GLI1 0.046 0.11 0.45 5 -0.47 6 11
RAB23 0.029 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
IFT172 0.029 0.005 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.036 0.08 -10000 0 -0.44 9 9
GNAZ 0.026 0.052 -10000 0 -0.64 3 3
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
CSNK1G1 0.03 0.003 -10000 0 -10000 0 0
PIAS1 0.03 0.003 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GLI2/SPOP 0.082 0.068 0.29 6 -10000 0 6
STK36 0.03 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.029 0.039 -10000 0 -0.36 2 2
PTCH1 0.046 0.11 0.45 5 -0.74 2 7
MIM/GLI1 0.047 0.14 0.45 2 -0.55 5 7
CREBBP 0.031 0.043 -10000 0 -0.36 2 2
Su(fu)/SIN3/HDAC complex 0.029 0.1 0.26 1 -0.54 10 11
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.023 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.05 0.03 -10000 0 -0.37 1 1
CDKN1B 0.017 0.082 -10000 0 -0.59 2 2
CDKN1A 0.018 0.076 -10000 0 -0.59 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
FOXO3 0.018 0.072 -10000 0 -0.59 2 2
AKT1 0.026 0.016 -10000 0 -10000 0 0
BAD 0.027 0.041 -10000 0 -0.61 2 2
AKT3 0.019 0.018 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.016 0.081 -10000 0 -0.59 2 2
AKT1/ASK1 0.025 0.093 -10000 0 -0.51 4 4
BAD/YWHAZ 0.056 0.032 -10000 0 -0.39 2 2
RICTOR 0.027 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.014 -10000 0 -10000 0 0
JNK cascade -0.024 0.09 0.49 4 -10000 0 4
TSC1 0.021 0.062 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.019 0.092 -10000 0 -0.52 4 4
EP300 0.028 0.03 -10000 0 -0.64 1 1
mol:GDP 0.012 0.073 -10000 0 -0.61 2 2
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.013 0.08 -10000 0 -0.59 2 2
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.017 0.016 -10000 0 -0.32 1 1
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
MAPKAP1 0.029 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.085 0.45 3 -0.26 9 12
YWHAH 0.03 0.004 -10000 0 -10000 0 0
AKT1S1 0.016 0.08 -10000 0 -0.59 2 2
CASP9 0.02 0.069 -10000 0 -0.59 1 1
YWHAB 0.029 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.032 0.097 0.34 5 -0.49 4 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.052 0.029 -10000 0 -0.41 1 1
YWHAE 0.029 0.005 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.016 0.079 -10000 0 -0.47 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.027 -10000 0 -10000 0 0
CHUK 0.017 0.077 -10000 0 -0.59 2 2
BAD/BCL-XL 0.038 0.094 -10000 0 -0.47 5 5
mTORC2 0.033 0.013 -10000 0 -10000 0 0
AKT2 0.02 0.018 -10000 0 -0.37 1 1
FOXO1-3a-4/14-3-3 family 0.034 0.11 0.32 7 -0.43 10 17
PDPK1 0.027 0.031 -10000 0 -0.64 1 1
MDM2 0.018 0.082 -10000 0 -0.59 2 2
MAPKKK cascade -0.019 0.091 0.51 4 -10000 0 4
MDM2/Cbp/p300 0.046 0.097 0.32 3 -0.47 5 8
TSC1/TSC2 0.027 0.071 0.28 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.093 0.31 3 -0.45 5 8
glucose import 0.01 0.06 -10000 0 -0.36 10 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.054 0.24 3 -0.33 2 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.008 0.056 -10000 0 -0.36 10 10
GSK3A 0.016 0.081 -10000 0 -0.59 2 2
FOXO1 0.016 0.08 -10000 0 -0.59 2 2
GSK3B 0.018 0.074 -10000 0 -0.59 2 2
SFN -0.043 0.2 -10000 0 -0.59 58 58
G1/S transition of mitotic cell cycle 0.024 0.081 0.34 3 -0.53 3 6
p27Kip1/14-3-3 family 0.038 0.071 0.29 1 -0.41 2 3
PRKACA 0.03 0.002 -10000 0 -10000 0 0
KPNA1 0.028 0.008 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
RHEB 0.027 0.009 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.068 0.84 1 -10000 0 1
VDR 0.025 0.052 -10000 0 -0.64 3 3
FAM120B 0.028 0.008 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.056 0.048 -10000 0 -0.34 1 1
RXRs/LXRs/DNA/Oxysterols 0.06 0.057 -10000 0 -0.36 4 4
MED1 0.029 0.005 -10000 0 -10000 0 0
mol:9cRA 0.006 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.013 0.074 -10000 0 -10000 0 0
RXRs/NUR77 0.063 0.087 -10000 0 -0.36 14 14
RXRs/PPAR 0.033 0.04 -10000 0 -0.55 1 1
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.039 -10000 0 -0.48 3 3
RARs/VDR/DNA/Vit D3 0.045 0.051 -10000 0 -0.34 5 5
RARA 0.029 0.005 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.052 -10000 0 -0.64 3 3
RARs/RARs/DNA/9cRA 0.037 0.037 -10000 0 -0.35 2 2
RARG 0.029 0.005 -10000 0 -10000 0 0
RPS6KB1 0.02 0.069 0.5 8 -0.43 1 9
RARs/THRs/DNA/SMRT 0.013 0.074 -10000 0 -10000 0 0
THRA 0.028 0.03 -10000 0 -0.64 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.039 -10000 0 -0.48 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.066 0.051 0.33 1 -0.34 3 4
NR1H4 0.01 0.11 -10000 0 -0.64 14 14
RXRs/LXRs/DNA 0.099 0.063 -10000 0 -10000 0 0
NR1H2 0.034 0.032 -10000 0 -0.63 1 1
NR1H3 0.036 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.068 0.055 -10000 0 -0.34 4 4
NR4A1 0.011 0.11 -10000 0 -0.63 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.025 0.076 -10000 0 -0.37 14 14
RXRG 0.027 0.059 -10000 0 -0.61 4 4
RXR alpha/CCPG 0.044 0.017 -10000 0 -10000 0 0
RXRA 0.034 0.012 -10000 0 -10000 0 0
RXRB 0.035 0.012 -10000 0 -10000 0 0
THRB -0.014 0.14 -10000 0 -0.56 30 30
PPARG 0.021 0.014 -10000 0 -10000 0 0
PPARD 0.029 0.006 -10000 0 -10000 0 0
TNF 0.054 0.11 -10000 0 -1 4 4
mol:Oxysterols 0.006 0.006 -10000 0 -10000 0 0
cholesterol transport 0.061 0.057 -10000 0 -0.35 4 4
PPARA 0.03 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.044 -10000 0 -0.64 2 2
RXRs/NUR77/BCL2 0.026 0.06 -10000 0 -0.3 14 14
