PARADIGM pathway analysis of mRNASeq expression and copy number data
Colorectal Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
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/C11N7ZTX
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 37 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
Signaling mediated by p38-alpha and p38-beta 86
IL4-mediated signaling events 80
IL23-mediated signaling events 77
Noncanonical Wnt signaling pathway 60
Endothelins 53
FOXA2 and FOXA3 transcription factor networks 50
Fc-epsilon receptor I signaling in mast cells 49
Wnt signaling 49
Ephrin B reverse signaling 48
TCR signaling in naïve CD8+ T cells 48
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 595 . 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 ( 595 ).

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
Signaling mediated by p38-alpha and p38-beta 0.1445 86 3801 44 -0.12 0.026 1000 -1000 -0.023 -1000
IL4-mediated signaling events 0.1345 80 7284 91 -0.57 0.48 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.1294 77 4644 60 -0.41 0.025 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 0.1008 60 1574 26 -0.072 0.025 1000 -1000 -0.035 -1000
Endothelins 0.0891 53 5127 96 -0.12 0.028 1000 -1000 -0.05 -1000
FOXA2 and FOXA3 transcription factor networks 0.0840 50 2322 46 -0.27 0.026 1000 -1000 -0.096 -1000
Fc-epsilon receptor I signaling in mast cells 0.0824 49 4815 97 -0.13 0.047 1000 -1000 -0.056 -1000
Wnt signaling 0.0824 49 345 7 -0.071 0.018 1000 -1000 -0.006 -1000
Ephrin B reverse signaling 0.0807 48 2312 48 -0.1 0.036 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 0.0807 48 4473 93 -0.088 0.038 1000 -1000 -0.044 -1000
Signaling events mediated by the Hedgehog family 0.0756 45 2366 52 -0.057 0.038 1000 -1000 -0.026 -1000
Reelin signaling pathway 0.0739 44 2486 56 -0.066 0.064 1000 -1000 -0.037 -1000
BCR signaling pathway 0.0739 44 4413 99 -0.13 0.029 1000 -1000 -0.061 -1000
IL12-mediated signaling events 0.0723 43 3813 87 -0.2 0.038 1000 -1000 -0.064 -1000
Osteopontin-mediated events 0.0723 43 1642 38 -0.085 0.029 1000 -1000 -0.04 -1000
TCGA08_p53 0.0723 43 307 7 -0.032 0.025 1000 -1000 -0.013 -1000
Glypican 1 network 0.0689 41 1998 48 -0.079 0.044 1000 -1000 -0.032 -1000
Syndecan-1-mediated signaling events 0.0655 39 1353 34 -0.046 0.026 1000 -1000 -0.038 -1000
amb2 Integrin signaling 0.0655 39 3236 82 -0.078 0.033 1000 -1000 -0.038 -1000
Syndecan-4-mediated signaling events 0.0655 39 2641 67 -0.064 0.037 1000 -1000 -0.031 -1000
Thromboxane A2 receptor signaling 0.0639 38 4022 105 -0.082 0.036 1000 -1000 -0.035 -1000
HIF-1-alpha transcription factor network 0.0639 38 2902 76 -0.15 0.028 1000 -1000 -0.085 -1000
EGFR-dependent Endothelin signaling events 0.0639 38 799 21 -0.049 0.038 1000 -1000 -0.037 -1000
Ephrin A reverse signaling 0.0622 37 263 7 -0.039 0.008 1000 -1000 -0.022 -1000
LPA receptor mediated events 0.0622 37 3809 102 -0.072 0.03 1000 -1000 -0.067 -1000
TCGA08_retinoblastoma 0.0622 37 296 8 -0.008 0.028 1000 -1000 -0.004 -1000
IL1-mediated signaling events 0.0605 36 2272 62 -0.046 0.089 1000 -1000 -0.047 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0571 34 1164 34 -0.038 0.046 1000 -1000 -0.022 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0555 33 2290 68 -0.16 0.062 1000 -1000 -0.06 -1000
PDGFR-beta signaling pathway 0.0555 33 3262 97 -0.085 0.075 1000 -1000 -0.054 -1000
JNK signaling in the CD4+ TCR pathway 0.0538 32 556 17 -0.045 0.026 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 0.0538 32 4100 125 -0.064 0.064 1000 -1000 -0.062 -1000
Glucocorticoid receptor regulatory network 0.0538 32 3701 114 -0.22 0.12 1000 -1000 -0.044 -1000
EPHB forward signaling 0.0538 32 2747 85 -0.047 0.077 1000 -1000 -0.061 -1000
Calcium signaling in the CD4+ TCR pathway 0.0521 31 971 31 -0.073 0.026 1000 -1000 -0.04 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0521 31 2438 78 -0.14 0.035 1000 -1000 -0.058 -1000
Signaling events regulated by Ret tyrosine kinase 0.0504 30 2508 82 -0.05 0.033 1000 -1000 -0.048 -1000
BMP receptor signaling 0.0471 28 2306 81 -0.051 0.041 1000 -1000 -0.038 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0471 28 2502 88 -0.055 0.037 1000 -1000 -0.062 -1000
Effects of Botulinum toxin 0.0454 27 708 26 -0.069 0.034 1000 -1000 -0.015 -1000
IGF1 pathway 0.0437 26 1505 57 -0.039 0.05 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0437 26 2252 86 -0.031 0.074 1000 -1000 -0.042 -1000
Caspase cascade in apoptosis 0.0420 25 1899 74 -0.057 0.051 1000 -1000 -0.033 -1000
Syndecan-2-mediated signaling events 0.0420 25 1780 69 -0.027 0.037 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 0.0420 25 1175 47 -0.12 0.04 1000 -1000 -0.041 -1000
Retinoic acid receptors-mediated signaling 0.0420 25 1474 58 -0.04 0.046 1000 -1000 -0.029 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0420 25 3081 120 -0.079 0.072 1000 -1000 -0.043 -1000
Visual signal transduction: Rods 0.0420 25 1343 52 -0.048 0.039 1000 -1000 -0.032 -1000
Integrins in angiogenesis 0.0403 24 2027 84 -0.082 0.054 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 0.0403 24 1232 51 -0.1 0.079 1000 -1000 -0.048 -1000
Nongenotropic Androgen signaling 0.0403 24 1293 52 -0.029 0.047 1000 -1000 -0.028 -1000
Cellular roles of Anthrax toxin 0.0387 23 905 39 -0.029 0.024 1000 -1000 -0.021 -1000
Ceramide signaling pathway 0.0387 23 1808 76 -0.039 0.065 1000 -1000 -0.03 -1000
VEGFR1 specific signals 0.0387 23 1296 56 -0.003 0.079 1000 -1000 -0.046 -1000
Arf6 signaling events 0.0370 22 1386 62 -0.047 0.057 1000 -1000 -0.031 -1000
IFN-gamma pathway 0.0370 22 1553 68 -0.047 0.036 1000 -1000 -0.051 -1000
Class I PI3K signaling events 0.0370 22 1676 73 -0.064 0.031 1000 -1000 -0.037 -1000
ErbB2/ErbB3 signaling events 0.0353 21 1371 65 -0.049 0.038 1000 -1000 -0.048 -1000
a4b1 and a4b7 Integrin signaling 0.0353 21 105 5 0.005 0.023 1000 -1000 0.01 -1000
Presenilin action in Notch and Wnt signaling 0.0353 21 1325 61 -0.038 0.064 1000 -1000 -0.041 -1000
IL6-mediated signaling events 0.0353 21 1584 75 -0.034 0.046 1000 -1000 -0.058 -1000
Ras signaling in the CD4+ TCR pathway 0.0353 21 367 17 -0.016 0.038 1000 -1000 -0.022 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0336 20 1125 54 -0.046 0.034 1000 -1000 -0.041 -1000
Signaling events mediated by PTP1B 0.0336 20 1528 76 -0.049 0.043 1000 -1000 -0.027 -1000
S1P1 pathway 0.0319 19 706 36 -0.06 0.034 1000 -1000 -0.039 -1000
IL27-mediated signaling events 0.0319 19 988 51 -0.1 0.026 1000 -1000 -0.053 -1000
Regulation of p38-alpha and p38-beta 0.0303 18 978 54 -0.063 0.049 1000 -1000 -0.043 -1000
Glypican 2 network 0.0303 18 72 4 0.013 0.023 1000 -1000 0.009 -1000
S1P4 pathway 0.0303 18 459 25 -0.017 0.034 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 0.0286 17 678 38 -0.02 0.039 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0286 17 648 37 -0.024 0.051 1000 -1000 -0.026 -1000
FOXM1 transcription factor network 0.0286 17 901 51 -0.1 0.045 1000 -1000 -0.13 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0269 16 1379 85 -0.055 0.047 1000 -1000 -0.037 -1000
EPO signaling pathway 0.0269 16 907 55 -0.017 0.058 1000 -1000 -0.039 -1000
PDGFR-alpha signaling pathway 0.0269 16 741 44 -0.033 0.056 1000 -1000 -0.041 -1000
Coregulation of Androgen receptor activity 0.0252 15 1212 76 -0.11 0.052 1000 -1000 -0.026 -1000
Nectin adhesion pathway 0.0252 15 950 63 -0.012 0.068 1000 -1000 -0.038 -1000
LPA4-mediated signaling events 0.0235 14 173 12 -0.044 0 1000 -1000 -0.024 -1000
PLK1 signaling events 0.0235 14 1226 85 -0.007 0.055 1000 -1000 -0.037 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0235 14 767 52 -0.028 0.073 1000 -1000 -0.04 -1000
Syndecan-3-mediated signaling events 0.0235 14 517 35 -0.017 0.064 1000 -1000 -0.021 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0235 14 639 45 -0.034 0.066 1000 -1000 -0.046 -1000
IL2 signaling events mediated by STAT5 0.0235 14 311 22 -0.032 0.026 1000 -1000 -0.034 -1000
Aurora B signaling 0.0235 14 960 67 -0.15 0.061 1000 -1000 -0.028 -1000
Arf6 downstream pathway 0.0218 13 581 43 -0.029 0.039 1000 -1000 -0.019 -1000
mTOR signaling pathway 0.0218 13 704 53 -0.071 0.028 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0218 13 911 68 -0.045 0.052 1000 -1000 -0.028 -1000
IL2 signaling events mediated by PI3K 0.0218 13 766 58 -0.016 0.042 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0218 13 448 33 -0.008 0.062 1000 -1000 -0.037 -1000
S1P5 pathway 0.0202 12 206 17 -0.008 0.028 1000 -1000 -0.01 -1000
Signaling mediated by p38-gamma and p38-delta 0.0202 12 182 15 -0.021 0.023 1000 -1000 -0.032 -1000
Paxillin-dependent events mediated by a4b1 0.0202 12 437 36 -0.04 0.042 1000 -1000 -0.031 -1000
S1P3 pathway 0.0202 12 504 42 -0.018 0.041 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 0.0202 12 413 34 -0.02 0.076 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 0.0202 12 36 3 -0.016 0.016 1000 -1000 -0.013 -1000
ErbB4 signaling events 0.0185 11 794 69 -0.077 0.049 1000 -1000 -0.034 -1000
ceramide signaling pathway 0.0185 11 557 49 -0.002 0.035 1000 -1000 -0.036 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0185 11 300 27 -0.026 0.04 1000 -1000 -0.036 -1000
Regulation of Telomerase 0.0185 11 1156 102 -0.057 0.049 1000 -1000 -0.038 -1000
Insulin Pathway 0.0185 11 850 74 -0.048 0.079 1000 -1000 -0.05 -1000
Regulation of Androgen receptor activity 0.0185 11 834 70 -0.14 0.057 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0168 10 292 28 -0.024 0.039 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0168 10 678 65 -0.018 0.046 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0168 10 340 32 -0.13 0.04 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0168 10 877 83 -0.049 0.055 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0168 10 791 74 -0.052 0.06 1000 -1000 -0.058 -1000
Arf6 trafficking events 0.0168 10 716 71 -0.041 0.045 1000 -1000 -0.03 -1000
Regulation of nuclear SMAD2/3 signaling 0.0151 9 1258 136 -0.055 0.05 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class III 0.0151 9 380 40 -0.044 0.047 1000 -1000 -0.032 -1000
FoxO family signaling 0.0134 8 545 64 -0.063 0.062 1000 -1000 -0.056 -1000
TCGA08_rtk_signaling 0.0134 8 231 26 -0.024 0.057 1000 -1000 -0.009 -1000
E-cadherin signaling in the nascent adherens junction 0.0134 8 660 76 -0.013 0.078 1000 -1000 -0.055 -1000
BARD1 signaling events 0.0118 7 450 57 -0.027 0.064 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 0.0118 7 331 43 -0.083 0.085 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class I 0.0118 7 793 104 -0.05 0.061 1000 -1000 -0.032 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0118 7 971 125 -0.022 0.093 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class II 0.0101 6 485 75 -0.022 0.068 1000 -1000 -0.032 -1000
Canonical NF-kappaB pathway 0.0084 5 223 39 -0.009 0.054 1000 -1000 -0.03 -1000
p38 MAPK signaling pathway 0.0084 5 235 44 -0.006 0.057 1000 -1000 -0.019 -1000
Arf1 pathway 0.0084 5 319 54 -0.004 0.039 1000 -1000 -0.016 -1000
Aurora C signaling 0.0067 4 31 7 0 0.034 1000 -1000 -0.015 -1000
PLK2 and PLK4 events 0.0050 3 9 3 -0.015 -1000 1000 -1000 -0.025 -1000
Aurora A signaling 0.0050 3 217 60 -0.013 0.07 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 0.0050 3 106 31 -0.01 0.047 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 0.0050 3 143 43 -0.038 0.078 1000 -1000 -0.03 -1000
TRAIL signaling pathway 0.0034 2 115 48 -0.014 0.055 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 0.0034 2 59 20 -0.015 0.029 1000 -1000 -0.014 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0017 1 26 23 0.012 0.036 1000 -1000 -0.022 -1000
Circadian rhythm pathway 0.0017 1 30 22 -0.006 0.057 1000 -1000 -0.034 -1000
E-cadherin signaling events 0.0017 1 5 5 0.025 0.05 1000 -1000 0.006 -1000
Alternative NF-kappaB pathway 0.0017 1 21 13 0 0.068 1000 -1000 0 -1000
Total NA 2935 175886 7203 -7.8 -990 131000 -131000 -4.8 -131000
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.096 0.31 -10000 0 -0.89 63 63
MKNK1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.026 0.14 -10000 0 -0.31 105 105
ATF2/c-Jun -0.035 0.13 -10000 0 -0.41 28 28
MAPK11 -0.025 0.14 -10000 0 -0.34 96 96
MITF -0.059 0.17 -10000 0 -0.38 124 124
MAPKAPK5 -0.048 0.16 -10000 0 -0.37 109 109
KRT8 -0.049 0.16 -10000 0 -0.38 110 110
MAPKAPK3 0.026 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.045 0.21 -10000 0 -0.46 110 110
CEBPB -0.027 0.12 0.2 2 -0.37 64 66
SLC9A1 -0.049 0.16 -10000 0 -0.39 105 105
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.047 0.16 -10000 0 -0.37 109 109
p38alpha-beta/MNK1 -0.021 0.18 -10000 0 -0.38 104 104
JUN -0.037 0.12 -10000 0 -0.4 28 28
PPARGC1A -0.072 0.18 -10000 0 -0.38 141 141
USF1 -0.044 0.16 -10000 0 -0.37 104 104
RAB5/GDP/GDI1 -0.03 0.13 -10000 0 -0.28 112 112
NOS2 -0.12 0.35 -10000 0 -0.84 100 100
DDIT3 -0.048 0.16 -10000 0 -0.37 109 109
RAB5A 0.022 0.043 -10000 0 -0.44 5 5
HSPB1 -0.041 0.14 0.27 17 -0.31 109 126
p38alpha-beta/HBP1 -0.021 0.17 -10000 0 -0.38 101 101
CREB1 -0.053 0.17 -10000 0 -0.4 106 106
RAB5/GDP 0.016 0.031 -10000 0 -0.32 5 5
EIF4E -0.054 0.14 -10000 0 -0.36 97 97
RPS6KA4 -0.048 0.16 -10000 0 -0.37 109 109
PLA2G4A -0.09 0.17 0.22 1 -0.36 140 141
GDI1 -0.047 0.16 -10000 0 -0.37 108 108
TP53 -0.083 0.2 -10000 0 -0.49 101 101
RPS6KA5 -0.049 0.16 -10000 0 -0.39 105 105
ESR1 -0.061 0.18 -10000 0 -0.38 125 125
HBP1 0.025 0.005 -10000 0 -10000 0 0
MEF2C -0.051 0.16 -10000 0 -0.38 112 112
MEF2A -0.049 0.16 -10000 0 -0.38 106 106
EIF4EBP1 -0.054 0.17 -10000 0 -0.41 104 104
KRT19 -0.048 0.16 -10000 0 -0.38 108 108
ELK4 -0.046 0.16 -10000 0 -0.38 105 105
ATF6 -0.044 0.16 -10000 0 -0.37 104 104
ATF1 -0.052 0.17 -10000 0 -0.4 106 106
p38alpha-beta/MAPKAPK2 -0.019 0.17 -10000 0 -0.38 100 100
p38alpha-beta/MAPKAPK3 -0.021 0.18 -10000 0 -0.38 104 104
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.36 0.59 -10000 0 -1.3 129 129
STAT6 (cleaved dimer) -0.44 0.59 -10000 0 -1.3 154 154
IGHG1 -0.12 0.2 -10000 0 -0.39 52 52
IGHG3 -0.41 0.54 -10000 0 -1.2 150 150
AKT1 -0.2 0.32 -10000 0 -0.81 76 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.28 -10000 0 -0.77 61 61
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 -10000 0 -0.83 71 71
THY1 -0.43 0.57 -10000 0 -1.3 139 139
MYB 0.019 0.055 -10000 0 -0.44 8 8
HMGA1 0.023 0.039 -10000 0 -0.44 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.25 0.37 -10000 0 -0.8 119 119
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.33 -10000 0 -0.81 78 78
SP1 0.024 0.032 -10000 0 -0.28 2 2
INPP5D 0.005 0.097 -10000 0 -0.44 26 26
SOCS5 0.024 0.034 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.43 0.6 -10000 0 -1.3 153 153
SOCS1 -0.28 0.36 -10000 0 -0.76 153 153
SOCS3 -0.22 0.32 -10000 0 -0.84 68 68
FCER2 -0.4 0.56 -10000 0 -1.2 159 159
PARP14 0.023 0.015 -10000 0 -10000 0 0
CCL17 -0.46 0.61 -10000 0 -1.3 151 151
GRB2 0.025 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.26 -10000 0 -0.62 74 74
T cell proliferation -0.42 0.59 -10000 0 -1.3 149 149
IL4R/JAK1 -0.43 0.57 -10000 0 -1.3 143 143
EGR2 -0.46 0.6 -10000 0 -1.3 149 149
JAK2 -0.028 0.088 -10000 0 -0.46 15 15
JAK3 0.018 0.055 -10000 0 -0.44 7 7
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
JAK1 0 0.034 -10000 0 -0.45 1 1
COL1A2 -0.14 0.32 -10000 0 -1.4 25 25
CCL26 -0.46 0.61 -10000 0 -1.3 156 156
IL4R -0.45 0.61 -10000 0 -1.4 143 143
PTPN6 0.032 0.017 -10000 0 -10000 0 0
IL13RA2 -0.48 0.64 -10000 0 -1.4 162 162
IL13RA1 -0.019 0.064 -10000 0 -0.45 4 4
IRF4 -0.21 0.49 -10000 0 -1.4 78 78
ARG1 -0.059 0.19 -10000 0 -0.66 21 21
CBL -0.24 0.34 -10000 0 -0.76 121 121
GTF3A 0.016 0.03 -10000 0 -0.15 3 3
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
IL13RA1/JAK2 -0.025 0.092 -10000 0 -0.34 17 17
IRF4/BCL6 -0.19 0.45 -10000 0 -1.3 77 77
CD40LG -0.015 0.12 -10000 0 -0.41 47 47
MAPK14 -0.24 0.35 -10000 0 -0.78 111 111
mitosis -0.18 0.3 -10000 0 -0.75 76 76
STAT6 -0.51 0.75 -10000 0 -1.6 148 148
SPI1 0.017 0.076 -10000 0 -0.44 15 15
RPS6KB1 -0.18 0.29 -10000 0 -0.74 73 73
STAT6 (dimer) -0.52 0.76 -10000 0 -1.6 148 148
STAT6 (dimer)/PARP14 -0.47 0.64 -10000 0 -1.4 147 147
mast cell activation 0.009 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.23 0.34 -10000 0 -0.8 95 95
FRAP1 -0.2 0.32 -10000 0 -0.81 76 76
LTA -0.45 0.6 -10000 0 -1.3 146 146
FES 0.019 0.055 -10000 0 -0.44 8 8
T-helper 1 cell differentiation 0.48 0.67 1.4 148 -10000 0 148
CCL11 -0.46 0.62 -10000 0 -1.4 157 157
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.32 -10000 0 -0.8 79 79
IL2RG 0.016 0.065 -10000 0 -0.43 11 11
IL10 -0.46 0.61 -10000 0 -1.3 152 152
IRS1 0.019 0.058 -10000 0 -0.44 9 9
IRS2 0.015 0.048 -10000 0 -0.44 6 6
IL4 -0.098 0.21 -10000 0 -1 17 17
IL5 -0.43 0.57 -10000 0 -1.3 143 143
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.32 0.44 -10000 0 -0.93 144 144
COL1A1 -0.18 0.38 -10000 0 -1.4 40 40
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.6 -10000 0 -1.3 138 138
IL2R gamma/JAK3 0.024 0.066 -10000 0 -0.32 18 18
TFF3 -0.46 0.61 -10000 0 -1.3 157 157
ALOX15 -0.5 0.64 -10000 0 -1.4 173 173
MYBL1 0.016 0.059 -10000 0 -0.44 9 9
T-helper 2 cell differentiation -0.34 0.47 -10000 0 -0.98 154 154
SHC1 0.025 0.004 -10000 0 -10000 0 0
CEBPB 0.015 0.024 -10000 0 -0.44 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.32 -10000 0 -0.82 65 65
mol:PI-3-4-5-P3 -0.2 0.32 -10000 0 -0.81 76 76
PI3K -0.21 0.35 -10000 0 -0.88 76 76
DOK2 0.011 0.065 -10000 0 -0.44 11 11
ETS1 0.021 0.041 -10000 0 -0.41 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.24 -10000 0 -0.57 76 76
ITGB3 -0.43 0.58 -10000 0 -1.3 144 144
PIGR -0.57 0.7 -10000 0 -1.4 212 212
IGHE 0.071 0.08 0.18 158 -0.25 1 159
MAPKKK cascade -0.15 0.23 -10000 0 -0.56 76 76
BCL6 0.027 0.008 -10000 0 -10000 0 0
OPRM1 -0.43 0.57 -10000 0 -1.3 143 143
RETNLB -0.55 0.68 -10000 0 -1.4 199 199
SELP -0.48 0.65 -10000 0 -1.4 156 156
AICDA -0.41 0.54 -10000 0 -1.2 141 141
IL23-mediated signaling events

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
CCL2 -0.32 0.53 -10000 0 -1.2 117 117
IL23A -0.33 0.54 -10000 0 -1.3 114 114
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.55 -10000 0 -1.2 126 126
positive regulation of T cell mediated cytotoxicity -0.36 0.62 -10000 0 -1.4 131 131
ITGA3 -0.31 0.51 -10000 0 -1.2 113 113
IL17F -0.21 0.33 -10000 0 -0.73 124 124
IL12B -0.005 0.051 -10000 0 -10000 0 0
STAT1 (dimer) -0.35 0.59 -10000 0 -1.3 132 132
CD4 -0.31 0.52 -10000 0 -1.2 111 111
IL23 -0.32 0.52 -10000 0 -1.2 113 113
IL23R -0.097 0.33 -10000 0 -1.3 39 39
IL1B -0.35 0.56 -10000 0 -1.3 115 115
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.4 0.6 -10000 0 -1.3 169 169
TYK2 -0.004 0.044 -10000 0 -0.47 1 1
STAT4 0.002 0.11 -10000 0 -0.44 31 31
STAT3 0.025 0.004 -10000 0 -10000 0 0
IL18RAP -0.002 0.11 -10000 0 -0.44 34 34
IL12RB1 -0.026 0.11 -10000 0 -0.46 32 32
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
IL12Rbeta1/TYK2 -0.018 0.096 -10000 0 -0.36 32 32
IL23R/JAK2 -0.1 0.32 -10000 0 -1.2 38 38
positive regulation of chronic inflammatory response -0.36 0.62 -10000 0 -1.4 131 131
natural killer cell activation 0.006 0.017 0.08 25 -10000 0 25
JAK2 -0.016 0.087 -10000 0 -0.47 15 15
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
NFKB1 0.018 0.025 -10000 0 -0.45 1 1
RELA 0.019 0.016 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.3 0.49 -10000 0 -1.1 113 113
ALOX12B -0.35 0.55 -10000 0 -1.2 139 139
CXCL1 -0.32 0.53 -10000 0 -1.2 114 114
T cell proliferation -0.36 0.62 -10000 0 -1.4 131 131
NFKBIA 0.018 0.016 -10000 0 -10000 0 0
IL17A -0.18 0.28 -10000 0 -0.59 129 129
PI3K -0.33 0.56 -10000 0 -1.2 125 125
IFNG -0.01 0.049 0.16 18 -0.12 47 65
STAT3 (dimer) -0.3 0.53 -10000 0 -1.2 124 124
IL18R1 0.008 0.087 -10000 0 -0.44 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.33 -10000 0 -0.76 98 98
IL18/IL18R 0.02 0.11 -10000 0 -0.3 52 52
macrophage activation -0.015 0.021 -10000 0 -0.045 105 105
TNF -0.34 0.55 -10000 0 -1.3 115 115
STAT3/STAT4 -0.33 0.57 -10000 0 -1.2 128 128
STAT4 (dimer) -0.35 0.6 -10000 0 -1.3 133 133
IL18 0.019 0.046 -10000 0 -0.44 5 5
IL19 -0.3 0.5 -10000 0 -1.2 107 107
STAT5A (dimer) -0.34 0.59 -10000 0 -1.3 126 126
STAT1 0.025 0.028 -10000 0 -0.44 2 2
SOCS3 0.023 0.045 -10000 0 -0.44 5 5
CXCL9 -0.36 0.57 -10000 0 -1.3 133 133
MPO -0.33 0.54 -10000 0 -1.2 125 125
positive regulation of humoral immune response -0.36 0.62 -10000 0 -1.4 131 131
IL23/IL23R/JAK2/TYK2 -0.41 0.74 -10000 0 -1.6 127 127
IL6 -0.34 0.57 -10000 0 -1.3 129 129
STAT5A 0.025 0.004 -10000 0 -10000 0 0
IL2 0.007 0.026 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.017 0.08 25 -10000 0 25
CD3E -0.32 0.52 -10000 0 -1.2 112 112
keratinocyte proliferation -0.36 0.62 -10000 0 -1.4 131 131
NOS2 -0.37 0.57 -10000 0 -1.2 147 147
Noncanonical Wnt signaling pathway

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
NFATC2 -0.015 0.11 -10000 0 -0.44 37 37
GNB1/GNG2 -0.06 0.16 -10000 0 -0.29 150 150
mol:DAG -0.061 0.13 -10000 0 -0.32 83 83
PLCG1 -0.062 0.14 -10000 0 -0.33 83 83
YES1 -0.072 0.15 0.19 1 -0.3 143 144
FZD3 0.013 0.055 -10000 0 -0.44 8 8
FZD6 0.018 0.044 -10000 0 -0.44 5 5
G protein -0.012 0.18 0.26 24 -0.38 57 81
MAP3K7 -0.064 0.11 0.15 1 -0.34 53 54
mol:Ca2+ -0.059 0.13 -10000 0 -0.31 83 83
mol:IP3 -0.061 0.13 -10000 0 -0.32 83 83
NLK -0.007 0.099 -10000 0 -0.79 9 9
GNB1 0.025 0.005 -10000 0 -10000 0 0
CAMK2A -0.064 0.12 0.16 1 -0.35 59 60
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.071 0.16 -10000 0 -0.32 148 148
CSNK1A1 0.024 0.028 -10000 0 -0.44 2 2
GNAS -0.054 0.15 0.19 24 -0.31 117 141
GO:0007205 -0.063 0.13 -10000 0 -0.38 53 53
WNT6 -0.001 0.13 -10000 0 -0.44 42 42
WNT4 -0.007 0.12 -10000 0 -0.44 43 43
NFAT1/CK1 alpha -0.068 0.16 -10000 0 -0.43 71 71
GNG2 0.021 0.044 -10000 0 -0.44 5 5
WNT5A 0.016 0.07 -10000 0 -0.44 13 13
WNT11 -0.034 0.17 -10000 0 -0.44 86 86
CDC42 -0.071 0.15 0.18 1 -0.34 89 90
Endothelins

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
AKT1 -0.027 0.18 0.25 53 -0.38 82 135
PTK2B 0.018 0.029 -10000 0 -0.45 2 2
mol:Ca2+ -0.027 0.24 0.37 1 -0.87 33 34
EDN1 0.007 0.13 0.22 52 -0.34 45 97
EDN3 -0.029 0.14 -10000 0 -0.44 56 56
EDN2 -0.007 0.13 -10000 0 -0.44 45 45
HRAS/GDP -0.027 0.18 0.33 9 -0.45 56 65
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.019 0.16 0.23 7 -0.41 51 58
ADCY4 -0.031 0.15 0.23 7 -0.43 47 54
ADCY5 -0.05 0.18 0.21 19 -0.41 73 92
ADCY6 -0.027 0.15 0.24 5 -0.43 45 50
ADCY7 -0.028 0.15 0.22 6 -0.43 46 52
ADCY1 -0.032 0.15 0.22 9 -0.42 48 57
ADCY2 -0.042 0.17 0.22 9 -0.43 67 76
ADCY3 -0.028 0.15 0.22 8 -0.42 48 56
ADCY8 -0.029 0.14 0.21 4 -0.43 40 44
ADCY9 -0.028 0.15 0.22 7 -0.41 49 56
arachidonic acid secretion -0.05 0.19 0.37 5 -0.48 63 68
ETB receptor/Endothelin-1/Gq/GTP -0.01 0.1 -10000 0 -0.34 37 37
GNAO1 0.016 0.087 -10000 0 -0.44 19 19
HRAS 0.025 0.02 -10000 0 -0.44 1 1
ETA receptor/Endothelin-1/G12/GTP 0.028 0.18 0.36 49 -0.41 53 102
ETA receptor/Endothelin-1/Gs/GTP 0.011 0.18 0.33 36 -0.36 70 106
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.035 0.21 0.25 54 -0.62 43 97
EDNRB 0.007 0.075 -10000 0 -0.43 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.044 0.2 0.26 38 -0.53 60 98
CYSLTR1 -0.045 0.22 0.25 54 -0.54 73 127
SLC9A1 -0.008 0.11 0.18 48 -0.28 54 102
mol:GDP -0.038 0.19 0.31 11 -0.47 58 69
SLC9A3 -0.12 0.31 -10000 0 -0.61 131 131
RAF1 -0.038 0.17 0.3 8 -0.42 62 70
JUN -0.015 0.2 -10000 0 -0.71 26 26
JAK2 -0.032 0.18 0.25 53 -0.38 90 143
mol:IP3 -0.018 0.15 0.23 10 -0.4 48 58
ETA receptor/Endothelin-1 0.018 0.23 0.41 53 -0.43 83 136
PLCB1 -0.004 0.1 -10000 0 -0.44 31 31
PLCB2 0.021 0.041 -10000 0 -0.45 4 4
ETA receptor/Endothelin-3 -0.023 0.13 0.22 1 -0.33 78 79
FOS -0.052 0.22 0.41 3 -0.8 34 37
Gai/GDP -0.009 0.2 -10000 0 -0.83 27 27
CRK 0.022 0.011 -10000 0 -10000 0 0
mol:Ca ++ -0.031 0.2 0.27 19 -0.52 62 81
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
PRKCB1 -0.013 0.14 0.22 10 -0.39 47 57
GNAQ 0.02 0.045 -10000 0 -0.45 5 5
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
GNAL 0.015 0.063 -10000 0 -0.44 10 10
Gs family/GDP -0.036 0.17 0.32 6 -0.43 60 66
ETA receptor/Endothelin-1/Gq/GTP -0.01 0.16 0.19 42 -0.42 45 87
MAPK14 -0.018 0.11 0.24 2 -0.37 34 36
TRPC6 -0.032 0.26 -10000 0 -0.96 32 32
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.016 0.064 -10000 0 -0.44 11 11
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.017 0.12 -10000 0 -0.36 41 41
ETB receptor/Endothelin-2 0.004 0.099 -10000 0 -0.33 44 44
ETB receptor/Endothelin-3 -0.021 0.11 -10000 0 -0.32 66 66
ETB receptor/Endothelin-1 0.012 0.11 0.23 4 -0.31 43 47
MAPK3 -0.046 0.2 0.44 3 -0.63 41 44
MAPK1 -0.053 0.21 0.44 3 -0.64 45 48
Rac1/GDP -0.031 0.17 0.29 7 -0.44 54 61
cAMP biosynthetic process -0.04 0.17 0.27 8 -0.46 53 61
MAPK8 -0.018 0.22 0.39 1 -0.66 44 45
SRC 0.015 0.023 -10000 0 -0.45 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.1 0.16 8 -0.37 30 38
p130Cas/CRK/Src/PYK2 -0.026 0.21 0.32 19 -0.54 52 71
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.031 0.17 0.31 6 -0.44 54 60
COL1A2 -0.027 0.23 0.29 43 -0.65 49 92
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.003 0.14 0.22 6 -0.32 76 82
mol:DAG -0.018 0.15 0.23 10 -0.4 48 58
MAP2K2 -0.043 0.18 0.38 5 -0.48 51 56
MAP2K1 -0.044 0.18 0.34 5 -0.46 60 65
EDNRA 0.005 0.14 0.21 53 -0.38 42 95
positive regulation of muscle contraction -0.011 0.16 0.22 86 -0.41 50 136
Gq family/GDP -0.024 0.17 0.26 1 -0.46 51 52
HRAS/GTP -0.034 0.17 0.29 11 -0.42 57 68
PRKCH -0.016 0.15 0.21 7 -0.4 49 56
RAC1 0.023 0.008 -10000 0 -10000 0 0
PRKCA -0.012 0.15 0.22 12 -0.39 45 57
PRKCB -0.026 0.17 0.22 8 -0.42 61 69
PRKCE -0.012 0.14 0.22 10 -0.39 46 56
PRKCD -0.013 0.15 0.22 10 -0.4 45 55
PRKCG -0.042 0.16 0.24 7 -0.39 62 69
regulation of vascular smooth muscle contraction -0.063 0.25 0.45 3 -0.93 34 37
PRKCQ -0.03 0.16 0.23 6 -0.42 58 64
PLA2G4A -0.055 0.2 0.38 5 -0.52 63 68
GNA14 0.012 0.076 -10000 0 -0.45 15 15
GNA15 0.014 0.073 -10000 0 -0.45 14 14
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.45 3 3
Rac1/GTP 0.027 0.18 0.36 48 -0.35 78 126
MMP1 -0.12 0.3 0.27 9 -0.82 85 94
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.17 0.33 -10000 0 -0.8 83 83
PCK1 -0.16 0.42 -10000 0 -1.3 63 63
HNF4A -0.16 0.4 0.5 7 -0.99 76 83
KCNJ11 -0.15 0.34 -10000 0 -0.89 54 54
AKT1 -0.11 0.2 -10000 0 -0.48 65 65
response to starvation -0.014 0.05 -10000 0 -0.23 24 24
DLK1 -0.15 0.33 -10000 0 -0.87 54 54
NKX2-1 -0.09 0.31 -10000 0 -1.2 27 27
ACADM -0.18 0.34 -10000 0 -0.82 85 85
TAT -0.095 0.2 -10000 0 -0.75 11 11
CEBPB 0.012 0.026 -10000 0 -0.44 1 1
CEBPA 0.009 0.079 -10000 0 -0.44 16 16
TTR -0.11 0.41 0.63 4 -1.1 63 67
PKLR -0.27 0.44 0.5 1 -0.91 158 159
APOA1 -0.19 0.44 -10000 0 -1.1 74 74
CPT1C -0.18 0.35 0.49 1 -0.86 83 84
ALAS1 -0.069 0.18 -10000 0 -0.63 5 5
TFRC -0.095 0.26 -10000 0 -1 16 16
FOXF1 0.023 0.081 0.24 23 -0.44 12 35
NF1 0.026 0.034 -10000 0 -0.44 3 3
HNF1A (dimer) 0.018 0.065 -10000 0 -0.26 23 23
CPT1A -0.17 0.33 -10000 0 -0.83 72 72
HMGCS1 -0.17 0.34 0.49 1 -0.82 78 79
NR3C1 0 0.098 -10000 0 -0.27 55 55
CPT1B -0.19 0.35 -10000 0 -0.82 94 94
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.018 0.051 -10000 0 -0.19 30 30
GCK -0.17 0.36 0.49 1 -0.85 85 86
CREB1 0.008 0.071 -10000 0 -0.2 56 56
IGFBP1 -0.17 0.38 -10000 0 -1.2 58 58
PDX1 -0.11 0.34 -10000 0 -1.3 34 34
UCP2 -0.18 0.34 -10000 0 -0.82 85 85
ALDOB -0.22 0.43 -10000 0 -0.99 106 106
AFP -0.031 0.11 -10000 0 -0.46 11 11
BDH1 -0.17 0.34 -10000 0 -0.84 76 76
HADH -0.15 0.32 -10000 0 -0.87 52 52
F2 -0.21 0.49 -10000 0 -1.2 87 87
HNF1A 0.018 0.065 -10000 0 -0.26 23 23
G6PC 0.024 0.12 -10000 0 -0.78 4 4
SLC2A2 -0.081 0.22 -10000 0 -0.73 16 16
INS -0.006 0.063 0.2 38 -0.45 1 39
FOXA1 -0.022 0.15 0.26 9 -0.44 65 74
FOXA3 0.006 0.098 -10000 0 -0.37 23 23
FOXA2 -0.18 0.36 -10000 0 -0.91 67 67
ABCC8 -0.15 0.34 -10000 0 -0.89 58 58
ALB -0.03 0.1 -10000 0 -0.5 5 5
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.02 -10000 0 -0.44 1 1
LAT2 -0.045 0.13 -10000 0 -0.36 67 67
AP1 -0.054 0.21 -10000 0 -0.58 63 63
mol:PIP3 -0.067 0.18 0.28 11 -0.45 79 90
IKBKB -0.021 0.12 0.2 51 -0.29 57 108
AKT1 -0.068 0.12 0.34 10 -0.38 31 41
IKBKG -0.034 0.11 0.2 18 -0.29 61 79
MS4A2 -0.027 0.14 -10000 0 -0.44 61 61
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.45 2 2
MAP3K1 -0.061 0.16 0.25 8 -0.45 62 70
mol:Ca2+ -0.048 0.14 0.26 11 -0.34 78 89
LYN 0.018 0.015 -10000 0 -10000 0 0
CBLB -0.046 0.14 -10000 0 -0.35 71 71
SHC1 0.025 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.047 0.03 -10000 0 -0.25 5 5
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.005 0.097 -10000 0 -0.44 26 26
PLD2 -0.062 0.12 0.34 11 -0.28 99 110
PTPN13 -0.069 0.18 0.32 1 -0.55 46 47
PTPN11 0.014 0.049 -10000 0 -0.46 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.049 0.11 0.36 5 -0.33 38 43
SYK 0.021 0.015 -10000 0 -10000 0 0
GRB2 0.025 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.039 0.2 0.19 1 -0.46 80 81
LAT -0.047 0.14 0.18 1 -0.35 74 75
PAK2 -0.063 0.18 0.27 8 -0.5 61 69
NFATC2 -0.044 0.14 -10000 0 -0.52 43 43
HRAS -0.067 0.19 0.29 5 -0.51 70 75
GAB2 0.024 0.028 -10000 0 -0.44 2 2
PLA2G1B 0.012 0.11 -10000 0 -0.86 9 9
Fc epsilon R1 -0.018 0.16 -10000 0 -0.33 112 112
Antigen/IgE/Fc epsilon R1 -0.015 0.14 0.18 1 -0.3 112 113
mol:GDP -0.073 0.21 0.23 2 -0.6 64 66
JUN 0.022 0.039 -10000 0 -0.44 4 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.45 2 2
FOS 0.013 0.08 -10000 0 -0.44 17 17
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.041 0.14 -10000 0 -0.35 76 76
CHUK -0.035 0.11 0.21 14 -0.3 60 74
KLRG1 -0.045 0.12 -10000 0 -0.26 116 116
VAV1 -0.059 0.15 -10000 0 -0.38 82 82
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.043 0.13 -10000 0 -0.34 72 72
negative regulation of mast cell degranulation -0.039 0.14 0.2 2 -0.31 79 81
BTK -0.071 0.23 -10000 0 -0.69 56 56
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.076 0.19 -10000 0 -0.38 129 129
GAB2/PI3K/SHP2 -0.079 0.1 -10000 0 -0.3 81 81
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.04 0.12 -10000 0 -0.3 80 80
RAF1 0.016 0.12 -10000 0 -0.94 9 9
Fc epsilon R1/FcgammaRIIB/SHIP -0.026 0.2 0.25 1 -0.34 150 151
FCER1G 0.008 0.086 -10000 0 -0.45 19 19
FCER1A -0.032 0.15 -10000 0 -0.46 64 64
Antigen/IgE/Fc epsilon R1/Fyn -0.006 0.14 -10000 0 -0.28 113 113
MAPK3 0.013 0.11 -10000 0 -0.86 9 9
MAPK1 0.008 0.12 -10000 0 -0.89 9 9
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MAPK8 -0.076 0.24 -10000 0 -0.64 63 63
DUSP1 0.025 0.036 -10000 0 -0.44 3 3
NF-kappa-B/RelA -0.012 0.071 0.12 3 -0.18 53 56
actin cytoskeleton reorganization -0.041 0.17 0.33 1 -0.54 40 41
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.047 0.18 0.28 2 -0.45 72 74
FER -0.045 0.13 -10000 0 -0.35 70 70
RELA 0.025 0.004 -10000 0 -10000 0 0
ITK -0.029 0.11 -10000 0 -0.4 40 40
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.022 0.22 0.26 15 -0.56 59 74
cytokine secretion -0.013 0.048 -10000 0 -0.15 19 19
SPHK1 -0.051 0.14 -10000 0 -0.37 75 75
PTK2 -0.044 0.18 0.34 1 -0.56 40 41
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.034 0.2 0.21 9 -0.47 80 89
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.06 0.18 0.28 10 -0.43 80 90
MAP2K2 0.009 0.11 -10000 0 -0.86 9 9
MAP2K1 0.007 0.11 -10000 0 -0.88 9 9
MAP2K7 0.025 0.02 -10000 0 -0.44 1 1
KLRG1/SHP2 -0.032 0.12 0.19 5 -0.29 72 77
MAP2K4 -0.13 0.36 -10000 0 -0.88 106 106
Fc epsilon R1/FcgammaRIIB -0.025 0.2 0.25 1 -0.36 131 132
mol:Choline -0.062 0.12 0.33 11 -0.27 99 110
SHC/Grb2/SOS1 -0.006 0.14 -10000 0 -0.35 66 66
FYN 0.022 0.039 -10000 0 -0.44 4 4
DOK1 0.026 0.001 -10000 0 -10000 0 0
PXN -0.042 0.16 0.44 2 -0.52 40 42
HCLS1 -0.048 0.14 -10000 0 -0.36 71 71
PRKCB -0.049 0.15 0.24 14 -0.38 73 87
FCGR2B -0.018 0.15 -10000 0 -0.44 60 60
IGHE -0.003 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.04 0.14 0.2 2 -0.32 79 81
LCP2 0.011 0.082 -10000 0 -0.45 18 18
PLA2G4A -0.074 0.16 0.17 2 -0.35 117 119
RASA1 0.024 0.028 -10000 0 -0.44 2 2
mol:Phosphatidic acid -0.062 0.12 0.33 11 -0.27 99 110
IKK complex -0.015 0.099 0.18 49 -0.22 50 99
WIPF1 0.019 0.058 -10000 0 -0.44 9 9
Wnt signaling

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
Noncanonical Wnts/FZD -0.071 0.16 -9999 0 -0.32 148 148
FZD6 0.018 0.044 -9999 0 -0.44 5 5
WNT6 -0.001 0.13 -9999 0 -0.44 42 42
WNT4 -0.007 0.12 -9999 0 -0.44 43 43
FZD3 0.013 0.055 -9999 0 -0.44 8 8
WNT5A 0.016 0.07 -9999 0 -0.44 13 13
WNT11 -0.034 0.17 -9999 0 -0.44 86 86
Ephrin B reverse 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
EFNB2 0.019 0.022 -10000 0 -0.44 1 1
EPHB2 0.018 0.059 -10000 0 -0.45 9 9
EFNB1 -0.004 0.041 0.23 2 -0.32 7 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.11 -10000 0 -0.26 64 64
Ephrin B2/EPHB1-2 0.021 0.082 -10000 0 -0.25 43 43
neuron projection morphogenesis 0.008 0.097 -10000 0 -0.24 64 64
Ephrin B1/EPHB1-2/Tiam1 0.022 0.11 0.21 1 -0.26 70 71
DNM1 0.023 0.049 -10000 0 -0.44 6 6
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.065 0.18 0.24 1 -0.49 79 80
YES1 -0.097 0.26 -10000 0 -0.73 85 85
Ephrin B1/EPHB1-2/NCK2 0.036 0.095 0.21 1 -0.25 49 50
PI3K -0.036 0.2 -10000 0 -0.48 89 89
mol:GDP 0.021 0.11 0.21 1 -0.26 70 71
ITGA2B 0.008 0.094 -10000 0 -0.44 23 23
endothelial cell proliferation 0.026 0.02 -10000 0 -0.27 1 1
FYN -0.096 0.26 -10000 0 -0.71 89 89
MAP3K7 -0.071 0.18 -10000 0 -0.52 82 82
FGR -0.1 0.26 -10000 0 -0.71 87 87
TIAM1 0.006 0.1 -10000 0 -0.44 28 28
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
RGS3 0.026 0.003 -10000 0 -10000 0 0
cell adhesion -0.059 0.19 -10000 0 -0.49 82 82
LYN -0.092 0.26 -10000 0 -0.7 88 88
Ephrin B1/EPHB1-2/Src Family Kinases -0.088 0.23 -10000 0 -0.64 86 86
Ephrin B1/EPHB1-2 -0.07 0.2 -10000 0 -0.57 75 75
SRC -0.086 0.25 -10000 0 -0.69 81 81
ITGB3 0.016 0.07 -10000 0 -0.44 13 13
EPHB1 0.006 0.12 -10000 0 -0.44 37 37
EPHB4 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.27 1 1
alphaIIb/beta3 Integrin 0.019 0.088 -10000 0 -0.32 36 36
BLK -0.1 0.26 -10000 0 -0.74 82 82
HCK -0.087 0.25 -10000 0 -0.71 77 77
regulation of stress fiber formation -0.035 0.093 0.25 49 -0.21 1 50
MAPK8 -0.066 0.17 -10000 0 -0.46 84 84
Ephrin B1/EPHB1-2/RGS3 0.036 0.092 -10000 0 -0.25 49 49
endothelial cell migration -0.023 0.17 0.24 45 -0.44 64 109
NCK2 0.025 0.019 -10000 0 -0.44 1 1
PTPN13 -0.049 0.19 -10000 0 -0.54 77 77
regulation of focal adhesion formation -0.035 0.093 0.25 49 -0.21 1 50
chemotaxis -0.034 0.09 0.24 49 -10000 0 49
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
Rac1/GTP 0.017 0.1 -10000 0 -0.25 64 64
angiogenesis -0.071 0.2 -10000 0 -0.57 77 77
LCK -0.099 0.26 -10000 0 -0.72 88 88
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.039 0.2 0.27 6 -0.52 67 73
FYN -0.074 0.25 0.25 3 -0.66 72 75
LAT/GRAP2/SLP76 -0.05 0.22 -10000 0 -0.55 76 76
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 -0.057 0.17 0.21 2 -0.43 83 85
B2M 0.022 0.023 -10000 0 -0.44 1 1
IKBKG -0.017 0.055 0.096 15 -0.14 61 76
MAP3K8 0.025 0.02 -10000 0 -0.44 1 1
mol:Ca2+ -0.018 0.024 0.088 8 -0.076 20 28
integrin-mediated signaling pathway 0.029 0.038 -10000 0 -0.27 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.085 0.25 0.24 2 -0.62 85 87
TRPV6 0.016 0.24 1.1 24 -0.44 14 38
CD28 -0.002 0.12 -10000 0 -0.45 36 36
SHC1 -0.074 0.24 0.28 6 -0.65 71 77
receptor internalization -0.078 0.27 -10000 0 -0.68 76 76
PRF1 -0.083 0.31 -10000 0 -0.95 56 56
KRAS 0.021 0.044 -10000 0 -0.44 5 5
GRB2 0.025 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.035 0.14 0.2 2 -0.34 82 84
LAT -0.078 0.25 -10000 0 -0.65 74 74
EntrezGene:6955 -0.001 0.003 -10000 0 -10000 0 0
CD3D 0.003 0.1 -10000 0 -0.45 28 28
CD3E 0.005 0.096 -10000 0 -0.46 24 24
CD3G -0.016 0.14 -10000 0 -0.45 51 51
RASGRP2 -0.008 0.048 -10000 0 -0.18 38 38
RASGRP1 -0.043 0.18 0.26 3 -0.45 78 81
HLA-A 0.019 0.046 -10000 0 -0.45 5 5
RASSF5 0.019 0.055 -10000 0 -0.44 8 8
RAP1A/GTP/RAPL 0.029 0.038 -10000 0 -0.27 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.063 0.14 16 -0.12 65 81
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.037 0.084 -10000 0 -0.23 78 78
PRKCA -0.002 0.11 0.15 35 -0.26 63 98
GRAP2 0.007 0.092 -10000 0 -0.44 23 23
mol:IP3 -0.041 0.15 0.2 9 -0.43 66 75
EntrezGene:6957 -0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.067 0.24 -10000 0 -0.67 64 64
ORAI1 -0.026 0.2 -10000 0 -0.96 24 24
CSK -0.075 0.25 0.23 2 -0.67 70 72
B7 family/CD28 -0.063 0.29 -10000 0 -0.7 81 81
CHUK 0.022 0.034 -10000 0 -0.44 3 3
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.087 0.29 -10000 0 -0.77 72 72
PTPN6 -0.077 0.25 0.25 2 -0.67 69 71
VAV1 -0.085 0.26 0.27 2 -0.67 77 79
Monovalent TCR/CD3 -0.039 0.19 -10000 0 -0.49 66 66
CBL 0.025 0.004 -10000 0 -10000 0 0
LCK -0.08 0.27 0.23 3 -0.68 74 77
PAG1 -0.065 0.25 0.26 2 -0.65 71 73
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
TCR/CD3/MHC I/CD8/LCK -0.087 0.29 0.19 1 -0.76 72 73
CD80 -0.009 0.12 -10000 0 -0.45 43 43
CD86 0.002 0.11 -10000 0 -0.45 32 32
PDK1/CARD11/BCL10/MALT1 -0.035 0.11 0.13 2 -0.27 81 83
HRAS 0.025 0.02 -10000 0 -0.44 1 1
GO:0035030 -0.077 0.22 -10000 0 -0.56 81 81
CD8A -0.008 0.13 -10000 0 -0.45 46 46
CD8B -0.011 0.13 -10000 0 -0.45 45 45
PTPRC -0.005 0.12 -10000 0 -0.45 39 39
PDK1/PKC theta -0.065 0.2 0.24 4 -0.52 82 86
CSK/PAG1 -0.063 0.24 0.25 5 -0.63 70 75
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.029 0.039 -10000 0 -0.33 5 5
GRAP2/SLP76 -0.056 0.25 -10000 0 -0.64 75 75
STIM1 0.003 0.11 1.2 4 -0.94 1 5
RAS family/GTP 0.001 0.081 0.16 10 -0.19 52 62
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.086 0.3 -10000 0 -0.75 76 76
mol:DAG -0.049 0.13 0.12 1 -0.38 66 67
RAP1A/GDP 0.005 0.031 0.079 10 -0.065 36 46
PLCG1 0.014 0.023 -10000 0 -0.44 1 1
CD247 0.01 0.085 -10000 0 -0.45 19 19
cytotoxic T cell degranulation -0.077 0.29 -10000 0 -0.88 56 56
RAP1A/GTP -0.003 0.018 -10000 0 -0.067 39 39
mol:PI-3-4-5-P3 -0.066 0.2 0.23 2 -0.5 85 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.053 0.2 0.22 8 -0.56 66 74
NRAS 0.018 0.058 -10000 0 -0.44 9 9
ZAP70 0.003 0.11 -10000 0 -0.45 31 31
GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.058 0.21 0.2 1 -0.54 78 79
MALT1 0.017 0.035 -10000 0 -0.44 3 3
TRAF6 0.025 0.02 -10000 0 -0.44 1 1
CD8 heterodimer -0.011 0.15 -10000 0 -0.39 73 73
CARD11 0.006 0.12 -10000 0 -0.44 36 36
PRKCB -0.009 0.13 0.15 39 -0.3 69 108
PRKCE -0.002 0.12 0.15 37 -0.27 64 101
PRKCQ -0.075 0.24 0.25 3 -0.59 84 87
LCP2 0.012 0.082 -10000 0 -0.44 18 18
BCL10 0.022 0.039 -10000 0 -0.44 4 4
regulation of survival gene product expression -0.046 0.14 0.2 2 -0.36 83 85
IKK complex 0.016 0.067 0.12 77 -0.11 46 123
RAS family/GDP -0.005 0.016 -10000 0 -0.07 12 12
MAP3K14 -0.03 0.1 0.17 2 -0.26 79 81
PDPK1 -0.052 0.16 0.19 4 -0.4 82 86
TCR/CD3/MHC I/CD8/Fyn -0.088 0.3 -10000 0 -0.73 81 81
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.032 0.17 -10000 0 -0.57 43 43
IHH -0.012 0.14 -10000 0 -0.47 42 42
SHH Np/Cholesterol/GAS1 -0.019 0.11 0.19 2 -0.26 99 101
LRPAP1 0.024 0.02 -10000 0 -0.44 1 1
dorsoventral neural tube patterning 0.02 0.11 0.26 99 -0.18 2 101
SMO/beta Arrestin2 -0.023 0.16 -10000 0 -0.46 48 48
SMO -0.037 0.16 -10000 0 -0.48 48 48
AKT1 -0.027 0.15 -10000 0 -0.44 42 42
ARRB2 0.022 0.01 -10000 0 -10000 0 0
BOC 0.022 0.068 -10000 0 -0.44 11 11
ADRBK1 0.025 0.02 -10000 0 -0.44 1 1
heart looping -0.035 0.16 -10000 0 -0.47 48 48
STIL -0.024 0.13 -10000 0 -0.34 55 55
DHH N/PTCH2 0.006 0.11 -10000 0 -0.34 51 51
DHH N/PTCH1 -0.014 0.14 -10000 0 -0.3 99 99
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
DHH 0.001 0.1 -10000 0 -0.44 30 30
PTHLH -0.057 0.24 -10000 0 -0.79 48 48
determination of left/right symmetry -0.035 0.16 -10000 0 -0.47 48 48
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
skeletal system development -0.056 0.24 -10000 0 -0.78 48 48
IHH N/Hhip -0.026 0.16 -10000 0 -0.37 92 92
DHH N/Hhip -0.016 0.14 -10000 0 -0.35 86 86
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.035 0.16 -10000 0 -0.47 48 48
pancreas development -0.024 0.15 -10000 0 -0.44 65 65
HHAT 0.02 0.048 -10000 0 -0.44 6 6
PI3K 0.034 0.031 -10000 0 -0.32 4 4
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.025 0.16 -10000 0 -0.44 75 75
somite specification -0.035 0.16 -10000 0 -0.47 48 48
SHH Np/Cholesterol/PTCH1 -0.023 0.13 -10000 0 -0.3 86 86
SHH Np/Cholesterol/PTCH2 -0.003 0.082 -10000 0 -0.25 53 53
SHH Np/Cholesterol/Megalin 0.008 0.065 0.19 1 -0.25 32 33
SHH -0.027 0.069 0.23 1 -0.32 30 31
catabolic process -0.019 0.12 -10000 0 -0.32 76 76
SMO/Vitamin D3 -0.031 0.15 -10000 0 -0.38 72 72
SHH Np/Cholesterol/Hhip -0.018 0.11 0.19 2 -0.27 85 87
LRP2 0.011 0.033 -10000 0 -10000 0 0
receptor-mediated endocytosis -0.035 0.15 -10000 0 -0.45 44 44
SHH Np/Cholesterol/BOC 0.007 0.075 0.19 2 -0.26 39 41
SHH Np/Cholesterol/CDO 0.006 0.069 -10000 0 -0.26 35 35
mesenchymal cell differentiation 0.018 0.11 0.27 85 -0.18 2 87
mol:Vitamin D3 -0.015 0.14 0.36 1 -0.3 86 87
IHH N/PTCH2 -0.002 0.12 -10000 0 -0.34 60 60
CDON 0.021 0.048 -10000 0 -0.44 6 6
IHH N/PTCH1 -0.008 0.13 -10000 0 -0.33 76 76
Megalin/LRPAP1 0.038 0.022 -10000 0 -0.32 1 1
PTCH2 0.007 0.096 -10000 0 -0.44 25 25
SHH Np/Cholesterol -0.001 0.058 -10000 0 -0.24 32 32
PTCH1 -0.019 0.12 -10000 0 -0.33 76 76
HHIP -0.024 0.15 -10000 0 -0.44 65 65
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.011 -10000 0 -10000 0 0
VLDLR -0.001 0.11 -10000 0 -0.44 35 35
CRKL 0.025 0.005 -10000 0 -10000 0 0
LRPAP1 0.024 0.02 -10000 0 -0.44 1 1
FYN 0.022 0.039 -10000 0 -0.44 4 4
ITGA3 0.024 0.028 -10000 0 -0.44 2 2
RELN/VLDLR/Fyn 0.002 0.13 -10000 0 -0.3 84 84
MAPK8IP1/MKK7/MAP3K11/JNK1 0.064 0.057 -10000 0 -0.27 13 13
AKT1 -0.043 0.11 -10000 0 -0.25 110 110
MAP2K7 0.025 0.02 -10000 0 -0.44 1 1
RAPGEF1 0.025 0.02 -10000 0 -0.44 1 1
DAB1 -0.009 0.12 -10000 0 -0.44 42 42
RELN/LRP8/DAB1 0.002 0.12 0.17 1 -0.27 92 93
LRPAP1/LRP8 0.034 0.031 -10000 0 -0.32 4 4
RELN/LRP8/DAB1/Fyn 0.01 0.12 -10000 0 -0.25 96 96
DAB1/alpha3/beta1 Integrin -0.007 0.13 -10000 0 -0.26 115 115
long-term memory -0.012 0.14 -10000 0 -0.26 132 132
DAB1/LIS1 -0.002 0.14 -10000 0 -0.26 115 115
DAB1/CRLK/C3G -0.007 0.13 -10000 0 -0.26 115 115
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
DAB1/NCK2 0.006 0.14 -10000 0 -0.27 116 116
ARHGEF2 0.025 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.013 0.05 -10000 0 -0.44 5 5
CDK5R1 0.026 0.007 -10000 0 -10000 0 0
RELN -0.015 0.14 -10000 0 -0.44 55 55
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
RELN/LRP8/Fyn 0.018 0.1 -10000 0 -0.27 62 62
GRIN2A/RELN/LRP8/DAB1/Fyn 0.018 0.13 -10000 0 -0.26 101 101
MAPK8 0.025 0.02 -10000 0 -0.44 1 1
RELN/VLDLR/DAB1 -0.013 0.14 -10000 0 -0.28 114 114
ITGB1 0.026 0.002 -10000 0 -10000 0 0
MAP1B -0.066 0.12 0.16 18 -0.28 120 138
RELN/LRP8 0.019 0.1 -10000 0 -0.27 59 59
GRIN2B/RELN/LRP8/DAB1/Fyn -0.001 0.15 -10000 0 -0.27 127 127
PI3K 0.034 0.031 -10000 0 -0.32 4 4
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.022 -10000 0 -0.32 2 2
RAP1A -0.062 0.11 0.32 7 -0.35 27 34
PAFAH1B1 0.022 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.017 0.068 -10000 0 -0.44 12 12
CRLK/C3G 0.036 0.017 -10000 0 -0.32 1 1
GRIN2B -0.008 0.12 -10000 0 -0.44 42 42
NCK2 0.025 0.019 -10000 0 -0.44 1 1
neuron differentiation -0.021 0.1 -10000 0 -0.37 22 22
neuron adhesion -0.064 0.12 0.33 9 -0.42 15 24
LRP8 0.023 0.034 -10000 0 -0.44 3 3
GSK3B -0.048 0.11 -10000 0 -0.25 111 111
RELN/VLDLR/DAB1/Fyn -0.006 0.14 -10000 0 -0.27 118 118
MAP3K11 0.025 0.02 -10000 0 -0.44 1 1
RELN/VLDLR/DAB1/P13K -0.039 0.12 -10000 0 -0.26 117 117
CDK5 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.023 0.14 0.78 8 -0.4 35 43
neuron migration -0.058 0.13 0.24 12 -0.31 89 101
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.02 0.1 -10000 0 -0.38 21 21
RELN/VLDLR 0.015 0.12 -10000 0 -0.27 84 84
BCR signaling pathway

