PARADIGM pathway analysis of mRNASeq expression and copy number data
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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/C1MS3RQ7
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 48 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
Ephrin A reverse signaling 94
Angiopoietin receptor Tie2-mediated signaling 90
Signaling mediated by p38-alpha and p38-beta 87
Endothelins 80
Glucocorticoid receptor regulatory network 66
Nephrin/Neph1 signaling in the kidney podocyte 56
Reelin signaling pathway 51
IL23-mediated signaling events 50
Thromboxane A2 receptor signaling 49
Integrins in angiogenesis 46
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 486 . 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 ( 486 ).

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
Ephrin A reverse signaling 0.1934 94 659 7 -0.048 0 1000 -1000 -0.012 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1852 90 7962 88 -0.3 0.075 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 0.1790 87 3867 44 -0.15 0.027 1000 -1000 -0.015 -1000
Endothelins 0.1646 80 7733 96 -0.19 0.028 1000 -1000 -0.029 -1000
Glucocorticoid receptor regulatory network 0.1358 66 7546 114 -0.41 0.22 1000 -1000 -0.043 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1152 56 1932 34 -0.051 0.03 1000 -1000 -0.028 -1000
Reelin signaling pathway 0.1049 51 2874 56 -0.094 0.066 1000 -1000 -0.022 -1000
IL23-mediated signaling events 0.1029 50 3015 60 -0.31 0.046 1000 -1000 -0.096 -1000
Thromboxane A2 receptor signaling 0.1008 49 5167 105 -0.12 0.037 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.0947 46 3910 84 -0.099 0.08 1000 -1000 -0.024 -1000
EPHB forward signaling 0.0947 46 3994 85 -0.073 0.092 1000 -1000 -0.044 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0905 44 3433 78 -0.12 0.062 1000 -1000 -0.047 -1000
S1P5 pathway 0.0864 42 720 17 -0.045 0.042 1000 -1000 -0.001 -1000
Aurora B signaling 0.0864 42 2876 67 -0.095 0.11 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 0.0844 41 700 17 -0.079 0.041 1000 -1000 -0.013 -1000
LPA receptor mediated events 0.0823 40 4118 102 -0.057 0.097 1000 -1000 -0.062 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0802 39 2664 68 -0.16 0.061 1000 -1000 -0.074 -1000
Noncanonical Wnt signaling pathway 0.0782 38 1006 26 -0.041 0.027 1000 -1000 -0.027 -1000
Ephrin B reverse signaling 0.0782 38 1860 48 -0.067 0.034 1000 -1000 -0.031 -1000
S1P1 pathway 0.0761 37 1332 36 -0.19 0.027 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 0.0741 36 4561 125 -0.073 0.073 1000 -1000 -0.05 -1000
IL6-mediated signaling events 0.0741 36 2746 75 -0.16 0.033 1000 -1000 -0.042 -1000
Signaling events mediated by the Hedgehog family 0.0720 35 1851 52 -0.041 0.037 1000 -1000 -0.02 -1000
HIF-1-alpha transcription factor network 0.0720 35 2716 76 -0.076 0.071 1000 -1000 -0.055 -1000
EPO signaling pathway 0.0720 35 1973 55 -0.019 0.048 1000 -1000 -0.021 -1000
Glypican 2 network 0.0720 35 142 4 0.031 0.06 1000 -1000 0.022 -1000
Glypican 1 network 0.0700 34 1632 48 -0.034 0.061 1000 -1000 -0.023 -1000
Nongenotropic Androgen signaling 0.0700 34 1805 52 -0.12 0.06 1000 -1000 -0.015 -1000
EGFR-dependent Endothelin signaling events 0.0700 34 722 21 -0.03 0.046 1000 -1000 -0.029 -1000
Osteopontin-mediated events 0.0679 33 1275 38 -0.053 0.05 1000 -1000 -0.021 -1000
amb2 Integrin signaling 0.0679 33 2718 82 -0.12 0.097 1000 -1000 -0.028 -1000
Wnt signaling 0.0679 33 236 7 -0.032 0.027 1000 -1000 -0.001 -1000
S1P4 pathway 0.0679 33 839 25 -0.045 0.048 1000 -1000 -0.014 -1000
Syndecan-1-mediated signaling events 0.0658 32 1096 34 -0.021 0.097 1000 -1000 -0.023 -1000
JNK signaling in the CD4+ TCR pathway 0.0658 32 555 17 -0.12 0.065 1000 -1000 -0.019 -1000
Calcium signaling in the CD4+ TCR pathway 0.0658 32 999 31 -0.089 0.032 1000 -1000 -0.032 -1000
BMP receptor signaling 0.0617 30 2470 81 -0.08 0.066 1000 -1000 -0.019 -1000
Effects of Botulinum toxin 0.0617 30 799 26 -0.028 0.049 1000 -1000 -0.011 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0617 30 3678 120 -0.075 0.085 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 0.0597 29 2444 82 -0.031 0.044 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0576 28 1498 52 -0.051 0.069 1000 -1000 -0.022 -1000
FOXM1 transcription factor network 0.0556 27 1378 51 -0.1 0.065 1000 -1000 -0.1 -1000
Arf6 signaling events 0.0535 26 1669 62 -0.036 0.043 1000 -1000 -0.024 -1000
Fc-epsilon receptor I signaling in mast cells 0.0535 26 2617 97 -0.068 0.04 1000 -1000 -0.051 -1000
PLK1 signaling events 0.0535 26 2260 85 -0.025 0.081 1000 -1000 -0.013 -1000
TCR signaling in naïve CD8+ T cells 0.0535 26 2488 93 -0.054 0.073 1000 -1000 -0.031 -1000
ErbB2/ErbB3 signaling events 0.0514 25 1626 65 -0.081 0.038 1000 -1000 -0.056 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0514 25 2175 85 -0.12 0.035 1000 -1000 -0.027 -1000
IL12-mediated signaling events 0.0494 24 2147 87 -0.18 0.065 1000 -1000 -0.053 -1000
Visual signal transduction: Cones 0.0494 24 913 38 -0.041 0.042 1000 -1000 -0.022 -1000
IL4-mediated signaling events 0.0494 24 2202 91 -0.26 0.13 1000 -1000 -0.14 -1000
Plasma membrane estrogen receptor signaling 0.0494 24 2093 86 -0.13 0.056 1000 -1000 -0.029 -1000
Aurora C signaling 0.0473 23 165 7 0 0.065 1000 -1000 -0.009 -1000
S1P3 pathway 0.0473 23 994 42 -0.027 0.04 1000 -1000 -0.019 -1000
Rapid glucocorticoid signaling 0.0473 23 478 20 -0.053 0.034 1000 -1000 -0.011 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0453 22 1208 54 -0.094 0.066 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 0.0453 22 1371 61 -0.12 0.074 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 0.0453 22 1001 44 -0.13 0.052 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 0.0453 22 1047 47 -0.23 0.042 1000 -1000 -0.035 -1000
Canonical Wnt signaling pathway 0.0453 22 1136 51 -0.12 0.11 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 0.0432 21 1507 69 -0.008 0.045 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 0.0432 21 1157 54 -0.099 0.06 1000 -1000 -0.039 -1000
BCR signaling pathway 0.0432 21 2102 99 -0.11 0.064 1000 -1000 -0.047 -1000
Visual signal transduction: Rods 0.0432 21 1101 52 -0.041 0.058 1000 -1000 -0.013 -1000
BARD1 signaling events 0.0412 20 1172 57 -0.03 0.046 1000 -1000 -0.042 -1000
Signaling events mediated by PTP1B 0.0412 20 1592 76 -0.14 0.094 1000 -1000 -0.024 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0391 19 2483 125 -0.059 0.052 1000 -1000 -0.028 -1000
Syndecan-4-mediated signaling events 0.0391 19 1308 67 -0.049 0.095 1000 -1000 -0.029 -1000
IGF1 pathway 0.0391 19 1130 57 -0.016 0.06 1000 -1000 -0.025 -1000
IL27-mediated signaling events 0.0370 18 933 51 -0.34 0.074 1000 -1000 -0.039 -1000
Insulin Pathway 0.0370 18 1349 74 -0.13 0.074 1000 -1000 -0.037 -1000
Caspase cascade in apoptosis 0.0350 17 1259 74 -0.038 0.064 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 0.0350 17 87 5 0.016 0.034 1000 -1000 0.02 -1000
Ceramide signaling pathway 0.0350 17 1305 76 -0.021 0.072 1000 -1000 -0.023 -1000
IL1-mediated signaling events 0.0350 17 1113 62 -0.037 0.067 1000 -1000 -0.023 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0350 17 1330 74 -0.14 0.053 1000 -1000 -0.044 -1000
TCGA08_retinoblastoma 0.0350 17 137 8 -0.009 0.056 1000 -1000 -0.002 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0350 17 576 33 -0.067 0.061 1000 -1000 -0.016 -1000
TCGA08_p53 0.0329 16 115 7 -0.014 0.026 1000 -1000 -0.01 -1000
VEGFR1 specific signals 0.0329 16 940 56 -0.055 0.041 1000 -1000 -0.032 -1000
Regulation of nuclear SMAD2/3 signaling 0.0309 15 2047 136 -0.069 0.15 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 0.0309 15 1166 76 -0.016 0.065 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0309 15 1060 69 -0.081 0.059 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0309 15 421 28 -0.027 0.052 1000 -1000 -0.02 -1000
Cellular roles of Anthrax toxin 0.0309 15 598 39 -0.023 0.026 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0309 15 1006 65 -0.22 0.066 1000 -1000 -0.031 -1000
Class I PI3K signaling events 0.0309 15 1120 73 -0.042 0.064 1000 -1000 -0.025 -1000
Aurora A signaling 0.0288 14 864 60 -0.063 0.072 1000 -1000 -0.024 -1000
mTOR signaling pathway 0.0288 14 774 53 -0.14 0.051 1000 -1000 -0.02 -1000
Nectin adhesion pathway 0.0288 14 929 63 -0.036 0.062 1000 -1000 -0.035 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0288 14 550 37 -0.019 0.062 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0288 14 730 49 0 0.038 1000 -1000 -0.025 -1000
HIF-2-alpha transcription factor network 0.0288 14 634 43 -0.048 0.049 1000 -1000 -0.039 -1000
IL2 signaling events mediated by PI3K 0.0288 14 830 58 -0.035 0.068 1000 -1000 -0.03 -1000
TCGA08_rtk_signaling 0.0288 14 372 26 -0.015 0.049 1000 -1000 -0.007 -1000
Regulation of Androgen receptor activity 0.0288 14 1017 70 -0.079 0.042 1000 -1000 -0.04 -1000
FOXA2 and FOXA3 transcription factor networks 0.0267 13 635 46 -0.063 0.043 1000 -1000 -0.082 -1000
Retinoic acid receptors-mediated signaling 0.0267 13 762 58 -0.042 0.05 1000 -1000 -0.028 -1000
IL2 signaling events mediated by STAT5 0.0247 12 283 22 -0.013 0.047 1000 -1000 -0.025 -1000
LPA4-mediated signaling events 0.0226 11 137 12 -0.03 0.021 1000 -1000 -0.018 -1000
IFN-gamma pathway 0.0226 11 781 68 -0.022 0.073 1000 -1000 -0.039 -1000
Signaling events mediated by PRL 0.0226 11 406 34 -0.036 0.046 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class III 0.0206 10 414 40 -0.07 0.051 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0206 10 845 83 -0.047 0.05 1000 -1000 -0.021 -1000
PDGFR-beta signaling pathway 0.0206 10 990 97 -0.1 0.07 1000 -1000 -0.039 -1000
Syndecan-3-mediated signaling events 0.0185 9 346 35 -0.022 0.073 1000 -1000 -0.014 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0185 9 425 45 -0.001 0.065 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 0.0185 9 730 76 -0.018 0.057 1000 -1000 -0.036 -1000
E-cadherin signaling in keratinocytes 0.0185 9 427 43 -0.015 0.046 1000 -1000 -0.012 -1000
Class I PI3K signaling events mediated by Akt 0.0165 8 599 68 -0.033 0.05 1000 -1000 -0.023 -1000
FoxO family signaling 0.0165 8 536 64 -0.023 0.058 1000 -1000 -0.049 -1000
Paxillin-dependent events mediated by a4b1 0.0165 8 317 36 -0.047 0.048 1000 -1000 -0.028 -1000
p38 MAPK signaling pathway 0.0165 8 357 44 -0.029 0.068 1000 -1000 -0.014 -1000
Atypical NF-kappaB pathway 0.0144 7 220 31 -0.009 0.032 1000 -1000 -0.021 -1000
Regulation of Telomerase 0.0144 7 760 102 -0.024 0.057 1000 -1000 -0.04 -1000
Canonical NF-kappaB pathway 0.0123 6 264 39 -0.004 0.057 1000 -1000 -0.019 -1000
Class IB PI3K non-lipid kinase events 0.0123 6 18 3 -0.028 0.028 1000 -1000 -0.019 -1000
Signaling mediated by p38-gamma and p38-delta 0.0103 5 78 15 -0.016 0.029 1000 -1000 -0.023 -1000
PLK2 and PLK4 events 0.0082 4 13 3 -0.013 0.027 1000 -1000 -0.019 -1000
Circadian rhythm pathway 0.0082 4 96 22 -0.007 0.04 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0082 4 197 48 -0.01 0.049 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0062 3 75 23 0.01 0.054 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class II 0.0062 3 251 75 -0.029 0.065 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 0.0062 3 126 32 -0.013 0.046 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class I 0.0062 3 337 104 -0.052 0.064 1000 -1000 -0.036 -1000
Arf6 trafficking events 0.0062 3 236 71 -0.047 0.05 1000 -1000 -0.035 -1000
Arf1 pathway 0.0041 2 111 54 -0.006 0.048 1000 -1000 -0.012 -1000
Arf6 downstream pathway 0.0021 1 58 43 -0.053 0.054 1000 -1000 -0.032 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 -0.011 0.06 1000 -1000 -0.027 -1000
E-cadherin signaling events 0.0000 0 0 5 0.024 0.047 1000 -1000 0.023 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.071 1000 -1000 0 -1000
Total NA 3050 181747 7203 -9 7.5 131000 -131000 -3.8 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.028 0.1 0.12 1 -0.19 134 135
EFNA5 -0.005 0.095 0.17 1 -0.31 43 44
FYN -0.045 0.073 0.18 3 -0.18 97 100
neuron projection morphogenesis -0.028 0.1 0.12 1 -0.19 134 135
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.028 0.1 0.12 1 -0.19 134 135
EPHA5 -0.048 0.14 0.17 2 -0.31 108 110
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.21 0.39 -10000 0 -0.8 143 143
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.39 136 136
NCK1/Dok-R -0.23 0.44 -10000 0 -0.9 141 141
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
mol:beta2-estradiol 0.067 0.11 0.24 142 -10000 0 142
RELA 0.026 0.006 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
F2 0.075 0.13 0.26 145 -10000 0 145
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.21 0.43 -10000 0 -0.86 143 143
FN1 0.021 0.05 0.17 4 -0.31 10 14
PLD2 -0.26 0.46 -10000 0 -0.94 143 143
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GRB14 0.048 0.06 0.17 82 -0.31 3 85
ELK1 -0.24 0.41 -10000 0 -0.86 142 142
GRB7 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.024 0.031 -10000 0 -0.31 4 4
Tie2/Ang1/alpha5/beta1 Integrin -0.23 0.46 -10000 0 -0.92 142 142
CDKN1A -0.15 0.28 -10000 0 -0.57 128 128
ITGA5 0.018 0.055 0.17 1 -0.31 13 14
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.45 -10000 0 -0.91 142 142
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO -0.15 0.3 0.43 1 -0.6 138 139
PLG -0.27 0.46 -10000 0 -0.95 143 143
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.2 0.37 -10000 0 -0.76 141 141
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.022 0.028 -10000 0 -0.31 3 3
ANGPT2 -0.15 0.26 -10000 0 -0.64 80 80
BMX -0.27 0.46 -10000 0 -0.95 143 143
ANGPT1 -0.3 0.49 -10000 0 -1.1 136 136
tube development -0.17 0.3 -10000 0 -0.62 139 139
ANGPT4 0.022 0.016 0.17 1 -10000 0 1
response to hypoxia -0.018 0.03 -10000 0 -0.071 13 13
Tie2/Ang1/GRB14 -0.25 0.49 -10000 0 -0.98 143 143
alpha5/beta1 Integrin 0.032 0.042 -10000 0 -0.21 13 13
FGF2 0.005 0.083 0.17 1 -0.31 32 33
STAT5A (dimer) -0.18 0.35 -10000 0 -0.72 134 134
mol:L-citrulline -0.15 0.3 0.43 1 -0.6 138 139
AGTR1 0.038 0.085 0.17 81 -0.31 17 98
MAPK14 -0.26 0.47 -10000 0 -0.95 143 143
Tie2/SHP2 -0.15 0.34 -10000 0 -0.94 68 68
TEK -0.16 0.38 -10000 0 -1 68 68
RPS6KB1 -0.2 0.38 0.4 1 -0.77 142 143
Angiotensin II/AT1 0.029 0.059 0.12 80 -0.2 18 98
Tie2/Ang1/GRB2 -0.26 0.48 -10000 0 -0.97 143 143
MAPK3 -0.25 0.42 -10000 0 -0.88 142 142
MAPK1 -0.25 0.42 -10000 0 -0.88 142 142
Tie2/Ang1/GRB7 -0.26 0.48 -10000 0 -0.97 143 143
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.27 0.46 -10000 0 -0.95 143 143
PI3K -0.24 0.44 -10000 0 -0.91 143 143
FES -0.26 0.47 -10000 0 -0.95 144 144
Crk/Dok-R -0.24 0.45 -10000 0 -0.9 143 143
Tie2/Ang1/ABIN2 -0.26 0.48 -10000 0 -0.97 143 143
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.19 0.35 -10000 0 -0.72 143 143
STAT5A 0.026 0.016 -10000 0 -0.31 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.18 0.38 0.39 3 -0.75 139 142
Tie2/Ang2 -0.23 0.41 -10000 0 -0.84 135 135
Tie2/Ang1 -0.28 0.5 -10000 0 -1 143 143
FOXO1 -0.19 0.35 -10000 0 -0.72 142 142
ELF1 0.008 0.048 -10000 0 -0.19 15 15
ELF2 -0.26 0.45 -10000 0 -0.92 143 143
mol:Choline -0.25 0.44 -10000 0 -0.91 143 143
cell migration -0.06 0.1 -10000 0 -0.22 139 139
FYN -0.19 0.34 -10000 0 -0.71 138 138
DOK2 0.02 0.017 0.17 3 -10000 0 3
negative regulation of cell cycle -0.13 0.25 -10000 0 -0.52 129 129
ETS1 -0.047 0.13 0.17 1 -0.25 131 132
PXN -0.14 0.32 0.42 7 -0.63 136 143
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 -0.17 0.33 0.44 1 -0.68 138 139
RAC1 0.025 0.008 -10000 0 -10000 0 0
TNF -0.066 0.15 0.18 10 -0.28 157 167
MAPKKK cascade -0.25 0.44 -10000 0 -0.91 143 143
RASA1 0.024 0.022 -10000 0 -0.31 2 2
Tie2/Ang1/Shc -0.26 0.48 -10000 0 -0.96 143 143
NCK1 0.025 0.007 -10000 0 -10000 0 0
vasculogenesis -0.13 0.27 0.42 1 -0.54 138 139
mol:Phosphatidic acid -0.25 0.44 -10000 0 -0.91 143 143
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP -0.15 0.3 0.43 1 -0.6 138 139
Rac1/GTP -0.18 0.35 -10000 0 -0.72 141 141
MMP2 -0.27 0.46 -10000 0 -0.95 143 143
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.37 -10000 0 -0.81 107 107
MKNK1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.034 0.14 -10000 0 -0.3 105 105
ATF2/c-Jun -0.053 0.15 -10000 0 -0.3 100 100
MAPK11 -0.032 0.14 0.19 5 -0.3 103 108
MITF -0.052 0.17 -10000 0 -0.36 100 100
MAPKAPK5 -0.05 0.16 -10000 0 -0.35 100 100
KRT8 -0.048 0.16 -10000 0 -0.35 99 99
MAPKAPK3 0.027 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.047 0.21 -10000 0 -0.43 105 105
CEBPB -0.047 0.16 -10000 0 -0.35 98 98
SLC9A1 -0.051 0.16 -10000 0 -0.35 104 104
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.069 0.19 -10000 0 -0.37 121 121
p38alpha-beta/MNK1 -0.02 0.18 -10000 0 -0.35 102 102
JUN -0.054 0.14 -10000 0 -0.3 100 100
PPARGC1A -0.13 0.24 -10000 0 -0.41 170 170
USF1 -0.051 0.16 -10000 0 -0.36 101 101
RAB5/GDP/GDI1 -0.026 0.12 -10000 0 -0.26 97 97
NOS2 -0.082 0.26 -10000 0 -0.51 98 98
DDIT3 -0.05 0.16 -10000 0 -0.35 103 103
RAB5A 0.026 0.005 -10000 0 -10000 0 0
HSPB1 -0.039 0.14 0.28 20 -0.31 85 105
p38alpha-beta/HBP1 -0.019 0.17 -10000 0 -0.35 92 92
CREB1 -0.055 0.17 -10000 0 -0.38 100 100
RAB5/GDP 0.02 0.004 -10000 0 -10000 0 0
EIF4E -0.05 0.14 0.22 1 -0.32 100 101
RPS6KA4 -0.049 0.16 0.26 1 -0.35 102 103
PLA2G4A -0.057 0.15 0.22 1 -0.33 104 105
GDI1 -0.05 0.16 -10000 0 -0.35 104 104
TP53 -0.072 0.18 -10000 0 -0.44 96 96
RPS6KA5 -0.057 0.17 -10000 0 -0.37 102 102
ESR1 -0.061 0.18 -10000 0 -0.37 111 111
HBP1 0.025 0.008 -10000 0 -10000 0 0
MEF2C -0.059 0.18 -10000 0 -0.38 106 106
MEF2A -0.053 0.16 -10000 0 -0.36 103 103
EIF4EBP1 -0.065 0.2 0.21 1 -0.43 98 99
KRT19 -0.074 0.2 -10000 0 -0.39 121 121
ELK4 -0.05 0.16 -10000 0 -0.35 100 100
ATF6 -0.052 0.16 -10000 0 -0.36 102 102
ATF1 -0.054 0.17 0.21 1 -0.38 99 100
p38alpha-beta/MAPKAPK2 -0.021 0.17 -10000 0 -0.34 102 102
p38alpha-beta/MAPKAPK3 -0.019 0.18 -10000 0 -0.36 97 97
Endothelins

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
AKT1 -0.04 0.14 0.26 23 -0.26 107 130
PTK2B 0.019 0.013 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.39 0.38 1 -0.92 94 95
EDN1 -0.006 0.11 0.2 33 -0.21 79 112
EDN3 -0.09 0.16 0.17 2 -0.31 168 170
EDN2 0.014 0.075 0.17 10 -0.31 23 33
HRAS/GDP -0.074 0.2 0.28 5 -0.42 91 96
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.04 0.15 0.17 20 -0.35 69 89
ADCY4 -0.063 0.16 0.19 32 -0.32 93 125
ADCY5 -0.075 0.18 0.2 28 -0.38 98 126
ADCY6 -0.061 0.16 0.2 32 -0.32 90 122
ADCY7 -0.061 0.15 0.19 29 -0.31 93 122
ADCY1 -0.055 0.15 0.19 28 -0.32 90 118
ADCY2 -0.062 0.16 0.2 31 -0.33 94 125
ADCY3 -0.061 0.15 0.2 31 -0.32 91 122
ADCY8 -0.058 0.14 0.18 18 -0.3 85 103
ADCY9 -0.061 0.15 0.19 30 -0.33 87 117
arachidonic acid secretion -0.13 0.28 0.3 6 -0.51 134 140
ETB receptor/Endothelin-1/Gq/GTP -0.04 0.13 -10000 0 -0.29 88 88
GNAO1 -0.024 0.12 -10000 0 -0.31 70 70
HRAS 0.028 0.015 0.17 5 -10000 0 5
ETA receptor/Endothelin-1/G12/GTP 0.002 0.15 0.33 20 -0.25 94 114
ETA receptor/Endothelin-1/Gs/GTP -0.036 0.18 0.31 19 -0.27 138 157
mol:GTP -0.002 0.007 -10000 0 -10000 0 0
COL3A1 -0.037 0.14 0.26 25 -0.34 53 78
EDNRB -0.011 0.1 0.17 1 -0.31 52 53
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.06 0.18 0.25 17 -0.43 78 95
CYSLTR1 -0.051 0.17 0.26 24 -0.41 61 85
SLC9A1 -0.019 0.09 0.18 23 -0.19 71 94
mol:GDP -0.086 0.21 0.28 8 -0.44 92 100
SLC9A3 -0.16 0.4 -10000 0 -0.86 97 97
RAF1 -0.094 0.22 0.27 10 -0.43 111 121
JUN -0.11 0.29 -10000 0 -0.69 73 73
JAK2 -0.041 0.14 0.26 23 -0.27 101 124
mol:IP3 -0.042 0.15 0.2 2 -0.35 65 67
ETA receptor/Endothelin-1 -0.016 0.18 0.38 23 -0.3 109 132
PLCB1 0.022 0.032 -10000 0 -0.31 4 4
PLCB2 0.021 0.019 0.17 2 -10000 0 2
ETA receptor/Endothelin-3 -0.078 0.16 0.17 16 -0.25 190 206
FOS -0.16 0.35 0.38 3 -0.84 90 93
Gai/GDP -0.17 0.37 -10000 0 -0.79 119 119
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.068 0.19 0.23 18 -0.43 78 96
BCAR1 0.022 0.011 -10000 0 -10000 0 0
PRKCB1 -0.046 0.14 0.2 2 -0.34 69 71
GNAQ 0.015 0.023 -10000 0 -10000 0 0
GNAZ -0.002 0.093 -10000 0 -0.31 41 41
GNAL -0.053 0.14 -10000 0 -0.31 114 114
Gs family/GDP -0.1 0.22 0.27 6 -0.43 116 122
ETA receptor/Endothelin-1/Gq/GTP -0.046 0.16 0.18 18 -0.35 77 95
MAPK14 -0.044 0.13 0.21 1 -0.3 71 72
TRPC6 -0.18 0.42 -10000 0 -0.99 94 94
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.039 0.13 -10000 0 -0.3 75 75
ETB receptor/Endothelin-2 0 0.093 0.14 11 -0.22 72 83
ETB receptor/Endothelin-3 -0.067 0.14 0.14 2 -0.24 181 183
ETB receptor/Endothelin-1 -0.009 0.12 0.17 18 -0.24 75 93
MAPK3 -0.15 0.32 0.34 5 -0.74 95 100
MAPK1 -0.15 0.33 0.33 5 -0.75 97 102
Rac1/GDP -0.073 0.19 0.28 5 -0.41 87 92
cAMP biosynthetic process -0.053 0.18 0.27 21 -0.37 84 105
MAPK8 -0.13 0.36 -10000 0 -0.73 102 102
SRC 0.026 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.059 0.16 0.16 2 -0.33 104 106
p130Cas/CRK/Src/PYK2 -0.14 0.28 0.3 7 -0.61 105 112
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.073 0.19 0.28 5 -0.42 84 89
COL1A2 -0.049 0.17 0.25 16 -0.4 63 79
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.008 0.12 0.17 21 -0.23 79 100
mol:DAG -0.043 0.15 0.2 2 -0.35 65 67
MAP2K2 -0.12 0.26 0.29 7 -0.55 107 114
MAP2K1 -0.12 0.26 0.33 6 -0.55 105 111
EDNRA -0.028 0.14 0.21 24 -0.26 100 124
positive regulation of muscle contraction -0.027 0.13 0.22 39 -0.24 87 126
Gq family/GDP -0.064 0.2 0.25 1 -0.42 87 88
HRAS/GTP -0.077 0.19 0.25 7 -0.41 88 95
PRKCH -0.047 0.14 0.21 3 -0.34 67 70
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.052 0.15 0.21 3 -0.36 71 74
PRKCB -0.07 0.18 0.21 6 -0.38 91 97
PRKCE -0.044 0.14 0.25 3 -0.33 66 69
PRKCD -0.047 0.15 0.21 5 -0.34 67 72
PRKCG -0.05 0.15 0.21 6 -0.34 69 75
regulation of vascular smooth muscle contraction -0.19 0.41 0.4 3 -1 88 91
PRKCQ -0.054 0.15 0.21 1 -0.37 65 66
PLA2G4A -0.14 0.32 0.31 6 -0.57 134 140
GNA14 0.015 0.023 -10000 0 -10000 0 0
GNA15 0.005 0.069 -10000 0 -0.31 20 20
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA11 0.009 0.059 -10000 0 -0.31 14 14
Rac1/GTP 0.002 0.15 0.33 20 -0.24 100 120
MMP1 -0.008 0.18 0.27 21 -0.68 27 48
Glucocorticoid receptor regulatory network

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
PCK2 0.076 0.1 0.3 14 -10000 0 14
SMARCC2 0.009 0.046 -10000 0 -0.11 49 49
SMARCC1 0.008 0.046 -10000 0 -0.11 54 54
TBX21 -0.081 0.16 0.43 2 -0.38 74 76
SUMO2 0.029 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.035 0.021 0.18 9 -10000 0 9
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 0.026 0.016 -10000 0 -0.31 1 1
GR alpha/HSP90/FKBP51/HSP90 0.11 0.12 0.28 98 -10000 0 98
PRL -0.067 0.12 -10000 0 -0.49 2 2
cortisol/GR alpha (dimer)/TIF2 0.12 0.24 0.51 104 -10000 0 104
RELA -0.029 0.1 -10000 0 -0.2 117 117
FGG 0.16 0.23 0.45 150 -0.28 1 151
GR beta/TIF2 0.05 0.14 0.28 82 -0.24 30 112
IFNG -0.21 0.29 0.35 1 -0.63 123 124
apoptosis 0.1 0.2 0.52 71 -0.42 2 73
CREB1 0.001 0.1 -10000 0 -0.28 52 52
histone acetylation -0.056 0.17 0.32 16 -0.38 72 88
BGLAP -0.09 0.15 -10000 0 -0.39 57 57
GR/PKAc 0.11 0.11 0.29 88 -10000 0 88
NF kappa B1 p50/RelA -0.047 0.18 -10000 0 -0.33 128 128
SMARCD1 0.009 0.046 -10000 0 -0.12 40 40
MDM2 0.085 0.11 0.22 139 -10000 0 139
GATA3 -0.064 0.15 -10000 0 -0.31 135 135
AKT1 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.072 0.13 -10000 0 -0.46 19 19
GSK3B 0.028 0.019 -10000 0 -10000 0 0
NR1I3 0.1 0.2 0.5 68 -0.7 3 71
CSN2 0.13 0.19 0.38 142 -10000 0 142
BRG1/BAF155/BAF170/BAF60A 0.014 0.14 -10000 0 -0.3 71 71
NFATC1 0.025 0.009 -10000 0 -10000 0 0
POU2F1 0.026 0.007 -10000 0 -10000 0 0
CDKN1A -0.028 0.15 -10000 0 -1.4 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.005 0.014 -10000 0 -10000 0 0
SFN -0.006 0.1 -10000 0 -0.31 48 48
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.11 0.29 74 -0.18 2 76
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.066 0.27 0.47 74 -0.65 35 109
JUN -0.12 0.18 0.29 1 -0.38 124 125
IL4 -0.09 0.15 -10000 0 -0.46 30 30
CDK5R1 0.036 0.032 0.17 23 -10000 0 23
PRKACA 0.027 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.069 0.11 0.18 25 -0.25 91 116
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.29 86 -10000 0 86
cortisol/GR alpha (monomer) 0.22 0.31 0.6 155 -10000 0 155
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.067 0.14 0.19 4 -0.27 123 127
AP-1/NFAT1-c-4 -0.21 0.29 -10000 0 -0.55 171 171
AFP -0.088 0.13 -10000 0 -0.49 6 6
SUV420H1 0.026 0.006 -10000 0 -10000 0 0
IRF1 0.13 0.16 0.4 81 -10000 0 81
TP53 0.032 0.014 -10000 0 -10000 0 0
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.32 0.44 -10000 0 -0.92 143 143
KRT14 -0.35 0.53 -10000 0 -1.1 144 144
TBP 0.032 0.013 -10000 0 -0.21 1 1
CREBBP 0.05 0.14 0.26 102 -0.26 40 142
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.023 0.009 -10000 0 -10000 0 0
AP-1 -0.21 0.29 -10000 0 -0.55 172 172
MAPK14 0.029 0.017 -10000 0 -10000 0 0
MAPK10 0.026 0.036 -10000 0 -0.3 4 4
MAPK11 0.032 0.026 0.16 8 -10000 0 8
KRT5 -0.41 0.5 -10000 0 -1 186 186
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.035 0.021 0.18 9 -10000 0 9
CGA -0.16 0.31 -10000 0 -0.81 73 73
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.067 0.17 0.38 71 -0.38 7 78
MAPK3 0.03 0.019 -10000 0 -10000 0 0
MAPK1 0.029 0.017 -10000 0 -10000 0 0
ICAM1 -0.15 0.24 -10000 0 -0.53 107 107
NFKB1 -0.03 0.11 -10000 0 -0.2 113 113
MAPK8 -0.11 0.18 0.34 2 -0.35 136 138
MAPK9 0.029 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.1 0.21 0.52 71 -0.43 2 73
BAX -0.02 0.076 -10000 0 -10000 0 0
POMC -0.24 0.45 0.41 1 -1.4 59 60
EP300 0.05 0.14 0.26 105 -0.27 43 148
cortisol/GR alpha (dimer)/p53 0.16 0.25 0.53 119 -10000 0 119
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.088 0.19 93 -10000 0 93
SGK1 -0.077 0.46 0.44 4 -1.1 75 79
IL13 -0.28 0.36 -10000 0 -0.8 133 133
IL6 -0.24 0.39 -10000 0 -0.83 129 129
PRKACG 0.019 0.005 -10000 0 -10000 0 0
IL5 -0.24 0.3 -10000 0 -0.69 123 123
IL2 -0.22 0.29 -10000 0 -0.63 130 130
CDK5 0.027 0.011 -10000 0 -10000 0 0
PRKACB 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.31 -10000 0 -0.62 123 123
CDK5R1/CDK5 0.046 0.031 0.15 22 -10000 0 22
NF kappa B1 p50/RelA/PKAc -0.007 0.16 -10000 0 -0.27 98 98
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.24 0.49 144 -10000 0 144
SMARCA4 0.009 0.046 -10000 0 -0.13 30 30
chromatin remodeling 0.065 0.2 0.36 90 -0.36 28 118
NF kappa B1 p50/RelA/Cbp -0.011 0.22 0.35 36 -0.38 81 117
JUN (dimer) -0.12 0.18 0.29 1 -0.38 124 125
YWHAH 0.027 0.004 -10000 0 -10000 0 0
VIPR1 -0.075 0.15 0.34 3 -0.36 66 69
NR3C1 0.14 0.2 0.4 137 -10000 0 137
NR4A1 -0.024 0.16 -10000 0 -0.43 59 59
TIF2/SUV420H1 0.004 0.078 -10000 0 -0.21 53 53
MAPKKK cascade 0.1 0.2 0.52 71 -0.42 2 73
cortisol/GR alpha (dimer)/Src-1 0.19 0.26 0.51 153 -10000 0 153
PBX1 0.026 0.016 -10000 0 -0.31 1 1
POU1F1 0.021 0.012 0.18 2 -10000 0 2
SELE -0.26 0.4 -10000 0 -0.85 132 132
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.065 0.2 0.36 90 -0.37 28 118
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.24 0.49 144 -10000 0 144
mol:cortisol 0.13 0.19 0.35 157 -10000 0 157
MMP1 -0.1 0.28 -10000 0 -0.98 42 42
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.009 0.11 0.22 90 -0.15 10 100
KIRREL -0.036 0.13 -10000 0 -0.32 90 90
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.009 0.11 0.15 10 -0.22 90 100
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.025 0.007 -10000 0 -10000 0 0
WASL 0.025 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.021 0.095 0.22 1 -0.17 89 90
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.015 0.078 -10000 0 -0.19 79 79
FYN -0.029 0.068 0.22 12 -0.16 72 84
mol:Ca2+ 0.02 0.093 0.21 1 -0.17 88 89
mol:DAG 0.021 0.094 0.22 1 -0.17 88 89
NPHS2 -0.003 0.033 0.17 3 -10000 0 3
mol:IP3 0.021 0.094 0.22 1 -0.17 88 89
regulation of endocytosis 0.007 0.08 -10000 0 -0.15 89 89
Nephrin/NEPH1/podocin/Cholesterol 0.01 0.087 0.2 1 -0.16 90 91
