Glioblastoma Multiforme: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 99 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
HIF-1-alpha transcription factor network 136
FOXM1 transcription factor network 107
Angiopoietin receptor Tie2-mediated signaling 87
Endothelins 84
Thromboxane A2 receptor signaling 76
HIF-2-alpha transcription factor network 75
TCGA08_rtk_signaling 74
TCGA08_p53 73
EGFR-dependent Endothelin signaling events 71
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 71
Results

The following list describes the columns found in Table 2.

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

  • 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.

Pathway.Name 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
HIF-1-alpha transcription factor network 136 10381 76 -0.08 0.1 1000 -1000 -0.01 -1000
FOXM1 transcription factor network 107 5496 51 -0.32 0.062 1000 -1000 -0.042 -1000
Angiopoietin receptor Tie2-mediated signaling 87 7719 88 -0.29 0.053 1000 -1000 -0.046 -1000
Endothelins 84 8148 96 -0.14 0.036 1000 -1000 -0.025 -1000
Thromboxane A2 receptor signaling 76 8039 105 -0.068 0.044 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 75 3225 43 -0.077 0.047 1000 -1000 -0.05 -1000
TCGA08_rtk_signaling 74 1942 26 -0.026 0.095 1000 -1000 -0.01 -1000
TCGA08_p53 73 513 7 -0.001 0.034 1000 -1000 -0.01 -1000
EGFR-dependent Endothelin signaling events 71 1502 21 -0.005 0.092 1000 -1000 -0.012 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 71 2358 33 -0.074 0.068 1000 -1000 -0.013 -1000
Effects of Botulinum toxin 70 1825 26 -0.008 0.053 1000 -1000 -0.01 -1000
Syndecan-3-mediated signaling events 66 2311 35 -0.072 0.08 1000 -1000 -0.029 -1000
PDGFR-alpha signaling pathway 64 2856 44 -0.093 0.036 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 64 3307 51 -0.1 0.074 1000 -1000 -0.023 -1000
TCGA08_retinoblastoma 64 513 8 -0.047 0.057 1000 -1000 -0.001 -1000
Arf6 signaling events 62 3870 62 -0.005 0.093 1000 -1000 -0.006 -1000
Ras signaling in the CD4+ TCR pathway 62 1069 17 -0.001 0.041 1000 -1000 -0.01 -1000
Syndecan-4-mediated signaling events 60 4022 67 -0.14 0.036 1000 -1000 -0.031 -1000
LPA receptor mediated events 59 6025 102 -0.13 0.037 1000 -1000 -0.052 -1000
S1P5 pathway 58 998 17 -0.009 0.036 1000 -1000 -0.008 -1000
S1P4 pathway 58 1471 25 -0.013 0.041 1000 -1000 -0.01 -1000
Syndecan-1-mediated signaling events 57 1961 34 -0.003 0.035 1000 -1000 -0.016 -1000
Nongenotropic Androgen signaling 56 2960 52 -0.084 0.058 1000 -1000 -0.021 -1000
Wnt signaling 55 390 7 -0.006 0.037 1000 -1000 -0.007 -1000
amb2 Integrin signaling 54 4496 82 -0.015 0.076 1000 -1000 -0.023 -1000
EPO signaling pathway 53 2961 55 -0.001 0.082 1000 -1000 -0.015 -1000
Fc-epsilon receptor I signaling in mast cells 53 5149 97 -0.12 0.048 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 53 1174 22 -0.072 0.042 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 52 900 17 -0.14 0.063 1000 -1000 -0.01 -1000
Syndecan-2-mediated signaling events 51 3554 69 -0.026 0.037 1000 -1000 -0.026 -1000
Glypican 2 network 51 206 4 0 0.007 1000 -1000 0 -1000
IL23-mediated signaling events 51 3079 60 -0.064 0.15 1000 -1000 -0.026 -1000
Osteopontin-mediated events 49 1896 38 -0.073 0.05 1000 -1000 -0.02 -1000
PLK2 and PLK4 events 48 145 3 -0.011 0.035 1000 -1000 -0.015 -1000
Presenilin action in Notch and Wnt signaling 45 2758 61 -0.082 0.079 1000 -1000 -0.028 -1000
FoxO family signaling 45 2930 64 -0.17 0.053 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 45 5702 125 -0.045 0.06 1000 -1000 -0.04 -1000
Arf6 downstream pathway 44 1893 43 -0.025 0.05 1000 -1000 -0.032 -1000
Ephrin B reverse signaling 44 2125 48 -0.065 0.068 1000 -1000 -0.045 -1000
IL2 signaling events mediated by PI3K 44 2552 58 -0.069 0.038 1000 -1000 -0.019 -1000
EPHB forward signaling 44 3780 85 -0.053 0.082 1000 -1000 -0.042 -1000
BCR signaling pathway 44 4438 99 -0.059 0.05 1000 -1000 -0.031 -1000
E-cadherin signaling in keratinocytes 44 1910 43 -0.039 0.064 1000 -1000 -0.012 -1000
IL12-mediated signaling events 43 3773 87 -0.11 0.095 1000 -1000 -0.019 -1000
Regulation of nuclear SMAD2/3 signaling 42 5787 136 -0.21 0.2 1000 -1000 -0.042 -1000
Reelin signaling pathway 42 2376 56 -0.014 0.068 1000 -1000 -0.014 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 41 2224 54 -0.037 0.077 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 41 3149 76 -0.032 0.06 1000 -1000 -0.031 -1000
Paxillin-dependent events mediated by a4b1 41 1500 36 -0.053 0.053 1000 -1000 -0.041 -1000
Class I PI3K signaling events 41 3029 73 -0.05 0.067 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 40 1135 28 -0.011 0.036 1000 -1000 -0.014 -1000
BMP receptor signaling 40 3258 81 -0.033 0.055 1000 -1000 -0.012 -1000
Paxillin-independent events mediated by a4b1 and a4b7 40 1500 37 -0.034 0.082 1000 -1000 -0.013 -1000
FAS signaling pathway (CD95) 40 1890 47 -0.16 0.048 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 40 2725 68 -0.1 0.046 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 39 2555 65 -0.045 0.036 1000 -1000 -0.061 -1000
mTOR signaling pathway 39 2087 53 -0.031 0.046 1000 -1000 -0.022 -1000
IL1-mediated signaling events 39 2473 62 -0.045 0.074 1000 -1000 -0.033 -1000
IL6-mediated signaling events 39 2931 75 -0.076 0.1 1000 -1000 -0.028 -1000
p38 MAPK signaling pathway 39 1720 44 0 0.044 1000 -1000 -0.008 -1000
Glypican 1 network 38 1869 48 -0.032 0.052 1000 -1000 -0.033 -1000
S1P1 pathway 38 1371 36 -0.004 0.054 1000 -1000 -0.02 -1000
PLK1 signaling events 37 3225 85 -0.049 0.054 1000 -1000 -0.022 -1000
IFN-gamma pathway 37 2556 68 -0.04 0.065 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 37 2555 68 -0.029 0.064 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 37 1999 54 0 0.047 1000 -1000 -0.009 -1000
S1P3 pathway 37 1593 42 -0.019 0.037 1000 -1000 -0.016 -1000
TCR signaling in naïve CD8+ T cells 36 3379 93 -0.34 0.39 1000 -1000 -0.025 -1000
Stabilization and expansion of the E-cadherin adherens junction 36 2710 74 -0.13 0.079 1000 -1000 -0.051 -1000
Neurotrophic factor-mediated Trk receptor signaling 36 4433 120 -0.035 0.087 1000 -1000 -0.029 -1000
PDGFR-beta signaling pathway 36 3495 97 -0.052 0.066 1000 -1000 -0.04 -1000
Hedgehog signaling events mediated by Gli proteins 35 2305 65 -0.017 0.057 1000 -1000 -0.019 -1000
IGF1 pathway 35 2036 57 -0.046 0.067 1000 -1000 -0.028 -1000
Plasma membrane estrogen receptor signaling 35 3090 86 -0.067 0.052 1000 -1000 -0.035 -1000
Noncanonical Wnt signaling pathway 34 901 26 -0.037 0.037 1000 -1000 -0.036 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 34 2907 85 -0.12 0.11 1000 -1000 -0.021 -1000
Alternative NF-kappaB pathway 34 442 13 0 0.065 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 33 169 5 0.027 0.052 1000 -1000 0.033 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 33 2634 78 -0.022 0.073 1000 -1000 -0.018 -1000
IL4-mediated signaling events 32 2937 91 -0.32 0.063 1000 -1000 -0.056 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 32 1468 45 -0.034 0.076 1000 -1000 -0.026 -1000
Caspase cascade in apoptosis 31 2350 74 -0.079 0.065 1000 -1000 -0.021 -1000
Signaling events regulated by Ret tyrosine kinase 31 2608 82 -0.058 0.062 1000 -1000 -0.027 -1000
E-cadherin signaling in the nascent adherens junction 31 2387 76 -0.041 0.091 1000 -1000 -0.034 -1000
ErbB4 signaling events 30 2111 69 -0.07 0.064 1000 -1000 -0.023 -1000
Aurora A signaling 30 1836 60 -0.028 0.058 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class III 30 1222 40 -0.048 0.049 1000 -1000 -0.049 -1000
Signaling mediated by p38-gamma and p38-delta 30 450 15 -0.025 0.036 1000 -1000 -0.022 -1000
Integrins in angiogenesis 30 2529 84 -0.046 0.071 1000 -1000 -0.015 -1000
Insulin Pathway 30 2234 74 -0.034 0.084 1000 -1000 -0.031 -1000
Signaling events mediated by PRL 30 1028 34 -0.036 0.047 1000 -1000 -0.026 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 29 680 23 -0.018 0.054 1000 -1000 -0.005 -1000
p75(NTR)-mediated signaling 29 3652 125 -0.023 0.088 1000 -1000 -0.041 -1000
Regulation of Telomerase 29 3003 102 -0.028 0.076 1000 -1000 -0.026 -1000
Aurora B signaling 29 1963 67 -0.033 0.062 1000 -1000 -0.017 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 28 2375 83 -0.035 0.068 1000 -1000 -0.015 -1000
BARD1 signaling events 27 1565 57 -0.064 0.085 1000 -1000 -0.058 -1000
TRAIL signaling pathway 27 1315 48 -0.033 0.087 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 27 1623 58 -0.054 0.06 1000 -1000 -0.019 -1000
Visual signal transduction: Cones 26 1019 38 -0.013 0.059 1000 -1000 -0.011 -1000
Insulin-mediated glucose transport 25 801 32 -0.016 0.042 1000 -1000 -0.015 -1000
Nectin adhesion pathway 25 1577 63 -0.01 0.083 1000 -1000 -0.024 -1000
Glucocorticoid receptor regulatory network 25 2953 114 -0.12 0.064 1000 -1000 -0.046 -1000
Calcium signaling in the CD4+ TCR pathway 24 746 31 -0.021 0.09 1000 -1000 -0.035 -1000
Coregulation of Androgen receptor activity 23 1767 76 -0.011 0.07 1000 -1000 -0.01 -1000
Signaling events mediated by HDAC Class I 23 2405 104 -0.029 0.066 1000 -1000 -0.025 -1000
IL27-mediated signaling events 23 1188 51 -0.016 0.063 1000 -1000 -0.031 -1000
Regulation of Androgen receptor activity 23 1645 70 -0.032 0.066 1000 -1000 -0.025 -1000
Ceramide signaling pathway 21 1640 76 -0.039 0.07 1000 -1000 -0.019 -1000
E-cadherin signaling events 21 109 5 0.033 0.063 1000 -1000 0.033 -1000
RXR and RAR heterodimerization with other nuclear receptor 20 1056 52 -0.044 0.1 1000 -1000 -0.023 -1000
Arf6 trafficking events 20 1445 71 -0.038 0.046 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 19 1480 75 -0.03 0.093 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 19 762 39 -0.068 0.037 1000 -1000 -0.01 -1000
Atypical NF-kappaB pathway 19 613 31 -0.021 0.037 1000 -1000 -0.014 -1000
Arf1 pathway 19 1033 54 -0.073 0.044 1000 -1000 -0.012 -1000
Canonical NF-kappaB pathway 18 730 39 -0.033 0.066 1000 -1000 -0.016 -1000
Circadian rhythm pathway 18 416 22 -0.01 0.056 1000 -1000 -0.017 -1000
Signaling mediated by p38-alpha and p38-beta 18 831 44 -0.015 0.084 1000 -1000 -0.013 -1000
VEGFR1 specific signals 18 1010 56 -0.031 0.042 1000 -1000 -0.026 -1000
Signaling events mediated by the Hedgehog family 17 889 52 -0.015 0.09 1000 -1000 -0.02 -1000
ceramide signaling pathway 17 872 49 -0.015 0.053 1000 -1000 -0.027 -1000
Sumoylation by RanBP2 regulates transcriptional repression 16 451 27 -0.033 0.077 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 16 320 20 -0.011 0.036 1000 -1000 -0.01 -1000
Nephrin/Neph1 signaling in the kidney podocyte 15 516 34 -0.054 0.095 1000 -1000 -0.04 -1000
FOXA2 and FOXA3 transcription factor networks 14 651 46 0 0.1 1000 -1000 -0.026 -1000
Aurora C signaling 10 75 7 0 0.063 1000 -1000 -0.005 -1000
Class IB PI3K non-lipid kinase events 10 30 3 -0.036 0.036 1000 -1000 -0.032 -1000
LPA4-mediated signaling events 8 99 12 -0.017 0.017 1000 -1000 -0.012 -1000
Visual signal transduction: Rods 8 430 52 -0.034 0.085 1000 -1000 -0.011 -1000
Ephrin A reverse signaling 2 17 7 -0.019 0.048 1000 -1000 -0.014 -1000
Total 5159 291242 7203 -7 8.6 131000 -131000 -3 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.028 0.46 0.58 107 -0.74 89 196
HDAC7 -0.001 0.005 -10000 0 -0.051 3 3
HIF1A/ARNT/Cbp/p300/Src-1 -0.029 0.39 0.56 52 -0.68 78 130
SMAD4 0.034 0.014 0.08 10 -10000 0 10
ID2 0.048 0.48 0.6 122 -0.73 91 213
AP1 0.013 0.083 -10000 0 -0.18 73 73
ABCG2 0.014 0.47 0.6 103 -0.74 91 194
HIF1A 0.044 0.13 0.22 100 -0.16 58 158
TFF3 0.042 0.47 0.6 116 -0.73 89 205
GATA2 0.038 0.014 0.077 19 -0.077 2 21
AKT1 0.052 0.14 0.24 93 -0.19 42 135
response to hypoxia 0.012 0.09 0.17 89 -0.12 51 140
MCL1 0.054 0.48 0.61 122 -0.74 88 210
NDRG1 -0.002 0.46 0.59 90 -0.74 95 185
SERPINE1 -0.067 0.39 0.56 45 -0.75 84 129
FECH 0.043 0.47 0.6 115 -0.72 90 205
FURIN 0.052 0.48 0.6 123 -0.73 90 213
NCOA2 0.037 0.006 -10000 0 -10000 0 0
EP300 0.073 0.18 0.34 115 -0.31 29 144
HMOX1 -0.02 0.45 0.6 80 -0.78 89 169
BHLHE40 -0.056 0.41 0.55 75 -0.71 94 169
BHLHE41 -0.056 0.41 0.55 75 -0.71 94 169
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.069 0.18 0.36 46 -0.23 37 83
ENG 0.03 0.15 0.29 55 -0.25 19 74
JUN 0.035 0.013 -10000 0 -0.051 2 2
RORA 0.024 0.46 0.6 105 -0.74 91 196
ABCB1 -0.057 0.22 -10000 0 -0.83 29 29
TFRC 0.031 0.47 0.6 112 -0.73 92 204
CXCR4 0.014 0.47 0.6 102 -0.75 94 196
TF -0.08 0.41 0.62 45 -0.75 93 138
CITED2 0.012 0.46 0.6 97 -0.74 91 188
HIF1A/ARNT -0.078 0.45 0.66 18 -0.87 77 95
LDHA -0.065 0.28 -10000 0 -0.97 40 40
ETS1 0.057 0.48 0.6 125 -0.74 88 213
PGK1 0.046 0.48 0.6 123 -0.75 89 212
NOS2 -0.056 0.41 0.55 75 -0.71 94 169
ITGB2 0.005 0.46 0.59 97 -0.76 91 188
ALDOA 0.055 0.48 0.61 121 -0.74 88 209
Cbp/p300/CITED2 -0.022 0.46 0.59 79 -0.79 88 167
FOS 0.026 0.018 -10000 0 -0.043 1 1
HK2 0.056 0.48 0.6 126 -0.74 88 214
SP1 0.033 0.059 0.11 38 -0.15 40 78
GCK 0.1 0.25 0.55 64 -0.48 11 75
HK1 -0.001 0.45 0.61 92 -0.73 90 182
NPM1 0.051 0.48 0.6 123 -0.73 90 213
EGLN1 0.048 0.47 0.6 117 -0.74 87 204
CREB1 0.032 0.034 -10000 0 -0.099 30 30
PGM1 0.051 0.48 0.61 121 -0.74 90 211
SMAD3 0.037 0.008 0.08 10 -10000 0 10
EDN1 0.054 0.22 0.51 18 -0.61 13 31
IGFBP1 -0.012 0.42 0.6 74 -0.72 82 156
VEGFA -0.015 0.34 0.48 85 -0.57 87 172
HIF1A/JAB1 0.043 0.1 0.2 58 -0.18 18 76
CP -0.035 0.44 0.59 76 -0.75 95 171
CXCL12 -0.038 0.41 0.58 62 -0.73 88 150
COPS5 0.037 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.053 0.14 6 -0.14 35 41
BNIP3 -0.008 0.45 0.61 89 -0.74 88 177
EGLN3 0.005 0.45 0.6 93 -0.73 91 184
CA9 -0.016 0.43 0.58 78 -0.74 85 163
TERT 0.05 0.48 0.6 125 -0.73 90 215
ENO1 0.046 0.48 0.61 121 -0.74 88 209
PFKL 0.054 0.48 0.61 124 -0.74 88 212
NCOA1 0.033 0.011 -10000 0 -10000 0 0
ADM -0.019 0.46 0.6 85 -0.75 97 182
ARNT 0.048 0.13 0.23 93 -0.14 59 152
HNF4A 0.037 0.012 0.083 9 -10000 0 9
ADFP -0.03 0.44 0.59 75 -0.74 95 170
SLC2A1 0.014 0.37 0.51 96 -0.59 87 183
LEP 0.007 0.43 0.6 87 -0.74 79 166
HIF1A/ARNT/Cbp/p300 -0.039 0.38 0.56 53 -0.7 79 132
EPO 0.02 0.31 0.55 55 -0.59 42 97
CREBBP 0.078 0.18 0.33 123 -0.27 30 153
HIF1A/ARNT/Cbp/p300/HDAC7 -0.043 0.38 0.54 52 -0.68 82 134
PFKFB3 0.007 0.46 0.61 96 -0.75 86 182
NT5E -0.028 0.44 0.6 76 -0.73 96 172
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.089 0.66 1 34 -1.2 98 132
PLK1 0.062 0.16 0.67 14 -0.81 5 19
BIRC5 -0.065 0.44 0.68 14 -1.2 59 73
HSPA1B -0.09 0.66 0.95 38 -1.2 103 141
MAP2K1 0.045 0.1 0.25 56 -10000 0 56
BRCA2 -0.088 0.66 1 33 -1.2 101 134
FOXM1 -0.24 0.98 1.2 31 -1.9 103 134
XRCC1 -0.086 0.67 1 35 -1.2 97 132
FOXM1B/p19 -0.32 0.57 -10000 0 -1.4 101 101
Cyclin D1/CDK4 -0.11 0.59 0.87 29 -1.1 105 134
CDC2 -0.11 0.74 1.1 36 -1.3 105 141
TGFA -0.072 0.58 0.86 41 -1 102 143
SKP2 -0.091 0.66 1 33 -1.2 98 131
CCNE1 0.024 0.037 0.1 21 -0.034 114 135
CKS1B -0.098 0.68 1.1 33 -1.2 103 136
RB1 -0.073 0.37 0.49 18 -1 50 68
FOXM1C/SP1 -0.17 0.76 0.9 28 -1.5 104 132
AURKB 0.058 0.16 0.67 14 -0.95 4 18
CENPF -0.11 0.71 1.1 35 -1.2 114 149
CDK4 0.025 0.052 0.15 31 -10000 0 31
MYC -0.11 0.57 0.82 34 -1 107 141
CHEK2 0.037 0.093 0.23 51 -10000 0 51
ONECUT1 -0.091 0.64 0.91 39 -1.2 103 142
CDKN2A 0.003 0.018 -10000 0 -0.14 4 4
LAMA4 -0.094 0.66 0.97 36 -1.2 100 136
FOXM1B/HNF6 -0.17 0.78 0.94 36 -1.5 103 139
FOS -0.15 0.7 1 32 -1.2 128 160
SP1 0.034 0.019 0.073 3 -0.045 24 27
CDC25B -0.086 0.69 1 38 -1.3 99 137
response to radiation 0.024 0.068 0.15 73 -10000 0 73
CENPB -0.077 0.68 1 39 -1.2 100 139
CENPA -0.093 0.67 1.1 33 -1.2 99 132
NEK2 -0.081 0.67 1.1 34 -1.2 98 132
HIST1H2BA -0.09 0.66 0.95 38 -1.2 103 141
CCNA2 0.022 0.031 0.094 5 -0.034 77 82
EP300 0.033 0.011 -10000 0 -10000 0 0
CCNB1/CDK1 -0.19 0.85 1.1 29 -1.6 111 140
CCNB2 -0.11 0.7 1 36 -1.3 104 140
CCNB1 -0.12 0.75 1.1 36 -1.4 107 143
ETV5 -0.12 0.69 1 33 -1.2 120 153
ESR1 -0.092 0.66 0.99 33 -1.2 103 136
CCND1 -0.098 0.62 0.9 39 -1.1 105 144
GSK3A 0.037 0.085 0.21 51 -10000 0 51
Cyclin A-E1/CDK1-2 0.047 0.1 0.26 24 -0.16 43 67
CDK2 0.024 0.037 0.099 18 -0.034 118 136
G2/M transition of mitotic cell cycle 0.028 0.082 0.18 75 -10000 0 75
FOXM1B/Cbp/p300 -0.17 0.69 0.8 18 -1.4 103 121
GAS1 -0.093 0.68 1 36 -1.2 101 137
MMP2 -0.12 0.7 1 36 -1.2 113 149
RB1/FOXM1C -0.14 0.62 0.85 25 -1.2 103 128
CREBBP 0.036 0.005 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.23 0.41 -10000 0 -0.83 141 141
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.38 132 132
NCK1/Dok-R -0.14 0.35 -10000 0 -0.86 96 96
PIK3CA 0.031 0.014 -10000 0 0 82 82
mol:beta2-estradiol 0.031 0.098 0.23 96 -10000 0 96
RELA 0.036 0.004 -10000 0 0 7 7
SHC1 0.032 0.011 -10000 0 0 52 52
Rac/GDP 0.017 0.02 -10000 0 -0.13 5 5
F2 0.053 0.11 0.28 87 -0.091 64 151
TNIP2 0.036 0.006 -10000 0 0 12 12
NF kappa B/RelA -0.11 0.36 -10000 0 -0.83 96 96
FN1 0.035 0.009 -10000 0 0 30 30
PLD2 -0.15 0.36 -10000 0 -0.89 96 96
PTPN11 0.036 0.005 -10000 0 0 11 11
GRB14 0.032 0.013 -10000 0 0 70 70
ELK1 -0.14 0.33 -10000 0 -0.82 96 96
GRB7 0.036 0.006 -10000 0 0 15 15
PAK1 0.036 0.006 -10000 0 0 16 16
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.86 96 96
CDKN1A -0.19 0.36 -10000 0 -0.69 146 146
ITGA5 0.033 0.012 -10000 0 0 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.36 -10000 0 -0.86 96 96
CRK 0.035 0.008 -10000 0 0 23 23
mol:NO -0.12 0.32 0.38 3 -0.59 137 140
PLG -0.15 0.36 -10000 0 -0.89 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.75 123 123
GRB2 0.035 0.007 -10000 0 0 18 18
PIK3R1 0.032 0.012 -10000 0 0 63 63
ANGPT2 -0.22 0.45 -10000 0 -1.1 102 102
BMX -0.15 0.36 -10000 0 -0.89 96 96
ANGPT1 -0.16 0.42 -10000 0 -1 95 95
tube development -0.21 0.36 -10000 0 -0.7 164 164
ANGPT4 0.022 0.029 -10000 0 -0.025 128 128
response to hypoxia -0.013 0.026 -10000 0 -0.063 96 96
Tie2/Ang1/GRB14 -0.14 0.37 -10000 0 -0.9 96 96
alpha5/beta1 Integrin 0.029 0.043 -10000 0 -0.14 21 21
FGF2 0.035 0.017 -10000 0 -0.014 47 47
STAT5A (dimer) -0.24 0.44 -10000 0 -0.82 170 170
mol:L-citrulline -0.12 0.32 0.38 3 -0.59 137 140
AGTR1 0.022 0.034 -10000 0 -0.048 92 92
MAPK14 -0.16 0.37 -10000 0 -0.9 96 96
Tie2/SHP2 -0.08 0.24 -10000 0 -0.84 33 33
TEK -0.086 0.25 -10000 0 -0.96 30 30
RPS6KB1 -0.2 0.37 -10000 0 -0.77 136 136
Angiotensin II/AT1 0.014 0.036 0.085 1 -0.061 69 70
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -0.9 96 96
MAPK3 -0.15 0.34 -10000 0 -0.84 96 96
MAPK1 -0.15 0.34 -10000 0 -0.84 96 96
Tie2/Ang1/GRB7 -0.14 0.38 -10000 0 -0.91 96 96
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.15 0.36 -10000 0 -0.89 96 96
PI3K -0.24 0.44 -10000 0 -0.91 133 133
FES -0.16 0.38 -10000 0 -0.9 97 97
Crk/Dok-R -0.14 0.36 -10000 0 -0.86 96 96
Tie2/Ang1/ABIN2 -0.14 0.38 -10000 0 -0.9 96 96
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.2 0.36 -10000 0 -0.74 141 141
STAT5A 0.036 0.004 -10000 0 0 5 5
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.37 -10000 0 -0.77 136 136
Tie2/Ang2 -0.29 0.5 -10000 0 -0.98 161 161
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 96 96
FOXO1 -0.22 0.39 -10000 0 -0.75 166 166
ELF1 0.028 0.036 0.11 4 -0.046 81 85
ELF2 -0.14 0.35 -10000 0 -0.87 96 96
mol:Choline -0.15 0.35 -10000 0 -0.86 96 96
cell migration -0.066 0.097 -10000 0 -0.21 137 137
FYN -0.25 0.41 -10000 0 -0.81 164 164
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.17 0.32 0.39 3 -0.62 147 150
ETS1 -0.002 0.12 -10000 0 -0.25 93 93
PXN -0.17 0.31 -10000 0 -0.65 134 134
ITGB1 0.027 0.017 -10000 0 0 142 142
NOS3 -0.15 0.35 0.4 1 -0.67 135 136
RAC1 0.025 0.017 -10000 0 0 162 162
TNF -0.003 0.12 -10000 0 -0.25 92 92
MAPKKK cascade -0.15 0.35 -10000 0 -0.86 96 96
RASA1 0.035 0.009 -10000 0 0 30 30
Tie2/Ang1/Shc -0.15 0.37 -10000 0 -0.91 96 96
NCK1 0.035 0.008 -10000 0 0 27 27
vasculogenesis -0.11 0.29 0.36 4 -0.53 138 142
mol:Phosphatidic acid -0.15 0.35 -10000 0 -0.86 96 96
mol:Angiotensin II -0.004 0.013 0.023 2 -0.032 75 77
mol:NADP -0.12 0.32 0.38 3 -0.59 137 140
Rac1/GTP -0.18 0.34 -10000 0 -0.7 132 132
MMP2 -0.15 0.36 -10000 0 -0.9 96 96
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 -0.022 0.15 0.2 87 -0.26 92 179
PTK2B 0.036 0.006 -10000 0 0 16 16
mol:Ca2+ -0.099 0.24 -10000 0 -0.57 52 52
EDN1 0.004 0.093 0.14 13 -0.16 105 118
EDN3 0.033 0.011 -10000 0 0 53 53
EDN2 0.036 0.006 -10000 0 0 12 12
HRAS/GDP -0.014 0.17 0.31 16 -0.37 55 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.003 0.12 0.2 18 -0.26 55 73
ADCY4 -0.037 0.098 0.14 38 -0.2 105 143
ADCY5 -0.037 0.098 0.14 38 -0.2 105 143
ADCY6 -0.009 0.13 0.19 87 -0.23 67 154
ADCY7 -0.015 0.13 0.2 60 -0.24 68 128
ADCY1 -0.001 0.11 0.2 45 -0.25 40 85
ADCY2 -0.008 0.13 0.19 85 -0.24 68 153
ADCY3 -0.037 0.098 0.14 38 -0.2 105 143
ADCY8 -0.012 0.13 0.19 78 -0.23 61 139
ADCY9 -0.01 0.13 0.21 54 -0.24 67 121
arachidonic acid secretion -0.079 0.26 0.32 25 -0.53 95 120
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.11 0.19 10 -0.26 46 56
GNAO1 0.031 0.014 -10000 0 0 87 87
HRAS 0.034 0.01 -10000 0 0 36 36
ETA receptor/Endothelin-1/G12/GTP 0.005 0.12 -10000 0 -0.22 76 76
ETA receptor/Endothelin-1/Gs/GTP 0.004 0.12 -10000 0 -0.21 108 108
mol:GTP 0 0.007 0.026 3 -0.026 3 6
COL3A1 -0.077 0.16 0.18 10 -0.37 103 113
EDNRB 0.023 0.045 0.097 61 -0.084 47 108
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.018 0.14 0.21 76 -0.26 88 164
CYSLTR1 -0.036 0.12 0.19 44 -0.24 104 148
SLC9A1 -0.014 0.087 0.13 31 -0.16 107 138
mol:GDP -0.022 0.17 0.3 20 -0.39 54 74
SLC9A3 -0.11 0.28 -10000 0 -0.65 78 78
RAF1 -0.034 0.2 0.31 25 -0.42 81 106
JUN -0.14 0.32 0.48 1 -0.65 108 109
JAK2 -0.022 0.14 0.21 68 -0.26 88 156
mol:IP3 -0.001 0.12 0.23 15 -0.29 38 53
ETA receptor/Endothelin-1 -0.022 0.15 -10000 0 -0.27 116 116
PLCB1 0.032 0.014 -10000 0 -0.004 58 58
PLCB2 0.029 0.023 -10000 0 -0.023 79 79
ETA receptor/Endothelin-3 0.006 0.09 -10000 0 -0.15 109 109
FOS -0.094 0.35 0.39 19 -0.84 83 102
Gai/GDP -0.069 0.27 -10000 0 -0.73 67 67
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca ++ -0.018 0.18 0.26 56 -0.34 76 132
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 0 0.13 0.24 26 -0.3 40 66
GNAQ 0.027 0.026 -10000 0 -0.034 70 70
GNAZ 0.031 0.013 -10000 0 0 80 80
GNAL 0.036 0.006 -10000 0 0 14 14
Gs family/GDP -0.011 0.16 0.28 19 -0.36 54 73
ETA receptor/Endothelin-1/Gq/GTP -0.005 0.13 0.21 13 -0.27 58 71
MAPK14 -0.011 0.1 0.18 6 -0.26 43 49
TRPC6 -0.1 0.25 -10000 0 -0.61 49 49
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
GNAI1 0.018 0.018 -10000 0 0 261 261
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.001 0.1 0.18 14 -0.25 43 57
ETB receptor/Endothelin-2 0.017 0.071 -10000 0 -0.12 87 87
ETB receptor/Endothelin-3 0.015 0.07 -10000 0 -0.12 80 80
ETB receptor/Endothelin-1 -0.001 0.1 0.18 26 -0.17 97 123
MAPK3 -0.076 0.32 0.38 20 -0.73 84 104
MAPK1 -0.09 0.34 0.38 19 -0.77 86 105
Rac1/GDP -0.009 0.15 0.31 15 -0.38 38 53
cAMP biosynthetic process 0.018 0.12 0.21 63 -0.22 48 111
MAPK8 -0.13 0.3 0.37 1 -0.57 130 131
SRC 0.034 0.009 -10000 0 0 34 34
ETB receptor/Endothelin-1/Gi/GTP -0.03 0.14 0.16 5 -0.35 57 62
p130Cas/CRK/Src/PYK2 -0.019 0.18 0.35 12 -0.48 42 54
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.013 0.15 0.31 13 -0.38 42 55
COL1A2 -0.052 0.17 0.22 1 -0.47 58 59
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.005 0.093 -10000 0 -0.15 117 117
mol:DAG -0.001 0.12 0.23 15 -0.29 38 53
MAP2K2 -0.052 0.26 0.34 32 -0.56 82 114
MAP2K1 -0.063 0.26 0.34 22 -0.58 85 107
EDNRA -0.011 0.11 0.14 25 -0.2 105 130
positive regulation of muscle contraction 0.027 0.15 0.22 146 -0.24 58 204
Gq family/GDP 0.006 0.16 0.31 5 -0.37 50 55
HRAS/GTP -0.014 0.16 0.28 24 -0.36 56 80
PRKCH -0.006 0.12 0.25 16 -0.31 38 54
RAC1 0.025 0.017 -10000 0 0 162 162
PRKCA -0.009 0.12 0.22 18 -0.31 40 58
PRKCB -0.003 0.12 0.22 17 -0.29 44 61
PRKCE -0.01 0.12 0.22 17 -0.3 42 59
PRKCD -0.004 0.13 0.26 23 -0.3 39 62
PRKCG -0.01 0.12 0.22 17 -0.31 40 57
regulation of vascular smooth muscle contraction -0.12 0.42 0.43 14 -1 83 97
PRKCQ -0.002 0.11 0.25 20 -0.3 31 51
PLA2G4A -0.089 0.28 0.34 20 -0.58 95 115
GNA14 0.027 0.026 -10000 0 -0.034 70 70
GNA15 0.031 0.019 -10000 0 -0.035 24 24
GNA12 0.023 0.018 -10000 0 0 188 188
GNA11 0.032 0.017 -10000 0 -0.036 16 16
Rac1/GTP 0.007 0.12 -10000 0 -0.22 73 73
MMP1 0.02 0.075 0.19 30 -10000 0 30
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.034 0.01 -10000 0 0 41 41
GNB1/GNG2 -0.046 0.077 -10000 0 -0.17 134 134
AKT1 -0.004 0.16 0.27 37 -0.27 52 89
EGF 0.035 0.008 -10000 0 0 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.016 0.067 0.24 23 -0.17 3 26
mol:Ca2+ -0.001 0.19 0.32 33 -0.27 136 169
LYN -0.016 0.07 0.25 22 -0.17 6 28
RhoA/GTP 0 0.083 0.16 26 -0.13 97 123
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.017 0.2 0.35 32 -0.32 130 162
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.035 0.008 -10000 0 0 25 25
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.076 -10000 0 -0.24 32 32
G beta5/gamma2 -0.054 0.1 -10000 0 -0.22 134 134
PRKCH -0.016 0.2 0.35 25 -0.32 137 162
DNM1 0.035 0.008 -10000 0 0 26 26
TXA2/TP beta/beta Arrestin3 0.015 0.018 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.005 57 -0.002 5 62
PTGDR 0.035 0.008 -10000 0 0 28 28
G12 family/GTP -0.044 0.14 -10000 0 -0.28 102 102
ADRBK1 0.036 0.005 -10000 0 0 10 10
ADRBK2 0.035 0.009 -10000 0 0 29 29
RhoA/GTP/ROCK1 0.044 0.027 -10000 0 -0.13 10 10
mol:GDP -0.008 0.13 0.4 15 -0.26 22 37
mol:NADP 0.025 0.017 -10000 0 0 167 167
RAB11A 0.036 0.007 -10000 0 0 17 17
PRKG1 0.026 0.017 -10000 0 0 147 147
mol:IP3 -0.013 0.22 0.37 24 -0.33 136 160
cell morphogenesis 0.044 0.027 -10000 0 -0.13 10 10
PLCB2 -0.036 0.27 0.41 21 -0.44 136 157
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.015 0.069 0.24 26 -10000 0 26
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.02 0.054 0.23 12 -0.17 8 20
RHOA 0.035 0.007 -10000 0 0 21 21
PTGIR 0.035 0.009 -10000 0 0 32 32
PRKCB1 -0.017 0.22 0.36 26 -0.34 133 159
GNAQ 0.035 0.009 -10000 0 0 30 30
mol:L-citrulline 0.025 0.017 -10000 0 0 167 167
TXA2/TXA2-R family -0.048 0.28 0.41 22 -0.47 136 158
LCK -0.016 0.067 0.25 23 -10000 0 23
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.032 0.039 0.19 3 -10000 0 3
TXA2-R family/G12 family/GDP/G beta/gamma -0.02 0.14 -10000 0 -0.46 45 45
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.041 0.19 3 -0.15 1 4
MAPK14 -0.004 0.15 0.28 36 -0.22 129 165
TGM2/GTP -0.016 0.24 0.4 23 -0.37 127 150
MAPK11 -0.006 0.15 0.28 33 -0.22 128 161
ARHGEF1 0.01 0.12 0.21 53 -0.17 99 152
GNAI2 0.034 0.01 -10000 0 0 44 44
JNK cascade -0.021 0.22 0.37 27 -0.35 136 163
RAB11/GDP 0.034 0.009 -10000 0 -0.007 22 22
ICAM1 -0.005 0.18 0.3 42 -0.27 127 169
cAMP biosynthetic process -0.013 0.2 0.35 24 -0.31 128 152
Gq family/GTP/EBP50 0.013 0.054 0.24 7 -0.16 31 38
actin cytoskeleton reorganization 0.044 0.027 -10000 0 -0.13 10 10
SRC -0.02 0.055 0.21 18 -10000 0 18
GNB5 0.035 0.008 -10000 0 0 23 23
GNB1 0.035 0.007 -10000 0 0 20 20
EGF/EGFR -0.009 0.11 0.28 21 -0.23 41 62
VCAM1 -0.023 0.21 0.3 43 -0.33 136 179
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.076 -10000 0 -0.24 32 32
platelet activation -0.009 0.19 0.35 30 -0.28 130 160
PGI2/IP 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.014 0.023 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.006 0.067 -10000 0 -0.21 32 32
TXA2/TP beta/beta Arrestin2 0.004 0.049 -10000 0 -0.26 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.02 -10000 0 -10000 0 0
mol:DAG -0.022 0.24 0.38 24 -0.37 138 162
EGFR 0.009 0.016 -10000 0 0 380 380
TXA2/TP alpha -0.029 0.26 0.41 21 -0.41 128 149
Gq family/GTP 0.009 0.047 0.21 9 -0.29 2 11
YES1 -0.015 0.069 0.25 22 -0.17 3 25
GNAI2/GTP 0.007 0.048 -10000 0 -0.14 1 1
PGD2/DP 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.009 -10000 0 0 36 36
FYN -0.017 0.07 0.25 22 -0.17 7 29
mol:NO 0.025 0.017 -10000 0 0 167 167
GNA15 0.033 0.011 -10000 0 0 51 51
PGK/cGMP 0.028 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.01 -10000 0 -0.006 26 26
TP alpha/TGM2/GDP/G beta/gamma 0.029 0.042 0.18 2 -10000 0 2
NOS3 0.025 0.017 -10000 0 0 167 167
RAC1 0.025 0.017 -10000 0 0 162 162
PRKCA -0.015 0.2 0.34 26 -0.32 135 161
PRKCB -0.016 0.21 0.33 31 -0.32 136 167
PRKCE -0.017 0.21 0.34 27 -0.33 133 160
PRKCD -0.019 0.22 0.35 30 -0.35 134 164
PRKCG -0.022 0.22 0.36 24 -0.35 137 161
muscle contraction -0.042 0.26 0.4 22 -0.43 138 160
PRKCZ -0.016 0.2 0.33 32 -0.31 136 168
ARR3 0.037 0 -10000 0 -10000 0 0
TXA2/TP beta 0.036 0.038 0.19 2 -0.14 1 3
PRKCQ -0.026 0.2 0.35 25 -0.32 128 153
MAPKKK cascade -0.032 0.24 0.39 22 -0.39 138 160
SELE -0.01 0.18 0.3 36 -0.27 134 170
TP beta/GNAI2/GDP/G beta/gamma 0.025 0.053 0.19 2 -0.17 13 15
ROCK1 0.036 0.006 -10000 0 0 15 15
GNA14 0.035 0.009 -10000 0 0 29 29
chemotaxis -0.068 0.32 0.44 21 -0.56 136 157
GNA12 0.023 0.018 -10000 0 0 188 188
GNA13 0.035 0.007 -10000 0 0 20 20
GNA11 0.033 0.011 -10000 0 0 51 51
Rac1/GTP 0.017 0.02 -10000 0 -0.14 5 5
HIF-2-alpha transcription factor network