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
JUN -0.069 0.16 0.38 2 -0.44 66 68
IKBKB -0.01 0.1 0.27 10 -0.3 27 37
AKT1 -0.044 0.095 0.26 10 -0.24 60 70
IKBKG -0.007 0.092 0.27 7 -0.27 26 33
CALM1 -0.021 0.15 0.25 20 -0.47 40 60
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
MAP3K1 -0.076 0.22 0.35 5 -0.53 84 89
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.16 0.26 22 -0.47 44 66
DOK1 0.026 0.001 -10000 0 -10000 0 0
AP-1 -0.038 0.1 0.22 7 -0.26 50 57
LYN 0.023 0.009 -10000 0 -10000 0 0
BLNK 0.01 0.083 -10000 0 -0.44 19 19
SHC1 0.025 0.004 -10000 0 -10000 0 0
BCR complex -0.016 0.15 -10000 0 -0.37 85 85
CD22 -0.085 0.22 -10000 0 -0.6 69 69
CAMK2G -0.021 0.14 0.28 9 -0.44 40 49
CSNK2A1 0.021 0.01 -10000 0 -10000 0 0
INPP5D 0.005 0.097 -10000 0 -0.44 26 26
SHC/GRB2/SOS1 -0.021 0.1 -10000 0 -0.27 67 67
GO:0007205 -0.021 0.16 0.26 22 -0.48 44 66
SYK 0.026 0.004 -10000 0 -10000 0 0
ELK1 -0.022 0.15 0.23 21 -0.47 42 63
NFATC1 -0.088 0.2 0.3 3 -0.48 88 91
B-cell antigen/BCR complex -0.016 0.15 -10000 0 -0.37 85 85
PAG1/CSK 0.028 0.038 -10000 0 -0.32 6 6
NFKBIB 0.008 0.049 0.14 12 -0.13 30 42
HRAS -0.017 0.14 0.28 11 -0.42 38 49
NFKBIA 0.009 0.048 0.14 12 -0.12 31 43
NF-kappa-B/RelA/I kappa B beta 0.014 0.043 0.14 13 -0.15 1 14
RasGAP/Csk 0.001 0.17 -10000 0 -0.34 105 105
mol:GDP -0.016 0.16 0.26 22 -0.47 41 63
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B 0.012 0.087 -10000 0 -0.44 20 20
NF-kappa-B/RelA/I kappa B alpha 0.014 0.042 0.14 13 -0.15 1 14
GRB2 0.025 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.076 0.2 0.4 2 -0.53 73 75
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:IP3 -0.02 0.16 0.26 22 -0.49 44 66
CSK 0.024 0.02 -10000 0 -0.44 1 1
FOS -0.029 0.14 0.22 17 -0.45 43 60
CHUK -0.018 0.11 0.27 7 -0.31 47 54
IBTK 0.017 0.061 -10000 0 -0.44 10 10
CARD11/BCL10/MALT1/TAK1 -0.016 0.15 0.28 6 -0.44 48 54
PTPN6 -0.084 0.2 -10000 0 -0.59 65 65
RELA 0.025 0.004 -10000 0 -10000 0 0
BCL2A1 0.007 0.033 0.097 1 -0.11 2 3
VAV2 -0.1 0.23 -10000 0 -0.58 86 86
ubiquitin-dependent protein catabolic process 0.011 0.049 0.14 12 -0.12 30 42
BTK -0.031 0.27 -10000 0 -1.1 36 36
CD19 -0.09 0.22 -10000 0 -0.54 85 85
MAP4K1 -0.009 0.13 -10000 0 -0.44 45 45
CD72 0.022 0.049 -10000 0 -0.44 6 6
PAG1 0.018 0.044 -10000 0 -0.44 5 5
MAPK14 -0.064 0.18 0.35 6 -0.44 83 89
SH3BP5 0.018 0.058 -10000 0 -0.44 9 9
PIK3AP1 -0.024 0.16 0.28 5 -0.5 44 49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.041 0.21 0.21 1 -0.5 77 78
RAF1 -0.018 0.13 0.26 11 -0.41 36 47
RasGAP/p62DOK/SHIP -0.008 0.18 -10000 0 -0.32 125 125
CD79A -0.035 0.17 -10000 0 -0.44 82 82
re-entry into mitotic cell cycle -0.037 0.1 0.22 7 -0.26 49 56
RASA1 0.024 0.028 -10000 0 -0.44 2 2
MAPK3 -0.018 0.11 0.25 10 -0.37 28 38
MAPK1 -0.018 0.11 0.23 10 -0.38 25 35
CD72/SHP1 -0.066 0.2 0.27 2 -0.59 59 61
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MAPK8 -0.065 0.18 0.33 5 -0.45 82 87
actin cytoskeleton organization -0.074 0.2 0.36 6 -0.49 82 88
NF-kappa-B/RelA 0.029 0.082 0.25 12 -0.2 14 26
Calcineurin -0.005 0.13 0.3 3 -0.41 38 41
PI3K -0.084 0.17 -10000 0 -0.47 75 75
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.02 0.16 0.3 4 -0.5 44 48
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.33 -10000 0 -0.81 95 95
DAPP1 -0.13 0.36 -10000 0 -0.95 86 86
cytokine secretion -0.081 0.18 0.3 3 -0.44 88 91
mol:DAG -0.02 0.16 0.26 22 -0.49 44 66
PLCG2 0.013 0.08 -10000 0 -0.44 17 17
MAP2K1 -0.02 0.12 0.24 10 -0.39 33 43
B-cell antigen/BCR complex/FcgammaRIIB -0.02 0.18 0.2 5 -0.39 103 108
mol:PI-3-4-5-P3 -0.072 0.11 0.18 3 -0.33 68 71
ETS1 -0.021 0.13 0.28 8 -0.41 37 45
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.018 0.13 -10000 0 -0.28 78 78
B-cell antigen/BCR complex/LYN -0.057 0.2 -10000 0 -0.5 78 78
MALT1 0.017 0.035 -10000 0 -0.44 3 3
TRAF6 0.025 0.02 -10000 0 -0.44 1 1
RAC1 -0.082 0.21 0.31 4 -0.53 83 87
B-cell antigen/BCR complex/LYN/SYK -0.043 0.21 -10000 0 -0.59 58 58
CARD11 -0.024 0.18 0.26 35 -0.49 53 88
FCGR2B -0.018 0.15 -10000 0 -0.44 60 60
PPP3CA 0.025 0.004 -10000 0 -10000 0 0
BCL10 0.022 0.039 -10000 0 -0.44 4 4
IKK complex 0 0.05 0.15 18 -0.12 11 29
PTPRC -0.004 0.12 -10000 0 -0.44 39 39
PDPK1 -0.051 0.081 0.18 7 -0.23 61 68
PPP3CB 0.025 0.004 -10000 0 -10000 0 0
PPP3CC 0.016 0.04 -10000 0 -0.44 4 4
POU2F2 0.01 0.034 0.2 3 -0.1 1 4
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.038 0.16 0.2 1 -0.41 63 64
TBX21 -0.17 0.47 0.54 1 -1.1 92 93
B2M 0.018 0.03 -10000 0 -0.44 1 1
TYK2 0.013 0.041 -10000 0 -0.46 1 1
IL12RB1 -0.009 0.12 -10000 0 -0.47 31 31
GADD45B -0.1 0.35 -10000 0 -0.9 70 70
IL12RB2 -0.001 0.1 -10000 0 -0.46 23 23
GADD45G -0.1 0.35 -10000 0 -0.89 69 69
natural killer cell activation -0.001 0.019 -10000 0 -10000 0 0
RELB 0.025 0.02 -10000 0 -0.44 1 1
RELA 0.025 0.004 -10000 0 -10000 0 0
IL18 0.016 0.049 -10000 0 -0.36 7 7
IL2RA -0.007 0.12 -10000 0 -0.44 43 43
IFNG -0.006 0.12 -10000 0 -0.44 37 37
STAT3 (dimer) -0.11 0.34 -10000 0 -0.78 92 92
HLA-DRB5 -0.013 0.14 -10000 0 -0.44 54 54
FASLG -0.17 0.48 -10000 0 -1.1 96 96
NF kappa B2 p52/RelB -0.14 0.42 -10000 0 -0.96 97 97
CD4 0.008 0.088 -10000 0 -0.44 21 21
SOCS1 0.02 0.069 -10000 0 -0.44 12 12
EntrezGene:6955 -0.003 0.013 -10000 0 -10000 0 0
CD3D -0.003 0.1 -10000 0 -0.45 28 28
CD3E 0.001 0.097 -10000 0 -0.45 24 24
CD3G -0.021 0.14 -10000 0 -0.45 51 51
IL12Rbeta2/JAK2 0.003 0.1 -10000 0 -0.34 38 38
CCL3 -0.17 0.46 0.54 1 -1.1 94 95
CCL4 -0.16 0.45 0.54 1 -1.1 90 91
HLA-A 0.016 0.049 -10000 0 -0.44 5 5
IL18/IL18R 0.023 0.12 -10000 0 -0.32 52 52
NOS2 -0.2 0.52 -10000 0 -1.2 112 112
IL12/IL12R/TYK2/JAK2/SPHK2 -0.032 0.14 0.2 1 -0.39 56 57
IL1R1 -0.15 0.42 -10000 0 -1.1 85 85
IL4 -0.005 0.034 -10000 0 -10000 0 0
JAK2 0.001 0.084 -10000 0 -0.46 15 15
EntrezGene:6957 -0.003 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.14 0.4 -10000 0 -0.95 93 93
RAB7A -0.085 0.3 0.49 1 -0.75 67 68
lysosomal transport -0.078 0.28 0.49 1 -0.71 67 68
FOS -0.15 0.41 -10000 0 -1 85 85
STAT4 (dimer) -0.12 0.38 0.38 2 -0.87 94 96
STAT5A (dimer) -0.14 0.43 -10000 0 -0.98 98 98
GZMA -0.17 0.46 -10000 0 -1.2 85 85
GZMB -0.18 0.47 -10000 0 -1.2 87 87
HLX 0.022 0.039 -10000 0 -0.44 4 4
LCK -0.17 0.47 -10000 0 -1.1 99 99
TCR/CD3/MHC II/CD4 -0.08 0.27 0.21 1 -0.66 78 79
IL2/IL2R 0.024 0.12 -10000 0 -0.31 57 57
MAPK14 -0.11 0.37 -10000 0 -0.88 82 82
CCR5 -0.12 0.39 -10000 0 -1 69 69
IL1B -0.015 0.13 -10000 0 -0.47 39 39
STAT6 -0.014 0.11 -10000 0 -0.3 1 1
STAT4 0.002 0.11 -10000 0 -0.44 31 31
STAT3 0.025 0.004 -10000 0 -10000 0 0
STAT1 0.025 0.028 -10000 0 -0.44 2 2
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
NFKB2 0.024 0.02 -10000 0 -0.44 1 1
IL12B 0.013 0.039 -10000 0 -10000 0 0
CD8A -0.013 0.13 -10000 0 -0.45 46 46
CD8B -0.014 0.13 -10000 0 -0.45 45 45
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.038 0.16 0.41 63 -0.2 1 64
IL2RB 0.011 0.084 -10000 0 -0.44 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.1 0.34 0.38 2 -0.77 94 96
IL2RG 0.017 0.064 -10000 0 -0.44 11 11
IL12 0.001 0.1 -10000 0 -0.33 39 39
STAT5A 0.025 0.004 -10000 0 -10000 0 0
CD247 0.005 0.087 -10000 0 -0.45 19 19
IL2 -0.006 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.02 -10000 0 -0.44 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.018 0.12 -10000 0 -0.46 39 39
IL12/IL12R/TYK2/JAK2 -0.18 0.54 -10000 0 -1.2 99 99
MAP2K3 -0.13 0.39 -10000 0 -0.9 92 92
RIPK2 0.022 0.009 -10000 0 -10000 0 0
MAP2K6 -0.11 0.37 -10000 0 -0.88 82 82
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.005 0.1 -10000 0 -0.44 28 28
IL18RAP -0.006 0.11 -10000 0 -0.45 34 34
IL12Rbeta1/TYK2 0.006 0.099 -10000 0 -0.36 32 32
EOMES -0.12 0.38 -10000 0 -1.2 61 61
STAT1 (dimer) -0.12 0.35 -10000 0 -0.78 104 104
T cell proliferation -0.076 0.27 0.33 2 -0.6 97 99
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.089 -10000 0 -0.44 21 21
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.095 0.3 -10000 0 -0.68 95 95
ATF2 -0.1 0.34 -10000 0 -0.83 77 77
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.033 0.11 -10000 0 -0.26 98 98
NF kappa B1 p50/RelA/I kappa B alpha -0.03 0.12 0.31 3 -0.4 21 24
alphaV/beta3 Integrin/Osteopontin/Src -0.011 0.14 -10000 0 -0.32 98 98
AP1 -0.028 0.15 -10000 0 -0.47 33 33
ILK -0.043 0.11 -10000 0 -0.27 99 99
bone resorption -0.043 0.11 -10000 0 -0.4 19 19
PTK2B 0.018 0.029 -10000 0 -0.44 2 2
PYK2/p130Cas 0.009 0.13 -10000 0 -0.25 98 98
ITGAV 0.018 0.064 -10000 0 -0.44 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.059 -10000 0 -0.34 14 14
alphaV/beta3 Integrin/Osteopontin 0.005 0.14 -10000 0 -0.29 101 101
MAP3K1 -0.046 0.12 0.19 5 -0.28 102 107
JUN 0.022 0.04 -10000 0 -0.45 4 4
MAPK3 -0.057 0.098 0.19 2 -0.34 27 29
MAPK1 -0.057 0.098 0.19 2 -0.35 25 27
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MAPK8 -0.06 0.1 0.18 5 -0.27 95 100
ITGB3 0.017 0.071 -10000 0 -0.45 13 13
NFKBIA -0.048 0.11 -10000 0 -0.4 24 24
FOS 0.012 0.081 -10000 0 -0.44 17 17
CD44 0.023 0.039 -10000 0 -0.44 4 4
CHUK 0.022 0.034 -10000 0 -0.44 3 3
PLAU -0.047 0.14 -10000 0 -0.82 10 10
NF kappa B1 p50/RelA -0.019 0.12 -10000 0 -0.46 15 15
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
RELA 0.025 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.027 0.074 -10000 0 -0.33 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.043 0.11 0.18 5 -0.27 100 105
VAV3 -0.085 0.12 0.18 4 -0.26 162 166
MAP3K14 -0.043 0.11 0.19 2 -0.27 100 102
ROCK2 0.017 0.064 -10000 0 -0.44 11 11
SPP1 -0.032 0.18 -10000 0 -0.44 88 88
RAC1 0.023 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.061 0.12 0.17 3 -0.24 150 153
MMP2 -0.077 0.14 -10000 0 -0.49 41 41
TCGA08_p53

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
CDKN2A -0.031 0.077 -10000 0 -0.32 38 38
TP53 -0.032 0.095 0.19 2 -0.27 73 75
Senescence -0.032 0.095 0.19 2 -0.27 73 75
Apoptosis -0.032 0.095 0.19 2 -0.27 73 75
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.007 0.059 0.21 41 -0.32 2 43
MDM4 0.025 0.02 -10000 0 -0.44 1 1
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.026 0.09 -10000 0 -0.3 37 37
fibroblast growth factor receptor signaling pathway 0.025 0.09 -10000 0 -0.3 37 37
LAMA1 -0.003 0.11 -10000 0 -0.44 33 33
PRNP 0.013 0.061 -10000 0 -0.44 10 10
GPC1/SLIT2 -0.012 0.14 -10000 0 -0.33 88 88
SMAD2 -0.016 0.037 0.18 3 -0.24 13 16
GPC1/PrPc/Cu2+ 0.018 0.055 -10000 0 -0.26 20 20
GPC1/Laminin alpha1 0.007 0.095 -10000 0 -0.32 43 43
TDGF1 -0.037 0.16 -10000 0 -0.44 78 78
CRIPTO/GPC1 -0.016 0.13 -10000 0 -0.32 88 88
APP/GPC1 0.03 0.05 -10000 0 -0.32 11 11
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.051 0.095 -10000 0 -0.27 89 89
FLT1 0.019 0.023 -10000 0 -0.44 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.044 0.049 -10000 0 -0.27 13 13
SERPINC1 0.012 0.027 -10000 0 -10000 0 0
FYN -0.055 0.094 -10000 0 -0.27 92 92
FGR -0.064 0.1 -10000 0 -0.28 110 110
positive regulation of MAPKKK cascade -0.026 0.18 0.29 16 -0.37 95 111
SLIT2 -0.033 0.17 -10000 0 -0.44 81 81
GPC1/NRG 0.002 0.1 -10000 0 -0.33 48 48
NRG1 -0.009 0.12 -10000 0 -0.44 40 40
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.034 0.044 -10000 0 -0.27 8 8
LYN -0.049 0.091 -10000 0 -0.27 83 83
mol:Spermine -0.011 0.04 -10000 0 -0.32 10 10
cell growth 0.025 0.09 -10000 0 -0.3 37 37
BMP signaling pathway -0.018 0.061 0.44 10 -10000 0 10
SRC -0.044 0.093 -10000 0 -0.28 80 80
TGFBR1 0.023 0.034 -10000 0 -0.44 3 3
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.067 0.2 -10000 0 -0.44 127 127
GPC1 0.018 0.061 -10000 0 -0.44 10 10
TGFBR1 (dimer) 0.023 0.034 -10000 0 -0.44 3 3
VEGFA 0.025 0.004 -10000 0 -10000 0 0
BLK -0.079 0.12 -10000 0 -0.3 132 132
HCK -0.051 0.1 -10000 0 -0.28 93 93
FGF2 0.008 0.099 -10000 0 -0.44 26 26
FGFR1 0.017 0.059 -10000 0 -0.44 9 9
VEGFR1 homodimer 0.019 0.022 -10000 0 -0.44 1 1
TGFBR2 0.026 0.004 -10000 0 -10000 0 0
cell death 0.03 0.049 -10000 0 -0.32 11 11
ATIII/GPC1 0.031 0.048 -10000 0 -0.32 10 10
PLA2G2A/GPC1 -0.04 0.16 -10000 0 -0.33 134 134
LCK -0.063 0.1 -10000 0 -0.28 106 106
neuron differentiation 0.002 0.1 -10000 0 -0.33 48 48
PrPc/Cu2+ 0.01 0.044 -10000 0 -0.32 10 10
APP 0.024 0.02 -10000 0 -0.44 1 1
TGFBR2 (dimer) 0.026 0.004 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.017 0.064 -10000 0 -0.44 11 11
CCL5 0.011 0.092 -10000 0 -0.44 22 22
SDCBP 0.015 0.061 -10000 0 -0.44 10 10
FGFR/FGF2/Syndecan-1 -0.013 0.15 0.21 6 -0.32 75 81
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 -0.046 0.13 -10000 0 -0.43 39 39
Syndecan-1/Syntenin -0.02 0.15 0.23 6 -0.39 44 50
MAPK3 -0.019 0.14 0.21 4 -0.37 42 46
HGF/MET 0.018 0.082 -10000 0 -0.32 32 32
TGFB1/TGF beta receptor Type II 0.017 0.064 -10000 0 -0.44 11 11
BSG 0.025 0.02 -10000 0 -0.44 1 1
keratinocyte migration -0.046 0.13 -10000 0 -0.42 39 39
Syndecan-1/RANTES -0.02 0.16 0.22 7 -0.37 65 72
Syndecan-1/CD147 -0.005 0.15 0.32 1 -0.38 43 44
Syndecan-1/Syntenin/PIP2 -0.021 0.14 0.21 6 -0.38 44 50
LAMA5 -0.003 0.09 -10000 0 -0.44 23 23
positive regulation of cell-cell adhesion -0.02 0.14 0.21 6 -0.37 44 50
MMP7 -0.026 0.16 -10000 0 -0.44 77 77
HGF 0.001 0.11 -10000 0 -0.44 32 32
Syndecan-1/CASK -0.028 0.14 -10000 0 -0.3 80 80
Syndecan-1/HGF/MET -0.014 0.17 0.24 5 -0.41 53 58
regulation of cell adhesion -0.026 0.13 0.34 3 -0.37 39 42
HPSE 0.021 0.052 -10000 0 -0.44 7 7
positive regulation of cell migration -0.013 0.15 0.21 6 -0.32 75 81
SDC1 -0.013 0.15 0.2 1 -0.31 79 80
Syndecan-1/Collagen -0.013 0.15 0.21 6 -0.32 75 81
PPIB 0.025 0.005 -10000 0 -10000 0 0
MET 0.024 0.02 -10000 0 -0.44 1 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
MMP9 0.003 0.085 -10000 0 -0.44 19 19
MAPK1 -0.02 0.14 0.2 5 -0.37 43 48
homophilic cell adhesion -0.019 0.15 0.24 8 -0.32 76 84
MMP1 -0.033 0.17 -10000 0 -0.44 82 82
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.002 0.16 0.2 6 -0.4 60 66
alphaM/beta2 Integrin/GPIbA -0.002 0.14 0.2 4 -0.36 59 63
alphaM/beta2 Integrin/proMMP-9 -0.003 0.13 0.2 12 -0.39 43 55
PLAUR 0.026 0.005 -10000 0 -10000 0 0
HMGB1 0.001 0.077 -10000 0 -0.45 15 15
alphaM/beta2 Integrin/Talin 0.007 0.13 -10000 0 -0.37 48 48
AGER 0.005 0.076 -10000 0 -0.46 13 13
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
SELPLG 0.015 0.072 -10000 0 -0.44 14 14
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.01 0.15 -10000 0 -0.3 103 103
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.003 0.085 -10000 0 -0.44 19 19
CYR61 0.025 0.051 -10000 0 -0.44 6 6
TLN1 0.025 0.02 -10000 0 -0.44 1 1
Rap1/GTP -0.054 0.15 -10000 0 -0.39 72 72
RHOA 0.025 0.02 -10000 0 -0.44 1 1
P-selectin oligomer -0.03 0.16 -10000 0 -0.44 72 72
MYH2 -0.075 0.16 0.24 3 -0.44 61 64
MST1R 0.022 0.039 -10000 0 -0.44 4 4
leukocyte activation during inflammatory response -0.007 0.14 -10000 0 -0.3 93 93
APOB -0.016 0.14 -10000 0 -0.44 51 51
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.007 0.1 -10000 0 -0.44 27 27
JAM3 0.026 0.008 -10000 0 -10000 0 0
GP1BA 0.009 0.069 -10000 0 -0.44 12 12
alphaM/beta2 Integrin/CTGF 0.009 0.13 0.2 5 -0.37 49 54
alphaM/beta2 Integrin -0.076 0.17 -10000 0 -0.44 72 72
JAM3 homodimer 0.026 0.008 -10000 0 -10000 0 0
ICAM2 0.023 0.04 -10000 0 -0.44 4 4
ICAM1 0.024 0.034 -10000 0 -0.44 3 3
phagocytosis triggered by activation of immune response cell surface activating receptor -0.075 0.16 -10000 0 -0.44 72 72
cell adhesion -0.002 0.13 0.2 4 -0.36 59 63
NFKB1 -0.039 0.2 0.41 5 -0.45 72 77
THY1 0.02 0.052 -10000 0 -0.44 7 7
RhoA/GDP 0.018 0.014 -10000 0 -0.32 1 1
Lipoprotein(a) 0.014 0.091 -10000 0 -0.27 51 51
alphaM/beta2 Integrin/LRP/tPA 0.012 0.13 -10000 0 -0.35 51 51
IL6 -0.076 0.25 0.32 5 -0.67 73 78
ITGB2 -0.001 0.096 -10000 0 -0.42 24 24
elevation of cytosolic calcium ion concentration 0.017 0.13 0.24 1 -0.35 49 50
alphaM/beta2 Integrin/JAM2/JAM3 0.005 0.16 0.22 4 -0.38 67 71
JAM2 -0.005 0.12 -10000 0 -0.44 39 39
alphaM/beta2 Integrin/ICAM1 0.018 0.14 -10000 0 -0.32 68 68
alphaM/beta2 Integrin/uPA/Plg -0.003 0.15 -10000 0 -0.34 81 81
RhoA/GTP -0.078 0.17 0.24 1 -0.45 68 69
positive regulation of phagocytosis -0.055 0.15 0.18 2 -0.4 70 72
Ron/MSP 0.026 0.074 -10000 0 -0.33 23 23
alphaM/beta2 Integrin/uPAR/uPA 0.019 0.13 0.24 1 -0.35 49 50
alphaM/beta2 Integrin/uPAR 0.008 0.13 0.19 1 -0.36 49 50
PLAU 0.023 0.045 -10000 0 -0.44 5 5
PLAT 0.018 0.048 -10000 0 -0.44 6 6
actin filament polymerization -0.072 0.15 0.22 4 -0.43 61 65
MST1 0.013 0.088 -10000 0 -0.44 20 20
alphaM/beta2 Integrin/lipoprotein(a) -0.003 0.15 -10000 0 -0.3 93 93
TNF -0.053 0.22 0.35 4 -0.53 66 70
RAP1B 0.026 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.007 0.14 0.2 3 -0.38 51 54
fibrinolysis -0.005 0.15 -10000 0 -0.33 81 81
HCK 0.005 0.072 -10000 0 -0.44 14 14
dendritic cell antigen processing and presentation -0.075 0.16 -10000 0 -0.44 72 72
VTN 0.006 0.095 -10000 0 -0.44 23 23
alphaM/beta2 Integrin/CYR61 0.007 0.14 0.2 8 -0.37 52 60
LPA 0.01 0.037 -10000 0 -0.44 1 1
LRP1 0.022 0.044 -10000 0 -0.44 5 5
cell migration -0.019 0.15 0.22 17 -0.43 49 66
FN1 -0.011 0.14 -10000 0 -0.44 54 54
alphaM/beta2 Integrin/Thy1 0.006 0.14 0.2 1 -0.39 49 50
MPO 0.001 0.1 -10000 0 -0.44 30 30
KNG1 -0.027 0.15 -10000 0 -0.44 65 65
RAP1/GDP 0.033 0.014 -10000 0 -0.27 1 1
ROCK1 -0.074 0.16 0.23 3 -0.44 62 65
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.029 0.11 -10000 0 -0.44 38 38
CTGF 0.027 0.024 -10000 0 -0.44 1 1
alphaM/beta2 Integrin/Hck -0.002 0.12 0.21 7 -0.4 39 46
ITGAM -0.016 0.13 -10000 0 -0.46 41 41
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.015 0.18 0.25 2 -0.36 99 101
HP -0.005 0.12 -10000 0 -0.44 38 38
leukocyte adhesion -0.03 0.17 0.22 2 -0.42 67 69
SELP -0.03 0.16 -10000 0 -0.44 72 72
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.029 0.15 -10000 0 -0.45 56 56
Syndecan-4/Syndesmos 0.002 0.21 0.35 1 -0.44 71 72
positive regulation of JNK cascade 0.005 0.2 0.31 2 -0.42 74 76
Syndecan-4/ADAM12 -0.012 0.23 0.31 4 -0.47 83 87
CCL5 0.011 0.092 -10000 0 -0.44 22 22
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
DNM2 0.025 0.02 -10000 0 -0.44 1 1
ITGA5 0.025 0.041 -10000 0 -0.44 4 4
SDCBP 0.015 0.061 -10000 0 -0.44 10 10
PLG -0.034 0.11 -10000 0 -0.41 41 41
ADAM12 -0.004 0.13 -10000 0 -0.44 45 45
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.024 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.028 0.21 0.3 2 -0.46 77 79
Syndecan-4/CXCL12/CXCR4 0.006 0.21 0.33 2 -0.45 74 76
Syndecan-4/Laminin alpha3 -0.018 0.2 0.3 1 -0.46 69 70
MDK 0.02 0.059 -10000 0 -0.44 9 9
Syndecan-4/FZD7 0 0.21 0.32 3 -0.45 70 73
Syndecan-4/Midkine -0.001 0.21 0.33 2 -0.45 74 76
FZD7 0.023 0.044 -10000 0 -0.44 5 5
Syndecan-4/FGFR1/FGF -0.013 0.2 0.33 1 -0.44 73 74
THBS1 0.02 0.052 -10000 0 -0.44 7 7
integrin-mediated signaling pathway -0.01 0.22 0.29 3 -0.45 79 82
positive regulation of MAPKKK cascade 0.005 0.2 0.31 2 -0.42 74 76
Syndecan-4/TACI -0.022 0.21 0.3 1 -0.45 78 79
CXCR4 0.021 0.06 -10000 0 -0.44 9 9
cell adhesion -0.015 0.088 0.19 12 -0.28 49 61
Syndecan-4/Dynamin 0.001 0.21 0.33 2 -0.45 71 73
Syndecan-4/TSP1 -0.003 0.21 0.33 2 -0.46 71 73
Syndecan-4/GIPC -0.001 0.21 0.33 2 -0.45 71 73
Syndecan-4/RANTES -0.005 0.21 0.32 2 -0.45 73 75
ITGB1 0.026 0.002 -10000 0 -10000 0 0
LAMA1 -0.003 0.11 -10000 0 -0.44 33 33
LAMA3 0.017 0.057 -10000 0 -0.44 8 8
RAC1 0.023 0.008 -10000 0 -10000 0 0
PRKCA 0.022 0.13 0.82 14 -0.47 1 15
Syndecan-4/alpha-Actinin -0.004 0.2 0.3 1 -0.44 71 72
TFPI 0.016 0.07 -10000 0 -0.44 13 13
F2 0.005 0.14 0.14 41 -0.41 57 98
alpha5/beta1 Integrin 0.037 0.031 -10000 0 -0.32 4 4
positive regulation of cell adhesion -0.034 0.2 0.29 1 -0.45 77 78
ACTN1 0.025 0.006 -10000 0 -10000 0 0
TNC -0.001 0.12 -10000 0 -0.44 39 39
Syndecan-4/CXCL12 -0.001 0.21 0.33 2 -0.45 71 73
FGF6 -0.017 0.008 -10000 0 -10000 0 0
RHOA 0.025 0.02 -10000 0 -0.44 1 1
CXCL12 0.022 0.057 -10000 0 -0.44 8 8
TNFRSF13B -0.002 0.11 -10000 0 -0.44 30 30
FGF2 0.008 0.099 -10000 0 -0.44 26 26
FGFR1 0.017 0.059 -10000 0 -0.44 9 9
Syndecan-4/PI-4-5-P2 -0.064 0.16 -10000 0 -0.44 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.045 0.13 -10000 0 -0.42 57 57
cell migration -0.01 0.014 -10000 0 -10000 0 0
PRKCD 0.005 0.029 -10000 0 -10000 0 0
vasculogenesis -0.002 0.2 0.32 2 -0.44 73 75
SDC4 -0.04 0.18 -10000 0 -0.47 68 68
Syndecan-4/Tenascin C -0.011 0.22 0.3 2 -0.47 78 80
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.02 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.011 0.2 0.33 2 -0.45 66 68
MMP9 -0.001 0.084 -10000 0 -0.44 19 19
Rac1/GTP -0.016 0.09 0.19 12 -0.29 49 61
cytoskeleton organization 0.003 0.2 0.35 1 -0.43 71 72
GIPC1 0.022 0.039 -10000 0 -0.44 4 4
Syndecan-4/TFPI -0.003 0.21 0.33 2 -0.45 72 74
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.007 0.062 -10000 0 -0.45 10 10
GNB1/GNG2 -0.035 0.066 -10000 0 -0.19 73 73
AKT1 -0.03 0.11 0.29 5 -0.24 77 82
EGF -0.031 0.17 -10000 0 -0.44 84 84
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.035 0.082 0.26 3 -0.31 24 27
mol:Ca2+ -0.039 0.13 0.31 4 -0.3 96 100
LYN -0.024 0.061 0.26 3 -0.35 5 8
RhoA/GTP -0.017 0.053 -10000 0 -0.13 73 73
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.045 0.14 0.31 5 -0.34 77 82
GNG2 0.021 0.044 -10000 0 -0.44 5 5
ARRB2 0.022 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.021 0.12 -10000 0 -0.51 25 25
G beta5/gamma2 -0.04 0.088 -10000 0 -0.25 71 71
PRKCH -0.044 0.14 0.29 4 -0.36 79 83
DNM1 0.022 0.049 -10000 0 -0.44 6 6
TXA2/TP beta/beta Arrestin3 0.005 0.041 -10000 0 -0.43 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.004 0.14 -10000 0 -0.44 48 48
G12 family/GTP -0.044 0.12 -10000 0 -0.31 77 77
ADRBK1 0.025 0.02 -10000 0 -0.44 1 1
ADRBK2 0.018 0.058 -10000 0 -0.44 9 9
RhoA/GTP/ROCK1 0.025 0.037 -10000 0 -0.32 5 5
mol:GDP 0.036 0.12 0.36 44 -0.27 3 47
mol:NADP 0.016 0.067 -10000 0 -0.44 12 12
RAB11A 0.025 0.005 -10000 0 -10000 0 0
PRKG1 0.003 0.099 -10000 0 -0.44 27 27
mol:IP3 -0.052 0.16 0.33 4 -0.37 96 100
cell morphogenesis 0.024 0.036 -10000 0 -0.32 5 5
PLCB2 -0.082 0.2 0.41 2 -0.51 94 96
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.041 0.093 0.32 2 -0.28 42 44
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.024 0.06 -10000 0 -0.3 14 14
RHOA 0.025 0.02 -10000 0 -0.44 1 1
PTGIR 0.021 0.053 -10000 0 -0.45 7 7
PRKCB1 -0.048 0.15 0.31 4 -0.38 79 83
GNAQ 0.022 0.043 -10000 0 -0.44 5 5
mol:L-citrulline 0.016 0.067 -10000 0 -0.44 12 12
TXA2/TXA2-R family -0.072 0.2 0.43 2 -0.53 77 79
LCK -0.033 0.08 0.32 2 -0.33 18 20
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.005 0.079 -10000 0 -0.23 46 46
TXA2-R family/G12 family/GDP/G beta/gamma -0.005 0.095 -10000 0 -0.41 26 26
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.002 0.077 -10000 0 -0.23 44 44
MAPK14 -0.029 0.095 0.31 5 -0.23 73 78
TGM2/GTP -0.065 0.16 0.3 2 -0.43 84 86
MAPK11 -0.031 0.095 0.25 5 -0.24 74 79
ARHGEF1 -0.026 0.071 -10000 0 -0.18 76 76
GNAI2 0.026 0.003 -10000 0 -10000 0 0
JNK cascade -0.05 0.15 0.33 4 -0.39 78 82
RAB11/GDP 0.025 0.006 -10000 0 -10000 0 0
ICAM1 -0.033 0.11 0.28 4 -0.29 69 73
cAMP biosynthetic process -0.051 0.15 0.32 4 -0.36 89 93
Gq family/GTP/EBP50 0.003 0.069 0.23 4 -0.29 20 24
actin cytoskeleton reorganization 0.024 0.036 -10000 0 -0.32 5 5
SRC -0.021 0.051 -10000 0 -0.35 5 5
GNB5 0.023 0.028 -10000 0 -0.44 2 2
GNB1 0.025 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.023 0.11 0.19 22 -0.28 44 66
VCAM1 -0.039 0.12 0.29 4 -0.32 73 77
TP beta/Gq family/GDP/G beta5/gamma2 -0.021 0.12 -10000 0 -0.51 25 25
platelet activation -0.039 0.13 0.34 6 -0.3 79 85
PGI2/IP 0.016 0.038 -10000 0 -0.32 7 7
PRKACA -0.01 0.081 -10000 0 -0.26 50 50
Gq family/GDP/G beta5/gamma2 -0.019 0.12 -10000 0 -0.48 24 24
TXA2/TP beta/beta Arrestin2 -0.017 0.077 -10000 0 -0.47 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.021 0.077 -10000 0 -0.25 50 50
mol:DAG -0.056 0.17 0.33 4 -0.42 80 84
EGFR 0.02 0.044 -10000 0 -0.44 5 5
TXA2/TP alpha -0.072 0.2 0.37 4 -0.49 89 93
Gq family/GTP -0.007 0.073 -10000 0 -0.24 39 39
YES1 -0.026 0.067 0.27 2 -0.39 7 9
GNAI2/GTP -0.01 0.079 -10000 0 -0.22 58 58
PGD2/DP -0.002 0.096 -10000 0 -0.32 48 48
SLC9A3R1 0.025 0.004 -10000 0 -10000 0 0
FYN -0.03 0.069 0.26 3 -0.32 10 13
mol:NO 0.016 0.067 -10000 0 -0.44 12 12
GNA15 0.015 0.073 -10000 0 -0.44 14 14
PGK/cGMP 0.011 0.077 -10000 0 -0.27 39 39
RhoA/GDP 0.025 0.02 -10000 0 -0.44 1 1
TP alpha/TGM2/GDP/G beta/gamma 0.007 0.078 -10000 0 -0.26 33 33
NOS3 0.016 0.068 -10000 0 -0.45 12 12
RAC1 0.023 0.008 -10000 0 -10000 0 0
PRKCA -0.043 0.14 0.32 5 -0.35 78 83
PRKCB -0.05 0.15 0.34 5 -0.38 79 84
PRKCE -0.042 0.14 0.33 2 -0.35 77 79
PRKCD -0.046 0.15 0.29 4 -0.38 78 82
PRKCG -0.061 0.16 0.34 4 -0.41 83 87
muscle contraction -0.07 0.19 0.37 4 -0.5 78 82
PRKCZ -0.046 0.14 0.31 4 -0.35 76 80
ARR3 -0.006 0.022 -10000 0 -10000 0 0
TXA2/TP beta 0 0.088 -10000 0 -0.23 59 59
PRKCQ -0.054 0.15 0.34 4 -0.38 80 84
MAPKKK cascade -0.065 0.18 0.34 4 -0.47 80 84
SELE -0.046 0.14 0.29 4 -0.38 69 73
TP beta/GNAI2/GDP/G beta/gamma 0.015 0.09 -10000 0 -0.24 50 50
ROCK1 0.017 0.044 -10000 0 -0.44 5 5
GNA14 0.014 0.075 -10000 0 -0.44 15 15
chemotaxis -0.08 0.22 0.44 2 -0.61 72 74
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.028 -10000 0 -0.44 2 2
GNA11 0.023 0.034 -10000 0 -0.44 3 3
Rac1/GTP 0.017 0.006 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.11 0.31 -10000 0 -0.82 49 49
HDAC7 0.026 0.02 -10000 0 -0.44 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.059 0.32 -10000 0 -0.79 47 47
SMAD4 0.019 0.012 -10000 0 -10000 0 0
ID2 -0.11 0.31 -10000 0 -0.82 49 49
AP1 0.023 0.069 -10000 0 -0.32 21 21
ABCG2 -0.12 0.32 -10000 0 -0.83 56 56
HIF1A -0.012 0.086 -10000 0 -0.53 6 6
TFF3 -0.12 0.32 -10000 0 -0.82 58 58
GATA2 0.006 0.095 -10000 0 -0.45 24 24
AKT1 -0.009 0.08 -10000 0 -0.25 13 13
response to hypoxia -0.02 0.064 -10000 0 -0.19 22 22
MCL1 -0.11 0.3 -10000 0 -0.81 49 49
NDRG1 -0.11 0.29 -10000 0 -0.82 44 44
SERPINE1 -0.11 0.31 -10000 0 -0.83 51 51
FECH -0.12 0.3 -10000 0 -0.81 49 49
FURIN -0.11 0.31 -10000 0 -0.82 49 49
NCOA2 0.018 0.048 -10000 0 -0.44 6 6
EP300 -0.012 0.1 -10000 0 -0.31 34 34
HMOX1 -0.11 0.31 -10000 0 -0.84 49 49
BHLHE40 -0.11 0.31 -10000 0 -0.82 49 49
BHLHE41 -0.12 0.32 -10000 0 -0.86 55 55
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.004 0.12 -10000 0 -0.46 6 6
ENG -0.021 0.094 0.38 2 -0.43 6 8
JUN 0.021 0.04 -10000 0 -0.44 4 4
RORA -0.12 0.32 -10000 0 -0.82 54 54
ABCB1 -0.13 0.34 -10000 0 -0.98 78 78
TFRC -0.11 0.31 -10000 0 -0.82 50 50
CXCR4 -0.11 0.32 -10000 0 -0.84 51 51
TF -0.12 0.33 -10000 0 -0.81 61 61
CITED2 -0.11 0.31 -10000 0 -0.82 49 49
HIF1A/ARNT -0.062 0.39 -10000 0 -0.94 45 45
LDHA 0.013 0.088 -10000 0 -1 2 2
ETS1 -0.11 0.31 -10000 0 -0.83 49 49
PGK1 -0.11 0.31 -10000 0 -0.82 49 49
NOS2 -0.13 0.34 -10000 0 -0.81 69 69
ITGB2 -0.12 0.32 -10000 0 -0.81 60 60
ALDOA -0.11 0.31 -10000 0 -0.82 49 49
Cbp/p300/CITED2 -0.11 0.34 -10000 0 -0.89 52 52
FOS 0.012 0.081 -10000 0 -0.44 17 17
HK2 -0.11 0.31 -10000 0 -0.82 50 50
SP1 0.01 0.055 -10000 0 -0.15 32 32
GCK -0.028 0.26 -10000 0 -1.3 19 19
HK1 -0.11 0.31 -10000 0 -0.82 49 49
NPM1 -0.11 0.31 -10000 0 -0.82 51 51
EGLN1 -0.11 0.3 -10000 0 -0.81 49 49
CREB1 0.028 0.028 -10000 0 -0.44 2 2
PGM1 -0.11 0.31 -10000 0 -0.8 52 52
SMAD3 0.025 0.008 -10000 0 -10000 0 0
EDN1 -0.063 0.25 -10000 0 -1 29 29
IGFBP1 -0.12 0.32 -10000 0 -0.79 67 67
VEGFA -0.074 0.26 0.4 1 -0.67 47 48
HIF1A/JAB1 0.007 0.063 -10000 0 -0.34 5 5
CP -0.14 0.34 -10000 0 -0.83 71 71
CXCL12 -0.11 0.31 -10000 0 -0.83 51 51
COPS5 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.028 0.019 -10000 0 -10000 0 0
BNIP3 -0.12 0.32 -10000 0 -0.83 57 57
EGLN3 -0.11 0.31 -10000 0 -0.82 52 52
CA9 -0.15 0.35 -10000 0 -0.79 83 83
TERT -0.12 0.32 -10000 0 -0.83 55 55
ENO1 -0.11 0.31 -10000 0 -0.81 49 49
PFKL -0.11 0.31 -10000 0 -0.82 49 49
NCOA1 0.025 0.019 -10000 0 -0.44 1 1
ADM -0.11 0.31 -10000 0 -0.82 49 49
ARNT -0.01 0.072 -10000 0 -0.5 1 1
HNF4A 0.007 0.054 -10000 0 -0.44 7 7
ADFP -0.12 0.3 -10000 0 -0.79 53 53
SLC2A1 -0.075 0.26 0.4 1 -0.67 48 49
LEP -0.11 0.31 -10000 0 -0.81 49 49
HIF1A/ARNT/Cbp/p300 -0.068 0.32 -10000 0 -0.8 49 49
EPO -0.05 0.22 -10000 0 -0.86 15 15
CREBBP -0.01 0.099 -10000 0 -0.34 25 25
HIF1A/ARNT/Cbp/p300/HDAC7 -0.055 0.32 -10000 0 -0.8 45 45
PFKFB3 -0.11 0.31 -10000 0 -0.82 49 49
NT5E -0.12 0.32 -10000 0 -0.83 56 56
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.02 -10000 0 -0.44 1 1
EGFR 0.02 0.044 -10000 0 -0.44 5 5
EGF/EGFR -0.002 0.12 -10000 0 -0.24 106 106
EGF/EGFR dimer/SHC/GRB2/SOS1 0.03 0.11 -10000 0 -0.24 76 76
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.015 0.078 -10000 0 -0.44 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.031 0.17 -10000 0 -0.44 84 84
EGF/EGFR dimer/SHC 0.01 0.12 -10000 0 -0.27 76 76
mol:GDP 0.025 0.11 -10000 0 -0.24 76 76
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.013 0.083 -10000 0 -0.44 18 18
GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
HRAS/GTP 0.009 0.094 -10000 0 -0.22 76 76
SHC1 0.025 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.1 -10000 0 -0.23 76 76
FRAP1 -0.049 0.071 0.15 3 -0.23 76 79
EGF/EGFR dimer -0.005 0.13 -10000 0 -0.32 78 78
SOS1 0.026 0.002 -10000 0 -10000 0 0
GRB2 0.025 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.02 0.088 -10000 0 -0.34 32 32
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.008 0.089 -10000 0 -0.27 52 52
EFNA5 -0.01 0.14 -10000 0 -0.44 52 52
FYN -0.039 0.07 0.18 1 -0.25 54 55
neuron projection morphogenesis 0.008 0.089 -10000 0 -0.27 52 52
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.008 0.09 -10000 0 -0.27 52 52
EPHA5 0.007 0.025 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.02 0.097 -10000 0 -0.26 54 54
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.11 0.28 2 -0.3 36 38
AP1 -0.013 0.12 -10000 0 -0.25 100 100
mol:PIP3 -0.04 0.09 -10000 0 -0.25 67 67
AKT1 -0.013 0.08 0.24 6 -0.33 14 20
PTK2B -0.053 0.12 0.18 2 -0.29 63 65
RHOA -0.001 0.067 0.23 6 -0.33 11 17
PIK3CB 0.023 0.034 -10000 0 -0.44 3 3
mol:Ca2+ -0.018 0.081 0.2 4 -0.27 30 34
MAGI3 0.024 0.028 -10000 0 -0.44 2 2
RELA 0.025 0.004 -10000 0 -10000 0 0
apoptosis -0.03 0.11 -10000 0 -0.27 86 86
HRAS/GDP 0.019 0.014 -10000 0 -0.32 1 1
positive regulation of microtubule depolymerization -0.066 0.12 0.24 4 -0.33 51 55
NF kappa B1 p50/RelA -0.018 0.12 -10000 0 -0.34 41 41
endothelial cell migration -0.027 0.14 -10000 0 -0.42 53 53
ADCY4 -0.038 0.13 0.24 1 -0.38 57 58
ADCY5 -0.054 0.16 0.24 1 -0.44 63 64
ADCY6 -0.031 0.13 0.24 1 -0.38 55 56
ADCY7 -0.032 0.13 0.24 1 -0.38 55 56
ADCY1 -0.036 0.13 -10000 0 -0.39 54 54
ADCY2 -0.046 0.15 0.24 1 -0.44 60 61
ADCY3 -0.032 0.13 0.24 1 -0.38 56 57
ADCY8 -0.032 0.12 0.23 2 -0.42 39 41
ADCY9 -0.033 0.13 0.24 1 -0.38 56 57
GSK3B -0.053 0.11 0.18 3 -0.3 50 53
arachidonic acid secretion -0.034 0.13 -10000 0 -0.42 41 41
GNG2 0.021 0.044 -10000 0 -0.44 5 5
TRIP6 -0.005 0.078 -10000 0 -0.37 23 23
GNAO1 -0.026 0.1 -10000 0 -0.3 64 64
HRAS 0.025 0.02 -10000 0 -0.44 1 1
NFKBIA -0.031 0.11 0.24 4 -0.31 49 53
GAB1 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.048 0.28 -10000 0 -0.85 61 61
JUN 0.022 0.039 -10000 0 -0.44 4 4
LPA/LPA2/NHERF2 0.03 0.034 -10000 0 -0.5 1 1
TIAM1 -0.072 0.32 -10000 0 -1 61 61
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:IP3 -0.023 0.08 0.2 4 -0.28 30 34
PLCB3 0.005 0.042 0.18 7 -0.46 2 9
FOS 0.013 0.08 -10000 0 -0.44 17 17
positive regulation of mitosis -0.034 0.13 -10000 0 -0.42 41 41
LPA/LPA1-2-3 0.008 0.12 -10000 0 -0.27 87 87
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
stress fiber formation -0.032 0.099 0.21 2 -0.31 39 41
GNAZ -0.02 0.096 -10000 0 -0.28 65 65
EGFR/PI3K-beta/Gab1 -0.026 0.1 -10000 0 -0.26 67 67
positive regulation of dendritic cell cytokine production 0.006 0.12 -10000 0 -0.26 87 87
LPA/LPA2/MAGI-3 0.029 0.034 -10000 0 -0.28 3 3
ARHGEF1 0.003 0.1 0.19 58 -0.24 51 109
GNAI2 -0.012 0.085 -10000 0 -0.28 50 50
GNAI3 -0.013 0.087 -10000 0 -0.28 53 53
GNAI1 -0.017 0.1 -10000 0 -0.3 56 56
LPA/LPA3 -0.003 0.088 -10000 0 -0.25 57 57
LPA/LPA2 0.015 0.029 -10000 0 -0.12 22 22
LPA/LPA1 -0.01 0.1 -10000 0 -0.32 53 53
HB-EGF/EGFR 0 0.054 0.16 2 -0.27 18 20
HBEGF -0.014 0.07 0.23 16 -0.32 19 35
mol:DAG -0.023 0.08 0.2 4 -0.28 30 34
cAMP biosynthetic process -0.04 0.14 0.3 5 -0.4 55 60
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
SRC 0.015 0.023 -10000 0 -0.44 1 1
GNB1 0.025 0.006 -10000 0 -10000 0 0
LYN -0.014 0.11 0.26 6 -0.31 42 48
GNAQ -0.014 0.074 -10000 0 -0.26 43 43
LPAR2 0.024 0.023 -10000 0 -0.44 1 1
LPAR3 -0.007 0.12 -10000 0 -0.44 38 38
LPAR1 -0.009 0.12 -10000 0 -0.35 53 53
IL8 -0.044 0.19 0.32 2 -0.46 80 82
PTK2 -0.032 0.092 0.18 3 -0.25 73 76
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
CASP3 -0.03 0.11 -10000 0 -0.27 86 86
EGFR 0.019 0.044 -10000 0 -0.44 5 5
PLCG1 -0.018 0.078 -10000 0 -0.27 43 43
PLD2 -0.037 0.096 0.17 4 -0.25 85 89
G12/G13 0.021 0.091 -10000 0 -0.26 52 52
PI3K-beta -0.007 0.079 -10000 0 -0.34 16 16
cell migration -0.013 0.096 -10000 0 -0.25 59 59
SLC9A3R2 0.025 0.02 -10000 0 -0.44 1 1
PXN -0.033 0.1 0.21 2 -0.31 39 41
HRAS/GTP -0.035 0.13 -10000 0 -0.44 41 41
RAC1 0.023 0.008 -10000 0 -10000 0 0
MMP9 0.001 0.085 -10000 0 -0.44 19 19
PRKCE 0.026 0.002 -10000 0 -10000 0 0
PRKCD -0.019 0.081 0.22 6 -0.27 28 34
Gi(beta/gamma) -0.032 0.13 -10000 0 -0.4 48 48
mol:LPA -0.005 0.031 -10000 0 -0.16 21 21
TRIP6/p130 Cas/FAK1/Paxillin -0.005 0.12 -10000 0 -0.4 23 23
MAPKKK cascade -0.034 0.13 -10000 0 -0.42 41 41
contractile ring contraction involved in cytokinesis 0.001 0.068 0.23 6 -0.32 12 18
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.018 0.082 -10000 0 -0.26 53 53
GNA15 -0.018 0.081 -10000 0 -0.26 51 51
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.028 -10000 0 -0.44 2 2
MAPT -0.067 0.12 0.24 4 -0.34 51 55
GNA11 -0.013 0.072 -10000 0 -0.25 43 43
Rac1/GTP -0.052 0.29 -10000 0 -0.91 61 61
MMP2 -0.027 0.14 -10000 0 -0.43 53 53
TCGA08_retinoblastoma