establishment of cell polarity -0.009 0.11 0.15 10 -0.22 90 100
Nephrin/NEPH1/podocin/NCK1-2 0.03 0.093 0.23 1 -0.16 85 86
Nephrin/NEPH1/beta Arrestin2 0.008 0.081 -10000 0 -0.15 88 88
NPHS1 0.004 0.042 0.18 11 -10000 0 11
Nephrin/NEPH1/podocin 0.007 0.083 0.17 1 -0.16 90 91
TJP1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.022 0.094 0.22 1 -0.17 88 89
CD2AP 0.027 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.022 0.094 0.22 1 -0.17 87 88
GRB2 0.026 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.051 0.095 0.22 12 -0.2 115 127
cytoskeleton organization -0.027 0.076 0.2 3 -0.2 76 79
Nephrin/NEPH1 0 0.074 0.15 1 -0.15 90 91
Nephrin/NEPH1/ZO-1 0.01 0.091 0.18 1 -0.18 88 89
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.041 0.024 0.14 21 -10000 0 21
VLDLR 0.026 0.016 -10000 0 -0.31 1 1
CRKL 0.027 0.005 -10000 0 -10000 0 0
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
FYN 0.023 0.01 -10000 0 -10000 0 0
ITGA3 0.02 0.048 -10000 0 -0.31 10 10
RELN/VLDLR/Fyn 0.049 0.045 -10000 0 -0.18 5 5
MAPK8IP1/MKK7/MAP3K11/JNK1 0.065 0.045 -10000 0 -0.16 11 11
AKT1 -0.052 0.094 0.13 2 -0.18 146 148
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
DAB1 -0.094 0.16 0.17 2 -0.31 173 175
RELN/LRP8/DAB1 -0.019 0.11 0.22 2 -0.17 155 157
LRPAP1/LRP8 0.04 0.014 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.011 0.1 0.22 2 -0.16 153 155
DAB1/alpha3/beta1 Integrin -0.015 0.1 -10000 0 -0.16 139 139
long-term memory -0.039 0.13 0.32 1 -0.19 169 170
DAB1/LIS1 -0.004 0.11 0.22 1 -0.16 136 137
DAB1/CRLK/C3G -0.013 0.1 -10000 0 -0.16 137 137
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
DAB1/NCK2 -0.003 0.11 0.22 1 -0.16 144 145
ARHGEF2 0.026 0.006 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.041 0.13 0.17 1 -0.31 97 98
CDK5R1 0.034 0.03 0.17 23 -10000 0 23
RELN 0.039 0.056 0.17 58 -0.31 4 62
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
RELN/LRP8/Fyn 0.051 0.045 0.23 3 -0.16 4 7
GRIN2A/RELN/LRP8/DAB1/Fyn -0.035 0.14 -10000 0 -0.19 191 191
MAPK8 0.019 0.05 -10000 0 -0.31 11 11
RELN/VLDLR/DAB1 -0.021 0.11 -10000 0 -0.17 156 156
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.06 0.092 0.17 13 -0.19 138 151
RELN/LRP8 0.057 0.044 0.23 3 -0.16 5 8
GRIN2B/RELN/LRP8/DAB1/Fyn -0.007 0.11 0.24 2 -0.16 146 148
PI3K 0.032 0.033 -10000 0 -0.25 5 5
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.035 -10000 0 -0.21 9 9
RAP1A -0.044 0.1 0.34 13 -0.22 2 15
PAFAH1B1 0.025 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.008 0.17 1 -10000 0 1
CRLK/C3G 0.037 0.011 -10000 0 -10000 0 0
GRIN2B 0.018 0.01 0.17 1 -10000 0 1
NCK2 0.027 0.003 -10000 0 -10000 0 0
neuron differentiation -0.042 0.099 0.19 1 -0.26 39 40
neuron adhesion -0.048 0.1 0.33 15 -0.28 6 21
LRP8 0.029 0.017 0.17 7 -10000 0 7
GSK3B -0.051 0.089 0.14 3 -0.18 122 125
RELN/VLDLR/DAB1/Fyn -0.013 0.1 -10000 0 -0.16 154 154
MAP3K11 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.048 0.1 0.15 2 -0.19 150 152
CDK5 0.025 0.008 -10000 0 -10000 0 0
MAPT 0.004 0.06 0.75 3 -10000 0 3
neuron migration -0.058 0.11 0.28 9 -0.25 13 22
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.04 0.098 0.19 1 -0.26 38 39
RELN/VLDLR 0.066 0.048 0.24 3 -0.16 5 8
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.22 0.51 -10000 0 -1.2 81 81
IL23A -0.24 0.53 -10000 0 -1.3 74 74
NF kappa B1 p50/RelA/I kappa B alpha -0.21 0.52 -10000 0 -1.2 76 76
positive regulation of T cell mediated cytotoxicity -0.25 0.58 -10000 0 -1.4 78 78
ITGA3 -0.22 0.5 -10000 0 -1.2 79 79
IL17F -0.14 0.32 0.42 1 -0.73 75 76
IL12B 0.013 0.068 0.21 23 -0.14 3 26
STAT1 (dimer) -0.24 0.56 -10000 0 -1.3 78 78
CD4 -0.21 0.48 -10000 0 -1.1 75 75
IL23 -0.23 0.51 -10000 0 -1.2 74 74
IL23R -0.025 0.16 -10000 0 -0.77 13 13
IL1B -0.26 0.56 -10000 0 -1.3 81 81
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.48 -10000 0 -1.1 74 74
TYK2 0.006 0.042 -10000 0 -10000 0 0
STAT4 0.028 0.038 0.17 13 -0.31 4 17
STAT3 0.026 0.005 -10000 0 -10000 0 0
IL18RAP 0.021 0.066 0.17 16 -0.31 16 32
IL12RB1 0.006 0.064 0.19 15 -0.28 7 22
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
IL12Rbeta1/TYK2 0.011 0.065 0.17 12 -0.26 5 17
IL23R/JAK2 -0.017 0.17 -10000 0 -0.85 8 8
positive regulation of chronic inflammatory response -0.25 0.58 -10000 0 -1.4 78 78
natural killer cell activation 0.002 0.008 -10000 0 -10000 0 0
JAK2 0.006 0.054 -10000 0 -0.32 1 1
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
NFKB1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.025 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.48 -10000 0 -1.2 74 74
ALOX12B -0.22 0.5 -10000 0 -1.1 83 83
CXCL1 -0.31 0.6 -10000 0 -1.2 126 126
T cell proliferation -0.25 0.58 -10000 0 -1.4 78 78
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
IL17A -0.094 0.26 0.39 2 -0.56 71 73
PI3K -0.22 0.52 -10000 0 -1.2 76 76
IFNG 0 0.027 -10000 0 -0.1 6 6
STAT3 (dimer) -0.21 0.5 -10000 0 -1.2 75 75
IL18R1 0.024 0.037 -10000 0 -0.3 6 6
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.33 -10000 0 -0.74 74 74
IL18/IL18R 0.046 0.063 -10000 0 -0.18 28 28
macrophage activation -0.011 0.021 0.028 2 -0.045 74 76
TNF -0.25 0.54 -10000 0 -1.3 78 78
STAT3/STAT4 -0.22 0.53 -10000 0 -1.2 78 78
STAT4 (dimer) -0.24 0.56 -10000 0 -1.3 78 78
IL18 0.019 0.05 -10000 0 -0.31 11 11
IL19 -0.21 0.48 -10000 0 -1.1 74 74
STAT5A (dimer) -0.24 0.56 -10000 0 -1.3 78 78
STAT1 0.03 0.019 0.17 9 -10000 0 9
SOCS3 -0.012 0.11 0.17 6 -0.31 57 63
CXCL9 -0.21 0.49 -10000 0 -1.2 76 76
MPO -0.25 0.54 -10000 0 -1.2 97 97
positive regulation of humoral immune response -0.25 0.58 -10000 0 -1.4 78 78
IL23/IL23R/JAK2/TYK2 -0.28 0.66 -10000 0 -1.5 78 78
IL6 -0.3 0.61 -10000 0 -1.2 128 128
STAT5A 0.026 0.016 -10000 0 -0.31 1 1
IL2 0.016 0.023 0.17 2 -10000 0 2
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -10000 0 -10000 0 0
CD3E -0.21 0.49 -10000 0 -1.2 76 76
keratinocyte proliferation -0.25 0.58 -10000 0 -1.4 78 78
NOS2 -0.24 0.52 -10000 0 -1.2 91 91
Thromboxane A2 receptor 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
TGM2 0.027 0.023 0.17 7 -0.31 1 8
GNB1/GNG2 -0.046 0.078 -10000 0 -0.18 111 111
AKT1 -0.025 0.11 0.27 5 -0.23 21 26
EGF 0.023 0.08 0.17 38 -0.31 21 59
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.01 0.074 0.26 18 -0.24 5 23
mol:Ca2+ -0.051 0.15 0.3 6 -0.29 115 121
LYN -0.012 0.057 0.24 11 -0.23 4 15
RhoA/GTP -0.023 0.061 -10000 0 -0.13 98 98
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.059 0.17 0.32 12 -0.34 110 122
GNG2 0.023 0.034 -10000 0 -0.31 5 5
ARRB2 0.025 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.015 0.12 0.27 1 -0.36 44 45
G beta5/gamma2 -0.055 0.11 -10000 0 -0.24 110 110
PRKCH -0.062 0.17 0.32 7 -0.34 111 118
DNM1 0.025 0.018 0.17 1 -0.31 1 2
TXA2/TP beta/beta Arrestin3 0.011 0.016 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.004 0.084 0.17 1 -0.31 32 33
G12 family/GTP -0.059 0.14 -10000 0 -0.3 103 103
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
ADRBK2 0.026 0.016 -10000 0 -0.31 1 1
RhoA/GTP/ROCK1 0.034 0.014 -10000 0 -0.18 1 1
mol:GDP 0.03 0.11 0.32 28 -0.27 3 31
mol:NADP 0.027 0.019 0.17 7 -10000 0 7
RAB11A 0.027 0.003 -10000 0 -10000 0 0
PRKG1 -0.063 0.15 -10000 0 -0.31 128 128
mol:IP3 -0.067 0.18 0.34 5 -0.36 115 120
cell morphogenesis 0.033 0.014 -10000 0 -0.18 1 1
PLCB2 -0.097 0.24 0.38 4 -0.49 115 119
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.067 0.23 14 -0.23 8 22
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.013 0.068 0.24 14 -0.26 5 19
RHOA 0.027 0.005 -10000 0 -10000 0 0
PTGIR 0.037 0.051 0.17 44 -0.31 4 48
PRKCB1 -0.067 0.18 0.32 5 -0.36 113 118
GNAQ 0.026 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.019 0.17 7 -10000 0 7
TXA2/TXA2-R family -0.1 0.24 0.38 4 -0.51 114 118
LCK -0.011 0.065 0.21 18 -0.23 4 22
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.015 0.059 0.18 2 -0.18 28 30
TXA2-R family/G12 family/GDP/G beta/gamma 0.017 0.058 -10000 0 -0.41 7 7
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.016 0.057 -10000 0 -0.18 25 25
MAPK14 -0.037 0.12 0.27 14 -0.22 108 122
TGM2/GTP -0.08 0.2 0.39 1 -0.41 114 115
MAPK11 -0.038 0.12 0.26 13 -0.23 108 121
ARHGEF1 -0.034 0.082 0.2 1 -0.18 103 104
GNAI2 0.027 0.005 -10000 0 -10000 0 0
JNK cascade -0.071 0.18 0.34 5 -0.38 115 120
RAB11/GDP 0.027 0.004 -10000 0 -10000 0 0
ICAM1 -0.048 0.14 0.27 6 -0.28 111 117
cAMP biosynthetic process -0.067 0.17 0.33 5 -0.34 115 120
Gq family/GTP/EBP50 0.008 0.061 0.24 11 -0.18 33 44
actin cytoskeleton reorganization 0.033 0.014 -10000 0 -0.18 1 1
SRC -0.012 0.064 0.24 14 -0.23 4 18
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.027 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.016 0.097 0.29 19 -0.23 15 34
VCAM1 -0.052 0.14 0.28 5 -0.29 111 116
TP beta/Gq family/GDP/G beta5/gamma2 -0.015 0.12 0.27 1 -0.36 44 45
platelet activation -0.05 0.15 0.34 12 -0.29 112 124
PGI2/IP 0.027 0.036 0.12 44 -0.21 4 48
PRKACA 0.004 0.052 -10000 0 -0.18 36 36
Gq family/GDP/G beta5/gamma2 -0.009 0.11 0.23 2 -0.32 42 44
TXA2/TP beta/beta Arrestin2 0.004 0.043 -10000 0 -0.33 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.052 0.1 1 -0.18 38 39
mol:DAG -0.076 0.2 0.34 5 -0.41 113 118
EGFR -0.002 0.09 -10000 0 -0.31 38 38
TXA2/TP alpha -0.093 0.22 0.38 5 -0.46 115 120
Gq family/GTP -0.006 0.05 0.14 1 -0.16 45 46
YES1 -0.011 0.067 0.26 14 -0.23 4 18
GNAI2/GTP 0.002 0.054 -10000 0 -0.17 27 27
PGD2/DP 0.005 0.057 0.12 1 -0.21 32 33
SLC9A3R1 0.026 0.005 -10000 0 -10000 0 0
FYN -0.011 0.063 0.23 14 -0.23 4 18
mol:NO 0.027 0.019 0.17 7 -10000 0 7
GNA15 0.013 0.067 -10000 0 -0.31 20 20
PGK/cGMP -0.018 0.091 0.12 7 -0.18 116 123
RhoA/GDP 0.027 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.031 0.068 -10000 0 -0.19 26 26
NOS3 0.027 0.019 0.17 7 -10000 0 7
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.064 0.17 0.3 7 -0.34 114 121
PRKCB -0.08 0.18 0.28 5 -0.37 116 121
PRKCE -0.061 0.16 0.29 6 -0.34 110 116
PRKCD -0.069 0.18 0.32 4 -0.37 110 114
PRKCG -0.07 0.18 0.34 5 -0.37 114 119
muscle contraction -0.095 0.22 0.38 5 -0.47 114 119
PRKCZ -0.063 0.16 0.34 5 -0.34 113 118
ARR3 0.021 0.008 0.17 1 -10000 0 1
TXA2/TP beta 0.017 0.059 -10000 0 -0.18 28 28
PRKCQ -0.066 0.17 0.33 5 -0.35 114 119
MAPKKK cascade -0.089 0.21 0.35 5 -0.44 115 120
SELE -0.069 0.17 0.28 5 -0.36 113 118
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.067 -10000 0 -0.19 28 28
ROCK1 0.025 0.016 -10000 0 -0.31 1 1
GNA14 0.026 0.005 -10000 0 -10000 0 0
chemotaxis -0.12 0.27 0.39 3 -0.59 112 115
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.056 -10000 0 -0.31 14 14
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.016 0.08 -10000 0 -0.23 43 43
alphaV beta3 Integrin -0.002 0.11 -10000 0 -0.22 91 91
PTK2 -0.081 0.18 0.3 10 -0.41 88 98
IGF1R 0.027 0.017 0.17 1 -0.31 1 2
PI4KB 0.026 0.006 -10000 0 -10000 0 0
MFGE8 0.025 0.027 -10000 0 -0.31 3 3
SRC 0.026 0.006 -10000 0 -10000 0 0
CDKN1B -0.044 0.15 -10000 0 -0.41 62 62
VEGFA 0.01 0.077 0.17 5 -0.31 26 31
ILK -0.033 0.14 -10000 0 -0.42 47 47
ROCK1 0.025 0.016 -10000 0 -0.31 1 1
AKT1 -0.037 0.13 -10000 0 -0.39 47 47
PTK2B -0.038 0.073 0.18 4 -0.3 21 25
alphaV/beta3 Integrin/JAM-A -0.007 0.12 0.25 1 -0.2 121 122
CBL 0.025 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.028 0.12 -10000 0 -0.19 92 92
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.047 0.077 0.24 1 -0.19 39 40
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.042 0.12 -10000 0 -0.32 51 51
alphaV/beta3 Integrin/Syndecan-1 0.001 0.099 -10000 0 -0.19 100 100
PI4KA 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.006 0.13 -10000 0 -0.24 99 99
PI4 Kinase 0.038 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
alphaV/beta3 Integrin/Osteopontin 0.016 0.1 -10000 0 -0.18 89 89
RPS6KB1 -0.054 0.12 0.4 5 -0.34 42 47
TLN1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.09 0.2 -10000 0 -0.44 99 99
GPR124 0.015 0.044 -10000 0 -0.31 8 8
MAPK1 -0.091 0.2 -10000 0 -0.44 101 101
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
alphaV/beta3 Integrin/Tumstatin -0.002 0.11 -10000 0 -0.21 98 98
cell adhesion 0.003 0.1 -10000 0 -0.21 85 85
ANGPTL3 0.08 0.069 0.17 188 -10000 0 188
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.074 -10000 0 -0.2 43 43
IGF-1R heterotetramer 0.027 0.017 0.17 1 -0.31 1 2
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
TGFBR2 0.019 0.05 -10000 0 -0.31 11 11
ITGB3 -0.036 0.13 -10000 0 -0.31 90 90
IGF1 0.009 0.088 0.17 17 -0.31 32 49
RAC1 0.025 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.002 0.089 -10000 0 -0.18 83 83
apoptosis 0.026 0.005 -10000 0 -10000 0 0
CD47 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.009 0.089 -10000 0 -0.18 87 87
VCL 0.01 0.071 -10000 0 -0.31 23 23
alphaV/beta3 Integrin/Del1 -0.027 0.14 -10000 0 -0.24 123 123
CSF1 0.02 0.046 -10000 0 -0.31 9 9
PIK3C2A -0.031 0.13 -10000 0 -0.42 45 45
PI4 Kinase/Pyk2 -0.032 0.11 -10000 0 -0.27 55 55
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.006 0.12 -10000 0 -0.2 107 107
FAK1/Vinculin -0.059 0.16 0.29 13 -0.35 85 98
alphaV beta3/Integrin/ppsTEM5 0.002 0.089 -10000 0 -0.18 83 83
RHOA 0.027 0.005 -10000 0 -10000 0 0
VTN 0.006 0.12 0.17 49 -0.31 51 100
BCAR1 0.022 0.011 -10000 0 -10000 0 0
FGF2 0.004 0.084 0.17 1 -0.31 32 33
F11R -0.023 0.048 -10000 0 -0.21 28 28
alphaV/beta3 Integrin/Lactadherin 0.008 0.092 -10000 0 -0.18 87 87
alphaV/beta3 Integrin/TGFBR2 0.006 0.097 -10000 0 -0.2 84 84
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.051 0.042 -10000 0 -0.17 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.01 0.081 -10000 0 -0.16 87 87
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.05 0.17 4 -0.31 10 14
alphaV/beta3 Integrin/Pyk2 -0.012 0.094 0.18 2 -0.18 103 105
SDC1 0.014 0.065 -10000 0 -0.31 19 19
VAV3 -0.026 0.057 0.2 7 -0.3 6 13
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
IRS1 0.017 0.056 -10000 0 -0.31 14 14
FAK1/Paxillin -0.058 0.16 0.3 10 -0.34 84 94
cell migration -0.062 0.14 0.26 10 -0.33 81 91
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.001 0.12 0.22 1 -0.2 110 111
SPP1 0.043 0.058 0.17 67 -0.31 4 71
KDR 0.012 0.068 -10000 0 -0.31 21 21
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.005 -10000 0 -10000 0 0
COL4A3 0.008 0.079 0.17 1 -0.31 28 29
angiogenesis -0.099 0.21 0.25 2 -0.47 96 98
Rac1/GTP 0.006 0.059 0.18 7 -0.17 36 43
EDIL3 -0.036 0.13 0.17 1 -0.31 89 90
cell proliferation 0.006 0.097 -10000 0 -0.2 84 84
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.014 0.065 0.12 3 -0.19 43 46
cell-cell adhesion 0.058 0.07 0.17 98 -10000 0 98
Ephrin B/EPHB2/RasGAP 0.035 0.088 -10000 0 -0.17 58 58
ITSN1 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
SHC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.022 0.12 2 -0.18 4 6
Ephrin B1/EPHB1 -0.025 0.096 -10000 0 -0.18 133 133
HRAS/GDP -0.032 0.1 -10000 0 -0.23 57 57
Ephrin B/EPHB1/GRB7 -0.015 0.12 -10000 0 -0.18 152 152
Endophilin/SYNJ1 -0.025 0.062 0.19 9 -0.29 6 15
KRAS 0.025 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.014 0.12 -10000 0 -0.18 149 149
endothelial cell migration 0.045 0.034 -10000 0 -0.2 3 3
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.027 0.004 -10000 0 -10000 0 0
PAK1 -0.019 0.076 0.22 22 -0.35 4 26
HRAS 0.028 0.015 0.17 5 -10000 0 5
RRAS -0.028 0.064 0.18 8 -0.31 7 15
DNM1 0.025 0.018 0.17 1 -0.31 1 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.051 0.096 0.21 20 -0.26 30 50
lamellipodium assembly -0.058 0.07 -10000 0 -0.17 98 98
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.055 0.12 0.18 1 -0.23 122 123
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
EPHB2 0.026 0.029 0.17 3 -0.31 3 6
EPHB3 0.026 0.011 0.17 2 -10000 0 2
EPHB1 -0.068 0.15 -10000 0 -0.31 134 134
EPHB4 0.025 0.008 -10000 0 -10000 0 0
mol:GDP -0.046 0.09 0.19 9 -0.24 59 68
Ephrin B/EPHB2 0.027 0.08 -10000 0 -0.17 58 58
Ephrin B/EPHB3 0.028 0.074 -10000 0 -0.16 53 53
JNK cascade -0.044 0.096 0.32 17 -0.16 129 146
Ephrin B/EPHB1 -0.021 0.11 -10000 0 -0.17 159 159
RAP1/GDP -0.023 0.1 0.25 13 -0.25 34 47
EFNB2 0.03 0.026 0.17 16 -10000 0 16
EFNB3 -0.016 0.11 -10000 0 -0.31 57 57
EFNB1 0.024 0.034 -10000 0 -0.31 5 5
Ephrin B2/EPHB1-2 -0.01 0.097 -10000 0 -0.16 133 133
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.11 -10000 0 -0.25 49 49
Rap1/GTP -0.035 0.091 -10000 0 -0.25 28 28
axon guidance 0.014 0.065 0.12 3 -0.19 43 46
MAPK3 -0.061 0.11 0.18 3 -0.27 61 64
MAPK1 -0.062 0.11 0.18 2 -0.28 63 65
Rac1/GDP -0.036 0.095 0.26 5 -0.26 35 40
actin cytoskeleton reorganization -0.056 0.063 -10000 0 -0.2 47 47
CDC42/GDP -0.031 0.1 0.24 14 -0.26 37 51
PI3K 0.049 0.037 -10000 0 -0.2 3 3
EFNA5 -0.005 0.095 0.17 1 -0.31 43 44
Ephrin B2/EPHB4 0.034 0.02 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.004 0.079 -10000 0 -0.21 51 51
CDC42 0.027 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.065 0.07 -10000 0 -0.2 51 51
PTK2 0.092 0.22 0.59 74 -10000 0 74
MAP4K4 -0.045 0.097 0.32 17 -0.16 129 146
SRC 0.026 0.006 -10000 0 -10000 0 0
KALRN 0.026 0.012 0.17 2 -10000 0 2
Intersectin/N-WASP 0.036 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.043 0.11 0.32 19 -0.28 21 40
MAP2K1 -0.059 0.11 0.17 1 -0.29 60 61
WASL 0.025 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.001 0.11 -10000 0 -0.17 132 132
cell migration -0.073 0.14 0.27 12 -0.33 68 80
NRAS 0.026 0.016 -10000 0 -0.31 1 1
SYNJ1 -0.025 0.063 0.2 9 -0.29 6 15
PXN 0.026 0.006 -10000 0 -10000 0 0
TF -0.047 0.079 0.17 3 -0.27 34 37
HRAS/GTP -0.022 0.1 -10000 0 -0.18 112 112
Ephrin B1/EPHB1-2 -0.012 0.098 -10000 0 -0.17 133 133
cell adhesion mediated by integrin 0.018 0.061 0.18 32 -0.22 4 36
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.023 0.11 -10000 0 -0.17 151 151
RAC1-CDC42/GTP -0.063 0.071 -10000 0 -0.25 28 28
RASA1 0.024 0.022 -10000 0 -0.31 2 2
RAC1-CDC42/GDP -0.03 0.097 0.27 3 -0.25 35 38
ruffle organization -0.031 0.13 0.33 32 -0.29 20 52
NCK1 0.025 0.007 -10000 0 -10000 0 0
receptor internalization -0.029 0.057 0.16 6 -0.28 7 13
Ephrin B/EPHB2/KALRN 0.039 0.082 -10000 0 -0.17 51 51
ROCK1 -0.003 0.044 0.18 24 -0.16 3 27
RAS family/GDP -0.054 0.062 -10000 0 -0.2 44 44
Rac1/GTP -0.061 0.074 -10000 0 -0.18 98 98
Ephrin B/EPHB1/Src/Paxillin -0.061 0.13 -10000 0 -0.23 156 156
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.048 0.15 0.29 2 -0.43 57 59
CRKL -0.049 0.15 -10000 0 -0.44 57 57
HRAS -0.025 0.15 -10000 0 -0.41 56 56
mol:PIP3 -0.018 0.15 0.24 6 -0.39 55 61
SPRED1 0.023 0.034 -10000 0 -0.31 5 5
SPRED2 0.023 0.034 -10000 0 -0.31 5 5
GAB1 -0.049 0.16 -10000 0 -0.46 59 59
FOXO3 -0.019 0.15 0.26 4 -0.39 52 56
AKT1 -0.018 0.16 0.28 3 -0.42 53 56
BAD -0.014 0.16 0.32 11 -0.4 52 63
megakaryocyte differentiation -0.049 0.16 -10000 0 -0.44 61 61
GSK3B -0.012 0.16 0.33 7 -0.39 52 59
RAF1 -0.02 0.13 0.23 6 -0.33 56 62
SHC1 0.026 0.006 -10000 0 -10000 0 0
STAT3 -0.05 0.16 -10000 0 -0.46 60 60
STAT1 -0.12 0.36 -10000 0 -0.99 66 66
HRAS/SPRED1 -0.008 0.13 -10000 0 -0.34 55 55
cell proliferation -0.052 0.16 -10000 0 -0.45 62 62
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
TEC 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.031 0.17 -10000 0 -0.45 59 59
HRAS/SPRED2 -0.008 0.13 -10000 0 -0.34 56 56
LYN/TEC/p62DOK -0.007 0.16 -10000 0 -0.43 50 50
MAPK3 -0.007 0.1 0.26 14 -0.24 50 64
STAP1 -0.063 0.17 0.25 1 -0.49 59 60
GRAP2 0.016 0.061 0.17 2 -0.31 16 18
JAK2 -0.098 0.31 -10000 0 -0.88 61 61
STAT1 (dimer) -0.11 0.35 -10000 0 -0.96 66 66
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.013 0.18 -10000 0 -0.46 58 58
actin filament polymerization -0.045 0.15 0.22 3 -0.43 56 59
LYN 0.023 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.087 0.24 -10000 0 -0.67 64 64
PIK3R1 0.023 0.028 -10000 0 -0.31 3 3
CBL/CRKL/GRB2 -0.019 0.15 -10000 0 -0.41 57 57
PI3K -0.013 0.18 -10000 0 -0.45 56 56
PTEN 0.022 0.011 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.41 -10000 0 -1.2 58 58
MAPK8 -0.053 0.17 -10000 0 -0.46 62 62
STAT3 (dimer) -0.049 0.16 -10000 0 -0.45 60 60
positive regulation of transcription -0.003 0.087 0.24 14 -0.2 46 60
mol:GDP -0.023 0.16 -10000 0 -0.42 58 58
PIK3C2B -0.048 0.16 -10000 0 -0.46 58 58
CBL/CRKL -0.03 0.15 -10000 0 -0.42 58 58
FER -0.052 0.17 -10000 0 -0.45 65 65
SH2B3 -0.048 0.16 -10000 0 -0.45 60 60
PDPK1 -0.013 0.15 0.26 14 -0.37 53 67
SNAI2 -0.068 0.18 -10000 0 -0.49 64 64
positive regulation of cell proliferation -0.083 0.28 -10000 0 -0.76 65 65
KITLG 0.002 0.079 -10000 0 -0.33 23 23
cell motility -0.083 0.28 -10000 0 -0.76 65 65
PTPN6 0.026 0.012 -10000 0 -10000 0 0
EPOR -0.006 0.13 -10000 0 -1.1 1 1
STAT5A (dimer) -0.069 0.24 -10000 0 -0.65 64 64
SOCS1 0.027 0.02 0.17 3 -0.31 1 4
cell migration 0.062 0.16 0.45 65 -0.19 1 66
SOS1 0.026 0.005 -10000 0 -10000 0 0
EPO -0.003 0.1 0.17 24 -0.32 42 66
VAV1 0.013 0.067 0.17 1 -0.31 20 21
GRB10 -0.048 0.15 -10000 0 -0.44 58 58
PTPN11 0.026 0.018 -10000 0 -0.3 1 1
SCF/KIT -0.047 0.17 -10000 0 -0.48 60 60
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.012 0.11 0.27 12 -0.27 54 66
CBL 0.025 0.016 -10000 0 -0.31 1 1
KIT -0.12 0.41 -10000 0 -1.2 58 58
MAP2K2 -0.013 0.11 0.26 12 -0.27 54 66
SHC/Grb2/SOS1 -0.007 0.17 -10000 0 -0.44 56 56
STAT5A -0.072 0.25 -10000 0 -0.67 64 64
GRB2 0.026 0.005 -10000 0 -10000 0 0
response to radiation -0.067 0.17 -10000 0 -0.48 64 64
SHC/GRAP2 0.03 0.045 0.14 2 -0.21 15 17
PTPRO -0.049 0.16 -10000 0 -0.45 60 60
SH2B2 -0.046 0.16 0.22 3 -0.44 56 59
DOK1 0.027 0.004 -10000 0 -10000 0 0
MATK -0.063 0.17 -10000 0 -0.46 65 65
CREBBP 0.018 0.054 -10000 0 -0.15 17 17
BCL2 -0.1 0.36 -10000 0 -1.2 40 40
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.042 0.14 0.25 118 -10000 0 118
GNAI2 0.027 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.073 -10000 0 -0.18 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.024 0.12 -10000 0 -0.31 70 70
RhoA/GTP -0.042 0.14 -10000 0 -0.25 118 118
negative regulation of cAMP metabolic process -0.044 0.14 0.14 1 -0.27 112 113
GNAZ -0.002 0.093 -10000 0 -0.31 41 41
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.008 -10000 0 -10000 0 0
S1PR5 -0.027 0.12 -10000 0 -0.31 77 77
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.045 0.14 0.14 1 -0.27 112 113
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
Aurora B signaling

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
Condensin I complex 0.024 0.05 0.17 7 -0.18 10 17
STMN1 -0.021 0.029 0.24 1 -0.15 1 2
Aurora B/RasGAP/Survivin 0.087 0.097 0.24 109 -0.15 20 129
Chromosomal passenger complex/Cul3 protein complex 0.011 0.055 0.15 4 -0.2 12 16
BIRC5 0.073 0.071 0.17 162 -0.32 1 163
DES -0.095 0.28 -10000 0 -0.59 113 113
Aurora C/Aurora B/INCENP 0.066 0.055 0.15 33 -0.099 17 50
Aurora B/TACC1 0.039 0.052 0.13 91 -0.11 14 105
Aurora B/PP2A 0.06 0.058 0.15 40 -0.12 16 56
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.012 0.016 0.12 6 -10000 0 6
mitotic metaphase/anaphase transition -0.001 0.004 -10000 0 -10000 0 0
NDC80 -0.018 0.042 0.26 6 -0.22 2 8
Cul3 protein complex 0.042 0.053 -10000 0 -0.18 25 25
KIF2C 0.024 0.04 0.17 8 -0.29 2 10
PEBP1 0.025 0.007 -10000 0 -10000 0 0
KIF20A 0.076 0.068 0.17 170 -10000 0 170
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.057 0.059 0.14 122 -0.14 13 135
SEPT1 0.029 0.02 0.17 10 -10000 0 10
SMC2 0.026 0.006 -10000 0 -10000 0 0
SMC4 0.026 0.009 0.17 1 -10000 0 1
NSUN2/NPM1/Nucleolin -0.007 0.17 0.3 8 -0.46 53 61
PSMA3 0.027 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.021 0.024 0.14 5 -0.15 3 8
AURKB 0.067 0.068 0.17 140 -10000 0 140
AURKC 0.026 0.024 0.17 2 -0.31 2 4
CDCA8 0.043 0.044 0.17 51 -10000 0 51
cytokinesis 0.03 0.065 0.22 11 -0.25 13 24
Aurora B/Septin1 0.057 0.11 0.26 23 -0.25 20 43
AURKA 0.034 0.032 0.17 26 -10000 0 26
INCENP 0.027 0.006 -10000 0 -10000 0 0
KLHL13 0.009 0.076 -10000 0 -0.31 26 26
BUB1 0.056 0.058 0.17 101 -10000 0 101
hSgo1/Aurora B/Survivin 0.1 0.11 0.26 131 -0.16 16 147
EVI5 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.056 0.066 0.21 16 -0.24 4 20
SGOL1 0.052 0.054 0.17 88 -10000 0 88
CENPA 0.027 0.068 0.23 8 -0.19 9 17
NCAPG 0.071 0.065 0.17 154 -10000 0 154
Aurora B/HC8 Proteasome 0.061 0.058 0.14 132 -0.11 15 147
NCAPD2 0.025 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.059 0.056 0.15 41 -0.11 12 53
RHOA 0.027 0.005 -10000 0 -10000 0 0
NCAPH 0.062 0.061 0.17 123 -10000 0 123
NPM1 -0.001 0.11 -10000 0 -0.3 48 48
RASA1 0.024 0.022 -10000 0 -0.31 2 2
KLHL9 0.027 0.005 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.061 0.058 0.14 132 -0.11 15 147
PPP1CC 0.026 0.006 -10000 0 -10000 0 0
Centraspindlin 0.054 0.072 0.23 22 -0.24 5 27
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
NSUN2 0 0.1 0.2 1 -0.28 48 49
MYLK -0.035 0.11 0.14 7 -0.25 98 105
KIF23 0.037 0.035 0.17 31 -10000 0 31
VIM -0.02 0.03 0.26 2 -10000 0 2
RACGAP1 0.029 0.013 0.17 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.003 0.1 -10000 0 -0.29 50 50
Chromosomal passenger complex 0.023 0.059 0.18 15 -0.2 8 23
Chromosomal passenger complex/EVI5 0.11 0.11 0.27 119 -0.15 17 136
TACC1 0.018 0.028 -10000 0 -0.31 3 3
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.027 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.047 0.18 0.26 1 -0.38 87 88
MAP3K8 0.018 0.053 0.17 1 -0.31 12 13
FOS -0.038 0.14 0.24 2 -0.37 52 54
PRKCA 0.006 0.068 -10000 0 -0.31 20 20
PTPN7 0.024 0.037 0.16 21 -10000 0 21
HRAS 0.028 0.015 0.16 5 -10000 0 5
PRKCB -0.051 0.14 -10000 0 -0.31 105 105
NRAS 0.026 0.016 -10000 0 -0.32 1 1
RAS family/GTP 0.041 0.028 -10000 0 -10000 0 0
MAPK3 -0.01 0.092 -10000 0 -0.41 6 6
MAP2K1 -0.079 0.2 -10000 0 -0.42 103 103
ELK1 0.018 0.023 -10000 0 -10000 0 0
BRAF -0.063 0.18 -10000 0 -0.4 88 88
mol:GTP -0.001 0.002 -10000 0 -0.004 82 82
MAPK1 -0.015 0.11 -10000 0 -0.43 15 15
RAF1 -0.069 0.18 -10000 0 -0.39 99 99
KRAS 0.025 0.007 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.031 0.071 -10000 0 -0.18 42 42
NF kappa B1 p50/RelA/I kappa B alpha -0.004 0.1 0.26 5 -0.25 29 34
AP1 -0.02 0.11 -10000 0 -0.19 129 129
mol:PIP3 -0.044 0.072 -10000 0 -0.23 40 40
AKT1 0.007 0.09 0.28 22 -0.23 7 29
PTK2B -0.054 0.12 0.24 2 -0.29 67 69
RHOA 0.006 0.044 0.19 8 -0.25 4 12
PIK3CB 0.025 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.085 0.22 23 -0.26 15 38
MAGI3 0.027 0.004 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.025 0.091 -10000 0 -0.21 88 88
HRAS/GDP 0.021 0.01 0.12 5 -10000 0 5
positive regulation of microtubule depolymerization -0.044 0.11 0.25 12 -0.28 51 63
NF kappa B1 p50/RelA -0.012 0.094 -10000 0 -0.22 62 62
endothelial cell migration -0.004 0.076 -10000 0 -0.25 34 34
ADCY4 -0.036 0.15 0.23 2 -0.42 53 55
ADCY5 -0.057 0.19 0.23 1 -0.49 65 66
ADCY6 -0.034 0.15 0.23 3 -0.41 52 55
ADCY7 -0.035 0.15 0.23 3 -0.41 52 55
ADCY1 -0.036 0.14 0.23 1 -0.42 49 50
ADCY2 -0.042 0.16 0.23 3 -0.43 57 60
ADCY3 -0.035 0.15 0.23 3 -0.41 53 56
ADCY8 -0.033 0.13 -10000 0 -0.4 47 47
ADCY9 -0.036 0.15 0.23 2 -0.41 53 55
GSK3B -0.046 0.12 0.25 11 -0.29 58 69
arachidonic acid secretion -0.042 0.14 -10000 0 -0.41 54 54
GNG2 0.023 0.034 -10000 0 -0.31 5 5
TRIP6 0.014 0.033 -10000 0 -0.26 6 6
GNAO1 -0.025 0.1 -10000 0 -0.25 71 71
HRAS 0.028 0.015 0.17 5 -10000 0 5
NFKBIA -0.02 0.11 0.3 13 -0.24 53 66
GAB1 0.026 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.19 -10000 0 -0.81 24 24
JUN 0.024 0.031 0.17 1 -0.31 4 5
LPA/LPA2/NHERF2 0.035 0.022 0.13 5 -0.11 5 10
TIAM1 -0.016 0.21 -10000 0 -0.95 24 24
PIK3R1 0.022 0.028 -10000 0 -0.31 3 3
mol:IP3 -0.017 0.079 0.19 21 -0.26 15 36
PLCB3 0.016 0.037 0.18 20 -10000 0 20
FOS -0.025 0.12 0.17 4 -0.31 76 80
positive regulation of mitosis -0.042 0.14 -10000 0 -0.41 54 54
LPA/LPA1-2-3 0.008 0.098 -10000 0 -0.18 90 90
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.011 -10000 0 -10000 0 0
stress fiber formation -0.029 0.12 0.29 9 -0.31 41 50
GNAZ -0.017 0.09 -10000 0 -0.24 60 60
EGFR/PI3K-beta/Gab1 -0.016 0.088 -10000 0 -0.21 61 61
positive regulation of dendritic cell cytokine production 0.007 0.097 -10000 0 -0.18 90 90