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
MMP14 -0.02 0.17 -10000 0 -0.67 30 30
oxygen homeostasis 0.004 0.021 0.045 66 -0.024 26 92
TCEB2 0.036 0.004 -10000 0 0 7 7
TCEB1 0.035 0.007 -10000 0 0 22 22
VHL/Elongin B/Elongin C/HIF2A 0.003 0.14 0.3 23 -0.23 55 78
EPO -0.043 0.2 0.4 17 -0.44 52 69
FIH (dimer) 0.015 0.039 0.11 18 -0.04 59 77
APEX1 0.016 0.043 0.11 8 -0.05 41 49
SERPINE1 -0.077 0.2 0.32 7 -0.45 84 91
FLT1 -0.014 0.16 -10000 0 -0.65 28 28
ADORA2A -0.038 0.24 0.44 35 -0.42 77 112
germ cell development -0.037 0.23 0.4 41 -0.41 80 121
SLC11A2 -0.035 0.25 0.42 43 -0.43 79 122
BHLHE40 -0.04 0.24 0.41 40 -0.42 80 120
HIF1AN 0.016 0.039 0.11 18 -0.04 59 77
HIF2A/ARNT/SIRT1 -0.017 0.17 0.35 25 -0.29 61 86
ETS1 0.047 0.033 0.12 43 -0.11 11 54
CITED2 -0.056 0.26 -10000 0 -0.82 48 48
KDR -0.002 0.16 -10000 0 -0.83 16 16
PGK1 -0.041 0.26 0.43 42 -0.44 86 128
SIRT1 0.024 0.017 -10000 0 0 172 172
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.03 0.27 0.48 13 -0.47 80 93
EPAS1 0 0.13 0.31 35 -0.22 63 98
SP1 0.041 0.011 0.11 8 -10000 0 8
ABCG2 -0.047 0.26 0.43 40 -0.44 96 136
EFNA1 -0.041 0.24 0.41 38 -0.44 81 119
FXN -0.04 0.24 0.44 35 -0.41 79 114
POU5F1 -0.04 0.24 0.41 40 -0.42 80 120
neuron apoptosis 0.03 0.26 0.46 79 -0.47 13 92
EP300 0.033 0.011 -10000 0 0 50 50
EGLN3 0.019 0.04 0.11 15 -0.04 62 77
EGLN2 0.022 0.042 0.11 20 -0.039 61 81
EGLN1 0.022 0.042 0.11 19 -0.04 68 87
VHL/Elongin B/Elongin C 0.045 0.024 -10000 0 -0.12 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.016 0.043 0.11 7 -0.05 43 50
SLC2A1 -0.052 0.24 0.44 27 -0.44 81 108
TWIST1 -0.065 0.21 0.39 19 -0.43 87 106
ELK1 0.038 0.036 0.12 29 -0.095 25 54
HIF2A/ARNT/Cbp/p300 0 0.19 0.38 31 -0.3 64 95
VEGFA -0.04 0.24 0.41 40 -0.42 80 120
CREBBP 0.036 0.005 -10000 0 0 9 9
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.025 0.017 -10000 0 0 166 166
HRAS 0.034 0.009 -10000 0 0 36 36
EGFR 0.009 0.016 -10000 0 0 380 380
AKT 0.092 0.12 0.25 128 -0.18 11 139
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.033 0.011 -10000 0 0 54 54
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.035 0.007 -10000 0 0 20 20
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.023 0.018 -10000 0 0 189 189
PIK3CA 0.031 0.014 -10000 0 0 82 82
PIK3CB 0.036 0.007 -10000 0 0 17 17
NRAS 0.032 0.012 -10000 0 0 63 63
PIK3CG 0.025 0.017 -10000 0 0 164 164
PIK3R3 0.036 0.006 -10000 0 0 15 15
PIK3R2 0.035 0.008 -10000 0 0 26 26
NF1 0.037 0.003 -10000 0 0 4 4
RAS -0.003 0.054 0.14 3 -0.24 11 14
ERBB2 0.036 0.004 -10000 0 0 6 6
proliferation/survival/translation -0.026 0.052 0.22 4 -0.2 13 17
PI3K 0.04 0.093 0.22 77 -0.15 12 89
PIK3R1 0.032 0.012 -10000 0 0 63 63
KRAS 0.034 0.009 -10000 0 0 35 35
FOXO 0.095 0.093 0.2 169 -10000 0 169
AKT2 0.035 0.008 -10000 0 0 28 28
PTEN 0.025 0.017 -10000 0 0 166 166
TCGA08_p53

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
CDKN2A -0.001 0.004 0 449 -10000 0 449
TP53 0.005 0.032 -10000 0 -0.23 7 7
Senescence 0.004 0.034 -10000 0 -0.22 9 9
Apoptosis 0.004 0.034 -10000 0 -0.22 9 9
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.019 0.3 2 -10000 0 2
MDM4 0.034 0.01 -10000 0 0 37 37
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.009 -10000 0 0 36 36
EGFR 0.009 0.016 -10000 0 0 380 380
EGF/EGFR 0 0.054 -10000 0 -0.11 65 65
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.058 -10000 0 -0.12 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.016 -10000 0 0 123 123
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.035 0.008 -10000 0 0 25 25
EGF/EGFR dimer/SHC 0 0.056 -10000 0 -0.13 61 61
mol:GDP 0.004 0.056 -10000 0 -0.12 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.033 0.011 -10000 0 0 52 52
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
HRAS/GTP -0.004 0.052 -10000 0 -0.12 69 69
SHC1 0.033 0.011 -10000 0 0 52 52
HRAS/GDP -0.001 0.058 -10000 0 -0.12 69 69
FRAP1 0.092 0.12 0.18 303 -0.19 4 307
EGF/EGFR dimer -0.005 0.057 -10000 0 -0.14 64 64
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 18 18
ETA receptor/Endothelin-1 0.023 0.06 -10000 0 -0.14 51 51
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.034 0.01 -9999 0 0 40 40
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.036 0.004 -9999 0 0 7 7
TCEB1 0.035 0.007 -9999 0 0 22 22
HIF1A/p53 -0.062 0.14 -9999 0 -0.27 137 137
HIF1A -0.058 0.12 -9999 0 -0.28 119 119
COPS5 0.036 0.006 -9999 0 0 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2 0.047 0.06 -9999 0 -0.13 22 22
FIH (dimer) 0.026 0.017 -9999 0 0 154 154
CDKN2A 0.004 0.012 -9999 0 0 449 449
ARNT/IPAS 0.05 0.015 -9999 0 -10000 0 0
HIF1AN 0.026 0.017 -9999 0 0 154 154
GNB2L1 0.037 0.002 -9999 0 0 2 2
HIF1A/ARNT -0.06 0.14 -9999 0 -0.28 138 138
CUL2 0.026 0.017 -9999 0 0 156 156
OS9 0.032 0.013 -9999 0 0 73 73
RACK1/Elongin B/Elongin C 0.068 0.032 -9999 0 -0.14 10 10
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.074 0.13 -9999 0 -0.27 139 139
PHD1-3/OS9 0.062 0.065 -9999 0 -0.14 30 30
HIF1A/RACK1/Elongin B/Elongin C -0.041 0.15 -9999 0 -0.27 137 137
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.062 0.14 -9999 0 -0.28 141 141
EGLN3 0.03 0.014 -9999 0 0 92 92
EGLN2 0.035 0.009 -9999 0 0 29 29
EGLN1 0.034 0.009 -9999 0 0 34 34
TP53 0.032 0.013 -9999 0 0 73 73
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.005 0.1 -9999 0 -0.61 12 12
ARNT 0.036 0.004 -9999 0 0 6 6
ARD1A 0.037 0.003 -9999 0 0 4 4
RBX1 0.033 0.011 -9999 0 0 47 47
HIF1A/p19ARF -0.064 0.12 -9999 0 -0.26 117 117
Effects of Botulinum toxin

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
STX1A -0.008 0.006 0 178 -10000 0 178
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.04 0.04 -10000 0 -0.14 18 18
STXBP1 0.029 0.015 -10000 0 0 107 107
ACh/CHRNA1 0.028 0.054 0.097 55 -0.076 90 145
RAB3GAP2/RIMS1/UNC13B 0.053 0.05 -10000 0 -0.13 23 23
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 0.035 0.007 -10000 0 0 21 21
mol:ACh 0.018 0.066 0.098 150 -0.09 87 237
RAB3GAP2 0.035 0.009 -10000 0 0 29 29
STX1A/SNAP25/VAMP2 0.025 0.1 0.18 18 -0.16 75 93
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.054 0.096 55 -0.076 90 145
UNC13B 0.032 0.013 -10000 0 0 69 69
CHRNA1 0.035 0.007 -10000 0 0 18 18
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.014 0.043 0.1 22 -0.086 40 62
SNAP25 0.002 0.003 -10000 0 0 274 274
VAMP2 0.004 0.001 -10000 0 0 49 49
SYT1 0.018 0.018 -10000 0 0 264 264
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.017 0.016 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.1 0.18 18 -0.16 75 93
Syndecan-3-mediated signaling events

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.036 0.006 -9999 0 0 13 13
Syndecan-3/Src/Cortactin -0.026 0.18 -9999 0 -0.45 74 74
Syndecan-3/Neurocan -0.066 0.18 -9999 0 -0.48 79 79
POMC 0.036 0.006 -9999 0 0 13 13
EGFR 0.009 0.016 -9999 0 0 380 380
Syndecan-3/EGFR -0.058 0.16 -9999 0 -0.42 78 78
AGRP 0.036 0.005 -9999 0 0 8 8
NCSTN 0.035 0.009 -9999 0 0 29 29
PSENEN 0.035 0.009 -9999 0 0 31 31
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.036 0.006 -9999 0 0 15 15
APH1A 0.036 0.006 -9999 0 0 12 12
NCAN 0 0 -9999 0 -10000 0 0
long-term memory -0.034 0.2 -9999 0 -0.5 79 79
Syndecan-3/IL8 -0.057 0.18 -9999 0 -0.48 79 79
PSEN1 0.033 0.011 -9999 0 0 47 47
Src/Cortactin 0.049 0.018 -9999 0 -0.14 1 1
FYN 0.03 0.014 -9999 0 0 88 88
limb bud formation -0.067 0.18 -9999 0 -0.5 79 79
MC4R 0.035 0.007 -9999 0 0 21 21
SRC 0.034 0.009 -9999 0 0 34 34
PTN 0.022 0.018 -9999 0 0 204 204
FGFR/FGF/Syndecan-3 -0.067 0.19 -9999 0 -0.5 79 79
neuron projection morphogenesis -0.072 0.16 -9999 0 -0.45 70 70
Syndecan-3/AgRP -0.044 0.19 -9999 0 -0.49 79 79
Syndecan-3/AgRP/MC4R -0.025 0.2 -9999 0 -0.48 78 78
Fyn/Cortactin 0.029 0.062 -9999 0 -0.15 53 53
SDC3 -0.068 0.19 -9999 0 -0.51 79 79
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.056 0.18 -9999 0 -0.47 79 79
IL8 0.019 0.018 -9999 0 0 244 244
Syndecan-3/Fyn/Cortactin -0.034 0.21 -9999 0 -0.51 79 79
Syndecan-3/CASK -0.066 0.18 -9999 0 -0.48 79 79
alpha-MSH/MC4R 0.051 0.014 -9999 0 -10000 0 0
Gamma Secretase 0.08 0.072 -9999 0 -0.16 28 28
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.017 0.032 0.082 4 -0.056 53 57
PDGF/PDGFRA/CRKL 0.007 0.069 -10000 0 -0.14 68 68
positive regulation of JUN kinase activity 0.024 0.063 -10000 0 -0.12 69 69
CRKL 0.035 0.008 -10000 0 0 28 28
PDGF/PDGFRA/Caveolin-3 0.009 0.069 -10000 0 -0.14 68 68
AP1 -0.079 0.24 0.3 12 -0.59 77 89
mol:IP3 -0.015 0.047 0.096 25 -0.12 39 64
PLCG1 -0.015 0.047 0.096 25 -0.12 39 64
PDGF/PDGFRA/alphaV Integrin 0.004 0.077 -10000 0 -0.16 78 78
RAPGEF1 0.035 0.007 -10000 0 0 18 18
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca2+ -0.015 0.047 0.096 25 -0.12 39 64
CAV3 0.036 0.005 -10000 0 0 11 11
CAV1 0.016 0.018 -10000 0 0 288 288
SHC/Grb2/SOS1 0.028 0.065 -10000 0 -0.12 69 69
PDGF/PDGFRA/Shf -0.005 0.055 -10000 0 -0.11 95 95
FOS -0.093 0.22 0.29 3 -0.6 72 75
JUN -0.026 0.058 0.21 10 -0.2 18 28
oligodendrocyte development 0.003 0.077 -10000 0 -0.16 78 78
GRB2 0.035 0.007 -10000 0 0 18 18
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:DAG -0.015 0.047 0.096 25 -0.12 39 64
PDGF/PDGFRA 0.017 0.032 0.082 4 -0.056 53 57
actin cytoskeleton reorganization 0.006 0.067 -10000 0 -0.14 66 66
SRF -0.015 0.021 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 52 52
PI3K 0.007 0.091 -10000 0 -0.15 107 107
PDGF/PDGFRA/Crk/C3G 0.027 0.073 -10000 0 -0.13 76 76
JAK1 -0.006 0.03 0.082 31 -10000 0 31
ELK1/SRF -0.02 0.084 0.14 67 -0.16 59 126
SHB 0.033 0.011 -10000 0 0 51 51
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.034 -10000 0 -0.032 101 101
GO:0007205 -0.028 0.071 0.11 25 -0.2 55 80
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.063 -10000 0 -0.12 69 69
PDGF/PDGFRA/SHB 0.006 0.067 -10000 0 -0.14 66 66
PDGF/PDGFRA/Caveolin-1 -0.015 0.078 -10000 0 -0.17 88 88
ITGAV 0.035 0.009 -10000 0 0 31 31
ELK1 -0.033 0.069 0.13 7 -0.16 84 91
PIK3CA 0.031 0.014 -10000 0 0 82 82
PDGF/PDGFRA/Crk 0.005 0.074 -10000 0 -0.15 77 77
JAK-STAT cascade -0.006 0.03 0.082 31 -10000 0 31
cell proliferation -0.005 0.055 -10000 0 -0.11 95 95
Canonical Wnt signaling pathway