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
CDKN2B 0.009 0.07 -10000 0 -0.4 14 14
CDKN2C 0.028 0.018 -10000 0 -10000 0 0
CDKN2A -0.008 0.11 -10000 0 -0.42 38 38
CCND2 0.006 0.058 0.18 42 -0.18 1 43
RB1 -0.006 0.07 0.26 12 -0.2 41 53
CDK4 0.011 0.062 0.2 48 -0.14 1 49
CDK6 0.011 0.063 0.21 42 -0.17 1 43
G1/S progression -0.001 0.077 0.2 44 -0.27 12 56
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.022 0.035 -10000 0 -0.32 3 3
PRKCZ 0.024 0.02 -10000 0 -0.44 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.001 0.067 -10000 0 -0.25 22 22
IRAK/TOLLIP 0.018 0.054 0.18 34 -0.3 4 38
IKBKB 0.023 0.009 -10000 0 -10000 0 0
IKBKG 0.025 0.02 -10000 0 -0.44 1 1
IL1 alpha/IL1R2 -0.005 0.14 -10000 0 -0.36 78 78
IL1A -0.01 0.14 -10000 0 -0.44 53 53
IL1B -0.046 0.099 -10000 0 -0.35 53 53
IRAK/TRAF6/p62/Atypical PKCs 0.089 0.086 -10000 0 -0.3 6 6
IL1R2 0.002 0.12 -10000 0 -0.44 36 36
IL1R1 0.021 0.056 -10000 0 -0.44 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.029 0.073 0.24 8 -0.3 5 13
TOLLIP 0.025 0.02 -10000 0 -0.44 1 1
TICAM2 0.004 0.086 -10000 0 -0.44 20 20
MAP3K3 0.024 0.028 -10000 0 -0.44 2 2
TAK1/TAB1/TAB2 0.017 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.057 0.1 0.27 8 -0.45 5 13
JUN 0.039 0.097 0.15 230 -0.23 14 244
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.024 0.11 -10000 0 -0.26 72 72
IL1 alpha/IL1R1/IL1RAP/MYD88 0.034 0.11 -10000 0 -0.26 67 67
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.043 0.11 -10000 0 -0.25 67 67
IL1 beta fragment/IL1R1/IL1RAP -0.004 0.11 -10000 0 -0.28 70 70
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MAPK8 0.048 0.1 0.16 239 -0.22 13 252
IRAK1 -0.002 0.057 0.2 35 -0.27 4 39
IL1RN/IL1R1 0.016 0.1 -10000 0 -0.34 41 41
IRAK4 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.023 0.034 -10000 0 -0.44 3 3
TRAF6 0.025 0.02 -10000 0 -0.44 1 1
PI3K 0.034 0.031 -10000 0 -0.32 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.077 -10000 0 -0.27 28 28
CHUK 0.022 0.034 -10000 0 -0.44 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.004 0.11 -10000 0 -0.28 70 70
IL1 beta/IL1R2 -0.019 0.14 -10000 0 -0.34 77 77
IRAK/TRAF6/TAK1/TAB1/TAB2 0.02 0.048 0.16 33 -0.23 5 38
NF kappa B1 p50/RelA 0.004 0.1 -10000 0 -0.25 70 70
IRAK3 0.007 0.098 -10000 0 -0.44 26 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.016 0.12 -10000 0 -0.26 85 85
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.088 -10000 0 -0.24 68 68
IL1 alpha/IL1R1/IL1RAP 0.019 0.11 -10000 0 -0.29 67 67
RELA 0.025 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.003 -10000 0 -10000 0 0
MYD88 0.026 0.002 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.083 0.085 0.19 30 -0.25 6 36
IL1RAP 0.018 0.061 -10000 0 -0.44 10 10
UBE2N 0.025 0.02 -10000 0 -0.44 1 1
IRAK/TRAF6 -0.021 0.078 -10000 0 -0.28 22 22
CASP1 0.009 0.09 -10000 0 -0.44 22 22
IL1RN/IL1R2 0.003 0.13 -10000 0 -0.38 59 59
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.009 0.11 -10000 0 -0.27 70 70
TMEM189-UBE2V1 0.005 0.044 -10000 0 -0.44 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.034 0.088 -10000 0 -0.34 9 9
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
IL1RN 0.001 0.12 -10000 0 -0.44 36 36
TRAF6/TAK1/TAB1/TAB2 0.028 0.036 -10000 0 -0.24 4 4
MAP2K6 0.055 0.1 0.17 242 -0.23 13 255
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.006 0.12 0.35 52 -10000 0 52
KIRREL -0.002 0.11 -10000 0 -0.44 32 32
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.006 0.12 -10000 0 -0.35 52 52
PLCG1 0.014 0.023 -10000 0 -0.44 1 1
ARRB2 0.022 0.01 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.019 0.12 -10000 0 -0.28 76 76
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.084 -10000 0 -0.26 51 51
FYN -0.024 0.09 0.2 24 -0.25 54 78
mol:Ca2+ 0.015 0.087 -10000 0 -0.28 37 37
mol:DAG 0.016 0.088 -10000 0 -0.28 37 37
NPHS2 -0.005 0.037 -10000 0 -0.14 3 3
mol:IP3 0.016 0.088 -10000 0 -0.28 37 37
regulation of endocytosis 0.018 0.089 -10000 0 -0.24 54 54
Nephrin/NEPH1/podocin/Cholesterol 0.021 0.094 0.17 1 -0.26 51 52
establishment of cell polarity 0.006 0.12 -10000 0 -0.35 52 52
Nephrin/NEPH1/podocin/NCK1-2 0.046 0.1 -10000 0 -0.25 52 52
Nephrin/NEPH1/beta Arrestin2 0.02 0.091 -10000 0 -0.24 54 54
NPHS1 0.001 0.11 -10000 0 -0.45 28 28
Nephrin/NEPH1/podocin 0.021 0.093 -10000 0 -0.26 54 54
TJP1 0.024 0.02 -10000 0 -0.44 1 1
NCK1 0.024 0.028 -10000 0 -0.44 2 2
NCK2 0.025 0.019 -10000 0 -0.44 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.016 0.089 -10000 0 -0.28 37 37
CD2AP 0.004 0.099 -10000 0 -0.44 27 27
Nephrin/NEPH1/podocin/GRB2 0.034 0.1 -10000 0 -0.27 51 51
GRB2 0.025 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.038 0.1 0.22 22 -0.28 63 85
cytoskeleton organization -0.021 0.094 0.2 5 -0.31 49 54
Nephrin/NEPH1 0.01 0.083 -10000 0 -0.24 52 52
Nephrin/NEPH1/ZO-1 0.021 0.1 -10000 0 -0.29 52 52
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.013 0.14 -10000 0 -0.46 48 48
NFATC2 -0.028 0.17 -10000 0 -0.48 49 49
NFATC3 0 0.077 -10000 0 -0.27 22 22
CD40LG -0.12 0.32 -10000 0 -0.8 76 76
ITCH 0.007 0.057 -10000 0 -0.49 5 5
CBLB 0.017 0.064 -10000 0 -0.37 11 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.16 0.38 -10000 0 -1 76 76
JUNB 0.024 0.034 -10000 0 -0.44 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.025 0.06 -10000 0 -0.34 13 13
T cell anergy 0.005 0.086 -10000 0 -0.45 13 13
TLE4 -0.025 0.13 -10000 0 -0.48 26 26
Jun/NFAT1-c-4/p21SNFT -0.069 0.25 -10000 0 -0.76 45 45
AP-1/NFAT1-c-4 -0.12 0.33 -10000 0 -0.87 66 66
IKZF1 -0.025 0.14 -10000 0 -0.52 26 26
T-helper 2 cell differentiation -0.068 0.22 -10000 0 -0.68 50 50
AP-1/NFAT1 -0.022 0.14 -10000 0 -0.4 38 38
CALM1 0.027 0.036 -10000 0 -0.2 12 12
EGR2 -0.07 0.26 -10000 0 -1 31 31
EGR3 -0.075 0.27 -10000 0 -1 34 34
NFAT1/FOXP3 -0.028 0.17 -10000 0 -0.51 47 47
EGR1 0.019 0.057 -10000 0 -0.41 9 9
JUN -0.002 0.056 -10000 0 -0.47 4 4
EGR4 0.002 0.11 -10000 0 -0.44 31 31
mol:Ca2+ 0.003 0.03 -10000 0 -0.19 13 13
GBP3 -0.047 0.19 -10000 0 -0.6 51 51
FOSL1 0.016 0.076 -10000 0 -0.44 15 15
NFAT1-c-4/MAF/IRF4 -0.065 0.26 -10000 0 -0.81 46 46
DGKA -0.021 0.11 -10000 0 -0.41 24 24
CREM 0.026 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.057 0.22 -10000 0 -0.76 36 36
CTLA4 -0.048 0.18 -10000 0 -0.55 47 47
NFAT1-c-4 (dimer)/EGR1 -0.056 0.23 -10000 0 -0.76 39 39
NFAT1-c-4 (dimer)/EGR4 -0.066 0.24 -10000 0 -0.77 40 40
FOS -0.013 0.09 -10000 0 -0.47 17 17
IFNG -0.13 0.34 -10000 0 -0.9 81 81
T cell activation 0 0.16 -10000 0 -0.62 5 5
MAF 0.021 0.052 -10000 0 -0.44 7 7
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.062 0.22 0.78 37 -10000 0 37
TNF -0.087 0.23 -10000 0 -0.75 46 46
FASLG -0.15 0.46 -10000 0 -1.3 68 68
TBX21 -0.009 0.12 -10000 0 -0.33 63 63
BATF3 0.021 0.053 -10000 0 -0.44 7 7
PRKCQ -0.021 0.14 -10000 0 -0.45 52 52
PTPN1 -0.021 0.11 -10000 0 -0.42 22 22
NFAT1-c-4/ICER1 -0.055 0.22 -10000 0 -0.76 36 36
GATA3 0.015 0.078 -10000 0 -0.44 16 16
T-helper 1 cell differentiation -0.13 0.33 -10000 0 -0.86 83 83
IL2RA -0.15 0.36 -10000 0 -0.94 79 79
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.021 0.11 -10000 0 -0.42 23 23
E2F1 0.017 0.024 -10000 0 -0.44 1 1
PPARG 0.02 0.051 -10000 0 -0.44 7 7
SLC3A2 -0.021 0.11 -10000 0 -0.42 22 22
IRF4 -0.017 0.14 -10000 0 -0.44 58 58
PTGS2 -0.12 0.32 -10000 0 -0.77 80 80
CSF2 -0.12 0.33 -10000 0 -0.78 82 82
JunB/Fra1/NFAT1-c-4 -0.052 0.22 -10000 0 -0.73 38 38
IL4 -0.071 0.24 -10000 0 -0.72 49 49
IL5 -0.1 0.3 -10000 0 -0.76 67 67
IL2 0 0.16 -10000 0 -0.63 5 5
IL3 -0.032 0.12 -10000 0 -0.62 16 16
RNF128 0.013 0.078 -10000 0 -0.54 11 11
NFATC1 -0.062 0.22 -10000 0 -0.79 37 37
CDK4 0.039 0.13 0.56 19 -10000 0 19
PTPRK -0.019 0.11 -10000 0 -0.42 24 24
IL8 -0.12 0.33 -10000 0 -0.8 79 79
POU2F1 0.02 0.052 -10000 0 -0.44 7 7
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.033 0.12 0.22 18 -0.38 21 39
PDGFB-D/PDGFRB/SLAP 0.024 0.063 -10000 0 -0.32 17 17
PDGFB-D/PDGFRB/APS/CBL 0.039 0.064 -10000 0 -0.27 22 22
AKT1 0.043 0.098 0.24 18 -0.4 1 19
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.063 0.14 0.24 90 -0.42 21 111
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
FGR -0.015 0.18 -10000 0 -0.51 52 52
mol:Ca2+ 0.049 0.14 0.23 87 -0.49 16 103
MYC 0.075 0.18 0.38 76 -0.53 15 91
SHC1 0.025 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.056 0.079 0.17 2 -0.23 8 10
LRP1/PDGFRB/PDGFB 0.043 0.059 -10000 0 -0.3 15 15
GRB10 0.02 0.039 -10000 0 -0.44 4 4
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
GO:0007205 0.048 0.14 0.23 86 -0.5 16 102
PTEN 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.03 0.058 -10000 0 -0.32 15 15
PDGFB-D/PDGFRB/GRB10 0.029 0.053 -10000 0 -0.32 12 12
cell cycle arrest 0.024 0.063 -10000 0 -0.32 17 17
HRAS 0.025 0.02 -10000 0 -0.44 1 1
HIF1A 0.036 0.093 0.23 18 -0.3 5 23
GAB1 0.031 0.15 0.31 2 -0.45 21 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.045 0.14 0.22 97 -0.42 17 114
PDGFB-D/PDGFRB 0.022 0.045 -10000 0 -0.29 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.048 -10000 0 -0.32 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.001 0.087 0.23 2 -0.36 20 22
positive regulation of MAPKKK cascade 0.03 0.058 -10000 0 -0.32 15 15
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:IP3 0.049 0.14 0.23 86 -0.51 16 102
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.022 0.021 -10000 0 -0.44 1 1
PDGFB-D/PDGFRB/GRB7 0.033 0.046 -10000 0 -0.32 9 9
SHB 0.026 0.005 -10000 0 -10000 0 0
BLK -0.085 0.22 -10000 0 -0.49 121 121
PTPN2 0.022 0.023 -10000 0 -0.43 1 1
PDGFB-D/PDGFRB/SNX15 0.033 0.048 -10000 0 -0.32 10 10
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
VAV2 0.038 0.16 0.26 39 -0.48 23 62
CBL 0.025 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.033 0.05 -10000 0 -0.32 11 11
LCK 0 0.14 -10000 0 -0.47 38 38
PDGFRB 0.02 0.063 -10000 0 -0.45 10 10
ACP1 0.026 0.002 -10000 0 -10000 0 0
HCK -0.01 0.12 -10000 0 -0.6 20 20
ABL1 0.03 0.15 0.22 90 -0.41 29 119
PDGFB-D/PDGFRB/CBL 0.02 0.16 0.37 1 -0.5 24 25
PTPN1 0.014 0.014 -10000 0 -10000 0 0
SNX15 0.025 0.004 -10000 0 -10000 0 0
STAT3 0.025 0.004 -10000 0 -10000 0 0
STAT1 0.025 0.028 -10000 0 -0.44 2 2
cell proliferation 0.075 0.18 0.37 78 -0.47 16 94
SLA 0.015 0.062 -10000 0 -0.44 10 10
actin cytoskeleton reorganization 0.059 0.1 0.18 210 -0.27 7 217
SRC 0.006 0.056 -10000 0 -0.33 8 8
PI3K -0.017 0.032 -10000 0 -0.23 9 9
PDGFB-D/PDGFRB/GRB7/SHC 0.045 0.043 -10000 0 -0.27 9 9
SH2B2 0.017 0.068 -10000 0 -0.44 12 12
PLCgamma1/SPHK1 0.063 0.15 0.24 90 -0.44 20 110
LYN 0.011 0.087 -10000 0 -0.44 12 12
LRP1 0.022 0.044 -10000 0 -0.44 5 5
SOS1 0.026 0.002 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
STAT5A 0.025 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.034 0.056 -10000 0 -0.27 8 8
SPHK1 0.017 0.084 -10000 0 -0.44 18 18
EDG1 0.003 0.004 -10000 0 -10000 0 0
mol:DAG 0.049 0.14 0.23 86 -0.51 16 102
PLCG1 0.048 0.15 0.23 86 -0.52 16 102
NHERF/PDGFRB 0.045 0.046 -10000 0 -0.27 11 11
YES1 -0.016 0.16 -10000 0 -0.5 50 50
cell migration 0.045 0.046 -10000 0 -0.27 11 11
SHC/Grb2/SOS1 0.033 0.052 -10000 0 -0.24 7 7
SLC9A3R2 0.025 0.02 -10000 0 -0.44 1 1
SLC9A3R1 0.025 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.055 0.049 -10000 0 -0.25 11 11
FYN 0.004 0.11 -10000 0 -0.48 18 18
DOK1 0.041 0.091 0.17 176 -0.26 7 183
HRAS/GTP 0.019 0.014 -10000 0 -0.32 1 1
PDGFB 0.024 0.029 -10000 0 -0.44 2 2
RAC1 0.052 0.18 0.33 49 -0.48 21 70
PRKCD 0.042 0.093 0.18 174 -0.26 7 181
FER 0.04 0.094 0.18 171 -0.26 9 180
MAPKKK cascade 0.057 0.1 0.29 15 -0.23 7 22
RASA1 0.042 0.093 0.18 174 -0.26 7 181
NCK1 0.024 0.028 -10000 0 -0.44 2 2
NCK2 0.025 0.019 -10000 0 -0.44 1 1
p62DOK/Csk 0.058 0.078 0.17 72 -0.24 8 80
PDGFB-D/PDGFRB/SHB 0.033 0.048 -10000 0 -0.32 10 10
chemotaxis 0.03 0.15 0.22 90 -0.4 29 119
STAT1-3-5/STAT1-3-5 0.028 0.047 -10000 0 -0.24 8 8
Bovine Papilomavirus E5/PDGFRB 0.014 0.045 -10000 0 -0.32 10 10
PTPRJ 0.025 0.02 -10000 0 -0.44 1 1
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.019 0.14 0.23 2 -0.36 62 64
MAP4K1 -0.009 0.13 -10000 0 -0.44 45 45
MAP3K8 0.025 0.02 -10000 0 -0.44 1 1
PRKCB -0.002 0.12 -10000 0 -0.44 37 37
DBNL 0.023 0.021 -10000 0 -0.44 1 1
CRKL 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 -0.027 0.13 -10000 0 -0.4 50 50
JUN -0.045 0.21 -10000 0 -0.69 53 53
MAP3K7 -0.026 0.13 -10000 0 -0.4 48 48
GRAP2 0.007 0.092 -10000 0 -0.44 23 23
CRK 0.022 0.01 -10000 0 -10000 0 0
MAP2K4 -0.034 0.14 0.24 3 -0.46 43 46
LAT 0.019 0.062 -10000 0 -0.44 10 10
LCP2 0.012 0.082 -10000 0 -0.44 18 18
MAPK8 -0.041 0.22 -10000 0 -0.72 53 53
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.02 0.14 -10000 0 -0.42 48 48
LAT/GRAP2/SLP76/HPK1/HIP-55 0.026 0.13 0.25 1 -0.34 58 59
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.036 0.022 -10000 0 -0.32 2 2
Necdin/E2F1 0.019 0.034 -10000 0 -0.32 4 4
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.022 0.12 -10000 0 -0.27 80 80
NGF (dimer)/p75(NTR)/BEX1 0.008 0.13 0.2 5 -0.3 84 89
NT-4/5 (dimer)/p75(NTR) 0.016 0.095 -10000 0 -0.32 40 40
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 -0.044 0.077 0.17 7 -0.25 63 70
IKBKG 0.025 0.02 -10000 0 -0.44 1 1
BDNF 0.011 0.087 -10000 0 -0.44 20 20
MGDIs/NGR/p75(NTR)/LINGO1 0.031 0.097 0.2 1 -0.28 46 47
FURIN 0.024 0.02 -10000 0 -0.44 1 1
proBDNF (dimer)/p75(NTR)/Sortilin 0.023 0.11 -10000 0 -0.3 54 54
LINGO1 0.027 0.044 -10000 0 -0.44 4 4
Sortilin/TRAF6/NRIF 0.023 0.048 -10000 0 -0.25 14 14
proBDNF (dimer) 0.011 0.087 -10000 0 -0.44 20 20
NTRK1 0 0.1 -10000 0 -0.44 30 30
RTN4R 0.023 0.041 -10000 0 -0.44 4 4
neuron apoptosis -0.05 0.15 0.29 2 -0.48 36 38
IRAK1 0.025 0.02 -10000 0 -0.44 1 1
SHC1 -0.047 0.084 -10000 0 -0.28 59 59
ARHGDIA 0.023 0.034 -10000 0 -0.44 3 3
RhoA/GTP 0.018 0.014 -10000 0 -0.32 1 1
Gamma Secretase 0.064 0.039 -10000 0 -0.24 5 5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.031 0.11 -10000 0 -0.27 65 65
MAGEH1 0.019 0.055 -10000 0 -0.44 8 8
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.029 0.11 0.2 2 -0.27 63 65
Mammalian IAPs/DIABLO 0.051 0.08 -10000 0 -0.35 20 20
proNGF (dimer) 0.005 0.095 -10000 0 -0.44 24 24
MAGED1 0.026 0.003 -10000 0 -10000 0 0
APP 0.024 0.02 -10000 0 -0.44 1 1
NT-4/5 (dimer) 0.001 0.033 -10000 0 -0.44 1 1
ZNF274 0.018 0.058 -10000 0 -0.44 9 9
RhoA/GDP/RHOGDI -0.008 0.09 -10000 0 -0.24 64 64
NGF 0.005 0.095 -10000 0 -0.44 24 24
cell cycle arrest -0.042 0.075 0.2 7 -0.22 60 67
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.003 0.082 -10000 0 -0.24 54 54
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.03 0.087 -10000 0 -0.28 41 41
NCSTN 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0.005 0.13 -10000 0 -0.3 83 83
PSENEN 0.024 0.02 -10000 0 -0.44 1 1
mol:ceramide -0.044 0.08 0.18 6 -0.26 60 66
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.009 0.078 -10000 0 -0.38 9 9
p75(NTR)/beta APP 0.016 0.094 -10000 0 -0.32 41 41
BEX1 0.001 0.11 -10000 0 -0.44 29 29
mol:GDP -0.043 0.084 -10000 0 -0.28 61 61
NGF (dimer) -0.009 0.15 -10000 0 -0.28 125 125
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.043 0.099 -10000 0 -0.27 47 47
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
RAC1/GTP 0.015 0.091 -10000 0 -0.24 61 61
MYD88 0.026 0.002 -10000 0 -10000 0 0
CHUK 0.022 0.034 -10000 0 -0.44 3 3
NGF (dimer)/p75(NTR)/PKA 0.005 0.13 -10000 0 -0.3 83 83
RHOB 0.025 0.028 -10000 0 -0.44 2 2
RHOA 0.025 0.02 -10000 0 -0.44 1 1
MAGE-G1/E2F1 0.021 0.024 -10000 0 -0.32 1 1
NT3 (dimer) 0.009 0.087 -10000 0 -0.44 20 20
TP53 -0.055 0.098 0.23 8 -0.26 82 90
PRDM4 -0.045 0.081 0.18 7 -0.26 60 67
BDNF (dimer) -0.045 0.18 -10000 0 -0.3 185 185
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
SORT1 0.025 0.02 -10000 0 -0.44 1 1
activation of caspase activity 0.017 0.12 -10000 0 -0.26 80 80
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.034 0.11 -10000 0 -0.26 61 61
RHOC 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.02 -10000 0 -0.44 1 1
MAPK10 -0.042 0.13 0.32 5 -0.35 51 56
DIABLO 0.026 0.003 -10000 0 -10000 0 0
SMPD2 -0.045 0.081 0.18 6 -0.26 60 66
APH1B 0.022 0.039 -10000 0 -0.44 4 4
APH1A 0.025 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.021 0.11 -10000 0 -0.29 61 61
PSEN1 0.024 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.031 -10000 0 -0.32 4 4
NT3 (dimer)/p75(NTR) 0.007 0.12 -10000 0 -0.35 53 53
MAPK8 -0.031 0.11 0.32 5 -0.33 43 48
MAPK9 -0.031 0.11 0.32 5 -0.33 43 48
APAF1 0.023 0.034 -10000 0 -0.44 3 3
NTF3 0.009 0.087 -10000 0 -0.44 20 20
NTF4 0.001 0.034 -10000 0 -0.44 1 1
NDN 0.021 0.044 -10000 0 -0.44 5 5
RAC1/GDP 0.017 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.022 0.12 -10000 0 -0.25 85 85
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.053 -10000 0 -0.29 11 11
RhoA-B-C/GTP 0.004 0.13 -10000 0 -0.3 83 83
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.041 0.11 -10000 0 -0.28 60 60
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.036 0.11 -10000 0 -0.28 55 55
PRKACB 0.002 0.1 -10000 0 -0.44 30 30
proBDNF (dimer)/p75 ECD 0.026 0.069 -10000 0 -0.32 22 22
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.015 0.076 -10000 0 -0.44 15 15
BIRC2 0.015 0.07 -10000 0 -0.44 13 13
neuron projection morphogenesis -0.045 0.099 0.13 19 -0.27 78 97
BAD -0.037 0.12 0.33 7 -0.35 44 51
RIPK2 0.022 0.009 -10000 0 -10000 0 0
NGFR 0 0.12 -10000 0 -0.44 40 40
CYCS -0.048 0.082 0.17 5 -0.25 71 76
ADAM17 0.024 0.028 -10000 0 -0.44 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.029 0.099 -10000 0 -0.26 51 51
BCL2L11 -0.037 0.12 0.33 7 -0.35 44 51
BDNF (dimer)/p75(NTR) 0.008 0.12 -10000 0 -0.35 54 54
PI3K 0.031 0.11 -10000 0 -0.26 62 62
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.032 0.11 -10000 0 -0.26 60 60
NDNL2 0.024 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
PRKCI 0.023 0.034 -10000 0 -0.44 3 3
NGF (dimer)/p75(NTR) 0.005 0.12 -10000 0 -0.33 62 62
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.035 0.1 -10000 0 -0.27 58 58
TRAF6 0.025 0.02 -10000 0 -0.44 1 1
RAC1 0.023 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.02 -10000 0 -0.44 1 1
PLG -0.029 0.11 -10000 0 -0.44 38 38
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.029 0.11 0.15 1 -0.29 73 74
SQSTM1 0.026 0.003 -10000 0 -10000 0 0
NGFRAP1 0 0.11 -10000 0 -0.44 32 32
CASP3 -0.036 0.12 0.34 6 -0.33 48 54
E2F1 0.015 0.023 -10000 0 -0.44 1 1
CASP9 0.024 0.02 -10000 0 -0.44 1 1
IKK complex 0.008 0.12 -10000 0 -0.35 33 33
NGF (dimer)/TRKA 0.006 0.11 -10000 0 -0.33 53 53
MMP7 -0.026 0.16 -10000 0 -0.44 77 77
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.039 0.11 -10000 0 -0.26 64 64
MMP3 -0.039 0.17 -10000 0 -0.44 88 88
APAF-1/Caspase 9 -0.064 0.093 -10000 0 -0.41 21 21
Glucocorticoid receptor regulatory network

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.043 0.078 0.3 13 -10000 0 13
SMARCC2 0.026 0.007 -10000 0 -10000 0 0
SMARCC1 0.026 0.008 -10000 0 -10000 0 0
TBX21 -0.077 0.22 0.34 5 -0.73 47 52
SUMO2 0.024 0.022 -10000 0 -0.44 1 1
STAT1 (dimer) 0.029 0.028 -10000 0 -0.44 2 2
FKBP4 0.025 0.006 -10000 0 -10000 0 0
FKBP5 0.024 0.028 -10000 0 -0.44 2 2
GR alpha/HSP90/FKBP51/HSP90 0.072 0.099 0.3 38 -0.29 7 45
PRL -0.037 0.096 -10000 0 -0.47 4 4
cortisol/GR alpha (dimer)/TIF2 0.089 0.2 0.52 60 -0.45 2 62
RELA -0.008 0.095 -10000 0 -0.26 38 38
FGG 0.073 0.17 0.44 62 -0.3 2 64
GR beta/TIF2 0.04 0.11 0.29 46 -0.33 9 55
IFNG -0.16 0.33 -10000 0 -0.88 79 79
apoptosis 0.014 0.14 0.48 19 -0.44 12 31
CREB1 0.026 0.028 -10000 0 -0.44 2 2
histone acetylation -0.032 0.1 -10000 0 -0.36 29 29
BGLAP -0.039 0.12 -10000 0 -0.66 8 8
GR/PKAc 0.076 0.11 0.3 30 -0.26 23 53
NF kappa B1 p50/RelA -0.021 0.18 -10000 0 -0.37 95 95
SMARCD1 0.025 0.021 -10000 0 -0.44 1 1
MDM2 0.045 0.081 0.22 64 -0.26 2 66
GATA3 0.018 0.079 -10000 0 -0.44 16 16
AKT1 0.02 0.02 -10000 0 -0.45 1 1
CSF2 -0.15 0.36 -10000 0 -1.1 63 63
GSK3B 0.024 0.029 -10000 0 -0.44 2 2
NR1I3 0.009 0.16 0.47 18 -0.78 11 29
CSN2 0.059 0.14 0.36 66 -0.27 2 68
BRG1/BAF155/BAF170/BAF60A 0.066 0.032 -10000 0 -0.24 5 5
NFATC1 0.015 0.061 -10000 0 -0.44 9 9
POU2F1 0.022 0.052 -10000 0 -0.44 7 7
CDKN1A -0.043 0.15 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.024 0.022 -10000 0 -0.44 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.084 0.09 0.3 33 -0.26 8 41
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.006 0.15 0.43 18 -0.74 10 28
JUN -0.096 0.16 0.28 1 -0.42 67 68
IL4 -0.042 0.12 -10000 0 -0.5 21 21
CDK5R1 0.026 0.008 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.063 0.14 0.2 54 -0.33 64 118
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.09 0.089 0.31 35 -0.27 7 42
cortisol/GR alpha (monomer) 0.12 0.25 0.62 76 -0.35 2 78
NCOA2 0.018 0.048 -10000 0 -0.44 6 6
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.027 0.11 -10000 0 -0.32 36 36
AP-1/NFAT1-c-4 -0.15 0.26 -10000 0 -0.54 150 150
AFP -0.079 0.14 -10000 0 -0.8 4 4
SUV420H1 0.025 0.02 -10000 0 -0.44 1 1
IRF1 0.071 0.12 0.41 31 -0.5 1 32
TP53 -0.001 0.12 -10000 0 -0.44 39 39
PPP5C 0.026 0.003 -10000 0 -10000 0 0
KRT17 -0.22 0.41 -10000 0 -0.98 113 113
KRT14 -0.057 0.14 -10000 0 -0.73 10 10
TBP 0.029 0.024 -10000 0 -0.37 2 2
CREBBP 0.034 0.036 0.29 2 -0.27 3 5
HDAC1 0.024 0.005 -10000 0 -10000 0 0
HDAC2 0.032 0.025 0.15 1 -10000 0 1
AP-1 -0.15 0.27 -10000 0 -0.54 151 151
MAPK14 0.025 0.01 -10000 0 -10000 0 0
MAPK10 0.002 0.1 -10000 0 -0.44 30 30
MAPK11 0.024 0.037 -10000 0 -0.44 3 3
KRT5 -0.18 0.37 -10000 0 -0.94 89 89
interleukin-1 receptor activity 0.007 0.025 0.12 1 -10000 0 1
NCOA1 0.027 0.019 -10000 0 -0.44 1 1
STAT1 0.029 0.028 -10000 0 -0.44 2 2
CGA -0.045 0.11 -10000 0 -0.5 9 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.065 0.18 0.47 70 -0.44 8 78
MAPK3 0.024 0.022 -10000 0 -0.44 1 1
MAPK1 0.024 0.01 -10000 0 -10000 0 0
ICAM1 -0.084 0.21 -10000 0 -0.58 58 58
NFKB1 -0.009 0.098 -10000 0 -0.22 70 70
MAPK8 -0.072 0.15 0.34 1 -0.38 61 62
MAPK9 0.025 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.013 0.14 0.48 19 -0.46 13 32
BAX -0.037 0.12 -10000 0 -0.78 3 3
POMC -0.095 0.29 -10000 0 -1.4 24 24
EP300 0.033 0.049 0.3 3 -0.34 5 8
cortisol/GR alpha (dimer)/p53 0.07 0.21 0.56 53 -0.35 1 54
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.073 0.22 44 -0.23 2 46
SGK1 0.027 0.12 -10000 0 -1.1 4 4
IL13 -0.11 0.2 -10000 0 -0.64 38 38
IL6 -0.14 0.35 -10000 0 -1 71 71
PRKACG -0.005 0.021 -10000 0 -10000 0 0
IL5 -0.091 0.16 -10000 0 -0.55 29 29
IL2 -0.12 0.23 -10000 0 -0.66 52 52
CDK5 0.025 0.006 -10000 0 -10000 0 0
PRKACB 0.002 0.1 -10000 0 -0.44 30 30
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
IL8 -0.16 0.36 -10000 0 -0.92 90 90
CDK5R1/CDK5 0.037 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.003 0.17 -10000 0 -0.4 52 52
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.1 0.2 0.5 75 -10000 0 75
SMARCA4 0.025 0.021 -10000 0 -0.44 1 1
chromatin remodeling 0.071 0.13 0.35 61 -0.38 4 65
NF kappa B1 p50/RelA/Cbp 0.018 0.17 0.3 18 -0.46 35 53
JUN (dimer) -0.095 0.16 0.28 1 -0.42 67 68
YWHAH 0.025 0.005 -10000 0 -10000 0 0
VIPR1 -0.068 0.18 -10000 0 -0.67 36 36
NR3C1 0.067 0.17 0.4 71 -0.38 6 77
NR4A1 0.016 0.095 -10000 0 -0.47 21 21
TIF2/SUV420H1 0.029 0.038 -10000 0 -0.32 6 6
MAPKKK cascade 0.014 0.14 0.48 19 -0.44 12 31
cortisol/GR alpha (dimer)/Src-1 0.11 0.21 0.53 77 -0.36 1 78
PBX1 0.017 0.07 -10000 0 -0.44 13 13
POU1F1 0.004 0.021 -10000 0 -10000 0 0
SELE -0.14 0.35 -10000 0 -0.96 76 76
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.071 0.13 0.35 61 -0.38 4 65
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.1 0.2 0.5 75 -10000 0 75
mol:cortisol 0.067 0.15 0.36 76 -10000 0 76
MMP1 -0.19 0.42 -10000 0 -1.1 95 95
EPHB forward signaling

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
Ephrin A5/EPHB2 0.003 0.096 -10000 0 -0.27 61 61
cell-cell adhesion 0.037 0.061 0.23 45 -10000 0 45
Ephrin B/EPHB2/RasGAP 0.038 0.07 -10000 0 -0.26 20 20
ITSN1 0.025 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
SHC1 0.025 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.024 0.061 -10000 0 -0.28 22 22
Ephrin B1/EPHB1 0.023 0.079 -10000 0 -0.27 38 38
HRAS/GDP -0.004 0.091 -10000 0 -0.31 17 17
Ephrin B/EPHB1/GRB7 0.032 0.09 -10000 0 -0.25 41 41
Endophilin/SYNJ1 0.017 0.09 0.17 116 -0.25 19 135
KRAS 0.021 0.044 -10000 0 -0.44 5 5
Ephrin B/EPHB1/Src 0.019 0.083 -10000 0 -0.26 34 34
endothelial cell migration 0.038 0.038 -10000 0 -0.29 4 4
GRB2 0.025 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.005 -10000 0 -10000 0 0
PAK1 0.015 0.1 0.18 123 -0.28 19 142
HRAS 0.025 0.02 -10000 0 -0.44 1 1
RRAS 0.019 0.094 0.18 120 -0.26 18 138
DNM1 0.022 0.049 -10000 0 -0.44 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.004 0.098 0.18 76 -0.24 36 112
lamellipodium assembly -0.037 0.061 -10000 0 -0.23 45 45
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.083 0.21 1 -0.26 29 30
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
EPHB2 0.018 0.058 -10000 0 -0.44 9 9
EPHB3 0.009 0.09 -10000 0 -0.44 22 22
EPHB1 0.008 0.12 -10000 0 -0.44 37 37
EPHB4 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.004 0.084 0.32 5 -0.31 16 21
Ephrin B/EPHB2 0.03 0.062 -10000 0 -0.26 18 18
Ephrin B/EPHB3 0.027 0.074 -10000 0 -0.26 28 28
JNK cascade -0.039 0.071 0.35 4 -0.24 48 52
Ephrin B/EPHB1 0.023 0.085 -10000 0 -0.24 43 43
RAP1/GDP 0.007 0.11 0.31 19 -0.3 13 32
EFNB2 0.019 0.022 -10000 0 -0.44 1 1
EFNB3 0.013 0.071 -10000 0 -0.44 13 13
EFNB1 0.025 0.02 -10000 0 -0.44 1 1
Ephrin B2/EPHB1-2 0.02 0.082 -10000 0 -0.25 43 43
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
CDC42/GTP 0.002 0.095 -10000 0 -0.3 27 27
Rap1/GTP -0.015 0.074 -10000 0 -0.33 9 9
axon guidance 0.003 0.096 -10000 0 -0.27 61 61
MAPK3 0.004 0.079 0.18 4 -0.34 10 14
MAPK1 0.004 0.077 0.18 1 -0.34 10 11
Rac1/GDP -0.009 0.089 0.23 4 -0.29 14 18
actin cytoskeleton reorganization -0.046 0.065 -10000 0 -0.29 18 18
CDC42/GDP 0.001 0.11 0.3 22 -0.3 19 41
PI3K 0.042 0.04 -10000 0 -0.29 4 4
EFNA5 -0.01 0.14 -10000 0 -0.44 52 52
Ephrin B2/EPHB4 0.026 0.019 -10000 0 -0.27 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.003 0.058 -10000 0 -0.24 18 18
CDC42 0.021 0.039 -10000 0 -0.44 4 4
RAS family/GTP -0.045 0.072 -10000 0 -0.33 15 15
PTK2 0.077 0.2 0.56 87 -0.44 1 88
MAP4K4 -0.039 0.071 0.35 4 -0.24 48 52
SRC 0.015 0.023 -10000 0 -0.44 1 1
KALRN 0.022 0.043 -10000 0 -0.44 5 5
Intersectin/N-WASP 0.036 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.098 0.26 20 -0.38 8 28
MAP2K1 0.004 0.078 0.19 1 -0.26 28 29
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.043 0.094 -10000 0 -0.26 47 47
cell migration 0.029 0.12 0.26 21 -0.39 10 31
NRAS 0.018 0.058 -10000 0 -0.44 9 9
SYNJ1 0.017 0.091 0.18 116 -0.25 19 135
PXN 0.026 0.002 -10000 0 -10000 0 0
TF -0.003 0.1 0.16 108 -0.24 43 151
HRAS/GTP 0.009 0.085 -10000 0 -0.25 40 40
Ephrin B1/EPHB1-2 0.03 0.086 -10000 0 -0.25 45 45
cell adhesion mediated by integrin -0.024 0.094 0.26 11 -0.19 116 127
RAC1 0.023 0.008 -10000 0 -10000 0 0
mol:GTP 0.01 0.086 -10000 0 -0.24 51 51
RAC1-CDC42/GTP -0.047 0.077 -10000 0 -0.26 52 52
RASA1 0.024 0.028 -10000 0 -0.44 2 2
RAC1-CDC42/GDP -0.003 0.093 0.24 3 -0.29 17 20
ruffle organization 0.005 0.13 0.39 33 -0.39 5 38
NCK1 0.024 0.028 -10000 0 -0.44 2 2
receptor internalization 0.011 0.091 0.17 114 -0.24 22 136
Ephrin B/EPHB2/KALRN 0.037 0.077 -10000 0 -0.29 20 20
ROCK1 -0.021 0.055 0.18 1 -0.26 26 27
RAS family/GDP -0.045 0.064 -10000 0 -0.29 18 18
Rac1/GTP -0.038 0.064 -10000 0 -0.24 45 45
Ephrin B/EPHB1/Src/Paxillin 0.001 0.07 -10000 0 -0.26 34 34
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.014 0.05 -10000 0 -0.26 13 13
NFATC2 -0.023 0.074 -10000 0 -0.3 37 37
NFATC3 -0.012 0.036 -10000 0 -0.14 2 2
CD40LG -0.067 0.24 0.35 2 -0.56 81 83
PTGS2 -0.071 0.24 0.35 1 -0.54 83 84
JUNB 0.024 0.034 -10000 0 -0.44 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.029 -10000 0 -10000 0 0
CaM/Ca2+ 0.002 0.029 -10000 0 -10000 0 0
CALM1 0.01 0.027 -10000 0 -10000 0 0
JUN 0.007 0.047 -10000 0 -0.46 4 4
mol:Ca2+ -0.007 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 0.016 0.076 -10000 0 -0.44 15 15
CREM 0.026 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.012 0.15 -10000 0 -0.35 58 58
FOS -0.003 0.085 -10000 0 -0.46 17 17
IFNG -0.07 0.24 0.35 1 -0.52 90 91
AP-1/NFAT1-c-4 -0.054 0.25 -10000 0 -0.55 85 85
FASLG -0.068 0.24 0.35 1 -0.54 83 84
NFAT1-c-4/ICER1 -0.028 0.09 0.18 1 -0.27 49 50
IL2RA -0.069 0.24 0.35 2 -0.57 79 81
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSF2 -0.073 0.25 0.35 2 -0.56 89 91
JunB/Fra1/NFAT1-c-4 0.002 0.12 0.21 1 -0.29 48 49
IL4 -0.058 0.21 0.34 2 -0.51 71 73
IL2 -0.016 0.14 -10000 0 -0.87 16 16
IL3 -0.017 0.13 -10000 0 -0.66 21 21
FKBP1A 0.021 0.01 -10000 0 -10000 0 0
BATF3 0.021 0.053 -10000 0 -0.44 7 7
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.02 0.052 -10000 0 -0.44 7 7
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.035 0.12 -10000 0 -0.39 43 43
CRKL -0.021 0.11 -10000 0 -0.4 41 41
HRAS -0.02 0.13 -10000 0 -0.39 46 46
mol:PIP3 -0.009 0.11 0.26 2 -0.37 39 41
SPRED1 0.02 0.044 -10000 0 -0.44 5 5
SPRED2 0.024 0.034 -10000 0 -0.44 3 3
GAB1 -0.017 0.12 -10000 0 -0.42 40 40
FOXO3 -0.02 0.14 0.25 1 -0.4 53 54
AKT1 -0.019 0.16 0.26 1 -0.43 54 55
BAD -0.02 0.14 0.25 1 -0.41 53 54
megakaryocyte differentiation -0.055 0.14 -10000 0 -0.44 46 46
GSK3B -0.02 0.15 0.31 2 -0.4 55 57
RAF1 -0.022 0.11 0.23 1 -0.32 45 46
SHC1 0.025 0.004 -10000 0 -10000 0 0
STAT3 -0.018 0.12 -10000 0 -0.42 39 39
STAT1 -0.057 0.3 -10000 0 -0.97 49 49
HRAS/SPRED1 -0.007 0.12 -10000 0 -0.33 48 48
cell proliferation -0.017 0.11 -10000 0 -0.41 40 40
PIK3CA 0.024 0.028 -10000 0 -0.45 2 2
TEC 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.015 0.14 -10000 0 -0.44 46 46
HRAS/SPRED2 -0.007 0.12 -10000 0 -0.32 47 47
LYN/TEC/p62DOK 0.019 0.12 -10000 0 -0.39 35 35
MAPK3 -0.016 0.081 0.19 2 -0.26 27 29
STAP1 -0.032 0.13 -10000 0 -0.46 43 43
GRAP2 0.007 0.092 -10000 0 -0.44 23 23
JAK2 -0.047 0.27 -10000 0 -0.89 46 46
STAT1 (dimer) -0.055 0.29 -10000 0 -0.94 49 49
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.004 0.15 -10000 0 -0.42 48 48
actin filament polymerization -0.022 0.11 0.22 1 -0.4 39 40
LYN 0.023 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.042 0.18 -10000 0 -0.63 45 45
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
CBL/CRKL/GRB2 0.005 0.11 -10000 0 -0.37 39 39
PI3K 0.007 0.14 -10000 0 -0.43 43 43
PTEN 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.04 0.32 -10000 0 -1.2 36 36
MAPK8 -0.018 0.12 -10000 0 -0.41 40 40
STAT3 (dimer) -0.017 0.11 -10000 0 -0.41 39 39
positive regulation of transcription -0.012 0.068 0.18 2 -0.22 21 23
mol:GDP -0.015 0.14 -10000 0 -0.39 51 51
PIK3C2B -0.017 0.12 -10000 0 -0.42 39 39
CBL/CRKL -0.006 0.11 -10000 0 -0.38 40 40
FER -0.019 0.12 -10000 0 -0.42 41 41
SH2B3 -0.018 0.12 -10000 0 -0.41 40 40
PDPK1 -0.009 0.1 0.24 3 -0.36 34 37
SNAI2 -0.019 0.11 -10000 0 -0.4 41 41
positive regulation of cell proliferation -0.036 0.21 -10000 0 -0.71 46 46
KITLG 0.012 0.079 -10000 0 -0.46 15 15
cell motility -0.036 0.21 -10000 0 -0.71 46 46
PTPN6 0.026 0.008 -10000 0 -10000 0 0
EPOR 0.005 0.14 -10000 0 -1.2 4 4
STAT5A (dimer) -0.027 0.17 -10000 0 -0.6 42 42
SOCS1 0.02 0.069 -10000 0 -0.44 12 12
cell migration 0.035 0.13 0.43 44 -10000 0 44
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.018 0.019 -10000 0 -10000 0 0
VAV1 -0.002 0.11 -10000 0 -0.44 35 35
GRB10 -0.018 0.11 -10000 0 -0.41 38 38
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
SCF/KIT -0.014 0.12 -10000 0 -0.44 40 40
GO:0007205 0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.02 0.086 0.2 2 -0.26 42 44
CBL 0.025 0.004 -10000 0 -10000 0 0
KIT -0.053 0.32 -10000 0 -1.3 34 34
MAP2K2 -0.019 0.086 0.2 2 -0.27 41 43
SHC/Grb2/SOS1 0.021 0.12 -10000 0 -0.4 39 39
STAT5A -0.027 0.18 -10000 0 -0.62 42 42
GRB2 0.025 0.004 -10000 0 -10000 0 0
response to radiation -0.019 0.11 -10000 0 -0.39 41 41
SHC/GRAP2 0.022 0.07 -10000 0 -0.32 23 23
PTPRO -0.056 0.14 -10000 0 -0.45 46 46
SH2B2 -0.022 0.12 0.22 1 -0.41 39 40
DOK1 0.026 0.001 -10000 0 -10000 0 0
MATK -0.036 0.13 -10000 0 -0.44 44 44
CREBBP 0.027 0.039 -10000 0 -0.18 4 4
BCL2 -0.14 0.34 -10000 0 -1.1 40 40
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.001 0.071 -10000 0 -0.4 14 14
Crk/p130 Cas/Paxillin -0.029 0.096 -10000 0 -0.3 45 45
JUN -0.029 0.095 -10000 0 -0.42 16 16
HRAS 0.025 0.02 -10000 0 -0.44 1 1
RET51/GFRalpha1/GDNF/GRB10 0.02 0.13 -10000 0 -0.3 70 70
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
FRS2 0.024 0.028 -10000 0 -0.44 2 2
RAP1A/GDP 0.018 0.014 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/DOK1 0.026 0.12 -10000 0 -0.29 72 72
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.024 0.086 0.19 1 -0.25 48 49
RHOA 0.025 0.02 -10000 0 -0.44 1 1
RAP1A/GTP 0.022 0.11 -10000 0 -0.26 72 72
GRB7 0.025 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.025 0.12 -10000 0 -0.29 72 72
MAPKKK cascade -0.004 0.11 -10000 0 -0.29 66 66
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
RET9/GFRalpha1/GDNF/IRS1 0.021 0.092 -10000 0 -0.26 55 55
lamellipodium assembly -0.022 0.09 -10000 0 -0.28 46 46
RET51/GFRalpha1/GDNF/SHC 0.024 0.12 -10000 0 -0.29 72 72
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
RET9/GFRalpha1/GDNF/SHC 0.024 0.084 -10000 0 -0.25 48 48
RET9/GFRalpha1/GDNF/Shank3 0.023 0.086 -10000 0 -0.25 49 49
MAPK3 -0.05 0.088 -10000 0 -0.33 23 23
DOK1 0.026 0.001 -10000 0 -10000 0 0
DOK6 0.007 0.077 -10000 0 -0.44 16 16
PXN 0.026 0.002 -10000 0 -10000 0 0
neurite development -0.038 0.083 -10000 0 -0.36 18 18
DOK5 -0.005 0.099 -10000 0 -0.44 27 27
GFRA1 -0.008 0.13 -10000 0 -0.44 47 47
MAPK8 -0.023 0.096 -10000 0 -0.26 74 74
HRAS/GTP 0.016 0.13 -10000 0 -0.31 70 70
tube development 0.021 0.083 0.2 5 -0.24 49 54
MAPK1 -0.049 0.088 0.34 1 -0.35 19 20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.003 0.075 -10000 0 -0.23 53 53
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
SRC 0.015 0.023 -10000 0 -0.44 1 1
PDLIM7 0.026 0.021 -10000 0 -0.44 1 1
RET51/GFRalpha1/GDNF/Dok6 0.002 0.11 0.25 1 -0.29 58 59
SHC1 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.025 0.12 -10000 0 -0.29 71 71
RET51/GFRalpha1/GDNF/Dok5 -0.002 0.12 0.24 2 -0.3 68 70
PRKCA 0.024 0.02 -10000 0 -0.44 1 1
HRAS/GDP 0.019 0.014 -10000 0 -0.32 1 1
CREB1 -0.009 0.097 -10000 0 -0.3 48 48
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.002 0.073 -10000 0 -0.24 48 48
RET51/GFRalpha1/GDNF/Grb7 0.025 0.12 -10000 0 -0.29 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.004 0.12 -10000 0 -0.44 37 37
DOK4 0.025 0.02 -10000 0 -0.44 1 1
JNK cascade -0.028 0.093 -10000 0 -0.41 16 16
RET9/GFRalpha1/GDNF/FRS2 0.024 0.085 -10000 0 -0.25 49 49
SHANK3 0.023 0.028 -10000 0 -0.44 2 2
RASA1 0.024 0.028 -10000 0 -0.44 2 2
NCK1 0.024 0.028 -10000 0 -0.44 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.001 0.07 -10000 0 -0.23 48 48
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.015 0.1 -10000 0 -0.26 76 76
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.014 0.1 -10000 0 -0.26 76 76
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.013 0.11 -10000 0 -0.28 69 69
PI3K -0.034 0.13 -10000 0 -0.4 48 48
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.086 -10000 0 -0.24 49 49
GRB10 0.02 0.039 -10000 0 -0.44 4 4
activation of MAPKK activity -0.011 0.092 -10000 0 -0.26 54 54
RET51/GFRalpha1/GDNF/FRS2 0.024 0.12 -10000 0 -0.29 74 74
GAB1 0.025 0.004 -10000 0 -10000 0 0
IRS1 0.019 0.058 -10000 0 -0.44 9 9
IRS2 0.015 0.048 -10000 0 -0.44 6 6
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.11 -10000 0 -0.28 69 69
RET51/GFRalpha1/GDNF/PKC alpha 0.025 0.12 -10000 0 -0.29 68 68
GRB2 0.025 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GDNF 0.014 0.027 -10000 0 -0.44 1 1
RAC1 0.023 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.021 0.13 -10000 0 -0.3 76 76
Rac1/GTP -0.023 0.11 -10000 0 -0.33 45 45
RET9/GFRalpha1/GDNF 0.01 0.086 -10000 0 -0.27 48 48
GFRalpha1/GDNF 0.009 0.1 -10000 0 -0.32 48 48
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.021 0.14 -9999 0 -0.28 105 105
SMAD6-7/SMURF1 0.036 0.038 -9999 0 -0.35 3 3
NOG 0.013 0.058 -9999 0 -0.44 7 7
SMAD9 -0.044 0.17 -9999 0 -0.51 64 64
SMAD4 0.019 0.012 -9999 0 -10000 0 0
SMAD5 -0.04 0.14 -9999 0 -0.42 45 45
BMP7/USAG1 -0.051 0.15 -9999 0 -0.36 111 111
SMAD5/SKI -0.035 0.15 -9999 0 -0.4 52 52
SMAD1 -0.004 0.072 -9999 0 -0.42 10 10
BMP2 0.016 0.052 -9999 0 -0.44 7 7
SMAD1/SMAD1/SMAD4 0.01 0.068 -9999 0 -0.39 7 7
BMPR1A 0.024 0.02 -9999 0 -0.44 1 1
BMPR1B -0.007 0.13 -9999 0 -0.44 44 44
BMPR1A-1B/BAMBI 0.012 0.12 -9999 0 -0.29 76 76
AHSG 0.017 0.047 -9999 0 -0.44 3 3
CER1 -0.002 0.024 -9999 0 -10000 0 0
BMP2-4/CER1 0.031 0.055 -9999 0 -0.28 14 14
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.034 0.13 -9999 0 -0.37 47 47
BMP2-4 (homodimer) 0.023 0.058 -9999 0 -0.32 14 14
RGMB 0.027 0.032 -9999 0 -0.44 2 2
BMP6/BMPR2/BMPR1A-1B 0.035 0.1 -9999 0 -0.26 57 57
RGMA -0.018 0.14 -9999 0 -0.44 57 57
SMURF1 0.025 0.006 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.028 0.12 -9999 0 -0.34 43 43
BMP2-4/USAG1 -0.009 0.12 -9999 0 -0.28 84 84
SMAD6/SMURF1/SMAD5 -0.036 0.14 -9999 0 -0.39 54 54
SOSTDC1 -0.044 0.17 -9999 0 -0.44 85 85
BMP7/BMPR2/BMPR1A-1B -0.015 0.12 -9999 0 -0.28 89 89
SKI 0.025 0.005 -9999 0 -10000 0 0
BMP6 (homodimer) 0.018 0.065 -9999 0 -0.44 11 11
HFE2 -0.007 0.02 -9999 0 -10000 0 0
ZFYVE16 0.012 0.077 -9999 0 -0.44 16 16
MAP3K7 0.025 0.004 -9999 0 -10000 0 0
BMP2-4/CHRD 0.025 0.081 -9999 0 -0.29 31 31
SMAD5/SMAD5/SMAD4 -0.035 0.14 -9999 0 -0.42 45 45
MAPK1 0.025 0.005 -9999 0 -10000 0 0
TAK1/TAB family -0.016 0.11 -9999 0 -0.3 47 47
BMP7 (homodimer) -0.038 0.15 -9999 0 -0.44 69 69
NUP214 0.026 0.003 -9999 0 -10000 0 0
BMP6/FETUA 0.034 0.057 -9999 0 -0.32 13 13
SMAD1/SKI 0.007 0.074 -9999 0 -0.4 10 10
SMAD6 0.023 0.028 -9999 0 -0.44 2 2
CTDSP2 0.026 0.002 -9999 0 -10000 0 0
BMP2-4/FETUA 0.036 0.058 -9999 0 -0.27 15 15
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.02 0.15 -9999 0 -0.44 61 61
BMPR2 (homodimer) 0.022 0.043 -9999 0 -0.44 5 5
GADD34/PP1CA 0.041 0.054 -9999 0 -0.27 16 16
BMPR1A-1B (homodimer) 0.014 0.098 -9999 0 -0.32 45 45
CHRDL1 -0.038 0.18 -9999 0 -0.44 93 93
ENDOFIN/SMAD1 0.002 0.086 -9999 0 -0.44 10 10
SMAD6-7/SMURF1/SMAD1 0.019 0.08 -9999 0 -0.43 8 8
SMAD6/SMURF1 0.025 0.006 -9999 0 -10000 0 0
BAMBI 0 0.12 -9999 0 -0.44 36 36
SMURF2 0.023 0.034 -9999 0 -0.44 3 3
BMP2-4/CHRDL1 -0.004 0.13 -9999 0 -0.28 93 93
BMP2-4/GREM1 0.005 0.11 -9999 0 -0.28 68 68
SMAD7 0.018 0.029 -9999 0 -0.44 2 2
SMAD8A/SMAD8A/SMAD4 -0.042 0.18 -9999 0 -0.47 75 75
SMAD1/SMAD6 0.006 0.075 -9999 0 -0.39 11 11
TAK1/SMAD6 0.036 0.01 -9999 0 -10000 0 0
BMP7 -0.038 0.15 -9999 0 -0.44 69 69
BMP6 0.018 0.065 -9999 0 -0.44 11 11
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.041 0.13 -9999 0 -0.35 63 63
PPM1A 0.024 0.006 -9999 0 -10000 0 0
SMAD1/SMURF2 0.006 0.079 -9999 0 -0.4 12 12
SMAD7/SMURF1 0.026 0.027 -9999 0 -0.32 2 2
CTDSPL 0.026 0.002 -9999 0 -10000 0 0
PPP1CA 0.026 0.004 -9999 0 -10000 0 0
XIAP 0.025 0.02 -9999 0 -0.44 1 1
CTDSP1 0.025 0.019 -9999 0 -0.44 1 1
PPP1R15A 0.026 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.05 0.16 -9999 0 -0.43 64 64
CHRD 0.009 0.09 -9999 0 -0.44 22 22
BMPR2 0.022 0.043 -9999 0 -0.44 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.04 0.12 -9999 0 -0.38 41 41
BMP4 0.02 0.057 -9999 0 -0.44 8 8
FST -0.001 0.12 -9999 0 -0.44 37 37
BMP2-4/NOG 0.033 0.062 -9999 0 -0.28 17 17
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.008 0.12 -9999 0 -0.26 87 87
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.006 0.25 -10000 0 -0.83 40 40
NCK1/PAK1/Dok-R -0.035 0.1 -10000 0 -0.4 40 40
NCK1/Dok-R -0.014 0.28 -10000 0 -1 37 37
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
mol:beta2-estradiol 0.006 0.055 0.24 30 -10000 0 30
RELA 0.025 0.004 -10000 0 -10000 0 0
SHC1 0.026 0.004 -10000 0 -10000 0 0
Rac/GDP 0.017 0.006 -10000 0 -10000 0 0
F2 -0.043 0.14 0.28 28 -0.38 60 88
TNIP2 0.024 0.02 -10000 0 -0.44 1 1
NF kappa B/RelA 0.017 0.26 -10000 0 -0.94 37 37
FN1 -0.011 0.14 -10000 0 -0.44 54 54
PLD2 -0.042 0.27 -10000 0 -1 36 36
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
GRB14 -0.048 0.18 -10000 0 -0.44 94 94
ELK1 -0.017 0.25 -10000 0 -0.94 37 37
GRB7 0.025 0.005 -10000 0 -10000 0 0
PAK1 0.026 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.003 0.29 -10000 0 -1 39 39
CDKN1A 0.017 0.2 0.45 2 -0.64 29 31
ITGA5 0.025 0.041 -10000 0 -0.44 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.014 0.28 -10000 0 -1 37 37
CRK 0.022 0.01 -10000 0 -10000 0 0
mol:NO 0.022 0.2 0.35 16 -0.62 41 57
PLG -0.055 0.27 -10000 0 -1 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.002 0.23 -10000 0 -0.81 38 38
GRB2 0.025 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.028 -10000 0 -0.45 2 2
ANGPT2 -0.029 0.21 0.42 1 -0.71 26 27
BMX -0.055 0.28 -10000 0 -1.1 37 37
ANGPT1 -0.029 0.28 -10000 0 -1.2 30 30
tube development 0.005 0.2 0.4 4 -0.65 39 43
ANGPT4 0.013 0.018 -10000 0 -10000 0 0
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.035 0.3 -10000 0 -1.1 37 37
alpha5/beta1 Integrin 0.037 0.031 -10000 0 -0.32 4 4
FGF2 0.005 0.099 -10000 0 -0.44 26 26
STAT5A (dimer) 0.013 0.23 0.44 1 -0.73 40 41
mol:L-citrulline 0.022 0.2 0.35 16 -0.62 41 57
AGTR1 -0.008 0.14 -10000 0 -0.44 50 50
MAPK14 -0.022 0.28 -10000 0 -1 38 38
Tie2/SHP2 0.011 0.19 -10000 0 -0.96 17 17
TEK -0.01 0.2 -10000 0 -1.2 13 13
RPS6KB1 0.006 0.24 0.45 2 -0.81 39 41
Angiotensin II/AT1 -0.003 0.097 -10000 0 -0.31 50 50
Tie2/Ang1/GRB2 -0.007 0.29 -10000 0 -1.1 37 37
MAPK3 -0.039 0.25 -10000 0 -0.97 36 36
MAPK1 -0.039 0.25 -10000 0 -0.96 36 36
Tie2/Ang1/GRB7 -0.008 0.29 -10000 0 -1.1 37 37
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MAPK8 -0.043 0.27 -10000 0 -1 37 37
PI3K -0.005 0.28 -10000 0 -0.96 39 39
FES -0.035 0.3 -10000 0 -1.1 38 38
Crk/Dok-R -0.015 0.27 -10000 0 -1 37 37
Tie2/Ang1/ABIN2 -0.007 0.29 -10000 0 -1.1 37 37
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.015 0.23 0.37 1 -0.74 40 41
STAT5A 0.026 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.028 0.25 0.42 8 -0.79 39 47
Tie2/Ang2 -0.03 0.25 -10000 0 -0.89 37 37
Tie2/Ang1 -0.041 0.3 -10000 0 -1.1 37 37
FOXO1 0.028 0.24 0.41 5 -0.74 41 46
ELF1 0.017 0.042 -10000 0 -0.45 3 3
ELF2 -0.038 0.27 -10000 0 -1 37 37
mol:Choline -0.039 0.25 -10000 0 -1 36 36
cell migration -0.017 0.066 -10000 0 -0.22 45 45
FYN -0.002 0.23 0.43 2 -0.74 39 41
DOK2 0.011 0.065 -10000 0 -0.44 11 11
negative regulation of cell cycle 0.02 0.18 0.4 5 -0.55 35 40
ETS1 0.017 0.069 -10000 0 -0.26 31 31
PXN 0.033 0.22 0.37 21 -0.66 39 60
ITGB1 0.026 0.002 -10000 0 -10000 0 0
NOS3 0.015 0.22 0.38 6 -0.7 41 47
RAC1 0.023 0.008 -10000 0 -10000 0 0
TNF 0.003 0.11 -10000 0 -0.35 46 46
MAPKKK cascade -0.039 0.25 -10000 0 -1 36 36
RASA1 0.024 0.028 -10000 0 -0.44 2 2
Tie2/Ang1/Shc -0.005 0.29 -10000 0 -1.1 37 37
NCK1 0.024 0.028 -10000 0 -0.44 2 2
vasculogenesis 0.025 0.18 0.34 18 -0.55 41 59
mol:Phosphatidic acid -0.039 0.25 -10000 0 -1 36 36
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.022 0.2 0.35 16 -0.62 41 57
Rac1/GTP 0.008 0.22 -10000 0 -0.74 39 39
MMP2 -0.05 0.28 -10000 0 -1.1 37 37
Effects of Botulinum toxin