SREBF1 0.061 0.052 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.066 0.051 0.33 1 -0.34 3 4
ABCA1 0.06 0.06 -10000 0 -10000 0 0
RARs/THRs 0.037 0.1 -10000 0 -10000 0 0
RXRs/FXR 0.065 0.086 -10000 0 -0.36 15 15
BCL2 0.029 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.013 0.038 -10000 0 -0.41 4 4
SNTA1 0.026 0.041 -10000 0 -0.61 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.013 0.037 -10000 0 -0.4 4 4
MAPK12 0.009 0.052 -10000 0 -0.33 11 11
CCND1 0.013 0.047 -10000 0 -0.31 4 4
p38 gamma/SNTA1 0.031 0.068 0.29 2 -0.67 1 3
MAP2K3 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.03 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint 0.013 0.06 -10000 0 -0.33 11 11
MAP2K6 0.016 0.032 -10000 0 -0.39 3 3
MAPT 0.019 0.067 0.3 5 -0.45 6 11
MAPK13 0.018 0.045 -10000 0 -0.48 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.021 0.007 -10000 0 -10000 0 0
Insulin Pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.045 0.052 -10000 0 -10000 0 0
TC10/GTP 0.044 0.041 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.065 0.042 -10000 0 -0.38 3 3
HRAS 0.029 0.028 -10000 0 -0.59 1 1
APS homodimer 0.023 0.048 -10000 0 -0.58 3 3
GRB14 -0.007 0.15 -10000 0 -0.64 27 27
FOXO3 0 0.14 -10000 0 -0.6 26 26
AKT1 0.034 0.11 0.41 15 -0.58 2 17
INSR 0.033 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.065 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
SORBS1 0.028 0.03 -10000 0 -0.64 1 1
CRK 0.029 0.005 -10000 0 -10000 0 0
PTPN1 0.022 0.01 -10000 0 -10000 0 0
CAV1 0 0.088 -10000 0 -0.36 3 3
CBL/APS/CAP/Crk-II/C3G 0.07 0.052 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.066 0.041 -10000 0 -0.38 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.047 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.044 0.038 -10000 0 -10000 0 0
RPS6KB1 0.027 0.1 0.38 13 -0.52 2 15
PARD6A 0.025 0.052 -10000 0 -0.64 3 3
CBL 0.028 0.03 -10000 0 -0.64 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.057 -10000 0 -0.49 6 6
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.028 0.078 -10000 0 -0.53 2 2
HRAS/GTP 0.016 0.042 -10000 0 -0.55 1 1
Insulin Receptor 0.033 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.076 0.044 -10000 0 -10000 0 0
PRKCI 0.032 0.052 -10000 0 -0.48 2 2
Insulin Receptor/Insulin/GRB14/PDK1 0.012 0.085 -10000 0 -0.62 2 2
SHC1 0.029 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.039 0.064 -10000 0 -0.45 7 7
PI3K 0.058 0.049 -10000 0 -10000 0 0
NCK2 0.029 0.005 -10000 0 -10000 0 0
RHOQ 0.029 0.005 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
AKT2 0.04 0.12 0.41 19 -0.58 2 21
PRKCZ 0.03 0.069 -10000 0 -0.59 5 5
SH2B2 0.023 0.048 -10000 0 -0.59 3 3
SHC/SHIP 0.035 0.05 -10000 0 -0.63 1 1
F2RL2 -0.005 0.14 -10000 0 -0.59 26 26
TRIP10 0.03 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.052 0.016 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.08 0.027 -10000 0 -10000 0 0
RAPGEF1 0.029 0.006 -10000 0 -10000 0 0
RASA1 0.025 0.031 -10000 0 -0.64 1 1
NCK1 0.027 0.031 -10000 0 -0.64 1 1
CBL/APS/CAP/Crk-II 0.062 0.05 -10000 0 -0.37 2 2
TC10/GDP 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.064 0.027 -10000 0 -10000 0 0
INPP5D 0.019 0.05 -10000 0 -0.46 3 3
SOS1 0.029 0.005 -10000 0 -10000 0 0
SGK1 -0.032 0.17 -10000 0 -0.62 38 38
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IRS1 0.025 0.052 -10000 0 -0.64 3 3
p62DOK/RasGAP 0.039 0.065 -10000 0 -0.45 7 7
INS 0.023 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.05 -10000 0 -0.45 3 3
GRB2 0.029 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.013 0.12 0.4 13 -0.59 4 17
PTPRA 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
TC10/GTP/CIP4 0.039 0.008 -10000 0 -10000 0 0
PDPK1 0.027 0.031 -10000 0 -0.64 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.028 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.049 0.037 -10000 0 -0.39 3 3
Insulin Receptor/Insulin/IRS3 0.041 0.011 -10000 0 -10000 0 0
Par3/Par6 0.039 0.091 -10000 0 -0.32 25 25
Osteopontin-mediated events

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
IKK alpha homodimer 0.06 0.057 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.078 0.077 0.37 5 -0.59 1 6
alphaV/beta3 Integrin/Osteopontin/Src 0.047 0.044 -10000 0 -0.47 3 3
AP1 0.087 0.094 -10000 0 -0.68 1 1
ILK 0.049 0.051 -10000 0 -10000 0 0
bone resorption 0.045 0.084 -10000 0 -0.56 1 1
PTK2B 0.027 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.074 0.061 -10000 0 -10000 0 0
ITGAV 0.033 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.092 -10000 0 -0.43 19 19
alphaV/beta3 Integrin/Osteopontin 0.067 0.05 -10000 0 -0.38 4 4
MAP3K1 0.045 0.052 -10000 0 -10000 0 0
JUN 0.029 0.007 -10000 0 -10000 0 0
MAPK3 0.04 0.059 -10000 0 -10000 0 0
MAPK1 0.043 0.058 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
MAPK8 0.041 0.054 0.41 1 -10000 0 1
ITGB3 0.031 0.043 -10000 0 -0.63 2 2
NFKBIA 0.04 0.056 -10000 0 -10000 0 0
FOS 0.012 0.1 -10000 0 -0.63 12 12
CD44 0.008 0.12 -10000 0 -0.59 18 18
CHUK 0.029 0.006 -10000 0 -10000 0 0
PLAU 0.051 0.16 0.52 4 -1.1 8 12
NF kappa B1 p50/RelA 0.084 0.075 0.38 1 -0.57 1 2
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
RELA 0.03 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.048 0.036 -10000 0 -0.46 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.046 0.055 -10000 0 -10000 0 0
VAV3 0.03 0.08 -10000 0 -0.66 1 1