LPA/LPA2/MAGI-3 0.035 0.02 -10000 0 -0.12 4 4
ARHGEF1 0.015 0.079 0.2 47 -0.19 15 62
GNAI2 -0.003 0.06 -10000 0 -0.2 39 39
GNAI3 -0.003 0.062 -10000 0 -0.2 39 39
GNAI1 -0.002 0.06 -10000 0 -0.21 35 35
LPA/LPA3 -0.011 0.08 0.12 7 -0.2 69 76
LPA/LPA2 0.019 0.019 -10000 0 -0.13 5 5
LPA/LPA1 0.001 0.076 -10000 0 -0.23 44 44
HB-EGF/EGFR -0.03 0.07 0.19 6 -0.2 43 49
HBEGF -0.035 0.052 0.25 9 -0.22 8 17
mol:DAG -0.017 0.079 0.19 21 -0.26 15 36
cAMP biosynthetic process -0.035 0.17 0.32 13 -0.42 56 69
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.027 0.005 -10000 0 -10000 0 0
LYN -0.008 0.12 0.32 20 -0.25 43 63
GNAQ -0.011 0.065 -10000 0 -0.18 59 59
LPAR2 0.026 0.015 -10000 0 -0.31 1 1
LPAR3 -0.017 0.12 0.17 7 -0.31 65 72
LPAR1 -0.002 0.098 -10000 0 -0.31 42 42
IL8 -0.055 0.18 0.43 7 -0.41 75 82
PTK2 -0.017 0.067 0.18 6 -0.17 64 70
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
CASP3 -0.025 0.092 -10000 0 -0.21 88 88
EGFR -0.002 0.09 -10000 0 -0.31 38 38
PLCG1 -0.019 0.074 0.16 1 -0.21 57 58
PLD2 -0.019 0.082 0.19 13 -0.18 79 92
G12/G13 0.032 0.063 -10000 0 -0.18 35 35
PI3K-beta 0.006 0.052 -10000 0 -0.22 12 12
cell migration -0.005 0.066 -10000 0 -0.24 22 22
SLC9A3R2 0.028 0.015 0.17 5 -10000 0 5
PXN -0.029 0.12 0.29 9 -0.31 41 50
HRAS/GTP -0.044 0.15 -10000 0 -0.42 54 54
RAC1 0.025 0.008 -10000 0 -10000 0 0
MMP9 0.097 0.081 0.17 257 -0.31 5 262
PRKCE 0.026 0.006 -10000 0 -10000 0 0
PRKCD -0.016 0.089 0.23 25 -0.26 16 41
Gi(beta/gamma) -0.034 0.14 0.15 4 -0.39 54 58
mol:LPA 0 0.017 -10000 0 -0.13 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.012 0.096 -10000 0 -0.3 22 22
MAPKKK cascade -0.042 0.14 -10000 0 -0.41 54 54
contractile ring contraction involved in cytokinesis 0.007 0.045 0.19 7 -0.25 4 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.011 0.066 -10000 0 -0.18 60 60
GNA15 -0.017 0.077 -10000 0 -0.2 71 71
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.045 0.12 0.25 12 -0.29 51 63
GNA11 -0.015 0.076 -10000 0 -0.2 66 66
Rac1/GTP 0.002 0.2 -10000 0 -0.85 24 24
MMP2 -0.004 0.076 -10000 0 -0.25 34 34
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.031 0.043 0.18 13 -0.31 4 17
NFATC2 0.016 0.16 -10000 0 -0.44 30 30
NFATC3 0.023 0.062 -10000 0 -0.23 9 9
CD40LG -0.096 0.26 -10000 0 -0.75 44 44
ITCH -0.018 0.082 -10000 0 -0.18 92 92
CBLB -0.018 0.082 -10000 0 -0.18 93 93
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.08 0.26 -10000 0 -0.76 38 38
JUNB 0.022 0.057 0.17 12 -0.31 12 24
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.1 -10000 0 -0.22 98 98
T cell anergy -0.058 0.15 0.29 3 -0.33 96 99
TLE4 -0.004 0.11 0.31 1 -0.39 16 17
Jun/NFAT1-c-4/p21SNFT -0.014 0.24 -10000 0 -0.75 27 27
AP-1/NFAT1-c-4 -0.049 0.31 -10000 0 -0.83 42 42
IKZF1 0 0.11 0.28 1 -0.37 17 18
T-helper 2 cell differentiation -0.15 0.26 -10000 0 -0.68 50 50
AP-1/NFAT1 -0.014 0.17 0.37 1 -0.35 54 55
CALM1 -0.002 0.07 -10000 0 -0.14 98 98
EGR2 -0.06 0.27 -10000 0 -1 24 24
EGR3 -0.073 0.3 -10000 0 -1.1 33 33
NFAT1/FOXP3 0.019 0.15 0.3 7 -0.37 22 29
EGR1 0.005 0.097 0.17 24 -0.31 37 61
JUN 0.013 0.042 0.17 1 -0.32 4 5
EGR4 0.061 0.064 0.16 127 -10000 0 127
mol:Ca2+ -0.022 0.056 -10000 0 -0.13 104 104
GBP3 -0.04 0.19 -10000 0 -0.53 55 55
FOSL1 -0.013 0.13 0.17 34 -0.31 70 104
NFAT1-c-4/MAF/IRF4 -0.008 0.23 -10000 0 -0.74 26 26
DGKA -0.003 0.11 -10000 0 -0.34 17 17
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.021 0.23 -10000 0 -0.75 28 28
CTLA4 -0.005 0.12 0.34 3 -0.37 17 20
NFAT1-c-4 (dimer)/EGR1 -0.021 0.25 -10000 0 -0.79 31 31
NFAT1-c-4 (dimer)/EGR4 0 0.24 -10000 0 -0.74 27 27
FOS -0.035 0.13 0.17 4 -0.32 76 80
IFNG -0.052 0.19 -10000 0 -0.6 25 25
T cell activation -0.034 0.16 0.4 1 -0.61 12 13
MAF 0.021 0.024 -10000 0 -0.31 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.022 0.16 0.62 24 -10000 0 24
TNF -0.065 0.24 -10000 0 -0.73 36 36
FASLG -0.13 0.39 -10000 0 -1.2 46 46
TBX21 0.03 0.049 0.18 17 -0.31 7 24
BATF3 0.032 0.03 0.17 22 -10000 0 22
PRKCQ 0.008 0.086 0.17 10 -0.3 31 41
PTPN1 -0.004 0.11 -10000 0 -0.34 19 19
NFAT1-c-4/ICER1 -0.015 0.22 -10000 0 -0.74 27 27
GATA3 -0.067 0.15 -10000 0 -0.31 135 135
T-helper 1 cell differentiation -0.051 0.19 -10000 0 -0.59 25 25
IL2RA -0.068 0.26 -10000 0 -0.72 41 41
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.003 0.11 -10000 0 -0.36 14 14
E2F1 0.034 0.026 0.17 17 -10000 0 17
PPARG 0.011 0.074 0.17 3 -0.31 24 27
SLC3A2 -0.003 0.11 0.31 1 -0.34 19 20
IRF4 0.021 0.07 0.17 23 -0.31 17 40
PTGS2 -0.11 0.28 -10000 0 -0.76 52 52
CSF2 -0.094 0.24 -10000 0 -0.73 43 43
JunB/Fra1/NFAT1-c-4 -0.025 0.24 -10000 0 -0.76 30 30
IL4 -0.16 0.27 -10000 0 -0.74 45 45
IL5 -0.094 0.24 -10000 0 -0.73 43 43
IL2 -0.035 0.16 0.4 1 -0.62 12 13
IL3 -0.017 0.11 -10000 0 -0.54 16 16
RNF128 -0.066 0.18 0.27 1 -0.41 101 102
NFATC1 -0.022 0.16 -10000 0 -0.62 24 24
CDK4 0.041 0.14 0.59 10 -10000 0 10
PTPRK -0.004 0.11 -10000 0 -0.35 18 18
IL8 -0.097 0.26 -10000 0 -0.74 48 48
POU2F1 0.026 0.006 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.03 0.12 -10000 0 -0.31 81 81
GNB1/GNG2 -0.008 0.12 -10000 0 -0.3 37 37
mol:DAG -0.02 0.11 0.19 13 -0.28 37 50
PLCG1 -0.021 0.11 0.19 13 -0.29 37 50
YES1 -0.029 0.094 -10000 0 -0.23 67 67
FZD3 0.02 0.012 -10000 0 -10000 0 0
FZD6 0.021 0.011 -10000 0 -10000 0 0
G protein -0.005 0.12 0.28 3 -0.29 37 40
MAP3K7 -0.041 0.1 0.19 15 -0.27 48 63
mol:Ca2+ -0.02 0.1 0.18 13 -0.27 37 50
mol:IP3 -0.02 0.11 0.19 13 -0.28 37 50
NLK 0.003 0.081 -10000 0 -0.78 5 5
GNB1 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.039 0.12 0.21 18 -0.28 56 74
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.02 0.1 -10000 0 -0.24 71 71
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.031 0.096 -10000 0 -0.23 71 71
GO:0007205 -0.024 0.1 0.21 16 -0.27 38 54
WNT6 -0.032 0.13 0.17 7 -0.31 87 94
WNT4 0.023 0.037 -10000 0 -0.31 6 6
NFAT1/CK1 alpha -0.035 0.12 -10000 0 -0.3 40 40
GNG2 0.023 0.034 -10000 0 -0.31 5 5
WNT5A 0.015 0.074 0.17 12 -0.31 22 34
WNT11 0.027 0.053 0.17 23 -0.31 8 31
CDC42 -0.028 0.094 0.17 1 -0.29 32 33
Ephrin B reverse 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
EFNB2 0.03 0.026 0.17 16 -10000 0 16
EPHB2 0.026 0.029 0.17 3 -0.31 3 6
EFNB1 -0.01 0.026 -10000 0 -0.21 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.004 0.096 -10000 0 -0.16 112 112
Ephrin B2/EPHB1-2 -0.01 0.096 -10000 0 -0.16 133 133
neuron projection morphogenesis -0.009 0.083 -10000 0 -0.15 112 112
Ephrin B1/EPHB1-2/Tiam1 -0.005 0.097 -10000 0 -0.16 121 121
DNM1 0.025 0.018 0.17 1 -0.31 1 2
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.006 0.053 -10000 0 -0.44 7 7
YES1 0.003 0.084 -10000 0 -0.68 7 7
Ephrin B1/EPHB1-2/NCK2 -0.004 0.095 -10000 0 -0.16 121 121
PI3K 0.028 0.069 -10000 0 -0.49 7 7
mol:GDP -0.006 0.096 -10000 0 -0.16 121 121
ITGA2B 0.02 0.048 0.17 5 -0.31 9 14
endothelial cell proliferation 0.033 0.02 0.13 2 -10000 0 2
FYN 0.001 0.085 -10000 0 -0.68 7 7
MAP3K7 -0.004 0.054 -10000 0 -0.48 6 6
FGR 0.005 0.087 -10000 0 -0.65 8 8
TIAM1 0.024 0.027 -10000 0 -0.31 3 3
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
RGS3 0.026 0.007 -10000 0 -10000 0 0
cell adhesion -0.012 0.09 -10000 0 -0.42 11 11
LYN 0.004 0.082 -10000 0 -0.66 7 7
Ephrin B1/EPHB1-2/Src Family Kinases -0.004 0.084 -10000 0 -0.65 8 8
Ephrin B1/EPHB1-2 -0.003 0.062 -10000 0 -0.51 7 7
SRC 0.005 0.086 -10000 0 -0.65 8 8
ITGB3 -0.036 0.13 -10000 0 -0.31 90 90
EPHB1 -0.067 0.15 -10000 0 -0.31 133 133
EPHB4 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.02 0.13 3 -10000 0 3
alphaIIb/beta3 Integrin -0.014 0.1 -10000 0 -0.21 99 99
BLK -0.015 0.1 -10000 0 -0.68 8 8
HCK 0.003 0.088 -10000 0 -0.66 8 8
regulation of stress fiber formation 0.005 0.093 0.16 121 -10000 0 121
MAPK8 -0.007 0.062 0.21 5 -0.44 7 12
Ephrin B1/EPHB1-2/RGS3 -0.005 0.095 -10000 0 -0.16 123 123
endothelial cell migration 0.002 0.066 0.2 25 -0.38 7 32
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTPN13 0.026 0.03 -10000 0 -0.42 2 2
regulation of focal adhesion formation 0.005 0.093 0.16 121 -10000 0 121
chemotaxis 0.006 0.094 0.16 123 -10000 0 123
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
Rac1/GTP -0.003 0.089 -10000 0 -0.15 112 112
angiogenesis -0.002 0.062 -10000 0 -0.51 7 7
LCK 0.006 0.087 -10000 0 -0.65 8 8
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.01 0.081 -10000 0 -0.23 43 43
PDGFRB 0.025 0.013 0.16 2 -10000 0 2
SPHK1 -0.006 0.085 -10000 0 -0.63 7 7
mol:S1P -0.01 0.08 0.29 1 -0.52 7 8
S1P1/S1P/Gi -0.1 0.2 0.21 1 -0.42 114 115
GNAO1 -0.03 0.12 -10000 0 -0.31 70 70
PDGFB-D/PDGFRB/PLCgamma1 -0.077 0.18 0.24 4 -0.38 108 112
PLCG1 -0.095 0.19 0.21 1 -0.4 110 111
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 0.16 2 -10000 0 2
GNAI2 0.018 0.021 -10000 0 -10000 0 0
GNAI3 0.018 0.02 -10000 0 -10000 0 0
GNAI1 0.016 0.033 0.16 1 -0.32 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.027 0.055 -10000 0 -0.19 43 43
S1P1/S1P -0.027 0.092 0.18 8 -0.32 20 28
negative regulation of cAMP metabolic process -0.097 0.2 0.21 1 -0.41 114 115
MAPK3 -0.13 0.25 0.24 2 -0.55 113 115
calcium-dependent phospholipase C activity -0.002 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
KDR 0.008 0.069 -10000 0 -0.31 21 21
PLCB2 -0.018 0.09 0.21 13 -0.29 19 32
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.023 0.079 -10000 0 -0.28 20 20
receptor internalization -0.027 0.085 0.16 5 -0.3 20 25
PTGS2 -0.19 0.39 0.37 1 -0.95 93 94
Rac1/GTP -0.022 0.077 -10000 0 -0.28 19 19
RHOA 0.027 0.005 -10000 0 -10000 0 0
VEGFA 0.006 0.078 0.16 5 -0.31 26 31
negative regulation of T cell proliferation -0.097 0.2 0.21 1 -0.41 114 115
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.009 0.095 -10000 0 -0.32 41 41
MAPK1 -0.13 0.26 0.21 1 -0.56 113 114
S1P1/S1P/PDGFB-D/PDGFRB -0.022 0.1 0.22 8 -0.26 37 45
ABCC1 0.02 0.018 -10000 0 -10000 0 0
p75(NTR)-mediated 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
Sortilin/TRAF6 0.038 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.039 0.03 0.14 14 -0.24 3 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.044 0.08 -10000 0 -0.16 58 58
NGF (dimer)/p75(NTR)/BEX1 -0.038 0.13 -10000 0 -0.21 169 169
NT-4/5 (dimer)/p75(NTR) -0.032 0.13 -10000 0 -0.26 114 114
IKBKB 0.021 0.011 -10000 0 -10000 0 0
AKT1 -0.023 0.068 0.17 27 -0.17 47 74
IKBKG 0.027 0.002 -10000 0 -10000 0 0
BDNF -0.039 0.13 -10000 0 -0.31 95 95
MGDIs/NGR/p75(NTR)/LINGO1 0.041 0.073 -10000 0 -0.18 40 40
FURIN 0.027 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.008 0.11 -10000 0 -0.21 109 109
LINGO1 0.042 0.042 0.17 50 -10000 0 50
Sortilin/TRAF6/NRIF 0.033 0.014 -10000 0 -10000 0 0
proBDNF (dimer) -0.039 0.13 -10000 0 -0.31 95 95
NTRK1 0.009 0.081 0.17 8 -0.31 28 36
RTN4R 0.027 0.005 -10000 0 -10000 0 0
neuron apoptosis -0.042 0.13 0.35 6 -0.33 46 52
IRAK1 0.027 0.002 -10000 0 -10000 0 0
SHC1 -0.032 0.054 -10000 0 -0.18 53 53
ARHGDIA 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.073 0.025 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.038 0.081 -10000 0 -0.17 59 59
MAGEH1 0.029 0.023 0.17 7 -0.31 1 8
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.036 0.08 -10000 0 -0.17 58 58
Mammalian IAPs/DIABLO 0.064 0.023 -10000 0 -0.17 1 1
proNGF (dimer) 0.013 0.067 0.17 2 -0.31 20 22
MAGED1 0.028 0.007 0.17 1 -10000 0 1
APP 0.025 0.022 -10000 0 -0.31 2 2
NT-4/5 (dimer) -0.048 0.14 -10000 0 -0.31 108 108
ZNF274 0.027 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.011 0.063 -10000 0 -0.16 58 58
NGF 0.013 0.068 0.17 2 -0.31 20 22
cell cycle arrest 0.001 0.083 0.24 25 -0.26 1 26
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.004 0.063 0.15 6 -0.18 45 51
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.01 0.12 -10000 0 -0.22 111 111
NCSTN 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.022 0.078 -10000 0 -0.18 59 59
PSENEN 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide -0.023 0.054 0.18 10 -0.17 42 52
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.004 0.054 -10000 0 -0.29 2 2
p75(NTR)/beta APP 0.017 0.071 -10000 0 -0.22 39 39
BEX1 -0.073 0.16 0.17 5 -0.31 147 152
mol:GDP -0.03 0.056 -10000 0 -0.18 59 59
NGF (dimer) 0.049 0.086 0.24 2 -0.17 49 51
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.054 0.073 -10000 0 -0.17 39 39
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
RAC1/GTP 0.019 0.065 -10000 0 -0.15 55 55
MYD88 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.023 0.079 -10000 0 -0.18 59 59
RHOB 0.021 0.043 -10000 0 -0.31 8 8
RHOA 0.027 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.041 0.02 0.14 15 -10000 0 15
NT3 (dimer) -0.006 0.097 -10000 0 -0.31 45 45
TP53 -0.038 0.086 0.22 18 -0.27 19 37
PRDM4 -0.03 0.055 0.18 7 -0.17 54 61
BDNF (dimer) -0.002 0.14 0.24 7 -0.2 145 152
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.039 0.077 -10000 0 -0.16 58 58
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.037 0.077 -10000 0 -0.17 56 56
RHOC 0.027 0.004 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
MAPK10 -0.037 0.12 0.41 7 -0.29 44 51
DIABLO 0.026 0.006 -10000 0 -10000 0 0
SMPD2 -0.023 0.054 0.18 10 -0.17 42 52
APH1B 0.027 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.024 0.079 -10000 0 -0.18 59 59
PSEN1 0.027 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.004 0.1 -10000 0 -0.24 70 70
MAPK8 -0.04 0.12 0.44 6 -0.29 49 55
MAPK9 -0.036 0.11 0.4 7 -0.29 44 51
APAF1 0.026 0.006 -10000 0 -10000 0 0
NTF3 -0.006 0.097 -10000 0 -0.31 45 45
NTF4 -0.048 0.14 -10000 0 -0.31 108 108
NDN 0.024 0.027 -10000 0 -0.31 3 3
RAC1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.036 0.078 -10000 0 -0.16 61 61
p75 CTF/Sortilin/TRAF6/NRIF 0.063 0.03 -10000 0 -0.17 5 5
RhoA-B-C/GTP 0.022 0.078 -10000 0 -0.18 59 59
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.016 0.11 -10000 0 -0.18 108 108
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.006 0.11 -10000 0 -0.19 109 109
PRKACB 0.026 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.011 0.1 -10000 0 -0.22 94 94
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.02 0.17 3 -0.31 1 4
BIRC2 0.026 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.002 0.08 0.28 6 -0.19 29 35
BAD -0.034 0.13 0.34 17 -0.3 46 63
RIPK2 0.022 0.011 -10000 0 -10000 0 0
NGFR -0.001 0.092 -10000 0 -0.31 40 40
CYCS -0.029 0.055 0.2 8 -0.24 2 10
ADAM17 0.023 0.034 -10000 0 -0.31 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.03 0.072 -10000 0 -0.17 47 47
BCL2L11 -0.036 0.13 0.32 17 -0.3 46 63
BDNF (dimer)/p75(NTR) -0.027 0.12 -10000 0 -0.25 110 110
PI3K 0.03 0.079 -10000 0 -0.17 58 58
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.037 0.078 -10000 0 -0.17 57 57
NDNL2 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.025 0.01 0.17 1 -10000 0 1
NGF (dimer)/p75(NTR) 0.008 0.085 -10000 0 -0.22 59 59
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.037 0.079 -10000 0 -0.17 59 59
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
PLG 0.028 0.031 0.17 23 -10000 0 23
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.038 0.1 0.15 3 -0.21 119 122
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
NGFRAP1 0.027 0.001 -10000 0 -10000 0 0
CASP3 -0.031 0.12 0.33 16 -0.28 46 62
E2F1 0.031 0.026 0.17 17 -10000 0 17
CASP9 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.088 -10000 0 -0.23 26 26
NGF (dimer)/TRKA 0.015 0.08 0.14 10 -0.22 47 57
MMP7 0.016 0.099 0.17 49 -0.31 34 83
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.047 0.078 -10000 0 -0.16 55 55
MMP3 0.001 0.11 0.17 31 -0.31 47 78
APAF-1/Caspase 9 -0.039 0.041 -10000 0 -0.23 3 3
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.006 0.15 0.46 1 -0.66 4 5
CRP -0.005 0.16 0.53 3 -0.58 8 11
cell cycle arrest -0.011 0.16 -10000 0 -0.62 11 11
TIMP1 0 0.17 -10000 0 -0.8 9 9
IL6ST -0.033 0.12 -10000 0 -0.31 80 80
Rac1/GDP -0.055 0.17 -10000 0 -0.36 88 88
AP1 0.017 0.13 -10000 0 -0.53 13 13
GAB2 0.027 0.006 -10000 0 -10000 0 0
TNFSF11 -0.014 0.17 0.47 1 -0.71 13 14
HSP90B1 0.026 0.079 -10000 0 -0.63 3 3
GAB1 0.027 0.016 -10000 0 -0.31 1 1
MAPK14 -0.11 0.24 0.23 2 -0.58 86 88
AKT1 0.025 0.065 0.25 2 -0.48 4 6
FOXO1 0.018 0.061 0.24 1 -0.45 4 5
MAP2K6 -0.088 0.2 -10000 0 -0.45 95 95
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.045 0.16 0.3 3 -0.37 69 72
MITF -0.065 0.16 -10000 0 -0.37 90 90
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.004 -10000 0 -10000 0 0
A2M -0.059 0.3 -10000 0 -1.1 35 35
CEBPB 0.03 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.002 0.1 -10000 0 -0.46 13 13
STAT3 -0.017 0.17 -10000 0 -0.66 11 11
STAT1 0.015 0.075 -10000 0 -0.87 3 3
CEBPD 0.01 0.16 -10000 0 -0.68 4 4
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
PI3K 0.033 0.033 -10000 0 -0.25 5 5
JUN 0.024 0.031 0.17 1 -0.31 4 5
PIAS3/MITF -0.056 0.17 0.22 3 -0.36 89 92
MAPK11 -0.11 0.25 0.23 2 -0.59 86 88
STAT3 (dimer)/FOXO1 0.001 0.14 0.37 1 -0.51 7 8
GRB2/SOS1/GAB family -0.031 0.16 0.23 1 -0.32 83 84
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.06 0.16 0.16 3 -0.29 135 138
GRB2 0.027 0.005 -10000 0 -10000 0 0
JAK2 0.026 0.016 -10000 0 -0.31 1 1
LBP 0.005 0.14 0.46 1 -0.56 6 7
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
JAK1 0.021 0.021 -10000 0 -10000 0 0
MYC 0.024 0.17 0.51 4 -0.66 4 8
FGG -0.012 0.15 -10000 0 -0.68 4 4
macrophage differentiation -0.011 0.16 -10000 0 -0.62 11 11
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.01 0.15 -10000 0 -0.23 125 125
JUNB -0.021 0.2 0.51 1 -0.95 13 14
FOS -0.025 0.12 0.17 4 -0.31 76 80
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.063 0.18 -10000 0 -0.38 93 93
STAT1/PIAS1 -0.028 0.15 0.27 2 -0.33 57 59
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.068 -10000 0 -0.45 5 5
STAT3 (dimer) -0.012 0.17 -10000 0 -0.65 11 11
PRKCD -0.025 0.17 0.31 16 -0.47 28 44
IL6R -0.003 0.087 -10000 0 -0.31 35 35
SOCS3 -0.16 0.38 0.42 1 -1.1 60 61
gp130 (dimer)/JAK1/JAK1/LMO4 0.006 0.095 -10000 0 -0.18 84 84
Rac1/GTP -0.051 0.17 -10000 0 -0.37 82 82
HCK 0.025 0.028 0.17 1 -0.31 3 4
MAPKKK cascade 0.011 0.11 -10000 0 -0.55 12 12
bone resorption -0.01 0.16 0.46 1 -0.67 13 14
IRF1 -0.007 0.15 0.45 1 -0.68 4 5
mol:GDP -0.068 0.17 -10000 0 -0.37 94 94
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.069 0.17 -10000 0 -0.38 94 94
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.27 0.31 1 -0.58 97 98
PTPN11 0.007 0.087 -10000 0 -0.68 7 7
IL6/IL6RA -0.017 0.12 0.15 41 -0.23 112 153
gp130 (dimer)/TYK2/TYK2/LMO4 0.006 0.091 -10000 0 -0.18 81 81
gp130 (dimer)/JAK2/JAK2/LMO4 0.006 0.091 -10000 0 -0.18 80 80
IL6 -0.025 0.15 0.17 44 -0.32 90 134
PIAS3 0.026 0.005 -10000 0 -10000 0 0
PTPRE 0.019 0.028 0.15 1 -0.31 2 3
PIAS1 0.026 0.016 -10000 0 -0.31 1 1
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.059 0.15 0.15 3 -0.28 138 141
LMO4 0.022 0.03 -10000 0 -0.38 1 1
STAT3 (dimer)/PIAS3 -0.015 0.17 -10000 0 -0.6 13 13
MCL1 0.031 0.079 0.41 3 -0.8 1 4
Signaling events mediated by the Hedgehog family

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
TGFB2 0.007 0.12 -10000 0 -0.5 20 20
IHH 0.037 0.072 0.21 30 -0.19 21 51
SHH Np/Cholesterol/GAS1 -0.023 0.08 0.11 1 -0.17 95 96
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.023 0.08 0.17 95 -0.11 1 96
SMO/beta Arrestin2 0.015 0.095 -10000 0 -0.33 20 20
SMO 0 0.086 -10000 0 -0.34 20 20
AKT1 0.001 0.094 -10000 0 -0.39 13 13
ARRB2 0.025 0.007 -10000 0 -10000 0 0
BOC 0.018 0.052 -10000 0 -0.31 12 12
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
heart looping 0 0.085 -10000 0 -0.34 20 20
STIL -0.011 0.094 0.19 27 -0.28 21 48
DHH N/PTCH2 0.037 0.035 0.14 6 -0.21 8 14
DHH N/PTCH1 0.021 0.077 -10000 0 -0.23 34 34
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
DHH 0.024 0.039 0.17 3 -0.31 6 9
PTHLH -0.005 0.15 -10000 0 -0.64 20 20
determination of left/right symmetry 0 0.085 -10000 0 -0.34 20 20
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
skeletal system development -0.005 0.15 -10000 0 -0.63 20 20
IHH N/Hhip 0.016 0.11 0.19 2 -0.27 51 53
DHH N/Hhip 0.015 0.078 -10000 0 -0.21 49 49
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0 0.085 -10000 0 -0.34 20 20
pancreas development -0.002 0.096 0.17 3 -0.31 43 46
HHAT 0.023 0.034 -10000 0 -0.31 5 5
PI3K 0.032 0.033 -10000 0 -0.25 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.005 0.098 0.17 1 -0.31 45 46
somite specification 0 0.085 -10000 0 -0.34 20 20
SHH Np/Cholesterol/PTCH1 -0.009 0.087 0.18 2 -0.27 25 27
SHH Np/Cholesterol/PTCH2 -0.01 0.068 0.13 4 -0.16 70 74
SHH Np/Cholesterol/Megalin -0.021 0.081 0.12 8 -0.17 97 105
SHH -0.041 0.078 0.26 5 -0.22 67 72
catabolic process 0.008 0.079 -10000 0 -0.27 34 34
SMO/Vitamin D3 -0.011 0.094 0.3 1 -0.3 25 26
SHH Np/Cholesterol/Hhip -0.023 0.087 0.14 3 -0.19 89 92
LRP2 0.001 0.094 0.17 8 -0.31 39 47
receptor-mediated endocytosis -0.026 0.1 -10000 0 -0.32 29 29
SHH Np/Cholesterol/BOC -0.014 0.07 0.17 1 -0.16 76 77
SHH Np/Cholesterol/CDO -0.01 0.066 0.13 3 -0.16 70 73
mesenchymal cell differentiation 0.023 0.087 0.19 89 -0.14 3 92
mol:Vitamin D3 -0.004 0.098 0.2 25 -0.29 22 47
IHH N/PTCH2 0.037 0.065 0.15 27 -0.2 23 50
CDON 0.026 0.02 0.17 3 -0.31 1 4
IHH N/PTCH1 0.023 0.088 0.24 1 -0.27 34 35
Megalin/LRPAP1 0.018 0.071 0.14 8 -0.21 40 48
PTCH2 0.027 0.024 0.17 3 -0.31 2 5
SHH Np/Cholesterol -0.017 0.061 -10000 0 -0.16 71 71
PTCH1 0.008 0.08 -10000 0 -0.27 34 34
HHIP -0.002 0.096 0.17 3 -0.31 43 46
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.031 0.24 0.3 6 -0.59 45 51
HDAC7 0.025 0.013 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.024 0.3 -10000 0 -0.71 40 40
SMAD4 0.025 0.008 -10000 0 -10000 0 0
ID2 -0.021 0.25 0.35 4 -0.64 39 43
AP1 -0.002 0.1 0.17 4 -0.22 76 80
ABCG2 -0.031 0.27 0.35 4 -0.63 50 54
HIF1A 0.011 0.065 -10000 0 -0.2 6 6
TFF3 -0.004 0.26 0.36 6 -0.61 45 51
GATA2 0.023 0.018 0.17 1 -0.11 1 2
AKT1 0.008 0.077 -10000 0 -0.2 24 24
response to hypoxia -0.011 0.073 -10000 0 -0.17 50 50
MCL1 -0.023 0.24 0.36 3 -0.61 40 43
NDRG1 -0.021 0.22 0.33 1 -0.62 32 33
SERPINE1 -0.016 0.25 0.33 2 -0.61 41 43
FECH -0.019 0.24 0.35 5 -0.61 41 46
FURIN -0.018 0.25 0.35 4 -0.61 41 45
NCOA2 -0.019 0.1 -10000 0 -0.31 53 53
EP300 -0.002 0.11 -10000 0 -0.31 35 35
HMOX1 -0.017 0.25 0.35 5 -0.61 41 46
BHLHE40 -0.02 0.25 0.35 4 -0.64 39 43
BHLHE41 -0.02 0.25 0.36 6 -0.62 40 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.06 0.097 -10000 0 -0.21 1 1
ENG 0.014 0.076 0.25 17 -10000 0 17
JUN 0.022 0.034 0.17 1 -0.27 5 6
RORA -0.017 0.25 0.35 4 -0.62 40 44
ABCB1 0.001 0.17 -10000 0 -0.97 11 11
TFRC -0.017 0.24 0.35 5 -0.62 39 44
CXCR4 -0.019 0.25 0.33 4 -0.63 38 42
TF -0.043 0.27 0.35 5 -0.62 55 60
CITED2 -0.017 0.25 0.35 5 -0.62 39 44
HIF1A/ARNT 0.071 0.34 0.6 1 -0.79 25 26
LDHA 0.028 0.082 -10000 0 -0.8 2 2
ETS1 -0.021 0.25 0.35 4 -0.62 39 43
PGK1 -0.017 0.25 0.35 5 -0.61 41 46
NOS2 -0.022 0.26 0.35 5 -0.64 45 50
ITGB2 -0.016 0.25 0.35 4 -0.62 40 44
ALDOA -0.018 0.25 0.35 5 -0.62 40 45
Cbp/p300/CITED2 -0.024 0.3 -10000 0 -0.76 45 45
FOS -0.026 0.12 0.17 4 -0.31 76 80
HK2 -0.018 0.25 0.35 4 -0.61 42 46
SP1 0.029 0.018 -10000 0 -0.1 4 4
GCK -0.034 0.3 -10000 0 -1.3 24 24
HK1 -0.018 0.24 0.35 4 -0.61 40 44
NPM1 -0.019 0.25 0.33 3 -0.61 41 44
EGLN1 -0.022 0.24 0.36 3 -0.62 38 41
CREB1 0.031 0.004 -10000 0 -10000 0 0
PGM1 -0.019 0.25 0.35 4 -0.62 40 44
SMAD3 0.028 0.003 -10000 0 -10000 0 0
EDN1 -0.051 0.29 0.34 1 -0.87 43 44
IGFBP1 -0.019 0.24 0.37 3 -0.62 37 40
VEGFA -0.019 0.25 0.37 5 -0.65 39 44
HIF1A/JAB1 0.021 0.052 -10000 0 -0.19 2 2
CP -0.03 0.27 0.35 6 -0.64 50 56
CXCL12 -0.02 0.26 0.35 5 -0.63 44 49
COPS5 0.018 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.013 -10000 0 -10000 0 0
BNIP3 -0.018 0.25 0.35 4 -0.61 41 45
EGLN3 -0.021 0.25 0.33 4 -0.63 41 45
CA9 -0.022 0.25 0.34 4 -0.61 41 45
TERT -0.007 0.26 0.37 5 -0.61 42 47
ENO1 -0.018 0.25 0.35 5 -0.62 40 45
PFKL -0.017 0.25 0.35 4 -0.61 40 44
NCOA1 0.024 0.012 -10000 0 -10000 0 0
ADM -0.014 0.25 0.36 7 -0.62 39 46
ARNT 0.011 0.061 -10000 0 -0.21 2 2
HNF4A 0.024 0.044 0.17 25 -0.11 17 42
ADFP -0.031 0.24 0.3 6 -0.59 45 51
SLC2A1 -0.013 0.24 0.37 5 -0.64 36 41
LEP -0.018 0.24 0.33 2 -0.62 37 39
HIF1A/ARNT/Cbp/p300 0.016 0.3 -10000 0 -0.76 35 35
EPO -0.076 0.32 0.43 1 -0.79 63 64
CREBBP 0.002 0.099 -10000 0 -0.3 32 32
HIF1A/ARNT/Cbp/p300/HDAC7 0.024 0.3 -10000 0 -0.74 36 36
PFKFB3 -0.021 0.25 0.35 4 -0.64 40 44
NT5E -0.031 0.26 0.33 1 -0.63 46 47
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.025 0.12 0.42 5 -0.46 5 10
CRKL -0.003 0.079 0.18 49 -0.2 5 54
mol:DAG 0.005 0.078 0.17 1 -0.23 37 38
HRAS -0.005 0.088 0.28 21 -0.21 3 24
MAPK8 -0.002 0.084 0.18 64 -0.16 42 106
RAP1A -0.004 0.08 0.18 49 -0.21 5 54
GAB1 -0.004 0.081 0.18 50 -0.21 6 56
MAPK14 0.001 0.083 0.18 67 -0.16 35 102
EPO 0.004 0.1 0.18 24 -0.31 40 64
PLCG1 0.005 0.079 -10000 0 -0.24 37 37
EPOR/TRPC2/IP3 Receptors 0.028 0.031 0.18 10 -10000 0 10
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.012 0.099 0.2 2 -0.19 84 86
GAB1/SHC/GRB2/SOS1 0.034 0.071 0.27 2 -0.2 6 8
EPO/EPOR (dimer) 0.023 0.082 0.16 31 -0.22 41 72
IRS2 -0.008 0.074 0.17 39 -0.2 6 45
STAT1 0.008 0.089 0.21 4 -0.24 44 48
STAT5B 0.005 0.083 -10000 0 -0.24 37 37
cell proliferation 0.006 0.1 0.21 77 -0.17 11 88
GAB1/SHIP/PIK3R1/SHP2/SHC 0.011 0.077 -10000 0 -0.25 16 16
TEC -0.004 0.08 0.18 48 -0.21 5 53
SOCS3 -0.012 0.11 0.17 6 -0.31 57 63
STAT1 (dimer) 0.008 0.088 0.2 4 -0.24 44 48
JAK2 0.023 0.026 -10000 0 -0.31 1 1
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
EPO/EPOR (dimer)/JAK2 0.048 0.079 0.23 2 -0.16 42 44
EPO/EPOR 0.023 0.082 0.16 31 -0.22 41 72
LYN 0.022 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.017 0.068 0.24 6 -0.21 5 11
elevation of cytosolic calcium ion concentration 0.027 0.031 0.18 10 -10000 0 10
SHC1 0.026 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.032 0.072 0.19 1 -0.18 38 39
mol:IP3 0.005 0.078 0.17 1 -0.23 37 38
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.017 0.085 0.33 3 -0.24 17 20
SH2B3 0.022 0.02 -10000 0 -10000 0 0
NFKB1 0.002 0.083 0.18 68 -0.16 34 102
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.08 -10000 0 -0.19 79 79
PTPN6 0.009 0.073 0.17 49 -0.16 40 89
TEC/VAV2/GRB2 0.029 0.07 0.25 4 -0.2 5 9
EPOR 0.028 0.031 0.18 10 -10000 0 10
INPP5D 0.01 0.073 -10000 0 -0.31 24 24
mol:GDP 0.029 0.073 0.27 2 -0.2 6 8
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG2 0.021 0.026 0.17 2 -0.31 2 4
CRKL/CBL/C3G 0.028 0.069 0.25 4 -0.21 5 9
VAV2 -0.007 0.072 0.17 42 -0.21 5 47
CBL -0.008 0.076 0.18 41 -0.22 6 47
SHC/Grb2/SOS1 0.022 0.062 -10000 0 -0.15 39 39
STAT5A 0.004 0.083 -10000 0 -0.24 39 39
GRB2 0.026 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.018 0.093 -10000 0 -0.3 16 16
LYN/PLCgamma2 0.028 0.026 -10000 0 -0.22 2 2
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
BTK -0.002 0.083 0.18 51 -0.21 7 58
BCL2 0.001 0.18 0.37 8 -0.66 25 33
Glypican 2 network

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
MDK 0.031 0.026 0.17 16 -10000 0 16
GPC2 0.054 0.061 0.17 103 -0.31 1 104
GPC2/Midkine 0.06 0.054 0.25 9 -0.16 2 11
neuron projection morphogenesis 0.06 0.053 0.25 9 -0.16 2 11
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.057 -10000 0 -0.17 29 29
fibroblast growth factor receptor signaling pathway 0.029 0.057 -10000 0 -0.17 29 29
LAMA1 0.02 0.072 0.17 24 -0.31 18 42
PRNP 0.027 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 0.009 0.083 -10000 0 -0.22 57 57
SMAD2 -0.011 0.042 0.18 17 -0.16 9 26
GPC1/PrPc/Cu2+ 0.035 0.012 -10000 0 -0.18 1 1
GPC1/Laminin alpha1 0.033 0.055 0.14 24 -0.21 19 43
TDGF1 -0.009 0.11 0.17 6 -0.31 53 59
CRIPTO/GPC1 0.011 0.08 0.14 5 -0.21 53 58
APP/GPC1 0.037 0.019 -10000 0 -0.21 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.03 0.052 0.16 1 -0.18 50 51
FLT1 0.024 0.032 0.17 2 -0.31 4 6
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.035 -10000 0 -0.18 9 9
SERPINC1 0.032 0.032 0.17 26 -10000 0 26
FYN -0.027 0.05 0.16 1 -0.18 45 46
FGR -0.032 0.054 0.16 1 -0.18 54 55
positive regulation of MAPKKK cascade -0.034 0.11 0.29 9 -0.29 49 58