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
STX1A -0.008 0.019 -10000 0 -0.32 2 2
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.022 0.077 -10000 0 -0.32 27 27
STXBP1 0.015 0.072 -10000 0 -0.44 14 14
ACh/CHRNA1 0 0.076 0.12 3 -0.28 28 31
RAB3GAP2/RIMS1/UNC13B 0.034 0.073 -10000 0 -0.27 29 29
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.006 0.1 -10000 0 -0.44 26 26
mol:ACh -0.002 0.046 0.078 77 -0.11 45 122
RAB3GAP2 0.023 0.034 -10000 0 -0.44 3 3
STX1A/SNAP25/VAMP2 0.003 0.093 0.23 1 -0.24 40 41
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0 0.075 0.12 3 -0.28 28 31
UNC13B 0.025 0.02 -10000 0 -0.44 1 1
CHRNA1 0.007 0.099 -10000 0 -0.44 26 26
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.047 0.13 0.12 7 -0.24 153 160
SNAP25 -0.006 0.047 -10000 0 -0.26 19 19
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 -0.069 0.19 -10000 0 -0.44 119 119
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.049 -10000 0 -0.27 16 16
STX1A/SNAP25 fragment 1/VAMP2 0.003 0.093 0.23 1 -0.24 40 41
IGF1 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
NCK2 0.025 0.019 -10000 0 -0.44 1 1
PTK2 0.021 0.022 -10000 0 -0.44 1 1
CRKL -0.016 0.075 -10000 0 -0.24 52 52
GRB2/SOS1/SHC 0.05 0.012 -10000 0 -10000 0 0
HRAS 0.025 0.02 -10000 0 -0.44 1 1
IRS1/Crk -0.004 0.078 -10000 0 -0.23 57 57
IGF-1R heterotetramer/IGF1/PTP1B 0.013 0.074 -10000 0 -0.27 30 30
AKT1 -0.037 0.065 0.2 3 -0.23 42 45
BAD -0.039 0.063 0.18 3 -0.35 6 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.072 -10000 0 -0.24 50 50
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.003 0.087 -10000 0 -0.24 64 64
RAF1 -0.021 0.085 0.26 1 -0.44 11 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.033 0.091 -10000 0 -0.23 57 57
YWHAZ 0.021 0.029 -10000 0 -0.44 2 2
IGF-1R heterotetramer/IGF1/IRS1 0.008 0.09 -10000 0 -0.25 59 59
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
RPS6KB1 -0.039 0.068 0.2 3 -0.24 46 49
GNB2L1 0.026 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.008 0.08 0.24 4 -0.34 9 13
PXN 0.026 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
HRAS/GTP 0.007 0.075 -10000 0 -0.22 50 50
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.049 0.085 -10000 0 -0.22 48 48
IGF-1R heterotetramer 0.016 0.038 -10000 0 -0.51 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.02 0.091 -10000 0 -0.24 60 60
Crk/p130 Cas/Paxillin 0.031 0.088 -10000 0 -0.22 53 53
IGF1R 0.016 0.038 -10000 0 -0.52 1 1
IGF1 -0.013 0.14 -10000 0 -0.46 52 52
IRS2/Crk -0.004 0.069 -10000 0 -0.24 41 41
PI3K 0.029 0.094 -10000 0 -0.24 56 56
apoptosis 0.032 0.058 0.34 6 -0.23 1 7
HRAS/GDP 0.019 0.014 -10000 0 -0.32 1 1
PRKCD -0.024 0.11 -10000 0 -0.34 53 53
RAF1/14-3-3 E -0.009 0.08 0.25 2 -0.38 12 14
BAD/14-3-3 -0.034 0.061 0.24 1 -0.36 6 7
PRKCZ -0.037 0.064 0.2 3 -0.22 46 49
Crk/p130 Cas/Paxillin/FAK1 -0.004 0.072 -10000 0 -0.38 5 5
PTPN1 0.015 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.02 0.11 -10000 0 -0.35 55 55
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.035 0.086 -10000 0 -0.24 47 47
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.003 0.083 -10000 0 -0.24 60 60
GRB10 0.02 0.039 -10000 0 -0.44 4 4
PTPN11 -0.018 0.079 -10000 0 -0.24 64 64
IRS1 -0.017 0.083 0.12 5 -0.25 59 64
IRS2 -0.014 0.07 -10000 0 -0.25 41 41
IGF-1R heterotetramer/IGF1 0.005 0.11 -10000 0 -0.35 52 52
GRB2 0.025 0.004 -10000 0 -10000 0 0
PDPK1 -0.037 0.068 0.2 3 -0.23 53 56
YWHAE 0.022 0.01 -10000 0 -10000 0 0
PRKD1 -0.033 0.13 -10000 0 -0.39 56 56
SHC1 0.025 0.004 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.036 0.079 -10000 0 -0.24 38 38
ER alpha/Gai/GDP/Gbeta gamma -0.026 0.16 -10000 0 -0.49 39 39
AKT1 -0.015 0.2 -10000 0 -0.74 40 40
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.011 0.21 -10000 0 -0.75 40 40
mol:Ca2+ -0.009 0.11 -10000 0 -0.4 24 24
IGF1R 0.024 0.02 -10000 0 -0.44 1 1
E2/ER alpha (dimer)/Striatin 0.02 0.068 -10000 0 -0.27 29 29
SHC1 0.025 0.004 -10000 0 -10000 0 0
apoptosis 0.013 0.2 0.71 40 -10000 0 40
RhoA/GTP 0.003 0.069 -10000 0 -0.24 37 37
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.031 0.15 0.28 1 -0.46 28 29
regulation of stress fiber formation 0.029 0.072 0.34 11 -0.15 27 38
E2/ERA-ERB (dimer) 0.016 0.075 -10000 0 -0.28 34 34
KRAS 0.021 0.044 -10000 0 -0.44 5 5
G13/GTP 0.021 0.058 -10000 0 -0.24 26 26
pseudopodium formation -0.029 0.072 0.15 27 -0.34 11 38
E2/ER alpha (dimer)/PELP1 0.018 0.063 -10000 0 -0.26 26 26
GRB2 0.025 0.004 -10000 0 -10000 0 0
GNG2 0.021 0.044 -10000 0 -0.44 5 5
GNAO1 0.016 0.087 -10000 0 -0.44 19 19
HRAS 0.025 0.02 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.022 0.16 0.23 2 -0.47 47 49
E2/ER beta (dimer) 0.012 0.046 -10000 0 -0.32 11 11
mol:GDP -0.013 0.097 -10000 0 -0.34 39 39
mol:NADP -0.022 0.16 0.23 2 -0.47 47 49
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:IP3 -0.024 0.099 0.17 4 -0.41 24 28
IGF-1R heterotetramer 0.024 0.02 -10000 0 -0.44 1 1
PLCB1 -0.019 0.1 0.18 4 -0.42 24 28
PLCB2 -0.012 0.091 -10000 0 -0.41 22 22
IGF1 -0.011 0.14 -10000 0 -0.44 52 52
mol:L-citrulline -0.022 0.16 0.23 2 -0.47 47 49
RHOA 0.025 0.02 -10000 0 -0.44 1 1
Gai/GDP -0.006 0.17 -10000 0 -0.75 27 27
JNK cascade 0.012 0.046 -10000 0 -0.32 11 11
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
ESR2 0.016 0.065 -10000 0 -0.44 11 11
GNAQ 0.022 0.043 -10000 0 -0.44 5 5
ESR1 0.006 0.097 -10000 0 -0.44 25 25
Gq family/GDP/Gbeta gamma -0.014 0.15 -10000 0 -0.59 27 27
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.027 0.093 -10000 0 -0.43 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.031 0.15 0.28 1 -0.45 28 29
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
E2/ER alpha (dimer) 0.006 0.069 -10000 0 -0.32 25 25
STRN 0.023 0.039 -10000 0 -0.44 4 4
GNAL 0.015 0.063 -10000 0 -0.44 10 10
PELP1 0.021 0.022 -10000 0 -0.44 1 1
MAPK11 0.001 0.045 -10000 0 -0.27 14 14
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.016 0.064 -10000 0 -0.44 11 11
HBEGF 0.074 0.21 0.31 171 -0.49 25 196
cAMP biosynthetic process 0.007 0.07 -10000 0 -0.23 41 41
SRC 0.027 0.17 0.21 7 -0.46 31 38
PI3K 0.034 0.031 -10000 0 -0.32 4 4
GNB1 0.025 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.013 0.1 -10000 0 -0.31 42 42
SOS1 0.026 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.03 0.12 -10000 0 -0.38 42 42
Gs family/GTP 0.012 0.074 -10000 0 -0.24 41 41
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.039 0.053 -10000 0 -0.3 12 12
vasodilation -0.02 0.15 0.22 2 -0.44 48 50
mol:DAG -0.024 0.099 0.17 4 -0.41 24 28
Gs family/GDP/Gbeta gamma -0.009 0.095 -10000 0 -0.32 38 38
MSN -0.031 0.076 0.16 25 -0.37 11 36
Gq family/GTP -0.003 0.097 -10000 0 -0.43 22 22
mol:PI-3-4-5-P3 -0.009 0.2 -10000 0 -0.72 40 40
NRAS 0.018 0.058 -10000 0 -0.44 9 9
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.02 0.15 0.44 48 -0.22 2 50
GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
RhoA/GDP 0 0.1 -10000 0 -0.33 39 39
NOS3 -0.025 0.17 0.23 2 -0.49 47 49
GNA11 0.023 0.034 -10000 0 -0.44 3 3
MAPKKK cascade 0.014 0.17 0.34 1 -0.51 41 42
E2/ER alpha (dimer)/PELP1/Src 0.035 0.16 0.25 18 -0.46 29 47
ruffle organization -0.029 0.072 0.15 27 -0.34 11 38
ROCK2 -0.029 0.083 0.23 5 -0.38 12 17
GNA14 0.014 0.075 -10000 0 -0.44 15 15
GNA15 0.015 0.073 -10000 0 -0.44 14 14
GNA13 0.024 0.028 -10000 0 -0.44 2 2
MMP9 0.07 0.21 0.36 149 -0.46 28 177
MMP2 0.021 0.17 0.26 12 -0.46 36 48
Caspase cascade in apoptosis

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
TOP1 -0.029 0.11 -10000 0 -0.4 28 28
ACTA1 -0.042 0.12 -10000 0 -0.37 45 45
NUMA1 -0.027 0.13 -10000 0 -0.45 31 31
SPTAN1 -0.041 0.12 0.2 2 -0.37 46 48
LIMK1 -0.035 0.12 0.25 6 -0.36 46 52
BIRC3 0.015 0.076 -10000 0 -0.44 15 15
BIRC2 0.015 0.07 -10000 0 -0.45 13 13
BAX 0.025 0.02 -10000 0 -0.44 1 1
CASP10 -0.042 0.086 0.22 1 -0.31 47 48
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.02 -10000 0 -0.44 1 1
PTK2 -0.026 0.11 -10000 0 -0.42 27 27
DIABLO 0.026 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.04 0.11 0.2 2 -0.36 46 48
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
GSN -0.043 0.12 0.2 2 -0.37 47 49
MADD 0.026 0.003 -10000 0 -10000 0 0
TFAP2A -0.055 0.22 -10000 0 -0.54 90 90
BID -0.015 0.059 0.14 1 -0.2 47 48
MAP3K1 -0.016 0.085 -10000 0 -0.42 19 19
TRADD 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.031 -10000 0 -0.32 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.041 0.12 0.22 3 -0.38 47 50
CASP9 0.024 0.02 -10000 0 -0.44 1 1
DNA repair 0.002 0.042 0.21 2 -0.16 6 8
neuron apoptosis -0.023 0.17 -10000 0 -0.66 35 35
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.037 0.13 -10000 0 -0.38 50 50
APAF1 0.023 0.034 -10000 0 -0.44 3 3
CASP6 -0.022 0.16 0.33 1 -0.81 20 21
TRAF2 0.025 0.02 -10000 0 -0.44 1 1
ICAD/CAD -0.043 0.11 -10000 0 -0.36 45 45
CASP7 0.006 0.063 0.28 8 -0.24 11 19
KRT18 0.01 0.044 -10000 0 -0.52 2 2
apoptosis -0.046 0.12 0.35 1 -0.45 30 31
DFFA -0.041 0.11 -10000 0 -0.37 46 46
DFFB -0.041 0.11 -10000 0 -0.37 45 45
PARP1 -0.002 0.042 0.16 6 -0.21 2 8
actin filament polymerization 0.037 0.11 0.34 45 -0.29 2 47
TNF 0.009 0.088 -10000 0 -0.44 21 21
CYCS -0.012 0.065 0.18 1 -0.26 24 25
SATB1 -0.036 0.16 0.31 1 -0.76 20 21
SLK -0.049 0.12 0.36 1 -0.35 55 56
p15 BID/BAX -0.01 0.067 -10000 0 -0.19 54 54
CASP2 0.008 0.059 0.2 17 -0.24 4 21
JNK cascade 0.016 0.085 0.42 19 -10000 0 19
CASP3 -0.041 0.12 -10000 0 -0.38 49 49
LMNB2 0.003 0.11 0.38 3 -0.43 22 25
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CASP4 0.024 0.028 -10000 0 -0.44 2 2
Mammalian IAPs/DIABLO 0.051 0.081 -10000 0 -0.35 20 20
negative regulation of DNA binding -0.054 0.21 -10000 0 -0.54 90 90
stress fiber formation -0.048 0.12 0.36 1 -0.35 55 56
GZMB -0.045 0.1 0.23 1 -0.37 46 47
CASP1 -0.001 0.061 -10000 0 -0.3 24 24
LMNB1 -0.001 0.12 0.38 3 -0.5 19 22
APP -0.023 0.17 -10000 0 -0.67 35 35
TNFRSF1A 0.025 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.013 -10000 0 -0.32 1 1
VIM -0.035 0.12 -10000 0 -0.46 28 28
LMNA 0.01 0.079 0.37 3 -0.3 20 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.007 0.055 -10000 0 -0.2 23 23
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.039 0.11 -10000 0 -0.36 46 46
APAF-1/Caspase 9 -0.012 0.15 0.41 1 -0.61 31 32
nuclear fragmentation during apoptosis -0.027 0.12 -10000 0 -0.44 31 31
CFL2 -0.038 0.11 0.3 2 -0.35 45 47
GAS2 -0.057 0.12 0.22 1 -0.35 56 57
positive regulation of apoptosis 0.007 0.11 0.38 3 -0.44 20 23
PRF1 0.012 0.092 -10000 0 -0.44 22 22
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.001 0.099 0.2 3 -0.3 51 54
EPHB2 0.018 0.058 -10000 0 -0.44 9 9
Syndecan-2/TACI 0.002 0.077 0.2 1 -0.27 40 41
LAMA1 -0.003 0.11 -10000 0 -0.44 33 33
Syndecan-2/alpha2 ITGB1 0.029 0.061 0.19 1 -0.24 22 23
HRAS 0.025 0.02 -10000 0 -0.44 1 1
Syndecan-2/CASK 0 0.04 -10000 0 -0.26 14 14
ITGA5 0.025 0.041 -10000 0 -0.44 4 4
BAX -0.011 0.057 -10000 0 -1.1 1 1
EPB41 0.021 0.039 -10000 0 -0.44 4 4
positive regulation of cell-cell adhesion 0.01 0.053 -10000 0 -0.24 23 23
LAMA3 0.017 0.057 -10000 0 -0.44 8 8
EZR 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.049 -10000 0 -0.44 6 6
Syndecan-2/MMP2 0.008 0.082 0.2 1 -0.34 27 28
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.037 -10000 0 -0.32 6 6
dendrite morphogenesis 0.01 0.057 -10000 0 -0.27 22 22
Syndecan-2/GM-CSF -0.003 0.096 0.2 6 -0.27 63 69
determination of left/right symmetry 0.001 0.048 -10000 0 -0.3 14 14
Syndecan-2/PKC delta 0.016 0.044 -10000 0 -0.26 14 14
GNB2L1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.006 0.1 0.19 61 -0.24 64 125
MAPK1 -0.004 0.1 0.19 62 -0.24 62 124
Syndecan-2/RACK1 0.027 0.045 -10000 0 -0.24 14 14
NF1 0.023 0.034 -10000 0 -0.44 3 3
FGFR/FGF/Syndecan-2 0.001 0.048 -10000 0 -0.3 14 14
ITGA2 0.021 0.048 -10000 0 -0.44 6 6
MAPK8 -0.002 0.045 0.22 1 -0.27 15 16
Syndecan-2/alpha2/beta1 Integrin 0.017 0.083 0.19 1 -0.24 47 48
Syndecan-2/Kininogen -0.005 0.1 0.2 13 -0.27 70 83
ITGB1 0.026 0.002 -10000 0 -10000 0 0
SRC -0.003 0.051 0.18 23 -0.25 10 33
Syndecan-2/CASK/Protein 4.1 0.012 0.044 -10000 0 -0.23 17 17
extracellular matrix organization 0.012 0.062 -10000 0 -0.31 19 19
actin cytoskeleton reorganization -0.001 0.098 0.2 3 -0.3 51 54
Syndecan-2/Caveolin-2/Ras 0.027 0.051 -10000 0 -0.25 16 16
Syndecan-2/Laminin alpha3 0.011 0.052 -10000 0 -0.26 19 19
Syndecan-2/RasGAP 0.037 0.049 -10000 0 -0.23 15 15
alpha5/beta1 Integrin 0.037 0.031 -10000 0 -0.32 4 4
PRKCD 0.026 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.01 0.057 -10000 0 -0.27 22 22
GO:0007205 0.002 0.006 -10000 0 -0.13 1 1
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.012 0.043 0.18 1 -0.25 11 12
RHOA 0.025 0.02 -10000 0 -0.44 1 1
SDCBP 0.015 0.061 -10000 0 -0.44 10 10
TNFRSF13B -0.002 0.11 -10000 0 -0.44 30 30
RASA1 0.024 0.028 -10000 0 -0.44 2 2
alpha2/beta1 Integrin 0.034 0.037 -10000 0 -0.32 6 6
Syndecan-2/Synbindin 0.015 0.044 -10000 0 -0.26 14 14
TGFB1 0.017 0.064 -10000 0 -0.44 11 11
CASP3 0.024 0.069 0.19 64 -0.24 13 77
FN1 -0.011 0.14 -10000 0 -0.44 54 54
Syndecan-2/IL8 -0.002 0.1 0.21 6 -0.28 59 65
SDC2 0.001 0.048 -10000 0 -0.3 14 14
KNG1 -0.027 0.15 -10000 0 -0.44 65 65
Syndecan-2/Neurofibromin 0.015 0.046 -10000 0 -0.26 15 15
TRAPPC4 0.025 0.004 -10000 0 -10000 0 0
CSF2 -0.018 0.14 -10000 0 -0.44 59 59
Syndecan-2/TGFB1 0.012 0.062 -10000 0 -0.31 19 19
Syndecan-2/Syntenin/PI-4-5-P2 0.01 0.053 -10000 0 -0.24 23 23
Syndecan-2/Ezrin 0.028 0.043 -10000 0 -0.24 13 13
PRKACA 0.026 0.073 0.19 72 -0.24 15 87
angiogenesis -0.002 0.1 0.21 6 -0.28 59 65
MMP2 0.007 0.1 -10000 0 -0.44 27 27
IL8 -0.017 0.15 -10000 0 -0.44 63 63
calcineurin-NFAT signaling pathway 0.002 0.076 0.2 1 -0.27 40 41
FAS signaling pathway (CD95)

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
SPTAN1 -0.007 0.04 0.21 9 -0.19 14 23
RFC1 -0.008 0.041 0.21 7 -0.2 15 22
PRKDC 0.007 0.069 0.23 42 -0.24 2 44
RIPK1 0.026 0.005 -10000 0 -10000 0 0
CASP7 -0.006 0.1 -10000 0 -0.57 15 15
FASLG/FAS/FADD/FAF1 0.01 0.094 0.2 59 -0.26 32 91
MAP2K4 -0.043 0.14 0.24 1 -0.35 71 72
mol:ceramide -0.016 0.11 -10000 0 -0.34 45 45
GSN -0.007 0.044 0.21 10 -0.25 4 14
FASLG/FAS/FADD/FAF1/Caspase 8 0.002 0.1 0.18 2 -0.32 32 34
FAS 0.015 0.054 -10000 0 -0.45 7 7
BID -0.017 0.038 0.26 10 -0.28 1 11
MAP3K1 -0.014 0.095 0.22 3 -0.33 26 29
MAP3K7 0.022 0.012 -10000 0 -10000 0 0
RB1 0.013 0.087 0.22 66 -0.23 20 86
CFLAR 0.027 0.003 -10000 0 -10000 0 0
HGF/MET -0.006 0.13 -10000 0 -0.29 97 97
ARHGDIB -0.007 0.044 0.25 7 -0.32 2 9
FADD 0.02 0.017 -10000 0 -10000 0 0
actin filament polymerization 0.006 0.048 0.25 4 -0.22 14 18
NFKB1 -0.02 0.14 -10000 0 -0.69 17 17
MAPK8 -0.062 0.18 -10000 0 -0.48 73 73
DFFA -0.007 0.037 0.21 7 -0.18 14 21
DNA fragmentation during apoptosis -0.006 0.041 0.22 10 -0.23 1 11
FAS/FADD/MET 0.039 0.043 -10000 0 -0.28 6 6
CFLAR/RIP1 0.04 0.008 -10000 0 -10000 0 0
FAIM3 0.018 0.068 -10000 0 -0.44 12 12
FAF1 0.02 0.018 -10000 0 -10000 0 0
PARP1 -0.007 0.037 0.21 7 -0.18 14 21
DFFB -0.007 0.038 0.21 8 -0.21 2 10
CHUK -0.025 0.13 -10000 0 -0.64 18 18
FASLG -0.008 0.12 -10000 0 -0.44 40 40
FAS/FADD 0.026 0.045 -10000 0 -0.32 7 7
HGF 0.001 0.11 -10000 0 -0.44 32 32
LMNA -0.006 0.044 0.2 14 -0.23 2 16
CASP6 -0.007 0.037 0.21 7 -0.18 13 20
CASP10 0.02 0.026 -10000 0 -0.44 1 1
CASP3 0 0.034 0.26 7 -0.23 2 9
PTPN13 -0.035 0.16 -10000 0 -0.44 77 77
CASP8 -0.016 0.053 0.34 12 -0.33 1 13
IL6 -0.12 0.4 -10000 0 -1.2 71 71
MET 0.024 0.02 -10000 0 -0.44 1 1
ICAD/CAD -0.009 0.035 0.19 7 -0.22 1 8
FASLG/FAS/FADD/FAF1/Caspase 10 -0.017 0.11 -10000 0 -0.35 45 45
activation of caspase activity by cytochrome c -0.017 0.038 0.26 10 -0.28 1 11
PAK2 -0.007 0.042 0.21 9 -0.32 2 11
BCL2 0.014 0.052 -10000 0 -0.44 7 7
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR 0.025 0.02 -10000 0 -0.44 1 1
Cbp/p300/PCAF 0.039 0.059 -10000 0 -0.29 17 17
EP300 0.023 0.028 -10000 0 -0.44 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.06 -10000 0 -0.28 16 16
KAT2B 0.013 0.077 -10000 0 -0.44 16 16
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.007 0.077 0.2 22 -0.26 16 38
RAR alpha/9cRA/Cyclin H 0.007 0.1 -10000 0 -0.3 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.005 0.079 0.18 3 -0.31 21 24
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.002 0.076 -10000 0 -0.18 80 80
NCOR2 0.024 0.034 -10000 0 -0.44 3 3
VDR/VDR/Vit D3 0.019 0.014 -10000 0 -0.32 1 1
RXRs/RARs/NRIP1/9cRA -0.039 0.16 0.3 1 -0.39 87 88
NCOA2 0.018 0.048 -10000 0 -0.44 6 6
NCOA3 0.015 0.013 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.44 1 1
VDR/VDR/DNA 0.025 0.02 -10000 0 -0.44 1 1
RARG 0.021 0.048 -10000 0 -0.44 6 6
RAR gamma1/9cRA 0.032 0.031 -10000 0 -0.27 6 6
MAPK3 0.024 0.021 -10000 0 -0.44 1 1
MAPK1 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.024 0.021 -10000 0 -0.44 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.023 0.16 -10000 0 -0.38 86 86
RARA -0.015 0.083 0.15 6 -0.22 78 84
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.006 0.081 0.19 2 -0.35 19 21
PRKCA 0.024 0.023 -10000 0 -0.44 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.034 0.16 0.3 4 -0.39 84 88
RXRG -0.022 0.11 0.17 3 -0.29 78 81
RXRA -0.014 0.076 -10000 0 -0.19 79 79
RXRB -0.02 0.11 0.17 4 -0.29 78 82
VDR/Vit D3/DNA 0.019 0.014 -10000 0 -0.32 1 1
RBP1 0.015 0.1 -10000 0 -0.44 27 27
CRBP1/9-cic-RA 0.011 0.074 -10000 0 -0.32 27 27
RARB 0.019 0.062 -10000 0 -0.44 10 10
PRKCG -0.024 0.17 -10000 0 -0.44 78 78
MNAT1 0.024 0.021 -10000 0 -0.44 1 1
RAR alpha/RXRs -0.04 0.16 0.25 3 -0.4 86 89
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.03 0.14 0.24 1 -0.34 82 83
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.092 0.26 7 -0.3 16 23
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.034 0.16 0.3 4 -0.38 85 89
positive regulation of DNA binding -0.001 0.091 -10000 0 -0.28 8 8
NRIP1 -0.038 0.19 -10000 0 -1 11 11
RXRs/RARs -0.028 0.15 0.28 2 -0.36 85 87
RXRs/RXRs/DNA/9cRA -0.039 0.15 -10000 0 -0.39 87 87
PRKACA 0.026 0.003 -10000 0 -10000 0 0
CDK7 0.023 0.028 -10000 0 -0.44 2 2
TFIIH 0.046 0.032 -10000 0 -0.39 2 2
RAR alpha/9cRA 0.022 0.085 0.21 1 -0.33 3 4
CCNH 0.025 0.004 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.042 0.04 -10000 0 -0.25 8 8
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.016 0.09 -10000 0 -0.27 47 47
NT3 (dimer)/TRKC 0.012 0.1 -10000 0 -0.34 42 42
NT3 (dimer)/TRKB -0.01 0.16 0.2 2 -0.32 117 119
SHC/Grb2/SOS1/GAB1/PI3K 0.02 0.033 -10000 0 -0.25 4 4
RAPGEF1 0.025 0.02 -10000 0 -0.44 1 1
BDNF 0.011 0.087 -10000 0 -0.44 20 20
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
NTRK1 0 0.1 -10000 0 -0.44 30 30
NTRK2 -0.026 0.17 -10000 0 -0.44 84 84
NTRK3 0.001 0.099 -10000 0 -0.44 26 26
NT-4/5 (dimer)/TRKB -0.002 0.15 0.2 2 -0.3 108 110
neuron apoptosis 0.072 0.18 0.4 109 -10000 0 109
SHC 2-3/Grb2 -0.079 0.2 -10000 0 -0.43 109 109
SHC1 0.025 0.004 -10000 0 -10000 0 0
SHC2 -0.074 0.19 -10000 0 -0.5 79 79
SHC3 -0.076 0.2 -10000 0 -0.51 80 80
STAT3 (dimer) 0.03 0.013 -10000 0 -0.26 1 1
NT3 (dimer)/TRKA 0.009 0.13 0.2 1 -0.32 73 74
RIN/GDP 0.006 0.077 0.23 11 -0.23 15 26
GIPC1 0.022 0.039 -10000 0 -0.44 4 4
KRAS 0.021 0.044 -10000 0 -0.44 5 5
DNAJA3 -0.04 0.11 0.17 1 -0.28 82 83
RIN/GTP 0.01 0.007 -10000 0 -10000 0 0
CCND1 0.014 0.018 -10000 0 -0.43 1 1
MAGED1 0.026 0.003 -10000 0 -10000 0 0
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.001 0.033 -10000 0 -0.44 1 1
SHC/GRB2/SOS1 0.05 0.012 -10000 0 -10000 0 0
GRB2 0.025 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.003 0.13 0.2 2 -0.31 84 86
TRKA/NEDD4-2 0.012 0.079 -10000 0 -0.31 31 31
ELMO1 0.022 0.035 -10000 0 -0.44 3 3
RhoG/GTP/ELMO1/DOCK1 0.029 0.028 -10000 0 -0.27 4 4
NGF 0.005 0.095 -10000 0 -0.44 24 24
HRAS 0.025 0.02 -10000 0 -0.44 1 1
DOCK1 0.024 0.02 -10000 0 -0.44 1 1
GAB2 0.024 0.028 -10000 0 -0.44 2 2
RIT2 -0.011 0.013 -10000 0 -10000 0 0
RIT1 0.025 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.028 -10000 0 -0.44 2 2
DNM1 0.022 0.049 -10000 0 -0.44 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.019 0.11 -10000 0 -0.28 77 77
mol:GDP 0.003 0.11 0.29 12 -0.33 21 33
NGF (dimer) 0.005 0.095 -10000 0 -0.44 24 24
RhoG/GDP 0.016 0.025 -10000 0 -0.32 3 3
RIT1/GDP 0.009 0.079 0.19 11 -0.23 17 28
TIAM1 0.006 0.1 -10000 0 -0.44 28 28
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
BDNF (dimer)/TRKB 0.003 0.14 -10000 0 -0.29 97 97
KIDINS220/CRKL/C3G 0.036 0.017 -10000 0 -0.32 1 1
SHC/RasGAP 0.035 0.023 -10000 0 -0.32 2 2
FRS2 family/SHP2 0.047 0.039 -10000 0 -0.31 6 6
SHC/GRB2/SOS1/GAB1 0.062 0.018 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.009 0.087 -10000 0 -0.44 20 20
RAP1/GDP 0.005 0.065 0.13 1 -0.2 17 18
KIDINS220/CRKL 0.025 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.011 0.087 -10000 0 -0.44 20 20
ubiquitin-dependent protein catabolic process 0.011 0.096 -10000 0 -0.28 53 53
Schwann cell development -0.021 0.025 -10000 0 -10000 0 0
EHD4 0.024 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.062 0.028 -10000 0 -0.25 3 3
FRS2 family/SHP2/CRK family/C3G/GAB2 0.007 0.056 -10000 0 -0.33 8 8
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
CDC42/GTP -0.022 0.12 0.18 1 -0.26 100 101
ABL1 0.025 0.02 -10000 0 -0.44 1 1
SH2B family/GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.013 0.098 -10000 0 -0.43 16 16
STAT3 0.03 0.013 -10000 0 -0.26 1 1
axon guidance -0.032 0.11 -10000 0 -0.26 100 100
MAPK3 -0.055 0.1 0.18 9 -0.28 81 90
MAPK1 -0.057 0.1 0.18 7 -0.28 83 90
CDC42/GDP 0.012 0.086 0.23 15 -0.23 19 34
NTF3 0.009 0.087 -10000 0 -0.44 20 20
NTF4 0.001 0.034 -10000 0 -0.44 1 1
NGF (dimer)/TRKA/FAIM 0.019 0.1 -10000 0 -0.28 57 57
PI3K 0.034 0.031 -10000 0 -0.32 4 4
FRS3 0.025 0.02 -10000 0 -0.44 1 1
FAIM 0.022 0.043 -10000 0 -0.44 5 5
GAB1 0.025 0.004 -10000 0 -10000 0 0
RASGRF1 -0.053 0.12 -10000 0 -0.28 103 103
SOS1 0.026 0.002 -10000 0 -10000 0 0
MCF2L -0.03 0.071 0.18 2 -0.29 35 37
RGS19 0.011 0.048 -10000 0 -0.44 6 6
CDC42 0.021 0.039 -10000 0 -0.44 4 4
RAS family/GTP 0.004 0.093 0.5 1 -0.46 10 11
Rac1/GDP 0.007 0.077 0.23 9 -0.23 18 27
NGF (dimer)/TRKA/GRIT 0.008 0.092 -10000 0 -0.28 53 53
neuron projection morphogenesis -0.022 0.13 -10000 0 -0.62 12 12
NGF (dimer)/TRKA/NEDD4-2 0.011 0.097 -10000 0 -0.28 53 53
MAP2K1 -0.012 0.036 0.18 18 -0.24 2 20
NGFR 0 0.12 -10000 0 -0.44 40 40
NGF (dimer)/TRKA/GIPC/GAIP -0.007 0.076 -10000 0 -0.24 46 46
RAS family/GTP/PI3K 0.012 0.064 -10000 0 -0.35 13 13
FRS2 family/SHP2/GRB2/SOS1 0.069 0.041 -10000 0 -0.27 6 6
NRAS 0.018 0.058 -10000 0 -0.44 9 9
GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
PRKCI 0.023 0.034 -10000 0 -0.44 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.02 -10000 0 -0.44 1 1
MAPKKK cascade -0.067 0.2 -10000 0 -0.56 73 73
RASA1 0.024 0.028 -10000 0 -0.44 2 2
TRKA/c-Abl 0.019 0.081 -10000 0 -0.32 31 31
SQSTM1 0.026 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.017 0.13 -10000 0 -0.27 98 98
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.099 -10000 0 -0.25 56 56
MATK -0.006 0.13 -10000 0 -0.44 45 45
NEDD4L 0.018 0.022 -10000 0 -0.44 1 1
RAS family/GDP -0.017 0.049 -10000 0 -0.19 20 20
NGF (dimer)/TRKA -0.032 0.12 -10000 0 -0.29 83 83
Rac1/GTP -0.044 0.095 -10000 0 -0.27 55 55
FRS2 family/SHP2/CRK family 0.059 0.047 -10000 0 -0.28 6 6
Visual signal transduction: Rods

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
mol:K + 0.024 0.02 -10000 0 -0.44 1 1
GNAT1/GTP 0.014 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.025 0.006 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.017 0.063 -10000 0 -0.27 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.009 0.019 -10000 0 -10000 0 0
GRK1 -0.009 0.016 -10000 0 -10000 0 0
CNG Channel -0.027 0.14 -10000 0 -0.27 137 137
mol:Na + 0 0.093 -10000 0 -0.24 65 65
mol:ADP -0.009 0.016 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.027 0.084 -10000 0 -0.28 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.009 0.099 -10000 0 -0.25 65 65
CNGB1 0.006 0.026 -10000 0 -10000 0 0
RDH5 0.021 0.052 -10000 0 -0.44 7 7
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.092 0.34 13 -0.29 13 26
Na + (4 Units) -0.014 0.088 -10000 0 -0.24 62 62
RGS9 0.008 0.095 -10000 0 -0.44 24 24
GNB1/GNGT1 0.017 0.08 -10000 0 -0.32 30 30
GNAT1/GDP 0.033 0.076 -10000 0 -0.24 38 38
GUCY2D 0.015 0.026 -10000 0 -10000 0 0
GNGT1 -0.007 0.1 -10000 0 -0.44 30 30
GUCY2F -0.016 0.011 -10000 0 -10000 0 0
GNB5 0.023 0.028 -10000 0 -0.44 2 2
mol:GMP (4 units) -0.045 0.12 0.18 3 -0.27 113 116
mol:11-cis-retinal 0.021 0.052 -10000 0 -0.44 7 7
mol:cGMP 0.018 0.069 -10000 0 -0.24 30 30
GNB1 0.025 0.005 -10000 0 -10000 0 0
Rhodopsin 0.029 0.04 -10000 0 -0.32 7 7
SLC24A1 0.024 0.02 -10000 0 -0.44 1 1
CNGA1 -0.001 0.12 -10000 0 -0.44 37 37
Metarhodopsin II 0.019 0.012 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.036 0.073 -10000 0 -0.25 30 30
RGS9BP 0.009 0.073 -10000 0 -0.44 14 14
Metarhodopsin II/Transducin -0.002 0.054 -10000 0 -0.23 30 30
GCAP Family/Ca ++ 0.029 0.067 -10000 0 -0.25 30 30
PDE6A/B -0.021 0.15 -10000 0 -0.34 97 97
mol:Pi 0.026 0.083 -10000 0 -0.28 38 38
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.026 0.066 -10000 0 -0.25 30 30
PDE6B 0.008 0.095 -10000 0 -0.44 24 24
PDE6A -0.035 0.16 -10000 0 -0.44 80 80
PDE6G 0.005 0.098 -10000 0 -0.44 26 26
RHO -0.014 0.014 -10000 0 -10000 0 0
PDE6 -0.01 0.16 -10000 0 -0.28 135 135
GUCA1A 0.009 0.068 -10000 0 -0.44 11 11
GC2/GCAP Family 0.039 0.071 -10000 0 -0.26 30 30
GUCA1C -0.017 0.009 -10000 0 -10000 0 0
GUCA1B 0.011 0.084 -10000 0 -0.44 19 19
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.031 -10000 0 -0.32 4 4
alphaV beta3 Integrin 0.026 0.099 -10000 0 -0.31 42 42
PTK2 0.009 0.13 0.32 9 -0.45 22 31
IGF1R 0.024 0.02 -10000 0 -0.44 1 1
PI4KB 0.025 0.004 -10000 0 -10000 0 0
MFGE8 0.023 0.04 -10000 0 -0.44 4 4
SRC 0.015 0.023 -10000 0 -0.44 1 1
CDKN1B -0.008 0.1 -10000 0 -0.4 32 32
VEGFA 0.025 0.004 -10000 0 -10000 0 0
ILK -0.006 0.1 -10000 0 -0.46 23 23
ROCK1 0.017 0.044 -10000 0 -0.44 5 5
AKT1 -0.015 0.092 -10000 0 -0.42 25 25
PTK2B -0.021 0.06 0.19 12 -0.25 27 39
alphaV/beta3 Integrin/JAM-A 0.019 0.11 -10000 0 -0.28 56 56
CBL 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.035 0.066 -10000 0 -0.28 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.031 0.1 -10000 0 -0.26 64 64
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.02 0.1 -10000 0 -0.43 20 20
alphaV/beta3 Integrin/Syndecan-1 0.038 0.068 -10000 0 -0.28 24 24
PI4KA 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.011 0.16 -10000 0 -0.32 111 111
PI4 Kinase 0.036 0.009 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
alphaV/beta3 Integrin/Osteopontin -0.001 0.14 -10000 0 -0.29 101 101
RPS6KB1 -0.082 0.13 -10000 0 -0.45 45 45
TLN1 0.025 0.02 -10000 0 -0.44 1 1
MAPK3 -0.054 0.17 -10000 0 -0.56 49 49
GPR124 0.019 0.04 -10000 0 -0.44 4 4
MAPK1 -0.054 0.17 -10000 0 -0.56 49 49
PXN 0.026 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
alphaV/beta3 Integrin/Tumstatin 0.021 0.11 -10000 0 -0.28 59 59
cell adhesion 0.025 0.075 -10000 0 -0.3 27 27
ANGPTL3 -0.001 0.022 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.035 -10000 0 -0.27 3 3
IGF-1R heterotetramer 0.024 0.02 -10000 0 -0.44 1 1
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
TGFBR2 0.026 0.004 -10000 0 -10000 0 0
ITGB3 0.016 0.07 -10000 0 -0.44 13 13
IGF1 -0.011 0.14 -10000 0 -0.44 52 52
RAC1 0.023 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.029 0.074 -10000 0 -0.3 25 25
apoptosis 0.017 0.064 -10000 0 -0.44 11 11
CD47 0.024 0.028 -10000 0 -0.44 2 2
alphaV/beta3 Integrin/CD47 0.037 0.07 -10000 0 -0.29 24 24
VCL 0.024 0.028 -10000 0 -0.44 2 2
alphaV/beta3 Integrin/Del1 0.016 0.12 -10000 0 -0.33 54 54
CSF1 0.023 0.034 -10000 0 -0.44 3 3
PIK3C2A -0.023 0.14 -10000 0 -0.52 41 41
PI4 Kinase/Pyk2 -0.003 0.092 -10000 0 -0.28 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.07 -10000 0 -0.27 25 25
FAK1/Vinculin 0.025 0.12 0.29 13 -0.37 21 34
alphaV beta3/Integrin/ppsTEM5 0.03 0.075 -10000 0 -0.3 25 25
RHOA 0.025 0.02 -10000 0 -0.44 1 1
VTN 0.006 0.095 -10000 0 -0.44 23 23
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
FGF2 0.008 0.099 -10000 0 -0.44 26 26
F11R -0.026 0.064 0.21 1 -0.32 25 26
alphaV/beta3 Integrin/Lactadherin 0.035 0.073 -10000 0 -0.29 26 26
alphaV/beta3 Integrin/TGFBR2 0.038 0.067 -10000 0 -0.28 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.054 0.055 -10000 0 -0.26 16 16
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
alphaV/beta3 Integrin/Talin 0.036 0.062 -10000 0 -0.26 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.011 0.14 -10000 0 -0.44 54 54
alphaV/beta3 Integrin/Pyk2 0.023 0.066 -10000 0 -0.25 27 27
SDC1 0.025 0.019 -10000 0 -0.44 1 1
VAV3 -0.049 0.083 0.18 3 -0.24 85 88
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
IRS1 0.019 0.058 -10000 0 -0.44 9 9
FAK1/Paxillin 0.026 0.12 0.28 12 -0.36 21 33
cell migration 0.02 0.11 0.26 15 -0.34 20 35
ITGAV 0.017 0.064 -10000 0 -0.44 11 11
PI3K 0.031 0.11 -10000 0 -0.27 58 58
SPP1 -0.033 0.18 -10000 0 -0.44 88 88
KDR 0.022 0.039 -10000 0 -0.44 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.017 0.064 -10000 0 -0.44 11 11
COL4A3 -0.005 0.12 -10000 0 -0.44 38 38
angiogenesis -0.052 0.17 -10000 0 -0.57 49 49
Rac1/GTP -0.016 0.087 -10000 0 -0.23 81 81
EDIL3 -0.009 0.12 -10000 0 -0.44 43 43
cell proliferation 0.038 0.066 -10000 0 -0.28 23 23
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.03 0.025 0.2 3 -10000 0 3
AES 0.029 0.028 0.17 3 -0.44 1 4
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.031 -10000 0 -0.32 4 4
SMAD4 0.019 0.012 -10000 0 -10000 0 0
DKK2 -0.023 0.15 -10000 0 -0.44 65 65
TLE1 0.026 0.044 0.17 2 -0.45 4 6
MACF1 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.031 0.1 0.26 23 -0.43 8 31
WIF1 -0.037 0.17 -10000 0 -0.44 83 83
beta catenin/RanBP3 0.035 0.14 0.4 54 -0.43 5 59
KREMEN2 0.022 0.07 -10000 0 -0.44 12 12
DKK1 -0.028 0.16 -10000 0 -0.44 76 76
beta catenin/beta TrCP1 0.042 0.097 0.27 20 -0.43 6 26
FZD1 0.023 0.028 -10000 0 -0.45 2 2
AXIN2 -0.1 0.41 0.58 14 -1.4 53 67
AXIN1 0.025 0.02 -10000 0 -0.45 1 1
RAN 0.026 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.025 0.089 -10000 0 -0.62 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.028 0.16 0.31 3 -0.55 23 26
Axin1/APC/GSK3 0.032 0.084 0.2 16 -0.38 10 26
Axin1/APC/GSK3/beta catenin/Macf1 0.011 0.094 0.24 5 -0.43 10 15
HNF1A 0.026 0.046 0.18 3 -0.41 5 8
CTBP1 0.029 0.03 0.18 3 -0.45 1 4
MYC 0.079 0.28 0.59 101 -1.5 5 106
RANBP3 0.025 0.02 -10000 0 -0.44 1 1
DKK2/LRP6/Kremen 2 0.012 0.12 -10000 0 -0.28 77 77
NKD1 -0.033 0.17 -10000 0 -0.44 82 82
TCF4 0.02 0.048 0.2 4 -0.45 4 8
TCF3 0.029 0.029 0.18 3 -0.45 1 4
WNT1/LRP6/FZD1/Axin1 0.059 0.039 -10000 0 -0.26 6 6
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.008 0.16 0.44 49 -0.48 11 60
LEF1 0.016 0.074 0.18 3 -0.44 13 16
DVL1 0.019 0.083 0.18 2 -0.42 12 14
CSNK2A1 0.021 0.01 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.009 0.12 0.33 2 -0.54 12 14
DKK1/LRP6/Kremen 2 0.01 0.13 -10000 0 -0.28 88 88
LRP6 0.024 0.028 -10000 0 -0.45 2 2
CSNK1A1 0.029 0.037 0.19 3 -0.45 2 5
NLK 0.021 0.014 -10000 0 -10000 0 0
CCND1 -0.012 0.095 0.55 1 -0.71 4 5
WNT1 0.016 0.031 -10000 0 -0.44 1 1
GSK3A 0.026 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.028 -10000 0 -0.45 2 2
FRAT1 0.024 0.02 -10000 0 -0.44 1 1
PPP2R5D 0.057 0.094 0.27 74 -0.26 5 79
APC -0.011 0.077 0.22 32 -0.26 18 50
WNT1/LRP6/FZD1 0.039 0.081 0.2 76 -0.36 6 82
CREBBP 0.03 0.022 0.18 3 -10000 0 3
Nongenotropic Androgen signaling

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
PTK2 -0.005 0.013 -10000 0 -0.32 1 1
GNB1/GNG2 0.035 0.066 -10000 0 -0.26 25 25
regulation of S phase of mitotic cell cycle 0.007 0.043 -10000 0 -0.24 13 13
GNAO1 0.016 0.087 -10000 0 -0.44 19 19
HRAS 0.025 0.02 -10000 0 -0.44 1 1
SHBG/T-DHT 0.015 0.014 -10000 0 -0.07 4 4
PELP1 0.021 0.022 -10000 0 -0.44 1 1
AKT1 -0.006 0.013 -10000 0 -0.32 1 1
MAP2K1 0.04 0.098 0.17 189 -0.24 11 200
T-DHT/AR 0.009 0.065 -10000 0 -0.32 21 21
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.008 25 25
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNAI1 0.016 0.064 -10000 0 -0.44 11 11
mol:GDP -0.011 0.061 -10000 0 -0.31 22 22
cell proliferation 0.031 0.13 0.27 8 -0.4 20 28
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
FOS 0.008 0.18 -10000 0 -0.77 25 25
mol:Ca2+ -0.004 0.018 -10000 0 -0.062 38 38
MAPK3 0.037 0.11 0.27 10 -0.33 12 22
MAPK1 0.015 0.11 0.2 1 -0.42 20 21
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:IP3 0 0.001 -10000 0 -0.005 25 25
cAMP biosynthetic process -0.002 0.019 -10000 0 -10000 0 0
GNG2 0.021 0.044 -10000 0 -0.44 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 25 25
HRAS/GTP 0.021 0.053 -10000 0 -0.26 11 11
actin cytoskeleton reorganization 0.03 0.038 -10000 0 -0.29 6 6
SRC 0.015 0.023 -10000 0 -0.44 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 25 25
PI3K 0.031 0.026 -10000 0 -0.27 4 4
apoptosis -0.029 0.12 0.37 28 -0.22 5 33
T-DHT/AR/PELP1 0.021 0.06 -10000 0 -0.26 22 22
HRAS/GDP 0.001 0.066 -10000 0 -0.31 21 21
CREB1 0.028 0.12 0.23 5 -0.39 28 33
RAC1-CDC42/GTP 0.038 0.041 -10000 0 -0.3 6 6
AR 0.007 0.092 -10000 0 -0.44 21 21
GNB1 0.025 0.005 -10000 0 -10000 0 0
RAF1 0.047 0.1 0.18 198 -0.25 11 209
RAC1-CDC42/GDP 0.038 0.079 -10000 0 -0.29 22 22
T-DHT/AR/PELP1/Src 0.021 0.051 -10000 0 -0.27 11 11
MAP2K2 0.04 0.1 0.16 193 -0.26 11 204
T-DHT/AR/PELP1/Src/PI3K 0.007 0.043 -10000 0 -0.24 13 13
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
SHBG 0.018 0.024 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.004 0.11 -10000 0 -0.43 24 24
mol:T-DHT 0 0.001 -10000 0 -0.004 22 22
RAC1 0.023 0.008 -10000 0 -10000 0 0
GNRH1 -0.007 0.029 -10000 0 -0.32 5 5
Gi family/GTP -0.015 0.071 -10000 0 -0.22 45 45
CDC42 0.021 0.039 -10000 0 -0.44 4 4
Cellular roles of Anthrax toxin

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
ANTXR1 -0.001 0.12 -10000 0 -0.44 37 37
ANTXR2 0.023 0.039 -10000 0 -0.44 4 4
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.015 -10000 0 -0.061 41 41
monocyte activation -0.022 0.14 -10000 0 -0.42 55 55
MAP2K2 0.003 0.079 -10000 0 -0.59 10 10
MAP2K1 -0.009 0.019 -10000 0 -0.25 2 2
MAP2K7 -0.009 0.017 -10000 0 -0.23 1 1
MAP2K6 -0.013 0.032 -10000 0 -0.23 10 10
CYAA -0.024 0.056 -10000 0 -0.23 41 41
MAP2K4 -0.007 0.012 -10000 0 -10000 0 0
IL1B -0.029 0.062 -10000 0 -0.23 45 45
Channel 0.015 0.072 -10000 0 -0.24 41 41
NLRP1 -0.012 0.031 -10000 0 -0.19 12 12
CALM1 0.024 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.022 0.11 -10000 0 -0.41 39 39
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.015 0.061 41 -10000 0 41
MAPK3 -0.009 0.018 0.13 1 -0.23 1 2
MAPK1 -0.009 0.014 -10000 0 -0.1 1 1
PGR -0.023 0.056 -10000 0 -0.25 32 32
PA/Cellular Receptors 0.015 0.079 -10000 0 -0.27 41 41
apoptosis -0.006 0.015 -10000 0 -0.061 41 41
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.015 0.068 -10000 0 -0.23 41 41
macrophage activation -0.012 0.017 0.12 1 -0.22 1 2
TNF 0.009 0.088 -10000 0 -0.44 21 21
VCAM1 -0.021 0.14 -10000 0 -0.42 54 54
platelet activation -0.022 0.11 -10000 0 -0.41 39 39
MAPKKK cascade 0.008 0.022 0.14 2 -0.13 1 3
IL18 -0.013 0.032 -10000 0 -0.18 12 12
negative regulation of macrophage activation -0.006 0.015 -10000 0 -0.061 41 41
LEF -0.006 0.015 -10000 0 -0.061 41 41
CASP1 -0.009 0.025 -10000 0 -0.097 34 34
mol:cAMP -0.022 0.11 -10000 0 -0.41 39 39
necrosis -0.006 0.015 -10000 0 -0.061 41 41
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.016 0.068 -10000 0 -0.23 41 41
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.012 0.022 0.23 1 -0.32 2 3
MAP4K4 0 0.06 -10000 0 -0.31 7 7
BAG4 0.022 0.021 -10000 0 -0.44 1 1
PKC zeta/ceramide -0.013 0.075 -10000 0 -0.21 58 58
NFKBIA 0.024 0.006 -10000 0 -10000 0 0
BIRC3 0.015 0.076 -10000 0 -0.44 15 15
BAX -0.004 0.044 -10000 0 -0.31 7 7
RIPK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.006 0.02 -10000 0 -0.38 1 1
BAD -0.03 0.069 -10000 0 -0.21 59 59
SMPD1 0.012 0.055 0.2 8 -0.18 21 29
RB1 0.006 0.098 0.19 82 -0.21 47 129
FADD/Caspase 8 0.007 0.058 -10000 0 -0.32 4 4
MAP2K4 -0.031 0.067 -10000 0 -0.21 58 58
NSMAF 0.023 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.027 0.07 0.18 12 -0.2 57 69
EGF -0.031 0.17 -10000 0 -0.44 84 84
mol:ceramide -0.027 0.073 0.13 2 -0.22 59 61
MADD 0.026 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.009 0.018 0.23 1 -0.32 1 2
ASAH1 0.02 0.011 -10000 0 -10000 0 0
negative regulation of cell cycle 0.005 0.098 0.19 82 -0.21 47 129
cell proliferation -0.019 0.093 0.19 2 -0.22 55 57
BID -0.011 0.14 -10000 0 -0.58 27 27
MAP3K1 -0.031 0.071 -10000 0 -0.21 64 64
EIF2A -0.039 0.073 0.17 2 -0.26 30 32
TRADD 0.026 0.003 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.025 0.066 0.17 12 -0.24 18 30
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.029 0.068 0.17 10 -0.23 25 35
Cathepsin D/ceramide -0.013 0.076 -10000 0 -0.21 59 59
FADD 0.003 0.055 0.2 2 -0.29 4 6
KSR1 -0.025 0.072 0.19 10 -0.21 58 68
MAPK8 -0.028 0.073 -10000 0 -0.25 23 23
PRKRA -0.03 0.069 -10000 0 -0.21 60 60
PDGFA 0.023 0.022 -10000 0 -0.44 1 1
TRAF2 0.025 0.02 -10000 0 -0.44 1 1
IGF1 -0.011 0.14 -10000 0 -0.44 52 52
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.027 0.073 0.13 2 -0.22 59 61
CTSD 0.025 0.02 -10000 0 -0.44 1 1
regulation of nitric oxide biosynthetic process 0.036 0.017 -10000 0 -0.32 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.02 0.099 0.2 2 -0.24 54 56
PRKCD 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0.024 0.02 -10000 0 -0.44 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.009 0.018 0.23 1 -0.32 1 2
RelA/NF kappa B1 0.036 0.017 -10000 0 -0.32 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.025 0.02 -10000 0 -0.44 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.005 0.058 -10000 0 -0.32 5 5
TNFR1A/BAG4/TNF-alpha 0.034 0.061 -10000 0 -0.27 20 20
mol:Sphingosine-1-phosphate -0.012 0.022 0.23 1 -0.32 2 3
MAP2K1 -0.029 0.067 0.17 12 -0.2 49 61
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.004 -10000 0 -10000 0 0
CYCS 0.014 0.059 0.16 10 -0.18 15 25
TNFRSF1A 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
TNFR1A/BAG4 0.032 0.02 -10000 0 -0.32 1 1
EIF2AK2 -0.038 0.074 -10000 0 -0.22 66 66
TNF-alpha/TNFR1A/FAN 0.035 0.06 -10000 0 -0.27 19 19
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.069 -10000 0 -0.36 9 9
MAP2K2 -0.029 0.066 0.17 12 -0.2 45 57
SMPD3 0.007 0.065 0.16 2 -0.23 31 33
TNF 0.009 0.088 -10000 0 -0.44 21 21
PKC zeta/PAR4 0.035 0.023 -10000 0 -0.32 2 2
mol:PHOSPHOCHOLINE 0.025 0.08 0.21 75 -0.13 27 102
NF kappa B1/RelA/I kappa B alpha 0.065 0.036 -10000 0 -0.25 3 3
AIFM1 0.011 0.061 0.15 9 -0.19 9 18
BCL2 0.014 0.052 -10000 0 -0.44 7 7
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.017 0.043 -10000 0 -0.34 6 6
VEGFR1 homodimer/NRP1 0.004 0.039 -10000 0 -0.33 6 6
mol:DAG 0.004 0.064 0.19 43 -0.44 3 46
VEGFR1 homodimer/NRP1/VEGFR 121 0.016 0.038 -10000 0 -0.32 5 5
CaM/Ca2+ 0.022 0.06 -10000 0 -0.42 3 3
HIF1A 0.022 0.065 -10000 0 -0.49 9 9
GAB1 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.019 0.089 0.32 2 -0.42 7 9
PLCG1 0.004 0.064 0.19 43 -0.44 3 46
NOS3 0.066 0.13 0.28 79 -0.41 11 90
CBL 0.025 0.004 -10000 0 -10000 0 0
mol:NO 0.069 0.12 0.28 83 -0.4 11 94
FLT1 0.007 0.041 -10000 0 -0.39 5 5
PGF 0.025 0.03 -10000 0 -0.44 2 2
VEGFR1 homodimer/NRP2/VEGFR121 0.026 0.062 -10000 0 -0.29 14 14
CALM1 0.024 0.007 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
eNOS/Hsp90 0.079 0.13 0.29 85 -0.48 6 91
endothelial cell proliferation 0.065 0.13 0.32 71 -0.49 5 76
mol:Ca2+ 0.004 0.064 0.19 43 -0.44 3 46
MAPK3 0.001 0.06 0.31 1 -0.4 3 4
MAPK1 0.001 0.058 0.17 40 -0.4 3 43
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
PLGF homodimer 0.024 0.03 -10000 0 -0.44 2 2
PRKACA 0.026 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.022 0.045 -10000 0 -0.44 5 5
VEGFA homodimer 0.025 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.017 0.041 -10000 0 -0.35 5 5
platelet activating factor biosynthetic process -0.002 0.056 0.3 1 -0.46 2 3
PI3K 0.036 0.061 -10000 0 -0.35 9 9
PRKCA 0.003 0.061 0.18 43 -0.41 3 46
PRKCB -0.003 0.075 0.18 40 -0.48 3 43
VEGFR1 homodimer/PLGF homodimer 0.018 0.049 -10000 0 -0.32 8 8
VEGFA 0.025 0.004 -10000 0 -10000 0 0
VEGFB 0.025 0.004 -10000 0 -10000 0 0
mol:IP3 0.004 0.064 0.19 43 -0.44 3 46
RASA1 0.025 0.092 0.19 119 -0.45 3 122
NRP2 0.019 0.066 -10000 0 -0.44 11 11
VEGFR1 homodimer 0.007 0.041 -10000 0 -0.39 5 5
VEGFB homodimer 0.025 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.028 -10000 0 -0.44 2 2
eNOS/Caveolin-1 0.069 0.12 0.28 68 -0.5 6 74
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
mol:PI-3-4-5-P3 0.034 0.059 -10000 0 -0.35 9 9
mol:L-citrulline 0.069 0.12 0.28 83 -0.4 11 94
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.027 0.076 -10000 0 -0.3 22 22
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.047 -10000 0 -0.31 7 7
CD2AP 0.004 0.099 -10000 0 -0.44 27 27
PI3K/GAB1 0.076 0.075 -10000 0 -0.39 6 6
PDPK1 0.016 0.091 0.34 2 -0.42 5 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.026 0.055 -10000 0 -0.4 7 7
mol:NADP 0.069 0.12 0.28 83 -0.4 11 94
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
ubiquitin-dependent protein catabolic process 0.026 0.075 -10000 0 -0.3 22 22
VEGFR1 homodimer/NRP2 0.015 0.064 -10000 0 -0.31 15 15
Arf6 signaling events