MAP3K14 0.047 0.059 -10000 0 -10000 0 0
ROCK2 0.027 0.034 -10000 0 -0.48 2 2
SPP1 0.03 0.053 -10000 0 -0.64 3 3
RAC1 0.027 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.072 -10000 0 -0.61 1 1
MMP2 0.055 0.094 0.43 2 -0.79 1 3
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.014 0.1 -10000 0 -0.44 21 21
regulation of axonogenesis -0.01 0.053 -10000 0 -10000 0 0
myoblast fusion -0.017 0.062 0.32 5 -10000 0 5
mol:GTP 0.012 0.046 -10000 0 -0.31 2 2
regulation of calcium-dependent cell-cell adhesion -0.048 0.052 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.047 -10000 0 -0.32 1 1
mol:GM1 0.002 0.039 -10000 0 -0.32 1 1
mol:Choline 0.014 0.032 -10000 0 -10000 0 0
lamellipodium assembly 0.006 0.078 -10000 0 -0.33 15 15
MAPK3 0.021 0.057 -10000 0 -0.51 1 1
ARF6/GTP/NME1/Tiam1 0.049 0.053 -10000 0 -10000 0 0
ARF1 0.029 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.062 -10000 0 -0.32 5 5
ARF1/GDP 0.017 0.076 -10000 0 -0.38 2 2
ARF6 0.028 0.027 -10000 0 -10000 0 0
RAB11A 0.03 0.003 -10000 0 -10000 0 0
TIAM1 0.03 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.054 -10000 0 -0.3 1 1
actin filament bundle formation -0.009 0.075 0.38 2 -10000 0 2
KALRN 0.011 0.049 -10000 0 -0.36 2 2
RAB11FIP3/RAB11A 0.042 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.009 0.075 -10000 0 -0.38 2 2
NME1 0.031 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.07 -10000 0 -0.38 1 1
substrate adhesion-dependent cell spreading 0.012 0.046 -10000 0 -0.31 2 2
cortical actin cytoskeleton organization 0.005 0.078 -10000 0 -0.33 15 15
RAC1 0.027 0.009 -10000 0 -10000 0 0
liver development 0.012 0.046 -10000 0 -0.31 2 2
ARF6/GTP 0.012 0.046 -10000 0 -0.31 2 2
RhoA/GTP 0.017 0.045 -10000 0 -0.32 1 1
mol:GDP 0.003 0.07 -10000 0 -0.32 5 5
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.047 -10000 0 -0.28 1 1
RHOA 0.021 0.014 -10000 0 -10000 0 0
PLD1 0.016 0.038 -10000 0 -10000 0 0
RAB11FIP3 0.029 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.006 0.078 -10000 0 -0.33 15 15
ruffle organization 0.01 0.053 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.012 0.046 -10000 0 -0.31 2 2
PLD2 0.014 0.043 -10000 0 -0.3 1 1
PIP5K1A 0.01 0.053 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.014 0.032 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.078 -10000 0 -0.33 15 15
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.04 0.034 -10000 0 -0.47 2 2
PTK2 0.031 0.07 -10000 0 -10000 0 0
positive regulation of JNK cascade 0.011 0.1 -10000 0 -0.35 12 12
CDC42/GDP 0.037 0.14 0.37 3 -0.51 4 7
Rac1/GDP 0.031 0.13 -10000 0 -0.49 5 5
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.13 -10000 0 -0.43 12 12
nectin-3/I-afadin 0.037 0.03 -10000 0 -0.47 1 1
RAPGEF1 0.021 0.12 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0.12 -10000 0 -0.48 2 2
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
TLN1 0.016 0.013 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.087 -10000 0 -10000 0 0
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.02 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.037 0.03 -10000 0 -0.47 1 1
PVR 0.03 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.03 0.004 -10000 0 -10000 0 0
mol:GDP 0.023 0.16 0.39 3 -0.53 13 16
MLLT4 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
PI3K 0.057 0.053 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.014 0.1 -10000 0 -0.37 10 10
PVRL1 0.03 0.004 -10000 0 -10000 0 0
PVRL3 0.026 0.035 -10000 0 -0.64 1 1
PVRL2 0.03 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
CDH1 0.007 0.12 -10000 0 -0.62 17 17
CLDN1 0.022 0.065 -10000 0 -0.62 5 5
JAM-A/CLDN1 0.058 0.053 -10000 0 -0.36 4 4
SRC 0.009 0.13 -10000 0 -0.53 2 2
ITGB3 0.027 0.042 -10000 0 -0.64 2 2
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
FARP2 0.016 0.17 -10000 0 -0.65 14 14
RAC1 0.027 0.009 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.051 0.032 -10000 0 -0.41 1 1
nectin-1/I-afadin 0.041 0.013 -10000 0 -10000 0 0
nectin-2/I-afadin 0.041 0.013 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.051 0.032 -10000 0 -0.41 1 1
CDC42/GTP/IQGAP1/filamentous actin 0.039 0.009 -10000 0 -10000 0 0
F11R 0.029 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.011 0.1 -10000 0 -0.35 12 12
alphaV/beta3 Integrin/Talin 0.049 0.039 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.041 0.013 -10000 0 -10000 0 0
PIP5K1C 0.017 0.014 -10000 0 -10000 0 0
VAV2 0.016 0.17 -10000 0 -0.66 11 11
RAP1/GDP 0.038 0.12 -10000 0 -0.42 1 1
ITGAV 0.029 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.051 0.032 -10000 0 -0.41 1 1
nectin-3(dimer)/I-afadin/I-afadin 0.037 0.03 -10000 0 -0.47 1 1
Rac1/GTP 0.021 0.12 -10000 0 -0.46 9 9
PTPRM 0.019 0.016 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.041 0.075 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0.006 -10000 0 -10000 0 0
NFATC1 0.045 0.072 0.37 3 -0.44 1 4
NFATC2 0.038 0.066 0.22 8 -0.27 6 14
NFATC3 0.025 0.032 -10000 0 -0.35 3 3
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0 0.086 0.31 2 -0.35 12 14
Exportin 1/Ran/NUP214 0.056 0.018 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.025 0.08 -10000 0 -0.43 3 3
BCL2/BAX 0.043 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.021 0.01 -10000 0 -10000 0 0
BAX 0.03 0.003 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
BAD 0.027 0.041 -10000 0 -0.61 2 2