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
HDAC1 0.033 0.046 0.12 68 -0.039 84 152
AES 0.032 0.042 0.11 65 -0.036 80 145
FBXW11 0.035 0.007 -10000 0 0 22 22
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -10000 0 0
SMAD4 0.033 0.012 -10000 0 0 59 59
DKK2 0.035 0.009 -10000 0 0 31 31
TLE1 0.032 0.042 0.11 67 -0.036 85 152
MACF1 0.034 0.011 -10000 0 0 50 50
CTNNB1 0.048 0.11 0.27 21 -0.42 9 30
WIF1 0.028 0.015 -10000 0 0 112 112
beta catenin/RanBP3 0.074 0.16 0.42 65 -0.35 8 73
KREMEN2 0.036 0.005 -10000 0 0 9 9
DKK1 0.017 0.018 -10000 0 0 276 276
beta catenin/beta TrCP1 0.062 0.11 0.27 20 -0.4 10 30
FZD1 0.024 0.017 -10000 0 0 175 175
AXIN2 -0.024 0.094 -10000 0 -0.24 66 66
AXIN1 0.038 0.001 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
Axin1/APC/GSK3/beta catenin 0.017 0.16 -10000 0 -0.59 29 29
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.13 0.26 8 -0.44 18 26
Axin1/APC/GSK3 0.005 0.087 0.27 3 -0.38 16 19
Axin1/APC/GSK3/beta catenin/Macf1 0.033 0.14 0.27 10 -0.4 27 37
HNF1A 0.007 0.03 0.073 73 -0.046 1 74
CTBP1 0.031 0.042 0.11 61 -0.037 83 144
MYC -0.1 0.41 0.73 14 -1.3 51 65
RANBP3 0.035 0.008 -10000 0 0 22 22
DKK2/LRP6/Kremen 2 0.064 0.027 -10000 0 -0.12 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.03 0.039 0.11 59 -0.036 68 127
TCF3 0.033 0.043 0.11 67 -0.036 82 149
WNT1/LRP6/FZD1/Axin1 0.06 0.046 -10000 0 -10000 0 0
Ran/GTP 0.026 0.016 -10000 0 -0.13 5 5
CtBP/CBP/TCF/TLE1/AES 0.036 0.19 0.46 68 -0.35 18 86
LEF1 0.034 0.044 0.12 70 -0.037 86 156
DVL1 0.01 0.096 -10000 0 -0.47 14 14
CSNK2A1 0.033 0.011 -10000 0 0 51 51
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.009 0.16 0.27 7 -0.49 31 38
DKK1/LRP6/Kremen 2 0.031 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 40 40
CSNK1A1 0.035 0.047 0.12 69 -0.039 86 155
NLK 0.027 0.023 -10000 0 -0.032 57 57
CCND1 -0.083 0.36 0.89 2 -1.3 39 41
WNT1 0.036 0.007 -10000 0 0 18 18
GSK3A 0.035 0.009 -10000 0 0 28 28
GSK3B 0.034 0.01 -10000 0 0 39 39
FRAT1 0.025 0.017 -10000 0 0 161 161
PPP2R5D 0.025 0.042 -10000 0 -0.24 6 6
APC 0.041 0.11 0.18 163 -10000 0 163
WNT1/LRP6/FZD1 0.002 0.046 -10000 0 -0.24 10 10
CREBBP 0.034 0.043 0.11 68 -0.036 86 154
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.027 -10000 0 -0.052 58 58
CDKN2C -0.009 0.021 -10000 0 -0.035 124 124
CDKN2A 0.005 0.014 -10000 0 -10000 0 0
CCND2 -0.002 0.019 0.11 6 -10000 0 6
RB1 -0.047 0.092 0.16 2 -0.19 144 146
CDK4 -0.001 0.021 0.13 6 -10000 0 6
CDK6 -0.001 0.02 0.13 6 -10000 0 6
G1/S progression 0.057 0.098 0.19 165 -0.16 2 167
Arf6 signaling 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
CENTA1/KIF3B 0.014 0.035 -10000 0 -0.11 38 38
ARNO/beta Arrestin1-2 0.042 0.025 -10000 0 -0.095 7 7
EGFR 0.009 0.016 -10000 0 0 380 380
EPHA2 0.033 0.011 -10000 0 0 55 55
USP6 0.035 0.007 -10000 0 0 18 18
IQSEC1 0.036 0.007 -10000 0 0 19 19
EGFR/EGFR/EGF/EGF -0.005 0.057 -10000 0 -0.14 64 64
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
mol:GTP 0.002 0.011 -10000 0 -0.066 1 1
ARRB1 0.036 0.005 -10000 0 0 11 11
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.033 0.011 -10000 0 0 51 51
EGF 0.035 0.008 -10000 0 0 25 25
somatostatin receptor activity 0 0 0.001 138 0 5 143
ARAP2 0 0 0 88 0 3 91
mol:GDP 0.068 0.068 0.16 121 -0.2 1 122
mol:PI-3-4-5-P3 0 0 0 124 0 4 128
ITGA2B 0.037 0.003 -10000 0 0 3 3
ARF6 0.035 0.009 -10000 0 0 29 29
Ephrin A1/EPHA2/NCK1/GIT1 0.075 0.055 -10000 0 -0.13 25 25
ADAP1 0 0 0 62 0 1 63
KIF13B 0.032 0.012 -10000 0 0 63 63
HGF/MET 0.032 0.027 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 7 7
ARF6/GTP 0.084 0.088 0.2 124 -0.21 4 128
EGFR/EGFR/EGF/EGF/ARFGEP100 0.001 0.056 -10000 0 -0.13 62 62
ADRB2 0.034 0.01 -10000 0 0 40 40
receptor agonist activity 0 0 0 134 0 3 137
actin filament binding 0 0 0 135 0 5 140
SRC 0.034 0.009 -10000 0 0 34 34
ITGB3 0.037 0.003 -10000 0 0 4 4
GNAQ 0.035 0.009 -10000 0 0 30 30
EFA6/PI-4-5-P2 0.001 0.001 0.001 161 -0.001 3 164
ARF6/GDP 0.035 0.063 0.16 13 -0.19 16 29
ARF6/GDP/GULP/ACAP1 0.055 0.074 0.21 15 -0.19 1 16
alphaIIb/beta3 Integrin/paxillin/GIT1 0.093 0.01 -10000 0 -10000 0 0
ACAP1 0 0 0 49 -10000 0 49
ACAP2 0 0 0 74 0 3 77
LHCGR/beta Arrestin2 0.03 0.024 -10000 0 -0.14 7 7
EFNA1 0.033 0.011 -10000 0 0 52 52
HGF 0.024 0.018 -10000 0 0 177 177
CYTH3 0 0 0.001 137 -0.001 3 140
CYTH2 0 0.001 0.003 1 -0.004 5 6
NCK1 0.035 0.008 -10000 0 0 27 27
fibronectin binding 0 0 0 137 0 5 142
endosomal lumen acidification 0 0 0 135 0 3 138
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.025 0.017 -10000 0 0 168 168
GNAQ/ARNO 0.027 0.008 0.041 6 0 30 36
mol:Phosphatidic acid 0 0 0 74 0 3 77
PIP3-E 0.03 0.014 -10000 0 0 90 90
MET 0.023 0.018 -10000 0 0 189 189
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GIT1 0.037 0.003 -10000 0 0 3 3
mol:PI-4-5-P2 0 0 0.001 140 -0.001 4 144
GNA11 0.033 0.011 -10000 0 0 51 51
LHCGR 0.037 0.002 -10000 0 0 2 2
AGTR1 0.035 0.008 -10000 0 0 22 22
desensitization of G-protein coupled receptor protein signaling pathway 0.03 0.024 -10000 0 -0.14 7 7
IPCEF1/ARNO 0.007 0.044 -10000 0 -0.093 51 51
alphaIIb/beta3 Integrin 0.054 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.024 0.14 -10000 0 -0.36 23 23
MAP3K8 0.022 0.018 -10000 0 0 199 199
FOS 0.019 0.1 -10000 0 -0.35 15 15
PRKCA 0.029 0.026 -10000 0 -0.03 78 78
PTPN7 0.028 0.029 0.067 53 -0.03 90 143
HRAS 0.034 0.01 -10000 0 0 36 36
PRKCB 0 0.008 0.017 61 -0.012 79 140
NRAS 0.032 0.012 -10000 0 0 63 63
RAS family/GTP 0.041 0.067 -10000 0 -0.14 54 54
MAPK3 0.035 0.05 -10000 0 -0.35 1 1
MAP2K1 0.008 0.057 -10000 0 -0.22 13 13
ELK1 0.026 0.029 -10000 0 -0.04 81 81
BRAF 0.007 0.021 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.003 61 -0.004 80 141
MAPK1 0.008 0.12 -10000 0 -0.44 30 30
RAF1 -0.001 0.068 -10000 0 -0.34 17 17
KRAS 0.034 0.009 -10000 0 0 35 35
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.032 0.16 -10000 0 -0.46 43 43
Syndecan-4/Syndesmos -0.14 0.28 -10000 0 -0.73 64 64
positive regulation of JNK cascade -0.13 0.26 -10000 0 -0.61 78 78
Syndecan-4/ADAM12 -0.13 0.28 -10000 0 -0.74 63 63
CCL5 0.033 0.011 -10000 0 0 54 54
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
DNM2 0.035 0.008 -10000 0 0 27 27
ITGA5 0.033 0.012 -10000 0 0 58 58
SDCBP 0.035 0.007 -10000 0 0 21 21
PLG 0.028 0.024 -10000 0 -0.047 25 25
ADAM12 0.024 0.017 -10000 0 0 176 176
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.024 0.022 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.28 -10000 0 -0.73 64 64
Syndecan-4/CXCL12/CXCR4 -0.14 0.28 -10000 0 -0.66 78 78
Syndecan-4/Laminin alpha3 -0.12 0.29 -10000 0 -0.72 64 64
MDK 0.03 0.014 -10000 0 0 92 92
Syndecan-4/FZD7 -0.14 0.3 -10000 0 -0.63 93 93
Syndecan-4/Midkine -0.13 0.3 -10000 0 -0.67 81 81
FZD7 0.026 0.017 -10000 0 0 143 143
Syndecan-4/FGFR1/FGF -0.096 0.28 -10000 0 -0.69 61 61
THBS1 0.03 0.014 -10000 0 0 93 93
integrin-mediated signaling pathway -0.13 0.28 -10000 0 -0.63 83 83
positive regulation of MAPKKK cascade -0.13 0.26 -10000 0 -0.61 78 78
Syndecan-4/TACI -0.12 0.29 -10000 0 -0.73 64 64
CXCR4 0.029 0.015 -10000 0 0 103 103
cell adhesion -0.01 0.055 0.21 3 -0.25 18 21
Syndecan-4/Dynamin -0.12 0.29 -10000 0 -0.72 64 64
Syndecan-4/TSP1 -0.13 0.28 -10000 0 -0.74 62 62
Syndecan-4/GIPC -0.12 0.29 -10000 0 -0.72 64 64
Syndecan-4/RANTES -0.13 0.29 -10000 0 -0.73 64 64
ITGB1 0.027 0.017 -10000 0 0 142 142
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.033 0.011 -10000 0 0 48 48
RAC1 0.025 0.017 -10000 0 0 162 162
PRKCA 0.004 0.12 1 6 -10000 0 6
Syndecan-4/alpha-Actinin -0.13 0.3 -10000 0 -0.65 86 86
TFPI 0.029 0.015 -10000 0 0 103 103
F2 0.01 0.042 -10000 0 -0.046 171 171
alpha5/beta1 Integrin 0.029 0.043 -10000 0 -0.14 21 21
positive regulation of cell adhesion -0.13 0.27 -10000 0 -0.69 64 64
ACTN1 0.028 0.016 -10000 0 0 119 119
TNC 0.028 0.016 -10000 0 0 121 121
Syndecan-4/CXCL12 -0.14 0.28 -10000 0 -0.73 63 63
FGF6 0.035 0.008 -10000 0 0 28 28
RHOA 0.035 0.007 -10000 0 0 21 21
CXCL12 0.022 0.018 -10000 0 0 204 204
TNFRSF13B 0.036 0.005 -10000 0 0 9 9
FGF2 0.035 0.008 -10000 0 0 25 25
FGFR1 0.036 0.005 -10000 0 0 9 9
Syndecan-4/PI-4-5-P2 -0.14 0.28 -10000 0 -0.73 64 64
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.028 0.025 -10000 0 -0.045 41 41
cell migration -0.011 0.016 -10000 0 -10000 0 0
PRKCD 0.029 0.024 -10000 0 -0.044 37 37
vasculogenesis -0.13 0.27 -10000 0 -0.7 62 62
SDC4 -0.14 0.3 -10000 0 -0.79 63 63
Syndecan-4/Tenascin C -0.14 0.3 -10000 0 -0.66 83 83
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.12 0.29 -10000 0 -0.73 65 65
MMP9 0.011 0.024 -10000 0 -0.042 39 39
Rac1/GTP -0.01 0.057 0.21 3 -0.26 18 21
cytoskeleton organization -0.13 0.26 -10000 0 -0.69 64 64
GIPC1 0.035 0.008 -10000 0 0 24 24
Syndecan-4/TFPI -0.13 0.29 -10000 0 -0.7 71 71
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.006 0.058 -10000 0 -0.15 61 61
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.096 0.21 11 -0.22 36 47
AP1 -0.01 0.076 0.09 16 -0.15 93 109
mol:PIP3 -0.024 0.05 -10000 0 -0.13 77 77
AKT1 0 0.094 0.2 21 -0.24 30 51
PTK2B -0.002 0.058 0.13 5 -0.15 58 63
RHOA 0.02 0.077 0.18 19 -0.32 12 31
PIK3CB 0.036 0.007 -10000 0 0 17 17
mol:Ca2+ -0.009 0.038 0.17 4 -0.14 16 20
MAGI3 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
apoptosis 0.002 0.063 0.1 36 -0.16 54 90
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
positive regulation of microtubule depolymerization -0.021 0.074 0.17 10 -0.18 59 69
NF kappa B1 p50/RelA -0.02 0.067 0.081 53 -0.17 52 105
endothelial cell migration -0.018 0.099 -10000 0 -0.3 54 54
ADCY4 -0.006 0.089 0.17 9 -0.25 37 46
ADCY5 -0.006 0.089 0.17 9 -0.25 37 46
ADCY6 0 0.09 0.16 15 -0.24 36 51
ADCY7 -0.004 0.095 0.16 15 -0.24 43 58
ADCY1 -0.01 0.08 0.15 9 -0.25 33 42
ADCY2 -0.002 0.092 0.16 15 -0.24 39 54
ADCY3 -0.006 0.089 0.17 9 -0.25 37 46
ADCY8 -0.003 0.09 0.16 14 -0.25 36 50
ADCY9 -0.001 0.091 0.16 15 -0.25 36 51
GSK3B -0.009 0.065 0.18 7 -0.16 57 64
arachidonic acid secretion -0.019 0.11 0.15 14 -0.28 53 67
GNG2 0 0.001 -10000 0 -0.003 10 10
TRIP6 -0.017 0.085 -10000 0 -0.25 57 57
GNAO1 0.003 0.058 0.12 24 -0.16 48 72
HRAS 0.034 0.009 -10000 0 0 36 36
NFKBIA -0.017 0.084 0.18 15 -0.22 37 52
GAB1 0.033 0.011 -10000 0 0 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.21 -10000 0 -0.8 31 31
JUN 0.034 0.01 -10000 0 0 41 41
LPA/LPA2/NHERF2 0.019 0.029 -10000 0 -0.062 54 54
TIAM1 -0.013 0.25 -10000 0 -0.98 31 31
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 -0.008 0.037 0.2 2 -0.14 19 21
PLCB3 0.006 0.036 0.2 5 -0.064 12 17
FOS 0.025 0.017 -10000 0 0 162 162
positive regulation of mitosis -0.019 0.11 0.15 14 -0.28 53 67
LPA/LPA1-2-3 -0.008 0.041 -10000 0 -0.13 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -0.002 1 1
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.009 0.068 -10000 0 -0.28 10 10
GNAZ 0.002 0.064 0.12 28 -0.17 49 77
EGFR/PI3K-beta/Gab1 -0.02 0.054 -10000 0 -0.13 78 78
positive regulation of dendritic cell cytokine production -0.008 0.041 -10000 0 -0.12 54 54
LPA/LPA2/MAGI-3 -0.004 0.017 -10000 0 -0.052 54 54
ARHGEF1 0.037 0.12 0.2 149 -0.17 34 183
GNAI2 0.004 0.07 0.13 40 -0.18 54 94
GNAI3 0.006 0.064 0.13 39 -0.16 54 93
GNAI1 0.003 0.046 0.13 18 -0.16 28 46
LPA/LPA3 -0.006 0.021 -10000 0 -0.067 54 54
LPA/LPA2 -0.006 0.021 -10000 0 -0.066 54 54
LPA/LPA1 -0.012 0.055 -10000 0 -0.17 54 54
HB-EGF/EGFR -0.013 0.059 -10000 0 -0.14 77 77
HBEGF 0.011 0.045 0.094 114 -10000 0 114
mol:DAG -0.008 0.037 0.2 2 -0.14 19 21
cAMP biosynthetic process 0.001 0.11 0.18 35 -0.27 42 77
NFKB1 0.036 0.007 -10000 0 0 18 18
SRC 0.034 0.009 -10000 0 0 34 34
GNB1 0.035 0.007 -10000 0 0 20 20
LYN -0.023 0.096 0.17 18 -0.23 62 80
GNAQ 0.008 0.026 0.057 38 -0.058 56 94
LPAR2 0 0.001 -10000 0 -0.003 3 3
LPAR3 0 0.001 -10000 0 -0.002 4 4
LPAR1 -0.01 0.033 -10000 0 -0.11 54 54
IL8 -0.13 0.2 0.32 8 -0.4 158 166
PTK2 0.013 0.057 0.12 38 -0.14 50 88
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
CASP3 0.002 0.063 0.1 36 -0.16 54 90
EGFR 0.009 0.016 -10000 0 0 380 380
PLCG1 0.005 0.038 0.074 7 -0.13 24 31
PLD2 0.015 0.054 0.12 38 -0.12 53 91
G12/G13 0.019 0.063 -10000 0 -0.15 46 46
PI3K-beta -0.014 0.068 -10000 0 -0.23 30 30
cell migration -0.001 0.073 -10000 0 -0.25 28 28
SLC9A3R2 0.036 0.005 -10000 0 0 8 8
PXN 0.008 0.069 -10000 0 -0.29 10 10
HRAS/GTP -0.019 0.11 0.16 9 -0.28 53 62
RAC1 0.025 0.017 -10000 0 0 162 162
MMP9 0.017 0.018 -10000 0 0 280 280
PRKCE 0.036 0.003 -10000 0 0 3 3
PRKCD -0.004 0.054 0.19 14 -0.2 3 17
Gi(beta/gamma) -0.01 0.12 0.17 12 -0.27 57 69
mol:LPA -0.01 0.033 -10000 0 -0.11 54 54
TRIP6/p130 Cas/FAK1/Paxillin -0.01 0.08 -10000 0 -0.26 30 30
MAPKKK cascade -0.019 0.11 0.15 14 -0.28 53 67
contractile ring contraction involved in cytokinesis 0.02 0.079 0.18 17 -0.32 13 30
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.026 0.057 37 -0.058 56 93
GNA15 0.008 0.025 0.056 34 -0.058 52 86
GNA12 0.023 0.018 -10000 0 0 188 188
GNA13 0.035 0.007 -10000 0 0 20 20
MAPT -0.021 0.076 0.17 10 -0.19 60 70
GNA11 0.011 0.023 0.057 38 -0.058 35 73
Rac1/GTP -0.008 0.22 -10000 0 -0.85 31 31
MMP2 -0.018 0.1 -10000 0 -0.31 54 54
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.005 0.1 0.24 51 -10000 0 51
GNAI2 0.034 0.01 -10000 0 0 44 44
S1P/S1P5/G12 0.01 0.031 -10000 0 -0.11 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
RhoA/GTP 0.005 0.11 -10000 0 -0.24 51 51
negative regulation of cAMP metabolic process -0.009 0.099 -10000 0 -0.2 83 83
GNAZ 0.031 0.013 -10000 0 0 80 80
GNAI3 0.036 0.006 -10000 0 0 14 14
GNA12 0.023 0.018 -10000 0 0 188 188
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.009 0.099 -10000 0 -0.2 83 83
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
RHOA 0.035 0.007 -10000 0 0 21 21
GNAI1 0.018 0.018 -10000 0 0 261 261
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
CDC42/GTP 0.005 0.1 -10000 0 -0.27 39 39
PLCG1 -0.012 0.095 0.12 5 -0.2 84 89
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
G12/G13 0.026 0.048 -10000 0 -0.14 28 28
cell migration 0.005 0.1 -10000 0 -0.26 39 39
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.013 0.098 0.12 4 -0.2 89 93
MAPK1 -0.007 0.092 0.12 5 -0.19 79 84
S1P/S1P5/Gi -0.009 0.099 -10000 0 -0.2 83 83
GNAI1 0.018 0.018 -10000 0 0 261 261
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.031 -10000 0 -0.11 28 28
RHOA 0.041 0.1 0.19 155 -0.18 2 157
S1P/S1P4/Gi -0.009 0.099 -10000 0 -0.2 83 83
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.031 0.013 -10000 0 0 80 80
S1P/S1P4/G12/G13 0.023 0.038 -10000 0 -0.1 28 28
GNA12 0.023 0.018 -10000 0 0 188 188
GNA13 0.035 0.007 -10000 0 0 20 20
CDC42 0.035 0.008 -10000 0 0 26 26
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.012 -10000 0 0 66 66
CCL5 0.033 0.011 -10000 0 0 54 54
SDCBP 0.035 0.007 -10000 0 0 21 21
FGFR/FGF2/Syndecan-1 0.015 0.1 0.21 24 -0.24 13 37
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 0.017 0.1 0.22 19 -0.24 14 33
Syndecan-1/Syntenin 0.026 0.11 0.23 27 -0.24 17 44
MAPK3 0.005 0.1 0.2 21 -0.23 21 42
HGF/MET 0.032 0.027 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.012 -10000 0 0 66 66
BSG 0.032 0.012 -10000 0 0 62 62
keratinocyte migration 0.017 0.1 0.22 19 -0.24 14 33
Syndecan-1/RANTES 0.021 0.11 0.24 19 -0.24 14 33
Syndecan-1/CD147 0.026 0.12 0.24 14 -0.24 20 34
Syndecan-1/Syntenin/PIP2 0.024 0.11 0.22 26 -0.23 17 43
LAMA5 0.032 0.012 -10000 0 0 67 67
positive regulation of cell-cell adhesion 0.023 0.11 0.22 26 -0.22 17 43
MMP7 0.027 0.016 -10000 0 0 138 138
HGF 0.024 0.018 -10000 0 0 177 177
Syndecan-1/CASK -0.001 0.087 0.14 26 -0.23 14 40
Syndecan-1/HGF/MET 0.024 0.09 0.25 8 -0.25 6 14
regulation of cell adhesion -0.003 0.11 0.23 30 -0.23 22 52
HPSE 0.033 0.012 -10000 0 0 59 59
positive regulation of cell migration 0.015 0.1 0.21 24 -0.24 13 37
SDC1 0.012 0.097 0.17 36 -0.25 11 47
Syndecan-1/Collagen 0.015 0.1 0.21 24 -0.24 13 37
PPIB 0.034 0.01 -10000 0 0 37 37
MET 0.023 0.018 -10000 0 0 189 189
PRKACA 0.035 0.008 -10000 0 0 24 24
MMP9 0.017 0.018 -10000 0 0 280 280
MAPK1 0.004 0.1 0.2 18 -0.23 21 39
homophilic cell adhesion 0.017 0.1 0.22 28 -0.23 13 41
MMP1 0.032 0.013 -10000 0 0 72 72
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.003 0 34 -0.017 1 35
GNB1/GNG2 0.039 0.031 -10000 0 -0.11 20 20
regulation of S phase of mitotic cell cycle -0.004 0.08 -10000 0 -0.19 68 68
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.01 -10000 0 0 36 36
SHBG/T-DHT 0.024 0.004 -10000 0 -10000 0 0
PELP1 0.035 0.007 -10000 0 0 17 17
AKT1 -0.01 0.004 0 54 -10000 0 54
MAP2K1 -0.029 0.083 0.18 28 -0.18 61 89
T-DHT/AR 0.025 0.009 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.003 52 -0.007 78 130
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
GNAI1 0.018 0.018 -10000 0 0 261 261
mol:GDP -0.02 0.035 -10000 0 -0.15 15 15
cell proliferation -0.054 0.18 0.29 13 -0.41 86 99
PIK3CA 0.031 0.014 -10000 0 0 82 82
FOS -0.084 0.28 0.35 5 -0.69 84 89
mol:Ca2+ -0.004 0.02 0.029 3 -0.053 59 62
MAPK3 -0.038 0.14 0.27 15 -0.3 75 90
MAPK1 -0.036 0.16 0.24 5 -0.44 43 48
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0 0.002 0.003 59 -0.004 75 134
cAMP biosynthetic process -0.002 0.013 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 0.003 59 -0.004 75 134
HRAS/GTP 0.041 0.066 -10000 0 -0.098 66 66
actin cytoskeleton reorganization 0.021 0.054 -10000 0 -0.12 43 43
SRC 0.034 0.009 -10000 0 0 34 34
voltage-gated calcium channel activity 0 0.002 0.003 59 -0.004 75 134
PI3K 0.019 0.064 -10000 0 -0.13 72 72
apoptosis 0.043 0.19 0.42 85 -0.26 12 97
T-DHT/AR/PELP1 0.043 0.025 -10000 0 -0.12 7 7
HRAS/GDP 0.01 0.062 -10000 0 -0.18 17 17
CREB1 -0.064 0.19 0.27 12 -0.45 85 97
RAC1-CDC42/GTP 0.028 0.06 -10000 0 -0.13 43 43
AR 0.035 0.008 -10000 0 0 22 22
GNB1 0.035 0.007 -10000 0 0 20 20
RAF1 -0.02 0.078 0.19 29 -0.22 13 42
RAC1-CDC42/GDP 0.022 0.054 -10000 0 -0.17 12 12
T-DHT/AR/PELP1/Src 0.058 0.034 -10000 0 -0.12 7 7
MAP2K2 -0.032 0.076 0.17 20 -0.18 58 78
T-DHT/AR/PELP1/Src/PI3K -0.004 0.081 -10000 0 -0.19 68 68
GNAZ 0.031 0.013 -10000 0 0 80 80
SHBG 0.036 0.006 -10000 0 0 15 15
Gi family/GNB1/GNG2/GDP -0.038 0.17 -10000 0 -0.46 50 50
mol:T-DHT 0 0.001 0.002 1 -0.004 23 24
RAC1 0.025 0.017 -10000 0 0 162 162
GNRH1 -0.011 0.002 0 12 -10000 0 12
Gi family/GTP -0.006 0.082 -10000 0 -0.19 61 61
CDC42 0.035 0.008 -10000 0 0 26 26
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.006 0.089 -9999 0 -0.29 16 16
FZD6 0.027 0.016 -9999 0 0 130 130
WNT6 0.037 0.002 -9999 0 0 1 1
WNT4 0.035 0.007 -9999 0 0 20 20
FZD3 0.029 0.015 -9999 0 0 109 109
WNT5A 0.03 0.015 -9999 0 0 99 99
WNT11 0.036 0.006 -9999 0 0 15 15
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.028 0.087 -10000 0 -0.14 90 90
alphaM/beta2 Integrin/GPIbA 0.049 0.071 -10000 0 -0.12 61 61
alphaM/beta2 Integrin/proMMP-9 -0.01 0.09 -10000 0 -0.14 141 141
PLAUR 0.03 0.014 -10000 0 0 90 90
HMGB1 0.039 0.014 0.083 1 -10000 0 1
alphaM/beta2 Integrin/Talin 0.038 0.073 -10000 0 -0.13 57 57
AGER 0.042 0.01 0.08 2 -10000 0 2
RAP1A 0.036 0.005 -10000 0 0 10 10
SELPLG 0.036 0.004 -10000 0 0 7 7
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.075 0.086 -10000 0 -0.12 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.017 0.018 -10000 0 0 280 280
CYR61 0.025 0.017 -10000 0 0 166 166
TLN1 0.029 0.015 -10000 0 0 101 101
Rap1/GTP 0.028 0.072 -10000 0 -0.21 20 20
RHOA 0.035 0.007 -10000 0 0 21 21
P-selectin oligomer 0.036 0.006 -10000 0 0 15 15
MYH2 0.024 0.072 0.18 5 -0.23 15 20
MST1R 0.035 0.008 -10000 0 0 23 23
leukocyte activation during inflammatory response 0.055 0.066 -10000 0 -0.11 57 57
APOB 0.036 0.006 -10000 0 0 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.029 0.015 -10000 0 0 109 109
JAM3 0.033 0.011 -10000 0 0 52 52
GP1BA 0.036 0.005 -10000 0 0 10 10
alphaM/beta2 Integrin/CTGF 0.02 0.087 -10000 0 -0.13 102 102
alphaM/beta2 Integrin 0.024 0.072 0.16 3 -0.22 16 19
JAM3 homodimer 0.033 0.011 -10000 0 0 52 52
ICAM2 0.034 0.009 -10000 0 0 32 32
ICAM1 0.031 0.014 -10000 0 0 83 83
phagocytosis triggered by activation of immune response cell surface activating receptor 0.025 0.075 0.16 2 -0.23 18 20
cell adhesion 0.048 0.07 -10000 0 -0.12 61 61
NFKB1 -0.003 0.079 0.21 23 -0.2 2 25
THY1 0.031 0.014 -10000 0 0 82 82
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Lipoprotein(a) 0.045 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.037 0.1 -10000 0 -0.14 108 108
IL6 -0.015 0.039 -10000 0 -10000 0 0
ITGB2 0.033 0.019 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.026 0.09 -10000 0 -0.15 71 71
alphaM/beta2 Integrin/JAM2/JAM3 0.048 0.1 -10000 0 -0.15 88 88
JAM2 0.033 0.012 -10000 0 0 57 57
alphaM/beta2 Integrin/ICAM1 0.076 0.078 -10000 0 -0.12 48 48
alphaM/beta2 Integrin/uPA/Plg 0.037 0.085 -10000 0 -0.13 67 67
RhoA/GTP 0.029 0.073 0.17 11 -0.23 16 27
positive regulation of phagocytosis 0.016 0.1 0.19 2 -0.23 54 56
Ron/MSP 0.051 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.028 0.091 -10000 0 -0.15 71 71
alphaM/beta2 Integrin/uPAR 0.036 0.079 -10000 0 -0.14 68 68
PLAU 0.02 0.018 -10000 0 0 236 236
PLAT 0.027 0.016 -10000 0 0 129 129
actin filament polymerization 0.027 0.073 0.2 8 -0.22 15 23
MST1 0.035 0.008 -10000 0 0 27 27
alphaM/beta2 Integrin/lipoprotein(a) 0.062 0.069 -10000 0 -0.11 57 57
TNF 0.005 0.089 0.2 41 -10000 0 41
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.017 0.075 -10000 0 -0.14 67 67
fibrinolysis 0.035 0.083 -10000 0 -0.13 67 67
HCK 0.027 0.016 -10000 0 0 141 141
dendritic cell antigen processing and presentation 0.025 0.075 0.16 2 -0.23 18 20
VTN 0.036 0.004 -10000 0 0 5 5
alphaM/beta2 Integrin/CYR61 0.01 0.095 -10000 0 -0.14 124 124
LPA 0.034 0.009 -10000 0 0 34 34
LRP1 0.032 0.013 -10000 0 0 70 70
cell migration -0.001 0.11 0.15 36 -0.15 145 181
FN1 0.035 0.009 -10000 0 0 30 30
alphaM/beta2 Integrin/Thy1 0.029 0.087 -10000 0 -0.14 94 94
MPO 0.036 0.004 -10000 0 0 6 6
KNG1 0.035 0.008 -10000 0 0 28 28
RAP1/GDP 0.024 0.007 -10000 0 -0.11 1 1
ROCK1 0.024 0.073 0.18 5 -0.24 16 21
ELA2 0.035 0.008 -10000 0 0 28 28
PLG 0.034 0.009 -10000 0 0 36 36
CTGF 0.027 0.016 -10000 0 0 139 139
alphaM/beta2 Integrin/Hck 0.03 0.092 -10000 0 -0.18 70 70
ITGAM 0.042 0.01 0.08 2 -10000 0 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.073 -10000 0 -0.12 56 56
HP 0.027 0.016 -10000 0 0 137 137
leukocyte adhesion 0.021 0.12 -10000 0 -0.21 68 68
SELP 0.036 0.006 -10000 0 0 15 15
EPO signaling pathway