SLIT2 -0.013 0.11 -10000 0 -0.31 57 57
GPC1/NRG 0 0.079 -10000 0 -0.21 55 55
NRG1 -0.019 0.1 -10000 0 -0.31 55 55
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.04 0.06 0.23 1 -0.18 29 30
LYN -0.026 0.047 -10000 0 -0.18 40 40
mol:Spermine -0.006 0.009 -10000 0 -0.21 1 1
cell growth 0.029 0.057 -10000 0 -0.17 29 29
BMP signaling pathway -0.026 0.016 0.31 1 -10000 0 1
SRC -0.031 0.053 0.16 1 -0.18 52 53
TGFBR1 0.026 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.06 0.099 0.17 160 -0.31 19 179
GPC1 0.026 0.016 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.026 0.006 -10000 0 -10000 0 0
VEGFA 0.01 0.077 0.17 5 -0.31 26 31
BLK -0.033 0.074 0.26 1 -0.2 69 70
HCK -0.032 0.054 0.12 2 -0.18 54 56
FGF2 0.004 0.084 0.17 1 -0.31 32 33
FGFR1 0.019 0.024 -10000 0 -0.31 2 2
VEGFR1 homodimer 0.024 0.032 0.17 2 -0.31 4 6
TGFBR2 0.019 0.05 -10000 0 -0.31 11 11
cell death 0.037 0.019 -10000 0 -0.21 2 2
ATIII/GPC1 0.042 0.027 0.14 25 -0.21 1 26
PLA2G2A/GPC1 0.061 0.073 0.14 157 -0.21 20 177
LCK -0.031 0.054 0.16 1 -0.18 51 52
neuron differentiation 0 0.078 -10000 0 -0.21 55 55
PrPc/Cu2+ 0.02 0.003 -10000 0 -10000 0 0
APP 0.025 0.022 -10000 0 -0.31 2 2
TGFBR2 (dimer) 0.019 0.05 -10000 0 -0.31 11 11
Nongenotropic Androgen signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.005 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.065 -10000 0 -0.16 48 48
regulation of S phase of mitotic cell cycle -0.004 0.071 -10000 0 -0.21 45 45
GNAO1 -0.024 0.12 -10000 0 -0.31 70 70
HRAS 0.027 0.015 0.16 5 -10000 0 5
SHBG/T-DHT 0.015 0.019 0.11 5 -0.15 4 9
PELP1 0.024 0.01 -10000 0 -10000 0 0
AKT1 -0.004 0.004 -10000 0 -10000 0 0
MAP2K1 -0.039 0.065 0.21 7 -0.21 12 19
T-DHT/AR -0.002 0.065 -10000 0 -0.21 43 43
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 82 82
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
mol:GDP -0.029 0.097 -10000 0 -0.33 43 43
cell proliferation -0.07 0.16 0.31 8 -0.41 78 86
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
FOS -0.12 0.28 0.28 6 -0.73 82 88
mol:Ca2+ -0.011 0.027 -10000 0 -0.066 79 79
MAPK3 -0.049 0.12 0.28 12 -0.29 69 81
MAPK1 -0.03 0.096 0.2 5 -0.26 33 38
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
mol:IP3 -0.001 0.002 -10000 0 -0.005 82 82
cAMP biosynthetic process 0.001 0.024 0.086 4 -0.17 3 7
GNG2 0.023 0.034 -10000 0 -0.31 5 5
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 82 82
HRAS/GTP 0.014 0.068 -10000 0 -0.15 46 46
actin cytoskeleton reorganization 0.032 0.025 -10000 0 -0.19 3 3
SRC 0.025 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 82 82
PI3K 0.029 0.028 -10000 0 -0.21 5 5
apoptosis 0.06 0.17 0.4 82 -0.28 6 88
T-DHT/AR/PELP1 0.013 0.061 -10000 0 -0.18 43 43
HRAS/GDP -0.018 0.1 -10000 0 -0.32 43 43
CREB1 -0.065 0.18 0.28 6 -0.43 82 88
RAC1-CDC42/GTP 0.04 0.029 -10000 0 -0.19 3 3
AR -0.004 0.096 -10000 0 -0.31 43 43
GNB1 0.027 0.004 -10000 0 -10000 0 0
RAF1 -0.032 0.06 0.22 8 -0.2 10 18
RAC1-CDC42/GDP 0.006 0.1 -10000 0 -0.3 42 42
T-DHT/AR/PELP1/Src 0.024 0.062 -10000 0 -0.16 43 43
MAP2K2 -0.038 0.065 0.21 7 -0.21 14 21
T-DHT/AR/PELP1/Src/PI3K -0.004 0.071 -10000 0 -0.21 45 45
GNAZ -0.002 0.093 -10000 0 -0.31 41 41
SHBG 0.023 0.031 0.17 5 -0.31 3 8
Gi family/GNB1/GNG2/GDP -0.049 0.14 -10000 0 -0.34 77 77
mol:T-DHT 0 0.002 -10000 0 -0.003 64 64
RAC1 0.025 0.008 -10000 0 -10000 0 0
GNRH1 -0.005 0.008 -10000 0 -10000 0 0
Gi family/GTP -0.035 0.094 0.11 1 -0.22 79 80
CDC42 0.027 0.004 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.015 0.17 5 -10000 0 5
EGFR -0.002 0.09 -10000 0 -0.31 38 38
EGF/EGFR 0.005 0.1 0.19 2 -0.19 93 95
EGF/EGFR dimer/SHC/GRB2/SOS1 0.046 0.081 -10000 0 -0.17 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.008 0.1 -10000 0 -0.31 50 50
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.023 0.08 0.17 38 -0.31 21 59
EGF/EGFR dimer/SHC 0.027 0.081 -10000 0 -0.19 50 50
mol:GDP 0.041 0.078 -10000 0 -0.16 47 47
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.014 0.075 0.17 10 -0.31 23 33
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.066 -10000 0 -0.16 47 47
SHC1 0.026 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.04 0.075 -10000 0 -0.16 47 47
FRAP1 -0.03 0.044 -10000 0 -0.16 47 47
EGF/EGFR dimer 0.013 0.09 0.14 32 -0.22 54 86
SOS1 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.004 0.1 0.14 9 -0.25 62 71
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.01 0.08 0.21 7 -0.16 73 80
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.089 0.35 1 -0.28 16 17
alphaV/beta3 Integrin/Osteopontin/Src 0.05 0.046 -10000 0 -0.2 5 5
AP1 -0.018 0.12 -10000 0 -0.32 37 37
ILK -0.021 0.078 0.2 9 -0.2 20 29
bone resorption -0.027 0.094 0.17 3 -0.28 39 42
PTK2B 0.019 0.013 -10000 0 -10000 0 0
PYK2/p130Cas 0.021 0.093 0.26 2 -0.17 42 44
ITGAV 0.027 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.014 0.078 -10000 0 -0.23 45 45
alphaV/beta3 Integrin/Osteopontin 0.021 0.1 -10000 0 -0.18 87 87
MAP3K1 -0.019 0.072 0.18 6 -0.17 72 78
JUN 0.024 0.032 0.17 1 -0.31 4 5
MAPK3 -0.036 0.074 0.22 11 -0.23 16 27
MAPK1 -0.037 0.074 0.22 10 -0.25 13 23
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.036 0.07 0.18 8 -0.24 22 30
ITGB3 -0.036 0.13 -10000 0 -0.31 90 90
NFKBIA -0.03 0.081 0.19 9 -0.27 19 28
FOS -0.025 0.12 0.17 4 -0.31 76 80
CD44 0.021 0.043 -10000 0 -0.31 8 8
CHUK 0.025 0.007 -10000 0 -10000 0 0
PLAU -0.045 0.17 0.43 2 -1.1 11 13
NF kappa B1 p50/RelA 0.001 0.094 0.31 1 -0.35 11 12
BCAR1 0.022 0.011 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.007 0.099 -10000 0 -0.21 90 90
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.022 0.08 0.2 8 -0.18 82 90
VAV3 -0.05 0.093 0.22 10 -0.28 35 45
MAP3K14 -0.019 0.078 0.2 9 -0.17 78 87
ROCK2 -0.002 0.093 -10000 0 -0.31 41 41
SPP1 0.044 0.06 0.17 67 -0.31 4 71
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.03 0.09 0.19 7 -0.26 32 39
MMP2 -0.053 0.095 -10000 0 -0.31 32 32
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.02 0.066 0.28 2 -0.2 15 17
alphaM/beta2 Integrin/GPIbA 0.021 0.065 0.27 3 -0.18 13 16
alphaM/beta2 Integrin/proMMP-9 0.058 0.099 0.26 6 -0.13 47 53
PLAUR 0.029 0.018 0.17 8 -10000 0 8
HMGB1 0.007 0.036 -10000 0 -0.12 3 3
alphaM/beta2 Integrin/Talin 0.024 0.059 0.24 2 -0.17 6 8
AGER 0.012 0.052 0.16 18 -0.2 6 24
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.028 0.017 0.17 6 -10000 0 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.009 0.12 0.26 3 -0.2 114 117
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.097 0.081 0.17 257 -0.31 5 262
CYR61 0.021 0.053 0.17 7 -0.31 11 18
TLN1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.013 0.097 -10000 0 -0.24 40 40
RHOA 0.027 0.005 -10000 0 -10000 0 0
P-selectin oligomer 0.02 0.045 -10000 0 -0.31 9 9
MYH2 -0.051 0.11 0.16 1 -0.31 48 49
MST1R 0.019 0.054 0.17 4 -0.31 12 16
leukocyte activation during inflammatory response -0.03 0.11 -10000 0 -0.19 139 139
APOB -0.049 0.14 0.17 2 -0.31 109 111
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.049 0.17 1 -0.31 10 11
JAM3 0.015 0.06 -10000 0 -0.31 16 16
GP1BA 0.021 0.042 0.17 3 -0.31 7 10
alphaM/beta2 Integrin/CTGF 0.016 0.074 0.24 2 -0.18 33 35
alphaM/beta2 Integrin -0.029 0.098 -10000 0 -0.27 42 42
JAM3 homodimer 0.015 0.06 -10000 0 -0.31 16 16
ICAM2 0.025 0.023 0.17 1 -0.31 2 3
ICAM1 0.03 0.021 0.17 11 -10000 0 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.028 0.098 0.19 1 -0.27 42 43
cell adhesion 0.021 0.065 0.26 3 -0.18 13 16
NFKB1 -0.059 0.17 0.33 4 -0.34 116 120
THY1 0.028 0.019 0.17 8 -10000 0 8
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.034 0.11 -10000 0 -0.2 145 145
alphaM/beta2 Integrin/LRP/tPA 0.029 0.067 0.24 2 -0.19 11 13
IL6 -0.12 0.25 0.44 3 -0.55 107 110
ITGB2 0.009 0.039 0.16 5 -0.14 1 6
elevation of cytosolic calcium ion concentration 0.029 0.072 0.32 2 -0.18 16 18
alphaM/beta2 Integrin/JAM2/JAM3 0.027 0.078 0.24 2 -0.2 21 23
JAM2 0.023 0.031 -10000 0 -0.31 4 4
alphaM/beta2 Integrin/ICAM1 0.05 0.082 0.27 3 -0.17 17 20
alphaM/beta2 Integrin/uPA/Plg 0.032 0.074 0.28 2 -0.18 16 18
RhoA/GTP -0.037 0.11 0.17 1 -0.31 45 46
positive regulation of phagocytosis -0.014 0.089 0.17 6 -0.24 27 33
Ron/MSP 0.044 0.054 0.24 1 -0.22 12 13
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.073 0.33 2 -0.18 16 18
alphaM/beta2 Integrin/uPAR 0.025 0.062 0.28 2 -0.16 7 9
PLAU 0.02 0.048 0.17 1 -0.31 10 11
PLAT 0.022 0.039 0.17 12 -0.31 4 16
actin filament polymerization -0.049 0.11 -10000 0 -0.3 47 47
MST1 0.042 0.044 0.17 54 -10000 0 54
alphaM/beta2 Integrin/lipoprotein(a) -0.028 0.12 -10000 0 -0.19 139 139
TNF -0.088 0.19 0.36 5 -0.38 111 116
RAP1B 0.026 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.019 0.068 0.28 2 -0.19 17 19
fibrinolysis 0.03 0.072 0.28 2 -0.18 16 18
HCK 0.025 0.028 0.17 1 -0.31 3 4
dendritic cell antigen processing and presentation -0.028 0.098 0.19 1 -0.27 42 43
VTN 0.006 0.12 0.17 49 -0.31 51 100
alphaM/beta2 Integrin/CYR61 0.022 0.069 0.28 2 -0.2 15 17
LPA -0.012 0.11 0.17 7 -0.31 58 65
LRP1 0.026 0.017 0.17 1 -0.31 1 2
cell migration 0.015 0.072 0.19 8 -0.19 22 30
FN1 0.021 0.05 0.17 4 -0.31 10 14
alphaM/beta2 Integrin/Thy1 0.025 0.062 0.28 2 -0.17 6 8
MPO -0.001 0.09 -10000 0 -0.31 38 38
KNG1 0.035 0.046 0.17 53 -10000 0 53
RAP1/GDP 0.034 0.01 -10000 0 -10000 0 0
ROCK1 -0.036 0.11 0.16 4 -0.31 39 43
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.028 0.031 0.17 23 -10000 0 23
CTGF 0.014 0.066 0.17 1 -0.31 19 20
alphaM/beta2 Integrin/Hck 0.023 0.062 0.28 2 -0.17 10 12
ITGAM 0.005 0.047 0.17 2 -0.23 6 8
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.031 0.071 0.3 3 -0.21 9 12
HP 0.024 0.077 0.17 47 -0.31 17 64
leukocyte adhesion -0.004 0.11 0.26 2 -0.28 28 30
SELP 0.02 0.046 -10000 0 -0.31 9 9
Wnt 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
Noncanonical Wnts/FZD -0.02 0.1 -10000 0 -0.24 71 71
FZD6 0.021 0.011 -10000 0 -10000 0 0
WNT6 -0.032 0.13 0.17 7 -0.31 87 94
WNT4 0.023 0.037 -10000 0 -0.31 6 6
FZD3 0.02 0.012 -10000 0 -10000 0 0
WNT5A 0.015 0.074 0.17 12 -0.31 22 34
WNT11 0.027 0.053 0.17 23 -0.31 8 31
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.024 0.12 -10000 0 -0.31 70 70
CDC42/GTP -0.013 0.11 -10000 0 -0.24 68 68
PLCG1 -0.023 0.099 -10000 0 -0.25 66 66
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.013 -10000 0 -10000 0 0
cell migration -0.013 0.1 -10000 0 -0.24 68 68
S1PR5 -0.027 0.12 -10000 0 -0.31 77 77
S1PR4 0.032 0.032 0.17 20 -0.31 1 21
MAPK3 -0.023 0.099 -10000 0 -0.25 66 66
MAPK1 -0.021 0.097 -10000 0 -0.25 64 64
S1P/S1P5/Gi -0.045 0.14 0.14 1 -0.27 112 113
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
CDC42/GDP 0.02 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.073 -10000 0 -0.18 66 66
RHOA 0.002 0.06 0.19 42 -10000 0 42
S1P/S1P4/Gi -0.018 0.11 -10000 0 -0.25 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.093 -10000 0 -0.31 41 41
S1P/S1P4/G12/G13 0.048 0.025 -10000 0 -10000 0 0
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.004 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.004 -10000 0 -10000 0 0
CCL5 0.02 0.055 0.17 6 -0.31 12 18
SDCBP 0.023 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.016 0.095 0.24 5 -0.34 18 23
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 -0.003 0.1 0.21 10 -0.34 18 28
Syndecan-1/Syntenin -0.002 0.091 0.22 6 -0.3 17 23
MAPK3 -0.007 0.095 0.22 12 -0.31 17 29
HGF/MET 0.008 0.095 0.14 9 -0.26 48 57
TGFB1/TGF beta receptor Type II 0.027 0.004 -10000 0 -10000 0 0
BSG 0.027 0.007 0.17 1 -10000 0 1
keratinocyte migration -0.003 0.1 0.21 10 -0.33 18 28
Syndecan-1/RANTES -0.003 0.11 0.22 12 -0.32 25 37
Syndecan-1/CD147 0.012 0.11 0.28 6 -0.32 17 23
Syndecan-1/Syntenin/PIP2 -0.004 0.086 0.18 3 -0.31 15 18
LAMA5 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.004 0.085 0.18 3 -0.3 15 18
MMP7 0.016 0.099 0.17 49 -0.31 34 83
HGF 0.011 0.076 0.17 9 -0.31 24 33
Syndecan-1/CASK -0.021 0.089 0.19 1 -0.31 21 22
Syndecan-1/HGF/MET -0.011 0.12 0.2 3 -0.32 41 44
regulation of cell adhesion -0.014 0.092 0.23 13 -0.31 17 30
HPSE 0.016 0.066 0.17 8 -0.31 18 26
positive regulation of cell migration -0.016 0.095 0.24 5 -0.34 18 23
SDC1 -0.014 0.094 0.24 5 -0.22 53 58
Syndecan-1/Collagen -0.016 0.095 0.24 5 -0.34 18 23
PPIB 0.028 0.011 0.17 3 -10000 0 3
MET -0.002 0.091 -10000 0 -0.31 39 39
PRKACA 0.027 0.004 -10000 0 -10000 0 0
MMP9 0.097 0.081 0.17 257 -0.31 5 262
MAPK1 -0.007 0.096 0.22 13 -0.31 17 30
homophilic cell adhesion -0.013 0.098 0.24 10 -0.33 19 29
MMP1 0.023 0.096 0.17 59 -0.31 29 88
JNK 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
LAT/GRAP2/SLP76/HPK1 0.059 0.069 0.28 9 -0.19 21 30
MAP4K1 0.03 0.049 0.17 25 -0.31 6 31
MAP3K8 0.019 0.053 0.17 1 -0.31 12 13
PRKCB -0.047 0.14 -10000 0 -0.31 105 105
DBNL 0.025 0.008 -10000 0 -10000 0 0
CRKL 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.058 0.17 1 -0.25 15 16
JUN -0.12 0.25 0.35 1 -0.54 121 122
MAP3K7 0.009 0.05 0.17 1 -0.23 12 13
GRAP2 0.016 0.061 0.17 2 -0.31 16 18
CRK 0.025 0.007 -10000 0 -10000 0 0
MAP2K4 0.002 0.074 0.24 7 -0.33 12 19
LAT 0.027 0.034 0.17 11 -0.31 3 14
LCP2 0.026 0.025 0.17 4 -0.31 2 6
MAPK8 -0.12 0.26 -10000 0 -0.56 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.017 0.065 0.18 1 -0.24 18 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.065 0.069 0.28 8 -0.18 20 28
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0 0.021 -10000 0 -10000 0 0
NFATC2 -0.029 0.071 -10000 0 -0.19 77 77
NFATC3 0.001 0.02 -10000 0 -10000 0 0
CD40LG -0.075 0.15 0.33 1 -0.36 68 69
PTGS2 -0.089 0.17 0.33 1 -0.4 89 90
JUNB 0.022 0.057 0.17 12 -0.31 12 24
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.02 -10000 0 -10000 0 0
CALM1 0.02 0.018 -10000 0 -10000 0 0
JUN 0.018 0.036 0.17 1 -0.32 4 5
mol:Ca2+ -0.003 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.006 -10000 0 -10000 0 0
FOSL1 -0.013 0.13 0.17 34 -0.31 70 104
CREM 0.027 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.008 0.1 -10000 0 -0.25 32 32
FOS -0.031 0.12 0.17 4 -0.32 76 80
IFNG -0.068 0.13 0.33 1 -0.34 59 60
AP-1/NFAT1-c-4 -0.033 0.18 0.34 1 -0.38 66 67
FASLG -0.072 0.14 0.33 1 -0.36 63 64
NFAT1-c-4/ICER1 -0.019 0.078 -10000 0 -0.2 33 33
IL2RA -0.066 0.14 0.33 1 -0.35 61 62
FKBP12/FK506 0.02 0.003 -10000 0 -10000 0 0
CSF2 -0.071 0.13 -10000 0 -0.34 60 60
JunB/Fra1/NFAT1-c-4 -0.025 0.11 0.21 4 -0.24 55 59
IL4 -0.072 0.13 -10000 0 -0.34 60 60
IL2 -0.001 0.14 -10000 0 -0.92 10 10
IL3 -0.01 0.14 -10000 0 -0.64 21 21
FKBP1A 0.027 0.004 -10000 0 -10000 0 0
BATF3 0.032 0.03 0.17 22 -10000 0 22
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.006 -10000 0 -10000 0 0
BMP receptor signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.017 0.11 -10000 0 -0.18 100 100
SMAD6-7/SMURF1 0.041 0.036 -10000 0 -0.18 8 8
NOG -0.012 0.11 0.17 1 -0.31 55 56
SMAD9 -0.071 0.19 -10000 0 -0.43 99 99
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD5 -0.006 0.071 0.21 2 -0.28 16 18
BMP7/USAG1 -0.073 0.15 -10000 0 -0.27 172 172
SMAD5/SKI 0.007 0.079 0.23 3 -0.28 14 17
SMAD1 0.021 0.03 -10000 0 -10000 0 0
BMP2 0.008 0.079 0.17 1 -0.31 28 29
SMAD1/SMAD1/SMAD4 0.03 0.036 -10000 0 -10000 0 0
BMPR1A 0.024 0.017 -10000 0 -0.31 1 1
BMPR1B 0.025 0.029 0.17 3 -0.31 3 6
BMPR1A-1B/BAMBI 0.05 0.033 -10000 0 -0.17 4 4
AHSG 0.028 0.036 0.17 30 -10000 0 30
CER1 0.023 0.021 0.17 9 -10000 0 9
BMP2-4/CER1 0.027 0.078 -10000 0 -0.22 39 39
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.006 0.099 0.18 1 -0.32 31 32
BMP2-4 (homodimer) 0.015 0.086 -10000 0 -0.26 39 39
RGMB 0.024 0.009 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.066 0.042 -10000 0 -0.17 3 3
RGMA 0.013 0.067 -10000 0 -0.31 20 20
SMURF1 0.025 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.009 0.092 -10000 0 -0.31 31 31
BMP2-4/USAG1 -0.037 0.13 -10000 0 -0.22 153 153
SMAD6/SMURF1/SMAD5 0.006 0.072 0.26 1 -0.28 12 13
SOSTDC1 -0.08 0.15 -10000 0 -0.31 150 150
BMP7/BMPR2/BMPR1A-1B 0.02 0.09 -10000 0 -0.16 89 89
SKI 0.027 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.042 0.045 0.17 55 -10000 0 55
HFE2 0.036 0.044 0.17 49 -10000 0 49
ZFYVE16 0.026 0.007 -10000 0 -10000 0 0
MAP3K7 0.023 0.01 -10000 0 -10000 0 0
BMP2-4/CHRD 0.036 0.086 -10000 0 -0.22 39 39
SMAD5/SMAD5/SMAD4 0.008 0.077 0.29 2 -0.28 12 14
MAPK1 0.027 0.004 -10000 0 -10000 0 0
TAK1/TAB family 0.005 0.084 -10000 0 -0.29 22 22
BMP7 (homodimer) -0.034 0.13 0.17 1 -0.31 88 89
NUP214 0.026 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.049 0.043 0.26 4 -10000 0 4
SMAD1/SKI 0.037 0.043 0.29 3 -10000 0 3
SMAD6 0.022 0.043 -10000 0 -0.31 8 8
CTDSP2 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.031 0.081 -10000 0 -0.22 37 37
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.007 0.1 0.17 30 -0.31 40 70
BMPR2 (homodimer) 0.027 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.049 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.035 0.026 0.14 2 -0.2 4 6
CHRDL1 -0.058 0.15 -10000 0 -0.31 123 123
ENDOFIN/SMAD1 0.036 0.045 0.32 4 -10000 0 4
SMAD6-7/SMURF1/SMAD1 0.045 0.048 0.31 1 -10000 0 1
SMAD6/SMURF1 0.024 0.008 -10000 0 -10000 0 0
BAMBI 0.033 0.028 0.17 20 -10000 0 20
SMURF2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.021 0.13 -10000 0 -0.23 126 126
BMP2-4/GREM1 0.019 0.1 -10000 0 -0.22 69 69
SMAD7 0.025 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.063 0.19 -10000 0 -0.4 107 107
SMAD1/SMAD6 0.031 0.039 0.28 2 -10000 0 2
TAK1/SMAD6 0.031 0.017 -10000 0 -10000 0 0
BMP7 -0.034 0.13 0.17 1 -0.31 88 89
BMP6 0.042 0.045 0.17 55 -10000 0 55
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.007 0.093 -10000 0 -0.31 29 29
PPM1A 0.027 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.036 0.045 0.34 3 -10000 0 3
SMAD7/SMURF1 0.033 0.016 -10000 0 -10000 0 0
CTDSPL 0.027 0.005 -10000 0 -10000 0 0
PPP1CA 0.026 0.006 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
CTDSP1 0.027 0.003 -10000 0 -10000 0 0
PPP1R15A 0.028 0.013 0.17 4 -10000 0 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.032 0.14 -10000 0 -0.41 42 42
CHRD 0.035 0.048 0.17 41 -0.31 3 44
BMPR2 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.01 0.097 -10000 0 -0.34 30 30
BMP4 0.011 0.071 -10000 0 -0.31 23 23
FST 0.002 0.087 0.17 3 -0.31 34 37
BMP2-4/NOG 0.008 0.11 -10000 0 -0.24 74 74
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.03 0.086 -10000 0 -0.16 74 74
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A -0.005 0.012 0.25 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.031 -10000 0 -0.21 5 5
STXBP1 0.024 0.022 -10000 0 -0.31 2 2
ACh/CHRNA1 0.025 0.064 0.13 80 -0.09 58 138
RAB3GAP2/RIMS1/UNC13B 0.047 0.031 -10000 0 -0.18 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.041 0.17 6 -0.31 6 12
mol:ACh -0.01 0.048 0.088 34 -0.11 61 95
RAB3GAP2 0.026 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.015 0.068 -10000 0 -0.16 42 42
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.025 0.063 0.13 80 -0.09 58 138
UNC13B 0.027 0.01 0.17 2 -10000 0 2
CHRNA1 0.049 0.054 0.17 83 -10000 0 83
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.009 0.081 0.12 6 -0.18 71 77
SNAP25 -0.027 0.077 -10000 0 -0.22 67 67
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.028 0.13 0.17 8 -0.31 81 89
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.021 0.015 0.19 1 -0.18 1 2
STX1A/SNAP25 fragment 1/VAMP2 0.015 0.068 -10000 0 -0.16 42 42
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.013 0.074 -10000 0 -0.21 39 39
NT3 (dimer)/TRKC -0.027 0.13 -10000 0 -0.26 103 103
NT3 (dimer)/TRKB -0.011 0.12 -10000 0 -0.23 104 104
SHC/Grb2/SOS1/GAB1/PI3K 0.019 0.029 -10000 0 -0.2 6 6
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
BDNF -0.039 0.13 -10000 0 -0.31 95 95
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.009 0.081 0.17 8 -0.31 28 36
NTRK2 -0.015 0.11 0.17 1 -0.31 59 60
NTRK3 -0.037 0.13 -10000 0 -0.31 92 92
NT-4/5 (dimer)/TRKB -0.035 0.14 -10000 0 -0.24 143 143
neuron apoptosis 0.052 0.16 0.38 69 -0.23 1 70
SHC 2-3/Grb2 -0.057 0.18 0.24 1 -0.41 69 70
SHC1 0.026 0.006 -10000 0 -10000 0 0
SHC2 -0.05 0.15 -10000 0 -0.41 51 51
SHC3 -0.075 0.19 0.25 1 -0.47 72 73
STAT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.004 0.11 -10000 0 -0.22 83 83
RIN/GDP 0.006 0.094 0.27 15 -0.22 21 36
GIPC1 0.027 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.007 -10000 0 -10000 0 0
DNAJA3 -0.029 0.094 -10000 0 -0.24 64 64
RIN/GTP 0.022 0.027 0.12 31 -0.11 2 33
CCND1 0.015 0.005 -10000 0 -10000 0 0
MAGED1 0.028 0.007 0.17 1 -10000 0 1
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.048 0.14 -10000 0 -0.31 108 108
SHC/GRB2/SOS1 0.049 0.018 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.058 0.1 0.23 1 -0.2 50 51
TRKA/NEDD4-2 0.022 0.062 0.14 14 -0.21 27 41
ELMO1 0.024 0.017 -10000 0 -0.31 1 1
RhoG/GTP/ELMO1/DOCK1 0.03 0.021 -10000 0 -0.18 3 3
NGF 0.013 0.068 0.17 2 -0.31 20 22
HRAS 0.028 0.015 0.17 5 -10000 0 5
DOCK1 0.024 0.027 -10000 0 -0.31 3 3
GAB2 0.026 0.006 -10000 0 -10000 0 0
RIT2 0.031 0.036 0.17 31 -10000 0 31
RIT1 0.026 0.006 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
DNM1 0.025 0.018 0.17 1 -0.31 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.012 0.099 -10000 0 -0.24 66 66
mol:GDP -0.01 0.12 0.31 15 -0.32 25 40
NGF (dimer) 0.013 0.067 0.17 2 -0.31 20 22
RhoG/GDP 0.018 0.012 -10000 0 -0.21 1 1
RIT1/GDP 0 0.088 0.27 11 -0.22 21 32
TIAM1 0.024 0.027 -10000 0 -0.31 3 3
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
BDNF (dimer)/TRKB -0.015 0.13 -10000 0 -0.24 109 109
KIDINS220/CRKL/C3G 0.037 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.035 0.021 -10000 0 -0.21 2 2
FRS2 family/SHP2 0.051 0.018 -10000 0 -0.18 1 1
SHC/GRB2/SOS1/GAB1 0.062 0.025 -10000 0 -0.17 1 1
RIT1/GTP 0.019 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.006 0.097 -10000 0 -0.31 45 45
RAP1/GDP -0.004 0.068 0.14 3 -0.19 20 23
KIDINS220/CRKL 0.027 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.039 0.13 -10000 0 -0.31 95 95
ubiquitin-dependent protein catabolic process 0.025 0.074 -10000 0 -0.19 45 45
Schwann cell development -0.022 0.026 -10000 0 -0.096 12 12
EHD4 0.027 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.024 0.029 -10000 0 -0.17 2 2
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.044 0.14 -10000 0 -0.24 137 137
ABL1 0.026 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.084 -10000 0 -0.32 18 18
STAT3 0.031 0.007 -10000 0 -10000 0 0
axon guidance -0.05 0.13 -10000 0 -0.23 137 137
MAPK3 -0.04 0.06 0.18 10 -0.2 39 49
MAPK1 -0.041 0.062 0.18 11 -0.2 41 52
CDC42/GDP 0.003 0.092 0.25 15 -0.22 20 35
NTF3 -0.006 0.097 -10000 0 -0.31 45 45
NTF4 -0.048 0.14 -10000 0 -0.31 108 108
NGF (dimer)/TRKA/FAIM 0.028 0.072 -10000 0 -0.18 44 44
PI3K 0.032 0.033 -10000 0 -0.25 5 5
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.025 0.007 -10000 0 -10000 0 0
GAB1 0.026 0.016 -10000 0 -0.31 1 1
RASGRF1 -0.049 0.12 -10000 0 -0.29 70 70
SOS1 0.026 0.005 -10000 0 -10000 0 0
MCF2L -0.054 0.09 -10000 0 -0.22 94 94
RGS19 0.027 0.008 0.17 1 -10000 0 1
CDC42 0.027 0.004 -10000 0 -10000 0 0
RAS family/GTP 0 0.11 0.29 5 -0.43 14 19
Rac1/GDP 0 0.083 0.26 7 -0.22 21 28
NGF (dimer)/TRKA/GRIT 0.015 0.067 0.12 10 -0.18 47 57
neuron projection morphogenesis -0.034 0.18 -10000 0 -0.8 16 16
NGF (dimer)/TRKA/NEDD4-2 0.026 0.075 -10000 0 -0.19 45 45
MAP2K1 -0.001 0.07 0.23 35 -10000 0 35
NGFR -0.001 0.092 -10000 0 -0.31 40 40
NGF (dimer)/TRKA/GIPC/GAIP 0.006 0.061 -10000 0 -0.18 41 41
RAS family/GTP/PI3K 0.016 0.026 -10000 0 -0.21 5 5
FRS2 family/SHP2/GRB2/SOS1 0.071 0.03 -10000 0 -0.16 1 1
NRAS 0.026 0.016 -10000 0 -0.31 1 1
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.025 0.01 0.17 1 -10000 0 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.063 0.21 -10000 0 -0.54 71 71
RASA1 0.024 0.022 -10000 0 -0.31 2 2
TRKA/c-Abl 0.025 0.059 0.14 8 -0.21 26 34
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0 0.12 -10000 0 -0.22 110 110
NGF (dimer)/TRKA/p62/Atypical PKCs 0.047 0.074 -10000 0 -0.16 42 42
MATK 0.085 0.074 0.17 209 -0.31 2 211
NEDD4L 0.027 0.025 0.17 13 -10000 0 13
RAS family/GDP -0.021 0.052 -10000 0 -0.16 32 32
NGF (dimer)/TRKA -0.027 0.1 -10000 0 -0.25 71 71
Rac1/GTP -0.04 0.091 -10000 0 -0.22 74 74
FRS2 family/SHP2/CRK family 0.07 0.031 -10000 0 -0.16 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.01 0.045 -10000 0 -0.34 6 6
Crk/p130 Cas/Paxillin -0.021 0.084 -10000 0 -0.24 46 46
JUN -0.022 0.081 -10000 0 -0.3 23 23
HRAS 0.028 0.015 0.17 5 -10000 0 5
RET51/GFRalpha1/GDNF/GRB10 0.043 0.092 -10000 0 -0.19 52 52
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.044 0.097 0.24 1 -0.19 58 59
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.02 0.082 -10000 0 -0.19 58 58
RHOA 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.035 0.09 0.2 1 -0.18 57 58
GRB7 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.044 0.097 0.24 1 -0.19 59 60
MAPKKK cascade 0.012 0.081 -10000 0 -0.21 42 42
BCAR1 0.022 0.011 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.019 0.081 -10000 0 -0.18 62 62
lamellipodium assembly -0.011 0.084 -10000 0 -0.23 50 50
RET51/GFRalpha1/GDNF/SHC 0.042 0.096 0.24 1 -0.19 58 59
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
RET9/GFRalpha1/GDNF/SHC 0.022 0.072 -10000 0 -0.17 53 53
RET9/GFRalpha1/GDNF/Shank3 0.023 0.072 -10000 0 -0.17 55 55
MAPK3 -0.031 0.076 0.24 14 -0.28 11 25
DOK1 0.027 0.004 -10000 0 -10000 0 0
DOK6 0.018 0.064 0.17 14 -0.31 15 29
PXN 0.026 0.006 -10000 0 -10000 0 0
neurite development -0.028 0.068 0.22 10 -0.27 12 22
DOK5 0.014 0.072 0.17 9 -0.31 21 30
GFRA1 0 0.092 0.17 1 -0.31 39 40
MAPK8 -0.017 0.08 -10000 0 -0.3 20 20
HRAS/GTP 0.035 0.1 0.2 2 -0.22 51 53
tube development 0.023 0.072 0.21 9 -0.16 53 62
MAPK1 -0.03 0.078 0.23 17 -0.27 13 30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.002 0.066 -10000 0 -0.19 51 51
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
PDLIM7 0.02 0.051 0.17 2 -0.31 11 13
RET51/GFRalpha1/GDNF/Dok6 0.042 0.1 0.24 1 -0.19 65 66
SHC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.04 0.1 0.24 1 -0.2 58 59
RET51/GFRalpha1/GDNF/Dok5 0.039 0.11 0.24 6 -0.21 67 73
PRKCA 0.013 0.067 -10000 0 -0.31 20 20
HRAS/GDP 0.021 0.01 0.12 5 -10000 0 5
CREB1 -0.007 0.088 -10000 0 -0.23 52 52
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.003 0.07 -10000 0 -0.2 51 51
RET51/GFRalpha1/GDNF/Grb7 0.044 0.098 0.24 1 -0.19 60 61
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.043 0.073 0.17 81 -0.31 10 91
DOK4 0.022 0.031 -10000 0 -0.31 4 4
JNK cascade -0.021 0.08 0.18 1 -0.29 23 24
RET9/GFRalpha1/GDNF/FRS2 0.023 0.07 -10000 0 -0.17 53 53
SHANK3 0.027 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.022 -10000 0 -0.31 2 2
NCK1 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.003 0.07 -10000 0 -0.2 51 51
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0 0.078 -10000 0 -0.2 58 58
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.001 0.084 -10000 0 -0.22 54 54
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0 0.082 -10000 0 -0.21 57 57
PI3K -0.019 0.12 0.24 3 -0.32 53 56
SOS1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.073 -10000 0 -0.16 53 53
GRB10 0.025 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.006 0.081 -10000 0 -0.25 31 31
RET51/GFRalpha1/GDNF/FRS2 0.044 0.095 0.24 1 -0.18 58 59
GAB1 0.026 0.016 -10000 0 -0.31 1 1
IRS1 0.017 0.056 -10000 0 -0.31 14 14
IRS2 0.027 0.013 0.17 3 -10000 0 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.002 0.086 -10000 0 -0.22 59 59
RET51/GFRalpha1/GDNF/PKC alpha 0.036 0.11 0.24 1 -0.21 67 68
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.004 -10000 0 -10000 0 0
GDNF 0.009 0.072 0.17 1 -0.31 23 24
RAC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.039 0.11 0.24 1 -0.2 67 68
Rac1/GTP -0.011 0.099 -10000 0 -0.27 47 47
RET9/GFRalpha1/GDNF 0.009 0.073 -10000 0 -0.19 55 55
GFRalpha1/GDNF 0.007 0.086 -10000 0 -0.23 55 55
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.002 0.036 0.35 1 -10000 0 1