CABIN1/MEF2D 0.014 0.083 0.31 1 -0.38 6 7
Calcineurin A alpha-beta B1/BCL2 0.029 0.005 -10000 0 -10000 0 0
FKBP8 0.029 0.03 -10000 0 -0.64 1 1
activation-induced cell death of T cells -0.014 0.082 0.37 6 -0.31 1 7
KPNB1 0.029 0.005 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SFN -0.043 0.2 -10000 0 -0.59 58 58
MAP3K8 0.027 0.039 -10000 0 -0.58 2 2
NFAT4/CK1 alpha 0.032 0.03 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.074 0.089 -10000 0 -0.42 4 4
CABIN1 0 0.085 0.31 2 -0.36 11 13
CALM1 0.028 0.009 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
MAP3K1 0.028 0.008 -10000 0 -10000 0 0
CAMK4 0.023 0.032 -10000 0 -0.64 1 1
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.039 0.035 -10000 0 -0.47 2 2
YWHAB 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.03 0.006 -10000 0 -10000 0 0
MAPK9 0.023 0.013 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.07 0.079 -10000 0 -0.45 1 1
PRKCH 0.028 0.008 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.041 0.027 -10000 0 -0.47 1 1
CASP3 0.03 0.005 -10000 0 -10000 0 0
PIM1 0.029 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
apoptosis 0.025 0.017 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.063 -10000 0 -0.36 5 5
PRKCB 0.022 0.064 -10000 0 -0.61 5 5
PRKCE 0.028 0.03 -10000 0 -0.64 1 1
JNK2/NFAT4 0.026 0.045 -10000 0 -0.34 2 2
BAD/BCL-XL 0.041 0.033 -10000 0 -0.45 2 2
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
NUP214 0.029 0.006 -10000 0 -10000 0 0
PRKCZ 0.025 0.052 -10000 0 -0.64 3 3
PRKCA 0.029 0.005 -10000 0 -10000 0 0
PRKCG -0.001 0.12 -10000 0 -0.59 20 20
PRKCQ 0.013 0.1 -10000 0 -0.57 14 14
FKBP38/BCL2 0.042 0.025 -10000 0 -0.47 1 1
EP300 0.028 0.031 -10000 0 -0.64 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.058 0.072 0.35 2 -0.4 1 3
CaM/Ca2+/FKBP38 0.037 0.025 -10000 0 -0.42 1 1
FKBP12/FK506 0.022 0.004 -10000 0 -10000 0 0
CSNK1A1 0.017 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.031 0.026 -10000 0 -0.39 1 1
NFATc/ERK1 0.053 0.071 -10000 0 -0.41 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.024 0.081 -10000 0 -0.44 3 3
NR4A1 0.051 0.12 -10000 0 -0.58 13 13
GSK3B 0.028 0.008 -10000 0 -10000 0 0
positive T cell selection 0.025 0.032 -10000 0 -0.35 3 3
NFAT1/CK1 alpha 0.021 0.038 -10000 0 -10000 0 0
RCH1/ KPNB1 0.043 0.008 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.03 0.003 -10000 0 -10000 0 0
AKAP5 0.025 0.043 -10000 0 -0.64 2 2
MEF2D 0.029 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.06 0.072 0.37 3 -0.4 1 4
CREBBP 0.029 0.008 -10000 0 -10000 0 0
BCL2 0.029 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.013 -10000 0 -10000 0 0
VDR 0.025 0.052 -10000 0 -0.64 3 3
Cbp/p300/PCAF 0.04 0.046 -10000 0 -0.76 1 1
EP300 0.028 0.03 -10000 0 -0.64 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.027 0.052 -10000 0 -0.33 4 4
KAT2B 0.02 0.033 -10000 0 -0.64 1 1
MAPK14 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.001 0.054 0.22 1 -10000 0 1
RAR alpha/9cRA/Cyclin H 0.05 0.056 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.027 0.054 -10000 0 -0.44 1 1
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.027 0.046 -10000 0 -0.3 4 4
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.039 -10000 0 -0.48 3 3
RXRs/RARs/NRIP1/9cRA 0.028 0.079 0.31 1 -0.47 2 3
NCOA2 0.019 0.079 -10000 0 -0.64 7 7
NCOA3 0.029 0.006 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.052 -10000 0 -0.64 3 3
RARG 0.03 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.04 0.008 -10000 0 -10000 0 0
MAPK3 0.03 0.007 -10000 0 -10000 0 0
MAPK1 0.03 0.004 -10000 0 -10000 0 0
MAPK8 0.031 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.045 0.07 -10000 0 -0.47 2 2
RARA 0.023 0.037 -10000 0 -0.27 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.021 0.075 -10000 0 -0.49 6 6
PRKCA 0.033 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.005 0.1 0.36 1 -0.52 3 4
RXRG 0.017 0.063 -10000 0 -0.45 2 2
RXRA 0.029 0.041 -10000 0 -10000 0 0
RXRB 0.019 0.063 -10000 0 -0.5 3 3
VDR/Vit D3/DNA 0.019 0.039 -10000 0 -0.48 3 3
RBP1 0.024 0.056 -10000 0 -0.6 4 4
CRBP1/9-cic-RA 0.017 0.042 -10000 0 -0.44 4 4
RARB 0.021 0.044 -10000 0 -0.64 2 2
PRKCG 0.002 0.12 -10000 0 -0.59 20 20
MNAT1 0.028 0.008 -10000 0 -10000 0 0
RAR alpha/RXRs 0.024 0.075 -10000 0 -0.52 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.032 0.073 0.28 2 -0.4 3 5
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.11 0.27 10 -0.34 7 17
RXRs/RARs/NRIP1/9cRA/HDAC3 0.014 0.1 0.36 2 -0.48 3 5
positive regulation of DNA binding 0.037 0.049 -10000 0 -10000 0 0
NRIP1 -0.008 0.12 -10000 0 -10000 0 0
RXRs/RARs -0.014 0.12 0.3 1 -0.43 8 9
RXRs/RXRs/DNA/9cRA 0.028 0.062 -10000 0 -0.48 2 2
PRKACA 0.03 0.002 -10000 0 -10000 0 0
CDK7 0.027 0.009 -10000 0 -10000 0 0
TFIIH 0.051 0.023 -10000 0 -10000 0 0
RAR alpha/9cRA 0.053 0.054 -10000 0 -10000 0 0
CCNH 0.027 0.01 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.025 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.03 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.013 -9999 0 -10000 0 0
DOCK1 0.028 0.03 -9999 0 -0.64 1 1
ITGA4 0.01 0.1 -9999 0 -0.59 15 15
RAC1 0.027 0.009 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.027 0.081 -9999 0 -0.43 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.045 0.074 -9999 0 -0.36 15 15
alpha4/beta7 Integrin/Paxillin 0.04 0.067 -9999 0 -10000 0 0