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
BCL2L1 0.045 0.081 0.34 2 -10000 0 2
CRKL 0.043 0.089 0.16 176 -10000 0 176
mol:DAG 0.017 0.061 0.21 2 -0.19 26 28
HRAS 0.042 0.098 0.23 57 -0.19 2 59
MAPK8 0.01 0.075 0.16 80 -10000 0 80
RAP1A 0.048 0.093 0.16 186 -10000 0 186
GAB1 0.039 0.087 0.16 161 -10000 0 161
MAPK14 0.033 0.1 0.17 151 -10000 0 151
EPO 0.027 0.02 -10000 0 -0.033 2 2
PLCG1 0.017 0.061 0.22 2 -0.19 26 28
EPOR/TRPC2/IP3 Receptors 0.042 0.013 -10000 0 -0.033 2 2
RAPGEF1 0.035 0.007 -10000 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.051 0.039 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.062 0.071 0.22 27 -10000 0 27
EPO/EPOR (dimer) 0.039 0.03 -10000 0 -10000 0 0
IRS2 0.037 0.088 0.16 153 -0.16 4 157
STAT1 0.021 0.066 0.23 4 -0.22 9 13
STAT5B 0.02 0.066 0.24 3 -0.19 28 31
cell proliferation 0.007 0.074 0.16 81 -10000 0 81
GAB1/SHIP/PIK3R1/SHP2/SHC 0.039 0.063 0.16 3 -0.17 7 10
TEC 0.048 0.093 0.16 188 -10000 0 188
SOCS3 0.036 0.005 -10000 0 0 8 8
STAT1 (dimer) 0.021 0.065 0.23 4 -0.22 9 13
JAK2 0.037 0.018 0.076 2 -10000 0 2
PIK3R1 0.032 0.012 -10000 0 0 63 63
EPO/EPOR (dimer)/JAK2 0.048 0.053 0.22 11 -0.095 2 13
EPO/EPOR 0.039 0.03 -10000 0 -10000 0 0
LYN 0.033 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.06 0.069 0.2 37 -10000 0 37
elevation of cytosolic calcium ion concentration 0.042 0.013 -10000 0 -0.033 2 2
SHC1 0.033 0.011 -10000 0 0 52 52
EPO/EPOR (dimer)/LYN 0.041 0.059 -10000 0 -0.13 29 29
mol:IP3 0.017 0.061 0.21 2 -0.19 26 28
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.022 0.094 0.16 135 -0.17 12 147
SH2B3 -0.001 0.006 0.022 19 -10000 0 19
NFKB1 0.032 0.099 0.17 148 -10000 0 148
EPO/EPOR (dimer)/JAK2/SOCS3 0.015 0.015 -10000 0 -10000 0 0
PTPN6 0.046 0.092 0.17 162 -10000 0 162
TEC/VAV2/GRB2 0.082 0.07 0.23 34 -10000 0 34
EPOR 0.042 0.013 -10000 0 -0.033 2 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.061 0.071 0.22 27 -10000 0 27
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.032 0.012 -10000 0 0 63 63
CRKL/CBL/C3G 0.08 0.065 0.22 28 -10000 0 28
VAV2 0.045 0.092 0.16 181 -10000 0 181
CBL 0.047 0.092 0.16 184 -10000 0 184
SHC/Grb2/SOS1 0.023 0.034 -10000 0 -0.11 8 8
STAT5A 0.02 0.065 0.26 2 -0.19 27 29
GRB2 0.035 0.007 -10000 0 0 18 18
STAT5 (dimer) 0.036 0.072 0.27 5 -0.21 7 12
LYN/PLCgamma2 0.025 0.074 -10000 0 -0.18 55 55
PTPN11 0.036 0.005 -10000 0 0 11 11
BTK 0.045 0.093 0.16 185 -10000 0 185
BCL2 0.047 0.082 0.32 1 -10000 0 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.012 -10000 0 0 62 62
LAT2 -0.016 0.094 0.14 2 -0.28 47 49
AP1 -0.06 0.18 -10000 0 -0.39 74 74
mol:PIP3 0.021 0.14 0.25 41 -0.28 46 87
IKBKB 0.011 0.094 0.19 37 -0.19 37 74
AKT1 -0.055 0.1 0.24 12 -0.28 41 53
IKBKG 0.01 0.093 0.19 34 -0.19 37 71
MS4A2 0.04 0.007 0.06 30 0 4 34
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
MAP3K1 -0.023 0.12 0.23 9 -0.31 52 61
mol:Ca2+ 0.022 0.12 0.22 45 -0.24 36 81
LYN 0.03 0.015 -10000 0 -0.034 6 6
CBLB -0.022 0.11 0.16 2 -0.28 66 68
SHC1 0.033 0.011 -10000 0 0 52 52
RasGAP/p62DOK 0.048 0.053 -10000 0 -0.12 37 37
positive regulation of cell migration -0.011 0.003 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.032 0.072 0.26 15 -0.18 10 25
PTPN13 -0.036 0.19 -10000 0 -0.6 39 39
PTPN11 0.031 0.022 -10000 0 -0.035 47 47
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.036 0.11 0.24 7 -0.32 37 44
SYK 0.03 0.015 -10000 0 -0.033 7 7
GRB2 0.036 0.007 -10000 0 0 18 18
LAT/PLCgamma1/GRB2/SLP76/GADs 0.011 0.12 0.22 5 -0.28 54 59
LAT -0.021 0.11 0.16 2 -0.28 65 67
PAK2 -0.023 0.13 0.23 7 -0.33 53 60
NFATC2 -0.013 0.013 -10000 0 -0.043 71 71
HRAS -0.021 0.14 0.21 7 -0.34 56 63
GAB2 0.033 0.011 -10000 0 0 48 48
PLA2G1B -0.007 0.19 -10000 0 -0.92 20 20
Fc epsilon R1 0.042 0.068 -10000 0 -0.11 73 73
Antigen/IgE/Fc epsilon R1 0.044 0.061 -10000 0 -0.096 72 72
mol:GDP -0.013 0.14 0.21 10 -0.35 54 64
JUN 0.034 0.01 -10000 0 0 41 41
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
FOS 0.025 0.017 -10000 0 0 162 162
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.12 -10000 0 -0.28 71 71
CHUK 0.011 0.091 0.18 40 -0.19 38 78
KLRG1 -0.018 0.099 0.13 7 -0.23 70 77
VAV1 -0.021 0.11 0.16 4 -0.28 61 65
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.023 0.11 0.15 3 -0.28 68 71
negative regulation of mast cell degranulation -0.022 0.092 -10000 0 -0.24 56 56
BTK -0.012 0.14 -10000 0 -0.37 46 46
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.19 124 124
GAB2/PI3K/SHP2 -0.069 0.075 -10000 0 -0.22 72 72
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.005 0.078 -10000 0 -0.2 62 62
RAF1 -0.007 0.2 -10000 0 -0.97 20 20
Fc epsilon R1/FcgammaRIIB/SHIP 0.023 0.097 -10000 0 -0.13 130 130
FCER1G 0.029 0.016 -10000 0 0 113 113
FCER1A 0.033 0.013 -10000 0 -0.032 9 9
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.083 -10000 0 -0.11 102 102
MAPK3 -0.005 0.19 -10000 0 -0.9 20 20
MAPK1 -0.014 0.2 -10000 0 -0.95 20 20
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.12 0.28 -10000 0 -0.55 148 148
DUSP1 0.031 0.013 -10000 0 0 76 76
NF-kappa-B/RelA 0.018 0.066 0.14 30 -0.13 37 67
actin cytoskeleton reorganization -0.027 0.2 -10000 0 -0.6 38 38
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.011 0.15 0.23 7 -0.31 71 78
FER -0.021 0.12 0.16 3 -0.28 68 71
RELA 0.036 0.004 -10000 0 0 7 7
ITK 0.003 0.037 -10000 0 -0.14 13 13
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.002 0.14 0.24 15 -0.34 49 64
cytokine secretion 0.01 0.045 0.087 28 -0.094 38 66
SPHK1 -0.019 0.12 0.15 4 -0.28 66 70
PTK2 -0.03 0.2 -10000 0 -0.64 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.027 0.12 0.25 13 -0.29 47 60
EDG1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG 0.002 0.15 0.25 34 -0.32 48 82
MAP2K2 -0.006 0.19 -10000 0 -0.92 20 20
MAP2K1 -0.017 0.18 -10000 0 -0.92 20 20
MAP2K7 0.035 0.007 -10000 0 0 22 22
KLRG1/SHP2 0.002 0.097 0.2 10 -0.24 51 61
MAP2K4 0.024 0.14 -10000 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.025 0.1 -10000 0 -0.14 130 130
mol:Choline -0.032 0.071 0.25 15 -0.18 10 25
SHC/Grb2/SOS1 0.012 0.13 0.2 1 -0.27 68 69
FYN 0.03 0.014 -10000 0 0 88 88
DOK1 0.037 0.002 -10000 0 0 2 2
PXN -0.031 0.19 -10000 0 -0.58 38 38
HCLS1 -0.025 0.13 0.16 7 -0.32 67 74
PRKCB 0.013 0.12 0.21 41 -0.24 43 84
FCGR2B 0.02 0.018 -10000 0 0 226 226
IGHE -0.001 0.004 0.021 2 -10000 0 2
KLRG1/SHIP -0.022 0.094 0.12 2 -0.25 56 58
LCP2 0.032 0.013 -10000 0 0 75 75
PLA2G4A -0.016 0.12 0.16 10 -0.31 61 71
RASA1 0.035 0.009 -10000 0 0 30 30
mol:Phosphatidic acid -0.032 0.071 0.25 15 -0.18 10 25
IKK complex 0.008 0.079 0.18 30 -0.16 22 52
WIPF1 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.033 0.014 -10000 0 -0.005 57 57
ELF1 0.042 0.016 -10000 0 -10000 0 0
CCNA2 0.028 0.016 -10000 0 0 118 118
PIK3CA 0.03 0.015 -10000 0 -0.002 89 89
JAK3 0.034 0.012 -10000 0 -0.008 34 34
PIK3R1 0.032 0.014 -10000 0 -0.002 68 68
JAK1 0.034 0.012 -10000 0 -0.004 46 46
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.02 0.18 0.23 3 -0.52 40 43
SHC1 0.032 0.014 -10000 0 -0.004 60 60
SP1 -0.01 0.12 -10000 0 -0.27 87 87
IL2RA 0.011 0.012 -10000 0 -10000 0 0
IL2RB 0.032 0.014 -10000 0 -0.004 61 61
SOS1 0 0.002 -10000 0 -10000 0 0
IL2RG 0.035 0.011 -10000 0 -0.006 30 30
G1/S transition of mitotic cell cycle -0.068 0.27 0.28 8 -0.59 92 100
PTPN11 0.035 0.01 -10000 0 -0.012 18 18
CCND2 -0.072 0.19 -10000 0 -0.5 87 87
LCK 0.035 0.01 -10000 0 -0.008 25 25
GRB2 0.035 0.01 -10000 0 -0.008 25 25
IL2 0.036 0.009 -10000 0 -0.013 16 16
CDK6 0.024 0.018 -10000 0 0 177 177
CCND3 -0.026 0.2 0.34 4 -0.72 29 33
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.068 0.06 -10000 0 -0.12 33 33
MAP4K1 0.035 0.008 -10000 0 0 27 27
MAP3K8 0.022 0.018 -10000 0 0 198 198
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.035 0.008 -10000 0 0 28 28
MAP3K1 -0.001 0.055 0.13 1 -0.16 44 45
JUN -0.14 0.24 -10000 0 -0.52 141 141
MAP3K7 -0.001 0.053 -10000 0 -0.17 38 38
GRAP2 0.034 0.01 -10000 0 0 37 37
CRK 0.035 0.008 -10000 0 0 23 23
MAP2K4 -0.015 0.071 0.15 1 -0.24 25 26
LAT 0.036 0.005 -10000 0 0 9 9
LCP2 0.031 0.013 -10000 0 0 75 75
MAPK8 -0.14 0.25 -10000 0 -0.54 141 141
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.009 0.06 -10000 0 -0.16 46 46
LAT/GRAP2/SLP76/HPK1/HIP-55 0.063 0.056 -10000 0 -0.11 33 33
Syndecan-2-mediated signaling 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
Syndecan-2/Fibronectin 0.013 0.062 0.14 2 -0.13 70 72
EPHB2 0.034 0.01 -10000 0 0 40 40
Syndecan-2/TACI 0.017 0.056 0.14 2 -0.12 66 68
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.022 0.075 -10000 0 -0.12 84 84
HRAS 0.034 0.009 -10000 0 0 36 36
Syndecan-2/CASK -0.009 0.042 -10000 0 -0.11 69 69
ITGA5 0.033 0.012 -10000 0 0 58 58
BAX -0.009 0.073 -10000 0 -0.9 3 3
EPB41 0.036 0.005 -10000 0 0 10 10
positive regulation of cell-cell adhesion 0.012 0.055 -10000 0 -0.12 73 73
LAMA3 0.033 0.011 -10000 0 0 48 48
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.018 -10000 0 0 245 245
Syndecan-2/MMP2 0.008 0.063 0.14 1 -0.14 66 67
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.019 0.055 -10000 0 -0.14 42 42
dendrite morphogenesis 0.016 0.054 0.14 2 -0.12 61 63
Syndecan-2/GM-CSF 0.017 0.056 0.14 2 -0.12 65 67
determination of left/right symmetry 0.007 0.023 0.086 5 -0.24 4 9
Syndecan-2/PKC delta 0.016 0.055 0.14 1 -0.12 62 63
GNB2L1 0.037 0.002 -10000 0 0 2 2
MAPK3 -0.023 0.051 0.12 34 -0.19 4 38
MAPK1 -0.022 0.053 0.12 31 -0.19 10 41
Syndecan-2/RACK1 0.029 0.065 0.14 3 -0.11 78 81
NF1 0.037 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.023 0.086 5 -0.24 4 9
ITGA2 0.029 0.015 -10000 0 0 112 112
MAPK8 -0.005 0.038 0.13 3 -0.39 3 6
Syndecan-2/alpha2/beta1 Integrin 0.007 0.064 0.14 1 -0.11 92 93
Syndecan-2/Kininogen 0.017 0.055 0.14 2 -0.12 63 65
ITGB1 0.027 0.017 -10000 0 0 142 142
SRC -0.026 0.052 0.17 11 -0.19 8 19
Syndecan-2/CASK/Protein 4.1 0.015 0.05 -10000 0 -0.11 68 68
extracellular matrix organization 0.014 0.053 0.14 1 -0.12 57 58
actin cytoskeleton reorganization 0.013 0.062 0.14 2 -0.13 70 72
Syndecan-2/Caveolin-2/Ras 0.005 0.068 0.15 1 -0.13 79 80
Syndecan-2/Laminin alpha3 0.016 0.053 0.14 1 -0.12 61 62
Syndecan-2/RasGAP 0.037 0.08 -10000 0 -0.12 91 91
alpha5/beta1 Integrin 0.029 0.043 -10000 0 -0.14 21 21
PRKCD 0.034 0.01 -10000 0 0 40 40
Syndecan-2 dimer 0.016 0.054 0.14 2 -0.12 61 63
GO:0007205 0.001 0.01 -10000 0 -0.11 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.013 0.067 0.19 2 -0.2 17 19
RHOA 0.035 0.007 -10000 0 0 21 21
SDCBP 0.035 0.007 -10000 0 0 21 21
TNFRSF13B 0.036 0.005 -10000 0 0 9 9
RASA1 0.035 0.009 -10000 0 0 30 30
alpha2/beta1 Integrin 0.019 0.055 -10000 0 -0.14 42 42
Syndecan-2/Synbindin 0.016 0.06 0.14 2 -0.13 67 69
TGFB1 0.032 0.012 -10000 0 0 66 66
CASP3 -0.018 0.055 0.12 32 -0.18 11 43
FN1 0.035 0.009 -10000 0 0 30 30
Syndecan-2/IL8 -0.004 0.07 -10000 0 -0.18 62 62
SDC2 0.007 0.023 0.086 5 -0.24 4 9
KNG1 0.035 0.008 -10000 0 0 28 28
Syndecan-2/Neurofibromin 0.017 0.057 0.14 2 -0.12 68 70
TRAPPC4 0.036 0.006 -10000 0 0 16 16
CSF2 0.036 0.005 -10000 0 0 8 8
Syndecan-2/TGFB1 0.014 0.053 0.14 1 -0.12 57 58
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.055 -10000 0 -0.12 73 73
Syndecan-2/Ezrin 0.014 0.054 -10000 0 -0.11 70 70
PRKACA -0.021 0.052 0.12 35 -0.19 4 39
angiogenesis -0.004 0.07 -10000 0 -0.18 62 62
MMP2 0.029 0.015 -10000 0 0 109 109
IL8 0.019 0.018 -10000 0 0 244 244
calcineurin-NFAT signaling pathway 0.017 0.056 0.14 2 -0.12 66 68
Glypican 2 network

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
MDK 0.03 0.014 -9999 0 0 92 92
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.007 0.051 -9999 0 -0.13 57 57
neuron projection morphogenesis 0.007 0.051 -9999 0 -0.13 57 57
IL23-mediated signaling events

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
CCL2 -0.064 0.6 0.76 34 -1 129 163
IL23A 0.09 0.37 0.8 18 -0.97 21 39
NF kappa B1 p50/RelA/I kappa B alpha 0.083 0.34 0.62 30 -0.83 25 55
positive regulation of T cell mediated cytotoxicity 0.092 0.4 0.78 37 -0.92 25 62
ITGA3 0.09 0.36 0.75 23 -0.88 22 45
IL17F 0.036 0.27 0.52 33 -0.59 27 60
IL12B 0.061 0.081 0.2 69 -0.075 2 71
STAT1 (dimer) 0.072 0.36 0.65 36 -0.9 25 61
CD4 0.074 0.42 0.72 40 -1 34 74
IL23 0.098 0.36 0.74 16 -0.95 20 36
IL23R 0.068 0.14 0.29 90 -0.15 10 100
IL1B 0.085 0.4 0.76 30 -1.2 22 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.099 0.36 0.71 30 -0.84 21 51
TYK2 0.042 0.06 0.15 49 -10000 0 49
STAT4 0.035 0.009 -10000 0 0 29 29
STAT3 0.034 0.01 -10000 0 0 37 37
IL18RAP 0.035 0.008 -10000 0 -0.031 4 4
IL12RB1 0.045 0.06 0.15 52 -10000 0 52
PIK3CA 0.031 0.014 -10000 0 0 82 82
IL12Rbeta1/TYK2 0.054 0.076 0.19 37 -0.14 11 48
IL23R/JAK2 0.1 0.17 0.4 72 -0.19 12 84
positive regulation of chronic inflammatory response 0.092 0.4 0.78 37 -0.92 25 62
natural killer cell activation -0.005 0.011 -10000 0 -0.03 44 44
JAK2 0.056 0.081 0.2 68 -0.075 2 70
PIK3R1 0.032 0.012 -10000 0 0 63 63
NFKB1 0.039 0.009 0.066 3 0 18 21
RELA 0.04 0.008 0.066 3 0 7 10
positive regulation of dendritic cell antigen processing and presentation 0.099 0.35 0.73 18 -0.9 20 38
ALOX12B 0.088 0.36 0.71 30 -0.83 24 54
CXCL1 0.097 0.37 0.77 32 -0.88 19 51
T cell proliferation 0.092 0.4 0.78 37 -0.92 25 62
NFKBIA 0.036 0.014 0.067 2 0 57 59
IL17A 0.06 0.24 0.48 43 -0.47 26 69
PI3K 0.049 0.35 0.65 21 -0.86 25 46
IFNG 0.019 0.034 0.098 30 -0.076 9 39
STAT3 (dimer) 0.05 0.34 0.63 23 -0.84 26 49
IL18R1 0.035 0.008 -10000 0 -0.015 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.096 0.27 0.56 51 -0.51 19 70
IL18/IL18R 0.061 0.036 -10000 0 -0.12 7 7
macrophage activation -0.002 0.016 0.039 1 -0.042 18 19
TNF 0.093 0.36 0.78 19 -0.97 16 35
STAT3/STAT4 0.071 0.36 0.62 26 -0.88 25 51
STAT4 (dimer) 0.072 0.36 0.64 31 -0.9 25 56
IL18 0.031 0.013 -10000 0 0 75 75
IL19 0.1 0.36 0.75 21 -0.88 18 39
STAT5A (dimer) 0.086 0.37 0.65 33 -0.89 25 58
STAT1 0.034 0.01 -10000 0 0 40 40
SOCS3 0.036 0.005 -10000 0 0 8 8
CXCL9 0.1 0.36 0.74 33 -0.83 24 57
MPO 0.089 0.36 0.68 38 -0.82 25 63
positive regulation of humoral immune response 0.092 0.4 0.78 37 -0.92 25 62
IL23/IL23R/JAK2/TYK2 0.09 0.4 0.78 37 -0.96 24 61
IL6 0.15 0.37 0.76 44 -0.87 18 62
STAT5A 0.036 0.004 -10000 0 0 5 5
IL2 0.022 0.03 0.076 1 -0.036 103 104
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.03 44 44
CD3E 0.088 0.36 0.75 19 -0.89 18 37
keratinocyte proliferation 0.092 0.4 0.78 37 -0.92 25 62
NOS2 0.09 0.36 0.69 37 -0.82 25 62
Osteopontin-mediated events

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
IKK alpha homodimer 0.002 0.079 0.19 3 -0.19 39 42
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.12 0.25 1 -0.32 44 45
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.082 -10000 0 -0.15 80 80
AP1 -0.014 0.15 0.28 6 -0.28 83 89
ILK -0.032 0.073 0.2 2 -0.24 33 35
bone resorption -0.04 0.085 0.18 5 -0.24 36 41
PTK2B 0.036 0.006 -10000 0 0 16 16
PYK2/p130Cas 0.045 0.091 -10000 0 -0.16 63 63
ITGAV 0.031 0.026 -10000 0 -0.056 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.02 0.069 -10000 0 -0.14 73 73
alphaV/beta3 Integrin/Osteopontin 0.05 0.094 -10000 0 -0.16 77 77
MAP3K1 -0.03 0.064 0.22 1 -0.21 27 28
JUN 0.034 0.01 -10000 0 0 41 41
MAPK3 -0.032 0.086 0.18 6 -0.24 41 47
MAPK1 -0.03 0.088 0.17 12 -0.25 41 53
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.028 0.061 0.23 1 -0.21 27 28
ITGB3 0.032 0.026 -10000 0 -0.055 40 40
NFKBIA -0.039 0.11 0.19 5 -0.32 46 51
FOS 0.025 0.017 -10000 0 0 162 162
CD44 0.029 0.015 -10000 0 0 110 110
CHUK 0.025 0.017 -10000 0 0 163 163
PLAU -0.073 0.26 -10000 0 -1 32 32
NF kappa B1 p50/RelA -0.001 0.13 0.24 3 -0.33 40 43
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
alphaV beta3 Integrin 0.04 0.058 -10000 0 -0.12 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.032 0.066 0.19 2 -0.23 29 31
VAV3 -0.026 0.074 0.18 3 -0.23 34 37
MAP3K14 -0.028 0.076 0.17 5 -0.21 36 41
ROCK2 0.035 0.007 -10000 0 0 20 20
SPP1 0.03 0.026 -10000 0 -0.058 30 30
RAC1 0.025 0.017 -10000 0 0 162 162
Rac1/GTP -0.021 0.072 0.15 4 -0.22 30 34
MMP2 -0.062 0.12 -10000 0 -0.33 62 62
PLK2 and PLK4 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
PLK2 0.031 0.014 -10000 0 0 83 83
PLK4 0.035 0.007 -10000 0 0 19 19
regulation of centriole replication -0.011 0.032 0.093 43 -9999 0 43
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.031 0.17 -10000 0 -0.47 64 64
HDAC1 0.027 0.034 0.097 14 -0.039 84 98
AES 0.034 0.013 0.07 10 -0.004 43 53
FBXW11 0.035 0.007 -10000 0 0 22 22
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -10000 0 0
TLE1 0.034 0.013 0.07 9 -0.008 32 41
AP1 -0.012 0.078 -10000 0 -0.21 58 58
NCSTN 0.035 0.009 -10000 0 0 29 29
ADAM10 0.033 0.012 -10000 0 0 57 57
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.009 0.13 -10000 0 -0.46 18 18
NICD/RBPSUH -0.034 0.17 -10000 0 -0.47 64 64
WIF1 0.029 0.015 -10000 0 0 112 112
NOTCH1 -0.03 0.18 -10000 0 -0.49 63 63
PSENEN 0.035 0.009 -10000 0 0 31 31
KREMEN2 0.036 0.005 -10000 0 0 9 9
DKK1 0.017 0.018 -10000 0 0 276 276
beta catenin/beta TrCP1 0.064 0.093 0.25 17 -0.32 7 24
APH1B 0.036 0.006 -10000 0 0 15 15
APH1A 0.036 0.006 -10000 0 0 12 12
AXIN1 0.014 0.064 0.23 5 -10000 0 5
CtBP/CBP/TCF1/TLE1/AES 0.012 0.072 0.17 49 -0.18 17 66
PSEN1 0.033 0.011 -10000 0 0 47 47
FOS 0.025 0.017 -10000 0 0 162 162
JUN 0.034 0.01 -10000 0 0 41 41
MAP3K7 0.032 0.018 0.064 7 -0.01 62 69
CTNNB1 0.05 0.09 0.23 28 -0.32 5 33
MAPK3 0.037 0.003 -10000 0 0 4 4
DKK2/LRP6/Kremen 2 0.064 0.027 -10000 0 -0.13 1 1
HNF1A 0 0.006 0.033 10 -10000 0 10
CTBP1 0.034 0.013 0.07 9 -0.007 36 45
MYC -0.082 0.37 -10000 0 -1.2 52 52
NKD1 0 0.003 -10000 0 -10000 0 0
FZD1 0.024 0.017 -10000 0 0 175 175
NOTCH1 precursor/Deltex homolog 1 -0.034 0.17 -10000 0 -0.47 64 64
apoptosis -0.013 0.078 -10000 0 -0.21 59 59
Delta 1/NOTCHprecursor -0.034 0.17 -10000 0 -0.47 64 64
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.025 0.037 -10000 0 -10000 0 0
Gamma Secretase 0.079 0.072 -10000 0 -0.16 28 28
APC -0.021 0.17 -10000 0 -0.61 31 31
DVL1 0.019 0.087 -10000 0 -0.41 15 15
CSNK2A1 0.033 0.011 -10000 0 0 51 51
MAP3K7IP1 0.033 0.017 0.063 8 -0.011 54 62
DKK1/LRP6/Kremen 2 0.03 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 40 40
CSNK1A1 0.036 0.006 -10000 0 0 12 12
NLK 0.01 0.053 0.14 1 -0.21 22 23
CCND1 -0.047 0.34 -10000 0 -1.2 42 42
WNT1 0.035 0.007 -10000 0 0 18 18
Axin1/APC/beta catenin 0.016 0.13 -10000 0 -0.43 28 28
DKK2 0.035 0.009 -10000 0 0 31 31
NOTCH1 precursor/DVL1 -0.005 0.19 -10000 0 -0.49 54 54
GSK3B 0.034 0.01 -10000 0 0 39 39
FRAT1 0.025 0.017 -10000 0 0 161 161
NOTCH/Deltex homolog 1 -0.031 0.17 -10000 0 -0.47 64 64
PPP2R5D 0.026 0.037 -10000 0 -0.25 4 4
MAPK1 0.034 0.01 -10000 0 0 44 44
WNT1/LRP6/FZD1 0.057 0.046 -10000 0 -10000 0 0
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.032 0.022 0.07 5 -0.019 63 68
FoxO family signaling

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
G6PC 0 0.048 -10000 0 -10000 0 0
PLK1 -0.06 0.2 -10000 0 -0.74 14 14
CDKN1B -0.12 0.21 0.41 4 -0.37 137 141
FOXO3 -0.066 0.22 0.36 1 -0.48 83 84
KAT2B -0.001 0.021 0.047 17 -0.041 80 97
FOXO1/SIRT1 0.013 0.051 -10000 0 -0.27 5 5
CAT -0.076 0.26 -10000 0 -1 21 21
CTNNB1 0.036 0.006 -10000 0 0 15 15
AKT1 0.021 0.043 -10000 0 -0.062 63 63
FOXO1 0.003 0.053 0.22 1 -0.26 6 7
MAPK10 0.044 0.093 0.19 129 -0.15 19 148
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
FOXO4 -0.031 0.19 0.26 14 -0.43 66 80
response to oxidative stress 0 0.023 0.056 10 -0.049 35 45
FOXO3A/SIRT1 -0.062 0.22 -10000 0 -0.47 86 86
XPO1 0.036 0.004 -10000 0 0 5 5
EP300 0.034 0.011 -10000 0 -10000 0 0
BCL2L11 0.024 0.031 -10000 0 -10000 0 0
FOXO1/SKP2 0.019 0.056 -10000 0 -0.24 7 7
mol:GDP 0 0.023 0.056 10 -0.049 35 45
RAN 0.035 0.011 -10000 0 -0.015 20 20
GADD45A -0.16 0.33 0.48 1 -0.82 78 79
YWHAQ 0.036 0.005 -10000 0 0 8 8
FOXO1/14-3-3 family 0.007 0.15 -10000 0 -0.54 20 20
MST1 0.022 0.043 0.11 1 -0.059 90 91
CSNK1D 0.035 0.007 -10000 0 0 20 20
CSNK1E 0.032 0.013 -10000 0 0 68 68
FOXO4/14-3-3 family -0.004 0.15 -10000 0 -0.55 21 21
YWHAB 0.034 0.01 -10000 0 0 41 41
MAPK8 0.025 0.077 0.19 72 -0.14 12 84
MAPK9 0.053 0.097 0.19 153 -0.14 14 167
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
YWHAZ 0.035 0.007 -10000 0 0 21 21
SIRT1 0.019 0.023 -10000 0 -0.035 38 38
SOD2 -0.14 0.35 0.42 4 -0.81 90 94
RBL2 -0.073 0.28 -10000 0 -0.93 36 36
RAL/GDP 0.018 0.049 -10000 0 -0.14 19 19
CHUK 0.012 0.038 -10000 0 -0.059 77 77
Ran/GTP 0.018 0.025 -10000 0 -0.076 12 12
CSNK1G2 0.035 0.008 -10000 0 0 27 27
RAL/GTP 0.017 0.05 0.15 2 -0.12 19 21
CSNK1G1 0.036 0.006 -10000 0 0 12 12
FASLG 0.022 0.042 -10000 0 -0.59 1 1
SKP2 0.036 0.006 -10000 0 0 16 16
USP7 0.034 0.011 -10000 0 -0.012 23 23
IKBKB 0.023 0.044 0.11 1 -0.059 95 96
CCNB1 -0.17 0.42 0.5 1 -1.1 85 86
FOXO1-3a-4/beta catenin -0.04 0.21 0.38 10 -0.4 81 91
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.055 -10000 0 -0.24 7 7
CSNK1A1 0.036 0.006 -10000 0 0 12 12
SGK1 -0.001 0.021 0.047 17 -0.041 80 97
CSNK1G3 0.036 0.005 -10000 0 0 11 11
Ran/GTP/Exportin 1 0.039 0.036 -10000 0 -0.14 7 7
ZFAND5 -0.019 0.16 0.24 15 -0.34 65 80
SFN 0.031 0.013 -10000 0 0 80 80
CDK2 0.036 0.012 -10000 0 -0.031 3 3
FOXO3A/14-3-3 -0.013 0.16 -10000 0 -0.48 29 29
CREBBP 0.038 0.008 -10000 0 -0.031 3 3
FBXO32 -0.06 0.2 0.32 1 -0.44 83 84
BCL6 -0.093 0.32 -10000 0 -0.98 47 47
RALB 0.033 0.014 -10000 0 -0.016 32 32
RALA 0.023 0.018 -10000 0 -0.001 186 186
YWHAH 0.032 0.013 -10000 0 0 73 73
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.044 0.043 -10000 0 -0.14 24 24
AKT1 -0.013 0.17 0.28 19 -0.41 47 66
PTK2B -0.001 0.11 0.2 59 -0.36 13 72
VEGFR2 homodimer/Frs2 0.026 0.083 0.19 2 -0.32 16 18
CAV1 0.016 0.018 -10000 0 0 288 288
CALM1 0.033 0.012 -10000 0 0 57 57
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.022 0.086 0.18 2 -0.29 19 21
endothelial cell proliferation 0.018 0.15 0.3 34 -0.38 28 62
mol:Ca2+ 0.007 0.13 0.24 64 -0.32 20 84
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.02 0.087 0.2 2 -0.27 22 24
RP11-342D11.1 -0.004 0.1 0.17 68 -0.33 19 87
CDH5 0.03 0.014 -10000 0 0 92 92
VEGFA homodimer 0.036 0.034 -10000 0 -0.096 14 14
SHC1 0.033 0.011 -10000 0 0 52 52
SHC2 0.032 0.012 -10000 0 0 61 61
HRAS/GDP 0.004 0.091 -10000 0 -0.24 46 46
SH2D2A 0.036 0.006 -10000 0 0 15 15
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.021 0.11 0.28 2 -0.35 21 23
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.087 0.18 1 -0.31 18 19
VEGFR1 homodimer 0.034 0.009 -10000 0 0 35 35
SHC/GRB2/SOS1 0.036 0.1 -10000 0 -0.23 46 46
GRB10 -0.012 0.11 0.21 33 -0.33 32 65
PTPN11 0.036 0.005 -10000 0 0 11 11
GRB2 0.035 0.007 -10000 0 0 18 18
PAK1 0.036 0.006 -10000 0 0 16 16
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.038 0.12 0.24 1 -0.28 37 38
HRAS 0.034 0.009 -10000 0 0 36 36
VEGF/Rho/ROCK1/Integrin Complex 0.012 0.11 0.18 5 -0.32 30 35
HIF1A 0.034 0.01 -10000 0 0 44 44
FRS2 0.035 0.009 -10000 0 0 30 30
oxygen and reactive oxygen species metabolic process 0.018 0.085 0.2 2 -0.27 22 24
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.036 0.005 -10000 0 0 10 10
Nck/Pak 0.048 0.025 -10000 0 -0.14 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.01 0.1 0.18 1 -0.29 31 32
mol:GDP 0.017 0.093 -10000 0 -0.23 46 46
mol:NADP 0.035 0.12 0.3 28 -0.33 18 46
eNOS/Hsp90 0.032 0.12 0.28 28 -0.31 18 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.007 0.13 0.24 64 -0.32 20 84
HIF1A/ARNT 0.046 0.032 -10000 0 -0.14 11 11
SHB 0.033 0.011 -10000 0 0 51 51
VEGFA -0.003 0.013 -10000 0 -0.041 52 52
VEGFC 0.033 0.011 -10000 0 0 50 50
FAK1/Vinculin 0.013 0.12 0.26 14 -0.45 19 33
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.037 0.1 0.2 4 -0.28 26 30
PTPN6 0.033 0.011 -10000 0 0 53 53
EPAS1 0.033 0.062 -10000 0 -0.26 14 14
mol:L-citrulline 0.035 0.12 0.3 28 -0.33 18 46
ITGAV 0.035 0.009 -10000 0 0 31 31
PIK3CA 0.031 0.014 -10000 0 0 82 82
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.039 0.095 0.2 4 -0.29 21 25
VEGFR2 homodimer/VEGFA homodimer 0.012 0.099 -10000 0 -0.26 46 46
VEGFR2/3 heterodimer 0.026 0.085 0.19 2 -0.33 16 18
VEGFB 0.036 0.004 -10000 0 0 7 7
MAPK11 0.009 0.13 0.28 36 -0.35 20 56
VEGFR2 homodimer -0.005 0.082 0.2 1 -0.4 14 15
FLT1 0.034 0.009 -10000 0 0 35 35
NEDD4 0.029 0.034 0.089 9 -0.057 54 63
MAPK3 0.018 0.13 0.29 43 -0.3 20 63
MAPK1 0.015 0.13 0.28 46 -0.29 21 67
VEGFA145/NRP2 0.023 0.022 0.073 1 -0.036 51 52
VEGFR1/2 heterodimer 0.024 0.084 0.19 1 -0.33 16 17
KDR -0.005 0.082 0.2 1 -0.4 14 15
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.1 0.2 11 -0.23 46 57
SRC 0.034 0.009 -10000 0 0 34 34
platelet activating factor biosynthetic process 0.018 0.13 0.29 45 -0.31 20 65
PI3K 0.004 0.14 0.27 22 -0.36 36 58
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.021 0.087 0.18 1 -0.3 19 20
FES 0.008 0.13 0.24 69 -0.34 18 87
GAB1 0.013 0.12 0.26 12 -0.37 25 37
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.084 0.18 1 -0.3 19 20
CTNNB1 0.036 0.006 -10000 0 0 15 15
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.036 0.004 -10000 0 0 6 6
eNOS/Caveolin-1 0.01 0.095 0.29 6 -0.38 12 18
VEGFR2 homodimer/VEGFA homodimer/Yes 0.018 0.09 0.18 1 -0.31 20 21
PI3K/GAB1 0.001 0.16 0.27 27 -0.39 47 74
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.06 0.098 0.24 2 -0.26 19 21
PRKACA 0.035 0.008 -10000 0 0 24 24
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.081 0.2 1 -0.3 15 16
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.007 0.13 0.23 67 -0.34 18 85
actin cytoskeleton reorganization 0.023 0.086 0.18 1 -0.31 18 19
PTK2 0.013 0.13 0.24 27 -0.46 19 46
EDG1 0 0.14 0.23 66 -0.35 29 95
mol:DAG 0.007 0.13 0.24 64 -0.32 20 84
CaM/Ca2+ 0.019 0.12 0.26 25 -0.24 46 71
MAP2K3 0 0.12 0.23 63 -0.33 18 81
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.045 0.14 0.23 101 -0.3 43 144
PLCG1 0.006 0.13 0.24 64 -0.33 20 84
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.034 0.089 0.2 3 -0.28 19 22
IQGAP1 0.033 0.011 -10000 0 0 48 48
YES1 0.034 0.01 -10000 0 0 40 40
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.022 0.09 0.18 1 -0.3 21 22
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.019 0.086 0.18 1 -0.29 20 21
cell migration 0.006 0.13 0.26 23 -0.4 29 52
mol:PI-3-4-5-P3 0.005 0.14 0.25 26 -0.34 36 62
FYN 0.03 0.014 -10000 0 0 88 88
VEGFB/NRP1 0.006 0.12 0.22 67 -0.33 18 85
mol:NO 0.035 0.12 0.3 28 -0.33 18 46
PXN 0.036 0.004 -10000 0 0 7 7
HRAS/GTP -0.045 0.07 -10000 0 -0.24 43 43
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.006 0.098 -10000 0 -0.3 43 43
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.037 0.003 -10000 0 0 4 4
NOS3 0.034 0.13 0.32 22 -0.37 18 40
VEGFR2 homodimer/VEGFA homodimer/Sck 0.016 0.094 -10000 0 -0.29 27 27
RAC1 0.025 0.017 -10000 0 0 162 162
PRKCA 0.001 0.12 0.23 55 -0.31 20 75
PRKCB 0.005 0.12 0.22 64 -0.31 20 84
VCL 0.026 0.017 -10000 0 0 151 151
VEGFA165/NRP1 -0.025 0.083 0.12 38 -0.23 46 84
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.087 0.18 1 -0.3 19 20
VEGFA165/NRP2 0.023 0.022 0.073 1 -0.036 51 52
MAPKKK cascade -0.03 0.093 0.19 6 -0.32 32 38
NRP2 0.036 0.005 -10000 0 0 8 8
VEGFC homodimer 0.033 0.011 -10000 0 0 50 50
NCK1 0.035 0.008 -10000 0 0 27 27
ROCK1 0.036 0.006 -10000 0 0 15 15
FAK1/Paxillin 0.03 0.13 0.26 19 -0.44 19 38
MAP3K13 0.007 0.13 0.24 66 -0.34 18 84
PDPK1 -0.013 0.13 0.23 40 -0.33 33 73
Arf6 downstream pathway