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
CENTA1/KIF3B 0.024 0.027 -10000 0 -0.5 1 1
ARNO/beta Arrestin1-2 0.019 0.086 -10000 0 -0.85 3 3
EGFR 0.02 0.044 -10000 0 -0.44 5 5
EPHA2 0.023 0.028 -10000 0 -0.44 2 2
USP6 0.021 0.022 -10000 0 -0.44 1 1
IQSEC1 0.026 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.005 0.13 -10000 0 -0.32 78 78
ARRB2 0.007 0.003 -10000 0 -10000 0 0
mol:GTP -0.003 0.052 0.13 9 -0.2 17 26
ARRB1 0.024 0.028 -10000 0 -0.44 2 2
FBXO8 0.024 0.02 -10000 0 -0.44 1 1
TSHR 0.016 0.032 -10000 0 -0.44 1 1
EGF -0.031 0.17 -10000 0 -0.44 84 84
somatostatin receptor activity 0 0 0.001 41 -0.001 24 65
ARAP2 0.012 0.079 -10000 0 -0.44 17 17
mol:GDP -0.002 0.09 0.19 12 -0.26 32 44
mol:PI-3-4-5-P3 0 0 0.001 24 -0.001 14 38
ITGA2B 0.008 0.095 -10000 0 -0.44 23 23
ARF6 0.024 0.02 -10000 0 -0.44 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.038 -10000 0 -0.3 4 4
ADAP1 0.023 0.021 -10000 0 -0.44 1 1
KIF13B 0.019 0.022 -10000 0 -0.44 1 1
HGF/MET 0.018 0.083 -10000 0 -0.32 32 32
PXN 0.026 0.002 -10000 0 -10000 0 0
ARF6/GTP 0 0.1 0.21 34 -0.28 23 57
EGFR/EGFR/EGF/EGF/ARFGEP100 0.01 0.12 -10000 0 -0.27 78 78
ADRB2 0.002 0.1 -10000 0 -0.44 30 30
receptor agonist activity 0 0 0 15 0 19 34
actin filament binding 0 0 0 40 0 29 69
SRC 0.015 0.023 -10000 0 -0.44 1 1
ITGB3 0.016 0.07 -10000 0 -0.44 13 13
GNAQ 0.022 0.044 -10000 0 -0.45 5 5
EFA6/PI-4-5-P2 0 0.001 0.001 51 -0.001 14 65
ARF6/GDP -0.047 0.16 0.21 2 -0.42 72 74
ARF6/GDP/GULP/ACAP1 0.003 0.12 0.22 6 -0.32 33 39
alphaIIb/beta3 Integrin/paxillin/GIT1 0.048 0.079 -10000 0 -0.25 36 36
ACAP1 0.01 0.078 -10000 0 -0.44 16 16
ACAP2 0.018 0.061 -10000 0 -0.44 10 10
LHCGR/beta Arrestin2 0.006 0.027 -10000 0 -10000 0 0
EFNA1 0.025 0.004 -10000 0 -10000 0 0
HGF 0.001 0.11 -10000 0 -0.44 32 32
CYTH3 -0.006 0.018 -10000 0 -0.32 2 2
CYTH2 0.013 0.073 -10000 0 -1 3 3
NCK1 0.024 0.028 -10000 0 -0.44 2 2
fibronectin binding 0 0 0 40 0 21 61
endosomal lumen acidification 0 0 0 43 0 23 66
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 -0.007 0.13 -10000 0 -0.44 44 44
GNAQ/ARNO 0.027 0.073 -10000 0 -0.94 3 3
mol:Phosphatidic acid 0 0 0 9 -10000 0 9
PIP3-E 0 0 0 10 0 9 19
MET 0.024 0.02 -10000 0 -0.44 1 1
GNA14 0.014 0.075 -10000 0 -0.44 15 15
GNA15 0.015 0.073 -10000 0 -0.44 14 14
GIT1 0.024 0.02 -10000 0 -0.44 1 1
mol:PI-4-5-P2 0 0 0.001 47 -0.001 17 64
GNA11 0.023 0.034 -10000 0 -0.44 3 3
LHCGR -0.013 0.015 -10000 0 -10000 0 0
AGTR1 -0.014 0.14 -10000 0 -0.44 50 50
desensitization of G-protein coupled receptor protein signaling pathway 0.006 0.027 -10000 0 -10000 0 0
IPCEF1/ARNO 0.012 0.11 -10000 0 -0.91 3 3
alphaIIb/beta3 Integrin 0.019 0.088 -10000 0 -0.32 36 36
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.033 0.094 -10000 0 -0.24 54 54
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.01 0.092 0.29 1 -0.38 9 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.032 0.065 -10000 0 -0.3 15 15
antigen processing and presentation of peptide antigen via MHC class I -0.015 0.073 -10000 0 -0.23 26 26
CaM/Ca2+ 0.033 0.091 -10000 0 -0.23 53 53
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
STAT1 (dimer)/SHP2 -0.002 0.087 0.21 1 -0.24 53 54
AKT1 -0.033 0.078 0.31 3 -0.35 10 13
MAP2K1 -0.035 0.085 0.29 3 -0.25 48 51
MAP3K11 -0.032 0.075 0.19 9 -0.23 52 61
IFNGR1 0.02 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.017 0.13 -10000 0 -0.39 40 40
Rap1/GTP -0.04 0.054 -10000 0 -0.3 7 7
CRKL/C3G 0.036 0.017 -10000 0 -0.32 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.036 0.097 -10000 0 -0.24 52 52
CEBPB 0.001 0.16 0.38 3 -0.48 32 35
STAT3 0.025 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.21 -10000 0 -1.1 17 17
STAT1 -0.032 0.08 0.26 4 -0.24 53 57
CALM1 0.024 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.006 0.12 -10000 0 -0.45 37 37
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
STAT1 (dimer)/PIAS1 -0.003 0.085 0.3 3 -0.23 49 52
CEBPB/PTGES2/Cbp/p300 0.013 0.11 -10000 0 -0.37 19 19
mol:Ca2+ 0.03 0.092 -10000 0 -0.24 54 54
MAPK3 -0.022 0.12 0.38 1 -0.71 9 10
STAT1 (dimer) -0.014 0.1 -10000 0 -0.32 26 26
MAPK1 -0.047 0.18 0.4 1 -0.74 30 31
JAK2 0.009 0.078 -10000 0 -0.46 15 15
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
JAK1 0.02 0.029 -10000 0 -0.49 1 1
CAMK2D 0.022 0.039 -10000 0 -0.44 4 4
DAPK1 -0.002 0.15 0.32 7 -0.53 31 38
SMAD7 -0.008 0.042 0.17 3 -0.2 5 8
CBL/CRKL/C3G 0.007 0.083 0.34 2 -0.22 47 49
PI3K 0.03 0.096 -10000 0 -0.24 51 51
IFNG -0.006 0.12 -10000 0 -0.45 37 37
apoptosis -0.005 0.13 0.32 4 -0.42 38 42
CAMK2G 0.025 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.004 -10000 0 -10000 0 0
CAMK2A 0.008 0.085 -10000 0 -0.44 19 19
CAMK2B 0.006 0.093 -10000 0 -0.44 22 22
FRAP1 -0.032 0.072 0.3 3 -0.33 10 13
PRKCD -0.035 0.078 0.32 3 -0.37 9 12
RAP1B 0.026 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.015 0.073 -10000 0 -0.23 26 26
PTPN2 0.02 0.022 -10000 0 -0.44 1 1
EP300 0.023 0.028 -10000 0 -0.44 2 2
IRF1 -0.032 0.084 0.34 3 -0.38 17 20
STAT1 (dimer)/PIASy -0.006 0.087 0.23 6 -0.29 15 21
SOCS1 -0.013 0.23 -10000 0 -1.3 17 17
mol:GDP 0.005 0.078 0.27 1 -0.22 47 48
CASP1 -0.015 0.061 0.16 4 -0.24 27 31
PTGES2 0.025 0.02 -10000 0 -0.44 1 1
IRF9 0.013 0.055 0.17 10 -0.17 10 20
mol:PI-3-4-5-P3 0.016 0.088 -10000 0 -0.24 51 51
RAP1/GDP 0.007 0.075 -10000 0 -0.32 6 6
CBL -0.032 0.075 0.18 13 -0.23 51 64
MAP3K1 -0.034 0.083 0.22 6 -0.25 52 58
PIAS1 0.025 0.005 -10000 0 -10000 0 0
PIAS4 0.025 0.019 -10000 0 -0.43 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.015 0.073 -10000 0 -0.23 26 26
PTPN11 -0.031 0.075 0.16 15 -0.24 53 68
CREBBP 0.026 0.004 -10000 0 -10000 0 0
RAPGEF1 0.025 0.02 -10000 0 -0.44 1 1
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.02 0.068 0.2 3 -0.35 6 9
DAPP1 -0.026 0.18 0.24 15 -0.41 69 84
Src family/SYK family/BLNK-LAT/BTK-ITK -0.064 0.23 0.26 2 -0.53 80 82
mol:DAG 0.002 0.11 0.17 88 -0.27 36 124
HRAS 0.023 0.024 -10000 0 -0.45 1 1
RAP1A 0.023 0.024 -10000 0 -0.48 1 1
ARF5/GDP 0.024 0.12 0.21 2 -0.42 24 26
PLCG2 0.013 0.08 -10000 0 -0.44 17 17
PLCG1 0.014 0.023 -10000 0 -0.44 1 1
ARF5 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.025 0.055 0.15 14 -0.27 17 31
ARF1/GTP -0.01 0.062 0.24 3 -0.25 19 22
RHOA 0.025 0.02 -10000 0 -0.44 1 1
YES1 0.019 0.035 -10000 0 -0.44 3 3
RAP1A/GTP -0.026 0.054 0.16 13 -0.25 20 33
ADAP1 -0.026 0.054 0.28 1 -0.31 11 12
ARAP3 -0.025 0.054 0.15 14 -0.25 20 34
INPPL1 0.025 0.02 -10000 0 -0.44 1 1
PREX1 0.012 0.04 -10000 0 -0.44 4 4
ARHGEF6 0.017 0.067 -10000 0 -0.44 12 12
ARHGEF7 0.02 0.011 -10000 0 -10000 0 0
ARF1 0.025 0.005 -10000 0 -10000 0 0
NRAS 0.018 0.06 -10000 0 -0.45 9 9
FYN 0.022 0.039 -10000 0 -0.44 4 4
ARF6 0.024 0.02 -10000 0 -0.44 1 1
FGR 0.007 0.094 -10000 0 -0.44 24 24
mol:Ca2+ 0.004 0.061 0.15 26 -0.14 22 48
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.006 0.1 -10000 0 -0.44 28 28
ZAP70 0.003 0.11 -10000 0 -0.44 31 31
mol:IP3 -0.001 0.078 0.13 84 -0.19 30 114
LYN 0.023 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.025 0.12 0.2 4 -0.43 24 28
RhoA/GDP 0.028 0.091 0.21 13 -0.33 18 31
PDK1/Src/Hsp90 0.029 0.029 -10000 0 -0.27 1 1
BLNK 0.01 0.084 -10000 0 -0.44 19 19
actin cytoskeleton reorganization 0.021 0.11 0.22 36 -0.41 18 54
SRC 0.015 0.023 -10000 0 -0.44 1 1
PLEKHA2 -0.023 0.055 -10000 0 -0.28 24 24
RAC1 0.023 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.011 -10000 0 -10000 0 0
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
ARF6/GTP -0.027 0.058 0.29 1 -0.31 11 12
RhoA/GTP -0.027 0.057 0.16 14 -0.31 11 25
Src family/SYK family/BLNK-LAT -0.042 0.16 0.19 1 -0.45 54 55
BLK -0.021 0.14 -10000 0 -0.44 56 56
PDPK1 0.026 0.004 -10000 0 -10000 0 0
CYTH1 -0.027 0.052 0.28 1 -0.29 11 12
HCK 0.005 0.072 -10000 0 -0.44 14 14
CYTH3 -0.027 0.053 0.28 1 -0.28 13 14
CYTH2 -0.027 0.052 0.28 1 -0.29 11 12
KRAS 0.02 0.046 -10000 0 -0.46 5 5
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.059 -10000 0 -0.45 7 7
SGK1 0.001 0.07 -10000 0 -0.43 11 11
INPP5D 0.005 0.097 -10000 0 -0.44 26 26
mol:GDP 0.015 0.12 0.19 7 -0.4 29 36
SOS1 0.026 0.002 -10000 0 -10000 0 0
SYK 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.004 0.088 0.22 13 -0.34 17 30
mol:PI-3-4-5-P3 -0.026 0.054 0.28 1 -0.27 17 18
ARAP3/RAP1A/GTP -0.026 0.055 0.16 13 -0.26 20 33
VAV1 -0.002 0.11 -10000 0 -0.44 35 35
mol:PI-3-4-P2 -0.026 0.067 -10000 0 -0.33 26 26
RAS family/GTP/PI3K Class I 0.031 0.068 0.2 7 -0.26 20 27
PLEKHA1 -0.026 0.059 -10000 0 -0.28 29 29
Rac1/GDP 0.019 0.12 0.21 2 -0.43 24 26
LAT 0.019 0.062 -10000 0 -0.44 10 10
Rac1/GTP -0.016 0.11 -10000 0 -0.45 26 26
ITK -0.039 0.07 0.28 1 -0.26 38 39
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.13 0.19 80 -0.38 37 117
LCK 0.013 0.086 -10000 0 -0.44 19 19
BTK -0.039 0.069 0.28 1 -0.25 39 40
ErbB2/ErbB3 signaling events

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.01 0.022 -10000 0 -0.27 4 4
RAS family/GTP 0.005 0.096 -10000 0 -0.3 13 13
NFATC4 -0.028 0.067 0.25 3 -0.21 36 39
ERBB2IP 0.011 0.081 -10000 0 -0.44 18 18
HSP90 (dimer) 0.023 0.02 -10000 0 -0.44 1 1
mammary gland morphogenesis -0.004 0.081 0.22 8 -0.25 40 48
JUN -0.007 0.084 0.19 4 -0.33 19 23
HRAS 0.025 0.021 -10000 0 -0.45 1 1
DOCK7 -0.034 0.073 0.18 7 -0.24 39 46
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.023 0.087 0.25 13 -0.25 39 52
AKT1 -0.006 0.014 -10000 0 -0.32 1 1
BAD -0.01 0.021 -10000 0 -0.51 1 1
MAPK10 -0.021 0.067 0.2 6 -0.22 18 24
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.001 0.088 0.23 8 -0.26 40 48
RAF1 -0.013 0.09 0.28 4 -0.31 13 17
ErbB2/ErbB3/neuregulin 2 0.031 0.056 0.23 27 -0.27 2 29
STAT3 0.013 0.075 -10000 0 -0.86 4 4
cell migration -0.014 0.067 0.21 10 -0.22 11 21
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.041 0.2 0.35 2 -0.6 47 49
FOS -0.028 0.15 0.31 2 -0.4 62 64
NRAS 0.018 0.058 -10000 0 -0.44 9 9
mol:Ca2+ -0.004 0.081 0.22 8 -0.25 40 48
MAPK3 -0.026 0.15 0.34 2 -0.51 33 35
MAPK1 -0.04 0.18 0.34 2 -0.56 44 46
JAK2 -0.036 0.073 0.21 3 -0.25 44 47
NF2 0.002 0.057 -10000 0 -0.6 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.001 0.07 0.2 3 -0.24 39 42
NRG1 -0.01 0.12 -10000 0 -0.45 40 40
GRB2/SOS1 0.038 0.006 -10000 0 -10000 0 0
MAPK8 -0.02 0.094 0.29 1 -0.26 37 38
MAPK9 -0.014 0.056 0.2 6 -0.21 3 9
ERBB2 -0.01 0.068 0.35 18 -0.34 1 19
ERBB3 0.024 0.02 -10000 0 -0.45 1 1
SHC1 0.025 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.008 -10000 0 -10000 0 0
apoptosis 0.006 0.027 0.65 1 -10000 0 1
STAT3 (dimer) 0.013 0.074 -10000 0 -0.84 4 4
RNF41 -0.014 0.021 -10000 0 -0.24 4 4
FRAP1 -0.005 0.011 -10000 0 -0.27 1 1
RAC1-CDC42/GTP -0.034 0.047 -10000 0 -0.2 38 38
ErbB2/ErbB2/HSP90 (dimer) -0.012 0.046 0.25 15 -0.28 1 16
CHRNA1 -0.025 0.16 0.32 2 -0.57 34 36
myelination -0.024 0.071 0.27 5 -0.4 2 7
PPP3CB -0.031 0.068 0.17 8 -0.23 38 46
KRAS 0.021 0.044 -10000 0 -0.44 5 5
RAC1-CDC42/GDP 0.006 0.08 0.21 1 -0.22 37 38
NRG2 0.019 0.027 -10000 0 -10000 0 0
mol:GDP -0.002 0.07 0.2 3 -0.24 40 43
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.021 0.09 0.29 3 -0.33 15 18
SRC 0.015 0.023 -10000 0 -0.44 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.034 0.073 0.18 7 -0.24 41 48
MAP2K1 -0.049 0.19 0.35 1 -0.58 49 50
heart morphogenesis -0.004 0.081 0.22 8 -0.25 40 48
RAS family/GDP 0.009 0.098 -10000 0 -0.23 45 45
GRB2 0.025 0.004 -10000 0 -10000 0 0
PRKACA 0.006 0.06 -10000 0 -0.63 5 5
CHRNE -0.001 0.036 0.065 3 -0.18 18 21
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
activation of caspase activity 0.006 0.014 0.32 1 -10000 0 1
nervous system development -0.004 0.081 0.22 8 -0.25 40 48
CDC42 0.021 0.039 -10000 0 -0.44 4 4
a4b1 and a4b7 Integrin 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
ITGB1 0.026 0.002 -9999 0 -10000 0 0
ITGB7 0.014 0.078 -9999 0 -0.44 16 16
ITGA4 0.005 0.097 -9999 0 -0.44 26 26
alpha4/beta7 Integrin 0.015 0.099 -9999 0 -0.36 37 37
alpha4/beta1 Integrin 0.023 0.074 -9999 0 -0.32 26 26
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.012 0.13 -10000 0 -0.43 39 39
HDAC1 0.023 0.006 -10000 0 -10000 0 0
AES 0.024 0.02 -10000 0 -0.44 1 1
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.015 0.075 -10000 0 -0.44 15 15
LRP6/FZD1 0.034 0.031 -10000 0 -0.32 4 4
TLE1 0.022 0.039 -10000 0 -0.45 4 4
AP1 -0.031 0.1 -10000 0 -0.26 94 94
NCSTN 0.025 0.004 -10000 0 -10000 0 0
ADAM10 0.021 0.039 -10000 0 -0.44 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.022 0.096 -10000 0 -0.66 9 9
NICD/RBPSUH 0.011 0.12 -10000 0 -0.42 37 37
WIF1 -0.036 0.17 -10000 0 -0.44 83 83
NOTCH1 -0.005 0.12 -10000 0 -0.44 39 39
PSENEN 0.025 0.02 -10000 0 -0.44 1 1
KREMEN2 0.022 0.07 -10000 0 -0.44 12 12
DKK1 -0.028 0.16 -10000 0 -0.44 76 76
beta catenin/beta TrCP1 0.04 0.076 0.26 4 -0.45 1 5
APH1B 0.022 0.039 -10000 0 -0.44 4 4
APH1A 0.025 0.004 -10000 0 -10000 0 0
AXIN1 -0.01 0.073 -10000 0 -0.46 8 8
CtBP/CBP/TCF1/TLE1/AES 0.01 0.051 -10000 0 -0.32 9 9
PSEN1 0.024 0.006 -10000 0 -10000 0 0
FOS 0.013 0.08 -10000 0 -0.44 17 17
JUN 0.022 0.039 -10000 0 -0.44 4 4
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.029 0.077 0.25 6 -0.47 1 7
MAPK3 0.025 0.02 -10000 0 -0.44 1 1
DKK2/LRP6/Kremen 2 0.012 0.12 -10000 0 -0.28 77 77
HNF1A 0.021 0.044 -10000 0 -0.44 5 5
CTBP1 0.024 0.02 -10000 0 -0.44 1 1
MYC 0.013 0.12 -10000 0 -1.3 5 5
NKD1 -0.032 0.17 -10000 0 -0.44 82 82
FZD1 0.023 0.028 -10000 0 -0.44 2 2
NOTCH1 precursor/Deltex homolog 1 0.006 0.12 -10000 0 -0.42 39 39
apoptosis -0.03 0.1 -10000 0 -0.25 94 94
Delta 1/NOTCHprecursor 0.009 0.12 -10000 0 -0.43 39 39
DLL1 0.02 0.056 -10000 0 -0.44 8 8
PPARD 0.023 0.078 -10000 0 -0.87 4 4
Gamma Secretase 0.064 0.039 -10000 0 -0.24 5 5
APC -0.038 0.13 -10000 0 -0.42 50 50
DVL1 -0.01 0.083 -10000 0 -0.46 14 14
CSNK2A1 0.021 0.01 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.01 0.13 -10000 0 -0.28 88 88
LRP6 0.024 0.028 -10000 0 -0.44 2 2
CSNK1A1 0.024 0.028 -10000 0 -0.44 2 2
NLK 0.01 0.005 -10000 0 -10000 0 0
CCND1 0.013 0.13 -10000 0 -0.93 10 10
WNT1 0.014 0.032 -10000 0 -0.44 1 1
Axin1/APC/beta catenin -0.001 0.12 0.4 3 -0.44 21 24
DKK2 -0.023 0.15 -10000 0 -0.44 65 65
NOTCH1 precursor/DVL1 -0.015 0.16 -10000 0 -0.58 29 29
GSK3B 0.024 0.028 -10000 0 -0.44 2 2
FRAT1 0.024 0.02 -10000 0 -0.44 1 1
NOTCH/Deltex homolog 1 0.009 0.12 -10000 0 -0.42 39 39
PPP2R5D 0.043 0.086 0.25 74 -0.27 6 80
MAPK1 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.024 0.12 -10000 0 -0.26 83 83
RBPJ 0.025 0.02 -10000 0 -0.44 1 1
CREBBP 0.027 0.006 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.047 0.22 0.47 1 -0.72 14 15
CRP -0.018 0.2 0.46 1 -0.76 14 15
cell cycle arrest -0.023 0.22 -10000 0 -0.78 22 22
TIMP1 0.001 0.18 -10000 0 -0.63 16 16
IL6ST 0.012 0.072 -10000 0 -0.45 13 13
Rac1/GDP -0.025 0.15 -10000 0 -0.43 43 43
AP1 0.038 0.13 -10000 0 -0.56 13 13
GAB2 0.024 0.028 -10000 0 -0.44 2 2
TNFSF11 -0.03 0.33 0.46 1 -0.98 52 53
HSP90B1 0.015 0.14 -10000 0 -1.1 8 8
GAB1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.022 0.14 -10000 0 -0.53 22 22
AKT1 0.019 0.078 -10000 0 -0.53 8 8
FOXO1 0.046 0.1 -10000 0 -0.53 7 7
MAP2K6 -0.029 0.13 -10000 0 -0.42 39 39
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.032 0.15 0.39 2 -0.45 42 44
MITF -0.031 0.13 0.22 1 -0.4 45 46
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.02 -10000 0 -0.44 1 1
A2M 0.005 0.15 -10000 0 -1.2 9 9
CEBPB 0.014 0.026 -10000 0 -0.44 1 1
GRB2/SOS1/GAB family/SHP2 0.021 0.11 -10000 0 -0.52 12 12
STAT3 -0.034 0.22 -10000 0 -0.83 23 23
STAT1 0.015 0.067 -10000 0 -1.1 2 2
CEBPD -0.004 0.2 -10000 0 -0.78 15 15
PIK3CA 0.025 0.028 -10000 0 -0.44 2 2
PI3K 0.036 0.031 -10000 0 -0.32 4 4
JUN 0.022 0.039 -10000 0 -0.44 4 4
PIAS3/MITF -0.014 0.14 -10000 0 -0.41 39 39
MAPK11 -0.023 0.14 -10000 0 -0.57 20 20
STAT3 (dimer)/FOXO1 0.019 0.2 0.35 8 -0.6 19 27
GRB2/SOS1/GAB family 0.041 0.14 -10000 0 -0.43 29 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.02 0.13 -10000 0 -0.4 43 43
GRB2 0.026 0.004 -10000 0 -10000 0 0
JAK2 0.013 0.075 -10000 0 -0.44 15 15
LBP 0.01 0.32 0.43 2 -0.83 57 59
PIK3R1 0.024 0.028 -10000 0 -0.44 2 2
JAK1 0.022 0.025 -10000 0 -0.45 1 1
MYC 0.004 0.22 0.46 1 -0.82 17 18
FGG -0.023 0.19 -10000 0 -0.75 17 17
macrophage differentiation -0.023 0.22 -10000 0 -0.78 22 22
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.017 0.14 -10000 0 -0.29 80 80
JUNB -0.021 0.2 -10000 0 -0.77 17 17
FOS 0.012 0.08 -10000 0 -0.44 17 17
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.018 0.14 -10000 0 -0.42 40 40
STAT1/PIAS1 0.004 0.14 -10000 0 -0.42 32 32
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.081 -10000 0 -0.53 9 9
STAT3 (dimer) -0.027 0.22 -10000 0 -0.82 22 22
PRKCD -0.02 0.18 0.3 31 -0.52 33 64
IL6R 0.011 0.076 -10000 0 -0.45 15 15
SOCS3 -0.021 0.16 0.38 1 -0.82 12 13
gp130 (dimer)/JAK1/JAK1/LMO4 0.038 0.066 -10000 0 -0.3 14 14
Rac1/GTP -0.025 0.15 -10000 0 -0.44 44 44
HCK 0.005 0.072 -10000 0 -0.44 14 14
MAPKKK cascade 0.03 0.12 -10000 0 -0.63 12 12
bone resorption -0.023 0.31 0.45 1 -0.91 52 53
IRF1 -0.02 0.19 -10000 0 -0.76 14 14
mol:GDP -0.033 0.14 0.21 1 -0.42 49 50
SOS1 0.026 0.002 -10000 0 -10000 0 0
VAV1 -0.034 0.14 0.21 1 -0.42 49 50
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.023 0.16 -10000 0 -0.59 27 27
PTPN11 0.008 0.11 -10000 0 -0.93 7 7
IL6/IL6RA -0.008 0.13 -10000 0 -0.34 67 67
gp130 (dimer)/TYK2/TYK2/LMO4 0.041 0.058 -10000 0 -0.28 15 15
gp130 (dimer)/JAK2/JAK2/LMO4 0.034 0.078 -10000 0 -0.3 27 27
IL6 -0.02 0.14 -10000 0 -0.45 57 57
PIAS3 0.024 0.02 -10000 0 -0.44 1 1
PTPRE 0.02 0.023 -10000 0 -0.43 1 1
PIAS1 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.018 0.12 -10000 0 -0.31 62 62
LMO4 0.021 0.029 -10000 0 -0.44 1 1
STAT3 (dimer)/PIAS3 -0.017 0.22 -10000 0 -0.77 24 24
MCL1 0.019 0.075 -10000 0 -0.62 4 4
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.003 0.17 0.29 1 -0.58 35 36
MAP3K8 0.024 0.021 -10000 0 -0.44 1 1
FOS -0.012 0.16 0.29 2 -0.6 32 34
PRKCA 0.023 0.022 -10000 0 -0.44 1 1
PTPN7 0.012 0.092 -10000 0 -0.45 21 21
HRAS 0.025 0.02 -10000 0 -0.44 1 1
PRKCB -0.003 0.12 -10000 0 -0.45 37 37
NRAS 0.018 0.058 -10000 0 -0.44 9 9
RAS family/GTP 0.038 0.054 -10000 0 -0.3 12 12
MAPK3 -0.002 0.14 -10000 0 -0.6 26 26
MAP2K1 -0.011 0.11 -10000 0 -0.39 41 41
ELK1 0.023 0.023 -10000 0 -0.44 1 1
BRAF -0.009 0.099 -10000 0 -0.39 36 36
mol:GTP 0 0.001 -10000 0 -0.004 25 25
MAPK1 -0.016 0.17 -10000 0 -0.57 42 42
RAF1 -0.011 0.11 -10000 0 -0.39 39 39
KRAS 0.021 0.044 -10000 0 -0.44 5 5
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.007 -10000 0 -10000 0 0
VLDLR -0.001 0.11 -10000 0 -0.44 35 35
LRPAP1 0.024 0.02 -10000 0 -0.44 1 1
NUDC 0.024 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.019 0.1 -10000 0 -0.27 59 59
CaM/Ca2+ 0.018 0.005 -10000 0 -10000 0 0
KATNA1 0.025 0.02 -10000 0 -0.44 1 1
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.036 0.083 0.18 21 -0.25 59 80
IQGAP1/CaM 0.034 0.024 -10000 0 -0.32 2 2
DAB1 -0.009 0.12 -10000 0 -0.44 42 42
IQGAP1 0.023 0.028 -10000 0 -0.44 2 2
PLA2G7 0.004 0.1 -10000 0 -0.44 28 28
CALM1 0.024 0.007 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.031 -10000 0 -0.32 4 4
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.028 -10000 0 -0.44 2 2
CDK5R1 0.026 0.007 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.007 0.004 -10000 0 -10000 0 0
CDK5R2 0.005 0.099 -10000 0 -0.44 25 25
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.016 0.15 -10000 0 -0.31 114 114
YWHAE 0.022 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.014 0.1 0.31 16 -0.32 18 34
MAP1B 0 0.037 -10000 0 -0.28 9 9
RAC1 0.007 0.009 -10000 0 -0.15 1 1
p35/CDK5 -0.039 0.067 0.17 6 -0.23 55 61
RELN -0.015 0.14 -10000 0 -0.44 55 55
PAFAH/LIS1 0.009 0.057 0.21 1 -0.26 23 24
LIS1/CLIP170 0.019 0.017 -10000 0 -0.27 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.017 0.079 -10000 0 -0.32 8 8
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.031 0.13 -10000 0 -0.31 73 73
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.033 0.099 0.32 12 -0.33 22 34
LIS1/IQGAP1 0.019 0.017 -10000 0 -0.27 1 1
RHOA 0.007 0.029 -10000 0 -0.68 1 1
PAFAH1B1 -0.008 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.028 -10000 0 -0.44 2 2
PAFAH1B2 0.022 0.039 -10000 0 -0.44 4 4
MAP1B/LIS1/Dynein heavy chain 0.01 0.04 -10000 0 -0.2 8 8
NDEL1/Katanin 60/Dynein heavy chain -0.014 0.1 0.31 12 -0.33 16 28
LRP8 0.023 0.034 -10000 0 -0.44 3 3
NDEL1/Katanin 60 -0.024 0.1 0.31 13 -0.32 20 33
P39/CDK5 -0.046 0.09 0.2 9 -0.25 76 85
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.019 0.013 -10000 0 -10000 0 0
CDK5 -0.04 0.071 0.18 6 -0.24 58 64
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.016 0.015 -10000 0 -0.23 1 1
CSNK2A1 0.021 0.01 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.01 0.13 0.22 10 -0.27 102 112
RELN/VLDLR 0.015 0.12 -10000 0 -0.27 84 84
CDC42 0.005 0.044 -10000 0 -0.5 4 4
Signaling events mediated by PTP1B

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
PDGFRB 0.018 0.062 -10000 0 -0.44 10 10
Jak2/Leptin Receptor 0.002 0.13 0.27 1 -0.38 35 36
PTP1B/AKT1 0.025 0.089 0.22 4 -0.28 17 21
FYN 0.022 0.039 -10000 0 -0.44 4 4
p210 bcr-abl/PTP1B 0.019 0.095 0.2 17 -0.3 16 33
EGFR 0.015 0.047 -10000 0 -0.45 5 5
EGF/EGFR 0.009 0.13 0.2 1 -0.28 51 52
CSF1 0.023 0.034 -10000 0 -0.44 3 3
AKT1 0.024 0.021 -10000 0 -0.45 1 1
INSR 0.025 0.02 -10000 0 -0.45 1 1
PTP1B/N-cadherin 0.007 0.11 0.22 3 -0.32 35 38
Insulin Receptor/Insulin 0.03 0.083 0.23 1 -0.32 8 9
HCK 0.005 0.072 -10000 0 -0.44 14 14
CRK 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.015 0.093 0.3 6 -0.29 16 22
EGF -0.03 0.18 -10000 0 -0.45 84 84
YES1 0.019 0.035 -10000 0 -0.44 3 3
CAV1 0.029 0.12 0.24 32 -0.33 17 49
TXN 0.026 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.034 0.1 0.23 3 -0.3 20 23
cell migration -0.019 0.095 0.3 16 -0.2 17 33
STAT3 0.026 0.004 -10000 0 -10000 0 0
PRLR -0.015 0.13 -10000 0 -0.44 51 51
ITGA2B 0.006 0.095 -10000 0 -0.45 23 23
CSF1R 0.007 0.097 -10000 0 -0.44 25 25
Prolactin Receptor/Prolactin 0.004 0.1 -10000 0 -0.33 51 51
FGR 0.007 0.094 -10000 0 -0.44 24 24
PTP1B/p130 Cas 0.027 0.094 0.22 3 -0.29 17 20
Crk/p130 Cas 0.029 0.093 0.22 2 -0.29 15 17
DOK1 0.015 0.095 0.23 4 -0.31 19 23
JAK2 -0.005 0.13 0.26 1 -0.37 37 38
Jak2/Leptin Receptor/Leptin 0.02 0.11 -10000 0 -0.38 13 13
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
PTPN1 0.019 0.095 0.2 17 -0.3 16 33
LYN 0.023 0.009 -10000 0 -10000 0 0
CDH2 -0.01 0.12 -10000 0 -0.44 43 43
SRC 0.024 0.1 0.25 1 -0.48 15 16
ITGB3 0.015 0.07 -10000 0 -0.45 13 13
CAT1/PTP1B 0.014 0.18 0.23 97 -0.44 45 142
CAPN1 0.024 0.02 -10000 0 -0.46 1 1
CSK 0.024 0.02 -10000 0 -0.44 1 1
PI3K 0.033 0.087 -10000 0 -0.33 9 9
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.019 0.1 -10000 0 -0.36 13 13
negative regulation of transcription -0.004 0.13 0.22 3 -0.37 37 40
FCGR2A 0.009 0.091 -10000 0 -0.44 22 22
FER 0.023 0.029 -10000 0 -0.45 2 2
alphaIIb/beta3 Integrin 0.018 0.089 -10000 0 -0.32 36 36
BLK -0.021 0.14 -10000 0 -0.44 56 56
Insulin Receptor/Insulin/Shc 0.043 0.024 -10000 0 -0.28 2 2
RHOA 0.024 0.02 -10000 0 -0.45 1 1
LEPR 0.019 0.055 -10000 0 -0.44 8 8
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
p210 bcr-abl/Grb2 0.025 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.049 0.2 0.23 17 -0.47 71 88
PRL 0.006 0.028 -10000 0 -10000 0 0
SOCS3 -0.003 0.17 -10000 0 -1.1 13 13
SPRY2 0.018 0.03 -10000 0 -0.45 2 2
Insulin Receptor/Insulin/IRS1 0.038 0.046 -10000 0 -0.28 11 11
CSF1/CSF1R 0.027 0.12 0.24 4 -0.32 28 32
Ras protein signal transduction -0.011 0.058 0.47 6 -10000 0 6
IRS1 0.019 0.058 -10000 0 -0.44 9 9
INS 0.004 0.027 -10000 0 -0.45 1 1
LEP 0.016 0.034 -10000 0 -0.44 1 1
STAT5B 0.015 0.097 0.19 16 -0.29 19 35
STAT5A 0.015 0.097 0.19 16 -0.29 19 35
GRB2 0.025 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.1 0.22 6 -0.33 23 29
CSN2 -0.017 0.058 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
LAT 0.008 0.13 -10000 0 -0.49 32 32
YBX1 0.033 0.025 -10000 0 -0.56 1 1
LCK 0.013 0.086 -10000 0 -0.44 19 19
SHC1 0.025 0.004 -10000 0 -10000 0 0
NOX4 -0.009 0.13 -10000 0 -0.45 44 44
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.031 0.035 -10000 0 -0.32 4 4
PDGFRB 0.019 0.063 -10000 0 -0.45 10 10
SPHK1 -0.023 0.15 -10000 0 -0.69 25 25
mol:S1P -0.024 0.13 -10000 0 -0.59 25 25
S1P1/S1P/Gi -0.01 0.14 -10000 0 -0.38 52 52
GNAO1 0.013 0.089 -10000 0 -0.45 19 19
PDGFB-D/PDGFRB/PLCgamma1 0.034 0.16 0.29 20 -0.41 30 50
PLCG1 -0.027 0.11 0.28 1 -0.41 32 33
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.063 -10000 0 -0.45 10 10
GNAI2 0.023 0.015 -10000 0 -10000 0 0
GNAI3 0.023 0.014 -10000 0 -10000 0 0
GNAI1 0.014 0.066 -10000 0 -0.45 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.011 0.024 -10000 0 -0.27 4 4
S1P1/S1P -0.003 0.11 0.21 2 -0.42 26 28
negative regulation of cAMP metabolic process -0.009 0.14 -10000 0 -0.37 52 52
MAPK3 -0.033 0.18 0.24 1 -0.53 57 58
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.014 -10000 0 -0.32 1 1
KDR 0.02 0.041 -10000 0 -0.45 4 4
PLCB2 0.004 0.11 0.27 10 -0.38 26 36
RAC1 0.023 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.093 -10000 0 -0.36 26 26
receptor internalization -0.003 0.1 -10000 0 -0.39 27 27
PTGS2 -0.06 0.3 0.48 3 -0.96 52 55
Rac1/GTP -0.004 0.09 -10000 0 -0.36 24 24
RHOA 0.025 0.02 -10000 0 -0.44 1 1
VEGFA 0.023 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.009 0.14 -10000 0 -0.37 52 52
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.013 0.074 -10000 0 -0.45 14 14
MAPK1 -0.029 0.18 -10000 0 -0.53 53 53
S1P1/S1P/PDGFB-D/PDGFRB 0.021 0.13 0.29 13 -0.45 18 31
ABCC1 0.024 0.022 -10000 0 -0.45 1 1
IL27-mediated 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
TGFB1 -0.015 0.14 -10000 0 -0.43 56 56
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.02 0.12 0.5 13 -10000 0 13
IL27/IL27R/JAK1 0.024 0.14 -10000 0 -0.56 12 12
TBX21 -0.051 0.16 -10000 0 -0.53 37 37
IL12B 0.011 0.026 -10000 0 -10000 0 0
IL12A -0.021 0.08 -10000 0 -0.32 39 39
IL6ST 0.011 0.072 -10000 0 -0.46 13 13
IL27RA/JAK1 0.01 0.09 -10000 0 -1.1 3 3
IL27 0.016 0.027 -10000 0 -10000 0 0
TYK2 0.021 0.026 -10000 0 -0.45 1 1
T-helper cell lineage commitment -0.1 0.39 0.94 2 -1.3 50 52
T-helper 2 cell differentiation 0.02 0.12 0.5 13 -10000 0 13
T cell proliferation during immune response 0.02 0.12 0.5 13 -10000 0 13
MAPKKK cascade -0.02 0.12 -10000 0 -0.5 13 13
STAT3 0.025 0.004 -10000 0 -10000 0 0
STAT2 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.024 0.029 -10000 0 -0.44 2 2
IL12RB1 0 0.11 -10000 0 -0.44 31 31
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.048 0.15 0.36 1 -0.49 40 41
IL27/IL27R/JAK2/TYK2 -0.02 0.12 -10000 0 -0.51 13 13
positive regulation of T cell mediated cytotoxicity -0.02 0.12 -10000 0 -0.5 13 13
STAT1 (dimer) 0.014 0.2 0.48 7 -0.63 26 33
JAK2 0.01 0.076 -10000 0 -0.45 15 15
JAK1 0.024 0.021 -10000 0 -0.45 1 1
STAT2 (dimer) -0.008 0.12 -10000 0 -0.49 13 13
T cell proliferation -0.059 0.14 -10000 0 -0.46 39 39
IL12/IL12R/TYK2/JAK2 -0.032 0.19 -10000 0 -0.86 19 19
IL17A -0.1 0.39 0.95 2 -1.3 50 52
mast cell activation 0.02 0.12 0.5 13 -10000 0 13
IFNG -0.005 0.039 -10000 0 -0.12 44 44
T cell differentiation -0.002 0.006 -10000 0 -0.022 40 40
STAT3 (dimer) -0.008 0.12 -10000 0 -0.48 13 13
STAT5A (dimer) -0.008 0.12 -10000 0 -0.48 13 13
STAT4 (dimer) -0.018 0.14 -10000 0 -0.46 32 32
STAT4 0.002 0.11 -10000 0 -0.44 31 31
T cell activation -0.005 0.008 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 0.016 0.11 -10000 0 -0.74 6 6
GATA3 -0.035 0.21 0.53 2 -1.3 16 18
IL18 -0.009 0.029 -10000 0 -0.32 5 5
positive regulation of mast cell cytokine production -0.008 0.12 -10000 0 -0.48 13 13
IL27/EBI3 0.013 0.087 -10000 0 -0.33 32 32
IL27RA -0.003 0.091 -10000 0 -1.2 3 3
IL6 -0.045 0.19 -10000 0 -0.47 91 91
STAT5A 0.025 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.01 0.038 0.47 3 -10000 0 3
IL1B -0.03 0.078 -10000 0 -0.32 39 39
EBI3 -0.004 0.11 -10000 0 -0.45 32 32
TNF -0.018 0.058 -10000 0 -0.32 21 21
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.019 -10000 0 -0.27 2 2
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.061 -10000 0 -0.44 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.021 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.01 0.026 -10000 0 -0.26 4 4
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.019 0.035 -10000 0 -0.44 3 3
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.024 0.028 -10000 0 -0.44 2 2
FYN 0.022 0.039 -10000 0 -0.44 4 4
MAP3K12 0.021 0.048 -10000 0 -0.44 6 6
FGR 0.007 0.094 -10000 0 -0.44 24 24
p38 alpha/TAB1 -0.063 0.13 -10000 0 -0.33 80 80
PRKG1 0.003 0.099 -10000 0 -0.44 27 27
DUSP8 0.022 0.039 -10000 0 -0.44 4 4
PGK/cGMP/p38 alpha -0.03 0.16 0.16 12 -0.36 76 88
apoptosis -0.061 0.12 -10000 0 -0.32 80 80
RAL/GTP 0.032 0.01 -10000 0 -10000 0 0
LYN 0.023 0.009 -10000 0 -10000 0 0
DUSP1 0.025 0.036 -10000 0 -0.44 3 3
PAK1 0.026 0.003 -10000 0 -10000 0 0
SRC 0.015 0.023 -10000 0 -0.44 1 1
RAC1/OSM/MEKK3/MKK3 0.049 0.037 -10000 0 -0.26 3 3
TRAF6 0.025 0.02 -10000 0 -0.44 1 1
RAC1 0.023 0.008 -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 0.023 0.021 -10000 0 -0.44 1 1
RAC1-CDC42/GTP 0.028 0.028 -10000 0 -0.27 4 4
MAPK11 -0.009 0.16 0.25 28 -0.38 53 81
BLK -0.021 0.14 -10000 0 -0.44 56 56
HCK 0.005 0.072 -10000 0 -0.44 14 14
MAP2K3 0.022 0.009 -10000 0 -10000 0 0
DUSP16 0.025 0.004 -10000 0 -10000 0 0
DUSP10 0.024 0.028 -10000 0 -0.44 2 2
TRAF6/MEKK3 0.031 0.021 -10000 0 -0.24 3 3
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.17 0.22 27 -0.38 72 99
positive regulation of innate immune response -0.022 0.19 0.26 31 -0.44 61 92
LCK 0.013 0.086 -10000 0 -0.44 19 19
p38alpha-beta/MKP7 -0.013 0.19 0.28 19 -0.43 57 76
p38alpha-beta/MKP5 -0.012 0.19 0.28 21 -0.43 58 79
PGK/cGMP 0.003 0.071 -10000 0 -0.32 27 27
PAK2 0.025 0.02 -10000 0 -0.44 1 1
p38alpha-beta/MKP1 -0.012 0.19 0.29 21 -0.44 57 78
CDC42 0.021 0.039 -10000 0 -0.44 4 4
RALB 0.026 0.001 -10000 0 -10000 0 0
RALA 0.024 0.008 -10000 0 -10000 0 0
PAK3 0.01 0.024 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.02 0.059 -9999 0 -0.44 9 9
GPC2 0.013 0.075 -9999 0 -0.44 15 15
GPC2/Midkine 0.023 0.073 -9999 0 -0.32 24 24
neuron projection morphogenesis 0.023 0.072 -9999 0 -0.32 24 24
S1P4 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
GNAO1 0.016 0.087 -10000 0 -0.44 19 19
CDC42/GTP 0 0.096 -10000 0 -0.28 38 38
PLCG1 -0.007 0.082 0.19 17 -0.29 26 43
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.024 -10000 0 -0.32 2 2
cell migration -0.001 0.094 -10000 0 -0.28 38 38
S1PR5 0.021 0.052 -10000 0 -0.44 7 7
S1PR4 0.009 0.093 -10000 0 -0.44 23 23
MAPK3 -0.017 0.092 0.19 1 -0.3 37 38
MAPK1 -0.012 0.086 -10000 0 -0.4 15 15
S1P/S1P5/Gi -0.002 0.087 -10000 0 -0.26 45 45
GNAI1 0.016 0.064 -10000 0 -0.44 11 11
CDC42/GDP 0.016 0.028 -10000 0 -0.32 4 4
S1P/S1P5/G12 0.028 0.035 -10000 0 -0.27 7 7
RHOA -0.003 0.075 0.19 57 -0.23 20 77
S1P/S1P4/Gi -0.008 0.096 -10000 0 -0.27 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
S1P/S1P4/G12/G13 0.034 0.056 -10000 0 -0.25 19 19
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.028 -10000 0 -0.44 2 2
CDC42 0.021 0.039 -10000 0 -0.44 4 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.024 0.075 -10000 0 -0.24 40 40
RGS9BP 0.009 0.073 -10000 0 -0.44 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.009 0.016 -10000 0 -10000 0 0
mol:Na + 0.014 0.072 -10000 0 -0.27 32 32
mol:ADP -0.012 0.026 0.22 6 -10000 0 6
GNAT2 0.014 0.063 -10000 0 -0.44 10 10
RGS9-1/Gbeta5/R9AP 0.027 0.084 -10000 0 -0.28 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.04 -10000 0 -0.27 10 10
GRK7 0.012 0.024 -10000 0 -10000 0 0
CNGB3 0.002 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.015 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.089 0.18 72 -0.25 32 104
Cone PDE6 0.039 0.081 -10000 0 -0.25 38 38
Cone Metarhodopsin II 0.021 0.014 -10000 0 -10000 0 0
Na + (4 Units) 0.025 0.072 0.21 1 -0.25 32 33
GNAT2/GDP 0.03 0.084 -10000 0 -0.24 47 47
GNB5 0.023 0.028 -10000 0 -0.44 2 2
mol:GMP (4 units) -0.02 0.037 0.18 6 -0.25 10 16
Cone Transducin 0.026 0.08 -10000 0 -0.26 40 40
SLC24A2 0.009 0.037 -10000 0 -0.44 2 2
GNB3/GNGT2 0.018 0.086 -10000 0 -0.33 33 33
GNB3 0.011 0.087 -10000 0 -0.44 20 20
GNAT2/GTP 0.013 0.044 -10000 0 -0.32 10 10
CNGA3 -0.006 0.11 -10000 0 -0.44 34 34
ARR3 -0.006 0.022 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.015 0.072 -10000 0 -0.27 32 32
mol:Pi 0.026 0.083 -10000 0 -0.28 38 38
Cone CNG Channel 0.026 0.079 -10000 0 -0.25 38 38
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.009 0.037 -10000 0 -0.44 2 2
RGS9 0.008 0.095 -10000 0 -0.44 24 24
PDE6C -0.006 0.021 -10000 0 -10000 0 0
GNGT2 0.014 0.075 -10000 0 -0.44 15 15
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.015 0.012 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.002 0.082 -9999 0 -0.35 29 29
CRKL 0.025 0.005 -9999 0 -10000 0 0
Rac1/GDP 0.017 0.006 -9999 0 -10000 0 0
DOCK1 0.024 0.02 -9999 0 -0.44 1 1
ITGA4 0.005 0.097 -9999 0 -0.44 26 26
alpha4/beta7 Integrin/MAdCAM1 0.013 0.14 -9999 0 -0.28 98 98
EPO 0.007 0.023 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.015 0.099 -9999 0 -0.36 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.022 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.023 0.074 -9999 0 -0.32 26 26
EPO/EPOR (dimer) 0.034 0.024 -9999 0 -0.32 2 2
lamellipodium assembly 0 0.089 -9999 0 -0.32 29 29
PIK3CA 0.024 0.028 -9999 0 -0.44 2 2
PI3K 0.034 0.031 -9999 0 -0.32 4 4
ARF6 0.024 0.02 -9999 0 -0.44 1 1
JAK2 0.001 0.084 -9999 0 -0.31 35 35
PXN 0.026 0.002 -9999 0 -10000 0 0
PIK3R1 0.023 0.028 -9999 0 -0.44 2 2
MADCAM1 -0.021 0.15 -9999 0 -0.44 66 66
cell adhesion 0.012 0.13 -9999 0 -0.27 98 98
CRKL/CBL 0.036 0.009 -9999 0 -10000 0 0
ITGB1 0.026 0.002 -9999 0 -10000 0 0
SRC -0.023 0.069 -9999 0 -0.35 22 22
ITGB7 0.014 0.078 -9999 0 -0.44 16 16
RAC1 0.023 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.029 0.1 -9999 0 -0.36 34 34
p130Cas/Crk/Dock1 0.041 0.097 -9999 0 -0.34 20 20
VCAM1 0.011 0.087 -9999 0 -0.44 20 20
RHOA 0.025 0.02 -9999 0 -0.44 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.066 -9999 0 -0.25 25 25
BCAR1 -0.024 0.067 -9999 0 -0.34 22 22
EPOR 0.024 0.035 -9999 0 -0.44 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.025 0.004 -9999 0 -10000 0 0
GIT1 0.024 0.02 -9999 0 -0.44 1 1
Rac1/GTP -0.001 0.092 -9999 0 -0.34 28 28
FOXM1 transcription factor network