VDR 0.023 0.038 0.17 2 -0.31 6 8
FAM120B 0.027 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.019 0.1 -10000 0 -0.28 29 29
RXRs/LXRs/DNA/Oxysterols -0.018 0.12 -10000 0 -0.41 27 27
MED1 0.027 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.011 -10000 0 -0.069 1 1
RARs/THRs/DNA/Src-1 0.021 0.033 -10000 0 -0.18 12 12
RXRs/NUR77 0.015 0.1 0.25 1 -0.18 94 95
RXRs/PPAR -0.024 0.098 -10000 0 -0.2 102 102
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.017 0.026 0.12 2 -0.21 6 8
RARs/VDR/DNA/Vit D3 0.052 0.048 -10000 0 -0.19 14 14
RARA 0.027 0.004 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.038 0.17 2 -0.31 6 8
RARs/RARs/DNA/9cRA 0.038 0.038 -10000 0 -0.15 13 13
RARG 0.021 0.043 -10000 0 -0.31 8 8
RPS6KB1 0.011 0.056 0.53 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.02 0.034 -10000 0 -0.18 13 13
THRA 0.027 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.017 0.026 0.12 2 -0.21 6 8
RXRs/PPAR/9cRA/PGJ2/DNA 0.006 0.094 -10000 0 -0.16 111 111
NR1H4 -0.031 0.13 0.17 17 -0.31 86 103
RXRs/LXRs/DNA 0.025 0.11 -10000 0 -0.22 26 26
NR1H2 0.026 0.019 -10000 0 -10000 0 0
NR1H3 0.025 0.021 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.013 0.093 -10000 0 -0.16 96 96
NR4A1 0.02 0.058 0.17 10 -0.31 13 23
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.049 0.11 0.15 2 -0.19 155 157
RXRG -0.045 0.14 0.17 6 -0.31 102 108
RXR alpha/CCPG 0.035 0.021 -10000 0 -10000 0 0
RXRA 0.024 0.02 -10000 0 -10000 0 0
RXRB 0.025 0.02 -10000 0 -0.081 1 1
THRB 0.028 0.018 0.17 7 -10000 0 7
PPARG 0.011 0.074 0.17 3 -0.31 24 27
PPARD 0.027 0.004 -10000 0 -10000 0 0
TNF -0.051 0.23 0.33 1 -0.94 27 28
mol:Oxysterols 0.001 0.01 -10000 0 -10000 0 0
cholesterol transport -0.018 0.12 -10000 0 -0.41 27 27
PPARA 0.027 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.034 -10000 0 -0.31 5 5
RXRs/NUR77/BCL2 -0.029 0.1 -10000 0 -0.21 100 100
SREBF1 -0.021 0.11 -10000 0 -0.38 26 26
RXRs/RXRs/DNA/9cRA 0.006 0.094 -10000 0 -0.16 111 111
ABCA1 -0.023 0.12 -10000 0 -0.57 7 7
RARs/THRs 0.069 0.046 -10000 0 -0.16 13 13
RXRs/FXR -0.02 0.12 0.25 1 -0.18 156 157
BCL2 0.015 0.055 -10000 0 -0.31 13 13
FOXM1 transcription factor network

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
NFATC3 0.003 0.36 0.61 1 -1.1 26 27
PLK1 0.047 0.048 -10000 0 -10000 0 0
BIRC5 0.034 0.12 -10000 0 -0.72 10 10
HSPA1B 0.002 0.36 -10000 0 -1.1 29 29
MAP2K1 0.028 0.045 -10000 0 -10000 0 0
BRCA2 -0.016 0.4 -10000 0 -1.2 38 38
FOXM1 -0.018 0.45 -10000 0 -1.5 30 30
XRCC1 0.001 0.36 -10000 0 -1.1 28 28
FOXM1B/p19 -0.02 0.41 -10000 0 -1.3 32 32
Cyclin D1/CDK4 0.007 0.34 -10000 0 -1 29 29
CDC2 0 0.38 -10000 0 -1.2 30 30
TGFA -0.01 0.36 -10000 0 -0.99 37 37
SKP2 -0.002 0.38 0.63 2 -1.1 31 33
CCNE1 0.026 0.023 0.17 4 -10000 0 4
CKS1B 0.002 0.36 -10000 0 -1.1 31 31
RB1 -0.006 0.26 -10000 0 -0.88 26 26
FOXM1C/SP1 -0.005 0.4 -10000 0 -1.3 30 30
AURKB -0.044 0.28 -10000 0 -0.83 51 51
CENPF 0.008 0.36 0.62 1 -1.1 26 27
CDK4 0.023 0.026 -10000 0 -10000 0 0
MYC -0.003 0.31 0.53 1 -0.92 29 30
CHEK2 0.028 0.044 -10000 0 -0.15 1 1
ONECUT1 -0.001 0.36 -10000 0 -1.1 30 30
CDKN2A 0.046 0.06 0.16 97 -10000 0 97
LAMA4 -0.003 0.38 -10000 0 -1.2 28 28
FOXM1B/HNF6 -0.018 0.42 -10000 0 -1.4 29 29
FOS -0.1 0.5 0.57 1 -1.1 87 88
SP1 0.028 0.006 -10000 0 -10000 0 0
CDC25B 0.001 0.36 -10000 0 -1.1 29 29
response to radiation 0.01 0.024 -10000 0 -10000 0 0
CENPB 0.001 0.36 -10000 0 -1.1 29 29
CENPA 0.006 0.36 -10000 0 -1.1 26 26
NEK2 0.009 0.36 -10000 0 -1.1 27 27
HIST1H2BA -0.001 0.36 -10000 0 -1.1 27 27
CCNA2 0.046 0.054 0.17 70 -10000 0 70
EP300 0.025 0.027 -10000 0 -0.31 3 3
CCNB1/CDK1 -0.013 0.41 -10000 0 -1.4 27 27
CCNB2 0.003 0.36 0.62 1 -1.1 26 27
CCNB1 0 0.38 -10000 0 -1.2 27 27
ETV5 -0.016 0.42 0.64 1 -1.2 41 42
ESR1 -0.012 0.39 0.62 1 -1.2 34 35
CCND1 -0.003 0.34 -10000 0 -1 29 29
GSK3A 0.027 0.04 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.065 0.063 0.2 39 -10000 0 39
CDK2 0.025 0.019 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.011 0.029 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.001 0.39 -10000 0 -1.2 31 31
GAS1 -0.043 0.46 0.63 2 -1.2 54 56
MMP2 -0.006 0.38 0.61 1 -1.2 29 30
RB1/FOXM1C -0.026 0.36 -10000 0 -1.1 29 29
CREBBP 0.026 0.005 -10000 0 -10000 0 0
Arf6 signaling events

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.02 -10000 0 -0.18 1 1
ARNO/beta Arrestin1-2 0.028 0.098 -10000 0 -0.75 7 7
EGFR -0.002 0.09 -10000 0 -0.31 38 38
EPHA2 -0.002 0.096 0.17 3 -0.31 43 46
USP6 0.025 0.01 0.17 1 -10000 0 1
IQSEC1 0.027 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.013 0.09 0.14 32 -0.22 54 86
ARRB2 0.009 0.005 -10000 0 -10000 0 0
mol:GTP 0.007 0.04 0.13 13 -0.15 6 19
ARRB1 0.026 0.016 -10000 0 -0.31 1 1
FBXO8 0.026 0.005 -10000 0 -10000 0 0
TSHR 0.018 0.059 0.17 6 -0.31 14 20
EGF 0.023 0.08 0.17 38 -0.31 21 59
somatostatin receptor activity 0 0 0.001 36 0 23 59
ARAP2 0.026 0.016 -10000 0 -0.31 1 1
mol:GDP 0.01 0.087 0.22 27 -0.22 24 51
mol:PI-3-4-5-P3 0 0 0.001 31 -0.001 7 38
ITGA2B 0.02 0.048 0.17 5 -0.31 9 14
ARF6 0.027 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.067 -10000 0 -0.17 39 39
ADAP1 0.024 0.018 0.17 1 -0.31 1 2
KIF13B 0.02 0.012 -10000 0 -10000 0 0
HGF/MET 0.008 0.095 0.14 9 -0.26 48 57
PXN 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.016 0.1 0.27 37 -0.2 25 62
EGFR/EGFR/EGF/EGF/ARFGEP100 0.028 0.082 -10000 0 -0.19 52 52
ADRB2 0.028 0.015 0.17 5 -10000 0 5
receptor agonist activity 0 0 0 25 0 18 43
actin filament binding 0 0 0.001 37 0 23 60
SRC 0.026 0.006 -10000 0 -10000 0 0
ITGB3 -0.036 0.13 -10000 0 -0.31 90 90
GNAQ 0.026 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 47 -0.001 12 59
ARF6/GDP 0 0.12 0.29 12 -0.31 29 41
ARF6/GDP/GULP/ACAP1 0.034 0.092 0.23 20 -0.23 14 34
alphaIIb/beta3 Integrin/paxillin/GIT1 0.015 0.093 -10000 0 -0.16 97 97
ACAP1 0.029 0.03 0.17 20 -10000 0 20
ACAP2 0.025 0.017 -10000 0 -0.31 1 1
LHCGR/beta Arrestin2 0.015 0.022 0.14 4 -10000 0 4
EFNA1 0.026 0.006 -10000 0 -10000 0 0
HGF 0.011 0.076 0.17 9 -0.31 24 33
CYTH3 -0.004 0.017 0.25 2 -10000 0 2
CYTH2 0.005 0.12 -10000 0 -0.98 7 7
NCK1 0.025 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 41 0 15 56
endosomal lumen acidification 0 0 0.001 33 0 25 58
microtubule-based process 0 0 -10000 0 0 6 6
GULP1 0.027 0.018 0.17 2 -0.31 1 3
GNAQ/ARNO 0.022 0.11 -10000 0 -0.87 7 7
mol:Phosphatidic acid 0 0 0 14 -10000 0 14
PIP3-E 0 0 0 29 0 4 33
MET -0.002 0.091 -10000 0 -0.31 39 39
GNA14 0.026 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.067 -10000 0 -0.31 20 20
GIT1 0.027 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 44 -0.001 14 58
GNA11 0.017 0.056 -10000 0 -0.31 14 14
LHCGR 0.02 0.015 0.17 4 -10000 0 4
AGTR1 0.037 0.085 0.17 81 -0.31 17 98
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.022 0.14 4 -10000 0 4
IPCEF1/ARNO 0.017 0.12 -10000 0 -0.82 7 7
alphaIIb/beta3 Integrin -0.014 0.1 -10000 0 -0.21 99 99
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.016 0.17 4 -10000 0 4
LAT2 -0.009 0.085 0.21 3 -0.29 29 32
AP1 0.002 0.14 0.26 3 -0.4 32 35
mol:PIP3 0.012 0.15 0.33 41 -0.36 24 65
IKBKB 0.01 0.12 0.29 47 -0.21 33 80
AKT1 -0.004 0.12 0.35 32 -0.25 14 46
IKBKG -0.002 0.11 0.27 33 -0.22 35 68
MS4A2 0.014 0.068 0.17 4 -0.31 19 23
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
MAP3K1 0.01 0.11 0.27 32 -0.31 23 55
mol:Ca2+ 0.015 0.13 0.3 41 -0.28 23 64
LYN 0.023 0.012 -10000 0 -10000 0 0
CBLB -0.008 0.083 0.16 2 -0.28 28 30
SHC1 0.026 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.04 0.042 -10000 0 -0.16 18 18
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.01 0.073 -10000 0 -0.31 24 24
PLD2 -0.015 0.084 0.28 20 -0.24 15 35
PTPN13 0 0.13 0.39 1 -0.53 14 15
PTPN11 0.023 0.023 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.015 0.13 0.39 33 -0.28 16 49
SYK 0.024 0.037 0.16 1 -0.32 5 6
GRB2 0.027 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.004 0.1 0.17 1 -0.35 26 27
LAT -0.01 0.083 0.15 1 -0.28 29 30
PAK2 0.01 0.12 0.27 32 -0.33 27 59
NFATC2 -0.068 0.16 -10000 0 -0.43 78 78
HRAS 0.003 0.12 0.25 21 -0.33 32 53
GAB2 0.026 0.006 -10000 0 -10000 0 0
PLA2G1B 0.017 0.089 -10000 0 -0.81 5 5
Fc epsilon R1 0.02 0.092 -10000 0 -0.22 57 57
Antigen/IgE/Fc epsilon R1 0.021 0.082 -10000 0 -0.19 57 57
mol:GDP -0.002 0.11 0.26 3 -0.36 29 32
JUN 0.024 0.031 0.17 1 -0.31 4 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.028 -10000 0 -0.31 3 3
FOS -0.025 0.12 0.17 4 -0.31 76 80
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.003 0.089 0.16 2 -0.29 31 33
CHUK 0.001 0.11 0.26 39 -0.22 33 72
KLRG1 -0.004 0.075 0.16 4 -0.24 31 35
VAV1 -0.012 0.095 0.17 3 -0.31 32 35
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.009 0.085 0.16 3 -0.27 35 38
negative regulation of mast cell degranulation 0.002 0.099 0.18 7 -0.32 28 35
BTK 0.003 0.1 0.23 2 -0.4 18 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.023 0.12 -10000 0 -0.36 44 44
GAB2/PI3K/SHP2 -0.036 0.054 -10000 0 -0.22 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.091 -10000 0 -0.29 32 32
RAF1 0.017 0.095 -10000 0 -0.88 5 5
Fc epsilon R1/FcgammaRIIB/SHIP 0.035 0.12 0.24 3 -0.24 60 63
FCER1G 0.027 0.015 0.17 3 -10000 0 3
FCER1A -0.011 0.11 -10000 0 -0.32 52 52
Antigen/IgE/Fc epsilon R1/Fyn 0.027 0.08 -10000 0 -0.18 55 55
MAPK3 0.014 0.088 -10000 0 -0.8 5 5
MAPK1 0.013 0.091 -10000 0 -0.83 5 5
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.019 0.19 -10000 0 -0.58 39 39
DUSP1 0.015 0.062 -10000 0 -0.31 17 17
NF-kappa-B/RelA 0 0.054 0.12 8 -0.14 28 36
actin cytoskeleton reorganization 0 0.13 -10000 0 -0.54 14 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.009 0.11 0.24 4 -0.32 34 38
FER -0.009 0.085 0.16 3 -0.3 27 30
RELA 0.026 0.006 -10000 0 -10000 0 0
ITK 0 0.059 0.17 1 -0.32 13 14
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG1 0.006 0.12 0.27 20 -0.38 25 45
cytokine secretion -0.005 0.035 -10000 0 -0.11 19 19
SPHK1 -0.009 0.085 0.19 3 -0.28 30 33
PTK2 -0.001 0.13 -10000 0 -0.58 13 13
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.001 0.11 -10000 0 -0.35 28 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.006 0.14 0.32 33 -0.35 28 61
MAP2K2 0.01 0.089 -10000 0 -0.83 5 5
MAP2K1 0.011 0.09 -10000 0 -0.82 5 5
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 0.005 0.078 0.19 5 -0.26 24 29
MAP2K4 -0.036 0.25 -10000 0 -0.86 41 41
Fc epsilon R1/FcgammaRIIB 0.033 0.098 0.24 3 -0.21 57 60
mol:Choline -0.014 0.084 0.28 20 -0.24 15 35
SHC/Grb2/SOS1 0.033 0.097 0.24 2 -0.3 21 23
FYN 0.023 0.01 -10000 0 -10000 0 0
DOK1 0.027 0.004 -10000 0 -10000 0 0
PXN 0.005 0.13 0.38 8 -0.53 14 22
HCLS1 -0.007 0.081 0.16 2 -0.28 28 30
PRKCB -0.006 0.14 0.29 37 -0.29 40 77
FCGR2B 0.023 0.048 0.17 11 -0.31 8 19
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0.001 0.1 0.18 7 -0.32 28 35
LCP2 0.026 0.026 0.17 4 -0.31 2 6
PLA2G4A -0.014 0.1 0.16 3 -0.31 36 39
RASA1 0.024 0.022 -10000 0 -0.31 2 2
mol:Phosphatidic acid -0.014 0.084 0.28 20 -0.24 15 35
IKK complex 0.012 0.11 0.28 47 -0.18 18 65
WIPF1 0.023 0.031 -10000 0 -0.31 4 4
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.012 0.03 0.12 5 -0.16 13 18
BUB1B 0.014 0.033 0.16 12 -0.11 1 13
PLK1 0.015 0.028 0.11 24 -0.091 3 27
PLK1S1 0.012 0.026 0.13 6 -0.16 5 11
KIF2A 0.009 0.031 0.16 11 -0.11 1 12
regulation of mitotic centrosome separation 0.015 0.028 0.11 24 -0.091 3 27
GOLGA2 0.026 0.007 -10000 0 -10000 0 0
Hec1/SPC24 0.063 0.052 0.14 116 -0.13 3 119
WEE1 0.018 0.038 0.18 4 -0.33 3 7
cytokinesis 0.016 0.069 0.21 20 -0.2 3 23
PP2A-alpha B56 0.06 0.092 -10000 0 -0.5 11 11
AURKA 0.018 0.027 0.14 11 -0.14 1 12
PICH/PLK1 0.02 0.039 0.2 12 -0.14 2 14
CENPE 0.007 0.037 0.18 12 -0.11 1 13
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.01 0.032 0.16 11 -0.11 1 12
PPP2CA 0.026 0.005 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.026 0.034 0.16 16 -0.18 1 17
PAK1 0.023 0.032 -10000 0 -0.32 4 4
SPC24 0.065 0.062 0.17 133 -10000 0 133
FBXW11 0.027 0.005 -10000 0 -10000 0 0
CLSPN 0.015 0.042 0.13 4 -0.24 9 13
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.014 12 -0.013 1 13
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.016 0.057 28 -0.048 4 32
G2 phase of mitotic cell cycle -0.001 0.002 0.011 4 -10000 0 4
STAG2 0.027 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.017 0.037 -10000 0 -0.43 3 3
spindle elongation 0.015 0.028 0.11 24 -0.091 3 27
ODF2 0.026 0.007 -10000 0 -10000 0 0
BUB1 0.035 0.096 -10000 0 -0.55 11 11
TPT1 -0.025 0.076 0.11 4 -0.17 96 100
CDC25C 0.037 0.051 0.17 13 -0.25 8 21
CDC25B 0.024 0.022 0.17 1 -0.32 1 2
SGOL1 0.012 0.03 0.16 13 -0.12 5 18
RHOA 0.027 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.04 0.031 0.22 1 -0.17 3 4
CDC14B -0.008 0.021 -10000 0 -0.21 5 5
CDC20 0.073 0.065 0.17 160 -10000 0 160
PLK1/PBIP1 0.007 0.018 0.089 11 -0.081 2 13
mitosis -0.003 0.003 0.025 1 -10000 0 1
FBXO5 0.009 0.029 0.14 13 -10000 0 13
CDC2 0.001 0.002 0.011 1 -0.011 3 4
NDC80 0.024 0.022 -10000 0 -0.31 2 2
metaphase plate congression 0.015 0.025 0.13 1 -0.22 3 4
ERCC6L 0.018 0.042 0.22 6 -0.16 4 10
NLP/gamma Tubulin 0.007 0.022 0.087 12 -0.067 14 26
microtubule cytoskeleton organization -0.025 0.076 0.11 4 -0.17 96 100
G2/M transition DNA damage checkpoint -0.001 0.002 0.015 3 -10000 0 3
PPP1R12A 0.026 0.006 -10000 0 -10000 0 0
interphase -0.001 0.002 0.015 3 -10000 0 3
PLK1/PRC1-2 0.081 0.066 0.16 168 -0.1 2 170
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.023 0.17 1 -10000 0 1
RAB1A 0.027 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.011 0.025 0.096 26 -0.079 1 27
mitotic prometaphase -0.001 0.002 0.018 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.049 0.18 11 -0.36 3 14
microtubule-based process 0.061 0.057 0.13 170 -0.096 4 174
Golgi organization 0.015 0.028 0.11 24 -0.091 3 27
Cohesin/SA2 0.027 0.021 0.12 9 -0.097 1 10
PPP1CB/MYPT1 0.038 0.009 -10000 0 -10000 0 0
KIF20A 0.075 0.067 0.17 170 -10000 0 170
APC/C/CDC20 0.061 0.058 0.14 160 -0.1 3 163
PPP2R1A 0.027 0.004 -10000 0 -10000 0 0
chromosome segregation 0.007 0.018 0.088 11 -0.08 2 13
PRC1 0.034 0.031 0.17 25 -10000 0 25
ECT2 0.024 0.066 0.23 41 -0.11 1 42
C13orf34 0.012 0.024 0.095 24 -0.076 3 27
NUDC 0.015 0.025 0.13 1 -0.23 3 4
regulation of attachment of spindle microtubules to kinetochore 0.014 0.033 0.16 12 -0.11 1 13
spindle assembly 0.01 0.024 0.095 20 -0.079 3 23
spindle stabilization 0.012 0.026 0.13 6 -0.16 5 11
APC/C/HCDH1 0.02 0.021 -10000 0 -0.17 5 5
MKLP2/PLK1 0.062 0.058 0.13 170 -0.097 4 174
CCNB1 0.031 0.029 0.17 18 -10000 0 18
PPP1CB 0.027 0.003 -10000 0 -10000 0 0
BTRC 0.026 0.006 -10000 0 -10000 0 0
ROCK2 -0.009 0.11 0.18 5 -0.35 43 48
TUBG1 0.006 0.039 0.11 4 -0.17 19 23
G2/M transition of mitotic cell cycle 0.004 0.024 -10000 0 -0.17 3 3
MLF1IP -0.005 0.034 0.26 7 -10000 0 7
INCENP 0.026 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.026 0.13 0.29 21 -0.4 23 44
FYN 0.007 0.16 0.32 24 -0.49 26 50
LAT/GRAP2/SLP76 0.014 0.13 0.27 9 -0.44 22 31
IKBKB 0.021 0.011 -10000 0 -10000 0 0
AKT1 0.013 0.13 0.33 28 -0.36 24 52
B2M 0.027 0.008 -10000 0 -10000 0 0
IKBKG 0.006 0.041 0.11 28 -0.13 12 40
MAP3K8 0.019 0.053 0.17 1 -0.31 12 13
mol:Ca2+ -0.013 0.011 0.086 2 -0.052 7 9
integrin-mediated signaling pathway 0.025 0.043 -10000 0 -0.17 21 21
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.005 0.16 0.36 21 -0.52 25 46
TRPV6 0.073 0.3 1.1 36 -10000 0 36
CD28 0.032 0.06 0.17 36 -0.31 9 45
SHC1 0.004 0.15 0.27 24 -0.49 25 49
receptor internalization -0.008 0.15 0.35 1 -0.44 36 37
PRF1 -0.014 0.22 -10000 0 -0.89 22 22
KRAS 0.025 0.007 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
COT/AKT1 0.022 0.11 0.31 26 -0.3 23 49
LAT -0.001 0.14 0.26 14 -0.49 24 38
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.026 0.059 0.17 23 -0.32 10 33
CD3E 0.023 0.051 0.17 8 -0.32 9 17
CD3G 0.008 0.089 0.17 16 -0.31 32 48
RASGRP2 0 0.037 0.082 5 -0.17 20 25
RASGRP1 0.009 0.13 0.35 22 -0.38 24 46
HLA-A 0.001 0.004 -10000 0 -10000 0 0
RASSF5 0.012 0.068 -10000 0 -0.31 21 21
RAP1A/GTP/RAPL 0.026 0.044 -10000 0 -0.17 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.079 0.21 41 -0.13 15 56
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.047 -10000 0 -0.19 19 19
PRKCA -0.004 0.07 0.17 15 -0.23 24 39
GRAP2 0.016 0.061 0.17 2 -0.31 16 18
mol:IP3 -0.005 0.092 0.17 2 -0.34 23 25
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.007 0.13 -10000 0 -0.53 21 21
ORAI1 -0.054 0.25 0.35 16 -0.94 32 48
CSK 0.001 0.14 0.24 14 -0.49 24 38
B7 family/CD28 0.039 0.15 0.3 15 -0.46 23 38
CHUK 0.025 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.006 0.16 0.21 5 -0.52 28 33
PTPN6 -0.006 0.14 0.21 8 -0.51 23 31
VAV1 -0.006 0.15 0.25 9 -0.49 28 37
Monovalent TCR/CD3 -0.002 0.094 -10000 0 -0.26 42 42
CBL 0.025 0.016 -10000 0 -0.31 1 1
LCK 0.009 0.15 0.29 23 -0.51 22 45
PAG1 0.014 0.14 0.2 62 -0.53 19 81
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.007 0.15 0.21 6 -0.47 32 38
CD80 0.034 0.036 0.17 30 -10000 0 30
CD86 0.027 0.024 0.17 7 -0.31 1 8
PDK1/CARD11/BCL10/MALT1 0.001 0.06 -10000 0 -0.23 19 19
HRAS 0.028 0.015 0.17 5 -10000 0 5
GO:0035030 -0.003 0.11 0.25 6 -0.38 25 31
CD8A 0.023 0.05 0.17 5 -0.32 9 14
CD8B 0.025 0.046 0.17 9 -0.32 7 16
PTPRC 0.017 0.065 0.17 7 -0.31 17 24
PDK1/PKC theta 0.007 0.16 0.41 26 -0.47 22 48
CSK/PAG1 0.016 0.14 0.22 42 -0.51 19 61
SOS1 0.026 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.021 0.009 -10000 0 -10000 0 0
GRAP2/SLP76 0.015 0.14 0.26 1 -0.48 25 26
STIM1 -0.012 0.17 1.1 7 -0.94 5 12
RAS family/GTP 0.022 0.085 0.25 28 -0.16 28 56
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.011 0.16 -10000 0 -0.47 36 36
mol:DAG -0.016 0.077 -10000 0 -0.29 26 26
RAP1A/GDP 0.014 0.036 0.12 26 -0.06 10 36
PLCG1 0.026 0.005 -10000 0 -10000 0 0
CD247 0.027 0.044 0.17 16 -0.32 5 21
cytotoxic T cell degranulation -0.012 0.2 -10000 0 -0.8 24 24
RAP1A/GTP 0 0.014 -10000 0 -0.061 21 21
mol:PI-3-4-5-P3 0.009 0.14 0.33 23 -0.43 25 48
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0 0.12 0.2 1 -0.43 23 24
NRAS 0.026 0.016 -10000 0 -0.31 1 1
ZAP70 0.04 0.052 0.17 53 -0.31 3 56
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0 0.12 0.2 5 -0.43 23 28
MALT1 0.024 0.019 0.17 1 -0.31 1 2
TRAF6 0.027 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.036 0.057 0.22 4 -0.27 13 17
CARD11 0.021 0.046 0.17 6 -0.31 8 14
PRKCB -0.015 0.078 0.16 7 -0.23 40 47
PRKCE 0 0.067 0.17 15 -0.23 18 33
PRKCQ 0 0.16 0.39 20 -0.52 24 44
LCP2 0.026 0.025 0.17 4 -0.31 2 6
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.016 0.12 0.3 30 -0.31 24 54
IKK complex 0.005 0.084 0.25 31 -0.11 26 57
RAS family/GDP 0 0.01 -10000 0 -0.038 7 7
MAP3K14 0.013 0.091 0.26 26 -0.23 23 49
PDPK1 0.015 0.13 0.35 29 -0.34 24 53
TCR/CD3/MHC I/CD8/Fyn -0.011 0.18 0.29 1 -0.59 30 31
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.01 0.008 0.058 2 -10000 0 2
RAS family/GTP 0.001 0.091 -10000 0 -0.19 43 43
NFATC4 -0.035 0.062 0.29 5 -0.24 4 9
ERBB2IP 0.025 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.014 0.068 0.16 1 -0.19 50 51
JUN -0.009 0.071 0.22 7 -0.3 1 8
HRAS 0.028 0.015 0.17 5 -10000 0 5
DOCK7 -0.04 0.058 0.16 7 -0.18 48 55
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.011 0.067 -10000 0 -0.17 50 50
AKT1 -0.005 0.007 -10000 0 -10000 0 0
BAD -0.01 0.005 -10000 0 -10000 0 0
MAPK10 -0.017 0.06 0.19 19 -0.18 3 22
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.012 0.074 0.17 1 -0.2 50 51
RAF1 -0.013 0.092 0.3 9 -0.24 22 31
ErbB2/ErbB3/neuregulin 2 -0.029 0.092 -10000 0 -0.18 129 129
STAT3 -0.011 0.2 -10000 0 -0.9 22 22
cell migration -0.005 0.088 0.26 30 -0.18 3 33
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.035 0.18 0.38 6 -0.46 37 43
FOS -0.053 0.19 0.3 9 -0.45 83 92
NRAS 0.026 0.016 -10000 0 -0.32 1 1
mol:Ca2+ -0.014 0.068 0.16 1 -0.19 50 51
MAPK3 -0.018 0.14 0.38 6 -0.43 15 21
MAPK1 -0.021 0.15 0.36 7 -0.42 27 34
JAK2 -0.039 0.058 0.18 4 -0.2 15 19
NF2 0.003 0.055 -10000 0 -0.69 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.01 0.066 -10000 0 -0.2 47 47
NRG1 -0.018 0.1 -10000 0 -0.31 54 54
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
MAPK8 -0.042 0.095 0.2 1 -0.23 56 57
MAPK9 -0.016 0.057 0.18 19 -0.16 1 20
ERBB2 -0.022 0.016 -10000 0 -0.23 2 2
ERBB3 0.025 0.016 -10000 0 -0.31 1 1
SHC1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.009 0.01 -10000 0 -10000 0 0
STAT3 (dimer) -0.011 0.19 -10000 0 -0.86 23 23
RNF41 -0.014 0.007 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.036 0.04 -10000 0 -0.15 47 47
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.016 -10000 0 -0.19 2 2
CHRNA1 -0.009 0.12 0.34 7 -0.33 17 24
myelination -0.017 0.099 0.32 23 -0.24 3 26
PPP3CB -0.037 0.054 0.18 3 -0.18 45 48
KRAS 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.004 0.083 -10000 0 -0.19 47 47
NRG2 -0.081 0.16 -10000 0 -0.31 154 154
mol:GDP -0.01 0.066 -10000 0 -0.2 47 47
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.021 0.089 0.26 11 -0.25 21 32
SRC 0.026 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.039 0.057 0.16 6 -0.18 46 52
MAP2K1 -0.041 0.15 -10000 0 -0.52 14 14
heart morphogenesis -0.014 0.068 0.16 1 -0.19 50 51
RAS family/GDP 0.007 0.092 -10000 0 -0.19 45 45
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.007 0.058 -10000 0 -0.72 3 3
CHRNE 0.003 0.02 0.12 3 -0.16 1 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.005 0.007 -10000 0 -10000 0 0
nervous system development -0.014 0.068 0.16 1 -0.19 50 51
CDC42 0.027 0.004 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.017 0.067 -10000 0 -0.21 37 37
CRKL -0.004 0.12 0.29 5 -0.45 17 22
mol:PIP3 -0.005 0.068 -10000 0 -0.73 4 4
AKT1 -0.001 0.078 0.41 2 -0.6 4 6
PTK2B 0.019 0.013 -10000 0 -10000 0 0
RAPGEF1 0.003 0.12 0.34 14 -0.42 17 31
RANBP10 0.024 0.009 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
HGF/MET/SHIP2 0.024 0.085 -10000 0 -0.22 47 47
MAP3K5 0.005 0.12 0.31 13 -0.41 19 32
HGF/MET/CIN85/CBL/ENDOPHILINS 0.035 0.085 -10000 0 -0.2 46 46
AP1 -0.005 0.09 0.18 3 -0.2 67 70
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.12 0.32 -10000 0 -0.75 94 94
STAT3 (dimer) -0.022 0.1 -10000 0 -0.29 48 48
GAB1/CRKL/SHP2/PI3K 0.022 0.12 0.27 3 -0.43 17 20
INPP5D 0.01 0.073 -10000 0 -0.31 24 24
CBL/CRK 0.01 0.12 0.32 7 -0.43 17 24
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.011 -10000 0 -10000 0 0
ELK1 0.004 0.1 0.34 33 -10000 0 33
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.064 -10000 0 -0.27 18 18
PAK1 0.002 0.085 0.41 7 -0.58 3 10
HGF/MET/RANBP10 0.02 0.085 -10000 0 -0.22 47 47
HRAS -0.034 0.18 -10000 0 -0.53 48 48
DOCK1 -0.005 0.12 0.28 6 -0.43 17 23
GAB1 -0.006 0.12 0.26 5 -0.46 18 23
CRK -0.004 0.12 0.31 7 -0.45 17 24
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.032 0.17 -10000 0 -0.51 49 49
JUN 0.024 0.031 0.17 1 -0.31 4 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.073 -10000 0 -0.22 49 49
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
cell morphogenesis -0.009 0.14 0.33 23 -0.39 33 56
GRB2/SHC 0.019 0.08 0.19 1 -0.2 43 44
FOS -0.025 0.12 0.17 4 -0.31 76 80
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.004 0.1 0.34 33 -10000 0 33
HGF/MET/MUC20 0.009 0.08 0.12 9 -0.22 48 57
cell migration 0.019 0.079 0.19 1 -0.2 43 44
GRB2 0.026 0.005 -10000 0 -10000 0 0
CBL 0.025 0.016 -10000 0 -0.31 1 1
MET/RANBP10 0.013 0.067 -10000 0 -0.21 39 39
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.006 0.084 -10000 0 -0.27 39 39
MET/MUC20 0 0.062 -10000 0 -0.21 39 39
RAP1B 0.009 0.13 0.37 21 -0.39 17 38
RAP1A 0.004 0.12 0.32 19 -0.39 17 36
HGF/MET/RANBP9 0.024 0.087 -10000 0 -0.22 47 47
RAF1 -0.025 0.17 0.3 2 -0.52 46 48
STAT3 -0.023 0.1 -10000 0 -0.29 48 48
cell proliferation -0.015 0.15 0.31 21 -0.39 44 65
RPS6KB1 -0.001 0.045 -10000 0 -0.25 9 9
MAPK3 -0.007 0.099 0.48 6 -10000 0 6
MAPK1 0 0.12 0.5 15 -10000 0 15
RANBP9 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0 0.14 0.32 11 -0.41 27 38
SRC -0.02 0.08 -10000 0 -0.26 37 37
PI3K 0.017 0.084 0.17 14 -0.22 43 57
MET/Glomulin 0.016 0.026 -10000 0 -0.12 11 11
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K1 -0.018 0.17 0.32 9 -0.48 45 54
MET -0.002 0.091 -10000 0 -0.31 39 39
MAP4K1 0.006 0.13 0.31 9 -0.43 20 29
PTK2 0.022 0.011 -10000 0 -10000 0 0
MAP2K2 -0.018 0.17 0.33 9 -0.48 45 54
BAD 0.001 0.083 0.42 5 -0.64 3 8
MAP2K4 0.004 0.11 0.3 12 -0.38 18 30
SHP2/GRB2/SOS1/GAB1 0.008 0.12 -10000 0 -0.35 33 33
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.026 0.006 -10000 0 -10000 0 0
SH3KBP1 0.027 0.004 -10000 0 -10000 0 0
HGS -0.016 0.067 -10000 0 -0.21 46 46
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF 0.011 0.076 0.17 9 -0.31 24 33
RASA1 0.024 0.022 -10000 0 -0.31 2 2
NCK1 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.026 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.02 0.085 0.17 17 -0.21 44 61
PDPK1 -0.001 0.075 -10000 0 -0.63 4 4
HGF/MET/SHIP 0.016 0.1 -10000 0 -0.25 54 54
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.017 0.082 0.19 4 -0.26 16 20
TBX21 -0.035 0.3 -10000 0 -0.95 31 31
B2M 0.025 0.015 -10000 0 -10000 0 0
TYK2 0.02 0.032 -10000 0 -10000 0 0
IL12RB1 0.022 0.057 0.19 17 -0.34 5 22
GADD45B -0.013 0.25 -10000 0 -0.83 26 26
IL12RB2 0.01 0.069 0.19 5 -0.31 16 21
GADD45G -0.006 0.24 -10000 0 -0.85 22 22
natural killer cell activation 0.003 0.016 0.045 7 -0.039 18 25
RELB 0.027 0.004 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
IL18 0.018 0.053 -10000 0 -0.31 11 11
IL2RA 0.044 0.06 0.17 72 -0.31 4 76
IFNG 0.032 0.034 0.17 28 -10000 0 28
STAT3 (dimer) -0.015 0.24 -10000 0 -0.68 35 35
HLA-DRB5 -0.003 0.008 -10000 0 -0.022 67 67
FASLG -0.038 0.31 -10000 0 -1 30 30
NF kappa B2 p52/RelB -0.021 0.28 -10000 0 -0.83 33 33
CD4 0.018 0.03 0.17 5 -0.31 1 6
SOCS1 0.027 0.02 0.17 3 -0.31 1 4
EntrezGene:6955 -0.004 0.012 -10000 0 -0.027 86 86
CD3D 0.017 0.063 0.17 23 -0.32 10 33
CD3E 0.014 0.055 0.17 8 -0.27 11 19
CD3G 0 0.092 0.17 15 -0.32 32 47
IL12Rbeta2/JAK2 0.026 0.066 0.18 4 -0.22 17 21
CCL3 -0.04 0.31 -10000 0 -0.98 33 33
CCL4 -0.034 0.28 -10000 0 -0.96 27 27
HLA-A 0 0.008 -10000 0 -0.043 14 14
IL18/IL18R 0.056 0.079 0.21 3 -0.2 28 31
NOS2 -0.056 0.36 -10000 0 -1.1 41 41
IL12/IL12R/TYK2/JAK2/SPHK2 0.018 0.08 0.19 2 -0.25 15 17
IL1R1 -0.032 0.28 -10000 0 -0.91 28 28
IL4 -0.008 0.031 -10000 0 -10000 0 0
JAK2 0.02 0.035 -10000 0 -0.32 1 1
EntrezGene:6957 -0.003 0.011 -10000 0 -0.026 76 76
TCR/CD3/MHC I/CD8 -0.034 0.21 -10000 0 -0.67 34 34
RAB7A 0.017 0.22 0.49 1 -0.7 21 22
lysosomal transport 0.019 0.21 0.44 3 -0.66 21 24
FOS -0.18 0.48 -10000 0 -1.1 93 93
STAT4 (dimer) 0.01 0.25 -10000 0 -0.71 31 31
STAT5A (dimer) -0.017 0.28 -10000 0 -0.8 36 36
GZMA -0.035 0.29 -10000 0 -0.97 28 28
GZMB -0.051 0.32 -10000 0 -1 36 36
HLX 0.031 0.026 0.17 16 -10000 0 16
LCK -0.037 0.29 0.47 1 -0.86 37 38
TCR/CD3/MHC II/CD4 -0.038 0.13 -10000 0 -0.26 95 95
IL2/IL2R 0.065 0.081 0.28 13 -0.22 22 35
MAPK14 -0.001 0.26 -10000 0 -0.84 25 25
CCR5 -0.016 0.26 -10000 0 -0.97 20 20
IL1B -0.005 0.12 0.18 22 -0.33 48 70
STAT6 0.013 0.091 -10000 0 -0.41 3 3
STAT4 0.028 0.038 0.17 13 -0.31 4 17
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.019 0.17 9 -10000 0 9
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.013 0.17 3 -10000 0 3
IL12B 0.028 0.049 0.18 29 -10000 0 29
CD8A 0.021 0.051 0.17 5 -0.32 9 14
CD8B 0.023 0.047 0.17 9 -0.31 7 16
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.017 0.081 0.26 16 -0.19 4 20
IL2RB 0.014 0.071 0.17 6 -0.31 21 27
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.23 0.36 1 -0.65 31 32
IL2RG 0.028 0.042 0.17 15 -0.31 5 20
IL12 0.035 0.066 0.19 19 -0.22 8 27
STAT5A 0.026 0.016 -10000 0 -0.31 1 1
CD247 0.018 0.05 0.17 16 -0.32 5 21
IL2 0.022 0.011 0.17 2 -10000 0 2
SPHK2 0.027 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.056 0.18 5 -0.29 9 14
IL12/IL12R/TYK2/JAK2 -0.035 0.32 -10000 0 -0.92 37 37
MAP2K3 -0.007 0.26 -10000 0 -0.8 29 29
RIPK2 0.022 0.011 -10000 0 -10000 0 0
MAP2K6 -0.005 0.26 -10000 0 -0.87 24 24