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
PLAUR -0.017 0.2 -10000 0 -0.82 26 26
regulation of axonogenesis 0.004 0.066 0.21 39 -10000 0 39
myoblast fusion -0.014 0.094 0.35 28 -0.17 2 30
mol:GTP 0.014 0.067 -10000 0 -0.18 52 52
regulation of calcium-dependent cell-cell adhesion -0.025 0.075 0.15 65 -0.15 1 66
ARF1/GTP 0.034 0.063 -10000 0 -0.14 53 53
mol:GM1 0.002 0.048 -10000 0 -0.13 52 52
mol:Choline -0.016 0.042 0.086 3 -0.13 45 48
lamellipodium assembly -0.009 0.1 -10000 0 -0.36 36 36
MAPK3 0.011 0.084 0.14 37 -0.28 29 66
ARF6/GTP/NME1/Tiam1 0.026 0.075 0.15 1 -0.15 65 66
ARF1 0.035 0.008 -10000 0 0 24 24
ARF6/GDP 0.014 0.095 0.17 2 -0.35 28 30
ARF1/GDP 0.012 0.1 -10000 0 -0.28 50 50
ARF6 0.039 0.042 -10000 0 -0.13 26 26
RAB11A 0.036 0.007 -10000 0 0 17 17
TIAM1 0.029 0.023 -10000 0 -0.044 34 34
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.011 0.083 0.14 36 -0.29 28 64
actin filament bundle formation -0.017 0.11 0.28 52 -10000 0 52
KALRN 0.006 0.071 0.13 3 -0.26 29 32
RAB11FIP3/RAB11A 0.048 0.035 -10000 0 -0.16 12 12
RhoA/GDP 0.018 0.11 -10000 0 -0.28 52 52
NME1 -0.001 0.008 -10000 0 -0.031 25 25
Rac1/GDP 0.013 0.091 -10000 0 -0.28 35 35
substrate adhesion-dependent cell spreading 0.014 0.067 -10000 0 -0.18 52 52
cortical actin cytoskeleton organization -0.009 0.1 -10000 0 -0.36 36 36
RAC1 0.025 0.017 -10000 0 0 162 162
liver development 0.014 0.067 -10000 0 -0.18 52 52
ARF6/GTP 0.014 0.067 -10000 0 -0.18 52 52
RhoA/GTP 0.033 0.065 -10000 0 -0.14 55 55
mol:GDP -0.007 0.1 0.18 2 -0.3 50 52
ARF6/GTP/RAB11FIP3/RAB11A 0.05 0.07 -10000 0 -0.13 61 61
RHOA 0.035 0.007 -10000 0 0 21 21
PLD1 0.012 0.053 -10000 0 -0.14 48 48
RAB11FIP3 0.036 0.006 -10000 0 0 15 15
tube morphogenesis -0.009 0.1 -10000 0 -0.36 36 36
ruffle organization -0.004 0.066 -10000 0 -0.21 39 39
regulation of epithelial cell migration 0.014 0.067 -10000 0 -0.18 52 52
PLD2 0.012 0.053 -10000 0 -0.14 50 50
PIP5K1A -0.004 0.067 -10000 0 -0.21 39 39
mol:Phosphatidic acid -0.016 0.042 0.086 3 -0.13 45 48
Rac1/GTP -0.009 0.1 -10000 0 -0.36 36 36
Ephrin B reverse 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
EFNB2 0.028 0.015 -10000 0 0 115 115
EPHB2 0.034 0.01 -10000 0 0 40 40
EFNB1 -0.017 0.02 0.092 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.05 0.054 -10000 0 -0.14 9 9
Ephrin B2/EPHB1-2 0.031 0.057 -10000 0 -0.11 52 52
neuron projection morphogenesis 0.034 0.041 -10000 0 -0.12 13 13
Ephrin B1/EPHB1-2/Tiam1 0.058 0.049 -10000 0 -0.1 28 28
DNM1 0.035 0.008 -10000 0 0 26 26
cell-cell signaling 0 0.003 0.023 1 -10000 0 1
MAP2K4 -0.054 0.16 0.2 1 -0.52 52 53
YES1 -0.054 0.24 -10000 0 -0.75 52 52
Ephrin B1/EPHB1-2/NCK2 0.062 0.044 -10000 0 -0.1 20 20
PI3K -0.018 0.19 -10000 0 -0.56 51 51
mol:GDP 0.056 0.048 -10000 0 -0.1 28 28
ITGA2B 0.037 0.003 -10000 0 0 3 3
endothelial cell proliferation 0.016 0.047 -10000 0 -0.12 45 45
FYN -0.065 0.24 -10000 0 -0.77 52 52
MAP3K7 -0.051 0.16 -10000 0 -0.54 51 51
FGR -0.051 0.23 -10000 0 -0.72 51 51
TIAM1 0.033 0.011 -10000 0 0 46 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
RGS3 0.035 0.007 -10000 0 0 22 22
cell adhesion -0.031 0.17 -10000 0 -0.53 51 51
LYN -0.061 0.23 -10000 0 -0.74 52 52
Ephrin B1/EPHB1-2/Src Family Kinases -0.057 0.21 -10000 0 -0.68 52 52
Ephrin B1/EPHB1-2 -0.047 0.18 -10000 0 -0.57 51 51
SRC -0.05 0.23 -10000 0 -0.72 52 52
ITGB3 0.037 0.003 -10000 0 0 4 4
EPHB1 0.03 0.015 -10000 0 0 94 94
EPHB4 0.025 0.017 -10000 0 0 165 165
RAC1 0.025 0.017 -10000 0 0 162 162
Ephrin B2/EPHB4 0.016 0.047 -10000 0 -0.12 45 45
alphaIIb/beta3 Integrin 0.054 0.005 -10000 0 -10000 0 0
BLK -0.052 0.23 -10000 0 -0.72 52 52
HCK -0.065 0.23 -10000 0 -0.74 52 52
regulation of stress fiber formation -0.06 0.043 0.1 20 -10000 0 20
MAPK8 -0.056 0.15 -10000 0 -0.49 52 52
Ephrin B1/EPHB1-2/RGS3 0.068 0.034 -10000 0 -0.11 6 6
endothelial cell migration 0.007 0.17 0.22 45 -0.46 43 88
NCK2 0.036 0.007 -10000 0 0 17 17
PTPN13 0.034 0.014 -10000 0 0 60 60
regulation of focal adhesion formation -0.06 0.043 0.1 20 -10000 0 20
chemotaxis -0.065 0.033 0.11 6 -10000 0 6
PIK3CA 0.031 0.014 -10000 0 0 82 82
Rac1/GTP 0.042 0.048 -10000 0 -0.13 11 11
angiogenesis -0.048 0.18 -10000 0 -0.57 52 52
LCK -0.05 0.22 -10000 0 -0.72 51 51
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.098 0.33 2 -0.44 3 5
UGCG -0.026 0.19 -10000 0 -0.74 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT -0.007 0.13 0.26 10 -0.31 54 64
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.024 0.18 -10000 0 -0.73 30 30
mol:DAG -0.006 0.032 0.17 16 -10000 0 16
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.18 0.3 7 -0.42 63 70
FRAP1 -0.035 0.2 0.31 9 -0.47 63 72
FOXO3 -0.035 0.2 0.3 8 -0.47 65 73
AKT1 -0.04 0.21 0.32 7 -0.5 65 72
GAB2 0.03 0.019 -10000 0 -0.012 81 81
SMPD1 0.001 0.097 -10000 0 -0.51 15 15
SGMS1 -0.003 0.034 0.077 11 -0.074 61 72
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.028 0.046 0.095 5 -0.13 72 77
CALM1 0.033 0.012 -10000 0 0 57 57
cell proliferation -0.032 0.19 0.28 11 -0.39 70 81
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.078 -10000 0 -0.16 72 72
RPS6KB1 0.029 0.028 -10000 0 -10000 0 0
mol:sphingomyelin -0.006 0.032 0.17 16 -10000 0 16
natural killer cell activation 0 0.004 0.007 28 -0.01 47 75
JAK3 0.034 0.017 -10000 0 -0.028 25 25
PIK3R1 0.031 0.02 -10000 0 -0.029 26 26
JAK1 0.032 0.019 -10000 0 -0.028 30 30
NFKB1 0.035 0.007 -10000 0 0 18 18
MYC -0.069 0.3 0.45 7 -0.83 58 65
MYB 0.033 0.041 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.16 0.27 7 -0.4 49 56
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.16 0.28 8 -0.4 47 55
Rac1/GDP 0.005 0.05 0.12 6 -0.13 44 50
T cell proliferation -0.024 0.15 0.26 8 -0.38 44 52
SHC1 0.029 0.019 -10000 0 -0.011 85 85
RAC1 0.025 0.017 -10000 0 0 162 162
positive regulation of cyclin-dependent protein kinase activity 0.005 0.012 0.057 24 -10000 0 24
PRKCZ -0.025 0.16 0.26 8 -0.39 47 55
NF kappa B1 p50/RelA -0.013 0.19 0.32 7 -0.42 63 70
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.094 0.21 3 -0.31 21 24
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
IL2RA 0.021 0.021 -10000 0 -0.004 206 206
IL2RB 0.032 0.019 -10000 0 -0.028 25 25
TERT 0.036 0.006 -10000 0 0 15 15
E2F1 0.035 0.032 -10000 0 -10000 0 0
SOS1 0 0.003 0.008 32 -0.009 46 78
RPS6 0.031 0.014 -10000 0 0 85 85
mol:cAMP -0.003 0.007 -10000 0 -0.032 25 25
PTPN11 0.032 0.018 -10000 0 -0.023 44 44
IL2RG 0.034 0.017 -10000 0 -0.03 25 25
actin cytoskeleton organization -0.024 0.15 0.26 8 -0.38 44 52
GRB2 0.033 0.017 -10000 0 -0.018 46 46
IL2 0.035 0.016 -10000 0 -0.03 25 25
PIK3CA 0.029 0.02 -10000 0 -0.029 27 27
Rac1/GTP 0.028 0.064 0.16 5 -0.12 44 49
LCK 0.034 0.017 -10000 0 -0.03 26 26
BCL2 -0.022 0.16 0.32 3 -0.43 39 42
EPHB forward signaling

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
Ephrin A5/EPHB2 0.045 0.014 -10000 0 -10000 0 0
cell-cell adhesion 0.031 0.041 0.15 36 -10000 0 36
Ephrin B/EPHB2/RasGAP 0.06 0.091 -10000 0 -0.14 75 75
ITSN1 0.035 0.007 -10000 0 0 21 21
PIK3CA 0.031 0.014 -10000 0 0 82 82
SHC1 0.033 0.011 -10000 0 0 52 52
Ephrin B1/EPHB3 0.045 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.039 0.025 -10000 0 -0.12 6 6
HRAS/GDP 0.003 0.084 0.17 1 -0.22 43 44
Ephrin B/EPHB1/GRB7 0.068 0.076 -10000 0 -0.12 47 47
Endophilin/SYNJ1 -0.028 0.055 0.19 12 -0.19 2 14
KRAS 0.034 0.009 -10000 0 0 35 35
Ephrin B/EPHB1/Src 0.063 0.077 -10000 0 -0.12 52 52
endothelial cell migration 0.021 0.073 -10000 0 -0.14 63 63
GRB2 0.035 0.007 -10000 0 0 18 18
GRB7 0.036 0.006 -10000 0 0 15 15
PAK1 -0.03 0.06 0.19 16 -10000 0 16
HRAS 0.034 0.009 -10000 0 0 36 36
RRAS -0.027 0.055 0.21 8 -0.19 10 18
DNM1 0.035 0.008 -10000 0 0 26 26
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.02 0.065 0.18 18 -0.19 11 29
lamellipodium assembly -0.031 0.041 -10000 0 -0.15 36 36
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.075 -10000 0 -0.28 16 16
PIK3R1 0.032 0.012 -10000 0 0 63 63
EPHB2 0.034 0.01 -10000 0 0 40 40
EPHB3 0.033 0.011 -10000 0 0 52 52
EPHB1 0.03 0.014 -10000 0 0 94 94
EPHB4 0.025 0.017 -10000 0 0 165 165
mol:GDP 0.017 0.12 0.2 100 -0.24 35 135
Ephrin B/EPHB2 0.052 0.069 -10000 0 -0.11 65 65
Ephrin B/EPHB3 0.051 0.069 -10000 0 -0.11 64 64
JNK cascade -0.007 0.067 0.23 19 -0.2 4 23
Ephrin B/EPHB1 0.052 0.066 -10000 0 -0.11 54 54
RAP1/GDP 0.026 0.12 0.2 105 -0.23 37 142
EFNB2 0.028 0.015 -10000 0 0 115 115
EFNB3 0.035 0.009 -10000 0 0 29 29
EFNB1 0.037 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.031 0.059 -10000 0 -0.11 52 52
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 10 10
CDC42/GTP 0.043 0.084 -10000 0 -0.19 34 34
Rap1/GTP -0.045 0.053 0.053 9 -0.21 22 31
axon guidance 0.045 0.014 -10000 0 -10000 0 0
MAPK3 -0.007 0.072 0.16 3 -0.28 16 19
MAPK1 -0.007 0.075 0.17 2 -0.28 20 22
Rac1/GDP -0.01 0.094 0.24 21 -0.24 34 55
actin cytoskeleton reorganization -0.041 0.061 -10000 0 -0.2 45 45
CDC42/GDP 0.033 0.13 0.22 108 -0.23 36 144
PI3K 0.024 0.077 -10000 0 -0.14 63 63
EFNA5 0.036 0.004 -10000 0 0 5 5
Ephrin B2/EPHB4 0.016 0.048 -10000 0 -0.12 45 45
Ephrin B/EPHB2/Intersectin/N-WASP 0.001 0.063 -10000 0 -0.17 45 45
CDC42 0.035 0.008 -10000 0 0 26 26
RAS family/GTP -0.053 0.062 0.05 27 -0.24 24 51
PTK2 -0.014 0.084 0.53 10 -0.2 15 25
MAP4K4 -0.007 0.067 0.23 19 -0.2 4 23
SRC 0.034 0.009 -10000 0 0 34 34
KALRN 0.035 0.007 -10000 0 0 22 22
Intersectin/N-WASP 0.033 0.034 -10000 0 -0.14 8 8
neuron projection morphogenesis 0.058 0.17 0.34 119 -0.23 14 133
MAP2K1 0.001 0.073 -10000 0 -0.27 18 18
WASL 0.025 0.017 -10000 0 0 166 166
Ephrin B1/EPHB1-2/NCK1 0.082 0.039 -10000 0 -0.12 10 10
cell migration -0.012 0.087 0.22 1 -0.29 20 21
NRAS 0.032 0.012 -10000 0 0 63 63
SYNJ1 -0.028 0.056 0.2 12 -0.19 2 14
PXN 0.036 0.004 -10000 0 0 7 7
TF -0.023 0.051 0.2 5 -0.19 21 26
HRAS/GTP 0.033 0.08 -10000 0 -0.15 64 64
Ephrin B1/EPHB1-2 0.053 0.035 -10000 0 -0.11 6 6
cell adhesion mediated by integrin 0.019 0.046 0.15 7 -0.24 5 12
RAC1 0.025 0.017 -10000 0 0 162 162
mol:GTP 0.042 0.078 -10000 0 -0.14 62 62
RAC1-CDC42/GTP -0.032 0.047 -10000 0 -0.2 13 13
RASA1 0.035 0.009 -10000 0 0 30 30
RAC1-CDC42/GDP 0.01 0.096 0.24 20 -0.24 33 53
ruffle organization 0.067 0.17 0.31 138 -0.26 6 144
NCK1 0.035 0.008 -10000 0 0 27 27
receptor internalization -0.033 0.052 0.18 12 -0.19 2 14
Ephrin B/EPHB2/KALRN 0.066 0.08 -10000 0 -0.12 62 62
ROCK1 -0.009 0.045 0.12 47 -10000 0 47
RAS family/GDP -0.044 0.064 -10000 0 -0.21 46 46
Rac1/GTP -0.03 0.046 -10000 0 -0.15 36 36
Ephrin B/EPHB1/Src/Paxillin 0.009 0.064 -10000 0 -0.21 7 7
BCR signaling pathway