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
NFATC3 0.009 0.29 -9999 0 -1 17 17
PLK1 0.029 0.11 -9999 0 -1.1 4 4
BIRC5 0.025 0.11 -9999 0 -0.82 8 8
HSPA1B 0.007 0.3 -9999 0 -1 19 19
MAP2K1 0.025 0.049 -9999 0 -0.49 2 2
BRCA2 0.034 0.35 -9999 0 -1.1 27 27
FOXM1 0.001 0.35 -9999 0 -1.4 17 17
XRCC1 0.01 0.3 -9999 0 -1.1 18 18
FOXM1B/p19 -0.012 0.34 -9999 0 -1.1 24 24
Cyclin D1/CDK4 0.021 0.28 -9999 0 -0.94 17 17
CDC2 0.009 0.31 -9999 0 -1.1 17 17
TGFA 0.009 0.28 -9999 0 -0.91 20 20
SKP2 0.011 0.3 -9999 0 -1.1 14 14
CCNE1 0.024 0.016 -9999 0 -10000 0 0
CKS1B 0.013 0.3 -9999 0 -1 17 17
RB1 0.01 0.21 -9999 0 -0.86 20 20
FOXM1C/SP1 0.012 0.33 -9999 0 -1.2 17 17
AURKB -0.1 0.33 -9999 0 -0.82 96 96
CENPF 0.001 0.33 -9999 0 -1.2 23 23
CDK4 0.021 0.025 -9999 0 -10000 0 0
MYC 0 0.26 -9999 0 -0.89 19 19
CHEK2 0.026 0.044 -9999 0 -0.49 1 1
ONECUT1 0.01 0.29 -9999 0 -1 17 17
CDKN2A -0.015 0.12 -9999 0 -0.45 38 38
LAMA4 0.008 0.3 -9999 0 -1.1 17 17
FOXM1B/HNF6 0.003 0.32 -9999 0 -1.2 17 17
FOS -0.022 0.36 -9999 0 -1.1 40 40
SP1 0.025 0.02 -9999 0 -0.44 1 1
CDC25B 0.033 0.3 -9999 0 -1 17 17
response to radiation 0.008 0.02 -9999 0 -10000 0 0
CENPB 0.032 0.31 -9999 0 -1 18 18
CENPA 0.006 0.3 -9999 0 -1.1 18 18
NEK2 0.012 0.3 -9999 0 -1.1 15 15
HIST1H2BA 0.006 0.29 -9999 0 -1 17 17
CCNA2 0.023 0.026 -9999 0 -0.46 1 1
EP300 0.023 0.028 -9999 0 -0.44 2 2
CCNB1/CDK1 0 0.33 -9999 0 -1.2 17 17
CCNB2 0.007 0.3 -9999 0 -1.1 17 17
CCNB1 0.008 0.31 -9999 0 -1.1 17 17
ETV5 -0.002 0.33 -9999 0 -1.2 23 23
ESR1 -0.019 0.36 -9999 0 -1.2 37 37
CCND1 0.01 0.28 -9999 0 -0.95 17 17
GSK3A 0.025 0.036 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.045 0.053 -9999 0 -0.54 1 1
CDK2 0.023 0.025 -9999 0 -0.46 1 1
G2/M transition of mitotic cell cycle 0.009 0.024 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 0.017 0.32 -9999 0 -1.1 17 17
GAS1 -0.08 0.47 -9999 0 -1.2 83 83
MMP2 -0.018 0.37 -9999 0 -1.2 34 34
RB1/FOXM1C -0.007 0.29 -9999 0 -0.97 22 22
CREBBP 0.025 0.004 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.027 -10000 0 -0.58 1 1
CRKL 0.015 0.1 0.26 10 -0.42 16 26
mol:PIP3 0 0.037 -10000 0 -0.82 1 1
AKT1 -0.007 0.038 -10000 0 -0.72 1 1
PTK2B 0.018 0.029 -10000 0 -0.44 2 2
RAPGEF1 0.017 0.1 0.26 11 -0.4 16 27
RANBP10 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
HGF/MET/SHIP2 0.032 0.076 -10000 0 -0.27 33 33
MAP3K5 0.004 0.13 0.34 4 -0.44 25 29
HGF/MET/CIN85/CBL/ENDOPHILINS 0.045 0.075 -10000 0 -0.25 33 33
AP1 0.017 0.064 0.16 3 -0.27 21 24
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.004 -10000 0 -10000 0 0
apoptosis -0.055 0.26 -10000 0 -0.75 67 67
STAT3 (dimer) -0.005 0.068 -10000 0 -0.27 26 26
GAB1/CRKL/SHP2/PI3K 0.047 0.11 0.3 3 -0.44 15 18
INPP5D 0.005 0.097 -10000 0 -0.44 26 26
CBL/CRK 0.033 0.1 0.28 5 -0.41 15 20
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.014 0.023 -10000 0 -0.44 1 1
PTEN 0.025 0.006 -10000 0 -10000 0 0
ELK1 0.006 0.098 0.32 39 -0.43 1 40
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.054 -10000 0 -0.21 20 20
PAK1 -0.009 0.038 0.28 1 -0.69 1 2
HGF/MET/RANBP10 0.033 0.075 -10000 0 -0.27 32 32
HRAS 0.004 0.085 -10000 0 -0.44 8 8
DOCK1 0.016 0.097 0.25 9 -0.42 15 24
GAB1 0.008 0.094 -10000 0 -0.43 16 16
CRK 0.013 0.097 0.26 8 -0.42 15 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.12 -10000 0 -0.46 35 35
JUN 0.022 0.039 -10000 0 -0.44 4 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.02 0.051 -10000 0 -0.19 35 35
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
cell morphogenesis 0.027 0.12 0.33 13 -0.41 12 25
GRB2/SHC -0.002 0.063 -10000 0 -0.18 33 33
FOS 0.013 0.08 -10000 0 -0.44 17 17
GLMN -0.006 0.047 0.11 1 -0.27 18 19
cell motility 0.006 0.098 0.32 39 -0.43 1 40
HGF/MET/MUC20 0.018 0.07 -10000 0 -0.27 32 32
cell migration -0.002 0.062 -10000 0 -0.18 33 33
GRB2 0.025 0.004 -10000 0 -10000 0 0
CBL 0.025 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.036 0.017 -10000 0 -0.32 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.001 0.066 -10000 0 -0.25 32 32
MET/MUC20 0.018 0.015 -10000 0 -0.32 1 1
RAP1B 0.014 0.097 0.31 7 -0.39 15 22
RAP1A 0.013 0.095 0.29 6 -0.39 15 21
HGF/MET/RANBP9 0.032 0.078 -10000 0 -0.28 32 32
RAF1 0.006 0.086 -10000 0 -0.42 8 8
STAT3 -0.005 0.068 -10000 0 -0.27 26 26
cell proliferation 0.005 0.095 0.3 3 -0.34 29 32
RPS6KB1 -0.007 0.055 -10000 0 -0.27 18 18
MAPK3 -0.009 0.087 0.55 8 -10000 0 8
MAPK1 0.017 0.16 0.64 30 -10000 0 30
RANBP9 0.025 0.02 -10000 0 -0.44 1 1
MAPK8 0.011 0.12 0.34 4 -0.44 18 22
SRC -0.008 0.061 0.19 6 -0.25 26 32
PI3K -0.003 0.068 -10000 0 -0.2 33 33
MET/Glomulin -0.019 0.057 -10000 0 -0.2 27 27
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 0.004 0.084 0.3 1 -0.43 7 8
MET 0.024 0.02 -10000 0 -0.44 1 1
MAP4K1 0.007 0.13 0.27 4 -0.47 26 30
PTK2 0.021 0.022 -10000 0 -0.44 1 1
MAP2K2 0.005 0.084 0.3 1 -0.41 8 9
BAD -0.01 0.039 -10000 0 -0.55 2 2
MAP2K4 0 0.12 0.33 4 -0.41 24 28
SHP2/GRB2/SOS1/GAB1 0.035 0.094 -10000 0 -0.39 16 16
INPPL1 0.025 0.02 -10000 0 -0.44 1 1
PXN 0.026 0.002 -10000 0 -10000 0 0
SH3KBP1 0.025 0.02 -10000 0 -0.44 1 1
HGS -0.023 0.047 -10000 0 -0.18 33 33
PLCgamma1/PKC 0.011 0.017 -10000 0 -0.32 1 1
HGF 0.001 0.11 -10000 0 -0.44 32 32
RASA1 0.024 0.028 -10000 0 -0.44 2 2
NCK1 0.024 0.028 -10000 0 -0.44 2 2
PTPRJ 0.025 0.02 -10000 0 -0.44 1 1
NCK/PLCgamma1 0.015 0.049 -10000 0 -0.19 26 26
PDPK1 -0.004 0.04 -10000 0 -0.76 1 1
HGF/MET/SHIP 0.019 0.099 -10000 0 -0.28 56 56
EPO signaling pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.059 -10000 0 -0.39 1 1
CRKL -0.004 0.061 0.25 4 -0.28 3 7
mol:DAG 0.013 0.036 -10000 0 -0.28 2 2
HRAS -0.011 0.066 0.28 6 -0.27 2 8
MAPK8 0.01 0.069 0.18 80 -0.25 2 82
RAP1A -0.005 0.062 0.18 11 -0.24 17 28
GAB1 -0.004 0.06 0.18 11 -0.23 17 28
MAPK14 0.01 0.068 0.18 79 -0.24 1 80
EPO 0.018 0.021 -10000 0 -10000 0 0
PLCG1 0.013 0.036 -10000 0 -0.29 2 2
EPOR/TRPC2/IP3 Receptors 0.024 0.035 -10000 0 -0.4 3 3
RAPGEF1 0.025 0.02 -10000 0 -0.44 1 1
EPO/EPOR (dimer)/SOCS3 0.044 0.045 -10000 0 -0.28 7 7
GAB1/SHC/GRB2/SOS1 0.04 0.06 0.26 2 -0.26 4 6
EPO/EPOR (dimer) 0.034 0.032 0.19 1 -0.33 2 3
IRS2 -0.009 0.05 0.19 4 -0.23 13 17
STAT1 0.023 0.055 0.24 1 -0.38 3 4
STAT5B 0.021 0.048 -10000 0 -0.31 2 2
cell proliferation 0.01 0.074 0.18 84 -0.23 2 86
GAB1/SHIP/PIK3R1/SHP2/SHC 0.019 0.082 -10000 0 -0.39 7 7
TEC -0.005 0.06 0.18 11 -0.23 17 28
SOCS3 0.023 0.045 -10000 0 -0.44 5 5
STAT1 (dimer) 0.023 0.054 0.23 1 -0.38 3 4
JAK2 0.014 0.076 -10000 0 -0.45 15 15
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
EPO/EPOR (dimer)/JAK2 0.058 0.062 -10000 0 -0.24 17 17
EPO/EPOR 0.034 0.032 0.19 1 -0.33 2 3
LYN 0.023 0.011 -10000 0 -10000 0 0
TEC/VAV2 0.013 0.076 0.27 1 -0.23 41 42
elevation of cytosolic calcium ion concentration 0.024 0.035 -10000 0 -0.4 3 3
SHC1 0.025 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.044 0.033 -10000 0 -0.27 1 1
mol:IP3 0.013 0.036 -10000 0 -0.28 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.014 0.072 0.28 1 -0.26 10 11
SH2B3 0.026 0.014 -10000 0 -10000 0 0
NFKB1 0.009 0.068 0.18 77 -0.25 2 79
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.052 -10000 0 -0.24 22 22
PTPN6 0.003 0.06 0.3 2 -0.23 17 19
TEC/VAV2/GRB2 0.025 0.08 0.26 2 -0.22 39 41
EPOR 0.024 0.036 -10000 0 -0.4 3 3
INPP5D 0.005 0.097 -10000 0 -0.44 26 26
mol:GDP 0.04 0.06 0.26 2 -0.26 4 6
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG2 0.013 0.08 -10000 0 -0.44 17 17
CRKL/CBL/C3G 0.036 0.061 0.26 3 -0.27 3 6
VAV2 -0.014 0.076 0.2 11 -0.23 41 52
CBL -0.005 0.061 0.2 11 -0.23 16 27
SHC/Grb2/SOS1 0.032 0.051 -10000 0 -0.22 16 16
STAT5A 0.021 0.048 -10000 0 -0.31 2 2
GRB2 0.025 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.035 0.065 0.25 1 -0.35 4 5
LYN/PLCgamma2 0.026 0.056 -10000 0 -0.32 14 14
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
BTK -0.017 0.081 0.2 11 -0.25 33 44
BCL2 0.009 0.14 -10000 0 -0.73 16 16
PDGFR-alpha 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
PDGFRA 0.013 0.086 -10000 0 -0.44 19 19
PDGF/PDGFRA/CRKL 0.027 0.064 -10000 0 -0.31 19 19
positive regulation of JUN kinase activity 0.053 0.055 -10000 0 -0.24 18 18
CRKL 0.025 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.022 0.064 -10000 0 -0.31 19 19
AP1 -0.009 0.16 0.29 5 -0.66 24 29
mol:IP3 -0.016 0.054 -10000 0 -0.33 16 16
PLCG1 -0.016 0.054 -10000 0 -0.33 16 16
PDGF/PDGFRA/alphaV Integrin 0.021 0.081 -10000 0 -0.32 29 29
RAPGEF1 0.025 0.02 -10000 0 -0.44 1 1
CRK 0.022 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.054 -10000 0 -0.33 16 16
CAV3 -0.01 0.019 -10000 0 -10000 0 0
CAV1 0.022 0.045 -10000 0 -0.44 5 5
SHC/Grb2/SOS1 0.056 0.056 -10000 0 -0.24 18 18
PDGF/PDGFRA/Shf 0.024 0.08 -10000 0 -0.32 28 28
FOS -0.033 0.15 0.3 13 -0.66 24 37
JUN -0.012 0.037 -10000 0 -0.35 4 4
oligodendrocyte development 0.021 0.081 -10000 0 -0.32 29 29
GRB2 0.025 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:DAG -0.016 0.054 -10000 0 -0.33 16 16
PDGF/PDGFRA 0.013 0.086 -10000 0 -0.44 19 19
actin cytoskeleton reorganization 0.028 0.062 -10000 0 -0.31 18 18
SRF -0.008 0.015 0.23 1 -10000 0 1
SHC1 0.025 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.062 -10000 0 -0.26 22 22
PDGF/PDGFRA/Crk/C3G 0.036 0.058 -10000 0 -0.26 19 19
JAK1 -0.009 0.057 -10000 0 -0.31 18 18
ELK1/SRF 0.017 0.085 0.15 133 -0.26 15 148
SHB 0.026 0.005 -10000 0 -10000 0 0
SHF 0.023 0.062 -10000 0 -0.44 9 9
CSNK2A1 0.013 0.023 -10000 0 -10000 0 0
GO:0007205 -0.014 0.057 -10000 0 -0.35 16 16
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.053 0.055 -10000 0 -0.24 18 18
PDGF/PDGFRA/SHB 0.028 0.063 -10000 0 -0.31 18 18
PDGF/PDGFRA/Caveolin-1 0.027 0.071 -10000 0 -0.34 19 19
ITGAV 0.017 0.064 -10000 0 -0.44 11 11
ELK1 -0.015 0.052 0.24 1 -0.31 16 17
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
PDGF/PDGFRA/Crk 0.023 0.063 -10000 0 -0.3 19 19
JAK-STAT cascade -0.009 0.057 -10000 0 -0.31 18 18
cell proliferation 0.024 0.08 -10000 0 -0.32 28 28
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.009 0.061 -10000 0 -0.37 9 9
SVIL 0.016 0.036 -10000 0 -0.44 1 1
ZNF318 0.039 0.046 0.18 53 -10000 0 53
JMJD2C 0.005 0.009 0.036 22 -10000 0 22
T-DHT/AR/Ubc9 0.027 0.068 -10000 0 -0.26 23 23
CARM1 0.02 0.025 -10000 0 -0.44 1 1
PRDX1 0.026 0.02 -10000 0 -0.44 1 1
PELP1 0.023 0.023 -10000 0 -0.44 1 1
CTNNB1 0.018 0.027 -10000 0 -10000 0 0
AKT1 0.028 0.025 -10000 0 -0.44 1 1
PTK2B 0.013 0.035 -10000 0 -0.44 2 2
MED1 0.028 0.032 -10000 0 -0.44 2 2
MAK 0.03 0.075 0.19 51 -0.43 8 59
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.012 0.056 -10000 0 -0.46 6 6
GSN 0.012 0.056 -10000 0 -0.3 9 9
NCOA2 0.014 0.049 -10000 0 -0.45 6 6
NCOA6 0.011 0.03 -10000 0 -0.44 1 1
DNA-PK 0.052 0.049 0.2 35 -0.51 1 36
NCOA4 0.02 0.03 -10000 0 -0.44 2 2
PIAS3 0.016 0.034 -10000 0 -0.44 1 1
cell proliferation 0.013 0.097 0.22 1 -0.53 14 15
XRCC5 0.028 0.022 -10000 0 -0.44 1 1
UBE3A 0.012 0.05 -10000 0 -0.25 8 8
T-DHT/AR/SNURF -0.004 0.11 -10000 0 -0.28 75 75
FHL2 0.028 0.064 -10000 0 -1 1 1
RANBP9 0.015 0.039 -10000 0 -0.1 37 37
JMJD1A -0.001 0.03 -10000 0 -0.12 33 33
CDK6 0.025 0.007 -10000 0 -10000 0 0
TGFB1I1 0.015 0.045 -10000 0 -0.44 3 3
T-DHT/AR/CyclinD1 0.019 0.072 -10000 0 -0.26 25 25
XRCC6 0.028 0.012 -10000 0 -10000 0 0
T-DHT/AR 0.033 0.082 -10000 0 -0.22 51 51
CTDSP1 0.019 0.027 -10000 0 -0.44 1 1
CTDSP2 0.035 0.03 -10000 0 -10000 0 0
BRCA1 0.016 0.035 -10000 0 -0.44 1 1
TCF4 0.021 0.045 -10000 0 -0.43 4 4
CDKN2A 0.006 0.12 0.17 4 -0.44 38 42
SRF 0.034 0.018 -10000 0 -0.13 1 1
NKX3-1 -0.038 0.19 -10000 0 -0.75 37 37
KLK3 -0.11 0.4 -10000 0 -1.3 54 54
TMF1 0.016 0.049 -10000 0 -0.44 6 6
HNRNPA1 0.031 0.018 -10000 0 -10000 0 0
AOF2 -0.007 0.023 -10000 0 -0.079 54 54
APPL1 -0.006 0.056 0.12 41 -0.32 11 52
T-DHT/AR/Caspase 8 0.031 0.072 -10000 0 -0.27 22 22
AR 0.009 0.095 -10000 0 -0.43 22 22
UBA3 0.019 0.027 -10000 0 -0.44 1 1
PATZ1 0.03 0.019 -10000 0 -10000 0 0
PAWR 0.02 0.025 -10000 0 -0.44 1 1
PRKDC 0.024 0.023 -10000 0 -0.44 1 1
PA2G4 0.031 0.02 -10000 0 -10000 0 0
UBE2I 0.025 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.029 0.064 -10000 0 -0.23 23 23
RPS6KA3 0.012 0.052 -10000 0 -0.44 4 4
T-DHT/AR/ARA70 0.021 0.071 -10000 0 -0.27 25 25
LATS2 0.023 0.027 -10000 0 -0.44 1 1
T-DHT/AR/PRX1 0.032 0.069 0.16 13 -0.24 23 36
Cyclin D3/CDK11 p58 0.02 0.005 -10000 0 -10000 0 0
VAV3 -0.04 0.16 -10000 0 -0.44 73 73
KLK2 0.006 0.035 -10000 0 -0.31 1 1
CASP8 0.027 0.021 -10000 0 -0.44 1 1
T-DHT/AR/TIF2/CARM1 0.026 0.076 -10000 0 -0.26 24 24
TMPRSS2 -0.003 0.087 -10000 0 -0.6 7 7
CCND1 0.019 0.021 -10000 0 -10000 0 0
PIAS1 0.014 0.039 -10000 0 -0.11 49 49
mol:T-DHT -0.001 0.016 -10000 0 -0.063 33 33
CDC2L1 0 0.002 -10000 0 -10000 0 0
PIAS4 0.008 0.059 -10000 0 -0.18 51 51
T-DHT/AR/CDK6 0.028 0.068 -10000 0 -0.26 21 21
CMTM2 0.009 0.095 -10000 0 -0.44 24 24
SNURF -0.028 0.14 -10000 0 -0.44 55 55
ZMIZ1 0.023 0.023 -10000 0 -10000 0 0
CCND3 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.024 0.019 -10000 0 -10000 0 0
FKBP4 0.015 0.034 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.018 0.062 -10000 0 -0.44 10 10
alphaV beta3 Integrin 0.024 0.073 -10000 0 -0.33 23 23
PTK2 -0.003 0.097 -10000 0 -0.42 21 21
positive regulation of JNK cascade 0.014 0.083 -10000 0 -0.3 26 26
CDC42/GDP 0.034 0.12 0.3 1 -0.4 30 31
Rac1/GDP 0.028 0.12 0.26 1 -0.4 28 29
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.029 0.1 -10000 0 -0.36 26 26
nectin-3/I-afadin 0.022 0.073 -10000 0 -0.32 25 25
RAPGEF1 0.008 0.11 0.28 1 -0.42 28 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.009 0.11 -10000 0 -0.45 30 30
PDGFB-D/PDGFRB 0.018 0.062 -10000 0 -0.44 10 10
TLN1 -0.012 0.045 -10000 0 -0.38 5 5
Rap1/GTP 0.012 0.082 -10000 0 -0.31 28 28
IQGAP1 0.023 0.028 -10000 0 -0.44 2 2
Rap1/GTP/I-afadin 0.046 0.021 -10000 0 -0.25 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.073 -10000 0 -0.32 25 25
PVR 0.026 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.003 -10000 0 -10000 0 0
mol:GDP 0.024 0.14 0.31 1 -0.48 29 30
MLLT4 0.025 0.02 -10000 0 -0.44 1 1
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
PI3K 0.052 0.081 -10000 0 -0.25 37 37
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.027 -10000 0 -0.32 3 3
positive regulation of lamellipodium assembly 0.009 0.1 -10000 0 -0.31 35 35
PVRL1 0.024 0.028 -10000 0 -0.44 2 2
PVRL3 0.006 0.094 -10000 0 -0.44 24 24
PVRL2 0.025 0.02 -10000 0 -0.44 1 1
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
CDH1 0.025 0.02 -10000 0 -0.44 1 1
CLDN1 0.009 0.088 -10000 0 -0.44 21 21
JAM-A/CLDN1 0.04 0.084 -10000 0 -0.25 44 44
SRC -0.009 0.12 -10000 0 -0.48 33 33
ITGB3 0.016 0.07 -10000 0 -0.44 13 13
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.027 -10000 0 -0.32 3 3
FARP2 0.03 0.13 -10000 0 -0.49 22 22
RAC1 0.023 0.008 -10000 0 -10000 0 0
CTNNA1 0.024 0.028 -10000 0 -0.44 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.065 -10000 0 -0.27 24 24
nectin-1/I-afadin 0.035 0.027 -10000 0 -0.32 3 3
nectin-2/I-afadin 0.036 0.022 -10000 0 -0.32 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.029 0.021 -10000 0 -0.27 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.035 0.069 -10000 0 -0.27 27 27
CDC42/GTP/IQGAP1/filamentous actin 0.029 0.037 -10000 0 -0.39 4 4
F11R 0.025 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.014 0.083 -10000 0 -0.3 26 26
alphaV/beta3 Integrin/Talin -0.01 0.092 0.19 4 -0.29 26 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.022 -10000 0 -0.32 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.022 -10000 0 -0.32 2 2
PIP5K1C -0.005 0.046 -10000 0 -0.2 24 24
VAV2 0.012 0.17 -10000 0 -0.49 46 46
RAP1/GDP 0.038 0.11 0.27 2 -0.37 27 29
ITGAV 0.017 0.064 -10000 0 -0.44 11 11
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.067 -10000 0 -0.27 25 25
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.073 -10000 0 -0.32 25 25
Rac1/GTP 0.013 0.12 -10000 0 -0.38 35 35
PTPRM 0 0.05 -10000 0 -0.22 24 24
E-cadherin/beta catenin/alpha catenin 0.068 0.041 -10000 0 -0.27 6 6
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.039 -10000 0 -0.44 4 4
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.011 0.022 -10000 0 -0.27 4 4
ADCY5 -0.044 0.083 -10000 0 -0.27 68 68
ADCY6 -0.009 0.001 -10000 0 -10000 0 0
ADCY7 -0.01 0.011 -10000 0 -0.27 1 1
ADCY1 -0.015 0.042 0.22 5 -0.27 10 15
ADCY2 -0.028 0.067 -10000 0 -0.27 41 41
ADCY3 -0.01 0.011 -10000 0 -0.27 1 1
ADCY8 -0.011 0.012 0.22 1 -10000 0 1
PRKCE -0.006 0 -10000 0 -10000 0 0
ADCY9 -0.01 0.015 -10000 0 -0.27 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.004 0.073 0.19 24 -0.2 16 40
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.007 0.028 0.15 14 -0.11 2 16
BUB1B 0.014 0.043 0.11 4 -0.18 8 12
PLK1 0.022 0.028 0.069 71 -0.1 3 74
PLK1S1 0.02 0.051 0.13 7 -0.18 21 28
KIF2A 0.015 0.027 0.18 2 -10000 0 2
regulation of mitotic centrosome separation 0.022 0.028 0.069 71 -0.1 3 74
GOLGA2 0.024 0.028 -10000 0 -0.44 2 2
Hec1/SPC24 0.031 0.054 -10000 0 -0.21 21 21
WEE1 0.025 0.052 -10000 0 -0.39 6 6
cytokinesis 0.016 0.055 -10000 0 -0.34 6 6
PP2A-alpha B56 0.048 0.092 -10000 0 -0.53 13 13
AURKA 0.022 0.022 0.1 1 -10000 0 1
PICH/PLK1 0.011 0.044 0.15 4 -0.23 13 17
CENPE 0.008 0.048 0.11 1 -0.22 18 19
RhoA/GTP 0.018 0.014 -10000 0 -0.32 1 1
positive regulation of microtubule depolymerization 0.016 0.027 0.18 2 -10000 0 2
PPP2CA 0.025 0.004 -10000 0 -10000 0 0
FZR1 0.025 0.02 -10000 0 -0.44 1 1
TPX2 0.036 0.041 0.095 71 -0.25 2 73
PAK1 0.027 0.004 -10000 0 -10000 0 0
SPC24 0.016 0.067 -10000 0 -0.44 12 12
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN 0.014 0.042 -10000 0 -0.22 15 15
GORASP1 0.026 0.002 -10000 0 -10000 0 0
metaphase 0.001 0.002 0.018 7 -0.012 2 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.016 0.038 71 -0.055 3 74
G2 phase of mitotic cell cycle 0.001 0.003 0.015 9 -10000 0 9
STAG2 0.023 0.039 -10000 0 -0.44 4 4
GRASP65/GM130/RAB1/GTP 0.012 0.041 -10000 0 -0.44 4 4
spindle elongation 0.022 0.028 0.069 71 -0.1 3 74
ODF2 0.028 0.004 -10000 0 -10000 0 0
BUB1 0.015 0.09 -10000 0 -0.57 13 13
TPT1 0.025 0.037 0.12 5 -0.17 8 13
CDC25C 0.016 0.042 -10000 0 -0.25 12 12
CDC25B 0.021 0.013 -10000 0 -10000 0 0
SGOL1 0.007 0.028 0.11 2 -0.15 14 16
RHOA 0.025 0.02 -10000 0 -0.44 1 1
CCNB1/CDK1 0.032 0.033 -10000 0 -0.21 3 3
CDC14B -0.002 0.024 -10000 0 -0.32 3 3
CDC20 0.026 0.003 -10000 0 -10000 0 0
PLK1/PBIP1 0.011 0.036 0.089 3 -0.2 11 14
mitosis -0.001 0.002 -10000 0 -10000 0 0
FBXO5 0.013 0.037 0.15 5 -0.24 4 9
CDC2 0.002 0.002 0.009 1 -0.01 1 2
NDC80 0.014 0.058 -10000 0 -0.44 9 9
metaphase plate congression 0.006 0.064 -10000 0 -0.22 40 40
ERCC6L 0.011 0.047 0.16 1 -0.24 13 14
NLP/gamma Tubulin 0.011 0.017 0.074 8 -0.091 1 9
microtubule cytoskeleton organization 0.025 0.037 0.12 5 -0.17 8 13
G2/M transition DNA damage checkpoint 0 0.002 0.013 10 -10000 0 10
PPP1R12A 0.024 0.034 -10000 0 -0.45 3 3
interphase 0 0.002 0.013 10 -10000 0 10
PLK1/PRC1-2 0.045 0.032 -10000 0 -0.21 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.055 0.029 -10000 0 -0.2 2 2
RAB1A 0.025 0.019 -10000 0 -0.44 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.025 0.031 0.073 77 -10000 0 77
mitotic prometaphase 0.001 0.005 0.018 40 -10000 0 40
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.033 0.17 2 -0.21 3 5
microtubule-based process 0.033 0.03 0.12 1 -0.21 2 3
Golgi organization 0.022 0.028 0.069 71 -0.1 3 74
Cohesin/SA2 0.031 0.029 0.1 2 -0.2 4 6
PPP1CB/MYPT1 0.036 0.039 -10000 0 -0.37 5 5
KIF20A 0.024 0.028 -10000 0 -0.44 2 2
APC/C/CDC20 0.035 0.026 0.12 1 -10000 0 1
PPP2R1A 0.025 0.02 -10000 0 -0.44 1 1
chromosome segregation 0.011 0.036 0.088 3 -0.2 11 14
PRC1 0.025 0.005 -10000 0 -10000 0 0
ECT2 0.011 0.046 0.21 4 -0.22 13 17
C13orf34 0.021 0.026 0.063 71 -0.074 3 74
NUDC 0.006 0.065 -10000 0 -0.22 40 40
regulation of attachment of spindle microtubules to kinetochore 0.014 0.043 0.11 4 -0.18 8 12
spindle assembly 0.016 0.024 0.092 13 -0.089 3 16
spindle stabilization 0.02 0.05 0.13 7 -0.18 21 28
APC/C/HCDH1 0.021 0.025 -10000 0 -0.27 4 4
MKLP2/PLK1 0.033 0.03 0.12 1 -0.21 2 3
CCNB1 0.025 0.011 -10000 0 -10000 0 0
PPP1CB 0.024 0.034 -10000 0 -0.45 3 3
BTRC 0.024 0.02 -10000 0 -0.44 1 1
ROCK2 0.016 0.066 -10000 0 -0.4 12 12
TUBG1 0.017 0.021 0.11 2 -0.16 3 5
G2/M transition of mitotic cell cycle 0.007 0.028 0.17 1 -0.21 3 4
MLF1IP -0.007 0.044 -10000 0 -0.32 11 11
INCENP 0.026 0.004 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.019 0.18 0.81 3 -1.2 11 14
VDR 0.025 0.02 -10000 0 -0.44 1 1
FAM120B 0.025 0.02 -10000 0 -0.44 1 1
RXRs/LXRs/DNA/9cRA 0.02 0.072 -10000 0 -0.29 25 25
RXRs/LXRs/DNA/Oxysterols 0.017 0.1 -10000 0 -0.41 29 29
MED1 0.023 0.028 -10000 0 -0.44 2 2
mol:9cRA 0.001 0.012 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.012 0.097 -10000 0 -0.24 82 82
RXRs/NUR77 0.065 0.052 -10000 0 -0.37 2 2
RXRs/PPAR 0.018 0.047 -10000 0 -0.26 9 9
NCOR2 0.024 0.034 -10000 0 -0.44 3 3
VDR/VDR/Vit D3 0.019 0.014 -10000 0 -0.32 1 1
RARs/VDR/DNA/Vit D3 0.05 0.054 -10000 0 -0.25 16 16
RARA 0.024 0.02 -10000 0 -0.44 1 1
NCOA1 0.025 0.019 -10000 0 -0.44 1 1
VDR/VDR/DNA 0.025 0.02 -10000 0 -0.44 1 1
RARs/RARs/DNA/9cRA 0.035 0.051 -10000 0 -0.25 15 15
RARG 0.021 0.048 -10000 0 -0.44 6 6
RPS6KB1 -0.005 0.098 0.54 9 -0.42 16 25
RARs/THRs/DNA/SMRT -0.013 0.099 -10000 0 -0.24 82 82
THRA 0.024 0.02 -10000 0 -0.44 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.014 -10000 0 -0.32 1 1
RXRs/PPAR/9cRA/PGJ2/DNA 0.051 0.056 0.29 8 -0.24 4 12
NR1H4 -0.015 0.14 -10000 0 -0.44 55 55
RXRs/LXRs/DNA 0.073 0.073 -10000 0 -0.35 4 4
NR1H2 0.024 0.027 -10000 0 -0.47 1 1
NR1H3 0.025 0.02 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.058 0.044 -10000 0 -0.24 3 3
NR4A1 0.029 0.026 -10000 0 -0.44 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.003 0.079 -10000 0 -0.22 55 55
RXRG 0.024 0.031 -10000 0 -0.44 1 1
RXR alpha/CCPG 0.036 0.023 -10000 0 -0.33 1 1
RXRA 0.024 0.027 -10000 0 -0.45 1 1
RXRB 0.025 0.02 -10000 0 -10000 0 0
THRB -0.028 0.15 -10000 0 -0.44 69 69
PPARG 0.02 0.051 -10000 0 -0.44 7 7
PPARD 0.025 0.02 -10000 0 -0.44 1 1
TNF -0.012 0.2 -10000 0 -1 22 22
mol:Oxysterols 0.001 0.01 -10000 0 -10000 0 0
cholesterol transport 0.017 0.1 -10000 0 -0.41 29 29
PPARA 0.024 0.02 -10000 0 -0.44 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.018 0.062 -10000 0 -0.44 10 10
RXRs/NUR77/BCL2 0.006 0.046 -10000 0 -0.24 11 11
SREBF1 0.006 0.1 -10000 0 -0.89 3 3
RXRs/RXRs/DNA/9cRA 0.051 0.056 0.28 8 -0.24 4 12
ABCA1 0.002 0.15 -10000 0 -1 10 10
RARs/THRs 0.03 0.12 -10000 0 -0.25 79 79
RXRs/FXR 0.04 0.1 -10000 0 -0.25 54 54
BCL2 0.014 0.052 -10000 0 -0.44 7 7
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.025 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.009 0.088 -9999 0 -0.36 17 17
Syndecan-3/Neurocan 0.006 0.088 -9999 0 -0.38 27 27
POMC 0.01 0.089 -9999 0 -0.44 21 21
EGFR 0.02 0.044 -9999 0 -0.44 5 5
Syndecan-3/EGFR 0.004 0.089 -9999 0 -0.38 25 25
AGRP -0.001 0.024 -9999 0 -10000 0 0
NCSTN 0.025 0.004 -9999 0 -10000 0 0
PSENEN 0.024 0.02 -9999 0 -0.44 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.022 0.039 -9999 0 -0.44 4 4
APH1A 0.025 0.004 -9999 0 -10000 0 0
NCAN 0.004 0.026 -9999 0 -10000 0 0
long-term memory 0.021 0.09 -9999 0 -0.36 28 28
Syndecan-3/IL8 -0.011 0.12 -9999 0 -0.4 31 31
PSEN1 0.024 0.006 -9999 0 -10000 0 0
Src/Cortactin 0.022 0.024 -9999 0 -0.32 1 1
FYN 0.022 0.039 -9999 0 -0.44 4 4
limb bud formation -0.007 0.084 -9999 0 -0.39 26 26
MC4R -0.004 0.021 -9999 0 -10000 0 0
SRC 0.015 0.023 -9999 0 -0.44 1 1
PTN 0.007 0.094 -9999 0 -0.44 24 24
FGFR/FGF/Syndecan-3 -0.007 0.085 -9999 0 -0.4 26 26
neuron projection morphogenesis 0.043 0.11 -9999 0 -0.36 16 16
Syndecan-3/AgRP 0.005 0.087 -9999 0 -0.38 28 28
Syndecan-3/AgRP/MC4R 0.011 0.085 -9999 0 -0.36 26 26
Fyn/Cortactin 0.034 0.031 -9999 0 -0.32 4 4
SDC3 -0.007 0.085 -9999 0 -0.4 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.12 -9999 0 -0.39 31 31
IL8 -0.017 0.15 -9999 0 -0.44 63 63
Syndecan-3/Fyn/Cortactin 0.022 0.092 -9999 0 -0.37 28 28
Syndecan-3/CASK -0.009 0.082 -9999 0 -0.37 28 28
alpha-MSH/MC4R 0.015 0.066 -9999 0 -0.31 21 21
Gamma Secretase 0.064 0.039 -9999 0 -0.24 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.021 -10000 0 -0.44 1 1
Caspase 8 (4 units) 0.017 0.085 -10000 0 -0.38 11 11
NEF -0.009 0.039 -10000 0 -0.17 30 30
NFKBIA 0.021 0.022 -10000 0 -10000 0 0
BIRC3 -0.001 0.083 -10000 0 -0.48 16 16
CYCS -0.007 0.098 0.18 43 -0.29 40 83
RIPK1 0.026 0.004 -10000 0 -10000 0 0
CD247 -0.004 0.11 -10000 0 -0.32 47 47
MAP2K7 0.003 0.12 0.27 1 -0.6 14 15
protein ubiquitination 0.009 0.065 0.41 3 -0.31 5 8
CRADD 0.026 0.003 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.019 0.052 -10000 0 -0.44 7 7
BID -0.01 0.084 0.17 8 -0.28 43 51
NF-kappa-B/RelA/I kappa B alpha 0.044 0.055 -10000 0 -0.26 16 16
TRADD 0.026 0.003 -10000 0 -10000 0 0
MAP3K5 0.024 0.028 -10000 0 -0.44 2 2
CFLAR 0.026 0 -10000 0 -10000 0 0
FADD 0.026 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.055 -10000 0 -0.26 16 16
MAPK8 0.002 0.11 0.34 2 -0.56 14 16
APAF1 0.023 0.034 -10000 0 -0.44 3 3
TRAF1 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.02 -10000 0 -0.44 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.004 0.09 0.19 7 -0.29 45 52
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.063 -10000 0 -0.33 6 6
CHUK 0.007 0.061 0.21 1 -0.33 5 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.066 0.047 -10000 0 -0.26 9 9
TCRz/NEF -0.01 0.11 -10000 0 -0.35 47 47
TNF 0.009 0.088 -10000 0 -0.44 21 21
FASLG -0.034 0.16 -10000 0 -0.54 47 47
NFKB1 0.021 0.029 -10000 0 -0.44 1 1
TNFR1A/BAG4/TNF-alpha 0.034 0.061 -10000 0 -0.27 20 20
CASP6 0.02 0.11 -10000 0 -0.56 11 11
CASP7 -0.01 0.12 0.34 2 -0.46 25 27
RELA 0.022 0.022 -10000 0 -10000 0 0
CASP2 0.025 0.005 -10000 0 -10000 0 0
CASP3 -0.014 0.12 0.34 2 -0.5 22 24
TNFRSF1A 0.025 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.02 -10000 0 -0.32 1 1
CASP8 0.025 0.019 -10000 0 -0.44 1 1
CASP9 0.024 0.02 -10000 0 -0.44 1 1
MAP3K14 0.011 0.063 -10000 0 -0.33 5 5
APAF-1/Caspase 9 -0.001 0.1 -10000 0 -0.4 20 20
BCL2 -0.006 0.1 0.33 2 -0.5 15 17
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.024 0.028 -10000 0 -0.44 2 2
ELF1 0.004 0.085 -10000 0 -0.34 32 32
CCNA2 0.024 0.02 -10000 0 -0.44 1 1
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
JAK3 0.021 0.052 -10000 0 -0.44 7 7
PIK3R1 0.024 0.028 -10000 0 -0.44 2 2
JAK1 0.025 0.02 -10000 0 -0.44 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.004 0.14 -10000 0 -0.44 34 34
SHC1 0.026 0.004 -10000 0 -10000 0 0
SP1 0.006 0.092 -10000 0 -0.33 40 40
IL2RA -0.027 0.16 0.24 1 -0.67 32 33
IL2RB 0.011 0.084 -10000 0 -0.44 19 19
SOS1 0.026 0.002 -10000 0 -10000 0 0
IL2RG 0.018 0.064 -10000 0 -0.44 11 11
G1/S transition of mitotic cell cycle -0.025 0.18 0.37 2 -0.65 42 44
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
CCND2 -0.032 0.18 0.25 3 -0.69 40 43
LCK 0.014 0.086 -10000 0 -0.44 19 19
GRB2 0.026 0.004 -10000 0 -10000 0 0
IL2 -0.005 0.02 -10000 0 -10000 0 0
CDK6 0.025 0.007 -10000 0 -10000 0 0
CCND3 0.006 0.12 0.4 1 -0.47 15 16
Aurora B signaling

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
Condensin I complex -0.006 0.085 -9999 0 -0.35 20 20
STMN1 -0.012 0.044 -9999 0 -0.32 11 11
Aurora B/RasGAP/Survivin 0.043 0.029 -9999 0 -0.3 2 2
Chromosomal passenger complex/Cul3 protein complex -0.014 0.077 -9999 0 -0.22 56 56
BIRC5 0.026 0.006 -9999 0 -10000 0 0
DES -0.15 0.31 -9999 0 -0.62 171 171
Aurora C/Aurora B/INCENP 0.034 0.05 -9999 0 -0.24 15 15
Aurora B/TACC1 0.024 0.034 -9999 0 -0.27 6 6
Aurora B/PP2A 0.032 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.006 0.011 -9999 0 -0.25 1 1
mitotic metaphase/anaphase transition 0.001 0.004 -9999 0 -10000 0 0
NDC80 -0.01 0.038 -9999 0 -0.32 8 8
Cul3 protein complex 0.032 0.095 -9999 0 -0.28 47 47
KIF2C 0.009 0.048 -9999 0 -0.37 7 7
PEBP1 0.027 0.003 -9999 0 -10000 0 0
KIF20A 0.025 0.028 -9999 0 -0.45 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.031 0.026 -9999 0 -0.32 2 2
SEPT1 0.017 0.068 -9999 0 -0.44 12 12
SMC2 0.019 0.055 -9999 0 -0.44 8 8
SMC4 0.014 0.074 -9999 0 -0.44 15 15
NSUN2/NPM1/Nucleolin -0.068 0.2 -9999 0 -0.5 96 96
PSMA3 0.024 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B 0.01 0.005 -9999 0 -10000 0 0
AURKB 0.022 0.012 -9999 0 -10000 0 0
AURKC 0.012 0.075 -9999 0 -0.44 15 15
CDCA8 0.026 0.005 -9999 0 -10000 0 0
cytokinesis 0.002 0.066 -9999 0 -0.3 15 15
Aurora B/Septin1 0 0.11 -9999 0 -0.31 22 22
AURKA 0.015 0.013 -9999 0 -10000 0 0
INCENP 0.026 0.004 -9999 0 -10000 0 0
KLHL13 0.001 0.13 -9999 0 -0.44 46 46
BUB1 0.027 0.02 -9999 0 -0.45 1 1
hSgo1/Aurora B/Survivin 0.039 0.033 -9999 0 -0.24 5 5
EVI5 0.02 0.052 -9999 0 -0.45 7 7
RhoA/GTP 0.035 0.062 -9999 0 -0.23 2 2
SGOL1 0.021 0.044 -9999 0 -0.44 5 5
CENPA 0.025 0.059 -9999 0 -0.21 11 11
NCAPG 0.023 0.034 -9999 0 -0.44 3 3
Aurora B/HC8 Proteasome 0.032 0.015 -9999 0 -10000 0 0
NCAPD2 0.025 0.005 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.032 0.021 -9999 0 -0.32 1 1
RHOA 0.025 0.02 -9999 0 -0.44 1 1
NCAPH 0.025 0.019 -9999 0 -0.44 1 1
NPM1 -0.048 0.16 -9999 0 -0.35 102 102
RASA1 0.024 0.028 -9999 0 -0.44 2 2
KLHL9 0.024 0.02 -9999 0 -0.44 1 1
mitotic prometaphase 0 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.015 -9999 0 -10000 0 0
PPP1CC 0.025 0.02 -9999 0 -0.44 1 1
Centraspindlin 0.03 0.061 -9999 0 -0.23 2 2
RhoA/GDP 0.018 0.014 -9999 0 -0.32 1 1
NSUN2 -0.032 0.11 -9999 0 -0.28 94 94
MYLK 0.002 0.056 -9999 0 -0.33 15 15
KIF23 0.025 0.006 -9999 0 -10000 0 0
VIM -0.008 0.022 -9999 0 -0.32 2 2
RACGAP1 0.026 0.004 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.032 0.11 -9999 0 -0.28 97 97
Chromosomal passenger complex 0.009 0.05 -9999 0 -0.19 14 14
Chromosomal passenger complex/EVI5 0.061 0.051 -9999 0 -0.24 7 7
TACC1 0.018 0.048 -9999 0 -0.44 6 6
PPP2R5D 0.025 0.004 -9999 0 -10000 0 0
CUL3 0.024 0.028 -9999 0 -0.44 2 2
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.009 0.047 -10000 0 -0.87 1 1
regulation of axonogenesis -0.004 0.045 0.31 9 -10000 0 9
myoblast fusion -0.021 0.036 0.47 2 -10000 0 2
mol:GTP 0.01 0.044 -10000 0 -0.16 32 32
regulation of calcium-dependent cell-cell adhesion -0.029 0.075 0.26 29 -10000 0 29
ARF1/GTP 0.026 0.039 -10000 0 -0.23 3 3
mol:GM1 0.002 0.032 -10000 0 -0.26 2 2
mol:Choline 0.004 0.028 -10000 0 -0.32 3 3
lamellipodium assembly -0.002 0.087 -10000 0 -0.36 29 29
MAPK3 0.012 0.035 -10000 0 -0.3 3 3
ARF6/GTP/NME1/Tiam1 0.03 0.076 -10000 0 -0.26 29 29
ARF1 0.025 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.036 -10000 0 -0.48 2 2
ARF1/GDP 0.017 0.063 -10000 0 -0.22 32 32
ARF6 0.03 0.026 -10000 0 -0.54 1 1
RAB11A 0.025 0.005 -10000 0 -10000 0 0
TIAM1 0.006 0.1 -10000 0 -0.44 28 28
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.031 -10000 0 -0.3 2 2
actin filament bundle formation -0.019 0.066 0.23 31 -10000 0 31
KALRN 0.012 0.038 -10000 0 -0.28 8 8
RAB11FIP3/RAB11A 0.036 0.018 -10000 0 -0.32 1 1
RhoA/GDP 0.02 0.066 -10000 0 -0.23 31 31
NME1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.061 -10000 0 -0.22 29 29
substrate adhesion-dependent cell spreading 0.01 0.044 -10000 0 -0.16 32 32
cortical actin cytoskeleton organization -0.001 0.087 -10000 0 -0.37 28 28
RAC1 0.023 0.008 -10000 0 -10000 0 0
liver development 0.01 0.044 -10000 0 -0.16 32 32
ARF6/GTP 0.01 0.044 -10000 0 -0.16 32 32
RhoA/GTP 0.025 0.044 -10000 0 -0.38 2 2
mol:GDP 0.005 0.057 -10000 0 -0.23 26 26
ARF6/GTP/RAB11FIP3/RAB11A 0.039 0.041 -10000 0 -0.24 3 3
RHOA 0.025 0.02 -10000 0 -0.44 1 1
PLD1 0.008 0.043 -10000 0 -0.34 4 4
RAB11FIP3 0.025 0.02 -10000 0 -0.44 1 1
tube morphogenesis -0.002 0.087 -10000 0 -0.36 29 29
ruffle organization 0.004 0.045 -10000 0 -0.31 9 9
regulation of epithelial cell migration 0.01 0.044 -10000 0 -0.16 32 32
PLD2 0.013 0.023 -10000 0 -0.26 2 2
PIP5K1A 0.004 0.046 -10000 0 -0.31 9 9
mol:Phosphatidic acid 0.004 0.028 -10000 0 -0.32 3 3
Rac1/GTP -0.002 0.088 -10000 0 -0.37 29 29
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.012 0.04 -10000 0 -0.26 12 12
FRAP1 -0.014 0.11 -10000 0 -0.45 35 35
AKT1 -0.007 0.051 0.15 17 -0.26 13 30
INSR 0.025 0.02 -10000 0 -0.44 1 1
Insulin Receptor/Insulin 0.027 0.019 -10000 0 -0.27 2 2
mol:GTP 0.021 0.055 0.19 3 -0.24 10 13
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.048 -10000 0 -0.22 13 13
TSC2 0.025 0.02 -10000 0 -0.44 1 1
RHEB/GDP 0.012 0.043 -10000 0 -0.22 9 9
TSC1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.016 0.046 -10000 0 -0.29 12 12
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.009 0.058 -10000 0 -0.25 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.02 -10000 0 -0.44 1 1
RPS6KB1 -0.002 0.087 0.23 4 -0.34 24 28
MAP3K5 0.003 0.035 0.19 4 -0.2 12 16
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
apoptosis 0.003 0.035 0.19 4 -0.2 12 16
mol:LY294002 0 0 0.001 1 -0.001 11 12
EIF4B -0.002 0.08 0.28 4 -0.3 23 27
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.017 0.08 0.24 2 -0.29 23 25
eIF4E/eIF4G1/eIF4A1 0 0.071 -10000 0 -0.27 36 36
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.051 -10000 0 -0.26 15 15
mTOR/RHEB/GTP/Raptor/GBL 0.003 0.036 0.2 7 -0.18 2 9
FKBP1A 0.021 0.01 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.05 0.2 1 -0.28 4 5
mol:Amino Acids 0 0 0.001 1 -0.001 11 12
FKBP12/Rapamycin 0.015 0.008 -10000 0 -10000 0 0
PDPK1 -0.014 0.039 0.15 4 -0.25 12 16
EIF4E 0.024 0.028 -10000 0 -0.44 2 2
ASK1/PP5C 0.001 0.13 -10000 0 -0.44 44 44
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.007 0.049 -10000 0 -0.25 18 18
TSC1/TSC2 0.023 0.059 0.21 3 -0.26 10 13
tumor necrosis factor receptor activity 0 0 0.001 11 -0.001 1 12
RPS6 0.026 0.008 -10000 0 -10000 0 0
PPP5C 0.026 0.003 -10000 0 -10000 0 0
EIF4G1 0.026 0.002 -10000 0 -10000 0 0
IRS1 0 0.045 -10000 0 -0.32 11 11
INS -0.017 0.02 -10000 0 -0.44 1 1
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.014 0.041 0.15 4 -0.24 14 18
EIF4EBP1 -0.071 0.3 -10000 0 -1 51 51
PIK3CA 0.024 0.028 -10000 0 -0.45 2 2
PPP2R5D -0.011 0.11 0.25 4 -0.4 35 39
peptide biosynthetic process -0.01 0.04 0.18 20 -0.25 3 23
RHEB 0.025 0.005 -10000 0 -10000 0 0
EIF4A1 0.022 0.01 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 25 -0.003 10 35
EEF2 -0.01 0.04 0.18 20 -0.25 3 23
eIF4E/4E-BP1 -0.055 0.29 -10000 0 -0.98 51 51
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.007 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.022 0.027 -10000 0 -0.25 2 2
CDKN1B 0.017 0.075 -10000 0 -0.35 17 17
CDKN1A 0.016 0.078 0.19 2 -0.34 19 21
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.021 -10000 0 -0.44 1 1
FOXO3 0.019 0.067 0.19 1 -0.34 14 15
AKT1 -0.003 0.07 -10000 0 -0.36 19 19
BAD 0.025 0.02 -10000 0 -0.44 1 1
AKT3 0.006 0.044 -10000 0 -0.3 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.017 0.076 -10000 0 -0.34 18 18
AKT1/ASK1 0.033 0.1 0.23 1 -0.34 22 23
BAD/YWHAZ 0.042 0.03 -10000 0 -0.27 3 3
RICTOR 0.009 0.086 -10000 0 -0.44 20 20
RAF1 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.031 0.096 0.33 22 -10000 0 22
TSC1 0.016 0.077 -10000 0 -0.34 19 19
YWHAZ 0.021 0.029 -10000 0 -0.44 2 2
AKT1/RAF1 0.038 0.1 0.24 3 -0.36 19 22
EP300 0.023 0.028 -10000 0 -0.44 2 2
mol:GDP 0.02 0.079 -10000 0 -0.35 19 19
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.017 0.078 -10000 0 -0.36 17 17
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
TBC1D4 0.001 0.024 -10000 0 -0.26 5 5
MAP3K5 0.024 0.028 -10000 0 -0.44 2 2
MAPKAP1 0.026 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.045 0.095 0.3 13 -0.2 51 64
YWHAH 0.025 0.005 -10000 0 -10000 0 0
AKT1S1 0.016 0.079 -10000 0 -0.36 18 18
CASP9 0.016 0.073 -10000 0 -0.36 15 15
YWHAB 0.015 0.013 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.035 0.1 0.31 6 -0.38 17 23
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.029 0.029 -10000 0 -0.27 1 1
YWHAE 0.022 0.01 -10000 0 -10000 0 0
SRC 0.015 0.023 -10000 0 -0.44 1 1
AKT2/p21CIP1 0.013 0.083 0.19 1 -0.36 14 15
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.013 0.033 -10000 0 -0.27 2 2
CHUK 0.02 0.067 -10000 0 -0.37 10 10
BAD/BCL-XL 0.01 0.074 -10000 0 -0.36 14 14
mTORC2 0.023 0.05 -10000 0 -0.24 20 20
AKT2 0.011 0.013 -10000 0 -0.3 1 1
FOXO1-3a-4/14-3-3 family 0.052 0.13 0.26 53 -0.39 19 72
PDPK1 0.026 0.004 -10000 0 -10000 0 0
MDM2 0.016 0.078 -10000 0 -0.34 19 19
MAPKKK cascade -0.037 0.099 0.35 19 -0.23 3 22
MDM2/Cbp/p300 0.041 0.1 0.26 1 -0.36 16 17
TSC1/TSC2 0.013 0.079 0.27 3 -0.37 15 18
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.097 0.25 1 -0.35 16 17
glucose import 0.023 0.084 0.2 91 -0.24 12 103
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.019 0.054 0.18 4 -0.27 8 12
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.023 0.084 0.2 91 -0.24 12 103
GSK3A 0.018 0.076 -10000 0 -0.35 17 17
FOXO1 0.022 0.076 0.2 3 -0.35 12 15
GSK3B 0.016 0.08 0.19 1 -0.35 20 21
SFN 0.024 0.022 -10000 0 -0.44 1 1
G1/S transition of mitotic cell cycle 0.019 0.098 0.27 7 -0.37 17 24
p27Kip1/14-3-3 family 0.043 0.052 0.27 1 -10000 0 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.028 -10000 0 -0.44 2 2
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
YWHAG 0.025 0.005 -10000 0 -10000 0 0
RHEB 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.059 0.12 -10000 0 -0.48 6 6
UGCG 0.009 0.08 -10000 0 -0.71 6 6
AKT1/mTOR/p70S6K/Hsp90/TERT -0.016 0.15 0.22 1 -0.47 37 38
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.009 0.079 -10000 0 -0.69 6 6
mol:DAG -0.007 0.12 -10000 0 -0.83 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.14 -10000 0 -0.45 37 37
FRAP1 -0.011 0.16 -10000 0 -0.51 39 39
FOXO3 -0.012 0.14 0.35 1 -0.44 37 38
AKT1 -0.01 0.15 -10000 0 -0.47 37 37
GAB2 0.024 0.028 -10000 0 -0.45 2 2
SMPD1 0.01 0.074 -10000 0 -0.73 5 5
SGMS1 0.004 0.092 -10000 0 -0.63 11 11
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 -0.008 0.022 -10000 0 -0.27 4 4
CALM1 0.024 0.007 -10000 0 -10000 0 0
cell proliferation 0.017 0.1 -10000 0 -0.49 11 11
EIF3A 0.025 0.02 -10000 0 -0.44 1 1
PI3K 0.037 0.032 -10000 0 -0.32 4 4
RPS6KB1 -0.001 0.14 -10000 0 -0.88 13 13
mol:sphingomyelin -0.007 0.12 -10000 0 -0.83 11 11
natural killer cell activation 0 0.001 -10000 0 -0.011 3 3
JAK3 0.022 0.052 -10000 0 -0.44 7 7
PIK3R1 0.025 0.028 -10000 0 -0.44 2 2
JAK1 0.026 0.02 -10000 0 -0.44 1 1
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MYC 0.016 0.16 -10000 0 -0.61 17 17
MYB 0.004 0.15 -10000 0 -1.2 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.007 0.13 -10000 0 -0.4 45 45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.13 -10000 0 -0.81 13 13
mol:PI-3-4-5-P3 -0.007 0.13 -10000 0 -0.39 45 45
Rac1/GDP 0.017 0.024 -10000 0 -0.25 4 4
T cell proliferation -0.008 0.12 0.22 1 -0.41 32 33
SHC1 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.008 -10000 0 -0.065 9 9
PRKCZ -0.009 0.12 0.23 1 -0.4 37 38
NF kappa B1 p50/RelA 0.01 0.15 -10000 0 -0.46 35 35
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.002 0.094 -10000 0 -0.42 19 19
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
RELA 0.025 0.004 -10000 0 -10000 0 0
IL2RA -0.008 0.12 -10000 0 -0.44 43 43
IL2RB 0.012 0.084 -10000 0 -0.44 19 19
TERT 0.007 0.1 -10000 0 -0.44 27 27
E2F1 0.005 0.065 -10000 0 -0.42 10 10
SOS1 0.026 0.004 -10000 0 -10000 0 0
RPS6 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.004 0.032 9 -10000 0 9
PTPN11 0.022 0.044 -10000 0 -0.45 5 5
IL2RG 0.019 0.064 -10000 0 -0.44 11 11
actin cytoskeleton organization -0.008 0.12 0.22 1 -0.41 32 33
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.019 0.011 -10000 0 -10000 0 0
PIK3CA 0.026 0.028 -10000 0 -0.44 2 2
Rac1/GTP 0.042 0.031 -10000 0 -0.23 4 4
LCK 0.013 0.086 -10000 0 -0.44 19 19
BCL2 -0.013 0.17 -10000 0 -0.74 22 22
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0 0.12 -10000 0 -0.44 40 40
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.021 -10000 0 -0.44 1 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
HIF1A/p53 -0.008 0.084 0.26 1 -0.24 61 62
HIF1A -0.004 0.054 -10000 0 -0.25 24 24
COPS5 0.023 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.062 0.037 -10000 0 -0.26 2 2
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A 0.001 0.12 -10000 0 -0.44 38 38
ARNT/IPAS 0.018 0.094 -10000 0 -0.32 40 40
HIF1AN 0.025 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/ARNT 0.003 0.068 -10000 0 -0.28 26 26
CUL2 0.026 0.002 -10000 0 -10000 0 0
OS9 0.026 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.045 0.024 -10000 0 -0.27 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.008 0.067 0.26 1 -0.26 30 31
PHD1-3/OS9 0.057 0.037 -10000 0 -0.25 5 5
HIF1A/RACK1/Elongin B/Elongin C 0.022 0.072 -10000 0 -0.26 27 27
VHL 0.025 0.02 -10000 0 -0.44 1 1
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
HIF1A/JAB1 0.005 0.064 0.26 1 -0.26 25 26
EGLN3 0.021 0.045 -10000 0 -0.44 5 5
EGLN2 0.025 0.02 -10000 0 -0.44 1 1
EGLN1 0.025 0.005 -10000 0 -10000 0 0
TP53 -0.007 0.11 -10000 0 -0.44 36 36
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.022 0.083 -10000 0 -0.54 11 11
ARNT 0.025 0.02 -10000 0 -0.44 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.024 0.02 -10000 0 -0.44 1 1
HIF1A/p19ARF -0.006 0.092 0.24 2 -0.24 66 68
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.008 0.084 0.28 28 -10000 0 28
GNAI2 0.026 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.028 0.035 -10000 0 -0.27 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.087 -10000 0 -0.44 19 19
RhoA/GTP 0.008 0.086 -10000 0 -0.28 28 28
negative regulation of cAMP metabolic process -0.002 0.087 -10000 0 -0.26 45 45
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.008 -10000 0 -10000 0 0
S1PR5 0.021 0.052 -10000 0 -0.44 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.002 0.087 -10000 0 -0.26 45 45
RhoA/GDP 0.018 0.014 -10000 0 -0.32 1 1
RHOA 0.025 0.02 -10000 0 -0.44 1 1
GNAI1 0.016 0.064 -10000 0 -0.44 11 11
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.012 0.012 -10000 0 -0.27 1 1
SNTA1 0.013 0.035 -10000 0 -0.44 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.039 -10000 0 -0.3 10 10
MAPK12 -0.012 0.054 0.2 9 -0.25 22 31
CCND1 0.001 0.048 -10000 0 -0.36 7 7
p38 gamma/SNTA1 0 0.052 0.19 5 -0.24 20 25
MAP2K3 0.022 0.009 -10000 0 -10000 0 0
PKN1 0.023 0.034 -10000 0 -0.44 3 3
G2/M transition checkpoint -0.012 0.054 0.2 9 -0.25 22 31
MAP2K6 -0.004 0.045 -10000 0 -0.26 18 18
MAPT -0.021 0.085 0.25 6 -0.3 38 44
MAPK13 -0.01 0.014 -10000 0 -0.32 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.008 0.036 -10000 0 -0.3 8 8
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.012 -10000 0 -10000 0 0
DOCK1 0.024 0.02 -10000 0 -0.44 1 1
ITGA4 0.005 0.097 -10000 0 -0.44 26 26
RAC1 0.023 0.008 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.015 0.099 -10000 0 -0.36 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.068 -10000 0 -0.27 26 26
alpha4/beta7 Integrin/Paxillin 0.022 0.082 -10000 0 -0.28 37 37
lamellipodium assembly -0.003 0.092 -10000 0 -0.42 20 20
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
PI3K 0.034 0.031 -10000 0 -0.32 4 4
ARF6 0.024 0.02 -10000 0 -0.44 1 1
TLN1 0.025 0.02 -10000 0 -0.44 1 1
PXN -0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
ARF6/GTP 0.038 0.059 -10000 0 -0.22 26 26
cell adhesion 0.039 0.062 -10000 0 -0.24 27 27
CRKL/CBL 0.036 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.029 0.061 -10000 0 -0.25 26 26
ITGB1 0.026 0.002 -10000 0 -10000 0 0
ITGB7 0.014 0.078 -10000 0 -0.44 16 16
ARF6/GDP 0.026 0.022 -10000 0 -0.44 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.034 0.091 -10000 0 -0.31 34 34
p130Cas/Crk/Dock1 0.042 0.031 -10000 0 -0.29 3 3
VCAM1 0.011 0.087 -10000 0 -0.44 20 20
alpha4/beta1 Integrin/Paxillin/Talin 0.041 0.063 -10000 0 -0.24 27 27
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.061 -10000 0 -0.24 25 25
BCAR1 0.024 0.028 -10000 0 -0.44 2 2
mol:GDP -0.04 0.06 0.24 25 -10000 0 25
CBL 0.025 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GIT1 0.024 0.02 -10000 0 -0.44 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.041 0.063 -10000 0 -0.24 27 27
Rac1/GTP -0.005 0.1 -10000 0 -0.47 20 20
S1P3 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
PDGFRB 0.018 0.062 -10000 0 -0.44 10 10
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.001 0.074 -10000 0 -0.25 40 40
GNAO1 0.016 0.088 -10000 0 -0.45 19 19
S1P/S1P3/G12/G13 0.041 0.037 -10000 0 -0.26 6 6
AKT1 -0.018 0.15 -10000 0 -0.44 54 54
AKT3 -0.005 0.18 -10000 0 -1.2 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.062 -10000 0 -0.44 10 10
GNAI2 0.025 0.01 -10000 0 -10000 0 0
GNAI3 0.025 0.01 -10000 0 -10000 0 0
GNAI1 0.016 0.065 -10000 0 -0.44 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.022 0.041 -10000 0 -0.46 4 4
S1PR2 0.026 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.1 -10000 0 -0.35 28 28
MAPK3 -0.01 0.096 0.2 1 -0.4 21 22
MAPK1 -0.005 0.091 -10000 0 -0.39 19 19
JAK2 0.028 0.12 0.22 9 -0.48 17 26
CXCR4 -0.014 0.1 -10000 0 -0.4 25 25
FLT1 0.019 0.025 -10000 0 -0.46 1 1
RhoA/GDP 0.018 0.014 -10000 0 -0.32 1 1
Rac1/GDP 0.017 0.006 -10000 0 -10000 0 0
SRC -0.004 0.089 0.2 20 -0.37 17 37
S1P/S1P3/Gi -0.001 0.1 -10000 0 -0.36 28 28
RAC1 0.023 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.01 0.098 -10000 0 -0.38 20 20
VEGFA 0.025 0.011 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.001 0.084 -10000 0 -0.32 21 21
VEGFR1 homodimer/VEGFA homodimer 0.029 0.027 -10000 0 -0.35 1 1
RHOA 0.025 0.02 -10000 0 -0.44 1 1
S1P/S1P3/Gq 0.004 0.082 -10000 0 -0.29 34 34
GNAQ 0.022 0.043 -10000 0 -0.44 5 5
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
G12/G13 0.033 0.024 -10000 0 -0.32 2 2
GNA14 0.014 0.075 -10000 0 -0.44 15 15
GNA15 0.015 0.073 -10000 0 -0.44 14 14
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.028 -10000 0 -0.44 2 2
GNA11 0.023 0.034 -10000 0 -0.44 3 3
Rac1/GTP 0.005 0.096 -10000 0 -0.39 19 19
Signaling events mediated by PRL