lamellipodium assembly 0.037 0.062 -9999 0 -0.62 2 2
PIK3CA 0.027 0.031 -9999 0 -0.64 1 1
PI3K 0.037 0.036 -9999 0 -0.47 2 2
ARF6 0.028 0.008 -9999 0 -10000 0 0
TLN1 0.029 0.006 -9999 0 -10000 0 0
PXN 0.023 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.031 -9999 0 -0.64 1 1
ARF6/GTP 0.049 0.064 -9999 0 -10000 0 0
cell adhesion 0.051 0.067 -9999 0 -10000 0 0
CRKL/CBL 0.043 0.024 -9999 0 -0.47 1 1
alpha4/beta1 Integrin/Paxillin 0.04 0.067 -9999 0 -10000 0 0
ITGB1 0.03 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ARF6/GDP 0.024 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.045 0.086 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 0.054 0.034 -9999 0 -0.41 2 2
VCAM1 0.015 0.091 -9999 0 -0.53 13 13
alpha4/beta1 Integrin/Paxillin/Talin 0.053 0.068 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.068 -9999 0 -10000 0 0
BCAR1 0.028 0.03 -9999 0 -0.64 1 1
mol:GDP -0.052 0.067 -9999 0 -10000 0 0
CBL 0.028 0.03 -9999 0 -0.64 1 1
PRKACA 0.03 0.002 -9999 0 -10000 0 0
GIT1 0.029 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.053 0.068 -9999 0 -10000 0 0
Rac1/GTP 0.038 0.069 -9999 0 -0.72 2 2
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.029 0.005 -10000 0 -10000 0 0
PTK2 0.029 0.007 -10000 0 -10000 0 0
CRKL 0.025 0.037 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.056 0.017 -10000 0 -10000 0 0
HRAS 0.029 0.028 -10000 0 -0.59 1 1
IRS1/Crk 0.031 0.034 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/PTP1B 0.053 0.042 -10000 0 -0.31 5 5
AKT1 0.036 0.068 0.31 6 -0.61 1 7
BAD 0.031 0.072 0.3 6 -0.82 1 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.036 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.035 0.035 -10000 0 -10000 0 0
RAF1 -0.047 0.18 0.32 4 -0.51 4 8
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.065 0.041 -10000 0 -10000 0 0
YWHAZ 0.029 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.034 0.038 -10000 0 -0.27 5 5
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
RPS6KB1 0.041 0.07 0.32 7 -0.61 1 8
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.038 0.16 0.32 9 -0.44 3 12
PXN 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.031 0.033 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.078 0.042 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.051 0.039 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin 0.065 0.044 -10000 0 -10000 0 0
IGF1R 0.032 0.015 -10000 0 -10000 0 0
IGF1 0.026 0.061 -10000 0 -0.56 5 5
IRS2/Crk 0.032 0.055 -10000 0 -0.37 1 1
PI3K 0.058 0.051 -10000 0 -0.34 1 1
apoptosis -0.048 0.072 0.66 1 -0.3 12 13
HRAS/GDP 0.021 0.02 -10000 0 -0.43 1 1
PRKCD 0.029 0.05 -10000 0 -0.63 1 1
RAF1/14-3-3 E -0.037 0.18 0.32 7 -0.46 3 10
BAD/14-3-3 0.05 0.076 0.31 12 -0.73 1 13
PRKCZ 0.037 0.069 0.32 5 -0.61 1 6
Crk/p130 Cas/Paxillin/FAK1 0.041 0.045 -10000 0 -0.51 1 1
PTPN1 0.029 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.025 0.04 -10000 0 -0.36 3 3
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.061 0.044 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
IRS1/NCK2 0.039 0.038 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
PTPN11 0.026 0.037 -10000 0 -10000 0 0
IRS1 0.023 0.04 -10000 0 -0.27 5 5
IRS2 0.02 0.057 -10000 0 -0.34 6 6
IGF-1R heterotetramer/IGF1 0.039 0.049 -10000 0 -0.4 5 5
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDPK1 0.043 0.071 0.32 7 -0.65 1 8
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKD1 0.041 0.051 -10000 0 -0.44 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.029 0.005 -9999 0 -10000 0 0
SMAD2 -0.027 0.065 -9999 0 -10000 0 0
SMAD3 0.027 0.023 -9999 0 -10000 0 0
SMAD3/SMAD4 0.033 0.092 -9999 0 -0.42 18 18
SMAD4/Ubc9/PIASy 0.056 0.017 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.021 0.084 -9999 0 -0.4 1 1
PPM1A 0.028 0.008 -9999 0 -10000 0 0
CALM1 0.028 0.008 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.018 0.078 -9999 0 -0.37 3 3
MAP3K1 0.028 0.008 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.042 0.015 -9999 0 -10000 0 0
MAPK3 0.029 0.006 -9999 0 -10000 0 0
MAPK1 0.03 0.004 -9999 0 -10000 0 0
NUP214 0.029 0.006 -9999 0 -10000 0 0
CTDSP1 0.029 0.007 -9999 0 -10000 0 0
CTDSP2 0.029 0.005 -9999 0 -10000 0 0
CTDSPL 0.021 0.014 -9999 0 -10000 0 0
KPNB1 0.029 0.005 -9999 0 -10000 0 0
TGFBRAP1 0.029 0.017 -9999 0 -0.33 1 1
UBE2I 0.029 0.006 -9999 0 -10000 0 0
NUP153 0.029 0.006 -9999 0 -10000 0 0
KPNA2 0.029 0.005 -9999 0 -10000 0 0
PIAS4 0.03 0.003 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.068 0.032 -10000 0 -0.37 1 1
HDAC3 0.023 0.013 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.023 0.089 -10000 0 -0.43 18 18
GATA1/HDAC5 0.023 0.094 -10000 0 -0.43 20 20
GATA2/HDAC5 0.03 0.075 -10000 0 -0.47 10 10
HDAC5/BCL6/BCoR 0.056 0.026 -10000 0 -0.41 1 1
HDAC9 0.027 0.009 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.033 -10000 0 -0.36 1 1
HDAC4/ANKRA2 0.038 0.016 -10000 0 -10000 0 0
HDAC5/YWHAB 0.041 0.026 -10000 0 -0.47 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
GATA2 0.014 0.095 -10000 0 -0.61 11 11
HDAC4/RFXANK 0.041 0.024 -10000 0 -0.43 1 1
BCOR 0.03 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.028 0.03 -10000 0 -0.64 1 1
HDAC5 0.028 0.03 -10000 0 -0.64 1 1
GNB1/GNG2 0.04 0.014 -10000 0 -10000 0 0
Histones 0.031 0.047 -10000 0 -0.73 1 1
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