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.003 0.009 -10000 0 -0.025 73 73
IL18RAP 0.02 0.069 0.18 16 -0.31 16 32
IL12Rbeta1/TYK2 0.032 0.057 0.16 15 -0.26 5 20
EOMES -0.028 0.22 -10000 0 -1.1 19 19
STAT1 (dimer) 0.004 0.24 0.4 2 -0.67 34 36
T cell proliferation 0.009 0.2 0.34 1 -0.55 30 31
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.023 0.041 -10000 0 -0.31 6 6
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.21 -10000 0 -0.62 24 24
ATF2 -0.006 0.24 0.41 2 -0.77 25 27
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.028 0.056 -10000 0 -0.15 38 38
RGS9BP 0.026 0.024 0.17 2 -0.31 2 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.02 0.015 0.17 4 -10000 0 4
mol:Na + 0.027 0.025 0.14 7 -10000 0 7
mol:ADP -0.016 0.008 -10000 0 -10000 0 0
GNAT2 0.026 0.014 0.17 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.005 0.096 -10000 0 -0.18 99 99
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.029 0.017 0.14 6 -10000 0 6
GRK7 0.022 0.01 0.17 1 -10000 0 1
CNGB3 0.019 0.023 0.17 10 -10000 0 10
Cone Metarhodopsin II/X-Arrestin 0.016 0.006 0.12 1 -10000 0 1
mol:Ca2+ 0.029 0.086 0.19 96 -10000 0 96
Cone PDE6 0.018 0.09 -10000 0 -0.16 93 93
Cone Metarhodopsin II 0.026 0.014 0.12 3 -10000 0 3
Na + (4 Units) 0.042 0.038 0.24 3 -10000 0 3
GNAT2/GDP 0.017 0.088 -10000 0 -0.15 98 98
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.011 0.028 0.18 10 -10000 0 10
Cone Transducin 0.03 0.06 -10000 0 -0.16 38 38
SLC24A2 0.036 0.042 0.17 44 -10000 0 44
GNB3/GNGT2 0.017 0.07 -10000 0 -0.22 38 38
GNB3 0.002 0.086 -10000 0 -0.31 34 34
GNAT2/GTP 0.019 0.01 0.12 4 -10000 0 4
CNGA3 0.026 0.025 0.17 14 -10000 0 14
ARR3 0.021 0.008 0.17 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.027 0.025 0.14 7 -10000 0 7
mol:Pi 0.005 0.095 -10000 0 -0.18 99 99
Cone CNG Channel 0.039 0.033 0.22 1 -10000 0 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.036 0.042 0.17 44 -10000 0 44
RGS9 -0.041 0.14 0.17 3 -0.31 99 102
PDE6C 0.019 0.007 -10000 0 -10000 0 0
GNGT2 0.024 0.035 0.17 1 -0.31 5 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.015 0.17 4 -10000 0 4
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.12 0.41 -10000 0 -1.2 29 29
STAT6 (cleaved dimer) -0.15 0.43 -10000 0 -1.2 45 45
IGHG1 -0.015 0.17 -10000 0 -0.48 7 7
IGHG3 -0.12 0.39 -10000 0 -1.1 36 36
AKT1 -0.061 0.27 -10000 0 -0.77 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.04 0.24 -10000 0 -0.84 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.055 0.28 -10000 0 -1 14 14
THY1 -0.12 0.41 -10000 0 -1.2 29 29
MYB 0.033 0.029 0.17 22 -10000 0 22
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.084 0.33 -10000 0 -0.86 47 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.061 0.29 -10000 0 -0.92 22 22
SP1 0.03 0.008 -10000 0 -0.094 1 1
INPP5D 0.01 0.073 -10000 0 -0.31 24 24
SOCS5 0.011 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.13 0.43 -10000 0 -1.2 45 45
SOCS1 -0.08 0.29 -10000 0 -0.76 35 35
SOCS3 -0.15 0.45 -10000 0 -1.2 68 68
FCER2 -0.097 0.38 -10000 0 -1.1 39 39
PARP14 0.026 0.011 -10000 0 -10000 0 0
CCL17 -0.12 0.42 -10000 0 -1.3 31 31
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.04 0.24 0.36 1 -0.71 24 25
T cell proliferation -0.13 0.42 -10000 0 -1.2 37 37
IL4R/JAK1 -0.12 0.42 -10000 0 -1.2 35 35
EGR2 -0.13 0.45 -10000 0 -1.4 34 34
JAK2 0.009 0.055 -10000 0 -0.34 1 1
JAK3 0.021 0.04 0.17 10 -0.24 4 14
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
JAK1 0.014 0.032 -10000 0 -10000 0 0
COL1A2 -0.004 0.17 -10000 0 -1.1 2 2
CCL26 -0.11 0.42 -10000 0 -1.2 33 33
IL4R -0.13 0.44 -10000 0 -1.3 33 33
PTPN6 0.015 0.027 -10000 0 -10000 0 0
IL13RA2 -0.21 0.55 -10000 0 -1.3 75 75
IL13RA1 0.011 0.053 -10000 0 -10000 0 0
IRF4 -0.058 0.34 -10000 0 -1.3 27 27
ARG1 -0.002 0.15 -10000 0 -0.54 2 2
CBL -0.08 0.31 -10000 0 -0.8 47 47
GTF3A 0.032 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
IL13RA1/JAK2 0.022 0.077 -10000 0 -0.24 1 1
IRF4/BCL6 -0.051 0.32 -10000 0 -1.2 27 27
CD40LG 0.018 0.085 0.18 22 -0.24 36 58
MAPK14 -0.1 0.36 -10000 0 -0.9 58 58
mitosis -0.056 0.26 0.39 1 -0.72 27 28
STAT6 -0.14 0.48 -10000 0 -1.4 36 36
SPI1 0.031 0.015 0.17 4 -10000 0 4
RPS6KB1 -0.055 0.25 -10000 0 -0.69 26 26
STAT6 (dimer) -0.14 0.48 -10000 0 -1.4 36 36
STAT6 (dimer)/PARP14 -0.13 0.43 -10000 0 -1.3 34 34
mast cell activation 0.001 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.083 0.29 -10000 0 -0.78 36 36
FRAP1 -0.061 0.27 -10000 0 -0.77 27 27
LTA -0.12 0.42 -10000 0 -1.2 34 34
FES 0.024 0.031 -10000 0 -0.31 4 4
T-helper 1 cell differentiation 0.13 0.46 1.3 36 -10000 0 36
CCL11 -0.12 0.4 -10000 0 -1.2 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.047 0.27 -10000 0 -0.79 24 24
IL2RG 0.021 0.047 0.17 15 -0.3 5 20
IL10 -0.14 0.46 -10000 0 -1.3 43 43
IRS1 0.017 0.056 -10000 0 -0.31 14 14
IRS2 0.027 0.013 0.17 3 -10000 0 3
IL4 -0.015 0.17 -10000 0 -0.91 8 8
IL5 -0.12 0.41 -10000 0 -1.2 33 33
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.082 0.35 -10000 0 -0.93 31 31
COL1A1 -0.003 0.17 -10000 0 -0.84 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.13 0.42 -10000 0 -1.3 30 30
IL2R gamma/JAK3 0.033 0.058 0.22 14 -0.24 7 21
TFF3 -0.11 0.41 -10000 0 -1.2 34 34
ALOX15 -0.15 0.47 -10000 0 -1.3 48 48
MYBL1 0.021 0.019 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.11 0.37 -10000 0 -1 37 37
SHC1 0.026 0.006 -10000 0 -10000 0 0
CEBPB 0.03 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.049 0.26 -10000 0 -0.9 14 14
mol:PI-3-4-5-P3 -0.061 0.27 -10000 0 -0.77 27 27
PI3K -0.067 0.29 -10000 0 -0.84 27 27
DOK2 0.02 0.017 0.17 3 -10000 0 3
ETS1 0.004 0.04 0.14 1 -0.27 3 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.033 0.21 0.35 1 -0.62 22 23
ITGB3 -0.25 0.6 -10000 0 -1.3 100 100
PIGR -0.26 0.6 -10000 0 -1.3 106 106
IGHE -0.004 0.06 0.19 14 -0.14 1 15
MAPKKK cascade -0.032 0.21 0.35 1 -0.61 22 23
BCL6 0.025 0.007 -10000 0 -10000 0 0
OPRM1 -0.12 0.41 -10000 0 -1.2 31 31
RETNLB -0.12 0.41 -10000 0 -1.2 30 30
SELP -0.13 0.43 -10000 0 -1.3 33 33
AICDA -0.12 0.39 -10000 0 -1.2 33 33
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.056 0.049 -10000 0 -0.16 18 18
ER alpha/Gai/GDP/Gbeta gamma -0.047 0.16 -10000 0 -0.39 58 58
AKT1 -0.02 0.18 -10000 0 -0.72 26 26
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.015 0.18 -10000 0 -0.7 28 28
mol:Ca2+ -0.004 0.05 0.17 1 -0.34 4 5
IGF1R 0.027 0.017 0.17 1 -0.31 1 2
E2/ER alpha (dimer)/Striatin 0.014 0.068 0.12 1 -0.19 45 46
SHC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.019 0.17 0.66 28 -10000 0 28
RhoA/GTP 0.019 0.03 -10000 0 -0.15 13 13
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.015 0.13 0.24 1 -0.34 44 45
regulation of stress fiber formation 0.022 0.065 0.25 6 -0.17 27 33
E2/ERA-ERB (dimer) 0.033 0.042 0.12 22 -0.18 14 36
KRAS 0.025 0.007 -10000 0 -10000 0 0
G13/GTP 0.028 0.033 0.12 1 -0.16 14 15
pseudopodium formation -0.022 0.065 0.17 27 -0.25 6 33
E2/ER alpha (dimer)/PELP1 0.027 0.038 0.12 1 -0.17 15 16
GRB2 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.023 0.034 -10000 0 -0.31 5 5
GNAO1 -0.024 0.12 -10000 0 -0.31 70 70
HRAS 0.028 0.015 0.17 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.02 0.13 0.33 2 -0.43 27 29
E2/ER beta (dimer) 0.024 0.02 0.12 21 -10000 0 21
mol:GDP 0.01 0.057 0.15 1 -0.25 19 20
mol:NADP -0.02 0.13 0.33 2 -0.43 27 29
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
mol:IP3 -0.004 0.051 -10000 0 -0.35 4 4
IGF-1R heterotetramer 0.027 0.017 0.17 1 -0.31 1 2
PLCB1 0.002 0.054 -10000 0 -0.36 4 4
PLCB2 0.002 0.053 -10000 0 -0.33 4 4
IGF1 0.009 0.088 0.17 17 -0.31 32 49
mol:L-citrulline -0.02 0.13 0.33 2 -0.43 27 29
RHOA 0.027 0.005 -10000 0 -10000 0 0
Gai/GDP -0.13 0.29 -10000 0 -0.62 120 120
JNK cascade 0.024 0.02 0.12 21 -10000 0 21
BCAR1 0.022 0.011 -10000 0 -10000 0 0
ESR2 0.033 0.029 0.17 21 -10000 0 21
GNAQ 0.026 0.006 -10000 0 -10000 0 0
ESR1 0.017 0.059 0.17 1 -0.31 15 16
Gq family/GDP/Gbeta gamma -0.016 0.15 -10000 0 -0.43 47 47
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.073 -10000 0 -0.48 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.016 0.14 0.24 1 -0.34 48 49
GNAZ -0.002 0.093 -10000 0 -0.31 41 41
E2/ER alpha (dimer) 0.013 0.04 0.12 1 -0.21 15 16
STRN 0.002 0.087 -10000 0 -0.31 35 35
GNAL -0.053 0.14 -10000 0 -0.31 114 114
PELP1 0.025 0.007 -10000 0 -10000 0 0
MAPK11 0.01 0.014 -10000 0 -10000 0 0
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
HBEGF -0.047 0.15 0.38 6 -0.38 56 62
cAMP biosynthetic process -0.012 0.081 -10000 0 -0.15 116 116
SRC -0.048 0.15 0.2 2 -0.38 56 58
PI3K 0.032 0.033 -10000 0 -0.25 5 5
GNB1 0.027 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.039 0.063 -10000 0 -0.28 13 13
SOS1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.036 0.11 -10000 0 -0.3 54 54
Gs family/GTP -0.006 0.086 -10000 0 -0.15 116 116
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.019 -10000 0 -10000 0 0
vasodilation -0.018 0.13 0.33 2 -0.41 27 29
mol:DAG -0.004 0.051 -10000 0 -0.35 4 4
Gs family/GDP/Gbeta gamma -0.016 0.088 -10000 0 -0.29 22 22
MSN -0.023 0.068 0.18 27 -0.22 10 37
Gq family/GTP 0.009 0.058 -10000 0 -0.34 4 4
mol:PI-3-4-5-P3 -0.014 0.17 -10000 0 -0.67 28 28
NRAS 0.026 0.016 -10000 0 -0.31 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.018 0.13 0.41 27 -0.33 2 29
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.061 -10000 0 -0.29 13 13
NOS3 -0.022 0.14 0.33 2 -0.45 27 29
GNA11 0.017 0.056 -10000 0 -0.31 14 14
MAPKKK cascade -0.033 0.15 0.36 2 -0.48 32 34
E2/ER alpha (dimer)/PELP1/Src -0.018 0.14 0.27 3 -0.35 49 52
ruffle organization -0.022 0.065 0.17 27 -0.25 6 33
ROCK2 -0.019 0.069 0.19 27 -0.22 8 35
GNA14 0.026 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.067 -10000 0 -0.31 20 20
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.058 0.14 0.38 4 -0.37 55 59
MMP2 -0.039 0.15 0.26 3 -0.38 54 57
Aurora C signaling

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
INCENP 0.027 0.004 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.065 0.054 -10000 0 -0.096 17 17
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.005 0.031 -10000 0 -0.32 4 4
AURKB 0.065 0.065 0.17 140 -10000 0 140
AURKC 0.026 0.024 0.17 2 -0.31 2 4
S1P3 pathway

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
PDGFRB 0.027 0.01 0.17 2 -10000 0 2
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.025 0.1 0.14 1 -0.24 73 74
GNAO1 -0.024 0.12 -10000 0 -0.31 70 70
S1P/S1P3/G12/G13 0.04 0.039 -10000 0 -0.16 13 13
AKT1 0.007 0.07 -10000 0 -0.46 6 6
AKT3 -0.016 0.12 -10000 0 -0.49 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.01 0.17 2 -10000 0 2
GNAI2 0.027 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.029 0.17 1 -0.31 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.017 0.059 0.17 1 -0.31 15 16
S1PR2 0.027 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.12 -10000 0 -0.28 71 71
MAPK3 -0.026 0.11 -10000 0 -0.27 70 70
MAPK1 -0.023 0.11 -10000 0 -0.27 67 67
JAK2 -0.027 0.12 0.18 2 -0.35 47 49
CXCR4 -0.021 0.11 -10000 0 -0.28 59 59
FLT1 0.025 0.032 0.17 2 -0.31 4 6
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC -0.025 0.11 -10000 0 -0.27 68 68
S1P/S1P3/Gi -0.021 0.12 -10000 0 -0.28 71 71
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.12 -10000 0 -0.32 46 46
VEGFA 0.012 0.078 0.17 5 -0.31 26 31
S1P/S1P2/Gi -0.016 0.11 -10000 0 -0.25 73 73
VEGFR1 homodimer/VEGFA homodimer 0.029 0.064 0.24 1 -0.22 28 29
RHOA 0.027 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.003 0.07 -10000 0 -0.21 40 40
GNAQ 0.026 0.006 -10000 0 -10000 0 0
GNAZ -0.001 0.094 -10000 0 -0.31 41 41
G12/G13 0.036 0.013 -10000 0 -10000 0 0
GNA14 0.026 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.067 -10000 0 -0.31 20 20
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.056 -10000 0 -0.31 14 14
Rac1/GTP -0.015 0.12 -10000 0 -0.34 40 40
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.002 0.086 -10000 0 -0.16 112 112
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.013 0.25 1 -10000 0 1
GNB1/GNG2 0.034 0.023 -10000 0 -0.18 5 5
GNB1 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.024 0.073 -10000 0 -0.15 114 114
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 0.012 0.019 0.045 114 -10000 0 114
GNAL -0.053 0.14 -10000 0 -0.31 114 114
GNG2 0.023 0.034 -10000 0 -0.31 5 5
CRH 0.015 0.012 0.17 2 -10000 0 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.037 -10000 0 -0.24 11 11
MAPK11 0.007 0.004 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR 0.026 0.016 -10000 0 -0.31 1 1
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.002 -10000 0 -10000 0 0
RELN/LRP8 0.057 0.044 0.23 3 -0.16 5 8
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.005 0.056 0.18 37 -0.16 3 40
IQGAP1/CaM 0.039 0.009 -10000 0 -10000 0 0
DAB1 -0.094 0.16 0.17 2 -0.31 173 175
IQGAP1 0.027 0.003 -10000 0 -10000 0 0
PLA2G7 0.06 0.062 0.17 119 -0.31 1 120
CALM1 0.026 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.04 0.014 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.006 -10000 0 -10000 0 0
CDK5R1 0.034 0.03 0.17 23 -10000 0 23
LIS1/Poliovirus Protein 3A -0.009 0.003 -10000 0 -10000 0 0
CDK5R2 0.041 0.043 0.17 51 -10000 0 51
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.025 0.12 -10000 0 -0.19 156 156
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.031 0.077 0.27 34 -0.2 1 35
MAP1B -0.008 0.053 -10000 0 -0.22 29 29
RAC1 0.01 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.009 0.052 0.2 19 -10000 0 19
RELN 0.039 0.056 0.17 58 -0.31 4 62
PAFAH/LIS1 0.046 0.045 0.13 106 -0.18 1 107
LIS1/CLIP170 0.025 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.018 0.042 -10000 0 -0.19 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.048 0.1 -10000 0 -0.33 19 19
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.012 0.078 0.25 38 -0.2 1 39
LIS1/IQGAP1 0.026 0.009 -10000 0 -10000 0 0
RHOA 0.011 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.026 0.17 17 -10000 0 17
PAFAH1B2 0.016 0.058 -10000 0 -0.31 15 15
MAP1B/LIS1/Dynein heavy chain 0.007 0.048 -10000 0 -0.14 30 30
NDEL1/Katanin 60/Dynein heavy chain 0.033 0.074 0.31 17 -0.2 2 19
LRP8 0.029 0.017 0.17 7 -10000 0 7
NDEL1/Katanin 60 0.027 0.078 0.26 33 -0.2 2 35
P39/CDK5 0 0.068 0.23 23 -0.18 1 24
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.009 -10000 0 -10000 0 0
CDK5 -0.015 0.035 0.17 13 -0.16 3 16
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.015 0.11 -10000 0 -0.16 152 152
RELN/VLDLR 0.066 0.048 0.24 3 -0.16 5 8
CDC42 0.011 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.014 0.13 -10000 0 -0.49 28 28
HDAC1 0.025 0.003 -10000 0 -10000 0 0
AES 0.026 0.005 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
DTX1 0.031 0.031 0.17 18 -0.31 1 19
LRP6/FZD1 0.032 0.02 -10000 0 -0.21 1 1
TLE1 0.026 0.006 -10000 0 -10000 0 0
AP1 -0.026 0.1 -10000 0 -0.24 75 75
NCSTN 0.026 0.006 -10000 0 -10000 0 0
ADAM10 0.014 0.065 -10000 0 -0.31 19 19
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.039 -10000 0 -0.49 1 1
NICD/RBPSUH 0.013 0.12 -10000 0 -0.48 28 28
WIF1 -0.12 0.17 0.17 7 -0.31 215 222
NOTCH1 -0.005 0.12 -10000 0 -0.5 28 28
PSENEN 0.027 0.003 -10000 0 -10000 0 0
KREMEN2 0.023 0.062 0.17 20 -0.31 13 33
DKK1 -0.029 0.13 0.17 12 -0.31 85 97
beta catenin/beta TrCP1 0.04 0.056 0.24 7 -0.24 2 9
APH1B 0.027 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.006 -10000 0 -10000 0 0
AXIN1 0.003 0.066 0.25 3 -0.3 5 8
CtBP/CBP/TCF1/TLE1/AES 0.019 0.023 -10000 0 -0.16 1 1
PSEN1 0.027 0.004 -10000 0 -10000 0 0
FOS -0.025 0.12 0.17 4 -0.31 76 80
JUN 0.024 0.031 0.17 1 -0.31 4 5
MAP3K7 0.022 0.01 -10000 0 -10000 0 0
CTNNB1 0.027 0.059 0.24 9 -0.25 2 11
MAPK3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.068 0.23 2 -0.19 33 35
HNF1A 0.04 0.043 0.16 50 -10000 0 50
CTBP1 0.026 0.004 -10000 0 -10000 0 0
MYC 0.025 0.02 -10000 0 -10000 0 0
NKD1 0.005 0.083 0.17 6 -0.31 30 36
FZD1 0.024 0.017 -10000 0 -0.31 1 1
NOTCH1 precursor/Deltex homolog 1 0.016 0.13 -10000 0 -0.48 27 27
apoptosis -0.026 0.1 -10000 0 -0.24 75 75
Delta 1/NOTCHprecursor 0.012 0.13 -10000 0 -0.48 28 28
DLL1 0.022 0.037 -10000 0 -0.31 6 6
PPARD 0.025 0.053 -10000 0 -0.76 2 2
Gamma Secretase 0.074 0.025 -10000 0 -10000 0 0
APC -0.016 0.11 0.25 2 -0.36 30 32
DVL1 -0.001 0.032 -10000 0 -0.23 5 5
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.008 0.096 -10000 0 -0.18 89 89
LRP6 0.024 0.009 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
NLK 0.009 0.004 -10000 0 -10000 0 0
CCND1 0.027 0.014 -10000 0 -10000 0 0
WNT1 0.029 0.022 0.17 11 -10000 0 11
Axin1/APC/beta catenin 0.02 0.09 0.32 9 -0.37 7 16
DKK2 0.015 0.074 0.17 12 -0.31 22 34
NOTCH1 precursor/DVL1 -0.002 0.12 -10000 0 -0.44 28 28
GSK3B 0.025 0.007 -10000 0 -10000 0 0
FRAT1 0.025 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.018 0.13 -10000 0 -0.49 27 27
PPP2R5D 0.022 0.052 0.2 7 -0.37 3 10
MAPK1 0.027 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.033 0.11 -10000 0 -0.16 194 194
RBPJ 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA 0.001 0.077 0.14 1 -0.33 21 22
PDGF/PDGFRA/CRKL 0.019 0.057 -10000 0 -0.22 20 20
positive regulation of JUN kinase activity 0.05 0.047 -10000 0 -0.17 16 16
CRKL 0.027 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.025 0.11 0.14 15 -0.23 105 120
AP1 -0.13 0.27 -10000 0 -0.74 78 78
mol:IP3 -0.029 0.052 -10000 0 -0.24 22 22
PLCG1 -0.029 0.052 -10000 0 -0.24 22 22
PDGF/PDGFRA/alphaV Integrin 0.018 0.057 -10000 0 -0.22 21 21
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.052 -10000 0 -0.24 22 22
CAV3 -0.033 0.14 0.17 17 -0.31 91 108
CAV1 -0.013 0.1 -10000 0 -0.31 54 54
SHC/Grb2/SOS1 0.052 0.048 -10000 0 -0.17 16 16
PDGF/PDGFRA/Shf 0.019 0.058 0.14 1 -0.23 19 20
FOS -0.13 0.27 0.3 1 -0.72 80 81
JUN -0.031 0.03 -10000 0 -0.28 3 3
oligodendrocyte development 0.018 0.057 -10000 0 -0.22 21 21
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
mol:DAG -0.029 0.052 -10000 0 -0.24 22 22
PDGF/PDGFRA 0.001 0.076 0.14 1 -0.33 21 22
actin cytoskeleton reorganization 0.019 0.058 -10000 0 -0.23 19 19
SRF -0.005 0.017 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.034 0.056 -10000 0 -0.21 20 20
PDGF/PDGFRA/Crk/C3G 0.038 0.047 -10000 0 -0.18 18 18
JAK1 -0.022 0.043 -10000 0 -0.23 19 19
ELK1/SRF -0.026 0.048 0.15 10 -0.21 20 30
SHB 0.024 0.027 -10000 0 -0.31 3 3
SHF 0.026 0.017 0.17 1 -0.31 1 2
CSNK2A1 0.033 0.018 -10000 0 -10000 0 0
GO:0007205 -0.026 0.06 -10000 0 -0.28 21 21
SOS1 0.026 0.005 -10000 0 -10000 0 0
Ras protein signal transduction 0.05 0.047 -10000 0 -0.17 16 16
PDGF/PDGFRA/SHB 0.019 0.058 -10000 0 -0.23 19 19
PDGF/PDGFRA/Caveolin-1 -0.006 0.1 -10000 0 -0.27 56 56
ITGAV 0.026 0.005 -10000 0 -10000 0 0
ELK1 -0.031 0.06 0.23 1 -0.27 21 22
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
PDGF/PDGFRA/Crk 0.018 0.057 -10000 0 -0.22 21 21
JAK-STAT cascade -0.022 0.043 -10000 0 -0.23 19 19
cell proliferation 0.019 0.058 0.14 1 -0.23 19 20
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.05 0.19 26 -0.18 3 29
RFC1 -0.004 0.034 0.16 15 -0.18 3 18
PRKDC 0.017 0.07 0.2 58 -0.18 2 60
RIPK1 0.028 0.007 -10000 0 -10000 0 0
CASP7 -0.014 0.097 -10000 0 -0.55 13 13
FASLG/FAS/FADD/FAF1 -0.01 0.059 0.16 1 -0.22 21 22
MAP2K4 -0.064 0.16 0.21 5 -0.32 105 110
mol:ceramide -0.022 0.098 0.21 1 -0.26 34 35
GSN 0 0.044 0.19 22 -0.18 3 25
FASLG/FAS/FADD/FAF1/Caspase 8 -0.017 0.075 0.19 1 -0.28 17 18
FAS 0.011 0.04 -10000 0 -0.32 5 5
BID -0.024 0.013 -10000 0 -10000 0 0
MAP3K1 -0.022 0.098 0.27 4 -0.29 22 26
MAP3K7 0.017 0.017 -10000 0 -10000 0 0
RB1 -0.003 0.026 0.15 11 -0.16 1 12
CFLAR 0.029 0.005 -10000 0 -10000 0 0
HGF/MET 0.024 0.087 -10000 0 -0.22 45 45
ARHGDIB -0.002 0.04 0.19 15 -0.18 3 18
FADD 0.015 0.023 -10000 0 -10000 0 0
actin filament polymerization 0 0.045 0.18 3 -0.19 22 25
NFKB1 -0.021 0.1 -10000 0 -0.53 5 5
MAPK8 -0.1 0.21 0.31 2 -0.47 108 110
DFFA -0.004 0.032 0.16 14 -0.18 3 17
DNA fragmentation during apoptosis -0.003 0.038 0.17 17 -0.18 3 20
FAS/FADD/MET 0.015 0.069 -10000 0 -0.19 37 37
CFLAR/RIP1 0.042 0.011 -10000 0 -10000 0 0
FAIM3 0.03 0.021 0.17 10 -10000 0 10
FAF1 0.015 0.026 -10000 0 -10000 0 0
PARP1 -0.005 0.029 0.15 12 -0.18 3 15
DFFB -0.003 0.036 0.17 17 -0.18 3 20
CHUK -0.022 0.091 -10000 0 -0.5 5 5
FASLG 0.011 0.063 0.16 16 -0.32 12 28
FAS/FADD 0.019 0.04 -10000 0 -0.23 5 5
HGF 0.011 0.076 0.17 9 -0.31 24 33
LMNA -0.006 0.032 0.15 17 -0.17 1 18
CASP6 -0.004 0.029 0.15 13 -0.18 2 15
CASP10 0.012 0.044 0.17 1 -0.31 6 7
CASP3 0.001 0.032 0.19 13 -10000 0 13
PTPN13 0.025 0.022 -10000 0 -0.31 2 2
CASP8 -0.025 0.014 -10000 0 -10000 0 0
IL6 -0.23 0.48 -10000 0 -1.1 105 105
MET -0.002 0.091 -10000 0 -0.31 39 39
ICAD/CAD -0.005 0.035 0.24 4 -0.18 1 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.099 0.21 1 -0.26 34 35
activation of caspase activity by cytochrome c -0.024 0.013 -10000 0 -10000 0 0
PAK2 0.002 0.047 0.19 27 -0.19 2 29
BCL2 0.015 0.055 -10000 0 -0.31 13 13
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.024 0.008 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.02 -10000 0 -0.21 1 1
SMAD4 0.025 0.008 -10000 0 -10000 0 0
DKK2 0.015 0.074 0.17 12 -0.31 22 34
TLE1 0.024 0.008 -10000 0 -10000 0 0
MACF1 0.028 0.002 -10000 0 -10000 0 0
CTNNB1 0.071 0.099 0.3 37 -0.42 1 38
WIF1 -0.12 0.17 0.16 7 -0.31 215 222
beta catenin/RanBP3 0.029 0.068 0.45 5 -0.34 1 6
KREMEN2 0.023 0.062 0.17 20 -0.31 13 33
DKK1 -0.029 0.13 0.17 12 -0.31 85 97
beta catenin/beta TrCP1 0.075 0.091 0.3 27 -0.38 1 28
FZD1 0.024 0.017 -10000 0 -0.31 1 1
AXIN2 -0.005 0.15 0.5 9 -1.3 5 14
AXIN1 0.027 0.006 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.084 -10000 0 -0.5 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.11 0.3 9 -0.44 9 18
Axin1/APC/GSK3 0.043 0.057 0.24 11 -0.43 1 12
Axin1/APC/GSK3/beta catenin/Macf1 0.038 0.092 0.33 16 -0.36 6 22
HNF1A 0.038 0.044 0.16 50 -10000 0 50
CTBP1 0.024 0.006 -10000 0 -10000 0 0
MYC 0.11 0.22 0.55 91 -10000 0 91
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.068 0.23 2 -0.18 33 35
NKD1 0.005 0.083 0.16 6 -0.31 30 36
TCF4 0.02 0.028 -10000 0 -0.31 3 3
TCF3 0.024 0.007 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.056 0.034 -10000 0 -0.16 1 1
Ran/GTP 0.019 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.003 0.067 0.4 3 -0.35 2 5
LEF1 0.027 0.045 0.16 21 -0.31 5 26
DVL1 0.035 0.035 0.18 1 -10000 0 1
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.06 0.086 0.3 9 -0.37 3 12
DKK1/LRP6/Kremen 2 0.008 0.096 -10000 0 -0.18 89 89
LRP6 0.025 0.009 -10000 0 -10000 0 0
CSNK1A1 0.025 0.009 -10000 0 -10000 0 0
NLK 0.027 0.006 -10000 0 -10000 0 0
CCND1 0.022 0.11 0.55 17 -10000 0 17
WNT1 0.029 0.022 0.17 11 -10000 0 11
GSK3A 0.027 0.006 -10000 0 -10000 0 0
GSK3B 0.026 0.007 -10000 0 -10000 0 0
FRAT1 0.025 0.007 -10000 0 -10000 0 0
PPP2R5D 0.042 0.063 0.24 22 -0.34 3 25
APC 0.009 0.078 0.21 50 -0.15 1 51
WNT1/LRP6/FZD1 0.059 0.078 0.17 148 -10000 0 148
CREBBP 0.024 0.007 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.018 0.037 0.16 4 -0.21 9 13
EPHB2 0.026 0.029 0.17 3 -0.31 3 6
Syndecan-2/TACI 0.029 0.05 0.16 41 -0.17 8 49
LAMA1 0.02 0.072 0.17 24 -0.31 18 42
Syndecan-2/alpha2 ITGB1 0.018 0.075 -10000 0 -0.18 51 51
HRAS 0.028 0.015 0.17 5 -10000 0 5
Syndecan-2/CASK 0.004 0.016 -10000 0 -0.17 4 4
ITGA5 0.018 0.055 0.17 1 -0.31 13 14
BAX -0.008 0.024 -10000 0 -10000 0 0
EPB41 0.027 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.019 -10000 0 -0.15 4 4
LAMA3 0.001 0.088 0.17 1 -0.31 36 37
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.004 0.094 -10000 0 -0.31 42 42
Syndecan-2/MMP2 0.017 0.029 0.12 1 -0.17 9 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.013 0.074 -10000 0 -0.21 45 45
dendrite morphogenesis 0.02 0.026 0.12 3 -0.21 4 7
Syndecan-2/GM-CSF 0.018 0.027 0.16 6 -0.18 4 10
determination of left/right symmetry 0.006 0.02 -10000 0 -0.2 4 4
Syndecan-2/PKC delta 0.02 0.021 -10000 0 -0.17 4 4
GNB2L1 0.028 0.012 0.17 3 -10000 0 3
MAPK3 0.027 0.074 0.19 81 -0.16 4 85
MAPK1 0.029 0.076 0.19 88 -0.16 4 92
Syndecan-2/RACK1 0.032 0.028 0.23 1 -0.16 4 5
NF1 0.027 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.02 -10000 0 -0.2 4 4
ITGA2 -0.007 0.098 -10000 0 -0.31 46 46
MAPK8 0 0.028 -10000 0 -0.17 13 13
Syndecan-2/alpha2/beta1 Integrin 0.028 0.075 0.24 7 -0.17 43 50
Syndecan-2/Kininogen 0.031 0.051 0.16 53 -0.18 4 57
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.083 0.19 92 -0.15 4 96
Syndecan-2/CASK/Protein 4.1 0.018 0.019 -10000 0 -0.16 4 4
extracellular matrix organization 0.02 0.021 -10000 0 -0.17 4 4
actin cytoskeleton reorganization 0.018 0.037 0.16 4 -0.21 9 13
Syndecan-2/Caveolin-2/Ras 0.021 0.054 -10000 0 -0.18 27 27
Syndecan-2/Laminin alpha3 0.009 0.049 0.13 1 -0.18 29 30
Syndecan-2/RasGAP 0.04 0.034 0.23 1 -0.16 5 6
alpha5/beta1 Integrin 0.032 0.042 -10000 0 -0.21 13 13
PRKCD 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.02 0.026 0.12 3 -0.21 4 7
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.028 0.18 4 -0.16 5 9
RHOA 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.023 0.01 -10000 0 -10000 0 0
TNFRSF13B 0.032 0.055 0.17 41 -0.31 6 47
RASA1 0.024 0.022 -10000 0 -0.31 2 2
alpha2/beta1 Integrin 0.013 0.074 -10000 0 -0.21 45 45
Syndecan-2/Synbindin 0.02 0.021 -10000 0 -0.17 4 4
TGFB1 0.027 0.004 -10000 0 -10000 0 0
CASP3 0.04 0.07 0.19 84 -0.16 4 88
FN1 0.021 0.05 0.17 4 -0.31 10 14
Syndecan-2/IL8 0.018 0.057 0.15 25 -0.18 24 49
SDC2 0.006 0.02 -10000 0 -0.2 4 4
KNG1 0.035 0.046 0.17 53 -10000 0 53
Syndecan-2/Neurofibromin 0.02 0.021 -10000 0 -0.17 4 4
TRAPPC4 0.026 0.006 -10000 0 -10000 0 0
CSF2 0.022 0.017 0.17 6 -10000 0 6
Syndecan-2/TGFB1 0.02 0.021 -10000 0 -0.17 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.019 -10000 0 -0.16 4 4
Syndecan-2/Ezrin 0.032 0.026 -10000 0 -0.16 4 4
PRKACA 0.045 0.073 0.19 96 -0.16 4 100
angiogenesis 0.018 0.057 0.15 25 -0.18 24 49
MMP2 0.018 0.049 0.17 1 -0.31 10 11
IL8 0.01 0.093 0.17 25 -0.31 34 59
calcineurin-NFAT signaling pathway 0.028 0.05 0.16 41 -0.17 8 49
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.033 0.17 10 -0.31 3 13
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.045 0.083 -10000 0 -0.16 159 159
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
FYN 0.023 0.01 -10000 0 -10000 0 0
MAP3K12 0.022 0.037 -10000 0 -0.31 6 6
FGR 0.026 0.023 0.17 1 -0.31 2 3
p38 alpha/TAB1 -0.043 0.078 -10000 0 -0.26 39 39
PRKG1 -0.063 0.15 -10000 0 -0.31 128 128
DUSP8 0.028 0.015 0.17 5 -10000 0 5
PGK/cGMP/p38 alpha -0.045 0.12 0.17 3 -0.28 68 71
apoptosis -0.042 0.075 -10000 0 -0.25 39 39
RAL/GTP 0.032 0.013 -10000 0 -10000 0 0
LYN 0.023 0.01 -10000 0 -10000 0 0
DUSP1 0.015 0.062 -10000 0 -0.31 17 17
PAK1 0.024 0.031 -10000 0 -0.31 4 4
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.025 -10000 0 -10000 0 0
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 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 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.011 -10000 0 -10000 0 0
MAPK11 -0.022 0.12 0.27 15 -0.3 35 50
BLK -0.002 0.1 0.17 30 -0.31 43 73
HCK 0.025 0.028 0.17 1 -0.31 3 4
MAP2K3 0.026 0.005 -10000 0 -10000 0 0
DUSP16 0.024 0.009 -10000 0 -10000 0 0
DUSP10 0.026 0.006 -10000 0 -10000 0 0
TRAF6/MEKK3 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.013 0.11 0.24 18 -0.29 35 53
positive regulation of innate immune response -0.023 0.14 0.3 16 -0.34 35 51
LCK 0.029 0.018 0.17 8 -10000 0 8
p38alpha-beta/MKP7 -0.011 0.14 0.32 12 -0.34 30 42
p38alpha-beta/MKP5 -0.014 0.14 0.33 10 -0.34 32 42
PGK/cGMP -0.041 0.1 -10000 0 -0.21 128 128
PAK2 0.026 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.019 0.14 0.33 10 -0.36 31 41
CDC42 0.027 0.004 -10000 0 -10000 0 0
RALB 0.026 0.006 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
PAK3 -0.099 0.16 -10000 0 -0.31 181 181
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.028 0.12 0.29 10 -0.35 33 43
IKBKB -0.008 0.11 0.3 13 -0.27 37 50
AKT1 0.02 0.1 0.29 37 -0.2 6 43