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
JUN -0.009 0.12 0.26 3 -0.32 35 38
IKBKB 0.018 0.08 0.27 4 -0.25 12 16
AKT1 0.005 0.086 0.22 29 -0.19 13 42
IKBKG 0.01 0.072 0.25 1 -0.24 12 13
CALM1 -0.029 0.13 0.22 2 -0.36 44 46
PIK3CA 0.031 0.014 -10000 0 0 82 82
MAP3K1 0.021 0.13 0.29 7 -0.36 31 38
MAP3K7 0.034 0.01 -10000 0 0 43 43
mol:Ca2+ -0.026 0.14 0.22 5 -0.38 44 49
DOK1 0.037 0.002 -10000 0 0 2 2
AP-1 -0.017 0.096 0.19 10 -0.21 49 59
LYN 0.031 0.013 -10000 0 0 74 74
BLNK 0.019 0.018 -10000 0 0 246 246
SHC1 0.033 0.011 -10000 0 0 52 52
BCR complex 0.05 0.015 -10000 0 -10000 0 0
CD22 -0.016 0.093 -10000 0 -0.3 35 35
CAMK2G -0.019 0.12 0.21 3 -0.35 42 45
CSNK2A1 0.033 0.011 -10000 0 0 51 51
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.035 0.057 -10000 0 -0.2 24 24
GO:0007205 -0.028 0.14 0.23 4 -0.38 45 49
SYK 0.031 0.013 -10000 0 0 74 74
ELK1 -0.033 0.13 0.21 4 -0.37 45 49
NFATC1 -0.022 0.093 0.26 3 -0.28 31 34
B-cell antigen/BCR complex 0.05 0.015 -10000 0 -10000 0 0
PAG1/CSK 0.024 0.023 -10000 0 -0.13 10 10
NFKBIB 0.021 0.042 0.16 1 -0.13 17 18
HRAS -0.028 0.12 0.22 5 -0.32 47 52
NFKBIA 0.021 0.038 0.16 1 -0.12 13 14
NF-kappa-B/RelA/I kappa B beta 0.026 0.037 0.16 1 -0.1 17 18
RasGAP/Csk 0.044 0.098 -10000 0 -0.12 114 114
mol:GDP -0.026 0.13 0.22 5 -0.37 45 50
PTEN 0.025 0.017 -10000 0 0 166 166
CD79B 0.036 0.005 -10000 0 0 11 11
NF-kappa-B/RelA/I kappa B alpha 0.026 0.036 0.16 1 -0.1 12 13
GRB2 0.035 0.007 -10000 0 0 18 18
PI3K/BCAP/CD19 -0.038 0.16 0.38 1 -0.44 45 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 -0.026 0.14 0.23 4 -0.39 43 47
CSK 0.035 0.007 -10000 0 0 19 19
FOS -0.031 0.13 0.2 7 -0.35 48 55
CHUK -0.059 0.14 0.25 1 -0.25 141 142
IBTK 0.035 0.008 -10000 0 0 28 28
CARD11/BCL10/MALT1/TAK1 -0.004 0.13 0.24 1 -0.34 40 41
PTPN6 -0.024 0.091 0.16 2 -0.3 34 36
RELA 0.036 0.004 -10000 0 0 7 7
BCL2A1 0.018 0.034 0.096 13 -0.089 21 34
VAV2 -0.016 0.11 -10000 0 -0.33 33 33
ubiquitin-dependent protein catabolic process 0.022 0.041 0.16 1 -0.13 17 18
BTK 0.018 0.012 -10000 0 -10000 0 0
CD19 -0.018 0.096 -10000 0 -0.3 38 38
MAP4K1 0.035 0.008 -10000 0 0 27 27
CD72 0.033 0.011 -10000 0 0 55 55
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.017 0.12 0.27 7 -0.32 31 38
SH3BP5 0.033 0.011 -10000 0 0 52 52
PIK3AP1 -0.024 0.14 0.23 5 -0.42 42 47
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.036 0.18 -10000 0 -0.51 54 54
RAF1 -0.033 0.11 0.21 5 -0.32 46 51
RasGAP/p62DOK/SHIP 0.036 0.085 -10000 0 -0.11 113 113
CD79A 0.034 0.009 -10000 0 0 34 34
re-entry into mitotic cell cycle -0.018 0.095 0.19 10 -0.22 46 56
RASA1 0.035 0.009 -10000 0 0 30 30
MAPK3 -0.039 0.099 0.19 5 -0.3 38 43
MAPK1 -0.038 0.1 0.2 5 -0.31 40 45
CD72/SHP1 -0.003 0.11 0.26 8 -0.29 37 45
NFKB1 0.036 0.007 -10000 0 0 18 18
MAPK8 0.017 0.12 0.27 7 -0.32 30 37
actin cytoskeleton organization 0.028 0.11 0.27 12 -0.3 20 32
NF-kappa-B/RelA 0.044 0.087 0.28 1 -0.24 23 24
Calcineurin -0.01 0.13 0.23 1 -0.34 42 43
PI3K -0.034 0.087 -10000 0 -0.27 36 36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.02 0.14 0.24 4 -0.44 39 43
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.014 0.15 -10000 0 -0.61 10 10
DAPP1 -0.004 0.16 -10000 0 -0.72 9 9
cytokine secretion -0.021 0.089 0.26 3 -0.26 31 34
mol:DAG -0.026 0.14 0.23 4 -0.39 43 47
PLCG2 0.032 0.012 -10000 0 0 63 63
MAP2K1 -0.037 0.11 0.2 4 -0.33 39 43
B-cell antigen/BCR complex/FcgammaRIIB 0.015 0.075 -10000 0 -0.12 97 97
mol:PI-3-4-5-P3 -0.019 0.072 0.19 15 -0.22 19 34
ETS1 -0.029 0.11 0.2 2 -0.35 36 38
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.033 0.094 -10000 0 -0.16 61 61
B-cell antigen/BCR complex/LYN -0.012 0.1 -10000 0 -0.3 39 39
MALT1 0.034 0.009 -10000 0 0 34 34
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.026 0.11 0.27 11 -0.32 20 31
B-cell antigen/BCR complex/LYN/SYK 0.023 0.11 -10000 0 -0.28 34 34
CARD11 -0.027 0.13 0.21 5 -0.36 45 50
FCGR2B 0.02 0.018 -10000 0 0 226 226
PPP3CA 0.034 0.01 -10000 0 0 37 37
BCL10 0.035 0.007 -10000 0 0 19 19
IKK complex 0.004 0.044 0.13 5 -0.12 10 15
PTPRC 0.029 0.015 -10000 0 0 110 110
PDPK1 -0.016 0.056 0.15 16 -0.17 13 29
PPP3CB 0.026 0.017 -10000 0 0 155 155
PPP3CC 0.036 0.006 -10000 0 0 12 12
POU2F2 0.016 0.03 0.1 3 -0.08 23 26
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.02 0.11 0.2 3 -0.36 31 34
adherens junction organization 0.002 0.077 0.15 5 -0.31 19 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.11 0.17 121 -0.28 22 143
FMN1 0.01 0.065 0.15 5 -0.27 16 21
mol:IP3 -0.007 0.079 0.14 5 -0.26 29 34
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.015 0.068 0.16 4 -0.28 15 19
CTNNB1 0.036 0.006 -10000 0 0 15 15
AKT1 -0.002 0.09 0.14 6 -0.29 31 37
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.031 0.068 -10000 0 -0.49 4 4
CTNND1 0.035 0.009 -10000 0 0 31 31
mol:PI-4-5-P2 0.005 0.068 0.15 6 -0.27 18 24
VASP 0.004 0.065 0.14 5 -0.28 16 21
ZYX 0.008 0.054 0.15 5 -0.31 8 13
JUB 0.01 0.065 0.15 5 -0.27 16 21
EGFR(dimer) 0.001 0.062 -10000 0 -0.28 16 16
E-cadherin/beta catenin-gamma catenin 0.064 0.029 -10000 0 -0.12 3 3
mol:PI-3-4-5-P3 0.024 0.096 0.2 3 -0.3 23 26
PIK3CA 0.031 0.015 -10000 0 -0.002 86 86
PI3K 0.025 0.098 0.21 3 -0.3 23 26
FYN -0.039 0.13 0.25 1 -0.32 72 73
mol:Ca2+ -0.007 0.077 0.14 5 -0.26 29 34
JUP 0.033 0.011 0.056 1 0 51 52
PIK3R1 0.032 0.015 -10000 0 -0.003 70 70
mol:DAG -0.007 0.079 0.14 5 -0.26 29 34
CDH1 0.034 0.01 -10000 0 0 37 37
RhoA/GDP 0.057 0.12 0.19 93 -0.29 22 115
establishment of polarity of embryonic epithelium 0.003 0.065 0.14 5 -0.27 17 22
SRC 0.034 0.009 -10000 0 0 34 34
RAC1 0.025 0.017 -10000 0 0 162 162
RHOA 0.035 0.007 -10000 0 0 21 21
EGFR 0.009 0.016 -10000 0 0 380 380
CASR -0.023 0.076 0.14 20 -0.29 22 42
RhoA/GTP 0.01 0.086 -10000 0 -0.28 24 24
AKT2 -0.002 0.082 0.15 4 -0.26 30 34
actin cable formation 0.001 0.063 0.14 5 -0.27 17 22
apoptosis 0.007 0.099 0.34 27 -0.17 13 40
CTNNA1 0.036 0.008 -10000 0 -0.002 19 19
mol:GDP -0.021 0.072 0.19 4 -0.3 21 25
PIP5K1A 0.005 0.068 0.15 6 -0.27 17 23
PLCG1 -0.008 0.081 0.14 5 -0.27 29 34
Rac1/GTP -0.003 0.066 -10000 0 -0.28 15 15
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.041 0.088 0.22 29 -0.19 13 42
TBX21 0.069 0.2 0.53 11 -0.53 9 20
B2M 0.035 0.008 -10000 0 0 25 25
TYK2 0.036 0.039 0.12 17 -0.05 27 44
IL12RB1 0.037 0.04 0.12 18 -0.051 32 50
GADD45B 0.06 0.29 0.51 19 -0.99 24 43
IL12RB2 0.04 0.041 0.12 21 -0.05 31 52
GADD45G 0.092 0.18 0.52 11 -0.53 4 15
natural killer cell activation 0.012 0.024 0.056 74 -0.034 12 86
RELB 0.034 0.009 -10000 0 0 32 32
RELA 0.036 0.004 -10000 0 0 7 7
IL18 0.034 0.022 0.089 2 -0.043 17 19
IL2RA 0.024 0.018 -10000 0 0 178 178
IFNG 0.035 0.009 -10000 0 0 30 30
STAT3 (dimer) 0.073 0.22 0.44 32 -0.52 26 58
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 47 47
FASLG 0.073 0.2 0.51 14 -0.52 10 24
NF kappa B2 p52/RelB 0.051 0.18 0.42 15 -0.46 18 33
CD4 0.024 0.027 -10000 0 -0.017 130 130
SOCS1 0.036 0.005 -10000 0 0 9 9
EntrezGene:6955 -0.001 0.01 -10000 0 -0.025 61 61
CD3D 0.025 0.029 -10000 0 -0.025 110 110
CD3E 0.028 0.027 -10000 0 -0.035 78 78
CD3G 0.027 0.029 -10000 0 -0.034 86 86
IL12Rbeta2/JAK2 0.055 0.059 0.19 13 -10000 0 13
CCL3 0.072 0.2 0.44 31 -0.46 19 50
CCL4 0.041 0.33 0.57 16 -1 31 47
HLA-A 0.036 0.006 -10000 0 0 12 12
IL18/IL18R 0.095 0.063 0.21 29 -0.1 19 48
NOS2 0.074 0.19 0.42 38 -0.41 22 60
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.087 0.22 26 -0.2 13 39
IL1R1 0.071 0.2 0.53 14 -0.53 9 23
IL4 0.004 0.048 -10000 0 -0.074 82 82
JAK2 0.033 0.038 0.11 13 -0.051 22 35
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 47 47
TCR/CD3/MHC I/CD8 0.006 0.046 0.11 1 -0.18 16 17
RAB7A 0.092 0.2 0.44 29 -0.53 21 50
lysosomal transport 0.093 0.2 0.44 30 -0.5 21 51
FOS -0.11 0.49 0.48 17 -1 97 114
STAT4 (dimer) 0.086 0.2 0.44 34 -0.47 21 55
STAT5A (dimer) 0.078 0.19 0.43 11 -0.46 18 29
GZMA 0.069 0.2 0.53 16 -0.53 9 25
GZMB 0.068 0.2 0.57 12 -0.53 9 21
HLX 0 0 -10000 0 -10000 0 0
LCK 0.062 0.2 0.47 25 -0.48 19 44
TCR/CD3/MHC II/CD4 -0.022 0.12 0.17 22 -0.2 126 148
IL2/IL2R 0.059 0.05 -10000 0 -10000 0 0
MAPK14 0.094 0.23 0.48 28 -0.62 21 49
CCR5 0.077 0.18 0.39 41 -0.38 21 62
IL1B 0.029 0.037 0.11 9 -0.05 27 36
STAT6 0.052 0.099 0.32 11 -0.47 2 13
STAT4 0.035 0.009 -10000 0 0 29 29
STAT3 0.034 0.01 -10000 0 0 37 37
STAT1 0.034 0.01 -10000 0 0 40 40
NFKB1 0.035 0.007 -10000 0 0 18 18
NFKB2 0.026 0.017 -10000 0 0 155 155
IL12B 0.04 0.041 0.12 21 -0.05 30 51
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.041 0.088 0.19 13 -0.22 29 42
IL2RB 0.033 0.011 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.087 0.2 0.44 37 -0.44 21 58
IL2RG 0.035 0.008 -10000 0 0 24 24
IL12 0.062 0.06 0.18 20 -10000 0 20
STAT5A 0.036 0.004 -10000 0 0 5 5
CD247 -0.001 0.009 -10000 0 -0.023 47 47
IL2 0.036 0.005 -10000 0 0 9 9
SPHK2 0.034 0.009 -10000 0 0 32 32
FRAP1 0.036 0.006 -10000 0 0 16 16
IL12A 0.038 0.04 0.12 19 -0.051 33 52
IL12/IL12R/TYK2/JAK2 0.065 0.21 0.49 29 -0.5 19 48
MAP2K3 0.088 0.23 0.47 28 -0.63 21 49
RIPK2 0.036 0.006 -10000 0 0 14 14
MAP2K6 0.092 0.22 0.47 29 -0.57 21 50
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.021 0.027 -10000 0 -0.012 183 183
IL18RAP 0.039 0.02 0.084 3 -0.041 22 25
IL12Rbeta1/TYK2 0.049 0.063 0.18 7 -0.16 14 21
EOMES -0.019 0.038 0.075 2 -0.1 49 51
STAT1 (dimer) 0.086 0.19 0.43 28 -0.44 12 40
T cell proliferation 0.075 0.18 0.4 36 -0.4 23 59
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.039 0.02 0.084 3 -0.041 22 25
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.17 0.34 2 -0.46 27 29
ATF2 0.086 0.22 0.46 21 -0.58 21 42
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.038 -10000 0 -0.055 95 95
HSPA8 0.036 0.009 -10000 0 0 25 25
SMAD3/SMAD4/ER alpha 0.043 0.088 0.23 8 -0.15 32 40
AKT1 0.03 0.02 -10000 0 -0.029 34 34
GSC 0.001 0.028 0.11 11 -0.065 3 14
NKX2-5 0.034 0.017 0.071 8 -0.06 12 20
muscle cell differentiation -0.016 0.13 0.3 54 -10000 0 54
SMAD2-3/SMAD4/SP1 0.051 0.14 0.34 5 -0.24 50 55
SMAD4 0.021 0.057 0.14 1 -0.14 32 33
CBFB 0.036 0.006 -10000 0 0 14 14
SAP18 0.034 0.01 -10000 0 0 43 43
Cbp/p300/MSG1 0.01 0.088 -10000 0 -0.13 99 99
SMAD3/SMAD4/VDR 0.044 0.12 -10000 0 -0.2 34 34
MYC 0.029 0.014 -10000 0 -10000 0 0
CDKN2B -0.21 0.19 -10000 0 -0.52 31 31
AP1 -0.004 0.1 0.24 1 -0.24 53 54
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.012 0.13 -10000 0 -0.37 38 38
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.002 0.083 -10000 0 -0.28 31 31
SP3 0.035 0.016 0.081 11 -0.055 10 21
CREB1 0.036 0.004 -10000 0 0 7 7
FOXH1 0.035 0.016 0.072 9 -0.06 12 21
SMAD3/SMAD4/GR 0.039 0.093 0.26 1 -0.17 33 34
GATA3 0.027 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.004 0.094 -10000 0 -0.28 32 32
MEF2C/TIF2 -0.02 0.074 0.28 8 -0.22 18 26
endothelial cell migration 0.2 0.5 1.2 106 -10000 0 106
MAX 0.027 0.043 0.084 90 -0.054 89 179
RBBP7 0.037 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 57 57
RUNX2 0.037 0.002 -10000 0 0 1 1
RUNX3 0.034 0.009 -10000 0 0 34 34
RUNX1 0.036 0.005 -10000 0 0 10 10
CTBP1 0.035 0.008 -10000 0 0 28 28
NR3C1 0.027 0.043 0.085 88 -0.054 90 178
VDR 0.035 0.007 -10000 0 0 21 21
CDKN1A -0.11 0.36 0.4 1 -1.1 59 60
KAT2B -0.003 0.008 -10000 0 -0.024 12 12
SMAD2/SMAD2/SMAD4/FOXH1 0.048 0.079 0.2 2 -0.16 40 42
DCP1A 0.035 0.008 -10000 0 0 24 24
SKI 0.037 0.001 -10000 0 -10000 0 0
SERPINE1 -0.2 0.5 -10000 0 -1.2 106 106
SMAD3/SMAD4/ATF2 0.039 0.088 0.21 1 -0.15 48 49
SMAD3/SMAD4/ATF3 0.018 0.1 -10000 0 -0.18 79 79
SAP30 0.036 0.007 -10000 0 0 18 18
Cbp/p300/PIAS3 0.041 0.074 -10000 0 -0.094 94 94
JUN -0.015 0.1 0.2 7 -0.25 48 55
SMAD3/SMAD4/IRF7 0.043 0.092 -10000 0 -0.17 37 37
TFE3 0.016 0.06 0.11 8 -0.096 103 111
COL1A2 -0.041 0.2 -10000 0 -0.63 51 51
mesenchymal cell differentiation -0.04 0.088 0.15 47 -0.21 1 48
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.035 0.008 -10000 0 0 27 27
FOS 0.02 0.03 0.12 2 -0.046 46 48
SMAD3/SMAD4/Max 0.04 0.089 0.24 2 -0.16 30 32
Cbp/p300/SNIP1 0.043 0.056 -10000 0 -0.13 8 8
ZBTB17 0.035 0.006 -10000 0 -10000 0 0
LAMC1 -0.035 0.1 0.17 2 -0.31 40 42
TGIF2/HDAC complex/SMAD3/SMAD4 0.037 0.086 0.21 1 -0.15 50 51
IRF7 0.035 0.01 -10000 0 -10000 0 0
ESR1 0.037 0.039 0.12 66 -0.026 59 125
HNF4A 0.034 0.01 -10000 0 0 37 37
MEF2C -0.028 0.069 0.28 8 -0.23 20 28
SMAD2-3/SMAD4 0.041 0.097 0.25 1 -0.19 36 37
Cbp/p300/Src-1 0.031 0.076 -10000 0 -0.13 52 52
IGHV3OR16-13 0.005 0.057 -10000 0 -0.49 6 6
TGIF2/HDAC complex 0.034 0.01 -10000 0 0 44 44
CREBBP 0.022 0.034 -10000 0 -0.045 102 102
SKIL 0.036 0.006 -10000 0 0 13 13
HDAC1 0.036 0.008 -10000 0 0 21 21
HDAC2 0.033 0.012 -10000 0 0 59 59
SNIP1 0.036 0.007 -10000 0 0 15 15
GCN5L2 0.021 0.034 -10000 0 -0.045 102 102
SMAD3/SMAD4/TFE3 0.03 0.13 0.28 4 -0.23 54 58
MSG1/HSC70 0.008 0.081 -10000 0 -0.15 102 102
SMAD2 0.035 0.017 0.091 2 -0.049 11 13
SMAD3 0.018 0.06 0.14 1 -0.12 41 42
SMAD3/E2F4-5/DP1/p107/SMAD4 0.001 0.075 -10000 0 -0.18 48 48
SMAD2/SMAD2/SMAD4 -0.013 0.072 0.17 10 -0.2 44 54
NCOR1 0.035 0.008 -10000 0 0 27 27
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA1 0.033 0.011 -10000 0 0 49 49
MYOD/E2A 0.051 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.059 0.15 0.34 5 -0.24 46 51
IFNB1 -0.006 0.059 0.18 4 -0.19 5 9
SMAD3/SMAD4/MEF2C 0.026 0.095 0.24 7 -0.22 27 34
CITED1 0.026 0.017 -10000 0 0 153 153
SMAD2-3/SMAD4/ARC105 0.041 0.088 0.22 2 -0.17 34 36
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.1 -10000 0 -0.34 29 29
RUNX1-3/PEBPB2 0.067 0.023 -10000 0 -10000 0 0
SMAD7 -0.041 0.18 0.28 3 -0.44 60 63
MYC/MIZ-1 0.027 0.059 -10000 0 -0.15 49 49
SMAD3/SMAD4 -0.081 0.24 0.22 2 -0.47 115 117
IL10 -0.008 0.062 0.2 6 -0.2 4 10
PIASy/HDAC complex 0.028 0.031 0.07 12 -0.031 89 101
PIAS3 0.023 0.029 -10000 0 -0.031 109 109
CDK2 0.021 0.032 -10000 0 -0.043 91 91
IL5 -0.01 0.065 0.19 8 -0.2 4 12
CDK4 0.021 0.031 -10000 0 -0.046 73 73
PIAS4 0.028 0.031 0.069 15 -0.031 89 104
ATF3 0.028 0.016 -10000 0 0 128 128
SMAD3/SMAD4/SP1 0.031 0.14 0.27 9 -0.24 60 69
FOXG1 0.001 0.007 0.023 22 -10000 0 22
FOXO3 -0.008 0.008 -10000 0 -10000 0 0
FOXO1 -0.008 0.007 -10000 0 -10000 0 0
FOXO4 -0.008 0.007 -10000 0 -10000 0 0
heart looping -0.028 0.069 0.28 8 -0.23 20 28
CEBPB 0.032 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.024 0.075 0.18 2 -0.14 55 57
MYOD1 0.036 0.005 -10000 0 0 8 8
SMAD3/SMAD4/HNF4 0.037 0.087 0.21 1 -0.15 46 47
SMAD3/SMAD4/GATA3 0.032 0.087 -10000 0 -0.17 23 23
SnoN/SIN3/HDAC complex/NCoR1 0.036 0.006 -10000 0 0 13 13
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.069 0.095 -10000 0 -0.17 14 14
SMAD3/SMAD4/SP1-3 0.048 0.14 0.34 3 -0.24 50 53
MED15 0 0 -10000 0 -10000 0 0
SP1 0.015 0.075 0.12 18 -0.12 105 123
SIN3B 0.035 0.009 -10000 0 0 33 33
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.07 0.086 0.24 2 -0.16 39 41
ITGB5 -0.032 0.1 0.2 8 -0.26 41 49
TGIF/SIN3/HDAC complex/CtBP -0.01 0.099 -10000 0 -0.31 32 32
SMAD3/SMAD4/AR 0.039 0.088 0.21 1 -0.16 46 47
AR 0.035 0.007 -10000 0 0 22 22
negative regulation of cell growth -0.016 0.12 0.18 2 -0.3 59 61
SMAD3/SMAD4/MYOD 0.04 0.088 0.21 1 -0.15 52 53
E2F5 0.036 0.005 -10000 0 0 8 8
E2F4 0.036 0.005 -10000 0 0 10 10
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.061 0.099 0.24 1 -0.16 46 47
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.099 -10000 0 -0.31 32 32
TFDP1 0.033 0.011 -10000 0 0 54 54
SMAD3/SMAD4/AP1 0.022 0.12 0.25 2 -0.25 51 53
SMAD3/SMAD4/RUNX2 0.04 0.089 0.21 1 -0.16 46 47
TGIF2 0.034 0.01 -10000 0 0 44 44
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.005 -10000 0 0 11 11
Reelin signaling pathway

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
CDK5R1/CDK5 0.029 0.041 -10000 0 -0.14 17 17
VLDLR 0.027 0.016 -10000 0 0 137 137
CRKL 0.035 0.008 -10000 0 0 28 28
LRPAP1 0.036 0.007 -10000 0 0 17 17
FYN 0.03 0.014 -10000 0 0 88 88
ITGA3 0.033 0.012 -10000 0 0 56 56
RELN/VLDLR/Fyn 0.018 0.062 -10000 0 -0.13 53 53
MAPK8IP1/MKK7/MAP3K11/JNK1 0.068 0.062 -10000 0 -0.12 4 4
AKT1 -0.014 0.068 -10000 0 -0.19 50 50
MAP2K7 0.035 0.007 -10000 0 0 22 22
RAPGEF1 0.035 0.007 -10000 0 0 18 18
DAB1 0.036 0.005 -10000 0 0 8 8
RELN/LRP8/DAB1 0.042 0.036 -10000 0 -0.11 2 2
LRPAP1/LRP8 0.045 0.036 -10000 0 -0.15 14 14
RELN/LRP8/DAB1/Fyn 0.042 0.06 -10000 0 -0.12 33 33
DAB1/alpha3/beta1 Integrin 0.028 0.059 -10000 0 -0.12 21 21
long-term memory 0.043 0.064 -10000 0 -0.12 30 30
DAB1/LIS1 0.048 0.072 -10000 0 -0.13 31 31
DAB1/CRLK/C3G 0.038 0.059 -10000 0 -0.12 24 24
PIK3CA 0.031 0.014 -10000 0 0 82 82
DAB1/NCK2 0.049 0.072 -10000 0 -0.13 29 29
ARHGEF2 0.035 0.007 -10000 0 0 21 21
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.036 0.007 -10000 0 0 17 17
CDK5R1 0.035 0.008 -10000 0 0 25 25
RELN 0.023 0.018 -10000 0 0 185 185
PIK3R1 0.032 0.012 -10000 0 0 63 63
RELN/LRP8/Fyn 0.03 0.056 -10000 0 -0.13 33 33
GRIN2A/RELN/LRP8/DAB1/Fyn 0.052 0.071 -10000 0 -0.12 33 33
MAPK8 0.027 0.016 -10000 0 0 141 141
RELN/VLDLR/DAB1 0.03 0.046 -10000 0 -0.11 21 21
ITGB1 0.027 0.017 -10000 0 0 142 142
MAP1B 0.022 0.084 0.16 106 -0.21 4 110
RELN/LRP8 0.041 0.043 -10000 0 -0.13 10 10
GRIN2B/RELN/LRP8/DAB1/Fyn 0.052 0.07 -10000 0 -0.12 31 31
PI3K 0.018 0.076 -10000 0 -0.16 72 72
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.027 -10000 0 -0.14 1 1
RAP1A 0.03 0.11 0.24 42 -10000 0 42
PAFAH1B1 0.035 0.008 -10000 0 0 25 25
MAPK8IP1 0.035 0.008 -10000 0 0 24 24
CRLK/C3G 0.05 0.015 -10000 0 -10000 0 0
GRIN2B 0.035 0.008 -10000 0 0 23 23
NCK2 0.036 0.007 -10000 0 0 17 17
neuron differentiation 0.009 0.064 -10000 0 -0.22 15 15
neuron adhesion 0.031 0.11 0.25 42 -10000 0 42
LRP8 0.034 0.009 -10000 0 0 34 34
GSK3B -0.009 0.077 -10000 0 -0.2 45 45
RELN/VLDLR/DAB1/Fyn 0.03 0.066 -10000 0 -0.12 53 53
MAP3K11 0.036 0.005 -10000 0 0 8 8
RELN/VLDLR/DAB1/P13K -0.008 0.073 -10000 0 -0.19 55 55
CDK5 0.023 0.018 -10000 0 0 184 184
MAPT -0.014 0.069 0.72 1 -10000 0 1
neuron migration -0.001 0.12 0.21 67 -0.28 32 99
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.009 0.065 -10000 0 -0.23 14 14
RELN/VLDLR 0.044 0.06 -10000 0 -0.12 26 26
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.011 -10000 0 0 47 47
VLDLR 0.027 0.016 -10000 0 0 137 137
LRPAP1 0.036 0.007 -10000 0 0 17 17
NUDC 0.035 0.008 -10000 0 0 28 28
RELN/LRP8 0.041 0.043 -10000 0 -0.13 10 10
CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
KATNA1 0.033 0.011 -10000 0 0 46 46
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.036 0.1 0.19 137 -0.2 5 142
IQGAP1/CaM 0.031 0.059 -10000 0 -0.15 45 45
DAB1 0.036 0.005 -10000 0 0 8 8
IQGAP1 0.033 0.011 -10000 0 0 48 48
PLA2G7 0.033 0.011 -10000 0 0 51 51
CALM1 0.033 0.012 -10000 0 0 57 57
DYNLT1 0.034 0.01 -10000 0 0 45 45
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.045 0.036 -10000 0 -0.15 14 14
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.035 0.008 -10000 0 0 25 25
LIS1/Poliovirus Protein 3A -0.023 0.029 -10000 0 -0.14 24 24
CDK5R2 0.036 0.006 -10000 0 0 16 16
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.031 0.049 -10000 0 -0.13 21 21
YWHAE 0.035 0.008 -10000 0 0 27 27
NDEL1/14-3-3 E 0.059 0.17 0.32 134 -0.26 16 150
MAP1B -0.014 0.067 -10000 0 -0.2 51 51
RAC1 -0.003 0.051 -10000 0 -0.27 11 11
p35/CDK5 -0.026 0.055 0.2 7 -0.21 11 18
RELN 0.023 0.018 -10000 0 0 185 185
PAFAH/LIS1 0.021 0.04 -10000 0 -0.15 22 22
LIS1/CLIP170 -0.023 0.029 -10000 0 -0.14 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.037 0.074 0.14 7 -0.27 26 33
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.013 0.088 0.17 1 -0.23 54 55
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.052 0.16 0.31 121 -0.26 14 135
LIS1/IQGAP1 0.013 0.059 -10000 0 -0.15 50 50
RHOA -0.006 0.066 -10000 0 -0.29 17 17
PAFAH1B1 -0.02 0.008 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.013 -10000 0 0 78 78
PAFAH1B2 0.036 0.005 -10000 0 0 8 8
MAP1B/LIS1/Dynein heavy chain 0.005 0.079 -10000 0 -0.2 54 54
NDEL1/Katanin 60/Dynein heavy chain 0.077 0.15 0.33 105 -0.25 23 128
LRP8 0.034 0.009 -10000 0 0 34 34
NDEL1/Katanin 60 0.051 0.16 0.31 122 -0.26 17 139
P39/CDK5 -0.026 0.055 0.2 7 -0.21 11 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.053 -10000 0 -0.19 26 26
CDK5 -0.014 0.043 0.19 8 -0.2 5 13
PPP2R5D 0.036 0.004 -10000 0 0 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.018 0.024 -10000 0 -0.12 24 24
CSNK2A1 0.033 0.011 -10000 0 0 51 51
RELN/VLDLR/DAB1/LIS1 0.033 0.061 -10000 0 -0.14 33 33
RELN/VLDLR 0.044 0.06 -10000 0 -0.12 26 26
CDC42 -0.003 0.048 -10000 0 -0.22 14 14
Signaling events mediated by PTP1B

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
PDGFRB 0.035 0.008 -10000 0 0 26 26
Jak2/Leptin Receptor -0.001 0.13 -10000 0 -0.33 47 47
PTP1B/AKT1 0.003 0.11 0.19 1 -0.25 51 52
FYN 0.03 0.014 -10000 0 0 88 88
p210 bcr-abl/PTP1B -0.007 0.11 0.19 2 -0.27 43 45
EGFR 0.009 0.017 -10000 0 -0.031 3 3
EGF/EGFR -0.032 0.089 -10000 0 -0.28 37 37
CSF1 0.036 0.004 -10000 0 0 7 7
AKT1 0.033 0.012 -10000 0 0 54 54
INSR 0.035 0.008 -10000 0 -0.001 24 24
PTP1B/N-cadherin -0.002 0.12 0.2 1 -0.27 53 54
Insulin Receptor/Insulin 0.022 0.11 -10000 0 -0.26 33 33
HCK 0.027 0.016 -10000 0 0 141 141
CRK 0.035 0.008 -10000 0 0 23 23
TYK2 -0.007 0.12 0.28 20 -0.29 40 60
EGF 0.027 0.024 -10000 0 -0.023 92 92
YES1 0.034 0.01 -10000 0 0 40 40
CAV1 0.01 0.14 0.22 36 -0.29 51 87
TXN 0.035 0.01 -10000 0 0 37 37
PTP1B/IRS1/GRB2 0.01 0.12 0.21 1 -0.27 46 47
cell migration 0.007 0.11 0.27 43 -0.19 2 45
STAT3 0.034 0.01 -10000 0 0 37 37
PRLR 0.038 0.004 -10000 0 -10000 0 0
ITGA2B 0.036 0.003 -10000 0 0 3 3
CSF1R 0.027 0.016 -10000 0 0 132 132
Prolactin Receptor/Prolactin 0.057 0.012 -10000 0 -10000 0 0
FGR 0.033 0.012 -10000 0 0 56 56
PTP1B/p130 Cas -0.01 0.1 0.17 1 -0.26 43 44
Crk/p130 Cas 0.001 0.11 0.19 1 -0.26 46 47
DOK1 -0.006 0.1 0.19 3 -0.3 30 33
JAK2 -0.012 0.13 -10000 0 -0.34 50 50
Jak2/Leptin Receptor/Leptin -0.012 0.12 -10000 0 -0.31 31 31
PIK3R1 0.032 0.012 -10000 0 0 63 63
PTPN1 -0.008 0.11 0.19 2 -0.27 43 45
LYN 0.031 0.013 -10000 0 0 74 74
CDH2 0.033 0.011 -10000 0 0 55 55
SRC 0.016 0.095 -10000 0 -0.48 14 14
ITGB3 0.036 0.003 -10000 0 0 4 4
CAT1/PTP1B -0.005 0.17 0.26 28 -0.36 63 91
CAPN1 0.036 0.004 -10000 0 0 5 5
CSK 0.035 0.007 -10000 0 0 19 19
PI3K 0.013 0.13 -10000 0 -0.29 41 41
mol:H2O2 0.004 0.005 0.024 5 -10000 0 5
STAT3 (dimer) -0.01 0.11 -10000 0 -0.29 30 30
negative regulation of transcription -0.012 0.13 -10000 0 -0.33 50 50
FCGR2A 0.028 0.015 -10000 0 0 117 117
FER 0.037 0.007 -10000 0 0 13 13
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
BLK 0.036 0.007 -10000 0 0 17 17
Insulin Receptor/Insulin/Shc 0.06 0.036 -10000 0 -0.13 8 8
RHOA 0.035 0.007 -10000 0 0 21 21
LEPR 0.035 0.007 -10000 0 0 19 19
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.035 0.007 -10000 0 0 18 18
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.003 0.15 0.2 13 -0.35 58 71
PRL 0.038 0.007 -10000 0 -10000 0 0
SOCS3 0.022 0.051 -10000 0 -1.1 1 1
SPRY2 0.029 0.018 -10000 0 0 139 139
Insulin Receptor/Insulin/IRS1 0.056 0.046 -10000 0 -0.13 22 22
CSF1/CSF1R -0.001 0.13 0.21 1 -0.27 53 54
Ras protein signal transduction -0.009 0.074 0.58 6 -10000 0 6
IRS1 0.033 0.011 -10000 0 0 51 51
INS 0.036 0.007 -10000 0 -0.002 17 17
LEP 0.025 0.017 -10000 0 0 169 169
STAT5B -0.002 0.1 0.18 3 -0.28 31 34
STAT5A -0.002 0.1 0.19 1 -0.29 29 30
GRB2 0.035 0.007 -10000 0 0 18 18
PDGFB-D/PDGFRB 0.003 0.12 0.2 1 -0.27 45 46
CSN2 0.012 0.041 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
LAT -0.026 0.18 -10000 0 -0.46 65 65
YBX1 0.039 0.042 -10000 0 -0.29 8 8
LCK 0.035 0.007 -10000 0 0 18 18
SHC1 0.033 0.011 -10000 0 0 52 52
NOX4 0.034 0.016 -10000 0 0 82 82
Paxillin-dependent events mediated by a4b1

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
CRKL 0.035 0.008 -10000 0 0 28 28
Rac1/GDP 0.025 0.02 -10000 0 -0.025 11 11
DOCK1 0.024 0.018 -10000 0 0 182 182
ITGA4 0.036 0.006 -10000 0 0 13 13
RAC1 0.025 0.017 -10000 0 0 162 162
alpha4/beta7 Integrin 0.052 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.051 0.035 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.052 0.018 -10000 0 -10000 0 0
lamellipodium assembly -0.047 0.14 -10000 0 -0.35 80 80
PIK3CA 0.031 0.014 -10000 0 0 82 82
PI3K 0.018 0.076 -10000 0 -0.16 72 72
ARF6 0.035 0.009 -10000 0 0 29 29
TLN1 0.029 0.015 -10000 0 0 101 101
PXN -0.021 0.01 0.093 3 -10000 0 3
PIK3R1 0.032 0.012 -10000 0 0 63 63
ARF6/GTP 0.048 0.049 -10000 0 -0.12 1 1
cell adhesion 0.045 0.052 -10000 0 -0.12 12 12
CRKL/CBL 0.051 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.039 0.027 -10000 0 -10000 0 0
ITGB1 0.027 0.017 -10000 0 0 142 142
ITGB7 0.036 0.006 -10000 0 0 14 14
ARF6/GDP 0.035 0.015 -10000 0 -0.025 13 13
alpha4/beta1 Integrin/Paxillin/VCAM1 0.012 0.081 -10000 0 -0.12 117 117
p130Cas/Crk/Dock1 0.027 0.036 -10000 0 -0.11 18 18
VCAM1 0.023 0.018 -10000 0 0 195 195
alpha4/beta1 Integrin/Paxillin/Talin 0.046 0.053 -10000 0 -0.12 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.048 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.051 0.047 -10000 0 -10000 0 0
CBL 0.036 0.005 -10000 0 0 8 8
PRKACA 0.035 0.008 -10000 0 0 24 24
GIT1 0.037 0.003 -10000 0 0 3 3
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.046 0.053 -10000 0 -0.12 12 12
Rac1/GTP -0.053 0.16 -10000 0 -0.39 80 80
Class I PI3K signaling events