HDAC4 0.028 0.007 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.027 -10000 0 -0.47 1 1
HDAC4/Ubc9 0.04 0.013 -10000 0 -10000 0 0
HDAC7 0.029 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.042 0.024 -10000 0 -0.47 1 1
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
HDAC6 0.03 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.041 0.032 -10000 0 -0.45 2 2
CAMK4 0.023 0.032 -10000 0 -0.64 1 1
Tubulin/HDAC6 0.056 0.026 -10000 0 -0.41 1 1
SUMO1 0.029 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.029 0.006 -10000 0 -10000 0 0
GATA1 0.005 0.12 -10000 0 -0.59 19 19
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NR3C1 0.022 0.03 -10000 0 -0.59 1 1
SUMO1/HDAC4 0.052 0.028 -10000 0 -10000 0 0
SRF 0.029 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.041 0.013 -10000 0 -10000 0 0
Tubulin 0.041 0.026 -10000 0 -0.47 1 1
HDAC4/14-3-3 E 0.042 0.011 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
RANGAP1 0.03 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.044 0.028 -10000 0 -10000 0 0
HDAC4/SRF 0.045 0.033 -10000 0 -0.41 1 1
HDAC4/ER alpha 0.036 0.043 -10000 0 -0.46 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.031 0.047 -10000 0 -0.72 1 1
cell motility 0.055 0.026 -10000 0 -0.4 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.034 0.019 -10000 0 -10000 0 0
BCL6 0.029 0.007 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.041 0.012 -10000 0 -10000 0 0
ESR1 0.023 0.053 -10000 0 -0.55 4 4
HDAC6/HDAC11 0.03 0.033 -10000 0 -0.47 1 1
Ran/GTP/Exportin 1 0.052 0.03 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
MEF2C 0.027 0.01 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.041 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
NCOR2 0.029 0.005 -10000 0 -10000 0 0
TUBB2A 0.028 0.03 -10000 0 -0.64 1 1
HDAC11 0.019 0.044 -10000 0 -0.64 2 2
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
ANKRA2 0.027 0.009 -10000 0 -10000 0 0
RFXANK 0.029 0.028 -10000 0 -0.59 1 1
nuclear import -0.041 0.022 0.35 1 -10000 0 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.05 0.061 -10000 0 -0.41 3 3
Ran/GTP/Exportin 1/HDAC1 0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.055 -10000 0 -0.46 1 1
SUMO1 0.029 0.007 -10000 0 -10000 0 0
ZFPM1 0.025 0.052 -10000 0 -0.64 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
FKBP3 0.028 0.008 -10000 0 -10000 0 0
Histones 0.056 0.046 -10000 0 -10000 0 0
YY1/LSF 0.008 0.068 -10000 0 -0.64 1 1
SMG5 0.029 0.007 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.034 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.029 0.041 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
RELA 0.028 0.037 -10000 0 -10000 0 0
HDAC1/Smad7 0.052 0.022 -10000 0 -10000 0 0
RANGAP1 0.03 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.034 0.032 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.044 0.028 -10000 0 -0.32 1 1
NF kappa B1 p50/RelA 0.075 0.069 0.29 7 -0.55 1 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.014 0.095 -10000 0 -0.61 11 11
GATA1 0.005 0.12 -10000 0 -0.59 19 19
Mad/Max 0.04 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.05 0.054 -10000 0 -0.42 2 2
RBBP7 0.03 0.003 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
MAX 0.028 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
NFKBIA 0.021 0.03 -10000 0 -10000 0 0
KAT2B 0.02 0.033 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.034 0.046 -10000 0 -0.42 2 2
SIN3 complex 0.06 0.075 -10000 0 -10000 0 0
SMURF1 0.027 0.009 -10000 0 -10000 0 0
CHD3 0.029 0.005 -10000 0 -10000 0 0
SAP30 0.009 0.11 -10000 0 -0.59 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.029 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.018 0.052 -10000 0 -0.56 1 1
YY1/HDAC2 0.011 0.065 -10000 0 -0.64 1 1
YY1/HDAC1 0.009 0.067 -10000 0 -0.64 1 1
NuRD/MBD2 Complex (MeCP1) 0.044 0.022 -10000 0 -10000 0 0
PPARG 0.021 0.042 -10000 0 -0.35 2 2
HDAC8/hEST1B 0.058 0.014 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.034 0.032 -10000 0 -10000 0 0
MBD3L2 0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.022 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.046 0.062 -10000 0 -0.36 1 1
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.028 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
YY1 0.021 0.037 -10000 0 -0.72 1 1
HDAC8 0.03 0.001 -10000 0 -10000 0 0
SMAD7 0.029 0.005 -10000 0 -10000 0 0
NCOR2 0.029 0.005 -10000 0 -10000 0 0
MXD1 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.029 0.019 -10000 0 -0.36 1 1
NFKB1 0.028 0.03 -10000 0 -0.64 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.068 -10000 0 -0.6 1 1
YY1/SAP30/HDAC1 0.01 0.095 -10000 0 -0.46 6 6
EP300 0.028 0.03 -10000 0 -0.64 1 1
STAT3 (dimer non-phopshorylated) 0.029 0.019 -10000 0 -0.36 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.03 -10000 0 -10000 0 0
histone deacetylation 0.05 0.025 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.033 -10000 0 -10000 0 0
nuclear export -0.057 0.014 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GATAD2B 0.029 0.007 -10000 0 -10000 0 0
GATAD2A 0.03 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.027 0.058 -10000 0 -0.35 7 7
GATA1/HDAC1 0.023 0.091 -10000 0 -0.43 19 19
GATA1/HDAC3 0.023 0.066 -10000 0 -0.32 13 13
CHD4 0.029 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.063 -10000 0 -0.45 8 8
SIN3/HDAC complex/Mad/Max 0.038 0.043 -10000 0 -0.4 2 2