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
CCNE1 0.025 0.004 -10000 0 -10000 0 0
mol:Halofuginone 0.002 0.009 -10000 0 -0.21 1 1
ITGA1 0.022 0.043 -10000 0 -0.44 5 5
CDKN1A 0.003 0.055 -10000 0 -0.33 12 12
PRL-3/alpha Tubulin 0.022 0.059 -10000 0 -0.32 16 16
mol:Ca2+ -0.02 0.08 0.33 15 -0.33 19 34
AGT 0.009 0.093 -10000 0 -0.44 23 23
CCNA2 -0.007 0.043 -10000 0 -0.82 1 1
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
EGR1 0.005 0.042 -10000 0 -0.32 9 9
CDK2/Cyclin E1 0.065 0.081 -10000 0 -0.31 12 12
MAPK3 -0.013 0.065 0.23 14 -0.32 17 31
PRL-2 /Rab GGTase beta 0.035 0.027 -10000 0 -0.32 3 3
MAPK1 -0.013 0.063 0.23 13 -0.32 16 29
PTP4A1 -0.006 0.047 -10000 0 -0.86 1 1
PTP4A3 0.009 0.077 -10000 0 -0.44 16 16
PTP4A2 0.025 0.005 -10000 0 -10000 0 0
ITGB1 -0.013 0.064 0.23 14 -0.32 16 30
SRC 0.015 0.023 -10000 0 -0.44 1 1
RAC1 -0.003 0.077 -10000 0 -0.4 19 19
Rab GGTase beta/Rab GGTase alpha 0.033 0.031 -10000 0 -0.32 4 4
PRL-1/ATF-5 0.075 0.095 -10000 0 -0.82 1 1
RABGGTA 0.024 0.02 -10000 0 -0.44 1 1
BCAR1 -0.009 0.055 0.34 14 -10000 0 14
RHOC -0.006 0.085 -10000 0 -0.38 26 26
RHOA -0.004 0.08 -10000 0 -0.38 23 23
cell motility 0.029 0.13 0.26 12 -0.38 29 41
PRL-1/alpha Tubulin 0.076 0.096 -10000 0 -0.82 1 1
PRL-3/alpha1 Integrin 0.02 0.066 -10000 0 -0.32 20 20
ROCK1 0.032 0.12 0.26 10 -0.4 24 34
RABGGTB 0.023 0.034 -10000 0 -0.44 3 3
CDK2 0.025 0.02 -10000 0 -0.44 1 1
mitosis -0.006 0.047 -10000 0 -0.85 1 1
ATF5 0.026 0.005 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.016 0.067 0.44 12 -10000 0 12
PI3K Class IB/PDE3B 0.016 0.067 -10000 0 -0.44 12 12
PDE3B 0.016 0.067 -10000 0 -0.44 12 12
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.048 0.084 -10000 0 -0.75 4 4
epithelial cell differentiation 0.007 0.11 -10000 0 -0.58 8 8
ITCH 0.014 0.036 -10000 0 -0.44 3 3
WWP1 0.007 0.096 -10000 0 -1.2 3 3
FYN 0.022 0.039 -10000 0 -0.44 4 4
EGFR 0.02 0.044 -10000 0 -0.44 5 5
PRL 0.004 0.028 -10000 0 -10000 0 0
neuron projection morphogenesis 0.004 0.094 0.26 10 -0.62 4 14
PTPRZ1 -0.009 0.12 -10000 0 -0.44 38 38
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.028 0.098 -10000 0 -0.65 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0 0.094 -10000 0 -0.29 33 33
ADAM17 0.012 0.037 -10000 0 -0.38 3 3
ErbB4/ErbB4 0.007 0.078 -10000 0 -0.81 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.045 0.084 -10000 0 -0.76 4 4
NCOR1 0.022 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.011 0.098 -10000 0 -0.58 6 6
GRIN2B -0.011 0.11 0.25 7 -0.44 16 23
ErbB4/ErbB2/betacellulin 0.039 0.082 -10000 0 -0.83 3 3
STAT1 0.025 0.028 -10000 0 -0.44 2 2
HBEGF 0.027 0.011 -10000 0 -10000 0 0
PRLR -0.015 0.13 -10000 0 -0.44 51 51
E4ICDs/ETO2 0.035 0.11 -10000 0 -0.35 22 22
axon guidance 0 0.1 0.3 5 -0.73 6 11
NEDD4 0.01 0.034 -10000 0 -0.44 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.004 0.1 -10000 0 -0.33 51 51
CBFA2T3 0.002 0.12 -10000 0 -0.44 39 39
ErbB4/ErbB2/HBEGF 0.045 0.076 -10000 0 -0.83 3 3
MAPK3 0.009 0.093 0.25 7 -0.65 4 11
STAT1 (dimer) 0.048 0.092 -10000 0 -0.84 4 4
MAPK1 0.009 0.091 0.24 7 -0.73 3 10
JAK2 0.013 0.075 -10000 0 -0.44 15 15
ErbB4/ErbB2/neuregulin 1 beta 0.002 0.093 0.22 6 -0.61 5 11
NRG1 -0.034 0.083 -10000 0 -0.33 42 42
NRG3 0.007 0.025 -10000 0 -10000 0 0
NRG2 0.019 0.027 -10000 0 -10000 0 0
NRG4 0.017 0.042 -10000 0 -0.44 3 3
heart development 0 0.1 0.3 5 -0.73 6 11
neural crest cell migration 0.002 0.092 0.22 6 -0.6 5 11
ERBB2 -0.008 0.038 0.24 7 -0.35 3 10
WWOX/E4ICDs 0.043 0.084 -10000 0 -0.75 4 4
SHC1 0.025 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.049 0.092 -10000 0 -0.72 5 5
apoptosis -0.015 0.11 0.51 11 -10000 0 11
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.047 0.086 -10000 0 -0.78 4 4
ErbB4/ErbB2/epiregulin -0.009 0.14 -10000 0 -0.5 8 8
ErbB4/ErbB4/betacellulin/betacellulin 0.042 0.09 -10000 0 -0.75 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.043 0.13 -10000 0 -0.56 9 9
MDM2 0.002 0.078 0.25 1 -0.8 4 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.007 0.084 -10000 0 -0.28 36 36
STAT5A 0.006 0.1 0.28 4 -0.91 4 8
ErbB4/EGFR/neuregulin 1 beta 0.008 0.1 -10000 0 -0.62 6 6
DLG4 0.02 0.029 -10000 0 -0.44 2 2
GRB2/SHC 0.037 0.008 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.034 0.077 -10000 0 -0.7 4 4
STAT5A (dimer) 0.019 0.13 0.29 1 -0.66 8 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.031 0.11 0.28 4 -0.91 4 8
LRIG1 0.015 0.069 -10000 0 -0.44 13 13
EREG -0.077 0.2 -10000 0 -0.44 134 134
BTC 0.016 0.067 -10000 0 -0.44 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.004 0.1 0.32 2 -0.74 6 8
ERBB4 0.003 0.076 -10000 0 -0.82 4 4
STAT5B 0.026 0.004 -10000 0 -10000 0 0
YAP1 0.002 0.1 -10000 0 -0.57 13 13
GRB2 0.025 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.044 0.078 0.22 1 -0.84 3 4
glial cell differentiation -0.034 0.076 0.69 4 -10000 0 4
WWOX 0.023 0.008 -10000 0 -10000 0 0
cell proliferation 0 0.12 0.27 6 -0.76 5 11
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.005 0.071 -10000 0 -0.29 17 17
BAG4 0.022 0.021 -10000 0 -0.44 1 1
BAD 0.005 0.034 0.15 4 -0.4 1 5
NFKBIA 0.024 0.006 -10000 0 -10000 0 0
BIRC3 0.015 0.076 -10000 0 -0.44 15 15
BAX 0.006 0.044 0.21 9 -0.4 1 10
EnzymeConsortium:3.1.4.12 0.003 0.021 0.1 4 -0.075 9 13
IKBKB 0.017 0.08 0.26 3 -0.29 6 9
MAP2K2 0.002 0.047 0.19 17 -0.26 2 19
MAP2K1 0.001 0.045 0.19 15 -0.22 3 18
SMPD1 0.004 0.027 0.14 4 -0.18 3 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.009 0.073 -10000 0 -0.31 9 9
MAP2K4 0.001 0.035 0.18 3 -0.23 5 8
protein ubiquitination 0.009 0.076 0.32 3 -0.34 6 9
EnzymeConsortium:2.7.1.37 0.001 0.049 0.19 16 -0.23 3 19
response to UV 0 0.001 0.002 17 -0.002 1 18
RAF1 0.005 0.045 0.19 16 -0.18 3 19
CRADD 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide 0.008 0.034 0.14 6 -0.12 7 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.032 0.01 -10000 0 -10000 0 0
MADD 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.003 0.039 0.16 4 -0.23 6 10
TRADD 0.026 0.003 -10000 0 -10000 0 0
RELA/p50 0.025 0.004 -10000 0 -10000 0 0
MAPK3 0.005 0.047 0.19 16 -0.22 3 19
MAPK1 0.002 0.05 0.19 15 -0.22 5 20
p50/RELA/I-kappa-B-alpha 0.035 0.011 -10000 0 -10000 0 0
FADD 0.006 0.069 0.2 2 -0.28 14 16
KSR1 0.007 0.044 0.19 15 -0.19 3 18
MAPK8 -0.002 0.038 0.22 3 -0.22 6 9
TRAF2 0.025 0.02 -10000 0 -0.44 1 1
response to radiation 0 0 0.002 6 -10000 0 6
CHUK 0.001 0.071 0.22 2 -0.34 8 10
TNF R/SODD 0.032 0.02 -10000 0 -0.32 1 1
TNF 0.01 0.089 -10000 0 -0.45 21 21
CYCS 0.025 0.058 0.16 26 -0.26 4 30
IKBKG 0.003 0.073 0.23 2 -0.33 9 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.01 0.072 -10000 0 -0.28 18 18
RELA 0.025 0.004 -10000 0 -10000 0 0
RIPK1 0.026 0.004 -10000 0 -10000 0 0
AIFM1 0.023 0.049 0.14 23 -0.42 1 24
TNF/TNF R/SODD 0.034 0.061 -10000 0 -0.27 20 20
TNFRSF1A 0.025 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 6 -10000 0 6
CASP8 0.015 0.1 -10000 0 -0.59 16 16
NSMAF 0.024 0.085 0.2 55 -0.27 12 67
response to hydrogen peroxide 0 0.001 0.002 17 -0.002 1 18
BCL2 0.014 0.052 -10000 0 -0.44 7 7
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.025 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.026 0.072 -9999 0 -0.4 19 19
MDM2/SUMO1 0.017 0.098 -9999 0 -0.43 22 22
HDAC4 0.026 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.025 0.072 -9999 0 -0.4 19 19
SUMO1 0.011 0.084 -9999 0 -0.44 19 19
NPC/RanGAP1/SUMO1 -0.005 0.08 -9999 0 -0.37 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.016 0.099 -9999 0 -0.44 24 24
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.002 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0.081 -9999 0 -0.44 18 18
SUMO1/HDAC4 0.017 0.094 -9999 0 -0.43 21 21
SUMO1/HDAC1 0.018 0.093 -9999 0 -0.43 21 21
RANGAP1 0.024 0.02 -9999 0 -0.44 1 1
MDM2/SUMO1/SUMO1 0.04 0.064 -9999 0 -0.26 19 19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.004 0.08 -9999 0 -0.36 24 24
Ran/GTP 0.007 0.08 -9999 0 -0.33 25 25
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.024 0.028 -9999 0 -0.44 2 2
UBE2I 0.025 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0.098 -9999 0 -0.42 24 24
NPC 0.008 0.042 -9999 0 -0.22 18 18
PIAS2 0.02 0.012 -9999 0 -10000 0 0
PIAS1 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.049 0.26 0.39 1 -1.1 32 33
RAD9A 0.025 0.02 -10000 0 -0.44 1 1
AP1 0.022 0.069 -10000 0 -0.32 21 21
IFNAR2 0.022 0.024 -10000 0 -0.44 1 1
AKT1 0.003 0.046 -10000 0 -0.19 26 26
ER alpha/Oestrogen 0.004 0.069 -10000 0 -0.32 25 25
NFX1/SIN3/HDAC complex 0.03 0.055 0.18 1 -0.28 4 5
EGF -0.033 0.17 -10000 0 -0.43 89 89
SMG5 0.025 0.02 -10000 0 -0.44 1 1
SMG6 0.022 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.035 0.025 -10000 0 -0.32 1 1
TERT/c-Abl -0.04 0.25 -10000 0 -0.98 33 33
SAP18 0.02 0.011 -10000 0 -10000 0 0
MRN complex 0.031 0.075 -10000 0 -0.35 18 18
WT1 -0.057 0.19 -10000 0 -0.44 113 113
WRN 0.019 0.029 -10000 0 -0.44 2 2
SP1 0.023 0.026 -10000 0 -0.44 1 1
SP3 0.023 0.023 -10000 0 -0.44 1 1
TERF2IP 0.025 0.02 -10000 0 -0.44 1 1
Telomerase/Nucleolin -0.024 0.23 -10000 0 -0.88 33 33
Mad/Max 0.033 0.024 -10000 0 -0.32 1 1
TERT -0.052 0.28 0.39 1 -1.1 32 33
CCND1 -0.043 0.23 -10000 0 -0.95 31 31
MAX 0.022 0.013 -10000 0 -10000 0 0
RBBP7 0.025 0.02 -10000 0 -0.44 1 1
RBBP4 0.024 0.02 -10000 0 -0.44 1 1
TERF2 0.024 0.012 -10000 0 -10000 0 0
PTGES3 0.024 0.028 -10000 0 -0.44 2 2
SIN3A 0.024 0.02 -10000 0 -0.44 1 1
Telomerase/911 0.03 0.055 -10000 0 -0.4 3 3
CDKN1B -0.009 0.073 -10000 0 -0.27 37 37
RAD1 0.025 0.004 -10000 0 -10000 0 0
XRCC5 0.025 0.019 -10000 0 -0.44 1 1
XRCC6 0.025 0.006 -10000 0 -10000 0 0
SAP30 0.023 0.028 -10000 0 -0.44 2 2
TRF2/PARP2 0.035 0.018 -10000 0 -0.28 1 1
UBE3A 0.02 0.036 -10000 0 -0.44 3 3
JUN 0.02 0.04 -10000 0 -0.44 4 4
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.026 -10000 0 -0.32 3 3
FOS 0.01 0.081 -10000 0 -0.44 17 17
IFN-gamma/IRF1 0.02 0.091 -10000 0 -0.31 38 38
PARP2 0.024 0.02 -10000 0 -0.44 1 1
BLM 0.021 0.044 -10000 0 -0.44 5 5
Telomerase -0.006 0.11 -10000 0 -0.48 17 17
IRF1 0.026 0.015 -10000 0 -0.17 1 1
ESR1 0.004 0.097 -10000 0 -0.44 25 25
KU/TER 0.036 0.017 -10000 0 -0.32 1 1
ATM/TRF2 0.033 0.039 -10000 0 -0.26 9 9
ubiquitin-dependent protein catabolic process 0.024 0.062 -10000 0 -0.26 8 8
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.024 0.063 -10000 0 -0.27 8 8
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.023 0.016 -10000 0 -10000 0 0
ATM 0.005 0.043 -10000 0 -0.36 8 8
SMAD3 -0.014 0.037 -10000 0 -0.32 8 8
ABL1 0.025 0.02 -10000 0 -0.44 1 1
MXD1 0.023 0.023 -10000 0 -0.44 1 1
MRE11A 0.019 0.055 -10000 0 -0.44 8 8
HUS1 0.024 0.007 -10000 0 -10000 0 0
RPS6KB1 0.021 0.044 -10000 0 -0.44 5 5
TERT/NF kappa B1/14-3-3 -0.032 0.25 0.38 1 -0.97 32 33
NR2F2 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.011 0.019 -10000 0 -0.32 1 1
MAPK1 -0.01 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.017 0.064 -10000 0 -0.44 11 11
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
HNRNPC 0.024 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.005 0.043 -10000 0 -0.36 8 8
NBN 0.01 0.074 -10000 0 -0.44 15 15
EGFR 0.018 0.044 -10000 0 -0.44 5 5
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.007 0.13 -10000 0 -0.32 78 78
MYC 0.016 0.045 -10000 0 -0.45 5 5
IL2 0.017 0.018 -10000 0 -10000 0 0
KU 0.036 0.017 -10000 0 -0.32 1 1
RAD50 0.024 0.02 -10000 0 -0.44 1 1
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
TGFB1 0.017 0.064 -10000 0 -0.44 11 11
TRF2/BLM 0.034 0.033 -10000 0 -0.3 5 5
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.03 0.26 0.37 1 -1 32 33
SP1/HDAC2 0.035 0.028 -10000 0 -0.32 1 1
PINX1 0.016 0.044 -10000 0 -0.44 5 5
Telomerase/EST1A -0.027 0.23 -10000 0 -0.89 32 32
Smad3/Myc 0.012 0.047 -10000 0 -0.27 14 14
911 complex 0.046 0.022 -10000 0 -0.27 1 1
IFNG 0 0.12 -10000 0 -0.43 38 38
Telomerase/PinX1 -0.034 0.23 -10000 0 -0.89 33 33
Telomerase/AKT1/mTOR/p70S6K -0.009 0.11 0.27 1 -0.48 14 15
SIN3B 0.025 0.02 -10000 0 -0.44 1 1
YWHAE 0.022 0.01 -10000 0 -10000 0 0
Telomerase/EST1B -0.023 0.23 -10000 0 -0.85 35 35
response to DNA damage stimulus 0 0.023 -10000 0 -0.11 25 25
MRN complex/TRF2/Rap1 0.049 0.071 -10000 0 -0.3 18 18
TRF2/WRN 0.028 0.025 -10000 0 -0.29 2 2
Telomerase/hnRNP C1/C2 -0.023 0.23 -10000 0 -0.9 32 32
E2F1 0.013 0.025 -10000 0 -0.44 1 1
ZNFX1 0.015 0.013 -10000 0 -10000 0 0
PIF1 0.022 0.039 -10000 0 -0.44 4 4
NCL 0.026 0.002 -10000 0 -10000 0 0
DKC1 0.026 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.04 0.069 -10000 0 -0.23 30 30
TC10/GTP 0.029 0.056 -10000 0 -0.22 24 24
Insulin Receptor/Insulin/IRS1/Shp2 0.065 0.058 -10000 0 -0.24 16 16
HRAS 0.025 0.02 -10000 0 -0.44 1 1
APS homodimer 0.017 0.068 -10000 0 -0.44 12 12
GRB14 -0.048 0.18 -10000 0 -0.44 94 94
FOXO3 -0.002 0.12 -10000 0 -0.65 18 18
AKT1 -0.037 0.09 0.22 4 -10000 0 4
INSR 0.036 0.024 -10000 0 -0.42 1 1
Insulin Receptor/Insulin 0.073 0.073 0.25 1 -0.22 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.02 0.039 -10000 0 -0.44 4 4
SORBS1 0.017 0.068 -10000 0 -0.44 12 12
CRK 0.022 0.01 -10000 0 -10000 0 0
PTPN1 -0.001 0.03 0.3 1 -10000 0 1
CAV1 0.006 0.058 0.17 22 -0.23 15 37
CBL/APS/CAP/Crk-II/C3G 0.049 0.068 -10000 0 -0.23 24 24
Insulin Receptor/Insulin/IRS1/NCK2 0.067 0.053 -10000 0 -0.25 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.049 0.049 -10000 0 -0.22 15 15
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.054 0.078 -10000 0 -0.33 7 7
RPS6KB1 -0.044 0.083 0.2 4 -0.31 2 6
PARD6A 0.026 0.021 -10000 0 -0.44 1 1
CBL 0.025 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.01 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.014 0.095 0.17 2 -0.28 3 5
HRAS/GTP -0.017 0.057 -10000 0 -0.22 30 30
Insulin Receptor 0.036 0.024 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.074 0.053 -10000 0 -0.23 11 11
PRKCI 0.01 0.073 -10000 0 -0.45 9 9
Insulin Receptor/Insulin/GRB14/PDK1 -0.014 0.097 -10000 0 -0.22 87 87
SHC1 0.025 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.038 0.036 -10000 0 -0.36 1 1
PI3K 0.06 0.053 -10000 0 -0.22 15 15
NCK2 0.025 0.019 -10000 0 -0.44 1 1
RHOQ 0.026 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.32 1 1
AKT2 -0.038 0.089 0.21 3 -10000 0 3
PRKCZ 0.001 0.09 -10000 0 -0.44 11 11
SH2B2 0.017 0.068 -10000 0 -0.44 12 12
SHC/SHIP 0.025 0.072 0.19 11 -0.22 36 47
F2RL2 -0.004 0.12 -10000 0 -0.44 37 37
TRIP10 0.025 0.02 -10000 0 -0.44 1 1
Insulin Receptor/Insulin/Shc 0.055 0.03 -10000 0 -0.22 2 2
TC10/GTP/CIP4/Exocyst 0.034 0.014 -10000 0 -0.27 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.079 0.037 -10000 0 -0.21 2 2
RAPGEF1 0.025 0.02 -10000 0 -0.44 1 1
RASA1 0.024 0.028 -10000 0 -0.44 2 2
NCK1 0.024 0.028 -10000 0 -0.44 2 2
CBL/APS/CAP/Crk-II 0.042 0.065 -10000 0 -0.24 23 23
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.061 0.045 -10000 0 -0.23 6 6
INPP5D -0.001 0.074 0.17 23 -0.23 36 59
SOS1 0.026 0.002 -10000 0 -10000 0 0
SGK1 -0.003 0.11 -10000 0 -0.71 13 13
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
IRS1 0.019 0.058 -10000 0 -0.44 9 9
p62DOK/RasGAP 0.039 0.037 -10000 0 -0.37 1 1
INS 0.027 0.026 -10000 0 -0.45 1 1
mol:PI-3-4-P2 -0.001 0.073 0.17 23 -0.23 36 59
GRB2 0.025 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.039 0.079 0.18 4 -0.32 2 6
PTPRA 0.027 0.016 -10000 0 -10000 0 0
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
TC10/GTP/CIP4 0.034 0.014 -10000 0 -0.27 1 1
PDPK1 0.026 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.026 0.04 -10000 0 -0.22 10 10
Insulin Receptor/Insulin/IRS1 0.052 0.047 -10000 0 -0.24 11 11
Insulin Receptor/Insulin/IRS3 0.048 0.033 -10000 0 -0.3 2 2
Par3/Par6 0.04 0.075 -10000 0 -0.24 37 37
Regulation of Androgen receptor activity

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
HDAC1 -0.012 0.013 -10000 0 -0.32 1 1
SMARCC1 0.01 0.016 -10000 0 -10000 0 0
REL 0.025 0.034 -10000 0 -0.44 3 3
HDAC7 -0.029 0.071 -10000 0 -0.39 9 9
JUN 0.021 0.039 -10000 0 -0.44 4 4
EP300 0.023 0.028 -10000 0 -0.44 2 2
KAT2B 0.012 0.077 -10000 0 -0.44 16 16
KAT5 0.025 0.02 -10000 0 -0.44 1 1
MAPK14 -0.003 0.044 -10000 0 -0.34 9 9
FOXO1 0.019 0.022 -10000 0 -0.44 1 1
T-DHT/AR 0.006 0.087 -10000 0 -0.37 12 12
MAP2K6 0.014 0.064 -10000 0 -0.46 10 10
BRM/BAF57 0.027 0.04 -10000 0 -0.33 5 5
MAP2K4 0.019 0.015 -10000 0 -10000 0 0
SMARCA2 0.017 0.042 -10000 0 -0.45 4 4
PDE9A -0.077 0.29 -10000 0 -0.83 66 66
NCOA2 0.018 0.048 -10000 0 -0.44 6 6
CEBPA 0.013 0.077 -10000 0 -0.44 16 16
EHMT2 0.022 0.022 -10000 0 -0.44 1 1
cell proliferation 0.035 0.14 0.32 23 -0.41 17 40
NR0B1 -0.001 0.024 -10000 0 -10000 0 0
EGR1 0.017 0.058 -10000 0 -0.45 8 8
RXRs/9cRA 0.04 0.033 -10000 0 -0.25 2 2
AR/RACK1/Src 0.051 0.1 0.26 10 -0.32 9 19
AR/GR -0.007 0.08 0.23 1 -0.25 43 44
GNB2L1 0.026 0.005 -10000 0 -10000 0 0
PKN1 0.023 0.034 -10000 0 -0.44 3 3
RCHY1 0.025 0.02 -10000 0 -0.44 1 1
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0.002 0.02 -10000 0 -0.33 1 1
T-DHT/AR/TIF2/CARM1 0.005 0.069 -10000 0 -0.32 13 13
SRC -0.012 0.047 0.19 9 -0.29 10 19
NR3C1 0.013 0.08 -10000 0 -0.44 17 17
KLK3 -0.14 0.35 -10000 0 -1.1 61 61
APPBP2 0.019 0.041 -10000 0 -0.44 4 4
TRIM24 0.021 0.016 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.007 0.064 0.24 3 -0.35 9 12
TMPRSS2 -0.024 0.16 -10000 0 -0.59 34 34
RXRG 0.014 0.032 -10000 0 -0.44 1 1
mol:9cRA -0.001 0.002 -10000 0 -0.011 1 1
RXRA 0.025 0.02 -10000 0 -0.44 1 1
RXRB 0.025 0.004 -10000 0 -10000 0 0
CARM1 0.025 0.02 -10000 0 -0.45 1 1
NR2C2 0.025 0.02 -10000 0 -0.44 1 1
KLK2 0.029 0.074 0.28 2 -0.35 5 7
AR -0.009 0.061 0.15 3 -0.25 30 33
SENP1 0.025 0.02 -10000 0 -0.44 1 1
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
MDM2 0.027 0.029 -10000 0 -0.44 2 2
SRY 0.002 0.009 0.029 54 -10000 0 54
GATA2 0.007 0.094 -10000 0 -0.44 24 24
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.001 0.12 -10000 0 -0.39 45 45
T-DHT/AR/RACK1/Src 0.057 0.11 0.3 11 -0.32 9 20
positive regulation of transcription 0.007 0.094 -10000 0 -0.44 24 24
DNAJA1 0.023 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.034 -10000 0 -0.4 3 3
NCOA1 0.024 0.027 -10000 0 -0.48 1 1
SPDEF -0.052 0.18 -10000 0 -0.44 105 105
T-DHT/AR/TIF2 -0.007 0.1 0.28 5 -0.46 13 18
T-DHT/AR/Hsp90 -0.007 0.061 0.34 1 -0.33 10 11
GSK3B 0.024 0.028 -10000 0 -0.45 2 2
NR2C1 0.025 0.02 -10000 0 -0.44 1 1
mol:T-DHT -0.019 0.041 -10000 0 -0.31 9 9
SIRT1 0.022 0.039 -10000 0 -0.44 4 4
ZMIZ2 0.025 0.023 -10000 0 -0.44 1 1
POU2F1 0.02 0.062 -10000 0 -0.41 8 8
T-DHT/AR/DAX-1 -0.018 0.059 0.33 1 -0.33 9 10
CREBBP 0.025 0.004 -10000 0 -10000 0 0
SMARCE1 0.02 0.025 -10000 0 -0.44 1 1
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.025 0.02 -9999 0 -0.44 1 1
SPHK1 0.014 0.083 -9999 0 -0.44 18 18
GNAI2 0.026 0.003 -9999 0 -10000 0 0
mol:S1P 0.003 0.049 -9999 0 -0.26 20 20
GNAO1 0.016 0.087 -9999 0 -0.44 19 19
mol:Sphinganine-1-P -0.024 0.056 -9999 0 -0.32 19 19
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.039 0.053 -9999 0 -0.2 20 20
GNAI3 0.025 0.004 -9999 0 -10000 0 0
G12/G13 0.033 0.024 -9999 0 -0.32 2 2
S1PR3 0.023 0.039 -9999 0 -0.44 4 4
S1PR2 0.026 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.044 -9999 0 -0.21 22 22
S1PR5 0.021 0.052 -9999 0 -0.44 7 7
S1PR4 0.009 0.093 -9999 0 -0.44 23 23
GNAI1 0.016 0.064 -9999 0 -0.44 11 11
S1P/S1P5/G12 0.026 0.056 -9999 0 -0.21 24 24
S1P/S1P3/Gq 0.005 0.092 -9999 0 -0.36 23 23
S1P/S1P4/Gi -0.011 0.11 -9999 0 -0.39 25 25
GNAQ 0.022 0.043 -9999 0 -0.44 5 5
GNAZ 0.014 0.073 -9999 0 -0.44 14 14
GNA14 0.014 0.075 -9999 0 -0.44 15 15
GNA15 0.015 0.073 -9999 0 -0.44 14 14
GNA12 0.024 0.008 -9999 0 -10000 0 0
GNA13 0.024 0.028 -9999 0 -0.44 2 2
GNA11 0.023 0.034 -9999 0 -0.44 3 3
ABCC1 0.025 0.02 -9999 0 -0.44 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.025 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.032 0.068 -10000 0 -0.27 25 25
forebrain development -0.012 0.14 0.36 2 -0.5 29 31
GNAO1 0.016 0.087 -10000 0 -0.44 19 19
SMO/beta Arrestin2 0.02 0.066 -10000 0 -0.32 20 20
SMO 0.009 0.086 -10000 0 -0.44 20 20
ARRB2 0.022 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.035 0.1 0.25 2 -0.51 7 9
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.024 0.028 -10000 0 -0.44 2 2
GNAI2 0.025 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.046 0.039 -10000 0 -0.25 4 4
GNAI1 0.016 0.064 -10000 0 -0.44 11 11
XPO1 0.017 0.065 -10000 0 -0.44 11 11
GLI1/Su(fu) -0.018 0.14 -10000 0 -0.58 18 18
SAP30 0.023 0.028 -10000 0 -0.44 2 2
mol:GDP 0.009 0.086 -10000 0 -0.44 20 20
MIM/GLI2A 0.016 0.064 -10000 0 -0.32 16 16
IFT88 0.017 0.04 -10000 0 -0.44 4 4
GNAI3 0.025 0.006 -10000 0 -10000 0 0
GLI2 -0.004 0.076 -10000 0 -0.31 19 19
GLI3 0.026 0.11 0.26 5 -0.54 7 12
CSNK1D 0.026 0.004 -10000 0 -10000 0 0
CSNK1E 0.025 0.005 -10000 0 -10000 0 0
SAP18 0.02 0.011 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.017 0.04 -10000 0 -0.44 4 4
GNG2 0.021 0.044 -10000 0 -0.44 5 5
Gi family/GTP -0.009 0.1 -10000 0 -0.32 37 37
SIN3B 0.025 0.02 -10000 0 -0.44 1 1
SIN3A 0.024 0.02 -10000 0 -0.44 1 1
GLI3/Su(fu) 0.026 0.094 0.35 1 -0.42 10 11
GLI2/Su(fu) -0.002 0.088 -10000 0 -0.34 23 23
FOXA2 -0.018 0.19 -10000 0 -0.75 31 31
neural tube patterning -0.012 0.14 0.36 2 -0.5 29 31
SPOP 0.025 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.016 0.055 -10000 0 -0.36 2 2
GNB1 0.025 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.028 -10000 0 -0.44 2 2
CSNK1G3 0.024 0.02 -10000 0 -0.44 1 1
MTSS1 0.016 0.064 -10000 0 -0.32 16 16
embryonic limb morphogenesis -0.012 0.14 0.36 2 -0.5 29 31
SUFU 0.01 0.042 -10000 0 -0.29 4 4
LGALS3 0.024 0.021 -10000 0 -0.44 1 1
catabolic process 0.029 0.12 0.24 1 -0.38 28 29
GLI3A/CBP 0.02 0.062 -10000 0 -0.33 17 17
KIF3A 0.017 0.061 -10000 0 -0.44 10 10
GLI1 -0.013 0.14 0.36 2 -0.52 29 31
RAB23 0.023 0.039 -10000 0 -0.44 4 4
CSNK1A1 0.024 0.028 -10000 0 -0.44 2 2
IFT172 0.026 0 -10000 0 -10000 0 0
RBBP7 0.025 0.02 -10000 0 -0.44 1 1
Su(fu)/Galectin3 0.017 0.056 -10000 0 -0.32 3 3
GNAZ 0.014 0.073 -10000 0 -0.44 14 14
RBBP4 0.024 0.02 -10000 0 -0.44 1 1
CSNK1G1 0.024 0.02 -10000 0 -0.44 1 1
PIAS1 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.01 0.076 -10000 0 -0.3 19 19
STK36 0.026 0.009 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.01 0.1 -10000 0 -0.43 20 20
PTCH1 -0.016 0.16 0.38 1 -0.82 14 15
MIM/GLI1 -0.006 0.15 0.39 1 -0.56 27 28
CREBBP 0.02 0.062 -10000 0 -0.33 17 17
Su(fu)/SIN3/HDAC complex 0.017 0.081 -10000 0 -0.31 22 22
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.095 0.17 -9999 0 -0.4 96 96
CaM/Ca2+ 0.018 0.005 -9999 0 -10000 0 0
AKT1 0.024 0.02 -9999 0 -0.44 1 1
AKT2 0.025 0.02 -9999 0 -0.44 1 1
STXBP4 0.021 0.048 -9999 0 -0.44 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.11 0.17 -9999 0 -0.42 99 99
YWHAZ 0.021 0.029 -9999 0 -0.44 2 2
CALM1 0.024 0.007 -9999 0 -10000 0 0
YWHAQ 0.026 0.002 -9999 0 -10000 0 0
TBC1D4 -0.011 0.029 -9999 0 -0.32 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.025 0.005 -9999 0 -10000 0 0
YWHAB 0.015 0.013 -9999 0 -10000 0 0
SNARE/Synip 0.04 0.037 -9999 0 -0.26 6 6
YWHAG 0.025 0.005 -9999 0 -10000 0 0
ASIP 0.003 0.018 -9999 0 -10000 0 0
PRKCI 0.023 0.034 -9999 0 -0.44 3 3
AS160/CaM/Ca2+ 0.018 0.005 -9999 0 -10000 0 0
RHOQ 0.026 0.002 -9999 0 -10000 0 0
GYS1 0.005 0.032 -9999 0 -0.34 4 4
PRKCZ 0.024 0.02 -9999 0 -0.44 1 1
TRIP10 0.025 0.02 -9999 0 -0.44 1 1
TC10/GTP/CIP4/Exocyst 0.034 0.014 -9999 0 -0.27 1 1
AS160/14-3-3 0.008 0.048 -9999 0 -0.29 6 6
VAMP2 0.022 0.01 -9999 0 -10000 0 0
SLC2A4 -0.13 0.2 -9999 0 -0.48 99 99
STX4 0.026 0.003 -9999 0 -10000 0 0
GSK3B 0.015 0.034 -9999 0 -0.42 3 3
SFN 0.024 0.022 -9999 0 -0.44 1 1
LNPEP 0.021 0.044 -9999 0 -0.44 5 5
YWHAE 0.022 0.01 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0.013 -10000 0 -10000 0 0
NFATC1 -0.035 0.14 0.3 3 -0.4 40 43
NFATC2 0.021 0.063 0.16 4 -0.22 14 18
NFATC3 0.016 0.017 -10000 0 -0.35 1 1
YWHAE 0.022 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.048 0.13 0.2 5 -0.39 48 53
Exportin 1/Ran/NUP214 0.046 0.043 -10000 0 -0.27 10 10
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.024 0.14 0.23 1 -0.36 54 55
BCL2/BAX 0.024 0.044 -10000 0 -0.32 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.018 0.005 -10000 0 -10000 0 0
BAX 0.025 0.02 -10000 0 -0.44 1 1
MAPK14 0.026 0.003 -10000 0 -10000 0 0
BAD 0.025 0.02 -10000 0 -0.44 1 1
CABIN1/MEF2D -0.036 0.13 0.22 2 -0.38 47 49
Calcineurin A alpha-beta B1/BCL2 0.014 0.052 -10000 0 -0.44 7 7
FKBP8 0.024 0.028 -10000 0 -0.44 2 2
activation-induced cell death of T cells 0.035 0.13 0.38 47 -0.22 2 49
KPNB1 0.025 0.004 -10000 0 -10000 0 0
KPNA2 0.025 0.005 -10000 0 -10000 0 0
XPO1 0.017 0.064 -10000 0 -0.44 11 11
SFN 0.024 0.022 -10000 0 -0.44 1 1
MAP3K8 0.025 0.02 -10000 0 -0.44 1 1
NFAT4/CK1 alpha 0.02 0.04 -10000 0 -0.3 6 6
MEF2D/NFAT1/Cbp/p300 0.055 0.079 -10000 0 -0.39 5 5
CABIN1 -0.049 0.13 0.18 4 -0.4 47 51
CALM1 0.024 0.007 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
MAP3K1 0.021 0.044 -10000 0 -0.44 5 5
CAMK4 0.013 0.075 -10000 0 -0.44 15 15
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.025 0.02 -10000 0 -0.44 1 1
YWHAH 0.025 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.028 0.058 -10000 0 -0.32 15 15
YWHAB 0.015 0.013 -10000 0 -10000 0 0
MAPK8 0.025 0.02 -10000 0 -0.44 1 1
MAPK9 0.026 0.003 -10000 0 -10000 0 0
YWHAG 0.025 0.005 -10000 0 -10000 0 0
FKBP1A 0.021 0.01 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.011 0.13 0.42 1 -0.38 35 36
PRKCH 0.02 0.044 -10000 0 -0.44 5 5
CABIN1/Cbp/p300 0.035 0.023 -10000 0 -0.32 2 2
CASP3 0.024 0.006 -10000 0 -10000 0 0
PIM1 0.026 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.007 -10000 0 -10000 0 0
apoptosis 0.008 0.027 0.19 1 -0.52 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.027 0.052 -10000 0 -0.35 4 4
PRKCB -0.002 0.12 -10000 0 -0.44 37 37
PRKCE 0.026 0.002 -10000 0 -10000 0 0
JNK2/NFAT4 0.021 0.04 -10000 0 -0.32 1 1
BAD/BCL-XL 0.022 0.024 -10000 0 -0.32 1 1
PRKCD 0.026 0.004 -10000 0 -10000 0 0
NUP214 0.026 0.003 -10000 0 -10000 0 0
PRKCZ 0.024 0.021 -10000 0 -0.45 1 1
PRKCA 0.024 0.02 -10000 0 -0.44 1 1
PRKCG -0.026 0.16 -10000 0 -0.44 76 76
PRKCQ -0.016 0.13 -10000 0 -0.44 52 52
FKBP38/BCL2 0.023 0.047 -10000 0 -0.32 9 9
EP300 0.023 0.028 -10000 0 -0.44 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.021 0.01 -10000 0 -10000 0 0
NFATc/JNK1 -0.022 0.14 0.41 1 -0.38 39 40
CaM/Ca2+/FKBP38 0.032 0.02 -10000 0 -0.27 2 2
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSNK1A1 0.009 0.018 -10000 0 -0.27 2 2
CaM/Ca2+/CAMK IV 0.024 0.049 -10000 0 -0.26 15 15
NFATc/ERK1 -0.023 0.13 0.41 1 -0.39 38 39
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.14 0.23 1 -0.36 55 56
NR4A1 0.023 0.072 0.26 3 -0.44 4 7
GSK3B 0.024 0.028 -10000 0 -0.44 2 2
positive T cell selection 0.016 0.016 -10000 0 -0.35 1 1
NFAT1/CK1 alpha 0.02 0.052 0.15 1 -0.22 8 9
RCH1/ KPNB1 0.037 0.007 -10000 0 -10000 0 0
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
AKAP5 0.014 0.076 -10000 0 -0.44 15 15
MEF2D 0.025 0.02 -10000 0 -0.45 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.021 0.029 -10000 0 -0.44 2 2
NFATc/p38 alpha -0.023 0.14 0.41 1 -0.38 40 41
CREBBP 0.026 0.004 -10000 0 -10000 0 0
BCL2 0.014 0.052 -10000 0 -0.44 7 7
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.017 0.034 -10000 0 -0.23 10 10
epithelial cell differentiation 0.052 0.024 -10000 0 -0.23 3 3
CYFIP2 0.017 0.061 -10000 0 -0.44 10 10
ENAH -0.025 0.049 0.26 2 -0.39 4 6
EGFR 0.02 0.044 -10000 0 -0.44 5 5
EPHA2 0.023 0.028 -10000 0 -0.44 2 2
MYO6 -0.016 0.021 0.17 3 -0.23 3 6
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.044 0.051 -10000 0 -0.29 12 12
AQP5 -0.01 0.094 -10000 0 -0.45 24 24
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.016 0.025 0.17 5 -0.22 4 9
regulation of calcium-dependent cell-cell adhesion -0.03 0.059 0.18 5 -0.23 40 45
EGF -0.031 0.17 -10000 0 -0.44 84 84
NCKAP1 0.024 0.028 -10000 0 -0.44 2 2
AQP3 0.003 0.057 -10000 0 -0.44 8 8
cortical microtubule organization 0.052 0.024 -10000 0 -0.23 3 3
GO:0000145 -0.015 0.024 0.16 5 -0.21 4 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.057 0.026 -10000 0 -0.24 3 3
MLLT4 0.025 0.02 -10000 0 -0.44 1 1
ARF6/GDP -0.027 0.029 -10000 0 -0.39 2 2
ARF6 0.024 0.02 -10000 0 -0.44 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.038 -10000 0 -0.3 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.005 0.02 0.17 1 -0.23 1 2
PVRL2 0.025 0.02 -10000 0 -0.44 1 1
ZYX -0.017 0.02 0.17 1 -0.23 4 5
ARF6/GTP 0.06 0.044 -10000 0 -0.34 4 4
CDH1 0.025 0.02 -10000 0 -0.44 1 1
EGFR/EGFR/EGF/EGF 0.008 0.097 -10000 0 -0.22 81 81
RhoA/GDP 0.052 0.027 -10000 0 -0.23 4 4
actin cytoskeleton organization -0.017 0.022 0.16 2 -0.22 5 7
IGF-1R heterotetramer 0.024 0.02 -10000 0 -0.44 1 1
GIT1 0.024 0.02 -10000 0 -0.44 1 1
IGF1R 0.024 0.02 -10000 0 -0.44 1 1
IGF1 -0.011 0.14 -10000 0 -0.44 52 52
DIAPH1 0.025 0.13 -10000 0 -0.58 24 24
Wnt receptor signaling pathway -0.052 0.024 0.23 3 -10000 0 3
RHOA 0.025 0.02 -10000 0 -0.44 1 1
RhoA/GTP -0.028 0.029 -10000 0 -0.26 7 7
CTNNA1 0.024 0.028 -10000 0 -0.44 2 2
VCL -0.018 0.022 0.16 2 -0.22 5 7
EFNA1 0.025 0.004 -10000 0 -10000 0 0
LPP -0.018 0.025 0.16 5 -0.22 4 9
Ephrin A1/EPHA2 0.043 0.031 -10000 0 -0.22 5 5
SEC6/SEC8 -0.024 0.02 -10000 0 -0.22 5 5
MGAT3 -0.03 0.06 0.18 5 -0.23 40 45
HGF/MET 0.03 0.066 -10000 0 -0.22 35 35
HGF 0.001 0.11 -10000 0 -0.44 32 32
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.017 0.034 -10000 0 -0.23 10 10
actin cable formation -0.01 0.072 0.23 16 -0.31 9 25
KIAA1543 -0.015 0.024 0.16 5 -0.22 4 9
KIFC3 -0.019 0.028 0.17 1 -0.23 9 10
NCK1 0.024 0.028 -10000 0 -0.44 2 2
EXOC3 0.025 0.004 -10000 0 -10000 0 0
ACTN1 -0.015 0.024 0.17 5 -0.23 3 8
NCK1/GIT1 0.035 0.027 -10000 0 -0.32 3 3
mol:GDP 0.052 0.024 -10000 0 -0.23 3 3
EXOC4 0.025 0.006 -10000 0 -10000 0 0
STX4 -0.016 0.02 0.17 2 -0.23 3 5
PIP5K1C -0.016 0.026 0.17 5 -0.23 4 9
LIMA1 0.02 0.051 -10000 0 -0.44 7 7
ABI1 0.025 0.02 -10000 0 -0.44 1 1
ROCK1 -0.02 0.051 0.28 4 -0.43 2 6
adherens junction assembly -0.007 0.058 0.27 4 -0.4 6 10
IGF-1R heterotetramer/IGF1 0.023 0.081 -10000 0 -0.23 53 53
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.022 -10000 0 -0.32 2 2
MET 0.024 0.02 -10000 0 -0.44 1 1
PLEKHA7 -0.016 0.026 0.17 5 -0.23 4 9
mol:GTP 0.055 0.038 -10000 0 -0.3 4 4
establishment of epithelial cell apical/basal polarity -0.016 0.052 0.31 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.017 0.034 -10000 0 -0.23 10 10
regulation of cell-cell adhesion -0.017 0.022 0.16 2 -0.22 5 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.017 0.034 -10000 0 -0.23 10 10
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 0.016 0.063 -10000 0 -0.44 10 10
CLTC -0.003 0.1 0.22 1 -0.4 33 34
calcium ion-dependent exocytosis 0.007 0.05 -10000 0 -0.37 3 3
Dynamin 2/GTP 0.022 0.017 -10000 0 -0.25 2 2
EXOC4 0.025 0.006 -10000 0 -10000 0 0
CD59 -0.003 0.083 -10000 0 -0.34 30 30
CPE -0.018 0.079 -10000 0 -0.27 50 50
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
membrane fusion 0.014 0.031 -10000 0 -0.38 1 1
CTNND1 -0.012 0.026 0.18 8 -0.23 2 10
DNM2 0.025 0.02 -10000 0 -0.44 1 1
mol:PI-4-5-P2 0.001 0.064 -10000 0 -0.26 25 25
TSHR 0.001 0.023 -10000 0 -0.29 2 2
INS 0.004 0.052 -10000 0 -0.52 5 5
BIN1 0.022 0.043 -10000 0 -0.44 5 5
mol:Choline 0.014 0.031 -10000 0 -0.38 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.012 -10000 0 -0.27 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.02 -10000 0 -0.44 1 1
mol:Ca2+ 0.021 0.017 -10000 0 -0.24 2 2
JUP -0.004 0.082 -10000 0 -0.34 30 30
ASAP2/amphiphysin II 0.043 0.036 -10000 0 -0.25 8 8
ARF6/GTP 0.018 0.015 -10000 0 -0.32 1 1
CDH1 -0.004 0.082 -10000 0 -0.34 30 30
clathrin-independent pinocytosis 0.017 0.015 -10000 0 -0.32 1 1
MAPK8IP3 0.024 0.034 -10000 0 -0.44 3 3
positive regulation of endocytosis 0.017 0.015 -10000 0 -0.32 1 1
EXOC2 0.025 0.02 -10000 0 -0.44 1 1
substrate adhesion-dependent cell spreading 0.004 0.071 -10000 0 -0.41 8 8
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.025 0.02 -10000 0 -0.44 1 1
regulation of calcium-dependent cell-cell adhesion -0.018 0.089 0.32 33 -10000 0 33
positive regulation of phagocytosis 0.01 0.012 -10000 0 -0.27 1 1
ARF6/GTP/JIP3 0.031 0.027 -10000 0 -0.27 4 4
ACAP1 0.013 0.038 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.016 0.093 -10000 0 -0.35 30 30
clathrin heavy chain/ACAP1 -0.001 0.088 0.23 2 -0.34 31 33
JIP4/KLC1 0.045 0.023 -10000 0 -0.25 2 2
EXOC1 0.024 0.02 -10000 0 -0.44 1 1
exocyst 0.001 0.07 -10000 0 -0.42 8 8
RALA/GTP 0.017 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.031 0.02 -10000 0 -0.27 2 2
receptor recycling 0.017 0.015 -10000 0 -0.32 1 1
CTNNA1 -0.012 0.029 0.18 8 -0.24 4 12
NME1 0.01 0.012 -10000 0 -0.27 1 1
clathrin coat assembly -0.003 0.1 0.22 1 -0.39 34 35
IL2RA -0.016 0.097 -10000 0 -0.36 31 31
VAMP3 0.01 0.012 -10000 0 -0.27 1 1
GLUT4/clathrin heavy chain/ACAP1 0.006 0.091 -10000 0 -0.31 32 32
EXOC6 0.022 0.034 -10000 0 -0.44 3 3
PLD1 0.008 0.023 -10000 0 -0.47 1 1
PLD2 0.009 0.01 -10000 0 -0.14 1 1
EXOC5 0.013 0.072 -10000 0 -0.44 14 14
PIP5K1C 0.004 0.057 -10000 0 -0.24 22 22
SDC1 -0.004 0.082 -10000 0 -0.34 30 30
ARF6/GDP 0.021 0.014 -10000 0 -0.27 1 1
EXOC7 0.025 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.019 0.092 -10000 0 -0.34 31 31
mol:Phosphatidic acid 0.014 0.031 -10000 0 -0.38 1 1
endocytosis -0.041 0.036 0.25 8 -10000 0 8
SCAMP2 0.025 0.005 -10000 0 -10000 0 0
ADRB2 -0.018 0.11 0.38 1 -0.39 35 36
EXOC3 0.025 0.004 -10000 0 -10000 0 0
ASAP2 0.024 0.028 -10000 0 -0.44 2 2
Dynamin 2/GDP 0.025 0.018 -10000 0 -0.25 2 2
KLC1 0.024 0.006 -10000 0 -10000 0 0
AVPR2 -0.015 0.11 0.28 5 -0.38 33 38
RALA 0.024 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.012 0.087 -10000 0 -0.32 30 30
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.023 0.03 -10000 0 -0.44 2 2
HSPA8 0.024 0.028 -10000 0 -0.44 2 2
SMAD3/SMAD4/ER alpha 0.023 0.085 0.23 2 -0.28 25 27
AKT1 0.022 0.027 -10000 0 -0.3 2 2
GSC -0.013 0.14 -10000 0 -1.2 5 5
NKX2-5 0.02 0.02 -10000 0 -0.12 2 2
muscle cell differentiation 0.028 0.12 0.34 20 -10000 0 20
SMAD2-3/SMAD4/SP1 0.043 0.084 -10000 0 -0.28 12 12
SMAD4 0.015 0.037 -10000 0 -0.18 1 1
CBFB 0.023 0.034 -10000 0 -0.44 3 3
SAP18 0.02 0.011 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.039 0.075 -10000 0 -0.27 28 28
SMAD3/SMAD4/VDR 0.049 0.066 -10000 0 -0.36 2 2
MYC 0.018 0.046 -10000 0 -0.45 5 5
CDKN2B -0.029 0.22 -10000 0 -1.3 15 15
AP1 0.014 0.073 -10000 0 -0.37 10 10
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.022 0.12 -10000 0 -0.37 40 40
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.033 0.11 -10000 0 -0.35 39 39
SP3 0.026 0.019 -10000 0 -0.44 1 1
CREB1 0.024 0.028 -10000 0 -0.44 2 2
FOXH1 0.005 0.097 -10000 0 -0.44 25 25
SMAD3/SMAD4/GR 0.023 0.077 -10000 0 -0.3 15 15
GATA3 0.004 0.089 -10000 0 -0.45 17 17
SKI/SIN3/HDAC complex/NCoR1 0.011 0.075 -10000 0 -0.31 16 16
MEF2C/TIF2 0.003 0.083 -10000 0 -0.35 10 10
endothelial cell migration 0.006 0.18 1.2 12 -10000 0 12
MAX 0.024 0.009 -10000 0 -10000 0 0
RBBP7 0.025 0.02 -10000 0 -0.44 1 1
RBBP4 0.024 0.02 -10000 0 -0.44 1 1
RUNX2 0.017 0.067 -10000 0 -0.44 12 12
RUNX3 0.017 0.071 -10000 0 -0.44 13 13
RUNX1 0.025 0.006 -10000 0 -10000 0 0
CTBP1 0.024 0.02 -10000 0 -0.44 1 1
NR3C1 0.012 0.078 -10000 0 -0.43 17 17
VDR 0.025 0.02 -10000 0 -0.44 1 1
CDKN1A -0.003 0.11 -10000 0 -1.1 4 4
KAT2B 0.012 0.077 -10000 0 -0.45 16 16
SMAD2/SMAD2/SMAD4/FOXH1 0.018 0.08 -10000 0 -0.27 28 28
DCP1A 0.026 0.004 -10000 0 -10000 0 0
SKI 0.025 0.005 -10000 0 -10000 0 0
SERPINE1 -0.006 0.18 -10000 0 -1.2 12 12
SMAD3/SMAD4/ATF2 0.03 0.059 -10000 0 -0.26 4 4
SMAD3/SMAD4/ATF3 0.031 0.059 -10000 0 -0.26 3 3
SAP30 0.023 0.028 -10000 0 -0.44 2 2
Cbp/p300/PIAS3 0.045 0.033 -10000 0 -0.27 3 3
JUN -0.001 0.066 -10000 0 -0.37 10 10
SMAD3/SMAD4/IRF7 0.029 0.063 -10000 0 -0.3 5 5
TFE3 0.027 0.015 -10000 0 -10000 0 0
COL1A2 -0.014 0.17 -10000 0 -0.83 24 24
mesenchymal cell differentiation -0.025 0.07 0.26 14 -10000 0 14
DLX1 0.02 0.046 -10000 0 -0.44 3 3
TCF3 0.025 0.02 -10000 0 -0.44 1 1
FOS 0.009 0.084 -10000 0 -0.45 17 17
SMAD3/SMAD4/Max 0.031 0.057 -10000 0 -0.22 2 2
Cbp/p300/SNIP1 0.047 0.026 -10000 0 -0.27 2 2
ZBTB17 0.024 0.022 -10000 0 -0.45 1 1
LAMC1 0.005 0.038 0.2 2 -10000 0 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.018 0.053 -10000 0 -0.28 6 6
IRF7 0.022 0.04 -10000 0 -0.38 5 5
ESR1 -0.001 0.095 0.17 1 -0.42 25 26
HNF4A 0.009 0.052 -10000 0 -0.44 7 7
MEF2C 0.001 0.088 0.2 1 -0.31 14 15
SMAD2-3/SMAD4 0.032 0.062 -10000 0 -0.25 3 3
Cbp/p300/Src-1 0.047 0.033 -10000 0 -0.39 2 2
IGHV3OR16-13 0.005 0.044 -10000 0 -0.7 2 2
TGIF2/HDAC complex 0.011 0.044 -10000 0 -0.44 5 5
CREBBP 0.025 0.009 -10000 0 -10000 0 0
SKIL 0.017 0.064 -10000 0 -0.44 11 11
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.025 0.004 -10000 0 -10000 0 0
SNIP1 0.025 0.005 -10000 0 -10000 0 0
GCN5L2 0 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.035 0.058 -10000 0 -0.23 1 1
MSG1/HSC70 0.027 0.08 -10000 0 -0.32 28 28
SMAD2 0.018 0.029 -10000 0 -0.44 1 1
SMAD3 0.016 0.042 -10000 0 -0.2 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.002 0.053 -10000 0 -0.25 9 9
SMAD2/SMAD2/SMAD4 -0.055 0.12 -10000 0 -0.33 55 55
NCOR1 0.022 0.01 -10000 0 -10000 0 0
NCOA2 0.018 0.048 -10000 0 -0.44 6 6
NCOA1 0.025 0.019 -10000 0 -0.44 1 1
MYOD/E2A 0.031 0.016 -10000 0 -0.32 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.05 0.088 -10000 0 -0.28 10 10
IFNB1 -0.004 0.043 -10000 0 -0.3 3 3
SMAD3/SMAD4/MEF2C 0.023 0.099 -10000 0 -0.33 12 12
CITED1 0.014 0.1 -10000 0 -0.44 26 26
SMAD2-3/SMAD4/ARC105 0.041 0.065 -10000 0 -0.27 3 3
RBL1 0.014 0.03 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.11 -10000 0 -0.42 26 26
RUNX1-3/PEBPB2 0.04 0.055 -10000 0 -0.27 15 15
SMAD7 0.006 0.1 -10000 0 -0.63 5 5
MYC/MIZ-1 0.026 0.043 0.18 6 -0.32 6 12
SMAD3/SMAD4 -0.035 0.11 0.26 2 -0.5 17 19
IL10 -0.029 0.13 -10000 0 -0.47 41 41
PIASy/HDAC complex 0.024 0.022 -10000 0 -0.44 1 1
PIAS3 0.024 0.021 -10000 0 -0.44 1 1
CDK2 0.024 0.021 -10000 0 -0.44 1 1
IL5 -0.015 0.079 -10000 0 -0.3 20 20
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.024 0.022 -10000 0 -0.44 1 1
ATF3 0.027 0.023 -10000 0 -0.44 1 1
SMAD3/SMAD4/SP1 0.03 0.077 -10000 0 -0.26 15 15
FOXG1 -0.011 0.081 -10000 0 -0.45 16 16
FOXO3 0.008 0.022 -10000 0 -0.23 2 2
FOXO1 0.006 0.025 -10000 0 -0.32 2 2
FOXO4 0.008 0.027 -10000 0 -0.24 4 4
heart looping 0.001 0.087 0.2 1 -0.3 14 15
CEBPB 0.014 0.025 -10000 0 -0.44 1 1
SMAD3/SMAD4/DLX1 0.032 0.065 -10000 0 -0.25 6 6
MYOD1 -0.017 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.056 -10000 0 -0.3 8 8
SMAD3/SMAD4/GATA3 0.018 0.1 -10000 0 -0.28 47 47
SnoN/SIN3/HDAC complex/NCoR1 0.017 0.064 -10000 0 -0.44 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.041 0.078 -10000 0 -0.25 15 15
SMAD3/SMAD4/SP1-3 0.042 0.079 -10000 0 -0.26 8 8
MED15 0.024 0.02 -10000 0 -0.44 1 1
SP1 0.021 0.041 -10000 0 -0.17 17 17
SIN3B 0.025 0.02 -10000 0 -0.44 1 1
SIN3A 0.024 0.02 -10000 0 -0.44 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.026 0.083 -10000 0 -0.25 32 32
ITGB5 -0.002 0.051 -10000 0 -0.29 2 2
TGIF/SIN3/HDAC complex/CtBP 0.017 0.059 -10000 0 -0.37 4 4
SMAD3/SMAD4/AR 0.022 0.086 -10000 0 -0.29 23 23
AR 0.008 0.092 -10000 0 -0.44 21 21
negative regulation of cell growth -0.01 0.072 -10000 0 -0.3 16 16
SMAD3/SMAD4/MYOD 0.027 0.055 -10000 0 -0.22 2 2
E2F5 0.012 0.07 -10000 0 -0.44 13 13
E2F4 0.026 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.033 0.081 -10000 0 -0.24 27 27
SMAD2-3/SMAD4/FOXO1-3a-4 0.012 0.092 -10000 0 -0.4 20 20
TFDP1 0.02 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.029 0.082 -10000 0 -0.37 10 10
SMAD3/SMAD4/RUNX2 0.025 0.071 -10000 0 -0.26 14 14
TGIF2 0.011 0.044 -10000 0 -0.44 5 5
TGIF1 0.021 0.01 -10000 0 -10000 0 0
ATF2 0.024 0.028 -10000 0 -0.44 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.028 -10000 0 -0.44 2 2
HDAC4 0.026 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.019 0.047 0.32 12 -0.16 3 15
CDKN1A -0.001 0.045 -10000 0 -0.58 2 2
KAT2B 0.013 0.077 -10000 0 -0.44 16 16
BAX 0.025 0.02 -10000 0 -0.44 1 1
FOXO3 -0.003 0.027 0.44 2 -10000 0 2
FOXO1 0.019 0.022 -10000 0 -0.44 1 1
FOXO4 0.01 0.024 -10000 0 -0.31 3 3
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.025 0.006 -10000 0 -10000 0 0
TAT 0.017 0.028 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.025 0.05 -10000 0 -0.32 16 16
PPARGC1A -0.012 0.13 -10000 0 -0.44 47 47
FHL2 0.025 0.019 -10000 0 -0.44 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.033 0.031 -10000 0 -0.32 4 4
HIST2H4A -0.019 0.047 0.16 3 -0.32 12 15
SIRT1/FOXO3a 0.018 0.027 0.18 1 -0.25 2 3
SIRT1 0.02 0.04 0.2 1 -0.45 4 5
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.033 -10000 0 -0.27 5 5
SIRT1/Histone H1b 0.012 0.059 0.18 1 -0.25 20 21
apoptosis -0.044 0.033 0.27 5 -10000 0 5
SIRT1/PGC1A 0.006 0.086 -10000 0 -0.27 51 51
p53/SIRT1 0.003 0.091 0.39 1 -0.33 39 40
SIRT1/FOXO4 0.017 0.048 0.19 1 -0.31 7 8
FOXO1/FHL2/SIRT1 0.034 0.035 -10000 0 -0.25 5 5
HIST1H1E 0.004 0.043 -10000 0 -0.26 15 15
SIRT1/p300 0.032 0.043 -10000 0 -0.45 4 4
muscle cell differentiation -0.018 0.061 0.3 18 -0.21 3 21
TP53 -0.009 0.11 0.2 1 -0.45 36 37
KU70/SIRT1/BAX 0.045 0.034 -10000 0 -0.27 5 5
CREBBP 0.025 0.004 -10000 0 -10000 0 0
MEF2D 0.025 0.02 -10000 0 -0.44 1 1
HIV-1 Tat/SIRT1 0.035 0.034 -10000 0 -0.32 4 4
ACSS2 -0.009 0.024 0.13 1 -0.32 3 4
SIRT1/PCAF/MYOD 0.018 0.062 0.22 3 -0.31 18 21
FoxO family signaling