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
ARF5/GTP -0.022 0.053 0.16 16 -0.22 9 25
DAPP1 -0.022 0.13 0.18 1 -0.3 63 64
Src family/SYK family/BLNK-LAT/BTK-ITK -0.044 0.19 0.23 6 -0.45 67 73
mol:DAG -0.007 0.091 0.18 25 -0.2 52 77
HRAS 0.035 0.02 0.077 2 -0.032 25 27
RAP1A 0.038 0.014 0.063 4 -0.019 20 24
ARF5/GDP 0.001 0.095 -10000 0 -0.31 31 31
PLCG2 0.032 0.012 -10000 0 0 63 63
PLCG1 0.034 0.01 -10000 0 0 37 37
ARF5 0.025 0.017 -10000 0 0 170 170
mol:GTP -0.024 0.052 0.15 17 -0.2 10 27
ARF1/GTP -0.018 0.047 0.12 16 -0.2 12 28
RHOA 0.035 0.007 -10000 0 0 21 21
YES1 0.034 0.01 -10000 0 0 40 40
RAP1A/GTP -0.023 0.053 0.16 17 -0.2 10 27
ADAP1 -0.024 0.046 0.13 14 -0.19 10 24
ARAP3 -0.024 0.051 0.15 17 -0.2 10 27
INPPL1 0.036 0.006 -10000 0 0 13 13
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.033 0.011 -10000 0 0 48 48
ARHGEF7 0.033 0.012 -10000 0 0 57 57
ARF1 0.035 0.008 -10000 0 0 24 24
NRAS 0.035 0.018 0.068 1 -0.033 12 13
FYN 0.03 0.014 -10000 0 0 88 88
ARF6 0.035 0.009 -10000 0 0 29 29
FGR 0.033 0.012 -10000 0 0 56 56
mol:Ca2+ 0.007 0.061 0.14 44 -0.12 18 62
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.033 0.011 -10000 0 0 46 46
ZAP70 0.037 0.002 -10000 0 0 2 2
mol:IP3 -0.008 0.065 0.16 29 -0.16 26 55
LYN 0.031 0.013 -10000 0 0 74 74
ARF1/GDP 0.01 0.11 -10000 0 -0.34 34 34
RhoA/GDP 0.027 0.09 0.18 13 -0.22 30 43
PDK1/Src/Hsp90 0.046 0.014 -10000 0 -10000 0 0
BLNK 0.019 0.018 -10000 0 0 246 246
actin cytoskeleton reorganization 0.011 0.1 0.19 25 -0.29 26 51
SRC 0.034 0.009 -10000 0 0 34 34
PLEKHA2 -0.012 0.024 0.086 29 -10000 0 29
RAC1 0.025 0.017 -10000 0 0 162 162
PTEN 0.025 0.022 -10000 0 -0.033 17 17
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.026 0.055 0.16 17 -0.2 10 27
RhoA/GTP -0.026 0.058 0.17 18 -0.21 11 29
Src family/SYK family/BLNK-LAT -0.05 0.16 0.16 4 -0.34 85 89
BLK 0.036 0.007 -10000 0 0 17 17
PDPK1 0.036 0.005 -10000 0 0 8 8
CYTH1 -0.024 0.046 0.13 14 -0.19 10 24
HCK 0.027 0.016 -10000 0 0 141 141
CYTH3 -0.024 0.046 0.13 14 -0.19 10 24
CYTH2 -0.024 0.046 0.13 14 -0.19 10 24
KRAS 0.034 0.021 0.077 2 -0.032 30 32
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.003 0.031 0.21 2 -0.16 2 4
SGK1 0 0.03 0.21 1 -0.16 3 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.006 0.11 0.17 3 -0.34 35 38
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.031 0.013 -10000 0 0 74 74
ARF6/GDP -0.025 0.067 0.17 15 -0.22 26 41
mol:PI-3-4-5-P3 -0.025 0.049 0.14 14 -0.2 10 24
ARAP3/RAP1A/GTP -0.023 0.053 0.16 17 -0.2 10 27
VAV1 0.034 0.009 -10000 0 0 33 33
mol:PI-3-4-P2 -0.011 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.067 0.096 0.21 120 -0.14 41 161
PLEKHA1 -0.007 0.022 0.086 23 -10000 0 23
Rac1/GDP 0.002 0.098 -10000 0 -0.31 32 32
LAT 0.036 0.005 -10000 0 0 9 9
Rac1/GTP -0.005 0.15 0.16 1 -0.44 38 39
ITK -0.027 0.049 0.13 15 -0.2 10 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.021 0.11 0.23 10 -0.27 56 66
LCK 0.035 0.007 -10000 0 0 18 18
BTK -0.026 0.052 0.14 18 -0.2 10 28
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.009 -10000 0 0 32 32
SPHK1 0.033 0.011 -10000 0 0 51 51
GNAI2 0.034 0.01 -10000 0 0 44 44
mol:S1P 0.018 0.016 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
mol:Sphinganine-1-P -0.011 0.032 0.093 43 -10000 0 43
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.028 0.046 -10000 0 -0.18 3 3
GNAI3 0.036 0.006 -10000 0 0 14 14
G12/G13 0.026 0.048 -10000 0 -0.14 28 28
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.034 0.01 -10000 0 0 45 45
S1P1/S1P 0.035 0.033 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.018 0.018 -10000 0 0 261 261
S1P/S1P5/G12 0.017 0.037 -10000 0 -0.18 3 3
S1P/S1P3/Gq 0.027 0.04 -10000 0 -0.26 6 6
S1P/S1P4/Gi -0.005 0.11 0.14 7 -0.28 43 50
GNAQ 0.035 0.009 -10000 0 0 30 30
GNAZ 0.031 0.013 -10000 0 0 80 80
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GNA12 0.023 0.018 -10000 0 0 188 188
GNA13 0.035 0.007 -10000 0 0 20 20
GNA11 0.033 0.011 -10000 0 0 51 51
ABCC1 0.035 0.007 -10000 0 0 19 19
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS 0.063 0.065 -9999 0 -0.12 12 12
SMAD6-7/SMURF1 0.045 0.039 -9999 0 -0.13 3 3
NOG 0 0 -9999 0 -10000 0 0
SMAD9 -0.024 0.15 -9999 0 -0.44 54 54
SMAD4 0.033 0.012 -9999 0 0 59 59
SMAD5 -0.027 0.095 -9999 0 -0.32 36 36
BMP7/USAG1 0.033 0.027 -9999 0 -10000 0 0
SMAD5/SKI -0.021 0.11 -9999 0 -0.3 44 44
SMAD1 -0.033 0.15 -9999 0 -0.41 50 50
BMP2 0.028 0.016 -9999 0 0 125 125
SMAD1/SMAD1/SMAD4 -0.011 0.13 -9999 0 -0.37 42 42
BMPR1A 0.025 0.017 -9999 0 0 167 167
BMPR1B 0.036 0.006 -9999 0 0 12 12
BMPR1A-1B/BAMBI 0.021 0.061 -9999 0 -0.13 50 50
AHSG 0.035 0.009 -9999 0 0 29 29
CER1 0.032 0.013 -9999 0 0 69 69
BMP2-4/CER1 0.037 0.055 -9999 0 -0.12 34 34
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.077 -9999 0 -0.26 24 24
BMP2-4 (homodimer) 0.028 0.051 -9999 0 -0.14 34 34
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.055 0.057 -9999 0 -0.12 12 12
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.025 0.017 -9999 0 0 165 165
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.068 -9999 0 -0.16 58 58
BMP2-4/USAG1 0.033 0.045 -9999 0 -0.12 14 14
SMAD6/SMURF1/SMAD5 -0.012 0.09 -9999 0 -0.29 34 34
SOSTDC1 0.024 0.018 -9999 0 0 182 182
BMP7/BMPR2/BMPR1A-1B 0.055 0.057 -9999 0 -0.12 14 14
SKI 0.037 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.035 0.008 -9999 0 0 25 25
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.034 0.009 -9999 0 0 35 35
MAP3K7 0.034 0.01 -9999 0 0 43 43
BMP2-4/CHRD 0.041 0.055 -9999 0 -0.12 33 33
SMAD5/SMAD5/SMAD4 -0.022 0.11 -9999 0 -0.31 44 44
MAPK1 0.034 0.01 -9999 0 0 44 44
TAK1/TAB family 0.019 0.083 -9999 0 -0.2 18 18
BMP7 (homodimer) 0.034 0.01 -9999 0 0 42 42
NUP214 0.035 0.007 -9999 0 0 18 18
BMP6/FETUA 0.049 0.016 -9999 0 -10000 0 0
SMAD1/SKI -0.016 0.15 -9999 0 -0.39 51 51
SMAD6 0.036 0.005 -9999 0 0 10 10
CTDSP2 0.033 0.012 -9999 0 0 58 58
BMP2-4/FETUA 0.04 0.055 -9999 0 -0.12 34 34
MAP3K7IP1 0.034 0.009 -9999 0 0 36 36
GREM1 0.032 0.012 -9999 0 0 61 61
BMPR2 (homodimer) 0.036 0.005 -9999 0 0 10 10
GADD34/PP1CA 0.051 0.055 -9999 0 -0.13 33 33
BMPR1A-1B (homodimer) 0.034 0.032 -9999 0 -0.14 6 6
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.019 0.16 -9999 0 -0.4 53 53
SMAD6-7/SMURF1/SMAD1 0.003 0.14 -9999 0 -0.38 42 42
SMAD6/SMURF1 0.025 0.017 -9999 0 0 165 165
BAMBI 0.018 0.018 -9999 0 0 258 258
SMURF2 0.035 0.007 -9999 0 0 19 19
BMP2-4/CHRDL1 0.026 0.044 -9999 0 -0.12 34 34
BMP2-4/GREM1 0.037 0.055 -9999 0 -0.12 33 33
SMAD7 0.034 0.01 -9999 0 0 45 45
SMAD8A/SMAD8A/SMAD4 -0.014 0.15 -9999 0 -0.41 61 61
SMAD1/SMAD6 -0.016 0.14 -9999 0 -0.39 43 43
TAK1/SMAD6 0.033 0.034 -9999 0 -0.14 8 8
BMP7 0.034 0.01 -9999 0 0 42 42
BMP6 0.035 0.008 -9999 0 0 25 25
MAP3K7IP2 0.033 0.011 -9999 0 0 48 48
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.003 0.055 -9999 0 -0.22 16 16
PPM1A 0.035 0.009 -9999 0 0 31 31
SMAD1/SMURF2 -0.017 0.16 -9999 0 -0.41 50 50
SMAD7/SMURF1 0.033 0.03 -9999 0 -0.14 3 3
CTDSPL 0.036 0.006 -9999 0 0 13 13
PPP1CA 0.035 0.007 -9999 0 0 19 19
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.036 0.006 -9999 0 0 15 15
PPP1R15A 0.033 0.011 -9999 0 0 53 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.013 0.069 -9999 0 -0.21 28 28
CHRD 0.035 0.008 -9999 0 0 23 23
BMPR2 0.036 0.005 -9999 0 0 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.019 0.07 -9999 0 -0.17 55 55
BMP4 0.033 0.011 -9999 0 0 51 51
FST 0.033 0.011 -9999 0 0 48 48
BMP2-4/NOG 0.026 0.044 -9999 0 -0.12 34 34
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.051 0.062 -9999 0 -0.12 9 9
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.001 0.039 -10000 0 -10000 0 0
CRKL 0.035 0.008 -10000 0 0 28 28
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
DOCK1 0.024 0.018 -10000 0 0 182 182
ITGA4 0.036 0.006 -10000 0 0 13 13
alpha4/beta7 Integrin/MAdCAM1 0.082 0.038 -10000 0 -0.12 6 6
EPO 0.025 0.017 -10000 0 0 165 165
alpha4/beta7 Integrin 0.052 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.039 0.025 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.036 0.026 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.1 -10000 0 -0.31 36 36
PIK3CA 0.031 0.014 -10000 0 0 82 82
PI3K 0.018 0.076 -10000 0 -0.16 72 72
ARF6 0.035 0.009 -10000 0 0 29 29
JAK2 0.009 0.031 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 7 7
PIK3R1 0.032 0.012 -10000 0 0 63 63
MADCAM1 0.035 0.009 -10000 0 0 29 29
cell adhesion 0.079 0.037 -10000 0 -0.12 6 6
CRKL/CBL 0.051 0.014 -10000 0 -10000 0 0
ITGB1 0.027 0.017 -10000 0 0 142 142
SRC -0.034 0.059 0.19 4 -10000 0 4
ITGB7 0.036 0.006 -10000 0 0 14 14
RAC1 0.025 0.017 -10000 0 0 162 162
alpha4/beta1 Integrin/VCAM1 0.002 0.078 -10000 0 -0.12 126 126
p130Cas/Crk/Dock1 -0.031 0.065 0.18 6 -0.2 8 14
VCAM1 0.023 0.018 -10000 0 0 195 195
RHOA 0.035 0.007 -10000 0 0 21 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.05 -10000 0 -10000 0 0
BCAR1 -0.033 0.052 0.18 4 -10000 0 4
EPOR 0.035 0.008 -10000 0 0 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.036 0.005 -10000 0 0 8 8
GIT1 0.037 0.003 -10000 0 0 3 3
Rac1/GTP -0.016 0.11 -10000 0 -0.32 36 36
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.056 0.22 7 -0.21 21 28
RFC1 -0.02 0.048 0.18 2 -0.21 25 27
PRKDC -0.017 0.055 0.19 7 -0.21 24 31
RIPK1 0.028 0.021 -10000 0 -0.023 73 73
CASP7 -0.16 0.28 -10000 0 -0.58 162 162
FASLG/FAS/FADD/FAF1 -0.015 0.087 0.16 28 -0.18 51 79
MAP2K4 -0.045 0.14 0.21 3 -0.33 40 43
mol:ceramide 0.003 0.094 0.19 5 -0.24 22 27
GSN -0.008 0.058 0.19 11 -0.21 19 30
FASLG/FAS/FADD/FAF1/Caspase 8 -0.013 0.097 0.18 11 -0.25 26 37
FAS 0.021 0.02 -10000 0 -10000 0 0
BID -0.031 0.034 0.074 26 -0.13 23 49
MAP3K1 -0.1 0.19 -10000 0 -0.37 166 166
MAP3K7 0.035 0.011 -10000 0 0 43 43
RB1 -0.017 0.045 0.23 1 -0.21 23 24
CFLAR 0.029 0.021 -10000 0 -0.028 60 60
HGF/MET 0.035 0.049 -10000 0 -0.12 21 21
ARHGDIB -0.015 0.056 0.22 7 -0.22 21 28
FADD 0.038 0.007 -10000 0 0 12 12
actin filament polymerization 0.008 0.058 0.21 19 -0.19 11 30
NFKB1 0.029 0.11 -10000 0 -0.65 10 10
MAPK8 -0.036 0.14 0.24 2 -0.35 26 28
DFFA -0.017 0.048 0.22 3 -0.21 24 27
DNA fragmentation during apoptosis -0.016 0.046 0.22 2 -0.2 24 26
FAS/FADD/MET 0.025 0.053 -10000 0 -0.12 28 28
CFLAR/RIP1 0.048 0.02 -10000 0 -0.14 2 2
FAIM3 0.034 0.009 -10000 0 0 35 35
FAF1 0.038 0.011 -10000 0 -10000 0 0
PARP1 -0.019 0.048 0.22 1 -0.21 26 27
DFFB -0.016 0.045 0.22 2 -0.2 23 25
CHUK 0.016 0.099 -10000 0 -0.61 10 10
FASLG 0.039 0.008 -10000 0 -10000 0 0
FAS/FADD 0.021 0.054 -10000 0 -0.15 36 36
HGF 0.024 0.018 -10000 0 0 177 177
LMNA -0.02 0.049 0.2 5 -0.19 24 29
CASP6 -0.017 0.046 0.17 3 -0.2 24 27
CASP10 0.039 0.004 -10000 0 -10000 0 0
CASP3 -0.011 0.05 -10000 0 -0.22 25 25
PTPN13 0.032 0.012 -10000 0 0 60 60
CASP8 -0.029 0.013 0.085 3 -10000 0 3
IL6 0.02 0.13 -10000 0 -0.63 6 6
MET 0.023 0.018 -10000 0 0 189 189
ICAD/CAD -0.021 0.049 0.25 4 -0.2 23 27
FASLG/FAS/FADD/FAF1/Caspase 10 0.002 0.094 0.19 5 -0.24 22 27
activation of caspase activity by cytochrome c -0.031 0.033 0.074 26 -0.13 23 49
PAK2 -0.015 0.049 0.15 2 -0.2 25 27
BCL2 0.035 0.007 -10000 0 0 20 20
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.042 0.011 -10000 0 -10000 0 0
NFATC2 0.015 0.16 0.29 3 -0.36 41 44
NFATC3 0.018 0.13 0.27 24 -0.24 72 96
CD40LG -0.018 0.34 0.49 44 -0.69 71 115
ITCH 0.033 0.047 0.19 8 -10000 0 8
CBLB 0.036 0.049 0.2 11 -10000 0 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.054 0.26 0.38 13 -0.64 53 66
JUNB 0.031 0.014 -10000 0 0 84 84
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.029 -10000 0 -0.14 7 7
T cell anergy 0.016 0.067 0.26 9 -0.24 1 10
TLE4 0.01 0.11 -10000 0 -0.32 20 20
Jun/NFAT1-c-4/p21SNFT -0.018 0.33 0.45 2 -0.73 72 74
AP-1/NFAT1-c-4 -0.035 0.35 -10000 0 -0.79 67 67
IKZF1 0.006 0.1 0.18 4 -0.24 39 43
T-helper 2 cell differentiation -0.087 0.23 -10000 0 -0.65 40 40
AP-1/NFAT1 0.017 0.15 0.28 19 -0.29 49 68
CALM1 0.046 0.024 0.14 2 -10000 0 2
EGR2 -0.076 0.42 0.49 16 -0.97 76 92
EGR3 -0.055 0.42 0.51 13 -1 68 81
NFAT1/FOXP3 0.039 0.12 0.26 3 -0.27 31 34
EGR1 0.029 0.015 0.071 1 -10000 0 1
JUN 0.032 0.042 0.11 34 -0.052 13 47
EGR4 0.037 0.004 0.071 1 -10000 0 1
mol:Ca2+ 0.005 0.003 -10000 0 -10000 0 0
GBP3 0.006 0.1 0.18 4 -0.24 39 43
FOSL1 0.033 0.011 -10000 0 0 53 53
NFAT1-c-4/MAF/IRF4 0.009 0.33 -10000 0 -0.72 75 75
DGKA 0.011 0.1 -10000 0 -0.31 20 20
CREM 0.026 0.016 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.007 0.33 -10000 0 -0.73 74 74
CTLA4 0.009 0.093 -10000 0 -0.26 21 21
NFAT1-c-4 (dimer)/EGR1 -0.029 0.34 -10000 0 -0.77 75 75
NFAT1-c-4 (dimer)/EGR4 0.001 0.34 -10000 0 -0.74 74 74
FOS 0.023 0.038 0.11 19 -0.05 9 28
IFNG -0.01 0.13 -10000 0 -0.42 16 16
T cell activation -0.014 0.22 -10000 0 -0.56 29 29
MAF 0.035 0.009 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.28 0.6 72 -0.46 20 92
TNF -0.041 0.31 0.4 10 -0.71 75 85
FASLG -0.1 0.46 0.56 2 -1.1 75 77
TBX21 0.04 0.006 0.11 3 -10000 0 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.026 0.018 -10000 0 -10000 0 0
PTPN1 0.008 0.12 0.43 2 -0.35 26 28
NFAT1-c-4/ICER1 -0.033 0.32 -10000 0 -0.73 74 74
GATA3 0.027 0.018 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.004 0.14 -10000 0 -0.42 16 16
IL2RA -0.064 0.25 0.35 1 -0.61 60 61
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.008 0.11 -10000 0 -0.34 26 26
E2F1 0.036 0.051 -10000 0 -0.25 12 12
PPARG 0.035 0.008 -10000 0 -10000 0 0
SLC3A2 0.006 0.12 0.24 2 -0.36 31 33
IRF4 0.037 0.002 -10000 0 0 1 1
PTGS2 -0.074 0.28 0.44 3 -0.69 68 71
CSF2 -0.018 0.34 0.49 45 -0.69 72 117
JunB/Fra1/NFAT1-c-4 -0.014 0.31 -10000 0 -0.72 71 71
IL4 -0.091 0.24 -10000 0 -0.67 40 40
IL5 -0.019 0.34 0.49 45 -0.69 72 117
IL2 -0.015 0.22 -10000 0 -0.57 29 29
IL3 0.009 0.082 -10000 0 -0.66 4 4
RNF128 0.014 0.023 0.17 1 -10000 0 1
NFATC1 -0.006 0.28 0.46 20 -0.6 72 92
CDK4 -0.01 0.27 0.55 30 -1 14 44
PTPRK -0.002 0.14 -10000 0 -0.43 37 37
IL8 -0.1 0.3 0.46 8 -0.74 67 75
POU2F1 0.039 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.015 0.013 0.085 5 -10000 0 5
RAS family/GTP 0.012 0.11 0.22 1 -0.18 75 76
NFATC4 -0.023 0.068 0.18 17 -0.2 5 22
ERBB2IP 0.035 0.01 -10000 0 -0.001 37 37
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.03 0.078 0.19 6 -0.22 5 11
JUN -0.005 0.086 0.22 5 -0.36 7 12
HRAS 0.034 0.009 -10000 0 0 36 36
DOCK7 -0.037 0.068 0.16 9 -0.18 18 27
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.026 0.081 0.21 14 -0.13 86 100
AKT1 -0.01 0.008 0.014 27 -10000 0 27
BAD -0.015 0.014 0.085 7 -10000 0 7
MAPK10 0.003 0.07 0.16 34 -0.15 12 46
mol:GTP 0 0.002 0.003 2 -0.005 26 28
ErbB2/ErbB3/neuregulin 1 beta -0.032 0.083 0.2 6 -0.24 5 11
RAF1 -0.021 0.1 0.24 11 -0.24 34 45
ErbB2/ErbB3/neuregulin 2 0.001 0.073 0.21 15 -0.13 91 106
STAT3 -0.024 0.24 -10000 0 -0.9 35 35
cell migration -0.009 0.068 0.18 17 -0.16 21 38
mol:PI-3-4-5-P3 -0.001 0.002 0.004 18 -0.004 71 89
cell proliferation -0.043 0.24 0.42 4 -0.58 59 63
FOS -0.032 0.2 0.38 6 -0.42 93 99
NRAS 0.032 0.012 -10000 0 0 63 63
mol:Ca2+ -0.03 0.078 0.19 6 -0.22 5 11
MAPK3 -0.02 0.18 0.4 3 -0.48 40 43
MAPK1 -0.045 0.22 0.4 3 -0.57 52 55
JAK2 -0.029 0.076 0.17 15 -0.22 5 20
NF2 0.01 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.08 0.15 12 -0.17 89 101
NRG1 0.036 0.005 -10000 0 0 9 9
GRB2/SOS1 0.024 0.02 -10000 0 -0.14 8 8
MAPK8 -0.018 0.088 0.19 2 -0.23 47 49
MAPK9 0.01 0.074 0.16 45 -0.15 3 48
ERBB2 -0.016 0.069 0.26 30 -10000 0 30
ERBB3 0.018 0.018 -10000 0 0 257 257
SHC1 0.033 0.011 -10000 0 0 52 52
RAC1 0.025 0.017 -10000 0 0 162 162
apoptosis 0.012 0.03 0.2 10 -0.069 4 14
STAT3 (dimer) -0.022 0.24 -10000 0 -0.88 35 35
RNF41 -0.021 0.02 0.076 10 -0.12 6 16
FRAP1 -0.016 0.012 0.084 5 -10000 0 5
RAC1-CDC42/GTP -0.024 0.045 -10000 0 -0.13 47 47
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.008 -10000 0 -10000 0 0
CHRNA1 -0.008 0.15 0.37 4 -0.37 38 42
myelination -0.036 0.072 0.24 7 -0.23 3 10
PPP3CB -0.022 0.068 0.17 14 -0.22 5 19
KRAS 0.034 0.009 -10000 0 0 35 35
RAC1-CDC42/GDP 0.021 0.075 0.22 1 -0.16 49 50
NRG2 0.036 0.004 -10000 0 0 7 7
mol:GDP -0.005 0.08 0.15 12 -0.17 89 101
SOS1 0 0.001 -10000 0 -0.004 9 9
MAP2K2 -0.029 0.1 0.22 11 -0.25 41 52
SRC 0.034 0.009 -10000 0 0 34 34
mol:cAMP -0.001 0.001 0.003 6 -0.004 1 7
PTPN11 -0.033 0.082 0.18 18 -0.23 5 23
MAP2K1 -0.039 0.2 0.39 2 -0.55 39 41
heart morphogenesis -0.03 0.078 0.19 6 -0.22 5 11
RAS family/GDP 0.019 0.11 0.24 1 -0.18 77 78
GRB2 0.036 0.007 -10000 0 0 18 18
PRKACA 0.018 0.009 -10000 0 -10000 0 0
CHRNE 0.001 0.025 0.075 2 -0.13 7 9
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.008 -10000 0 -0.014 27 27
nervous system development -0.03 0.078 0.19 6 -0.22 5 11
CDC42 0.035 0.008 -10000 0 0 26 26
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.036 0.006 -10000 0 0 15 15
MKNK1 0.034 0.009 -10000 0 0 35 35
mol:PIP3 -0.019 0.058 0.095 4 -0.24 21 25
FRAP1 0.035 0.1 0.28 2 -0.5 11 13
AKT1 0.014 0.11 0.16 114 -0.26 30 144
INSR 0.035 0.008 -10000 0 0 23 23
Insulin Receptor/Insulin 0.046 0.013 -10000 0 -10000 0 0
mol:GTP 0.039 0.11 0.2 66 -0.26 29 95
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.046 -10000 0 -0.19 16 16
TSC2 0.035 0.008 -10000 0 0 28 28
RHEB/GDP 0.006 0.076 -10000 0 -0.22 30 30
TSC1 0.034 0.01 -10000 0 0 40 40
Insulin Receptor/IRS1 0.023 0.06 -10000 0 -0.25 22 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.071 -10000 0 -0.23 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.042 0.086 0.25 11 -0.28 6 17
MAP3K5 -0.027 0.085 0.16 1 -0.23 73 74
PIK3R1 0.033 0.012 -10000 0 0 63 63
apoptosis -0.026 0.085 0.16 1 -0.23 73 74
mol:LY294002 0 0 0.001 9 -0.001 18 27
EIF4B 0.036 0.082 0.23 13 -0.3 5 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.073 0.23 7 -0.24 6 13
eIF4E/eIF4G1/eIF4A1 0.011 0.074 -10000 0 -0.32 13 13
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.083 -10000 0 -0.23 32 32
mTOR/RHEB/GTP/Raptor/GBL 0.012 0.064 0.19 16 -0.21 10 26
FKBP1A 0.032 0.012 -10000 0 0 63 63
RHEB/GTP 0.022 0.088 0.23 6 -0.23 26 32
mol:Amino Acids 0 0 0.001 9 -0.001 18 27
FKBP12/Rapamycin 0.021 0.024 -10000 0 -0.14 10 10
PDPK1 -0.02 0.063 0.16 16 -0.24 19 35
EIF4E 0.034 0.01 -10000 0 0 38 38
ASK1/PP5C -0.031 0.24 -10000 0 -0.56 79 79
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.015 0.11 -10000 0 -0.34 31 31
TSC1/TSC2 0.043 0.12 0.22 66 -0.28 29 95
tumor necrosis factor receptor activity 0 0 0.001 18 -0.001 9 27
RPS6 0.031 0.014 -10000 0 0 85 85
PPP5C 0.034 0.01 -10000 0 0 40 40
EIF4G1 0.033 0.011 -10000 0 0 50 50
IRS1 0.001 0.059 -10000 0 -0.26 23 23
INS 0.036 0.006 -10000 0 0 16 16
PTEN 0.025 0.017 -10000 0 0 166 166
PDK2 -0.019 0.063 0.16 16 -0.24 19 35
EIF4EBP1 -0.024 0.26 -10000 0 -1.1 26 26
PIK3CA 0.031 0.014 -10000 0 0 82 82
PPP2R5D 0.029 0.094 0.27 3 -0.45 11 14
peptide biosynthetic process -0.021 0.017 0.18 3 -10000 0 3
RHEB 0.025 0.017 -10000 0 0 166 166
EIF4A1 0.035 0.007 -10000 0 0 18 18
mol:Rapamycin 0 0.001 0.003 26 -0.003 15 41
EEF2 -0.021 0.017 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.008 0.25 -10000 0 -1.1 26 26
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.025 0.019 -10000 0 -0.13 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.033 0.011 -10000 0 0 48 48
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.12 -10000 0 -0.27 67 67
IRAK/TOLLIP 0.028 0.033 -10000 0 -0.12 22 22
IKBKB 0.037 0.003 -10000 0 0 4 4
IKBKG 0.037 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.043 0.022 -10000 0 -10000 0 0
IL1A 0.035 0.007 -10000 0 0 22 22
IL1B 0.003 0.044 0.093 95 -10000 0 95
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.052 -10000 0 -0.13 30 30
IL1R2 0.03 0.014 -10000 0 0 90 90
IL1R1 0.036 0.006 -10000 0 0 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.1 -10000 0 -0.31 34 34
TOLLIP 0.035 0.009 -10000 0 0 31 31
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.005 -10000 0 0 8 8
TAK1/TAB1/TAB2 0.055 0.05 -10000 0 -0.15 21 21
IKK complex/ELKS -0.045 0.097 -10000 0 -0.26 17 17
JUN -0.04 0.042 0.15 2 -0.21 10 12
MAP3K7 0.034 0.01 -10000 0 0 43 43
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.031 0.11 -10000 0 -0.15 112 112
IL1 alpha/IL1R1/IL1RAP/MYD88 0.065 0.069 -10000 0 -0.13 49 49
PIK3R1 0.032 0.012 -10000 0 0 63 63
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.074 0.075 -10000 0 -0.13 48 48
IL1 beta fragment/IL1R1/IL1RAP 0.025 0.083 0.16 8 -0.14 87 95
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.034 0.036 0.17 2 -0.2 8 10
IRAK1 -0.018 0.011 -10000 0 -0.12 5 5
IL1RN/IL1R1 0.053 0.01 -10000 0 -10000 0 0
IRAK4 0.035 0.007 -10000 0 0 19 19
PRKCI 0.035 0.008 -10000 0 0 27 27
TRAF6 0.036 0.005 -10000 0 0 10 10
PI3K 0.018 0.076 -10000 0 -0.16 72 72
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.12 -10000 0 -0.28 59 59
CHUK 0.025 0.017 -10000 0 0 163 163
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.025 0.083 0.16 8 -0.14 87 95
IL1 beta/IL1R2 0.017 0.072 -10000 0 -0.14 71 71
IRAK/TRAF6/TAK1/TAB1/TAB2 0.058 0.069 -10000 0 -0.14 36 36
NF kappa B1 p50/RelA 0.015 0.1 -10000 0 -0.15 107 107
IRAK3 0.035 0.008 -10000 0 0 27 27
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.038 0.083 -10000 0 -0.13 81 81
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.075 -10000 0 -0.28 15 15
IL1 alpha/IL1R1/IL1RAP 0.049 0.054 -10000 0 -0.13 33 33
RELA 0.036 0.004 -10000 0 0 7 7
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
SQSTM1 0.034 0.009 -10000 0 0 35 35
MYD88 0.034 0.009 -10000 0 0 36 36
IRAK/TRAF6/MEKK3 0.05 0.038 -10000 0 -0.12 22 22
IL1RAP 0.03 0.014 -10000 0 0 95 95
UBE2N 0.036 0.006 -10000 0 0 12 12
IRAK/TRAF6 -0.039 0.063 0.063 70 -0.2 24 94
CASP1 0.029 0.015 -10000 0 0 110 110
IL1RN/IL1R2 0.045 0.021 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.097 -10000 0 -0.15 91 91
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.099 -10000 0 -0.32 35 35
PIK3CA 0.031 0.014 -10000 0 0 82 82
IL1RN 0.036 0.004 -10000 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.064 0.061 -10000 0 -0.14 24 24
MAP2K6 -0.039 0.034 0.19 2 -0.21 8 10
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.067 0.27 0.61 14 -0.74 20 34
CRP 0.057 0.26 0.61 10 -0.74 19 29
cell cycle arrest 0.05 0.29 0.56 14 -0.75 32 46
TIMP1 0.003 0.37 0.56 15 -0.79 72 87
IL6ST 0.028 0.033 0.091 1 -0.047 43 44
Rac1/GDP 0.041 0.11 0.3 16 -0.31 11 27
AP1 0.012 0.2 0.33 1 -0.56 38 39
GAB2 0.034 0.012 -10000 0 -0.041 1 1
TNFSF11 0.055 0.26 0.57 9 -0.75 19 28
HSP90B1 0.001 0.22 0.31 2 -0.84 30 32
GAB1 0.033 0.012 -10000 0 -0.001 56 56
MAPK14 0.027 0.067 -10000 0 -0.31 3 3
AKT1 -0.012 0.17 -10000 0 -0.56 31 31
FOXO1 -0.013 0.16 -10000 0 -0.53 31 31
MAP2K6 0.028 0.071 0.19 4 -0.26 8 12
mol:GTP 0 0.004 -10000 0 -0.022 1 1
MAP2K4 0.035 0.14 0.35 23 -0.35 17 40
MITF 0.03 0.084 0.22 11 -0.29 9 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.01 -10000 0 0 45 45
A2M -0.076 0.34 -10000 0 -1.2 44 44
CEBPB 0.031 0.014 -10000 0 0 82 82
GRB2/SOS1/GAB family/SHP2 0.021 0.13 0.27 2 -0.47 25 27
STAT3 0.04 0.3 0.56 14 -0.81 31 45
STAT1 0.022 0.065 -10000 0 -0.71 3 3
CEBPD 0.022 0.34 0.57 9 -0.88 44 53
PIK3CA 0.031 0.014 -10000 0 -0.041 1 1
PI3K 0.019 0.076 -10000 0 -0.16 72 72
JUN 0.034 0.01 -10000 0 0 41 41
PIAS3/MITF 0.077 0.11 0.27 24 -0.27 13 37
MAPK11 0.024 0.065 0.21 2 -0.31 3 5
STAT3 (dimer)/FOXO1 -0.021 0.26 0.46 7 -0.63 51 58
GRB2/SOS1/GAB family 0.043 0.13 0.24 3 -0.29 37 40
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.004 0.1 0.19 10 -0.27 41 51
GRB2 0.036 0.008 -10000 0 -0.042 1 1
JAK2 0.031 0.014 -10000 0 0 82 82
LBP 0.067 0.26 0.55 17 -0.66 23 40
PIK3R1 0.033 0.013 -10000 0 -0.001 64 64
JAK1 0.03 0.026 -10000 0 -0.043 47 47
MYC 0.01 0.37 0.59 12 -0.88 58 70
FGG 0.056 0.26 0.57 9 -0.74 20 29
macrophage differentiation 0.05 0.29 0.56 14 -0.75 32 46
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.074 -10000 0 -0.18 7 7
JUNB 0.051 0.3 0.52 24 -0.86 27 51
FOS 0.025 0.017 -10000 0 0 162 162
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.029 0.085 0.23 13 -0.29 10 23
STAT1/PIAS1 0.072 0.13 0.3 18 -0.35 7 25
GRB2/SOS1/GAB family/SHP2/PI3K 0 0.17 -10000 0 -0.52 32 32
STAT3 (dimer) 0.041 0.3 0.56 14 -0.8 31 45
PRKCD 0.1 0.22 0.42 91 -0.44 22 113
IL6R 0.031 0.027 -10000 0 -0.041 56 56
SOCS3 0.059 0.087 0.46 2 -10000 0 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.044 0.089 0.18 1 -0.17 46 47
Rac1/GTP 0.038 0.12 0.3 14 -0.33 11 25
HCK 0.027 0.017 -10000 0 0 141 141
MAPKKK cascade 0.013 0.19 0.34 2 -0.59 35 37
bone resorption 0.058 0.25 0.56 9 -0.7 20 29
IRF1 0.049 0.3 0.58 14 -0.88 25 39
mol:GDP 0.031 0.09 0.23 21 -0.28 10 31
SOS1 0.001 0.004 0.026 10 -0.022 1 11
VAV1 0.03 0.09 0.23 20 -0.28 10 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.02 0.078 -10000 0 -0.33 13 13
PTPN11 0.016 0.099 -10000 0 -0.73 8 8
IL6/IL6RA 0.023 0.038 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.047 0.075 -10000 0 -0.15 45 45
gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.064 -10000 0 -0.12 34 34
IL6 0.015 0.027 -10000 0 -0.041 25 25
PIAS3 0.036 0.006 -10000 0 0 15 15
PTPRE 0.01 0.03 -10000 0 -0.056 36 36
PIAS1 0.035 0.008 -10000 0 0 26 26
RAC1 0.026 0.018 -10000 0 0 162 162
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.057 0.17 6 -0.21 7 13
LMO4 0.029 0.033 0.09 2 -0.046 50 52
STAT3 (dimer)/PIAS3 0.012 0.27 0.49 3 -0.74 32 35
MCL1 -0.014 0.16 -10000 0 -0.7 17 17
p38 MAPK 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
TRAF6/ASK1 0.011 0.052 -10000 0 -0.12 47 47
TRAF2/ASK1 0.032 0.044 -10000 0 -0.12 36 36
ATM 0.034 0.01 -10000 0 0 37 37
MAP2K3 0.011 0.1 0.22 1 -0.3 29 30
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.093 0.19 2 -0.28 26 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.032 0.012 -10000 0 0 65 65
TXN 0.007 0.002 -10000 0 0 37 37
CALM1 0.033 0.012 -10000 0 0 57 57
GADD45A 0.031 0.013 -10000 0 0 77 77
GADD45B 0.031 0.014 -10000 0 0 84 84
MAP3K1 0.035 0.007 -10000 0 0 20 20
MAP3K6 0.035 0.007 -10000 0 0 22 22
MAP3K7 0.034 0.01 -10000 0 0 43 43
MAP3K4 0.032 0.012 -10000 0 0 66 66
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.054 -10000 0 -0.14 39 39
TAK1/TAB family 0.009 0.056 -10000 0 -0.33 11 11
RAC1/OSM/MEKK3 0.031 0.026 -10000 0 -0.1 5 5
TRAF2 0.036 0.006 -10000 0 0 16 16
RAC1/OSM/MEKK3/MKK3 0.011 0.078 -10000 0 -0.26 23 23
TRAF6 0.009 0.033 -10000 0 -0.2 12 12
RAC1 0.025 0.017 -10000 0 0 162 162
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.017 0.018 -10000 0 0 274 274
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.008 0.056 -10000 0 -0.14 53 53
MAPK11 0.033 0.011 -10000 0 0 53 53
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.01 0.069 -10000 0 -0.14 67 67
OSM/MEKK3 0.027 0.003 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 0 37 37
TAOK2 0.012 0.024 -10000 0 -0.2 6 6
TAOK3 0.006 0.041 -10000 0 -0.2 19 19
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
MAPK14 0.036 0.004 -10000 0 0 5 5
MAP3K7IP2 0.033 0.011 -10000 0 0 48 48
MAP3K5 0.03 0.014 -10000 0 0 90 90
MAP3K10 0.035 0.008 -10000 0 0 28 28
MAP3K3 0.036 0.005 -10000 0 0 8 8
TRX/ASK1 0.023 0.035 -10000 0 -0.17 13 13
GADD45/MTK1/MTK1 0.044 0.077 -10000 0 -0.13 66 66
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.056 -10000 0 -0.13 35 35
fibroblast growth factor receptor signaling pathway 0.052 0.056 -10000 0 -0.13 35 35
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.031 0.013 -10000 0 0 74 74
GPC1/SLIT2 0.032 0.046 -10000 0 -0.14 24 24
SMAD2 -0.023 0.049 0.18 11 -0.2 3 14
GPC1/PrPc/Cu2+ 0.024 0.058 -10000 0 -0.14 50 50
GPC1/Laminin alpha1 0.015 0.04 -10000 0 -0.13 34 34
TDGF1 0.035 0.007 -10000 0 0 18 18
CRIPTO/GPC1 0.038 0.047 -10000 0 -0.14 28 28
APP/GPC1 0.035 0.058 -10000 0 -0.16 37 37
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.023 0.033 0.09 22 -0.13 23 45
FLT1 0.034 0.009 -10000 0 0 35 35
GPC1/TGFB/TGFBR1/TGFBR2 0.052 0.053 -10000 0 -0.12 33 33
SERPINC1 0.036 0.006 -10000 0 0 12 12
FYN -0.018 0.029 0.09 24 -0.13 8 32
FGR -0.022 0.033 0.09 22 -0.13 21 43
positive regulation of MAPKKK cascade -0.031 0.13 0.19 22 -0.3 61 83
SLIT2 0.029 0.015 -10000 0 0 102 102
GPC1/NRG 0.037 0.051 -10000 0 -0.14 34 34
NRG1 0.036 0.005 -10000 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.032 0.043 -10000 0 -0.12 34 34
LYN -0.022 0.034 0.09 22 -0.13 23 45
mol:Spermine -0.01 0.004 -10000 0 -10000 0 0
cell growth 0.052 0.056 -10000 0 -0.13 35 35
BMP signaling pathway -0.032 0.012 0 64 -10000 0 64
SRC -0.024 0.035 0.09 23 -0.13 27 50
TGFBR1 0.036 0.006 -10000 0 0 16 16
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.018 0.018 -10000 0 0 264 264
GPC1 0.032 0.012 -10000 0 0 64 64
TGFBR1 (dimer) 0.036 0.006 -10000 0 0 16 16
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.025 0.035 0.09 24 -0.13 26 50
HCK -0.018 0.031 0.09 19 -0.13 16 35
FGF2 0.035 0.008 -10000 0 0 25 25
FGFR1 0.036 0.005 -10000 0 0 9 9
VEGFR1 homodimer 0.034 0.009 -10000 0 0 35 35
TGFBR2 0.035 0.009 -10000 0 0 29 29
cell death 0.034 0.058 -10000 0 -0.16 37 37
ATIII/GPC1 0.038 0.049 -10000 0 -0.14 31 31
PLA2G2A/GPC1 -0.005 0.075 -10000 0 -0.15 92 92
LCK -0.024 0.034 0.09 24 -0.13 24 48
neuron differentiation 0.037 0.051 -10000 0 -0.14 34 34
PrPc/Cu2+ 0.015 0.038 -10000 0 -0.13 30 30
APP 0.035 0.007 -10000 0 0 20 20
TGFBR2 (dimer) 0.035 0.009 -10000 0 0 29 29
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.052 -10000 0 -0.19 28 28
PDGFRB 0.036 0.009 -10000 0 -0.001 27 27
SPHK1 0.016 0.04 -10000 0 -0.76 1 1
mol:S1P 0.018 0.042 -10000 0 -0.68 1 1
S1P1/S1P/Gi -0.001 0.14 0.25 15 -0.47 27 42
GNAO1 0.033 0.015 0.064 1 0 87 88
PDGFB-D/PDGFRB/PLCgamma1 0.03 0.14 0.25 30 -0.39 28 58
PLCG1 -0.004 0.13 0.23 21 -0.43 27 48
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.036 0.009 -10000 0 -0.001 27 27
GNAI2 0.036 0.012 -10000 0 0 44 44
GNAI3 0.038 0.007 -10000 0 0 14 14
GNAI1 0.019 0.02 -10000 0 0 261 261
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.009 0.076 0.12 12 -0.28 28 40
S1P1/S1P 0.025 0.08 0.21 4 -0.28 19 23
negative regulation of cAMP metabolic process 0 0.14 0.24 17 -0.46 27 44
MAPK3 0.001 0.14 0.29 15 -0.46 24 39
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
KDR 0.027 0.035 0.094 1 -0.13 18 19
PLCB2 0.038 0.092 0.21 33 -0.26 18 51
RAC1 0.025 0.017 -10000 0 0 162 162
RhoA/GTP 0.017 0.068 -10000 0 -0.24 20 20
receptor internalization 0.024 0.076 0.2 4 -0.26 19 23
PTGS2 0.032 0.15 0.36 7 -0.48 14 21
Rac1/GTP 0.009 0.059 -10000 0 -0.26 14 14
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFA -0.001 0.022 -10000 0 -0.1 23 23
negative regulation of T cell proliferation 0 0.14 0.24 17 -0.46 27 44
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.033 0.015 -10000 0 0 80 80
MAPK1 0.004 0.14 0.29 15 -0.47 22 37
S1P1/S1P/PDGFB-D/PDGFRB 0.054 0.1 0.24 19 -0.3 21 40
ABCC1 0.037 0.008 -10000 0 0 19 19
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.009 0.026 1 -0.037 12 13
BUB1B -0.022 0.085 0.11 26 -0.22 64 90
PLK1 0.004 0.023 0.081 19 -0.072 3 22
PLK1S1 0.003 0.014 0.048 22 -0.044 1 23
KIF2A 0.005 0.021 0.071 19 -0.065 3 22
regulation of mitotic centrosome separation 0.005 0.024 0.081 19 -0.072 3 22
GOLGA2 0.035 0.008 -10000 0 0 27 27
Hec1/SPC24 -0.004 0.01 -10000 0 -0.055 6 6
WEE1 -0.031 0.13 -10000 0 -0.45 38 38
cytokinesis -0.022 0.11 0.15 15 -0.3 60 75
PP2A-alpha B56 0.054 0.08 -10000 0 -0.53 6 6
AURKA 0.003 0.016 0.055 22 -0.041 2 24
PICH/PLK1 -0.035 0.075 0.071 10 -0.18 88 98
CENPE 0.005 0.049 0.14 39 -0.11 6 45
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization 0.005 0.021 0.071 19 -0.064 3 22
PPP2CA 0.035 0.007 -10000 0 0 20 20
FZR1 0.035 0.008 -10000 0 0 25 25
TPX2 -0.026 0.089 0.1 3 -0.22 86 89
PAK1 0.036 0.007 -10000 0 0 16 16
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 22 22
CLSPN 0.01 0.027 -10000 0 -0.2 6 6
GORASP1 0.034 0.009 -10000 0 0 33 33
metaphase 0.001 0.003 0.016 9 -0.011 2 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.003 0.014 0.048 22 -0.044 1 23
G2 phase of mitotic cell cycle -0.001 0.002 0.01 7 -10000 0 7
STAG2 0.035 0.007 -10000 0 0 22 22
GRASP65/GM130/RAB1/GTP -0.02 0.14 -10000 0 -0.6 26 26
spindle elongation 0.005 0.024 0.081 19 -0.072 3 22
ODF2 0.035 0.009 -10000 0 0 29 29
BUB1 0.021 0.064 -10000 0 -0.58 5 5
TPT1 -0.003 0.052 -10000 0 -0.18 37 37
CDC25C 0.013 0.026 -10000 0 -0.22 5 5
CDC25B 0.012 0.031 -10000 0 -0.029 165 165
SGOL1 0.001 0.009 0.037 12 -0.026 1 13
RHOA 0.035 0.007 -10000 0 0 21 21
CCNB1/CDK1 -0.021 0.13 -10000 0 -0.24 93 93
CDC14B -0.011 0.004 0.01 8 -10000 0 8
CDC20 0.028 0.016 -10000 0 0 127 127
PLK1/PBIP1 -0.015 0.037 0.07 8 -0.091 77 85
mitosis -0.001 0.003 0.012 10 -10000 0 10
FBXO5 -0.016 0.063 0.12 17 -0.16 53 70
CDC2 0.015 0.023 -10000 0 -0.031 41 41
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.06 -10000 0 -0.26 24 24
ERCC6L -0.045 0.1 -10000 0 -0.23 93 93
NLP/gamma Tubulin 0.002 0.028 0.072 13 -0.1 21 34
microtubule cytoskeleton organization -0.003 0.052 -10000 0 -0.18 37 37
G2/M transition DNA damage checkpoint -0.001 0.002 0.01 6 -10000 0 6
PPP1R12A 0.036 0.008 -10000 0 0 22 22
interphase -0.001 0.002 0.01 6 -10000 0 6
PLK1/PRC1-2 0.008 0.077 0.13 1 -0.14 89 90
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.053 -10000 0 -0.13 26 26
RAB1A 0.035 0.007 -10000 0 0 19 19
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.019 0.065 20 -0.051 1 21
mitotic prometaphase 0 0.005 0.02 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process -0.049 0.1 0.18 2 -0.21 108 110
microtubule-based process 0.02 0.025 0.1 5 -0.067 2 7
Golgi organization 0.005 0.024 0.081 19 -0.072 3 22
Cohesin/SA2 0.021 0.033 0.096 6 -0.096 21 27
PPP1CB/MYPT1 0.047 0.036 -10000 0 -0.16 14 14
KIF20A 0.029 0.015 -10000 0 0 110 110
APC/C/CDC20 0.02 0.025 0.11 5 -10000 0 5
PPP2R1A 0.033 0.012 -10000 0 0 59 59
chromosome segregation -0.014 0.036 0.069 8 -0.09 77 85
PRC1 0.028 0.016 -10000 0 0 123 123
ECT2 0.002 0.061 0.15 48 -0.11 17 65
C13orf34 0.004 0.02 0.068 19 -0.062 1 20
NUDC 0.002 0.06 -10000 0 -0.26 24 24
regulation of attachment of spindle microtubules to kinetochore -0.022 0.085 0.11 26 -0.22 64 90
spindle assembly 0.002 0.026 0.083 16 -0.079 13 29
spindle stabilization 0.003 0.014 0.048 22 -0.044 1 23
APC/C/HCDH1 0.024 0.026 0.09 1 -0.12 15 16
MKLP2/PLK1 0.02 0.025 0.1 5 -0.067 2 7
CCNB1 0.015 0.027 -10000 0 -0.028 106 106
PPP1CB 0.036 0.006 -10000 0 0 14 14
BTRC 0.026 0.017 -10000 0 0 153 153
ROCK2 0.017 0.03 -10000 0 -0.21 3 3
TUBG1 0.002 0.05 0.1 1 -0.22 22 23
G2/M transition of mitotic cell cycle -0.046 0.11 0.14 17 -0.24 92 109
MLF1IP -0.009 0.006 0.01 2 -10000 0 2
INCENP 0.036 0.004 -10000 0 0 6 6
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.074 -10000 0 -0.13 40 40
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.035 0.008 -10000 0 0 28 28
STAT1 (dimer)/Cbp/p300 0.022 0.084 0.27 5 -0.22 19 24
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.063 -10000 0 -0.14 42 42
antigen processing and presentation of peptide antigen via MHC class I -0.026 0.08 0.13 5 -0.18 66 71
CaM/Ca2+ 0.046 0.08 -10000 0 -0.14 42 42
RAP1A 0.036 0.005 -10000 0 0 10 10
STAT1 (dimer)/SHP2 -0.023 0.06 0.16 17 -0.19 9 26
AKT1 -0.033 0.085 0.22 9 -0.23 32 41
MAP2K1 -0.029 0.056 0.15 17 -0.21 8 25
MAP3K11 -0.023 0.059 0.16 22 -0.18 7 29
IFNGR1 0.031 0.019 -10000 0 -0.037 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.03 0.12 -10000 0 -0.31 60 60
Rap1/GTP -0.04 0.037 0.05 1 -0.13 32 33
CRKL/C3G 0.05 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.065 0.077 -10000 0 -0.13 35 35
CEBPB -0.006 0.12 0.35 3 -0.44 21 24
STAT3 0.034 0.01 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.06 0.096 -10000 0 -0.74 4 4
STAT1 -0.026 0.06 0.17 19 -0.19 9 28
CALM1 0.033 0.012 -10000 0 0 57 57
IFN-gamma (dimer) 0.03 0.022 -10000 0 -0.037 39 39
PIK3CA 0.031 0.014 -10000 0 0 82 82
STAT1 (dimer)/PIAS1 -0.027 0.07 0.18 20 -0.21 17 37
CEBPB/PTGES2/Cbp/p300 0.009 0.09 -10000 0 -0.3 21 21
mol:Ca2+ 0.046 0.072 -10000 0 -0.12 40 40
MAPK3 0.007 0.074 0.34 1 -0.69 1 2
STAT1 (dimer) -0.027 0.11 0.19 7 -0.26 56 63
MAPK1 -0.04 0.2 0.34 1 -0.75 34 35
JAK2 0.027 0.022 -10000 0 -0.038 34 34
PIK3R1 0.032 0.012 -10000 0 0 63 63
JAK1 0.033 0.017 0.071 1 -0.036 18 19
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.001 0.096 0.3 4 -0.38 13 17
SMAD7 -0.009 0.061 0.16 22 -0.14 21 43
CBL/CRKL/C3G 0.019 0.071 0.25 5 -0.18 6 11
PI3K 0.027 0.095 -10000 0 -0.16 71 71
IFNG 0.03 0.022 -10000 0 -0.037 39 39
apoptosis 0.014 0.086 0.31 3 -0.39 9 12
CAMK2G 0.024 0.018 -10000 0 0 177 177
STAT3 (dimer) 0.034 0.01 -10000 0 0 37 37
CAMK2A 0.036 0.005 -10000 0 0 8 8
CAMK2B 0.017 0.018 -10000 0 0 274 274
FRAP1 -0.039 0.077 0.17 14 -0.23 32 46
PRKCD -0.033 0.081 0.24 8 -0.22 25 33
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.026 0.08 0.13 5 -0.18 66 71
PTPN2 0.036 0.007 -10000 0 0 18 18
EP300 0.034 0.011 -10000 0 0 50 50
IRF1 -0.036 0.059 0.21 3 -0.28 13 16
STAT1 (dimer)/PIASy -0.026 0.065 0.18 19 -0.19 8 27
SOCS1 0.017 0.095 -10000 0 -1 4 4
mol:GDP -0.023 0.066 0.17 22 -0.19 4 26
CASP1 -0.02 0.074 0.18 16 -0.16 65 81
PTGES2 0.035 0.007 -10000 0 0 20 20
IRF9 -0.002 0.044 0.13 15 -0.13 18 33
mol:PI-3-4-5-P3 0.014 0.084 -10000 0 -0.15 73 73
RAP1/GDP -0.032 0.052 0.11 18 -0.17 7 25
CBL -0.024 0.058 0.15 25 -0.18 6 31
MAP3K1 -0.023 0.056 0.15 18 -0.18 6 24
PIAS1 0.035 0.008 -10000 0 0 26 26
PIAS4 0.035 0.008 -10000 0 0 24 24
antigen processing and presentation of peptide antigen via MHC class II -0.026 0.08 0.13 5 -0.18 66 71
PTPN11 -0.018 0.06 0.16 25 -0.18 6 31
CREBBP 0.037 0.005 -10000 0 0 9 9
RAPGEF1 0.035 0.007 -10000 0 0 18 18
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.017 0.021 0.093 16 -10000 0 16
BAD/BCL-XL/YWHAZ 0.047 0.034 -10000 0 -0.13 11 11
CDKN1B -0.024 0.12 0.2 5 -0.33 57 62
CDKN1A -0.027 0.12 -10000 0 -0.33 60 60
FRAP1 0.036 0.006 -10000 0 0 16 16
PRKDC 0.034 0.01 -10000 0 0 45 45
FOXO3 -0.018 0.11 -10000 0 -0.31 61 61
AKT1 -0.018 0.12 -10000 0 -0.33 58 58
BAD 0.036 0.006 -10000 0 0 13 13
AKT3 0.015 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.018 0.11 -10000 0 -0.31 61 61
AKT1/ASK1 -0.009 0.13 0.25 1 -0.32 60 61
BAD/YWHAZ 0.064 0.037 -10000 0 -0.13 12 12
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.035 0.008 -10000 0 0 28 28
JNK cascade 0.009 0.12 0.31 60 -0.24 1 61
TSC1 -0.025 0.12 0.2 1 -0.33 59 60
YWHAZ 0.035 0.007 -10000 0 0 21 21
AKT1/RAF1 0 0.13 0.26 1 -0.34 61 62
EP300 0.033 0.011 -10000 0 0 50 50
mol:GDP -0.018 0.12 -10000 0 -0.32 60 60
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.026 0.12 -10000 0 -0.33 62 62
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.001 0.022 0.12 14 -10000 0 14
MAP3K5 0.03 0.014 -10000 0 0 90 90
MAPKAP1 0.034 0.009 -10000 0 0 32 32
negative regulation of cell cycle 0.003 0.11 0.36 24 -10000 0 24
YWHAH 0.032 0.013 -10000 0 0 73 73
AKT1S1 -0.018 0.11 -10000 0 -0.31 61 61
CASP9 -0.02 0.12 0.2 3 -0.32 59 62
YWHAB 0.034 0.01 -10000 0 0 41 41
p27Kip1/KPNA1 -0.006 0.13 0.29 4 -0.32 60 64
GBL 0.036 0.006 -10000 0 0 15 15
PDK1/Src/Hsp90 0.046 0.014 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
SRC 0.034 0.009 -10000 0 0 34 34
AKT2/p21CIP1 -0.024 0.11 0.24 1 -0.28 61 62
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.07 -10000 0 -0.44 8 8
CHUK -0.022 0.1 -10000 0 -0.33 47 47
BAD/BCL-XL 0.003 0.12 -10000 0 -0.32 56 56
mTORC2 0.06 0.032 -10000 0 -0.12 9 9
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.005 0.13 -10000 0 -0.42 28 28
PDPK1 0.036 0.005 -10000 0 0 8 8
MDM2 -0.016 0.12 0.2 10 -0.32 58 68
MAPKKK cascade 0 0.13 0.33 61 -0.26 1 62
MDM2/Cbp/p300 0.015 0.13 0.27 1 -0.31 59 60
TSC1/TSC2 -0.029 0.13 0.26 8 -0.34 62 70
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.12 0.26 1 -0.3 59 60
glucose import -0.008 0.022 0.2 3 -10000 0 3
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.013 0.084 -10000 0 -0.34 10 10
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.022 0.2 3 -10000 0 3
GSK3A -0.019 0.12 0.25 8 -0.32 57 65
FOXO1 -0.018 0.11 -10000 0 -0.31 61 61
GSK3B -0.024 0.12 0.2 4 -0.34 60 64
SFN 0.031 0.013 -10000 0 0 80 80
G1/S transition of mitotic cell cycle -0.028 0.13 0.25 9 -0.33 62 71
p27Kip1/14-3-3 family 0.011 0.11 -10000 0 -0.55 12 12
PRKACA 0.035 0.008 -10000 0 0 24 24
KPNA1 0.035 0.008 -10000 0 0 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.025 0.017 -10000 0 0 166 166
CREBBP 0.036 0.005 -10000 0 0 9 9
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.047 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 0 20 20
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.004 -10000 0 0 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.035 0.007 -10000 0 0 21 21
RAC1-CDC42/GTP/PAK family 0.002 0.049 -10000 0 -0.14 43 43
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.034 0.01 -10000 0 0 40 40
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.005 -10000 0 0 8 8
FYN 0.03 0.014 -10000 0 0 88 88
MAP3K12 0.036 0.006 -10000 0 0 12 12
FGR 0.033 0.012 -10000 0 0 56 56
p38 alpha/TAB1 0.02 0.11 0.18 6 -0.25 41 47
PRKG1 0.026 0.017 -10000 0 0 147 147
DUSP8 0.034 0.01 -10000 0 0 40 40
PGK/cGMP/p38 alpha 0.004 0.096 0.16 2 -0.25 39 41
apoptosis 0.018 0.1 0.18 6 -0.24 41 47
RAL/GTP 0.027 0.037 -10000 0 -0.12 19 19
LYN 0.031 0.013 -10000 0 0 74 74
DUSP1 0.031 0.013 -10000 0 0 76 76
PAK1 0.036 0.006 -10000 0 0 16 16
SRC 0.034 0.009 -10000 0 0 34 34
RAC1/OSM/MEKK3/MKK3 0.046 0.037 -10000 0 -0.11 5 5
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.025 0.017 -10000 0 0 162 162
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 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.031 0.028 -10000 0 -0.12 5 5
MAPK11 0.001 0.12 0.2 8 -0.3 47 55
BLK 0.036 0.007 -10000 0 0 17 17
HCK 0.027 0.016 -10000 0 0 141 141
MAP2K3 0.036 0.005 -10000 0 0 10 10
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.033 0.011 -10000 0 0 49 49
TRAF6/MEKK3 0.045 0.011 -10000 0 -0.1 1 1
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
MAPK14 0.012 0.11 0.18 11 -0.26 43 54
positive regulation of innate immune response 0.004 0.14 0.22 10 -0.33 47 57
LCK 0.035 0.007 -10000 0 0 18 18
p38alpha-beta/MKP7 0.002 0.13 0.2 11 -0.32 47 58
p38alpha-beta/MKP5 0.017 0.14 0.24 7 -0.33 40 47
PGK/cGMP 0.019 0.012 -10000 0 -10000 0 0
PAK2 0.035 0.007 -10000 0 0 21 21
p38alpha-beta/MKP1 0.008 0.14 0.24 6 -0.33 48 54
CDC42 0.035 0.008 -10000 0 0 26 26
RALB 0.036 0.006 -10000 0 0 16 16
RALA 0.024 0.018 -10000 0 0 182 182
PAK3 0.027 0.016 -10000 0 0 139 139
S1P3 pathway