NuRD Complex 0.051 0.06 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.054 0.044 -10000 0 -10000 0 0
SIN3B 0.03 0.003 -10000 0 -10000 0 0
MTA2 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.051 0.028 -10000 0 -10000 0 0
HDAC complex 0.069 0.031 -10000 0 -0.37 1 1
GATA1/Fog1 0.021 0.096 -10000 0 -0.44 20 20
FKBP25/HDAC1/HDAC2 0.053 0.021 -10000 0 -10000 0 0
TNF 0.019 0.081 -10000 0 -0.61 8 8
negative regulation of cell growth 0.038 0.054 -10000 0 -0.34 6 6
NuRD/MBD2/PRMT5 Complex 0.044 0.022 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.052 0.03 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.029 0.042 -10000 0 -0.34 2 2
SIN3/HDAC complex/NCoR1 0.038 0.041 -10000 0 -0.35 1 1
TFCP2 0.029 0.005 -10000 0 -10000 0 0
NR2C1 0.029 0.006 -10000 0 -10000 0 0
MBD3 0.027 0.041 -10000 0 -0.61 2 2
MBD2 0.029 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.042 0.031 -10000 0 -0.43 2 2
FBXW11 0.023 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.032 0.038 -10000 0 -0.41 3 3
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.062 -10000 0 -10000 0 0
NFKBIA 0.019 0.044 -10000 0 -0.33 2 2
MAPK14 0.029 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.027 -10000 0 -0.41 1 1
ARRB2 0.019 0.029 -10000 0 -0.62 1 1
REL 0.026 0.045 -10000 0 -0.53 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.034 0.033 -10000 0 -0.37 3 3
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.035 0.023 -10000 0 -0.41 1 1
PIK3CA 0.027 0.031 -10000 0 -0.64 1 1
NF kappa B1 p50 dimer 0.025 0.024 -10000 0 -0.47 1 1
PIK3R1 0.026 0.031 -10000 0 -0.64 1 1
NFKB1 0.02 0.023 -10000 0 -0.48 1 1
RELA 0.03 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.023 0.043 -10000 0 -0.29 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.035 0.07 -10000 0 -0.5 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.036 -10000 0 -0.47 2 2
NF kappa B1 p50/RelA 0.023 0.043 -10000 0 -0.29 2 2
IKBKB 0.028 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -10000 0 -10000 0 0
SYK 0.027 0.034 -10000 0 -0.48 2 2
I kappa B alpha/PIK3R1 0.021 0.065 0.28 1 -0.41 2 3
cell death 0.034 0.067 -10000 0 -0.47 1 1
NF kappa B1 p105/c-Rel 0.032 0.038 -10000 0 -0.41 3 3
LCK 0.002 0.13 -10000 0 -0.59 22 22
BCL3 0.027 0.039 -10000 0 -0.59 2 2
Arf1 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
coatomer protein complex 0.051 0.074 0.31 8 -0.45 1 9
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.017 0.051 -10000 0 -0.3 8 8
AP2 0.042 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.038 0.014 -10000 0 -10000 0 0
CLTB 0.023 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.014 -10000 0 -10000 0 0
CD4 0.019 0.077 -10000 0 -0.59 8 8
CLTA 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.011 0.022 -10000 0 -0.48 1 1
mol:PI-4-5-P2 0.011 0.017 -10000 0 -0.35 1 1
ARF1/GTP 0.035 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.022 -10000 0 -0.4 1 1
mol:Choline 0.011 0.016 -10000 0 -0.34 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.03 0.007 -10000 0 -10000 0 0
DDEF1 0.01 0.017 -10000 0 -0.35 1 1
ARF1/GDP 0.007 0.021 -10000 0 -0.39 1 1
AP2M1 0.029 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.017 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.042 0.023 -10000 0 -0.36 1 1
ARFIP2 0.027 0.008 -10000 0 -10000 0 0
COPA 0.029 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.037 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.02 0.005 -10000 0 -10000 0 0
GGA3 0.029 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.028 0.03 -10000 0 -0.23 6 6
AP2A1 0.03 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.017 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.028 0.038 -10000 0 -0.3 6 6
Arfaptin 2/Rac/GDP 0.036 0.013 -10000 0 -10000 0 0
CYTH2 0.031 0.005 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.039 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -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 0.023 0.027 -10000 0 -10000 0 0
PLD2 0.011 0.016 -10000 0 -0.34 1 1
ARF-GAP1/v-SNARE 0.011 0.022 -10000 0 -0.48 1 1
PIP5K1A 0.011 0.017 -10000 0 -0.35 1 1
ARF1/GTP/Membrin/GBF1/p115 0.027 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.016 -10000 0 -0.34 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.011 0.022 -10000 0 -0.48 1 1
GOSR2 0.018 0.009 -10000 0 -10000 0 0
USO1 0.016 0.026 -10000 0 -0.3 3 3
GBF1 0.01 0.05 -10000 0 -0.3 12 12
ARF1/GTP/Arfaptin 2 0.041 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.05 0.056 -10000 0 -0.36 8 8
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 0.066 0.029 -10000 0 -10000 0 0
CLOCK 0.032 0.03 -10000 0 -0.63 1 1
TIMELESS/CRY2 0.056 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 0.037 0.023 -10000 0 -0.43 1 1
ATR 0.028 0.007 -10000 0 -10000 0 0
NR1D1 0.035 0.063 -10000 0 -1.2 1 1
ARNTL 0.033 0.005 -10000 0 -10000 0 0
TIMELESS 0.038 0.023 -10000 0 -10000 0 0
NPAS2 0.023 0.073 -10000 0 -0.49 9 9
CRY2 0.03 0.003 -10000 0 -10000 0 0
mol:CO -0.014 0.007 0.14 1 -10000 0 1
CHEK1 0.03 0.003 -10000 0 -10000 0 0
mol:HEME 0.014 0.007 -10000 0 -0.14 1 1
PER1 0.029 0.005 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.069 0.052 -10000 0 -0.4 4 4
BMAL1/CLOCK 0.05 0.06 -10000 0 -0.8 1 1
S phase of mitotic cell cycle 0.066 0.029 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.067 0.03 -10000 0 -10000 0 0
mol:NADPH 0.014 0.007 -10000 0 -0.14 1 1