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
G6PC 0.024 0.066 0.5 2 -10000 0 2
PLK1 0.013 0.13 0.51 1 -0.7 5 6
CDKN1B 0.059 0.11 0.39 7 -0.37 15 22
FOXO3 0.024 0.12 -10000 0 -0.52 10 10
KAT2B 0.014 0.079 -10000 0 -0.44 16 16
FOXO1/SIRT1 0.04 0.06 0.25 3 -0.32 3 6
CAT 0.014 0.12 -10000 0 -0.69 2 2
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.026 0.027 -10000 0 -0.44 1 1
FOXO1 0.032 0.068 0.36 5 -0.28 1 6
MAPK10 0.02 0.075 0.19 50 -0.23 28 78
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.028 0.082 0.3 7 -0.48 3 10
response to oxidative stress 0.006 0.009 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.037 0.1 -10000 0 -0.47 7 7
XPO1 0.018 0.064 -10000 0 -0.44 11 11
EP300 0.024 0.028 -10000 0 -0.45 2 2
BCL2L11 0.027 0.025 -10000 0 -10000 0 0
FOXO1/SKP2 0.038 0.061 0.26 3 -0.35 3 6
mol:GDP 0.006 0.009 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
GADD45A 0.033 0.14 -10000 0 -0.59 19 19
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.033 0.12 0.32 2 -0.42 23 25
MST1 0.014 0.089 -10000 0 -0.44 20 20
CSNK1D 0.026 0.004 -10000 0 -10000 0 0
CSNK1E 0.025 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.013 0.11 -10000 0 -0.36 40 40
YWHAB 0.015 0.013 -10000 0 -10000 0 0
MAPK8 0.032 0.052 0.19 54 -0.27 1 55
MAPK9 0.032 0.051 0.19 54 -10000 0 54
YWHAG 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
YWHAZ 0.021 0.029 -10000 0 -0.44 2 2
SIRT1 0.023 0.041 -10000 0 -0.44 4 4
SOD2 0.054 0.11 0.5 3 -0.56 3 6
RBL2 0.033 0.13 -10000 0 -1.2 3 3
RAL/GDP 0.036 0.019 -10000 0 -10000 0 0
CHUK 0.024 0.038 -10000 0 -0.44 3 3
Ran/GTP 0.021 0.004 -10000 0 -10000 0 0
CSNK1G2 0.024 0.028 -10000 0 -0.44 2 2
RAL/GTP 0.039 0.016 -10000 0 -10000 0 0
CSNK1G1 0.024 0.02 -10000 0 -0.44 1 1
FASLG -0.063 0.34 -10000 0 -1.3 41 41
SKP2 0.023 0.034 -10000 0 -0.44 3 3
USP7 0.026 0.004 -10000 0 -10000 0 0
IKBKB 0.024 0.019 -10000 0 -10000 0 0
CCNB1 0.016 0.11 -10000 0 -0.69 2 2
FOXO1-3a-4/beta catenin 0.062 0.11 0.34 16 -0.43 2 18
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.061 0.26 3 -0.35 3 6
CSNK1A1 0.024 0.028 -10000 0 -0.44 2 2
SGK1 0.026 0.04 -10000 0 -0.44 3 3
CSNK1G3 0.024 0.02 -10000 0 -0.44 1 1
Ran/GTP/Exportin 1 0.032 0.042 -10000 0 -0.27 11 11
ZFAND5 0.026 0.081 0.3 8 -0.7 2 10
SFN 0.024 0.022 -10000 0 -0.44 1 1
CDK2 0.025 0.02 -10000 0 -0.44 1 1
FOXO3A/14-3-3 -0.007 0.097 -10000 0 -0.37 22 22
CREBBP 0.026 0.004 -10000 0 -10000 0 0
FBXO32 0.043 0.14 0.51 1 -0.69 2 3
BCL6 0.036 0.1 -10000 0 -0.78 2 2
RALB 0.027 0.002 -10000 0 -10000 0 0
RALA 0.024 0.008 -10000 0 -10000 0 0
YWHAH 0.025 0.005 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.01 0.084 -10000 0 -0.44 19 19
HRAS 0.025 0.02 -10000 0 -0.44 1 1
EGFR 0.02 0.044 -10000 0 -0.44 5 5
AKT 0.033 0.085 0.25 15 -0.31 15 30
FOXO3 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.024 0.02 -10000 0 -0.44 1 1
FOXO1 0.019 0.022 -10000 0 -0.44 1 1
AKT3 0.017 0.068 -10000 0 -0.44 12 12
FOXO4 0.025 0.02 -10000 0 -0.44 1 1
MET 0.024 0.02 -10000 0 -0.44 1 1
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
PIK3CB 0.023 0.034 -10000 0 -0.44 3 3
NRAS 0.018 0.058 -10000 0 -0.44 9 9
PIK3CG -0.005 0.12 -10000 0 -0.44 39 39
PIK3R3 0.023 0.034 -10000 0 -0.44 3 3
PIK3R2 0.025 0.02 -10000 0 -0.44 1 1
NF1 0.023 0.034 -10000 0 -0.44 3 3
RAS 0.014 0.052 0.16 3 -0.28 7 10
ERBB2 0.024 0.02 -10000 0 -0.44 1 1
proliferation/survival/translation -0.024 0.069 0.27 17 -0.22 3 20
PI3K 0.022 0.071 0.22 23 -0.27 11 34
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
KRAS 0.021 0.044 -10000 0 -0.44 5 5
FOXO 0.057 0.053 0.21 23 -0.12 4 27
AKT2 0.025 0.02 -10000 0 -0.44 1 1
PTEN 0.025 0.006 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0.04 -10000 0 -0.36 3 3
KLHL20 0.035 0.084 0.2 34 -0.23 26 60
CYFIP2 0.017 0.061 -10000 0 -0.44 10 10
Rac1/GDP 0.057 0.087 0.28 6 -0.34 2 8
ENAH 0.009 0.05 -10000 0 -0.37 4 4
AP1M1 0.025 0.02 -10000 0 -0.44 1 1
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.024 0.02 -10000 0 -0.44 1 1
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.011 0.031 -10000 0 -0.31 1 1
ABI1/Sra1/Nap1 -0.012 0.039 -10000 0 -0.17 28 28
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.053 -10000 0 -0.24 14 14
RAPGEF1 0.052 0.085 0.26 6 -0.35 3 9
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.024 0.04 -10000 0 -0.37 3 3
CRK 0.054 0.082 -10000 0 -0.36 2 2
E-cadherin/gamma catenin/alpha catenin 0.048 0.029 -10000 0 -0.27 4 4
alphaE/beta7 Integrin 0.025 0.058 -10000 0 -0.31 16 16
IQGAP1 0.023 0.028 -10000 0 -0.44 2 2
NCKAP1 0.024 0.028 -10000 0 -0.44 2 2
Rap1/GTP/I-afadin 0.046 0.021 -10000 0 -0.25 2 2
DLG1 0.012 0.043 -10000 0 -0.36 3 3
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.021 -10000 0 -0.22 2 2
MLLT4 0.025 0.02 -10000 0 -0.44 1 1
ARF6/GTP/NME1/Tiam1 0.032 0.066 -10000 0 -0.24 28 28
PI3K -0.013 0.027 -10000 0 -0.29 2 2
ARF6 0.024 0.02 -10000 0 -0.44 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.036 0.022 -10000 0 -0.32 2 2
TIAM1 0.006 0.1 -10000 0 -0.44 28 28
E-cadherin(dimer)/Ca2+ 0.057 0.026 -10000 0 -0.24 3 3
AKT1 0.017 0.049 -10000 0 -0.23 2 2
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
CDH1 0.025 0.02 -10000 0 -0.44 1 1
RhoA/GDP 0.069 0.091 0.3 9 -0.34 2 11
actin cytoskeleton organization 0.031 0.066 0.16 39 -0.17 26 65
CDC42/GDP 0.064 0.092 0.3 10 -0.34 2 12
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.015 0.02 -10000 0 -0.22 4 4
ITGB7 0.014 0.078 -10000 0 -0.44 16 16
RAC1 0.023 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.062 0.027 -10000 0 -0.25 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin 0.043 0.022 -10000 0 -0.23 3 3
mol:GDP 0.061 0.099 0.31 11 -0.4 2 13
CDC42/GTP/IQGAP1 0.029 0.037 -10000 0 -0.39 4 4
JUP 0.025 0.02 -10000 0 -0.44 1 1
p120 catenin/RhoA/GDP 0.078 0.092 0.3 9 -0.35 2 11
RAC1/GTP/IQGAP1 0.029 0.021 -10000 0 -0.27 2 2
PIP5K1C/AP1M1 0.037 0.026 -10000 0 -0.58 1 1
RHOA 0.025 0.02 -10000 0 -0.44 1 1
CDC42 0.021 0.039 -10000 0 -0.44 4 4
CTNNA1 0.024 0.028 -10000 0 -0.44 2 2
positive regulation of S phase of mitotic cell cycle 0.028 0.051 0.14 46 -0.12 21 67
NME1 0.026 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.012 0.041 -10000 0 -0.36 3 3
regulation of cell-cell adhesion 0.006 0.025 -10000 0 -0.23 2 2
WASF2 0.008 0.031 -10000 0 -0.11 5 5
Rap1/GTP 0.072 0.077 0.3 4 -0.35 1 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.057 -10000 0 -0.23 16 16
CCND1 0.032 0.059 0.15 44 -0.14 21 65
VAV2 0.049 0.18 0.4 1 -0.66 29 30
RAP1/GDP 0.078 0.087 0.31 8 -0.4 1 9
adherens junction assembly 0.012 0.04 -10000 0 -0.35 3 3
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.02 -10000 0 -0.44 1 1
PIP5K1C 0.025 0.02 -10000 0 -0.44 1 1
regulation of heterotypic cell-cell adhesion 0.042 0.051 -10000 0 -0.22 16 16
E-cadherin/beta catenin 0.011 0.02 -10000 0 -0.3 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.007 0.035 -10000 0 -0.36 3 3
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
Rac1/GTP -0.013 0.086 -10000 0 -0.38 26 26
E-cadherin/beta catenin/alpha catenin 0.049 0.025 -10000 0 -0.27 3 3
ITGAE 0.022 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.041 -10000 0 -0.38 3 3
BARD1 signaling events

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
BARD1/CSTF1 0.02 0.031 -10000 0 -0.32 3 3
ATM 0.019 0.055 -10000 0 -0.44 8 8
UBE2D3 0.025 0.004 -10000 0 -10000 0 0
PRKDC 0.022 0.021 -10000 0 -0.44 1 1
ATR 0.024 0.028 -10000 0 -0.44 2 2
UBE2L3 0.025 0.005 -10000 0 -10000 0 0
FANCD2 0.012 0.053 -10000 0 -0.38 9 9
protein ubiquitination 0.057 0.056 -10000 0 -0.26 15 15
XRCC5 0.025 0.019 -10000 0 -0.44 1 1
XRCC6 0.025 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.031 0.075 -10000 0 -0.35 18 18
MRE11A 0.019 0.055 -10000 0 -0.44 8 8
DNA-PK 0.044 0.03 -10000 0 -0.51 1 1
FA complex/FANCD2/Ubiquitin 0.016 0.062 -10000 0 -0.46 6 6
FANCF 0.021 0.048 -10000 0 -0.44 6 6
BRCA1 0.025 0.02 -10000 0 -0.44 1 1
CCNE1 0.025 0.004 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.016 -10000 0 -0.32 1 1
FANCG 0.026 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.033 0.042 -10000 0 -0.32 8 8
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.026 0.004 -10000 0 -10000 0 0
NBN 0.01 0.074 -10000 0 -0.44 15 15
FANCA 0.025 0.004 -10000 0 -10000 0 0
DNA repair 0.025 0.083 0.26 7 -0.46 5 12
BRCA1/BARD1/ubiquitin 0.033 0.042 -10000 0 -0.32 8 8
BARD1/DNA-PK 0.053 0.044 -10000 0 -0.28 6 6
FANCL 0.024 0.034 -10000 0 -0.44 3 3
mRNA polyadenylation -0.02 0.031 0.32 3 -10000 0 3
BRCA1/BARD1/CTIP/M/R/N Complex -0.001 0.13 -10000 0 -0.42 32 32
BRCA1/BACH1/BARD1/TopBP1 0.047 0.041 -10000 0 -0.27 9 9
BRCA1/BARD1/P53 0.029 0.091 -10000 0 -0.26 43 43
BARD1/CSTF1/BRCA1 0.028 0.035 -10000 0 -0.27 3 3
BRCA1/BACH1 0.025 0.02 -10000 0 -0.44 1 1
BARD1 0.02 0.051 -10000 0 -0.44 7 7
PCNA 0.021 0.01 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.046 0.039 -10000 0 -0.27 8 8
BRCA1/BARD1/UbcH7 0.045 0.04 -10000 0 -0.27 8 8
BRCA1/BARD1/RAD51/PCNA 0.047 0.043 -10000 0 -0.24 7 7
BARD1/DNA-PK/P53 0.036 0.082 -10000 0 -0.25 34 34
BRCA1/BARD1/Ubiquitin 0.033 0.042 -10000 0 -0.32 8 8
BRCA1/BARD1/CTIP 0.02 0.072 -10000 0 -0.31 21 21
FA complex 0.021 0.042 -10000 0 -0.5 2 2
BARD1/EWS 0.033 0.04 -10000 0 -0.32 7 7
RBBP8 -0.018 0.06 -10000 0 -0.4 13 13
TP53 -0.007 0.11 -10000 0 -0.44 36 36
TOPBP1 0.025 0.02 -10000 0 -0.44 1 1
G1/S transition of mitotic cell cycle -0.027 0.09 0.26 43 -10000 0 43
BRCA1/BARD1 0.064 0.058 -10000 0 -0.27 15 15
CSTF1 0.015 0.013 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.036 -10000 0 -0.32 7 7
CDK2 0.025 0.02 -10000 0 -0.44 1 1
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.024 0.006 -10000 0 -10000 0 0
RAD50 0.024 0.02 -10000 0 -0.44 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.042 -10000 0 -0.32 8 8
EWSR1 0.025 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.011 0.14 -10000 0 -0.57 31 31
oxygen homeostasis 0.003 0.008 -10000 0 -10000 0 0
TCEB2 0.026 0.021 -10000 0 -0.44 1 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.041 0.077 -10000 0 -0.4 2 2
EPO 0.045 0.12 -10000 0 -0.55 2 2
FIH (dimer) 0.024 0.02 -10000 0 -10000 0 0
APEX1 0.023 0.023 -10000 0 -10000 0 0
SERPINE1 0.037 0.14 -10000 0 -0.53 15 15
FLT1 0.018 0.12 -10000 0 -0.74 10 10
ADORA2A 0.032 0.12 0.32 5 -0.47 10 15
germ cell development 0.036 0.14 -10000 0 -0.48 21 21
SLC11A2 0.043 0.12 -10000 0 -0.46 9 9
BHLHE40 0.043 0.12 -10000 0 -0.46 9 9
HIF1AN 0.024 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.05 0.095 -10000 0 -0.37 4 4
ETS1 0.031 0.033 -10000 0 -0.44 2 2
CITED2 0.024 0.1 -10000 0 -0.61 11 11
KDR 0.016 0.15 -10000 0 -0.74 16 16
PGK1 0.043 0.12 -10000 0 -0.46 9 9
SIRT1 0.022 0.039 -10000 0 -0.44 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.085 0.15 -10000 0 -0.52 9 9
EPAS1 0.021 0.056 0.18 1 -0.31 3 4
SP1 0.029 0.02 -10000 0 -0.44 1 1
ABCG2 0.034 0.15 -10000 0 -0.49 27 27
EFNA1 0.043 0.12 -10000 0 -0.46 9 9
FXN 0.034 0.12 0.32 6 -0.45 10 16
POU5F1 0.035 0.14 -10000 0 -0.49 21 21
neuron apoptosis -0.083 0.15 0.51 9 -10000 0 9
EP300 0.023 0.028 -10000 0 -0.44 2 2
EGLN3 0.02 0.048 -10000 0 -0.44 5 5
EGLN2 0.023 0.028 -10000 0 -0.46 1 1
EGLN1 0.024 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.044 0.028 -10000 0 -0.29 2 2
VHL 0.025 0.02 -10000 0 -0.44 1 1
ARNT 0.023 0.029 -10000 0 -0.44 1 1
SLC2A1 0.033 0.12 0.32 5 -0.45 9 14
TWIST1 0.017 0.15 0.32 4 -0.48 31 35
ELK1 0.029 0.021 -10000 0 -0.44 1 1
HIF2A/ARNT/Cbp/p300 0.059 0.099 -10000 0 -0.37 3 3
VEGFA 0.042 0.12 -10000 0 -0.46 9 9
CREBBP 0.025 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.038 0.083 -10000 0 -0.31 24 24
Ran/GTP/Exportin 1/HDAC1 -0.022 0.054 -10000 0 -0.3 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.014 0.083 -10000 0 -0.31 24 24
SUMO1 0.011 0.084 -10000 0 -0.44 19 19
ZFPM1 0.024 0.04 -10000 0 -0.44 4 4
NPC/RanGAP1/SUMO1/Ubc9 -0.004 0.08 -10000 0 -0.36 24 24
FKBP3 0.015 0.064 -10000 0 -0.44 11 11
Histones 0.049 0.053 -10000 0 -0.33 1 1
YY1/LSF 0.006 0.073 -10000 0 -0.26 29 29
SMG5 0.025 0.02 -10000 0 -0.44 1 1
RAN 0.026 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.012 0.05 -10000 0 -0.24 21 21
I kappa B alpha/HDAC1 0.016 0.059 -10000 0 -0.37 1 1
SAP18 0.02 0.011 -10000 0 -10000 0 0
RELA 0.01 0.061 -10000 0 -0.25 23 23
HDAC1/Smad7 0.036 0.03 -10000 0 -0.27 2 2
RANGAP1 0.024 0.02 -10000 0 -0.44 1 1
HDAC3/TR2 0.024 0.05 -10000 0 -0.3 2 2
NuRD/MBD3 Complex 0.009 0.054 -10000 0 -0.28 7 7
NF kappa B1 p50/RelA 0.014 0.08 0.3 1 -0.33 15 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.007 0.094 -10000 0 -0.44 24 24
GATA1 0.011 0.031 -10000 0 -0.44 1 1
Mad/Max 0.036 0.018 -10000 0 -0.32 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.004 0.074 -10000 0 -0.39 7 7
RBBP7 0.025 0.02 -10000 0 -0.44 1 1
NPC 0.008 0.042 -10000 0 -0.22 18 18
RBBP4 0.024 0.02 -10000 0 -0.44 1 1
MAX 0.024 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NFKBIA 0.011 0.039 -10000 0 -0.4 1 1
KAT2B 0.013 0.077 -10000 0 -0.44 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.009 0.037 -10000 0 -0.36 1 1
SIN3 complex 0.046 0.039 -10000 0 -0.25 4 4
SMURF1 0.025 0.006 -10000 0 -10000 0 0
CHD3 0.022 0.01 -10000 0 -10000 0 0
SAP30 0.023 0.028 -10000 0 -0.44 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.01 -10000 0 -10000 0 0
YY1/HDAC3 0.002 0.067 -10000 0 -0.35 7 7
YY1/HDAC2 0.008 0.07 -10000 0 -0.26 26 26
YY1/HDAC1 0.008 0.069 -10000 0 -0.25 27 27
NuRD/MBD2 Complex (MeCP1) 0.001 0.065 -10000 0 -0.29 16 16
PPARG 0.002 0.081 -10000 0 -0.32 29 29
HDAC8/hEST1B 0.05 0.017 -10000 0 -0.27 1 1
UBE2I 0.025 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.023 0.052 -10000 0 -0.27 4 4
MBD3L2 -0.017 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.03 -10000 0 -0.27 2 2
CREBBP 0.025 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.005 0.073 -10000 0 -0.33 9 9
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC3 0.012 0.039 -10000 0 -0.18 21 21
HDAC2 0.025 0.004 -10000 0 -10000 0 0
YY1 0.006 0.055 -10000 0 -0.3 17 17
HDAC8 0.026 0.002 -10000 0 -10000 0 0
SMAD7 0.018 0.029 -10000 0 -0.44 2 2
NCOR2 0.024 0.034 -10000 0 -0.44 3 3
MXD1 0.025 0.02 -10000 0 -0.44 1 1
STAT3 0.016 0.019 -10000 0 -0.29 2 2
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.012 0.081 -10000 0 -0.44 18 18
YY1/LSF/HDAC1 0.02 0.073 -10000 0 -0.26 22 22
YY1/SAP30/HDAC1 0.02 0.071 -10000 0 -0.29 11 11
EP300 0.023 0.028 -10000 0 -0.44 2 2
STAT3 (dimer non-phopshorylated) 0.016 0.019 -10000 0 -0.29 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.039 -10000 0 -0.4 1 1
histone deacetylation 0.001 0.064 -10000 0 -0.28 16 16
STAT3 (dimer non-phopshorylated)/HDAC3 0.016 0.045 -10000 0 -0.32 2 2
nuclear export -0.05 0.017 0.27 1 -10000 0 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GATAD2B 0.025 0.004 -10000 0 -10000 0 0
GATAD2A 0.025 0.02 -10000 0 -0.44 1 1
GATA2/HDAC3 0.014 0.072 -10000 0 -0.25 23 23
GATA1/HDAC1 0.035 0.019 -10000 0 -0.32 1 1
GATA1/HDAC3 0.023 0.051 -10000 0 -0.3 2 2
CHD4 0.025 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.025 0.067 -10000 0 -0.32 21 21
SIN3/HDAC complex/Mad/Max 0.025 0.053 -10000 0 -0.28 5 5
NuRD Complex -0.017 0.096 -10000 0 -0.32 24 24
positive regulation of chromatin silencing 0.047 0.052 -10000 0 -0.32 1 1
SIN3B 0.025 0.02 -10000 0 -0.44 1 1
MTA2 0.025 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.02 -10000 0 -0.44 1 1
XPO1 0.017 0.064 -10000 0 -0.44 11 11
SUMO1/HDAC1 0.018 0.093 -10000 0 -0.43 21 21
HDAC complex 0.061 0.026 -10000 0 -0.25 2 2
GATA1/Fog1 0.035 0.036 -10000 0 -0.32 5 5
FKBP25/HDAC1/HDAC2 0.04 0.047 -10000 0 -0.27 11 11
TNF 0.009 0.088 -10000 0 -0.44 21 21
negative regulation of cell growth 0.025 0.052 -10000 0 -0.28 5 5
NuRD/MBD2/PRMT5 Complex 0.001 0.065 -10000 0 -0.29 16 16
Ran/GTP/Exportin 1 0.016 0.1 -10000 0 -0.41 25 25
NF kappa B/RelA/I kappa B alpha 0.003 0.075 -10000 0 -0.3 28 28
SIN3/HDAC complex/NCoR1 -0.002 0.06 -10000 0 -0.29 12 12
TFCP2 0.024 0.028 -10000 0 -0.44 2 2
NR2C1 0.025 0.02 -10000 0 -0.44 1 1
MBD3 0.023 0.034 -10000 0 -0.44 3 3
MBD2 0.018 0.022 -10000 0 -0.44 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.024 0.073 -10000 0 -0.33 23 23
AKT1 0.067 0.11 0.38 12 -0.47 8 20
PTK2B -0.02 0.074 0.34 1 -0.55 6 7
VEGFR2 homodimer/Frs2 0.024 0.064 -10000 0 -0.61 5 5
CAV1 0.022 0.045 -10000 0 -0.44 5 5
CALM1 0.024 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.039 0.065 -10000 0 -0.67 4 4
endothelial cell proliferation 0.093 0.15 0.32 91 -0.42 8 99
mol:Ca2+ 0.002 0.05 -10000 0 -0.52 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.046 0.066 -10000 0 -0.64 4 4
RP11-342D11.1 -0.01 0.055 -10000 0 -0.59 4 4
CDH5 0.025 0.028 -10000 0 -0.44 2 2
VEGFA homodimer 0.056 0.043 -10000 0 -0.29 6 6
SHC1 0.025 0.004 -10000 0 -10000 0 0
SHC2 0.002 0.11 -10000 0 -0.44 33 33
HRAS/GDP 0.036 0.058 -10000 0 -0.53 4 4
SH2D2A 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.074 0.11 0.3 2 -0.47 8 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.039 0.059 -10000 0 -0.62 4 4
VEGFR1 homodimer 0.019 0.022 -10000 0 -0.44 1 1
SHC/GRB2/SOS1 0.06 0.066 -10000 0 -0.58 4 4
GRB10 0.005 0.071 -10000 0 -0.59 7 7
PTPN11 0.022 0.043 -10000 0 -0.44 5 5
GRB2 0.025 0.004 -10000 0 -10000 0 0
PAK1 0.026 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.06 0.07 -10000 0 -0.67 4 4
HRAS 0.025 0.02 -10000 0 -0.44 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.022 0.12 -10000 0 -0.5 18 18
HIF1A 0.02 0.048 -10000 0 -0.44 6 6
FRS2 0.024 0.028 -10000 0 -0.44 2 2
oxygen and reactive oxygen species metabolic process 0.044 0.064 -10000 0 -0.63 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.019 0.062 -10000 0 -0.44 10 10
Nck/Pak 0.036 0.022 -10000 0 -0.32 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.038 0.064 -10000 0 -0.57 5 5
mol:GDP 0.047 0.061 -10000 0 -0.56 4 4
mol:NADP 0.064 0.12 0.32 13 -0.4 15 28
eNOS/Hsp90 0.069 0.11 0.32 12 -0.38 14 26
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
mol:IP3 0.002 0.051 -10000 0 -0.52 4 4
HIF1A/ARNT 0.031 0.043 -10000 0 -0.36 6 6
SHB 0.026 0.005 -10000 0 -10000 0 0
VEGFA 0.026 0.008 -10000 0 -10000 0 0
VEGFC 0.012 0.08 -10000 0 -0.44 17 17
FAK1/Vinculin 0.029 0.12 0.39 1 -0.54 11 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.02 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.042 0.086 -10000 0 -0.57 6 6
PTPN6 0.025 0.004 -10000 0 -10000 0 0
EPAS1 0.028 0.037 -10000 0 -0.36 5 5
mol:L-citrulline 0.064 0.12 0.32 13 -0.4 15 28
ITGAV 0.017 0.064 -10000 0 -0.44 11 11
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.052 0.065 -10000 0 -0.64 4 4
VEGFR2 homodimer/VEGFA homodimer 0.04 0.067 -10000 0 -0.52 6 6
VEGFR2/3 heterodimer 0.021 0.075 -10000 0 -0.43 12 12
VEGFB 0.025 0.004 -10000 0 -10000 0 0
MAPK11 -0.009 0.073 0.24 1 -0.48 10 11
VEGFR2 homodimer 0.011 0.062 -10000 0 -0.73 4 4
FLT1 0.019 0.023 -10000 0 -0.44 1 1
NEDD4 0.024 0.029 -10000 0 -0.44 2 2
MAPK3 0.038 0.097 0.31 10 -0.49 4 14
MAPK1 0.036 0.095 0.32 8 -0.49 4 12
VEGFA145/NRP2 0.033 0.05 -10000 0 -0.32 11 11
VEGFR1/2 heterodimer 0.018 0.057 -10000 0 -0.54 5 5
KDR 0.011 0.062 -10000 0 -0.73 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.037 0.076 -10000 0 -0.6 5 5
SRC 0.015 0.023 -10000 0 -0.44 1 1
platelet activating factor biosynthetic process 0.046 0.1 0.33 12 -0.5 4 16
PI3K 0.032 0.082 -10000 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.06 -10000 0 -0.62 4 4
FES 0.004 0.067 -10000 0 -0.58 5 5
GAB1 0.016 0.062 -10000 0 -0.61 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.023 0.055 -10000 0 -0.53 4 4
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.025 0.02 -10000 0 -0.44 1 1
eNOS/Caveolin-1 0.065 0.11 0.3 6 -0.39 15 21
VEGFR2 homodimer/VEGFA homodimer/Yes 0.032 0.066 -10000 0 -0.66 4 4
PI3K/GAB1 0.035 0.078 -10000 0 -0.52 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.062 0.068 -10000 0 -0.59 5 5
PRKACA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.027 0.093 -10000 0 -0.59 8 8
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
CDC42 0.007 0.066 -10000 0 -0.66 4 4
actin cytoskeleton reorganization 0.039 0.059 -10000 0 -0.61 4 4
PTK2 0.009 0.1 -10000 0 -0.57 10 10
EDG1 -0.01 0.055 -10000 0 -0.59 4 4
mol:DAG 0.002 0.051 -10000 0 -0.52 4 4
CaM/Ca2+ 0.011 0.051 -10000 0 -0.48 4 4
MAP2K3 -0.013 0.061 -10000 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.048 0.091 -10000 0 -0.6 7 7
PLCG1 0.002 0.051 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.03 0.057 -10000 0 -0.51 4 4
IQGAP1 0.023 0.028 -10000 0 -0.44 2 2
YES1 0.019 0.035 -10000 0 -0.44 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.038 0.067 -10000 0 -0.67 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.059 -10000 0 -0.62 4 4
cell migration 0.034 0.11 0.34 3 -0.52 9 12
mol:PI-3-4-5-P3 0.038 0.079 -10000 0 -0.51 5 5
FYN 0.022 0.039 -10000 0 -0.44 4 4
VEGFB/NRP1 0.014 0.056 -10000 0 -0.57 4 4
mol:NO 0.064 0.12 0.32 13 -0.4 15 28
PXN 0.026 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.054 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.025 0.075 -10000 0 -0.6 7 7
VHL 0.025 0.02 -10000 0 -0.44 1 1
ITGB3 0.016 0.07 -10000 0 -0.44 13 13
NOS3 0.065 0.12 0.34 11 -0.44 15 26
VEGFR2 homodimer/VEGFA homodimer/Sck 0.025 0.088 -10000 0 -0.55 5 5
RAC1 0.023 0.008 -10000 0 -10000 0 0
PRKCA -0.01 0.047 -10000 0 -0.49 4 4
PRKCB -0.017 0.063 -10000 0 -0.48 5 5
VCL 0.024 0.028 -10000 0 -0.44 2 2
VEGFA165/NRP1 0.017 0.059 -10000 0 -0.59 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0.03 0.058 -10000 0 -0.57 4 4
VEGFA165/NRP2 0.033 0.05 -10000 0 -0.32 11 11
MAPKKK cascade 0.016 0.068 -10000 0 -0.52 7 7
NRP2 0.019 0.066 -10000 0 -0.44 11 11
VEGFC homodimer 0.012 0.08 -10000 0 -0.44 17 17
NCK1 0.024 0.028 -10000 0 -0.44 2 2
ROCK1 0.017 0.044 -10000 0 -0.44 5 5
FAK1/Paxillin 0.029 0.11 0.39 1 -0.53 10 11
MAP3K13 0.008 0.062 -10000 0 -0.58 5 5
PDPK1 0.06 0.1 0.24 77 -0.5 4 81
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.055 0.043 -10000 0 -0.29 6 6
HDAC3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.022 0.054 -10000 0 -0.3 19 19
GATA1/HDAC4 0.037 0.018 -10000 0 -0.32 1 1
GATA1/HDAC5 0.035 0.024 -10000 0 -0.32 2 2
GATA2/HDAC5 0.023 0.074 -10000 0 -0.33 24 24
HDAC5/BCL6/BCoR 0.051 0.018 -10000 0 -0.27 1 1
HDAC9 -0.002 0.11 -10000 0 -0.44 33 33
Glucocorticoid receptor/Hsp90/HDAC6 0.039 0.057 -10000 0 -0.27 18 18
HDAC4/ANKRA2 0.037 0.017 -10000 0 -0.32 1 1
HDAC5/YWHAB 0.021 0.024 -10000 0 -0.32 1 1
NPC/RanGAP1/SUMO1/Ubc9 -0.004 0.08 -10000 0 -0.36 24 24
GATA2 0.007 0.094 -10000 0 -0.44 24 24
HDAC4/RFXANK 0.037 0.022 -10000 0 -0.32 2 2
BCOR 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.028 -10000 0 -0.44 2 2
HDAC5 0.025 0.02 -10000 0 -0.44 1 1
GNB1/GNG2 0.032 0.035 -10000 0 -0.32 5 5
Histones 0.01 0.082 -10000 0 -0.37 13 13
ADRBK1 0.025 0.02 -10000 0 -0.44 1 1
HDAC4 0.026 0.004 -10000 0 -10000 0 0
XPO1 0.017 0.064 -10000 0 -0.44 11 11
HDAC5/ANKRA2 0.036 0.023 -10000 0 -0.32 2 2
HDAC4/Ubc9 0.038 0.007 -10000 0 -10000 0 0
HDAC7 0.025 0.02 -10000 0 -0.44 1 1
HDAC5/14-3-3 E 0.032 0.021 -10000 0 -0.32 1 1
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
HDAC6 0.026 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.036 0.03 -10000 0 -0.45 2 2
CAMK4 0.013 0.075 -10000 0 -0.44 15 15
Tubulin/HDAC6 0.047 0.045 -10000 0 -0.27 10 10
SUMO1 0.011 0.084 -10000 0 -0.44 19 19
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.013 -10000 0 -10000 0 0
GATA1 0.011 0.031 -10000 0 -0.44 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
NR3C1 0.013 0.08 -10000 0 -0.44 17 17
SUMO1/HDAC4 0.017 0.094 -10000 0 -0.43 21 21
SRF 0.026 0.005 -10000 0 -10000 0 0
HDAC4/YWHAB 0.022 0.019 -10000 0 -10000 0 0
Tubulin 0.034 0.048 -10000 0 -0.32 10 10
HDAC4/14-3-3 E 0.032 0.015 -10000 0 -10000 0 0
GNB1 0.025 0.005 -10000 0 -10000 0 0
RANGAP1 0.024 0.02 -10000 0 -0.44 1 1
BCL6/BCoR 0.038 0.007 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.025 -10000 0 -0.27 3 3
HDAC4/SRF 0.041 0.054 -10000 0 -0.28 15 15
HDAC4/ER alpha 0.024 0.074 -10000 0 -0.32 25 25
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.009 0.083 -10000 0 -0.36 13 13
cell motility 0.047 0.045 -10000 0 -0.27 10 10
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.025 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.037 0.016 -10000 0 -0.32 1 1
BCL6 0.026 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.026 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.035 0.018 -10000 0 -0.32 1 1
ESR1 0.006 0.097 -10000 0 -0.44 25 25
HDAC6/HDAC11 0.036 0.022 -10000 0 -0.32 2 2
Ran/GTP/Exportin 1 0.016 0.1 -10000 0 -0.41 25 25
NPC 0.008 0.042 -10000 0 -0.22 18 18
MEF2C 0.021 0.048 -10000 0 -0.44 6 6
RAN 0.026 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.068 0.044 -10000 0 -0.24 9 9
GNG2 0.021 0.044 -10000 0 -0.44 5 5
NCOR2 0.024 0.034 -10000 0 -0.44 3 3
TUBB2A 0.021 0.063 -10000 0 -0.44 10 10
HDAC11 0.024 0.028 -10000 0 -0.44 2 2
HSP90AA1 0.024 0.02 -10000 0 -0.44 1 1
RANBP2 0.012 0.081 -10000 0 -0.44 18 18
ANKRA2 0.024 0.02 -10000 0 -0.44 1 1
RFXANK 0.024 0.028 -10000 0 -0.44 2 2
nuclear import -0.016 0.02 0.27 1 -10000 0 1
Canonical NF-kappaB pathway

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
FBXW11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.088 0.3 8 -0.31 7 15
ERC1 0.025 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.023 0.059 -10000 0 -0.32 16 16
NFKBIA -0.009 0.015 0.2 1 -0.24 1 2
BIRC2 0.015 0.07 -10000 0 -0.44 13 13
IKBKB 0.023 0.009 -10000 0 -10000 0 0
RIPK2 0.022 0.009 -10000 0 -10000 0 0
IKBKG 0.01 0.066 -10000 0 -0.39 6 6
IKK complex/A20 0.03 0.087 -10000 0 -0.37 8 8
NEMO/A20/RIP2 0.022 0.009 -10000 0 -10000 0 0
XPO1 0.017 0.064 -10000 0 -0.44 11 11
NEMO/ATM 0.025 0.084 0.26 2 -0.39 13 15
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.029 0.041 -10000 0 -0.27 11 11
IKK complex/ELKS 0.027 0.072 -10000 0 -0.4 7 7
BCL10/MALT1/TRAF6 0.035 0.049 -10000 0 -0.35 6 6
NOD2 0.011 0.084 -10000 0 -0.44 19 19
NFKB1 0.026 0.02 -10000 0 -0.44 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
MALT1 0.017 0.035 -10000 0 -0.44 3 3
cIAP1/UbcH5C 0.029 0.053 -10000 0 -0.32 13 13
ATM 0.019 0.055 -10000 0 -0.44 8 8
TNF/TNFR1A 0.025 0.067 -10000 0 -0.32 21 21
TRAF6 0.025 0.02 -10000 0 -0.44 1 1
PRKCA 0.024 0.02 -10000 0 -0.44 1 1
CHUK 0.022 0.034 -10000 0 -0.44 3 3
UBE2D3 0.025 0.004 -10000 0 -10000 0 0
TNF 0.009 0.088 -10000 0 -0.44 21 21
NF kappa B1 p50/RelA 0.054 0.02 -10000 0 -0.27 1 1
BCL10 0.022 0.039 -10000 0 -0.44 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.015 0.2 1 -0.24 1 2
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.004 -10000 0 -10000 0 0
IKK complex 0.029 0.077 -10000 0 -0.42 7 7
CYLD 0.025 0.02 -10000 0 -0.44 1 1
IKK complex/PKC alpha 0.035 0.079 -10000 0 -0.41 7 7
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.018 0.023 -10000 0 -0.33 2 2
TRAF2/ASK1 0.033 0.019 -10000 0 -0.27 2 2
ATM 0.019 0.055 -10000 0 -0.44 8 8
MAP2K3 -0.006 0.11 0.36 2 -0.38 30 32
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.002 0.097 0.28 4 -0.38 22 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.027 0.023 -10000 0 -0.44 1 1
TXN 0.006 0.001 -10000 0 -10000 0 0
CALM1 0.024 0.007 -10000 0 -10000 0 0
GADD45A 0.024 0.028 -10000 0 -0.44 2 2
GADD45B 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 0.021 0.044 -10000 0 -0.44 5 5
MAP3K6 0.021 0.039 -10000 0 -0.44 4 4
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
MAP3K4 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.038 -10000 0 -0.32 6 6
TAK1/TAB family 0 0.019 0.16 3 -0.13 1 4
RAC1/OSM/MEKK3 0.042 0.027 -10000 0 -0.26 3 3
TRAF2 0.025 0.02 -10000 0 -0.44 1 1
RAC1/OSM/MEKK3/MKK3 0.008 0.089 -10000 0 -0.35 22 22
TRAF6 0.006 0.013 -10000 0 -0.3 1 1
RAC1 0.023 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.006 0.093 -10000 0 -0.44 22 22
CCM2 0.023 0.021 -10000 0 -0.44 1 1
CaM/Ca2+/CAMKIIB 0.022 0.06 -10000 0 -0.27 22 22
MAPK11 0.024 0.036 -10000 0 -0.44 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.033 0.062 -10000 0 -0.25 24 24
OSM/MEKK3 0.032 0.029 -10000 0 -0.33 3 3
TAOK1 0.003 0.063 -10000 0 -0.38 13 13
TAOK2 0.007 0.038 -10000 0 -0.3 9 9
TAOK3 0.008 0.036 -10000 0 -0.3 8 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.024 0.028 -10000 0 -0.44 2 2
MAP3K10 0.023 0.034 -10000 0 -0.44 3 3
MAP3K3 0.024 0.028 -10000 0 -0.44 2 2
TRX/ASK1 0.022 0.015 -10000 0 -0.26 1 1
GADD45/MTK1/MTK1 0.057 0.029 -10000 0 -0.25 3 3
Arf1 pathway

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
coatomer protein complex 0.056 0.072 0.14 174 -0.5 1 175
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.007 0.039 0.14 11 -0.18 5 16
AP2 0.037 0.016 -10000 0 -0.32 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.013 -10000 0 -10000 0 0
CLTB 0.025 0.02 -10000 0 -0.44 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.016 0.011 -10000 0 -0.22 1 1
CD4 0.009 0.088 -10000 0 -0.44 21 21
CLTA 0.025 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 -0.004 0.013 -10000 0 -0.32 1 1
mol:PI-4-5-P2 0.003 0.018 -10000 0 -0.28 2 2
ARF1/GTP 0.033 0.013 -10000 0 -0.11 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.004 0.02 0.18 2 -0.38 1 3
mol:Choline 0.003 0.018 -10000 0 -0.28 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.027 0.007 -10000 0 -10000 0 0
DDEF1 0.002 0.019 -10000 0 -0.29 2 2
ARF1/GDP 0.001 0.014 -10000 0 -0.26 1 1
AP2M1 0.026 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.018 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.021 0.022 -10000 0 -0.24 1 1
ARFIP2 0.016 0.021 -10000 0 -10000 0 0
COPA 0.025 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0.018 0.13 1 -0.18 1 2
ARF1/GTP/ARHGAP10 0.019 0.006 -10000 0 -10000 0 0
GGA3 0.025 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.022 0.026 -10000 0 -0.25 4 4
AP2A1 0.025 0.02 -10000 0 -0.44 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.006 0.028 0.13 2 -0.36 2 4
ARF1/GDP/Membrin 0.016 0.034 -10000 0 -0.28 5 5
Arfaptin 2/Rac/GDP 0.03 0.012 -10000 0 -10000 0 0
CYTH2 0.027 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.035 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.006 -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 0.012 0.044 -10000 0 -0.2 21 21
PLD2 0.003 0.018 -10000 0 -0.28 2 2
ARF-GAP1/v-SNARE -0.004 0.013 -10000 0 -0.32 1 1
PIP5K1A 0.003 0.018 -10000 0 -0.29 2 2
ARF1/GTP/Membrin/GBF1/p115 0.009 0.031 -10000 0 -0.15 5 5
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.003 0.018 -10000 0 -0.28 2 2
KDEL Receptor/Ligand/ARF-GAP1 -0.004 0.013 -10000 0 -0.32 1 1
GOSR2 0.009 0.009 -10000 0 -10000 0 0
USO1 0.003 0.055 -10000 0 -0.42 9 9
GBF1 0.004 0.042 -10000 0 -0.32 9 9
ARF1/GTP/Arfaptin 2 0.035 0.01 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.039 0.063 -10000 0 -0.27 22 22
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.034 0.049 -9999 0 -0.24 15 15
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.007 0.019 -9999 0 -0.3 1 1
AURKB 0.022 0.01 -9999 0 -10000 0 0
AURKC 0.012 0.075 -9999 0 -0.44 15 15
PLK2 and PLK4 events

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
PLK2 0.025 0.036 -9999 0 -0.44 3 3
PLK4 0.024 0.028 -9999 0 -0.44 2 2
regulation of centriole replication -0.015 0.033 -9999 0 -0.38 4 4
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.045 0.038 -10000 0 -0.21 2 2
BIRC5 0.025 0.005 -10000 0 -10000 0 0
NFKBIA 0.003 0.012 0.24 1 -10000 0 1
CPEB1 -0.012 0.12 -10000 0 -0.44 40 40
AKT1 0.002 0.012 -10000 0 -0.26 1 1
NDEL1 0.022 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.015 0.019 -10000 0 -0.26 1 1
NDEL1/TACC3 0.051 0.035 -10000 0 -10000 0 0
GADD45A 0.024 0.028 -10000 0 -0.44 2 2
GSK3B 0.023 0.024 -10000 0 -0.39 2 2
PAK1/Aurora A 0.046 0.035 -10000 0 -10000 0 0
MDM2 0.024 0.028 -10000 0 -0.44 2 2
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.008 0.019 -10000 0 -0.32 2 2
TP53 -0.005 0.07 -10000 0 -0.29 30 30
DLG7 0.004 0.006 -10000 0 -10000 0 0
AURKAIP1 0.024 0.02 -10000 0 -0.44 1 1
ARHGEF7 0.02 0.011 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.054 0.037 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.019 -10000 0 -0.26 1 1
AURKA 0.009 0.01 -10000 0 -10000 0 0
AURKB 0.007 0.011 -10000 0 -0.14 2 2
CDC25B 0.008 0.009 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.007 -10000 0 -10000 0 0
mRNA polyadenylation 0.003 0.058 -10000 0 -0.23 22 22
Aurora A/CPEB 0.003 0.059 -10000 0 -0.23 22 22
Aurora A/TACC1/TRAP/chTOG 0.064 0.047 -10000 0 -0.24 3 3
BRCA1 0.025 0.02 -10000 0 -0.44 1 1
centrosome duplication 0.046 0.035 -10000 0 -10000 0 0
regulation of centrosome cycle 0.05 0.034 -10000 0 -10000 0 0
spindle assembly 0.062 0.046 -10000 0 -0.24 3 3
TDRD7 0.026 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.07 0.037 -10000 0 -0.2 2 2
CENPA 0.007 0.029 -10000 0 -0.32 4 4
Aurora A/PP2A 0.046 0.035 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.003 0.027 0.2 3 -10000 0 3
negative regulation of DNA binding -0.013 0.079 -10000 0 -0.24 54 54
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.028 0.022 -10000 0 -0.32 1 1
RASA1 0.024 0.028 -10000 0 -0.44 2 2
Ajuba/Aurora A 0.005 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0.01 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.01 -10000 0 -10000 0 0
TACC1 0.018 0.048 -10000 0 -0.44 6 6
TACC3 0.025 0.005 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.063 0.036 -10000 0 -0.24 1 1
Aurora A/RasGAP 0.045 0.037 -10000 0 -10000 0 0
OAZ1 0.026 0.004 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GIT1 0.024 0.02 -10000 0 -0.44 1 1
GIT1/beta-PIX/PAK1 0.039 0.027 -10000 0 -0.27 1 1
Importin alpha/Importin beta/TPX2 -0.008 0.019 -10000 0 -0.32 2 2
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.009 0.014 -10000 0 -0.17 2 2
PAK1 0.026 0.003 -10000 0 -10000 0 0
CKAP5 0.026 0.003 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.036 0.022 -10000 0 -0.32 2 2
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.026 -10000 0 -0.27 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.06 0.2 5 -0.21 5 10
NFKBIA 0.041 0.057 -10000 0 -0.2 6 6
MAPK14 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.022 0.016 -10000 0 -0.27 1 1
ARRB2 0.01 0.005 -10000 0 -10000 0 0
REL 0.023 0.034 -10000 0 -0.44 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.023 -10000 0 -0.27 3 3
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.022 0.016 -10000 0 -0.27 1 1
PIK3CA 0.024 0.028 -10000 0 -0.44 2 2
NF kappa B1 p50 dimer 0.015 0.016 -10000 0 -0.32 1 1
PIK3R1 0.023 0.028 -10000 0 -0.44 2 2
NFKB1 -0.01 0.017 0.23 1 -0.32 1 2
RELA 0.025 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.029 0.051 -10000 0 -0.2 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.037 0.059 0.19 4 -0.23 3 7
SRC 0.015 0.023 -10000 0 -0.44 1 1
PI3K 0.034 0.031 -10000 0 -0.32 4 4
NF kappa B1 p50/RelA 0.029 0.051 -10000 0 -0.2 6 6
IKBKB 0.023 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
SYK 0.026 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.047 0.065 0.21 5 -0.2 9 14
cell death 0.035 0.057 0.18 3 -0.22 3 6
NF kappa B1 p105/c-Rel 0.021 0.026 -10000 0 -0.27 4 4
LCK 0.013 0.086 -10000 0 -0.44 19 19
BCL3 0.024 0.028 -10000 0 -0.44 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.041 -10000 0 -0.4 3 3
adherens junction organization 0.027 0.047 -10000 0 -0.28 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.039 -10000 0 -0.35 3 3
FMN1 0.027 0.044 -10000 0 -0.31 2 2
mol:IP3 0.006 0.03 -10000 0 -0.24 5 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.036 0.043 -10000 0 -0.32 2 2
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.043 0.059 0.18 7 -0.38 2 9
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.059 0.07 -10000 0 -0.48 3 3
CTNND1 0.028 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.045 -10000 0 -0.28 4 4
VASP 0.029 0.041 -10000 0 -0.31 2 2
ZYX 0.028 0.045 -10000 0 -0.41 2 2
JUB 0.032 0.041 -10000 0 -0.3 2 2
EGFR(dimer) 0.04 0.053 -10000 0 -0.28 4 4
E-cadherin/beta catenin-gamma catenin 0.047 0.021 -10000 0 -0.26 2 2
mol:PI-3-4-5-P3 0.076 0.07 0.21 8 -0.26 3 11
PIK3CA 0.027 0.028 -10000 0 -0.44 2 2
PI3K 0.078 0.071 0.22 8 -0.27 3 11
FYN -0.001 0.038 -10000 0 -0.32 4 4
mol:Ca2+ 0.006 0.029 -10000 0 -0.24 5 5
JUP 0.025 0.02 -10000 0 -0.45 1 1
PIK3R1 0.027 0.029 -10000 0 -0.44 2 2
mol:DAG 0.006 0.03 -10000 0 -0.24 5 5
CDH1 0.026 0.02 -10000 0 -0.44 1 1
RhoA/GDP 0.012 0.046 -10000 0 -0.33 4 4
establishment of polarity of embryonic epithelium 0.03 0.042 -10000 0 -0.3 2 2
SRC 0.015 0.023 -10000 0 -0.44 1 1
RAC1 0.023 0.008 -10000 0 -10000 0 0
RHOA 0.025 0.02 -10000 0 -0.44 1 1
EGFR 0.02 0.044 -10000 0 -0.44 5 5
CASR -0.003 0.028 -10000 0 -0.38 1 1
RhoA/GTP 0.012 0.034 -10000 0 -0.32 2 2
AKT2 0.045 0.059 0.17 5 -0.32 3 8
actin cable formation 0.023 0.044 -10000 0 -0.3 2 2
apoptosis -0.038 0.061 0.38 3 -0.19 6 9
CTNNA1 0.026 0.029 -10000 0 -0.45 2 2
mol:GDP 0.002 0.037 0.17 3 -0.36 3 6
PIP5K1A 0.029 0.045 -10000 0 -0.28 4 4
PLCG1 0.006 0.03 -10000 0 -0.24 5 5
Rac1/GTP 0.046 0.052 -10000 0 -0.28 3 3
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.023 0.039 -9999 0 -0.44 4 4
positive regulation of NF-kappaB transcription factor activity 0.027 0.034 -9999 0 -0.32 4 4
MAP2K4 0.012 0.027 -9999 0 -10000 0 0
IKBKB 0.023 0.009 -9999 0 -10000 0 0
TNFRSF10B 0.02 0.011 -9999 0 -10000 0 0
TNFRSF10A 0.02 0.011 -9999 0 -10000 0 0
SMPD1 0.007 0.022 -9999 0 -0.21 5 5
IKBKG 0.025 0.02 -9999 0 -0.44 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.02 0.013 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.027 0.033 -9999 0 -0.32 4 4
TRAIL/TRAILR3 0.027 0.043 -9999 0 -0.32 7 7
TRAIL/TRAILR1 0.027 0.033 -9999 0 -0.32 4 4
TRAIL/TRAILR4 0.027 0.034 -9999 0 -0.32 4 4
TRAIL/TRAILR1/DAP3/GTP 0.035 0.032 -9999 0 -0.25 4 4
IKK complex 0.007 0.059 -9999 0 -0.38 4 4
RIPK1 0.026 0.004 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.019 0.003 -9999 0 -10000 0 0
MAPK3 -0.014 0.025 -9999 0 -0.32 4 4
MAP3K1 0.016 0.029 -9999 0 -0.22 5 5
TRAILR4 (trimer) 0.02 0.013 -9999 0 -10000 0 0
TRADD 0.026 0.003 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.011 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.016 0.03 -9999 0 -0.22 4 4
CFLAR 0.026 0 -9999 0 -10000 0 0
MAPK1 -0.013 0.026 -9999 0 -0.32 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.055 0.041 -9999 0 -0.24 3 3
mol:ceramide 0.007 0.022 -9999 0 -0.21 5 5
FADD 0.026 0.004 -9999 0 -10000 0 0
MAPK8 0 0.041 -9999 0 -0.3 1 1
TRAF2 0.025 0.02 -9999 0 -0.44 1 1
TRAILR3 (trimer) 0.02 0.038 -9999 0 -0.44 3 3
CHUK 0.022 0.034 -9999 0 -0.44 3 3
TRAIL/TRAILR1/FADD 0.037 0.035 -9999 0 -0.27 4 4
DAP3 0.025 0.004 -9999 0 -10000 0 0
CASP10 -0.007 0.029 -9999 0 -0.29 5 5
JNK cascade 0.027 0.034 -9999 0 -0.32 4 4
TRAIL (trimer) 0.023 0.039 -9999 0 -0.44 4 4
TNFRSF10C 0.02 0.038 -9999 0 -0.44 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD 0.043 0.036 -9999 0 -0.24 4 4
TRAIL/TRAILR2/FADD 0.037 0.035 -9999 0 -0.27 4 4
cell death 0.007 0.022 -9999 0 -0.21 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.016 0.031 -9999 0 -0.22 4 4
TRAILR2 (trimer) 0.02 0.011 -9999 0 -10000 0 0
CASP8 0.014 0.034 -9999 0 -0.76 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.055 0.041 -9999 0 -0.24 3 3
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.03 0.048 -10000 0 -0.23 15 15
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.03 -10000 0 -0.27 5 5
GNB1 0.025 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.01 0.035 -10000 0 -0.24 10 10
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 0.003 0.009 0.066 10 -10000 0 10
GNAL 0.015 0.063 -10000 0 -0.44 10 10
GNG2 0.021 0.044 -10000 0 -0.44 5 5
CRH -0.015 0.01 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.013 -10000 0 -0.3 1 1
MAPK11 0.004 0.022 -10000 0 -0.3 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0.012 -10000 0 -10000 0 0
SMAD2 0.012 0.035 0.2 1 -0.22 1 2
SMAD3 0.013 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4 0.018 0.064 -10000 0 -0.44 10 10
SMAD4/Ubc9/PIASy 0.036 0.029 -10000 0 -0.27 1 1
SMAD2/SMAD2/SMAD4 0.035 0.045 -10000 0 -10000 0 0
PPM1A 0.024 0.006 -10000 0 -10000 0 0
CALM1 0.024 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.012 0.028 -10000 0 -0.2 1 1
MAP3K1 0.021 0.044 -10000 0 -0.44 5 5
TRAP-1/SMAD4 0.026 0.027 -10000 0 -0.32 2 2
MAPK3 0.025 0.02 -10000 0 -0.44 1 1
MAPK1 0.025 0.005 -10000 0 -10000 0 0
NUP214 0.026 0.003 -10000 0 -10000 0 0
CTDSP1 0.025 0.019 -10000 0 -0.44 1 1
CTDSP2 0.026 0.002 -10000 0 -10000 0 0
CTDSPL 0.026 0.002 -10000 0 -10000 0 0
KPNB1 0.025 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.024 0.028 -10000 0 -0.44 2 2
UBE2I 0.025 0.004 -10000 0 -10000 0 0
NUP153 0.025 0.004 -10000 0 -10000 0 0
KPNA2 0.025 0.005 -10000 0 -10000 0 0
PIAS4 0.025 0.02 -10000 0 -0.44 1 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.043 0.055 -10000 0 -1.1 1 1
CLOCK 0.027 0.008 -10000 0 -10000 0 0
TIMELESS/CRY2 0.031 0.054 -10000 0 -1.2 1 1
DEC1/BMAL1 0.035 0.019 -10000 0 -0.32 1 1
ATR 0.024 0.028 -10000 0 -0.44 2 2
NR1D1 0.014 0.055 -10000 0 -0.8 2 2
ARNTL 0.025 0.028 -10000 0 -0.44 2 2
TIMELESS 0.015 0.055 -10000 0 -1.2 1 1
NPAS2 0.027 0.02 -10000 0 -0.44 1 1
CRY2 0.026 0.003 -10000 0 -10000 0 0
mol:CO -0.006 0.008 0.14 2 -10000 0 2
CHEK1 0.025 0.02 -10000 0 -0.44 1 1
mol:HEME 0.006 0.008 -10000 0 -0.14 2 2
PER1 0.022 0.023 -10000 0 -0.44 1 1
BMAL/CLOCK/NPAS2 0.057 0.029 -10000 0 -0.22 5 5
BMAL1/CLOCK 0.015 0.07 -10000 0 -0.84 2 2
S phase of mitotic cell cycle 0.043 0.055 -10000 0 -1.1 1 1
TIMELESS/CHEK1/ATR 0.043 0.057 -10000 0 -1.1 1 1
mol:NADPH 0.006 0.008 -10000 0 -0.14 2 2
PER1/TIMELESS 0.026 0.058 -10000 0 -0.86 2 2
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.001 0.024 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.05 0.022 -9999 0 -0.27 2 2
E-cadherin/beta catenin 0.037 0.016 -9999 0 -0.32 1 1
CTNNB1 0.026 0.003 -9999 0 -10000 0 0
JUP 0.025 0.02 -9999 0 -0.44 1 1
CDH1 0.025 0.02 -9999 0 -0.44 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 0.034 0.031 -10000 0 -0.32 4 4
FBXW11 0.026 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
CHUK 0.022 0.034 -10000 0 -0.44 3 3
NF kappa B2 p100/RelB 0.068 0.043 -10000 0 -0.34 4 4
NFKB1 0.024 0.02 -10000 0 -0.44 1 1
MAP3K14 0.025 0.02 -10000 0 -0.44 1 1
NF kappa B1 p50/RelB 0.036 0.022 -10000 0 -0.32 2 2
RELB 0.025 0.02 -10000 0 -0.44 1 1
NFKB2 0.024 0.02 -10000 0 -0.44 1 1
NF kappa B2 p52/RelB 0.033 0.024 0.13 1 -0.5 1 2
regulation of B cell activation 0.032 0.024 0.13 1 -0.5 1 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 584 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QG.A5Z2 TCGA.QG.A5Z1 TCGA.QG.A5YX TCGA.QG.A5YW
109_MAP3K5 0.023 -0.0032 0.031 0.023
47_PPARGC1A 0.026 0.026 0.026 0.026
105_BMP4 0.026 0.026 -0.44 0.026
105_BMP6 0.026 0.026 -0.44 0.026
105_BMP7 0.026 0 0.026 0.026
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0.067 0.067 -0.25 0.067
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.026 0.026
84_STAT5B -0.12 0.07 -0.12 0.039
84_STAT5A -0.12 0.07 -0.12 0.039
Methods & Data
Input
  • Expression Data Normalization = Tumor samples 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/COADREAD-TP/9908691/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COADREAD-TP/10005903/Gistic2_Analysis_10006139/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)