IKBKG 0.028 0.072 0.29 12 -0.25 5 17
CALM1 0.011 0.082 0.25 13 -0.31 9 22
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
MAP3K1 -0.055 0.18 0.34 7 -0.47 51 58
MAP3K7 0.023 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.01 0.079 0.24 10 -0.32 10 20
DOK1 0.027 0.004 -10000 0 -10000 0 0
AP-1 -0.011 0.079 0.26 9 -0.23 21 30
LYN 0.023 0.01 -10000 0 -10000 0 0
BLNK 0.025 0.017 -10000 0 -0.31 1 1
SHC1 0.026 0.006 -10000 0 -10000 0 0
BCR complex 0.039 0.077 0.17 52 -0.23 25 77
CD22 -0.013 0.092 -10000 0 -0.31 31 31
CAMK2G 0.009 0.076 0.27 8 -0.3 7 15
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
INPP5D 0.01 0.073 -10000 0 -0.31 24 24
SHC/GRB2/SOS1 0.022 0.045 -10000 0 -0.17 17 17
GO:0007205 0.011 0.082 0.23 11 -0.32 11 22
SYK 0.023 0.035 0.17 1 -0.31 5 6
ELK1 0.008 0.082 0.26 5 -0.31 11 16
NFATC1 0 0.098 0.29 14 -0.3 16 30
B-cell antigen/BCR complex 0.039 0.077 0.17 52 -0.23 25 77
PAG1/CSK 0.032 0.017 -10000 0 -10000 0 0
NFKBIB 0.015 0.046 0.15 14 -0.12 7 21
HRAS 0.019 0.076 0.25 15 -0.23 6 21
NFKBIA 0.016 0.045 0.15 14 -0.12 7 21
NF-kappa-B/RelA/I kappa B beta 0.02 0.041 0.15 16 -10000 0 16
RasGAP/Csk 0.064 0.082 0.25 18 -0.17 32 50
mol:GDP 0.013 0.083 0.23 11 -0.3 12 23
PTEN 0.022 0.011 -10000 0 -10000 0 0
CD79B 0.024 0.054 0.17 15 -0.31 10 25
NF-kappa-B/RelA/I kappa B alpha 0.02 0.04 0.15 16 -10000 0 16
GRB2 0.026 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.022 0.13 0.36 7 -0.41 24 31
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
mol:IP3 0.012 0.076 0.24 9 -0.33 10 19
CSK 0.027 0.003 -10000 0 -10000 0 0
FOS -0.011 0.092 0.28 6 -0.3 18 24
CHUK 0.014 0.1 0.29 13 -0.28 27 40
IBTK 0.023 0.01 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.025 0.074 0.25 4 -0.31 4 8
PTPN6 -0.019 0.087 -10000 0 -0.38 19 19
RELA 0.026 0.006 -10000 0 -10000 0 0
BCL2A1 0.015 0.029 0.12 10 -10000 0 10
VAV2 -0.018 0.094 -10000 0 -0.43 15 15
ubiquitin-dependent protein catabolic process 0.017 0.045 0.15 14 -0.12 7 21
BTK 0.026 0.088 -10000 0 -0.92 3 3
CD19 -0.025 0.094 0.2 1 -0.33 28 29
MAP4K1 0.03 0.049 0.17 25 -0.31 6 31
CD72 0.03 0.038 0.17 19 -0.31 3 22
PAG1 0.022 0.011 -10000 0 -10000 0 0
MAPK14 -0.046 0.15 0.32 8 -0.4 49 57
SH3BP5 0.027 0.005 -10000 0 -10000 0 0
PIK3AP1 0.01 0.079 0.29 3 -0.33 12 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.014 0.092 -10000 0 -0.33 23 23
RAF1 0.019 0.076 0.25 18 -0.24 4 22
RasGAP/p62DOK/SHIP 0.054 0.093 0.23 18 -0.2 40 58
CD79A 0.029 0.081 0.17 54 -0.31 19 73
re-entry into mitotic cell cycle -0.01 0.078 0.25 9 -0.23 19 28
RASA1 0.024 0.022 -10000 0 -0.31 2 2
MAPK3 0.017 0.078 0.27 20 -0.22 2 22
MAPK1 0.014 0.073 0.27 16 -0.22 2 18
CD72/SHP1 0.001 0.1 0.24 4 -0.36 20 24
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.048 0.16 0.32 9 -0.4 52 61
actin cytoskeleton organization -0.01 0.092 0.31 5 -0.37 13 18
NF-kappa-B/RelA 0.041 0.077 0.27 15 -0.18 4 19
Calcineurin 0.023 0.068 0.25 4 -0.29 5 9
PI3K -0.016 0.083 -10000 0 -0.3 20 20
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.008 0.077 0.22 1 -0.35 14 15
SOS1 0.026 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.081 0.3 -10000 0 -0.74 75 75
DAPP1 -0.11 0.32 -10000 0 -0.83 75 75
cytokine secretion 0.001 0.094 0.28 14 -0.28 16 30
mol:DAG 0.012 0.076 0.24 9 -0.33 10 19
PLCG2 0.021 0.026 0.17 2 -0.31 2 4
MAP2K1 0.016 0.073 0.26 14 -0.23 4 18
B-cell antigen/BCR complex/FcgammaRIIB 0.048 0.081 0.25 19 -0.19 31 50
mol:PI-3-4-5-P3 -0.023 0.059 0.18 6 -0.23 13 19
ETS1 0.01 0.08 0.28 14 -0.29 6 20
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.061 0.071 0.25 13 -0.17 19 32
B-cell antigen/BCR complex/LYN 0.002 0.09 -10000 0 -0.31 26 26
MALT1 0.024 0.019 0.17 1 -0.31 1 2
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 -0.015 0.09 0.27 2 -0.39 13 15
B-cell antigen/BCR complex/LYN/SYK 0.025 0.1 0.27 1 -0.33 19 20
CARD11 0.021 0.095 0.28 26 -0.32 7 33
FCGR2B 0.023 0.048 0.17 11 -0.31 8 19
PPP3CA 0.027 0.012 0.17 3 -10000 0 3
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.012 0.055 0.18 27 -0.11 6 33
PTPRC 0.017 0.064 0.17 7 -0.31 17 24
PDPK1 -0.013 0.059 0.21 13 -0.18 8 21
PPP3CB 0.026 0.005 -10000 0 -10000 0 0
PPP3CC 0.019 0.013 -10000 0 -10000 0 0
POU2F2 0.014 0.029 0.12 8 -0.091 2 10
Visual signal transduction: Rods

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
mol:K + 0.027 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.015 0.008 0.12 2 -10000 0 2
Metarhodopsin II/Arrestin 0.026 0.012 0.12 3 -10000 0 3
PDE6G/GNAT1/GTP 0.039 0.028 0.12 45 -10000 0 45
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.02 0.011 0.17 2 -10000 0 2
GRK1 0.02 0.015 0.17 4 -10000 0 4
CNG Channel 0.021 0.076 -10000 0 -0.17 56 56
mol:Na + 0.029 0.043 -10000 0 -0.15 9 9
mol:ADP 0.02 0.015 0.17 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.005 0.096 -10000 0 -0.18 99 99
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.044 0.044 -10000 0 -0.15 9 9
CNGB1 0.024 0.021 0.17 9 -10000 0 9
RDH5 0.015 0.065 0.17 3 -0.31 18 21
SAG 0.02 0.008 0.17 1 -10000 0 1
mol:Ca2+ -0.021 0.068 0.35 10 -10000 0 10
Na + (4 Units) 0.019 0.042 -10000 0 -0.15 8 8
RGS9 -0.041 0.14 0.17 3 -0.31 99 102
GNB1/GNGT1 0.031 0.013 -10000 0 -10000 0 0
GNAT1/GDP 0.014 0.087 -10000 0 -0.16 96 96
GUCY2D 0.035 0.057 0.17 52 -0.31 5 57
GNGT1 0.017 0.011 0.17 2 -10000 0 2
GUCY2F 0.019 0.007 0.17 1 -10000 0 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.067 0.16 3 -0.17 57 60
mol:11-cis-retinal 0.015 0.065 0.17 3 -0.31 18 21
mol:cGMP 0.034 0.039 -10000 0 -0.16 6 6
GNB1 0.027 0.004 -10000 0 -10000 0 0
Rhodopsin 0.026 0.046 0.14 2 -0.22 15 17
SLC24A1 0.027 0.003 -10000 0 -10000 0 0
CNGA1 0.025 0.033 0.17 3 -0.31 4 7
Metarhodopsin II 0.025 0.014 0.12 1 -10000 0 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.058 0.049 0.24 4 -0.17 6 10
RGS9BP 0.026 0.024 0.17 2 -0.31 2 4
Metarhodopsin II/Transducin 0.01 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.044 0.02 -10000 0 -0.16 1 1
PDE6A/B 0.002 0.096 -10000 0 -0.24 64 64
mol:Pi 0.005 0.095 -10000 0 -0.18 99 99
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.017 -10000 0 -10000 0 0
PDE6B -0.01 0.1 0.17 1 -0.31 53 54
PDE6A 0.013 0.069 0.17 3 -0.31 21 24
PDE6G 0.039 0.041 0.17 45 -10000 0 45
RHO 0.02 0.012 0.17 2 -10000 0 2
PDE6 0.009 0.13 0.22 1 -0.19 125 126
GUCA1A 0.023 0.011 0.17 2 -10000 0 2
GC2/GCAP Family 0.055 0.023 -10000 0 -0.17 1 1
GUCA1C 0.018 0.008 0.17 1 -10000 0 1
GUCA1B 0.031 0.029 0.17 15 -0.31 1 16
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.013 0.077 -10000 0 -0.21 50 50
ATM 0.025 0.017 -10000 0 -0.31 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.023 0.012 0.17 1 -10000 0 1
ATR 0.025 0.007 -10000 0 -10000 0 0
UBE2L3 0.027 0.005 -10000 0 -10000 0 0
FANCD2 0.017 0.011 0.2 1 -10000 0 1
protein ubiquitination 0.041 0.071 -10000 0 -0.16 48 48
XRCC5 0.027 0.004 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.042 0.024 -10000 0 -10000 0 0
MRE11A 0.026 0.006 -10000 0 -10000 0 0
DNA-PK 0.045 0.023 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.013 0.048 -10000 0 -0.3 1 1
FANCF 0.027 0.004 -10000 0 -10000 0 0
BRCA1 0.026 0.009 0.17 1 -10000 0 1
CCNE1 0.028 0.013 0.17 4 -10000 0 4
CDK2/Cyclin E1 0.04 0.012 -10000 0 -10000 0 0
FANCG 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.012 0.077 0.14 1 -0.21 50 51
FANCE 0.027 0.004 -10000 0 -10000 0 0
FANCC 0.026 0.006 -10000 0 -10000 0 0
NBN 0.022 0.011 -10000 0 -10000 0 0
FANCA 0.029 0.041 0.17 27 -0.31 2 29
DNA repair -0.009 0.067 0.62 1 -0.25 1 2
BRCA1/BARD1/ubiquitin 0.012 0.077 0.14 1 -0.21 50 51
BARD1/DNA-PK 0.034 0.072 -10000 0 -0.16 49 49
FANCL 0.027 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.013 0.077 0.21 50 -10000 0 50
BRCA1/BARD1/CTIP/M/R/N Complex 0.005 0.066 -10000 0 -0.18 46 46
BRCA1/BACH1/BARD1/TopBP1 0.026 0.071 -10000 0 -0.18 48 48
BRCA1/BARD1/P53 0.032 0.071 -10000 0 -0.16 48 48
BARD1/CSTF1/BRCA1 0.028 0.071 -10000 0 -0.18 48 48
BRCA1/BACH1 0.026 0.009 0.17 1 -10000 0 1
BARD1 -0.009 0.1 -10000 0 -0.31 52 52
PCNA 0.027 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.028 0.072 -10000 0 -0.18 50 50
BRCA1/BARD1/UbcH7 0.027 0.072 -10000 0 -0.18 50 50
BRCA1/BARD1/RAD51/PCNA 0.044 0.077 0.24 1 -0.17 48 49
BARD1/DNA-PK/P53 0.036 0.073 -10000 0 -0.15 49 49
BRCA1/BARD1/Ubiquitin 0.012 0.077 0.14 1 -0.21 50 51
BRCA1/BARD1/CTIP 0.016 0.064 -10000 0 -0.17 49 49
FA complex 0.023 0.035 0.18 3 -0.17 3 6
BARD1/EWS 0.012 0.078 -10000 0 -0.21 52 52
RBBP8 -0.011 0.01 -10000 0 -0.21 1 1
TP53 0.023 0.01 -10000 0 -10000 0 0
TOPBP1 0.025 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.03 0.069 0.16 48 -10000 0 48
BRCA1/BARD1 0.046 0.074 -10000 0 -0.16 48 48
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.005 0.071 -10000 0 -0.21 52 52
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.036 0.036 0.17 34 -10000 0 34
RAD50 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.012 0.077 0.14 1 -0.21 50 51
EWSR1 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.027 0.01 0.17 2 -10000 0 2
Jak2/Leptin Receptor 0.023 0.11 0.28 5 -0.38 14 19
PTP1B/AKT1 0.011 0.073 0.25 5 -0.21 12 17
FYN 0.023 0.01 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.002 0.074 0.23 7 -0.22 14 21
EGFR -0.003 0.092 -10000 0 -0.32 38 38
EGF/EGFR 0.003 0.097 -10000 0 -0.24 39 39
CSF1 0.02 0.046 -10000 0 -0.31 9 9
AKT1 0.027 0.005 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.008 0.096 0.27 3 -0.24 44 47
Insulin Receptor/Insulin 0.027 0.072 0.21 1 -0.21 5 6
HCK 0.025 0.028 0.17 1 -0.31 3 4
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 -0.001 0.073 0.3 5 -0.22 11 16
EGF 0.02 0.083 0.17 38 -0.31 21 59
YES1 0.026 0.007 -10000 0 -10000 0 0
CAV1 -0.007 0.11 0.26 15 -0.29 30 45
TXN 0.027 0.01 0.16 1 -10000 0 1
PTP1B/IRS1/GRB2 0.015 0.085 0.24 1 -0.27 14 15
cell migration -0.002 0.074 0.22 14 -0.23 7 21
STAT3 0.026 0.005 -10000 0 -10000 0 0
PRLR 0.02 0.076 0.17 22 -0.31 21 43
ITGA2B 0.02 0.048 0.16 5 -0.31 9 14
CSF1R 0.026 0.017 0.17 1 -0.31 1 2
Prolactin Receptor/Prolactin 0.032 0.058 -10000 0 -0.22 19 19
FGR 0.026 0.023 0.17 1 -0.31 2 3
PTP1B/p130 Cas 0.01 0.067 0.22 4 -0.22 10 14
Crk/p130 Cas 0.017 0.073 0.27 2 -0.22 8 10
DOK1 0.009 0.074 0.25 12 -0.22 7 19
JAK2 0.012 0.097 0.26 4 -0.37 14 18
Jak2/Leptin Receptor/Leptin -0.008 0.11 -10000 0 -0.31 24 24
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
PTPN1 0.002 0.074 0.23 7 -0.22 14 21
LYN 0.023 0.01 -10000 0 -10000 0 0
CDH2 -0.048 0.14 0.17 9 -0.31 109 118
SRC 0.016 0.073 -10000 0 -0.38 12 12
ITGB3 -0.036 0.13 -10000 0 -0.31 90 90
CAT1/PTP1B -0.003 0.11 0.29 17 -0.3 18 35
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.03 0.076 -10000 0 -0.31 4 4
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.011 0.11 -10000 0 -0.29 44 44
negative regulation of transcription 0.013 0.097 0.26 4 -0.37 14 18
FCGR2A 0.026 0.019 0.17 2 -0.31 1 3
FER 0.017 0.054 -10000 0 -0.31 12 12
alphaIIb/beta3 Integrin -0.014 0.1 -10000 0 -0.21 99 99
BLK -0.002 0.1 0.17 30 -0.31 43 73
Insulin Receptor/Insulin/Shc 0.048 0.022 -10000 0 -0.092 1 1
RHOA 0.027 0.006 -10000 0 -10000 0 0
LEPR 0.014 0.066 -10000 0 -0.3 20 20
BCAR1 0.022 0.011 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.03 0.13 0.25 7 -0.32 44 51
PRL 0.014 0.023 0.17 4 -10000 0 4
SOCS3 -0.14 0.41 -10000 0 -1.1 68 68
SPRY2 0.022 0.028 -10000 0 -0.31 3 3
Insulin Receptor/Insulin/IRS1 0.044 0.043 -10000 0 -0.18 14 14
CSF1/CSF1R 0.016 0.086 0.27 2 -0.28 13 15
Ras protein signal transduction 0.005 0.085 0.49 13 -10000 0 13
IRS1 0.017 0.056 -10000 0 -0.31 14 14
INS 0.016 0.029 0.17 12 -10000 0 12
LEP 0.018 0.027 0.17 10 -10000 0 10
STAT5B 0.009 0.079 0.24 8 -0.27 10 18
STAT5A 0.008 0.079 0.24 8 -0.27 10 18
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.076 0.25 4 -0.21 14 18
CSN2 0 0.047 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
LAT 0.012 0.091 -10000 0 -0.4 18 18
YBX1 0.033 0.005 -10000 0 -10000 0 0
LCK 0.029 0.018 0.17 8 -10000 0 8
SHC1 0.026 0.006 -10000 0 -10000 0 0
NOX4 0.094 0.071 0.17 227 -10000 0 227
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.009 0.098 -10000 0 -0.21 90 90
AKT1 -0.011 0.14 0.35 8 -0.42 39 47
PTK2B -0.045 0.11 -10000 0 -0.51 22 22
VEGFR2 homodimer/Frs2 0.009 0.1 -10000 0 -0.49 20 20
CAV1 -0.013 0.1 -10000 0 -0.31 54 54
CALM1 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.015 0.12 -10000 0 -0.48 20 20
endothelial cell proliferation -0.018 0.15 0.37 12 -0.47 28 40
mol:Ca2+ -0.013 0.11 0.18 6 -0.48 20 26
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.027 0.11 -10000 0 -0.46 20 20
RP11-342D11.1 -0.031 0.1 0.17 7 -0.47 21 28
CDH5 0.024 0.009 -10000 0 -10000 0 0
VEGFA homodimer 0.052 0.057 -10000 0 -0.16 27 27
SHC1 0.026 0.006 -10000 0 -10000 0 0
SHC2 0.029 0.025 0.17 10 -0.31 1 11
HRAS/GDP 0.017 0.1 -10000 0 -0.42 21 21
SH2D2A 0.03 0.04 0.17 21 -0.31 3 24
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.02 0.12 0.31 1 -0.43 22 23
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.017 0.12 -10000 0 -0.48 21 21
VEGFR1 homodimer 0.024 0.032 0.17 2 -0.31 4 6
SHC/GRB2/SOS1 0.038 0.12 -10000 0 -0.45 21 21
GRB10 -0.013 0.1 0.18 3 -0.47 20 23
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
PAK1 0.024 0.031 -10000 0 -0.31 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.12 -10000 0 -0.45 20 20
HRAS 0.028 0.015 0.17 5 -10000 0 5
VEGF/Rho/ROCK1/Integrin Complex -0.038 0.13 -10000 0 -0.41 34 34
HIF1A 0.026 0.016 -10000 0 -0.31 1 1
FRS2 0.026 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.025 0.11 -10000 0 -0.46 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.026 0.023 0.17 1 -0.31 2 3
Nck/Pak 0.034 0.026 -10000 0 -0.21 4 4
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.011 0.11 -10000 0 -0.49 20 20
mol:GDP 0.026 0.11 -10000 0 -0.44 21 21
mol:NADP 0.008 0.11 0.35 12 -0.37 22 34
eNOS/Hsp90 0.014 0.1 0.3 6 -0.35 22 28
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
mol:IP3 -0.014 0.11 0.18 6 -0.49 20 26
HIF1A/ARNT 0.037 0.016 -10000 0 -0.21 1 1
SHB 0.024 0.027 -10000 0 -0.31 3 3
VEGFA 0.011 0.077 0.17 5 -0.31 26 31
VEGFC 0.026 0.017 0.17 1 -0.31 1 2
FAK1/Vinculin -0.049 0.18 0.27 3 -0.54 41 44
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.006 0.14 -10000 0 -0.51 24 24
PTPN6 0.025 0.007 -10000 0 -10000 0 0
EPAS1 0.018 0.07 0.17 1 -0.31 20 21
mol:L-citrulline 0.008 0.11 0.35 12 -0.37 22 34
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.029 0.11 -10000 0 -0.45 20 20
VEGFR2 homodimer/VEGFA homodimer 0.017 0.12 -10000 0 -0.51 21 21
VEGFR2/3 heterodimer 0.008 0.11 -10000 0 -0.51 20 20
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 -0.028 0.11 0.24 3 -0.5 21 24
VEGFR2 homodimer -0.008 0.12 -10000 0 -0.57 20 20
FLT1 0.024 0.032 0.17 2 -0.31 4 6
NEDD4 0.022 0.043 -10000 0 -0.31 8 8
MAPK3 -0.044 0.11 0.27 4 -0.48 22 26
MAPK1 -0.043 0.11 0.27 5 -0.48 22 27
VEGFA145/NRP2 0.011 0.085 0.14 4 -0.22 55 59
VEGFR1/2 heterodimer 0.008 0.11 -10000 0 -0.53 20 20
KDR -0.008 0.12 -10000 0 -0.57 20 20
VEGFA165/NRP1/VEGFR2 homodimer 0.008 0.13 -10000 0 -0.52 22 22
SRC 0.026 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.039 0.12 0.25 10 -0.5 21 31
PI3K -0.01 0.14 -10000 0 -0.44 37 37
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.014 0.11 -10000 0 -0.48 20 20
FES -0.014 0.11 0.18 7 -0.49 21 28
GAB1 -0.009 0.14 -10000 0 -0.43 37 37
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.12 -10000 0 -0.49 20 20
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
ARNT 0.026 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.003 0.11 0.37 3 -0.41 22 25
VEGFR2 homodimer/VEGFA homodimer/Yes 0.014 0.12 -10000 0 -0.49 20 20
PI3K/GAB1 -0.01 0.15 -10000 0 -0.44 40 40
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.035 0.12 -10000 0 -0.46 19 19
PRKACA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.023 0.1 -10000 0 -0.47 20 20
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 -0.013 0.11 0.18 7 -0.5 20 27
actin cytoskeleton reorganization 0.017 0.12 -10000 0 -0.48 21 21
PTK2 -0.055 0.17 -10000 0 -0.57 36 36
EDG1 -0.031 0.1 0.17 7 -0.47 21 28
mol:DAG -0.014 0.11 0.18 6 -0.49 20 26
CaM/Ca2+ 0.001 0.1 -10000 0 -0.45 20 20
MAP2K3 -0.038 0.1 0.17 6 -0.46 22 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.027 0.12 -10000 0 -0.48 20 20
PLCG1 -0.014 0.11 0.18 6 -0.5 20 26
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.11 -10000 0 -0.45 20 20
IQGAP1 0.027 0.003 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.014 0.12 -10000 0 -0.5 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.013 0.12 -10000 0 -0.49 20 20
cell migration -0.043 0.17 0.26 1 -0.48 44 45
mol:PI-3-4-5-P3 -0.008 0.13 -10000 0 -0.41 37 37
FYN 0.023 0.01 -10000 0 -10000 0 0
VEGFB/NRP1 -0.006 0.1 0.18 6 -0.45 21 27
mol:NO 0.008 0.11 0.35 12 -0.37 22 34
PXN 0.026 0.006 -10000 0 -10000 0 0
HRAS/GTP 0 0.098 -10000 0 -0.42 21 21
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.007 0.11 -10000 0 -0.48 20 20
VHL 0.025 0.016 -10000 0 -0.31 1 1
ITGB3 -0.036 0.13 -10000 0 -0.31 90 90
NOS3 0.006 0.12 0.36 12 -0.41 22 34
VEGFR2 homodimer/VEGFA homodimer/Sck 0.016 0.12 -10000 0 -0.5 20 20
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.038 0.1 0.22 7 -0.48 20 27
PRKCB -0.059 0.12 0.17 5 -0.5 24 29
VCL 0.01 0.071 -10000 0 -0.31 23 23
VEGFA165/NRP1 -0.002 0.11 -10000 0 -0.47 21 21
VEGFR1/2 heterodimer/VEGFA homodimer 0.015 0.12 0.23 1 -0.52 20 21
VEGFA165/NRP2 0.011 0.085 0.14 4 -0.22 55 59
MAPKKK cascade 0.004 0.1 0.34 3 -0.43 19 22
NRP2 0.005 0.082 -10000 0 -0.31 31 31
VEGFC homodimer 0.026 0.017 0.17 1 -0.31 1 2
NCK1 0.025 0.007 -10000 0 -10000 0 0
ROCK1 0.025 0.016 -10000 0 -0.31 1 1
FAK1/Paxillin -0.046 0.17 0.3 3 -0.53 38 41
MAP3K13 -0.018 0.11 0.18 4 -0.49 22 26
PDPK1 -0.018 0.11 0.25 1 -0.36 37 38
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.026 0.079 0.21 2 -0.36 13 15
Syndecan-4/Syndesmos 0.036 0.12 0.32 5 -0.56 12 17
positive regulation of JNK cascade 0.039 0.12 0.31 2 -0.51 14 16
Syndecan-4/ADAM12 0.037 0.12 0.28 5 -0.54 14 19
CCL5 0.02 0.055 0.17 6 -0.31 12 18
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.004 -10000 0 -10000 0 0
ITGA5 0.018 0.055 0.17 1 -0.31 13 14
SDCBP 0.023 0.01 -10000 0 -10000 0 0
PLG 0.025 0.036 0.16 23 -0.12 2 25
ADAM12 0.028 0.044 0.17 19 -0.31 5 24
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.049 0.025 0.025 5 -0.09 28 33
Syndecan-4/Laminin alpha1 0.033 0.12 0.32 5 -0.52 15 20
Syndecan-4/CXCL12/CXCR4 0.041 0.12 0.32 2 -0.54 14 16
Syndecan-4/Laminin alpha3 0.027 0.12 0.27 3 -0.5 17 20
MDK 0.031 0.026 0.17 16 -10000 0 16
Syndecan-4/FZD7 0.034 0.13 0.31 6 -0.5 18 24
Syndecan-4/Midkine 0.04 0.12 0.31 5 -0.56 12 17
FZD7 0.016 0.06 -10000 0 -0.31 16 16
Syndecan-4/FGFR1/FGF 0.028 0.12 -10000 0 -0.51 15 15
THBS1 0.017 0.062 0.17 5 -0.31 16 21
integrin-mediated signaling pathway 0.031 0.12 0.32 5 -0.48 16 21
positive regulation of MAPKKK cascade 0.039 0.12 0.31 2 -0.51 14 16
Syndecan-4/TACI 0.041 0.13 0.31 6 -0.54 14 20
CXCR4 0.025 0.027 0.17 5 -0.31 2 7
cell adhesion 0.005 0.058 0.2 7 -0.26 15 22
Syndecan-4/Dynamin 0.037 0.12 0.31 6 -0.53 14 20
Syndecan-4/TSP1 0.034 0.12 0.32 4 -0.49 16 20
Syndecan-4/GIPC 0.036 0.12 0.31 6 -0.53 14 20
Syndecan-4/RANTES 0.036 0.13 0.31 5 -0.49 18 23
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 0.02 0.072 0.17 24 -0.31 18 42
LAMA3 0.001 0.088 0.17 1 -0.31 36 37
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.01 0.12 0.73 9 -0.29 16 25
Syndecan-4/alpha-Actinin 0.035 0.12 0.31 6 -0.52 15 21
TFPI 0.025 0.052 0.17 15 -0.31 9 24
F2 0.031 0.035 0.17 24 -0.14 1 25
alpha5/beta1 Integrin 0.032 0.042 -10000 0 -0.21 13 13
positive regulation of cell adhesion 0.016 0.12 0.27 3 -0.51 17 20
ACTN1 0.022 0.037 -10000 0 -0.31 6 6
TNC 0.008 0.076 -10000 0 -0.31 26 26
Syndecan-4/CXCL12 0.033 0.12 0.3 3 -0.52 15 18
FGF6 0.018 0.011 0.17 2 -10000 0 2
RHOA 0.027 0.005 -10000 0 -10000 0 0
CXCL12 0.016 0.06 0.17 1 -0.31 16 17
TNFRSF13B 0.032 0.055 0.17 41 -0.31 6 47
FGF2 0.004 0.084 0.17 1 -0.31 32 33
FGFR1 0.019 0.024 -10000 0 -0.31 2 2
Syndecan-4/PI-4-5-P2 0.017 0.12 0.3 3 -0.53 14 17
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.049 0.16 4 -0.27 11 15
cell migration -0.027 0.014 -10000 0 -10000 0 0
PRKCD 0.024 0.018 -10000 0 -0.13 2 2
vasculogenesis 0.034 0.12 0.32 4 -0.47 16 20
SDC4 0.021 0.12 0.33 3 -0.56 14 17
Syndecan-4/Tenascin C 0.031 0.12 0.32 5 -0.5 16 21
Syndecan-4/PI-4-5-P2/PKC alpha -0.04 0.02 -10000 0 -0.078 7 7
Syndecan-4/Syntenin 0.03 0.11 0.3 2 -0.54 11 13
MMP9 0.095 0.081 0.16 258 -0.31 5 263
Rac1/GTP 0.005 0.059 0.2 7 -0.26 15 22
cytoskeleton organization 0.036 0.12 0.32 5 -0.53 12 17
GIPC1 0.027 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.037 0.13 0.34 5 -0.51 16 21
IGF1 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
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTK2 0.022 0.011 -10000 0 -10000 0 0
CRKL 0 0.051 0.13 2 -0.19 28 30
GRB2/SOS1/SHC 0.049 0.018 -10000 0 -10000 0 0
HRAS 0.028 0.015 0.17 5 -10000 0 5
IRS1/Crk 0.009 0.055 -10000 0 -0.18 33 33
IGF-1R heterotetramer/IGF1/PTP1B 0.038 0.061 0.24 1 -0.18 29 30
AKT1 -0.012 0.068 0.18 28 -0.2 19 47
BAD -0.016 0.064 0.17 26 -0.27 7 33
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.001 0.049 -10000 0 -0.19 27 27
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.017 0.062 0.22 1 -0.19 31 32
RAF1 0.005 0.072 0.28 3 -0.4 6 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.068 0.23 1 -0.18 31 32
YWHAZ 0.021 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.02 0.065 0.14 15 -0.18 39 54
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
RPS6KB1 -0.012 0.069 0.18 29 -0.19 23 52
GNB2L1 0.028 0.012 0.17 3 -10000 0 3
positive regulation of MAPKKK cascade 0.01 0.081 0.29 13 -0.32 5 18
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.018 0.052 -10000 0 -0.17 27 27
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.06 0.062 0.25 1 -0.15 28 29
IGF-1R heterotetramer 0.023 0.027 0.19 1 -0.066 31 32
IGF-1R heterotetramer/IGF1/IRS/Nck 0.034 0.065 0.23 1 -0.19 30 31
Crk/p130 Cas/Paxillin 0.034 0.062 0.22 1 -0.17 30 31
IGF1R 0.023 0.027 0.19 1 -0.066 31 32
IGF1 0.026 0.054 0.19 17 -0.36 6 23
IRS2/Crk 0.009 0.053 0.16 3 -0.18 29 32
PI3K 0.038 0.071 0.23 1 -0.19 31 32
apoptosis 0.016 0.048 0.22 5 -0.15 13 18
HRAS/GDP 0.021 0.01 0.12 5 -10000 0 5
PRKCD -0.005 0.078 0.17 1 -0.29 29 30
RAF1/14-3-3 E 0.024 0.074 0.28 7 -0.34 6 13
BAD/14-3-3 -0.016 0.05 0.16 13 -0.23 5 18
PRKCZ -0.013 0.068 0.18 27 -0.19 23 50
Crk/p130 Cas/Paxillin/FAK1 0.016 0.052 0.14 3 -0.25 5 8
PTPN1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.003 0.083 -10000 0 -0.3 32 32
BCAR1 0.022 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.047 0.059 0.25 1 -0.16 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
IRS1/NCK2 0.019 0.059 0.14 2 -0.18 30 32
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 -0.002 0.053 -10000 0 -0.19 30 30
IRS1 0.004 0.059 0.12 19 -0.2 30 49
IRS2 -0.001 0.051 0.13 2 -0.19 29 31
IGF-1R heterotetramer/IGF1 0.024 0.074 0.2 3 -0.24 31 34
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDPK1 -0.015 0.064 0.18 17 -0.2 24 41
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.006 0.079 0.17 1 -0.29 31 32
SHC1 0.026 0.006 -10000 0 -10000 0 0
IL27-mediated signaling events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.006 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.007 0.14 0.69 12 -0.7 1 13
IL27/IL27R/JAK1 0.043 0.2 -10000 0 -0.9 10 10
TBX21 0.019 0.16 0.41 10 -0.51 12 22
IL12B 0.034 0.034 0.17 29 -10000 0 29
IL12A -0.001 0.03 0.25 1 -0.21 8 9
IL6ST -0.029 0.13 0.19 1 -0.31 79 80
IL27RA/JAK1 0.007 0.16 0.45 1 -1 10 11
IL27 0.029 0.031 0.18 15 -10000 0 15
TYK2 0.028 0.011 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.017 0.1 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.007 0.14 0.69 12 -0.7 1 13
T cell proliferation during immune response 0.007 0.14 0.69 12 -0.7 1 13
MAPKKK cascade -0.007 0.14 0.7 1 -0.69 12 13
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT2 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.032 0.02 0.16 10 -10000 0 10
IL12RB1 0.029 0.043 0.17 17 -0.31 5 22
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.018 0.17 0.49 10 -0.5 14 24
IL27/IL27R/JAK2/TYK2 -0.007 0.15 0.7 1 -0.7 12 13
positive regulation of T cell mediated cytotoxicity -0.007 0.14 0.7 1 -0.69 12 13
STAT1 (dimer) 0.074 0.24 0.5 78 -0.72 10 88
JAK2 0.026 0.018 -10000 0 -0.31 1 1
JAK1 0.029 0.009 0.14 1 -10000 0 1
STAT2 (dimer) -0.002 0.14 0.59 1 -0.66 12 13
T cell proliferation -0.026 0.15 0.41 5 -0.65 13 18
IL12/IL12R/TYK2/JAK2 0.038 0.087 -10000 0 -0.55 8 8
IL17A -0.018 0.1 -10000 0 -10000 0 0
mast cell activation 0.007 0.14 0.69 12 -0.7 1 13
IFNG 0.006 0.029 0.18 2 -0.095 7 9
T cell differentiation -0.002 0.005 0.013 6 -0.02 14 20
STAT3 (dimer) -0.003 0.15 0.59 1 -0.67 12 13
STAT5A (dimer) -0.003 0.15 0.59 1 -0.68 12 13
STAT4 (dimer) -0.001 0.15 0.59 1 -0.66 13 14
STAT4 0.028 0.038 0.17 13 -0.31 4 17
T cell activation -0.005 0.014 0.12 6 -10000 0 6
IL27R/JAK2/TYK2 0.002 0.16 -10000 0 -0.96 10 10
GATA3 -0.34 0.54 0.65 3 -1.2 141 144
IL18 -0.009 0.031 -10000 0 -0.21 11 11
positive regulation of mast cell cytokine production -0.002 0.14 0.58 1 -0.65 12 13
IL27/EBI3 0.045 0.036 0.17 3 -0.21 3 6
IL27RA -0.013 0.17 -10000 0 -1.1 10 10
IL6 -0.024 0.14 0.19 6 -0.31 90 96
STAT5A 0.026 0.016 -10000 0 -0.31 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.003 0.072 0.45 10 -10000 0 10
IL1B -0.027 0.062 -10000 0 -0.21 48 48
EBI3 0.029 0.037 0.17 8 -0.31 4 12
TNF -0.017 0.049 0.25 1 -0.21 27 28
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.019 0.079 -10000 0 -0.17 63 63
TC10/GTP 0.018 0.064 -10000 0 -0.15 53 53
Insulin Receptor/Insulin/IRS1/Shp2 0.056 0.048 -10000 0 -0.18 13 13
HRAS 0.028 0.015 0.17 5 -10000 0 5
APS homodimer 0.028 0.029 0.17 14 -0.31 1 15
GRB14 0.048 0.06 0.17 82 -0.31 3 85
FOXO3 -0.13 0.26 -10000 0 -0.56 127 127
AKT1 -0.01 0.08 0.2 40 -0.28 5 45
INSR 0.029 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.057 0.028 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.008 -10000 0 -10000 0 0
SORBS1 -0.022 0.12 -10000 0 -0.31 69 69
CRK 0.025 0.007 -10000 0 -10000 0 0
PTPN1 -0.006 0.021 0.15 8 -10000 0 8
CAV1 -0.03 0.058 0.2 4 -0.18 50 54
CBL/APS/CAP/Crk-II/C3G 0.038 0.08 -10000 0 -0.16 54 54
Insulin Receptor/Insulin/IRS1/NCK2 0.06 0.044 -10000 0 -0.17 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.04 0.048 -10000 0 -0.2 13 13
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.051 -10000 0 -0.32 4 4
RPS6KB1 -0.014 0.073 0.18 41 -0.27 5 46
PARD6A 0.025 0.016 0.17 4 -10000 0 4
CBL 0.025 0.016 -10000 0 -0.31 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.06 -10000 0 -0.57 5 5
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.023 0.061 0.16 9 -0.25 7 16
HRAS/GTP -0.032 0.038 -10000 0 -0.17 28 28
Insulin Receptor 0.029 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.066 0.048 -10000 0 -0.16 13 13
PRKCI 0.021 0.051 -10000 0 -0.3 9 9
Insulin Receptor/Insulin/GRB14/PDK1 0.025 0.048 -10000 0 -0.21 14 14
SHC1 0.026 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.036 0.055 -10000 0 -0.42 5 5
PI3K 0.05 0.053 -10000 0 -0.2 13 13
NCK2 0.027 0.003 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.01 0.12 5 -10000 0 5
AKT2 -0.011 0.076 0.22 20 -0.28 5 25
PRKCZ 0.022 0.05 -10000 0 -0.3 9 9
SH2B2 0.028 0.029 0.17 14 -0.31 1 15
SHC/SHIP 0.012 0.054 0.17 6 -0.18 29 35
F2RL2 0.074 0.068 0.17 169 -10000 0 169
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.047 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.07 0.031 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.022 -10000 0 -0.31 2 2
NCK1 0.025 0.007 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.028 0.079 -10000 0 -0.17 58 58
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.058 0.03 -10000 0 -10000 0 0
INPP5D -0.022 0.05 0.18 8 -0.18 28 36
SOS1 0.026 0.005 -10000 0 -10000 0 0
SGK1 -0.11 0.29 -10000 0 -0.77 80 80
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