PER1/TIMELESS 0.055 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.028 -10000 0 -0.59 1 1
TRAIL signaling 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
TNFSF10 0.027 0.031 -10000 0 -0.64 1 1
positive regulation of NF-kappaB transcription factor activity 0.037 0.028 -10000 0 -0.47 1 1
MAP2K4 0.037 0.031 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.029 -10000 0 -0.59 1 1
TNFRSF10A 0.026 0.018 -10000 0 -0.33 1 1
SMPD1 0.019 0.015 -10000 0 -0.23 1 1
IKBKG 0.03 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.03 -10000 0 -0.47 1 1
TRAIL/TRAILR3 0.038 0.028 -10000 0 -0.47 1 1
TRAIL/TRAILR1 0.038 0.028 -10000 0 -0.47 1 1
TRAIL/TRAILR4 0.038 0.028 -10000 0 -0.47 1 1
TRAIL/TRAILR1/DAP3/GTP 0.047 0.029 -10000 0 -0.37 1 1
IKK complex 0.039 0.028 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.005 -10000 0 -10000 0 0
MAPK3 0.02 0.023 -10000 0 -0.47 1 1
MAP3K1 0.038 0.032 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.027 0.009 -10000 0 -10000 0 0
TRADD 0.029 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.026 0.018 -10000 0 -0.33 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.036 0.023 -10000 0 -10000 0 0
CFLAR 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.021 0.023 -10000 0 -0.47 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.072 0.04 -10000 0 -10000 0 0
mol:ceramide 0.019 0.015 -10000 0 -0.23 1 1
FADD 0.03 0.004 -10000 0 -10000 0 0
MAPK8 0.038 0.035 0.29 1 -10000 0 1
TRAF2 0.029 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.027 0.009 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.052 0.03 -10000 0 -0.41 1 1
DAP3 0.029 0.007 -10000 0 -10000 0 0
CASP10 0.017 0.02 -10000 0 -0.4 1 1
JNK cascade 0.037 0.028 -10000 0 -0.47 1 1
TRAIL (trimer) 0.027 0.031 -10000 0 -0.64 1 1
TNFRSF10C 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.058 0.033 -10000 0 -0.35 1 1
TRAIL/TRAILR2/FADD 0.051 0.031 -10000 0 -0.41 1 1
cell death 0.019 0.015 -10000 0 -0.23 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.036 0.024 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.026 0.029 -10000 0 -0.58 1 1
CASP8 0.004 0.081 -10000 0 -0.58 9 9
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.072 0.041 -10000 0 -0.35 1 1
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 0.029 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -10000 0 -9999 0 0
MDM2/SUMO1 0.05 0.029 -10000 0 -9999 0 0
HDAC4 0.028 0.007 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -10000 0 -9999 0 0
SUMO1 0.029 0.007 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.016 0.023 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.022 0.008 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.029 0.006 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.029 0.005 -10000 0 -9999 0 0
SUMO1/HDAC4 0.052 0.028 -10000 0 -9999 0 0
SUMO1/HDAC1 0.051 0.028 -10000 0 -9999 0 0
RANGAP1 0.03 0.004 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.07 0.023 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.022 0.008 -10000 0 -9999 0 0
Ran/GTP 0.037 0.029 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.029 0.005 -10000 0 -9999 0 0
UBE2I 0.029 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.039 0.03 0.25 2 -9999 0 2
NPC 0.017 0.003 -10000 0 -9999 0 0
PIAS2 0.029 0.005 -10000 0 -9999 0 0
PIAS1 0.03 0.003 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.047 0.018 -10000 0 -10000 0 0
MAPK9 0.008 0.005 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.035 0.18 1 -0.43 3 4
GNB1/GNG2 0.036 0.013 -10000 0 -10000 0 0
GNB1 0.029 0.006 -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 0.01 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.019 0.003 -10000 0 -10000 0 0
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 0 -10000 0 -10000 0 0
GNAL 0.029 0.005 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
CRH 0.016 0.047 -10000 0 -0.59 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.011 0.002 -10000 0 -10000 0 0
MAPK11 0.01 0.012 -10000 0 -0.25 1 1
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 0.039 0.043 -9999 0 -0.43 4 4
FBXW11 0.023 0.013 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -9999 0 -10000 0 0
CHUK 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.062 0.048 -9999 0 -10000 0 0
NFKB1 0.028 0.03 -9999 0 -0.64 1 1
MAP3K14 0.025 0.055 -9999 0 -0.59 4 4
NF kappa B1 p50/RelB 0.043 0.024 -9999 0 -0.47 1 1
RELB 0.03 0.004 -9999 0 -10000 0 0
NFKB2 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.039 0.009 -9999 0 -10000 0 0
regulation of B cell activation 0.038 0.009 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 498 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MW.A4EC TCGA.MM.A564 TCGA.EU.5907 TCGA.EU.5906
109_MAP3K5 0.1 0.054 -0.3 0.054
47_PPARGC1A 0.03 0.03 0 0.03
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0 0.03
105_BMP7 0.018 -0.64 -0.64 -0.64
105_BMP2 0.03 0.03 0.03 0.03
131_RELN/VLDLR -0.37 -0.37 -0.33 0.078
30_TGFB1/TGF beta receptor Type II 0.03 0.034 0.03 0.03
84_STAT5B -0.052 -0.14 -0.075 -0.028
84_STAT5A -0.052 -0.14 -0.075 -0.028
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/KIRC-TP/6044644/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIRC-TP/6154568/GDAC_Gistic2Report_6156758/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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