IRS1 0.017 0.056 -10000 0 -0.31 14 14
p62DOK/RasGAP 0.036 0.055 -10000 0 -0.42 5 5
INS 0.024 0.025 0.18 12 -10000 0 12
mol:PI-3-4-P2 -0.022 0.05 0.18 8 -0.18 28 36
GRB2 0.026 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.059 0.18 21 -0.28 5 26
PTPRA 0.029 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
TC10/GTP/CIP4 0.035 0.008 -10000 0 -10000 0 0
PDPK1 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.017 0.037 -10000 0 -0.18 13 13
Insulin Receptor/Insulin/IRS1 0.043 0.04 -10000 0 -0.17 13 13
Insulin Receptor/Insulin/IRS3 0.038 0.02 0.15 12 -10000 0 12
Par3/Par6 0.073 0.059 0.22 2 -0.11 1 3
Caspase cascade in apoptosis

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
TOP1 0.005 0.076 0.22 4 -0.3 18 22
ACTA1 -0.038 0.094 0.18 10 -0.34 23 33
NUMA1 0.008 0.073 0.22 4 -0.34 12 16
SPTAN1 -0.005 0.09 0.21 25 -0.35 16 41
LIMK1 0.001 0.096 0.21 40 -0.33 18 58
BIRC3 0.026 0.02 0.17 3 -0.31 1 4
BIRC2 0.026 0.006 -10000 0 -10000 0 0
BAX 0.027 0.01 0.17 2 -10000 0 2
CASP10 -0.024 0.052 0.22 3 -0.23 22 25
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
PTK2 0.001 0.077 0.2 4 -0.3 20 24
DIABLO 0.026 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.089 0.2 25 -0.34 16 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.006 -10000 0 -10000 0 0
GSN -0.007 0.09 0.21 21 -0.35 16 37
MADD 0.026 0.005 -10000 0 -10000 0 0
TFAP2A -0.007 0.17 -10000 0 -0.57 36 36
BID -0.002 0.034 0.14 2 -0.17 16 18
MAP3K1 -0.035 0.12 -10000 0 -0.36 54 54
TRADD 0.024 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.012 0.087 0.24 11 -0.34 18 29
CASP9 0.027 0.004 -10000 0 -10000 0 0
DNA repair 0.003 0.048 0.21 13 -10000 0 13
neuron apoptosis 0.004 0.12 -10000 0 -0.63 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.084 0.24 9 -0.41 11 20
APAF1 0.026 0.006 -10000 0 -10000 0 0
CASP6 0.012 0.098 -10000 0 -0.86 4 4
TRAF2 0.026 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.015 0.085 0.28 8 -0.34 17 25
CASP7 -0.006 0.054 0.21 1 -0.21 22 23
KRT18 0.02 0.034 -10000 0 -0.48 1 1
apoptosis -0.004 0.083 0.32 6 -0.36 13 19
DFFA -0.015 0.083 0.23 6 -0.34 18 24
DFFB -0.013 0.085 0.24 9 -0.35 17 26
PARP1 -0.003 0.048 -10000 0 -0.22 13 13
actin filament polymerization -0.001 0.1 0.32 17 -0.22 41 58
TNF 0.011 0.081 0.17 11 -0.31 27 38
CYCS 0.004 0.037 0.18 4 -0.16 6 10
SATB1 0.011 0.1 0.37 4 -0.83 4 8
SLK -0.013 0.083 0.27 7 -0.34 18 25
p15 BID/BAX 0.013 0.044 -10000 0 -0.16 20 20
CASP2 0.005 0.059 0.2 13 -0.27 5 18
JNK cascade 0.034 0.12 0.36 54 -10000 0 54
CASP3 -0.013 0.085 0.19 9 -0.33 21 30
LMNB2 0.018 0.097 0.28 11 -0.4 8 19
RIPK1 0.027 0.005 -10000 0 -10000 0 0
CASP4 0.025 0.016 -10000 0 -0.31 1 1
Mammalian IAPs/DIABLO 0.064 0.023 -10000 0 -0.17 1 1
negative regulation of DNA binding -0.006 0.17 -10000 0 -0.56 36 36
stress fiber formation -0.012 0.082 0.27 7 -0.33 18 25
GZMB -0.023 0.055 0.26 2 -0.26 19 21
CASP1 0.005 0.046 -10000 0 -0.26 13 13
LMNB1 0.019 0.1 0.28 14 -0.35 14 28
APP 0.003 0.12 -10000 0 -0.64 16 16
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.003 -10000 0 -10000 0 0
VIM -0.003 0.08 0.26 4 -0.36 14 18
LMNA 0.022 0.081 0.26 15 -0.31 7 22
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.051 -10000 0 -0.29 3 3
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.013 0.084 0.2 12 -0.34 19 31
APAF-1/Caspase 9 0.011 0.074 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis 0.008 0.072 0.22 4 -0.34 12 16
CFL2 0.001 0.1 0.22 41 -0.33 17 58
GAS2 -0.015 0.08 0.18 8 -0.34 18 26
positive regulation of apoptosis 0.024 0.096 0.27 16 -0.4 6 22
PRF1 0.022 0.045 0.17 4 -0.31 8 12
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.016 0.063 0.17 3 -0.31 17 20
ITGA4 0.021 0.059 0.17 11 -0.31 13 24
alpha4/beta7 Integrin 0.026 0.066 0.24 3 -0.22 27 30
alpha4/beta1 Integrin 0.034 0.045 -10000 0 -0.21 13 13
Ceramide 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
SPHK2 -0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0 0.052 -10000 0 -0.29 4 4
BAG4 0.008 0.063 -10000 0 -0.31 18 18
PKC zeta/ceramide 0.003 0.07 -10000 0 -0.2 40 40
NFKBIA 0.027 0.004 -10000 0 -10000 0 0
BIRC3 0.026 0.02 0.17 3 -0.31 1 4
BAX -0.001 0.06 -10000 0 -0.34 12 12
RIPK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.006 0.11 0.73 10 -10000 0 10
BAD -0.011 0.071 0.2 10 -0.21 35 45
SMPD1 0.015 0.062 0.21 20 -0.15 5 25
RB1 -0.016 0.063 -10000 0 -0.19 40 40
FADD/Caspase 8 0.006 0.055 0.21 5 -0.3 4 9
MAP2K4 -0.017 0.061 0.18 1 -0.2 32 33
NSMAF 0.023 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.019 0.071 0.17 8 -0.21 38 46
EGF 0.023 0.08 0.17 38 -0.31 21 59
mol:ceramide -0.014 0.069 -10000 0 -0.21 41 41
MADD 0.026 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.008 0.006 -10000 0 -10000 0 0
ASAH1 0.019 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.062 -10000 0 -0.19 40 40
cell proliferation 0 0.078 0.2 2 -0.22 27 29
BID 0.005 0.11 -10000 0 -0.63 11 11
MAP3K1 -0.016 0.064 0.19 1 -0.2 39 40
EIF2A -0.007 0.071 0.18 25 -0.2 29 54
TRADD 0.024 0.009 -10000 0 -10000 0 0
CRADD 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.017 0.069 0.18 8 -0.22 25 33
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.071 0.18 8 -0.21 30 38
Cathepsin D/ceramide 0.004 0.069 -10000 0 -0.2 37 37
FADD 0.002 0.055 0.2 5 -0.29 4 9
KSR1 -0.021 0.073 0.19 1 -0.2 51 52
MAPK8 -0.012 0.074 -10000 0 -0.23 29 29
PRKRA -0.016 0.062 0.19 1 -0.2 38 39
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.026 0.006 -10000 0 -10000 0 0
IGF1 0.009 0.088 0.17 17 -0.31 32 49
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.069 -10000 0 -0.2 41 41
CTSD 0.027 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0 0.084 0.22 2 -0.23 26 28
PRKCD 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.008 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.008 0.048 -10000 0 -0.3 4 4
TNFR1A/BAG4/TNF-alpha 0.021 0.07 -10000 0 -0.18 44 44
mol:Sphingosine-1-phosphate -0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.021 0.068 0.17 8 -0.21 30 38
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
CYCS 0.015 0.055 0.14 20 -0.21 10 30
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.02 0.049 -10000 0 -0.21 18 18
EIF2AK2 -0.017 0.059 0.19 2 -0.19 35 37
TNF-alpha/TNFR1A/FAN 0.033 0.057 -10000 0 -0.18 26 26
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.037 -10000 0 -10000 0 0
MAP2K2 -0.021 0.069 0.19 7 -0.21 32 39
SMPD3 -0.003 0.084 0.2 4 -0.29 26 30
TNF 0.011 0.081 0.17 11 -0.31 27 38
PKC zeta/PAR4 0.038 0.009 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.006 0.061 0.17 19 -0.16 29 48
NF kappa B1/RelA/I kappa B alpha 0.072 0.026 -10000 0 -10000 0 0
AIFM1 0.008 0.061 0.14 14 -0.21 11 25
BCL2 0.015 0.055 -10000 0 -0.31 13 13
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.004 0.055 -10000 0 -0.21 14 14
IRAK/TOLLIP 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.021 0.011 -10000 0 -10000 0 0
IKBKG 0.027 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.012 0.1 0.14 3 -0.22 95 98
IL1A 0.022 0.029 0.17 3 -0.31 3 6
IL1B -0.037 0.074 0.25 1 -0.24 51 52
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.032 -10000 0 -10000 0 0
IL1R2 -0.037 0.13 -10000 0 -0.31 92 92
IL1R1 0.026 0.022 -10000 0 -0.31 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.047 -10000 0 -0.21 2 2
TOLLIP 0.027 0.004 -10000 0 -10000 0 0
TICAM2 0.021 0.04 -10000 0 -0.31 7 7
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.004 0.086 0.26 3 -0.31 11 14
JUN -0.007 0.055 0.18 27 -0.26 1 28
MAP3K7 0.023 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.033 0.082 -10000 0 -0.17 56 56
IL1 alpha/IL1R1/IL1RAP/MYD88 0.058 0.036 -10000 0 -0.19 6 6
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.067 0.039 -10000 0 -0.18 6 6
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.073 0.19 1 -0.18 55 56
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.001 0.055 0.19 28 -0.14 9 37
IRAK1 0.012 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.03 0.055 0.14 7 -0.21 22 29
IRAK4 0.027 0.004 -10000 0 -10000 0 0
PRKCI 0.025 0.01 0.17 1 -10000 0 1
TRAF6 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.033 -10000 0 -0.25 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.059 -10000 0 -0.22 13 13
CHUK 0.025 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.073 0.19 1 -0.18 55 56
IL1 beta/IL1R2 -0.031 0.11 -10000 0 -0.21 120 120
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.021 0.073 -10000 0 -0.17 46 46
IRAK3 0.013 0.064 -10000 0 -0.31 18 18
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.034 0.082 0.2 1 -0.16 59 60
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.028 -10000 0 -0.2 6 6
IL1 alpha/IL1R1/IL1RAP 0.046 0.034 -10000 0 -0.21 6 6
RELA 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
MYD88 0.027 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.049 0.03 0.18 21 -10000 0 21
IL1RAP 0.023 0.031 -10000 0 -0.31 4 4
UBE2N 0.026 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 0.004 0.064 -10000 0 -0.24 7 7
CASP1 0.017 0.054 -10000 0 -0.31 13 13
IL1RN/IL1R2 -0.017 0.11 0.14 6 -0.22 106 112
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.075 0.2 1 -0.17 52 53
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.024 0.043 -10000 0 -0.27 4 4
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
IL1RN 0.015 0.069 0.17 7 -0.31 20 27
TRAF6/TAK1/TAB1/TAB2 0.032 0.017 -10000 0 -10000 0 0
MAP2K6 0.007 0.055 0.2 29 -0.14 1 30
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.019 0.01 -10000 0 -10000 0 0
epithelial cell differentiation 0.048 0.024 -10000 0 -10000 0 0
CYFIP2 0.027 0.005 -10000 0 -10000 0 0
ENAH -0.008 0.088 0.38 15 -10000 0 15
EGFR -0.002 0.09 -10000 0 -0.31 38 38
EPHA2 -0.002 0.096 0.17 3 -0.31 43 46
MYO6 0.007 0.054 0.19 23 -10000 0 23
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.051 0.015 -10000 0 -10000 0 0
AQP5 -0.14 0.19 -10000 0 -0.39 181 181
CTNND1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.052 0.2 28 -10000 0 28
regulation of calcium-dependent cell-cell adhesion -0.003 0.057 0.2 28 -0.15 11 39
EGF 0.023 0.08 0.17 38 -0.31 21 59
NCKAP1 0.026 0.005 -10000 0 -10000 0 0
AQP3 0.003 0.067 0.35 2 -0.37 12 14
cortical microtubule organization 0.048 0.024 -10000 0 -10000 0 0
GO:0000145 -0.002 0.049 0.18 28 -10000 0 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.053 0.026 -10000 0 -10000 0 0
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.032 0.034 -10000 0 -0.15 27 27
ARF6 0.027 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.067 -10000 0 -0.17 39 39
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.035 0.17 10 -10000 0 10
PVRL2 0.027 0.004 -10000 0 -10000 0 0
ZYX -0.005 0.042 0.2 17 -10000 0 17
ARF6/GTP 0.048 0.067 -10000 0 -0.16 39 39
CDH1 0.024 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.022 0.067 -10000 0 -0.15 52 52
RhoA/GDP 0.049 0.024 -10000 0 -10000 0 0
actin cytoskeleton organization -0.013 0.041 0.16 18 -0.16 1 19
IGF-1R heterotetramer 0.027 0.017 0.17 1 -0.31 1 2
GIT1 0.027 0.002 -10000 0 -10000 0 0
IGF1R 0.027 0.017 0.17 1 -0.31 1 2
IGF1 0.009 0.088 0.17 17 -0.31 32 49
DIAPH1 0.025 0.12 -10000 0 -0.55 6 6
Wnt receptor signaling pathway -0.048 0.024 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.034 -10000 0 -0.15 27 27
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL -0.013 0.041 0.16 18 -0.16 1 19
EFNA1 0.026 0.006 -10000 0 -10000 0 0
LPP -0.014 0.047 0.18 15 -10000 0 15
Ephrin A1/EPHA2 0.027 0.057 -10000 0 -0.14 40 40
SEC6/SEC8 -0.02 0.011 -10000 0 -10000 0 0
MGAT3 -0.003 0.058 0.2 28 -0.15 11 39
HGF/MET 0.021 0.07 -10000 0 -0.18 44 44
HGF 0.011 0.076 0.17 9 -0.31 24 33
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.019 0.01 -10000 0 -10000 0 0
actin cable formation 0.017 0.11 0.31 41 -0.23 6 47
KIAA1543 -0.005 0.044 0.18 21 -0.14 1 22
KIFC3 -0.005 0.044 0.19 21 -10000 0 21
NCK1 0.025 0.007 -10000 0 -10000 0 0
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 -0.004 0.047 0.19 22 -10000 0 22
NCK1/GIT1 0.037 0.011 -10000 0 -10000 0 0
mol:GDP 0.048 0.024 -10000 0 -10000 0 0
EXOC4 0.025 0.008 -10000 0 -10000 0 0
STX4 -0.002 0.05 0.2 25 -10000 0 25
PIP5K1C -0.001 0.052 0.2 28 -10000 0 28
LIMA1 0.027 0.004 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 -0.004 0.097 0.4 15 -10000 0 15
adherens junction assembly -0.008 0.098 0.26 20 -0.5 8 28
IGF-1R heterotetramer/IGF1 0.032 0.049 0.16 1 -0.14 26 27
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.009 -10000 0 -10000 0 0
MET -0.002 0.091 -10000 0 -0.31 39 39
PLEKHA7 -0.004 0.046 0.2 21 -10000 0 21
mol:GTP 0.041 0.066 -10000 0 -0.16 39 39
establishment of epithelial cell apical/basal polarity 0.005 0.091 0.32 27 -10000 0 27
cortical actin cytoskeleton stabilization 0.019 0.01 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.013 0.041 0.16 18 -0.16 1 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.019 0.01 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.022 -10000 0 -10000 0 0
CDKN2C 0.031 0.017 0.15 3 -0.094 1 4
CDKN2A 0.056 0.057 0.17 96 -0.14 1 97
CCND2 -0.008 0.02 -10000 0 -0.1 15 15
RB1 0.005 0.019 0.14 4 -10000 0 4
CDK4 -0.006 0.014 -10000 0 -0.18 2 2
CDK6 -0.009 0.028 -10000 0 -0.17 12 12
G1/S progression -0.005 0.019 -10000 0 -0.15 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.067 0.15 0.17 1 -0.31 136 137
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.028 0.018 0.17 7 -10000 0 7
TCEB1 0.022 0.011 -10000 0 -10000 0 0
HIF1A/p53 0.011 0.067 0.25 3 -0.25 25 28
HIF1A -0.006 0.061 -10000 0 -0.26 24 24
COPS5 0.022 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.061 0.039 -10000 0 -0.19 1 1
FIH (dimer) 0.026 0.007 -10000 0 -10000 0 0
CDKN2A 0.054 0.056 0.17 97 -10000 0 97
ARNT/IPAS -0.029 0.11 -10000 0 -0.21 127 127
HIF1AN 0.026 0.007 -10000 0 -10000 0 0
GNB2L1 0.028 0.012 0.17 3 -10000 0 3
HIF1A/ARNT 0.01 0.065 0.25 1 -0.26 23 24
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.027 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.045 0.028 0.23 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.01 0.066 -10000 0 -0.26 25 25
PHD1-3/OS9 0.06 0.035 -10000 0 -0.16 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.027 0.065 -10000 0 -0.25 19 19
VHL 0.025 0.016 -10000 0 -0.31 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.006 0.061 -10000 0 -0.25 22 22
EGLN3 0.021 0.045 -10000 0 -0.31 9 9
EGLN2 0.027 0.004 -10000 0 -10000 0 0
EGLN1 0.026 0.006 -10000 0 -10000 0 0
TP53 0.023 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.021 0.083 -10000 0 -0.46 13 13
ARNT 0.026 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.027 0.082 0.23 5 -0.26 24 29
TCGA08_p53

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
CDKN2A -0.014 0.028 0.25 3 -10000 0 3
TP53 -0.004 0.045 -10000 0 -0.18 30 30
Senescence -0.004 0.045 -10000 0 -0.18 30 30
Apoptosis -0.004 0.045 -10000 0 -0.18 30 30
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0 0.063 0.3 20 -0.17 2 22
MDM4 0.026 0.005 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.052 -10000 0 -0.41 6 6
VEGFR1 homodimer/NRP1 0.006 0.049 -10000 0 -0.4 6 6
mol:DAG -0.031 0.067 0.19 6 -0.42 5 11
VEGFR1 homodimer/NRP1/VEGFR 121 0.014 0.066 -10000 0 -0.22 25 25
CaM/Ca2+ 0.002 0.073 0.18 6 -0.39 5 11
HIF1A 0.028 0.035 -10000 0 -0.28 6 6
GAB1 0.026 0.016 -10000 0 -0.31 1 1
AKT1 -0.025 0.078 0.29 2 -0.36 8 10
PLCG1 -0.031 0.067 0.19 6 -0.42 5 11
NOS3 -0.005 0.082 0.28 9 -0.44 4 13
CBL 0.025 0.016 -10000 0 -0.31 1 1
mol:NO 0 0.092 0.32 13 -0.43 5 18
FLT1 0.01 0.055 -10000 0 -0.51 5 5
PGF -0.012 0.11 0.17 2 -0.31 56 58
VEGFR1 homodimer/NRP2/VEGFR121 0.017 0.087 -10000 0 -0.21 50 50
CALM1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
eNOS/Hsp90 0.01 0.086 0.28 8 -0.41 5 13
endothelial cell proliferation -0.052 0.13 0.34 3 -0.39 44 47
mol:Ca2+ -0.03 0.066 0.19 6 -0.41 5 11
MAPK3 -0.034 0.074 0.22 7 -0.36 11 18
MAPK1 -0.033 0.075 0.23 8 -0.36 11 19
PIK3R1 0.023 0.027 -10000 0 -0.31 3 3
PLGF homodimer -0.012 0.11 0.17 2 -0.31 56 58
PRKACA 0.027 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.013 0.1 -10000 0 -0.31 54 54
VEGFA homodimer 0.01 0.077 0.17 5 -0.31 26 31
VEGFR1 homodimer/VEGFA homodimer 0.015 0.072 0.18 1 -0.24 25 26
platelet activating factor biosynthetic process -0.036 0.069 0.18 6 -0.35 11 17
PI3K 0.022 0.084 -10000 0 -0.36 8 8
PRKCA -0.034 0.075 0.21 6 -0.37 11 17
PRKCB -0.055 0.094 0.18 4 -0.31 38 42
VEGFR1 homodimer/PLGF homodimer 0.001 0.082 -10000 0 -0.2 59 59
VEGFA 0.01 0.077 0.17 5 -0.31 26 31
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.031 0.067 0.19 6 -0.42 5 11
RASA1 -0.013 0.053 0.19 10 -0.4 6 16
NRP2 0.005 0.082 -10000 0 -0.31 31 31
VEGFR1 homodimer 0.01 0.055 -10000 0 -0.51 5 5
VEGFB homodimer 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.001 0.1 0.38 5 -0.32 21 26
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
mol:PI-3-4-5-P3 0.021 0.082 -10000 0 -0.31 10 10
mol:L-citrulline 0 0.092 0.32 13 -0.43 5 18
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.073 -10000 0 -0.43 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.071 -10000 0 -0.23 25 25
CD2AP 0.027 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.031 0.087 -10000 0 -0.34 8 8
PDPK1 -0.024 0.073 0.22 8 -0.36 7 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.072 -10000 0 -0.23 24 24
mol:NADP 0 0.092 0.32 13 -0.43 5 18
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.071 -10000 0 -0.42 6 6
VEGFR1 homodimer/NRP2 0.012 0.073 -10000 0 -0.23 31 31
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.029 -10000 0 -0.31 3 3
HSPA8 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.034 0.063 -10000 0 -0.2 16 16
AKT1 0.028 0.008 -10000 0 -10000 0 0
GSC 0.031 0.11 0.89 1 -1.2 2 3
NKX2-5 0.001 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.07 0.27 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.075 0.054 -10000 0 -0.26 3 3
SMAD4 0.022 0.035 -10000 0 -0.15 4 4
CBFB 0.024 0.009 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.007 0.094 -10000 0 -0.18 91 91
SMAD3/SMAD4/VDR 0.064 0.058 -10000 0 -0.18 3 3
MYC 0.027 0.033 0.16 24 -10000 0 24
CDKN2B -0.023 0.13 -10000 0 -0.74 8 8
AP1 0.009 0.084 0.2 1 -0.29 12 13
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.075 -10000 0 -0.26 16 16
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.052 -10000 0 -0.24 3 3
SP3 0.027 0.006 -10000 0 -10000 0 0
CREB1 0.027 0.003 -10000 0 -10000 0 0
FOXH1 0.04 0.05 0.17 55 -0.19 1 56
SMAD3/SMAD4/GR 0.038 0.061 -10000 0 -0.21 12 12
GATA3 -0.069 0.15 -10000 0 -0.31 136 136
SKI/SIN3/HDAC complex/NCoR1 0.013 0.044 -10000 0 -10000 0 0
MEF2C/TIF2 0.006 0.069 0.23 7 -0.23 7 14
endothelial cell migration 0.013 0.21 1 18 -10000 0 18
MAX 0.027 0.01 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.022 -10000 0 -0.31 2 2
RUNX2 0.026 0.023 0.17 1 -0.31 2 3
RUNX3 0.027 0.032 0.17 8 -0.31 3 11
RUNX1 0.025 0.018 0.17 1 -0.31 1 2
CTBP1 0.027 0.004 -10000 0 -10000 0 0
NR3C1 0.019 0.051 -10000 0 -0.31 11 11
VDR 0.023 0.038 0.17 2 -0.31 6 8
CDKN1A 0.011 0.12 -10000 0 -1 5 5
KAT2B 0.025 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.059 0.054 -10000 0 -0.3 1 1
DCP1A 0.026 0.005 -10000 0 -10000 0 0
SKI 0.027 0.004 -10000 0 -10000 0 0
SERPINE1 -0.014 0.21 -10000 0 -1 18 18
SMAD3/SMAD4/ATF2 0.029 0.071 -10000 0 -0.19 28 28
SMAD3/SMAD4/ATF3 0.025 0.094 -10000 0 -0.21 49 49
SAP30 0.027 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.046 0.032 0.18 1 -0.18 3 4
JUN -0.004 0.075 0.16 1 -0.29 12 13
SMAD3/SMAD4/IRF7 0.048 0.051 -10000 0 -10000 0 0
TFE3 0.028 0.017 -10000 0 -10000 0 0
COL1A2 0.021 0.043 -10000 0 -0.84 1 1
mesenchymal cell differentiation -0.044 0.049 0.23 1 -10000 0 1
DLX1 0.15 0.051 0.17 416 -10000 0 416
TCF3 0.027 0.005 -10000 0 -10000 0 0
FOS -0.015 0.12 0.18 4 -0.32 61 65
SMAD3/SMAD4/Max 0.044 0.049 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.048 0.027 -10000 0 -0.18 3 3
ZBTB17 0.026 0.005 -10000 0 -10000 0 0
LAMC1 0.012 0.032 0.2 2 -10000 0 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.044 0.046 -10000 0 -10000 0 0
IRF7 0.034 0.03 0.17 23 -10000 0 23
ESR1 0.015 0.059 0.16 1 -0.31 15 16
HNF4A 0.028 0.033 0.17 26 -10000 0 26
MEF2C 0.032 0.075 0.2 61 -0.29 4 65
SMAD2-3/SMAD4 0.054 0.046 -10000 0 -0.26 1 1
Cbp/p300/Src-1 0.047 0.029 -10000 0 -0.18 3 3
IGHV3OR16-13 0.01 0.017 -10000 0 -0.33 1 1
TGIF2/HDAC complex 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.012 -10000 0 -10000 0 0
SKIL 0.021 0.042 0.17 3 -0.31 7 10
HDAC1 0.027 0.003 -10000 0 -10000 0 0
HDAC2 0.024 0.01 -10000 0 -10000 0 0
SNIP1 0.027 0.003 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.055 0.046 -10000 0 -0.18 1 1
MSG1/HSC70 -0.006 0.1 -10000 0 -0.21 91 91
SMAD2 0.028 0.018 -10000 0 -0.15 2 2
SMAD3 0.02 0.034 -10000 0 -0.14 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.012 0.048 0.18 2 -0.25 1 3
SMAD2/SMAD2/SMAD4 -0.002 0.055 0.22 2 -0.17 20 22
NCOR1 0.026 0.007 -10000 0 -10000 0 0
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
NCOA1 0.027 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.033 0.029 -10000 0 -0.21 4 4
SMAD2-3/SMAD4/SP1/MIZ-1 0.085 0.057 -10000 0 -0.27 2 2
IFNB1 0.004 0.035 0.2 3 -10000 0 3
SMAD3/SMAD4/MEF2C 0.06 0.073 0.23 17 -0.29 4 21
CITED1 -0.036 0.14 0.17 11 -0.31 96 107
SMAD2-3/SMAD4/ARC105 0.067 0.046 -10000 0 -0.23 1 1
RBL1 0.008 0.076 -10000 0 -0.31 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.009 0.052 0.22 1 -0.32 4 5
RUNX1-3/PEBPB2 0.046 0.031 -10000 0 -0.17 4 4
SMAD7 0.015 0.087 -10000 0 -0.38 8 8
MYC/MIZ-1 0.034 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.009 0.091 0.31 2 -0.41 15 17
IL10 -0.041 0.11 0.2 2 -0.38 20 22
PIASy/HDAC complex 0.028 0.008 -10000 0 -10000 0 0
PIAS3 0.025 0.01 -10000 0 -10000 0 0
CDK2 0.025 0.011 -10000 0 -10000 0 0
IL5 -0.038 0.091 0.19 2 -0.28 14 16
CDK4 0.025 0.011 -10000 0 -10000 0 0
PIAS4 0.028 0.008 -10000 0 -10000 0 0
ATF3 -0.004 0.11 0.17 24 -0.31 53 77
SMAD3/SMAD4/SP1 0.056 0.049 -10000 0 -0.25 3 3
FOXG1 0.003 0.045 0.17 29 -10000 0 29
FOXO3 0.011 0.006 -10000 0 -10000 0 0
FOXO1 0.01 0.008 -10000 0 -10000 0 0
FOXO4 0.012 0.006 -10000 0 -10000 0 0
heart looping 0.031 0.074 0.2 61 -0.29 4 65
CEBPB 0.027 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.11 0.084 -10000 0 -0.17 5 5
MYOD1 0.019 0.037 0.17 11 -0.31 4 15
SMAD3/SMAD4/HNF4 0.045 0.052 -10000 0 -0.17 1 1
SMAD3/SMAD4/GATA3 -0.016 0.12 -10000 0 -0.24 52 52
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.042 0.17 3 -0.31 7 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.064 0.055 -10000 0 -0.17 3 3
SMAD3/SMAD4/SP1-3 0.069 0.053 -10000 0 -0.25 2 2
MED15 0.027 0.005 -10000 0 -10000 0 0
SP1 0.03 0.015 -10000 0 -0.19 1 1
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.059 0.053 0.21 1 -0.23 3 4
ITGB5 0.015 0.042 0.2 9 -0.28 1 10
TGIF/SIN3/HDAC complex/CtBP 0.014 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.023 0.079 -10000 0 -0.19 40 40
AR -0.003 0.096 -10000 0 -0.31 43 43
negative regulation of cell growth -0.001 0.069 -10000 0 -0.27 7 7
SMAD3/SMAD4/MYOD 0.04 0.054 -10000 0 -0.18 5 5
E2F5 0.022 0.013 0.17 1 -10000 0 1
E2F4 0.024 0.009 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.085 0.065 -10000 0 -0.19 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.038 -10000 0 -0.32 4 4
TFDP1 0.026 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.028 0.093 -10000 0 -0.29 12 12
SMAD3/SMAD4/RUNX2 0.044 0.049 -10000 0 -0.23 1 1
TGIF2 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.026 0.007 -10000 0 -10000 0 0
ATF2 0.007 0.078 -10000 0 -0.31 28 28
Coregulation of Androgen receptor activity

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
NRIP1 0.025 0.017 -10000 0 -0.12 4 4
SVIL 0.014 0.063 -10000 0 -0.31 17 17
ZNF318 0.027 0.018 0.18 6 -10000 0 6
JMJD2C 0.004 0.009 -10000 0 -0.099 3 3
T-DHT/AR/Ubc9 0.016 0.065 -10000 0 -0.17 44 44
CARM1 0.026 0.008 -10000 0 -10000 0 0
PRDX1 0.027 0.003 -10000 0 -10000 0 0
PELP1 0.025 0.008 -10000 0 -10000 0 0
CTNNB1 0.026 0.011 -10000 0 -0.075 1 1
AKT1 0.027 0.008 -10000 0 -10000 0 0
PTK2B 0.019 0.015 -10000 0 -10000 0 0
MED1 0.027 0.007 -10000 0 -10000 0 0
MAK 0.065 0.065 0.17 137 -10000 0 137
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.016 0.054 -10000 0 -0.31 12 12
GSN 0.024 0.029 -10000 0 -0.31 3 3
NCOA2 -0.016 0.1 -10000 0 -0.31 53 53
NCOA6 0.026 0.013 -10000 0 -10000 0 0
DNA-PK 0.045 0.027 0.22 4 -10000 0 4
NCOA4 0.026 0.007 -10000 0 -10000 0 0
PIAS3 0.026 0.012 -10000 0 -10000 0 0
cell proliferation 0.034 0.068 0.25 2 -0.4 6 8
XRCC5 0.027 0.005 -10000 0 -10000 0 0
UBE3A 0.026 0.015 -10000 0 -0.11 5 5
T-DHT/AR/SNURF 0.01 0.077 -10000 0 -0.19 55 55
FHL2 -0.013 0.16 -10000 0 -0.75 20 20
RANBP9 0.026 0.013 -10000 0 -0.092 4 4
JMJD1A 0.003 0.011 -10000 0 -0.09 5 5
CDK6 0.016 0.055 -10000 0 -0.31 13 13
TGFB1I1 0 0.091 -10000 0 -0.31 38 38
T-DHT/AR/CyclinD1 0.017 0.065 -10000 0 -0.17 43 43
XRCC6 0.027 0.005 -10000 0 -10000 0 0
T-DHT/AR 0.019 0.077 -10000 0 -0.16 69 69
CTDSP1 0.027 0.008 -10000 0 -10000 0 0
CTDSP2 0.027 0.013 0.15 1 -10000 0 1
BRCA1 0.026 0.014 0.17 1 -0.088 2 3
TCF4 0.022 0.029 -10000 0 -0.31 3 3
CDKN2A 0.054 0.057 0.17 97 -10000 0 97
SRF 0.023 0.036 -10000 0 -0.15 20 20
NKX3-1 -0.007 0.035 -10000 0 -0.16 7 7
KLK3 -0.01 0.14 -10000 0 -1.2 6 6
TMF1 0.026 0.007 -10000 0 -10000 0 0
HNRNPA1 0.027 0.008 0.13 1 -10000 0 1
AOF2 0 0.009 -10000 0 -0.076 6 6
APPL1 -0.011 0.014 0.12 5 -10000 0 5
T-DHT/AR/Caspase 8 0.016 0.066 -10000 0 -0.17 44 44
AR -0.005 0.097 -10000 0 -0.31 43 43
UBA3 0.026 0.009 -10000 0 -10000 0 0
PATZ1 0.027 0.007 -10000 0 -10000 0 0
PAWR 0.026 0.008 -10000 0 -10000 0 0
PRKDC 0.023 0.013 0.2 1 -10000 0 1
PA2G4 0.027 0.009 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.017 0.059 -10000 0 -0.16 43 43
RPS6KA3 0.026 0.021 -10000 0 -0.16 4 4
T-DHT/AR/ARA70 0.016 0.065 -10000 0 -0.17 45 45
LATS2 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.016 0.06 0.15 2 -0.16 44 46
Cyclin D3/CDK11 p58 0.02 0.003 -10000 0 -10000 0 0
VAV3 -0.01 0.1 -10000 0 -0.31 52 52
KLK2 0.003 0.054 -10000 0 -0.67 2 2
CASP8 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.007 0.1 -10000 0 -0.25 55 55
TMPRSS2 -0.012 0.092 -10000 0 -0.41 20 20
CCND1 0.026 0.012 0.17 1 -10000 0 1
PIAS1 0.026 0.022 -10000 0 -0.15 6 6
mol:T-DHT -0.001 0.018 -10000 0 -0.066 29 29
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.026 0.022 -10000 0 -0.16 6 6
T-DHT/AR/CDK6 0.011 0.072 -10000 0 -0.18 51 51
CMTM2 0.023 0.02 0.17 2 -0.31 1 3
SNURF 0.015 0.06 -10000 0 -0.31 16 16
ZMIZ1 0.022 0.031 -10000 0 -0.2 4 4
CCND3 0.027 0.003 -10000 0 -10000 0 0
TGIF1 0.026 0.009 -10000 0 -10000 0 0
FKBP4 0.025 0.015 -10000 0 -0.1 2 2
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.032 0.061 -10000 0 -0.38 2 2
epithelial cell differentiation 0.042 0.064 -10000 0 -0.32 1 1
ITCH 0.031 0.016 0.13 1 -10000 0 1
WWP1 0.028 0.078 -10000 0 -0.44 1 1
FYN 0.023 0.01 -10000 0 -10000 0 0
EGFR -0.002 0.09 -10000 0 -0.31 38 38
PRL 0.02 0.014 0.17 4 -10000 0 4
neuron projection morphogenesis 0.002 0.092 0.26 25 -0.35 2 27
PTPRZ1 -0.072 0.16 0.17 11 -0.31 143 154
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.016 0.076 -10000 0 -0.32 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.006 0.065 -10000 0 -0.37 2 2
ADAM17 0.029 0.03 -10000 0 -0.31 3 3
ErbB4/ErbB4 0.02 0.061 -10000 0 -0.42 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.026 0.064 -10000 0 -0.37 3 3
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.003 0.065 -10000 0 -0.35 2 2
GRIN2B -0.005 0.06 0.24 3 -0.41 1 4
ErbB4/ErbB2/betacellulin 0.021 0.074 -10000 0 -0.37 7 7
STAT1 0.03 0.019 0.17 9 -10000 0 9
HBEGF 0.026 0.031 0.17 6 -0.31 3 9
PRLR 0.018 0.076 0.17 22 -0.31 21 43
E4ICDs/ETO2 0.028 0.052 -10000 0 -0.45 1 1
axon guidance 0.025 0.063 -10000 0 -0.37 1 1
NEDD4 0.026 0.035 -10000 0 -0.3 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.028 0.055 -10000 0 -0.22 19 19
CBFA2T3 0.021 0.028 -10000 0 -0.31 3 3
ErbB4/ErbB2/HBEGF 0.03 0.056 -10000 0 -0.37 2 2
MAPK3 0.007 0.082 0.25 16 -0.32 3 19
STAT1 (dimer) 0.034 0.063 -10000 0 -0.37 2 2
MAPK1 0.008 0.081 0.24 15