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
PDGFRB 0.035 0.008 -10000 0 0 26 26
mol:S1P 0.001 0.002 0.017 4 -10000 0 4
S1P1/S1P/Gi -0.019 0.11 -10000 0 -0.25 65 65
GNAO1 0.031 0.014 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.024 0.038 -10000 0 -0.1 28 28
AKT1 -0.014 0.16 -10000 0 -0.48 47 47
AKT3 0.009 0.077 -10000 0 -0.38 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.008 -10000 0 0 26 26
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.037 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.019 -10000 0 0 261 261
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 0.018 4 -10000 0 4
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.034 0.01 -10000 0 0 45 45
mol:Ca2+ -0.002 0.1 0.2 1 -0.29 36 37
MAPK3 -0.009 0.098 0.18 1 -0.28 38 39
MAPK1 -0.003 0.092 0.18 1 -0.27 31 32
JAK2 -0.009 0.11 0.2 6 -0.32 39 45
CXCR4 -0.007 0.098 0.18 1 -0.28 39 40
FLT1 0.036 0.01 0.07 1 -10000 0 1
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
SRC -0.01 0.096 -10000 0 -0.28 36 36
S1P/S1P3/Gi -0.002 0.1 0.2 1 -0.29 36 37
RAC1 0.025 0.017 -10000 0 0 162 162
RhoA/GTP 0.01 0.11 0.18 1 -0.27 40 41
VEGFA 0.002 0.002 0.032 3 -10000 0 3
S1P/S1P2/Gi -0.006 0.1 0.16 1 -0.26 47 48
VEGFR1 homodimer/VEGFA homodimer 0.029 0.01 0.11 3 -10000 0 3
RHOA 0.035 0.007 -10000 0 0 21 21
S1P/S1P3/Gq 0.015 0.04 -10000 0 -0.15 26 26
GNAQ 0.035 0.009 -10000 0 0 30 30
GNAZ 0.032 0.014 -10000 0 0 80 80
G12/G13 0.026 0.048 -10000 0 -0.14 28 28
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GNA12 0.023 0.018 -10000 0 0 188 188
GNA13 0.035 0.007 -10000 0 0 20 20
GNA11 0.033 0.011 -10000 0 0 51 51
Rac1/GTP 0 0.092 -10000 0 -0.3 25 25
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.028 0.074 0.2 22 -0.27 10 32
FYN -0.01 0.11 0.24 11 -0.3 34 45
LAT/GRAP2/SLP76 0.021 0.076 0.22 5 -0.29 12 17
IKBKB 0.037 0.003 -10000 0 0 4 4
AKT1 0.005 0.084 0.2 19 -0.23 25 44
B2M 0.037 0.009 -10000 0 0 25 25
IKBKG -0.003 0.035 0.09 18 -0.098 10 28
MAP3K8 0.022 0.018 -10000 0 0 198 198
mol:Ca2+ -0.01 0.009 -10000 0 -0.04 3 3
integrin-mediated signaling pathway 0.024 0.007 -10000 0 -0.11 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.007 0.1 0.24 18 -0.28 26 44
TRPV6 0.39 0.59 1.2 162 -10000 0 162
CD28 0.037 0.001 -10000 0 -10000 0 0
SHC1 0.019 0.079 0.2 31 -0.32 10 41
receptor internalization 0.019 0.064 0.17 10 -0.3 9 19
PRF1 -0.14 0.31 -10000 0 -0.61 144 144
KRAS 0.034 0.009 -10000 0 0 35 35
GRB2 0.035 0.007 -10000 0 0 18 18
COT/AKT1 0.006 0.064 0.19 6 -0.21 19 25
LAT 0.012 0.075 0.21 14 -0.3 12 26
EntrezGene:6955 0.001 0.004 0.014 41 -10000 0 41
CD3D 0.035 0.011 -10000 0 0 45 45
CD3E 0.038 0.007 -10000 0 0 10 10
CD3G 0.037 0.008 -10000 0 0 18 18
RASGRP2 0.006 0.018 0.073 1 -0.15 4 5
RASGRP1 -0.022 0.13 0.22 27 -0.25 94 121
HLA-A 0.038 0.007 -10000 0 0 12 12
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.024 0.007 -10000 0 -0.11 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.055 0.13 36 -0.1 19 55
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.037 -10000 0 -0.13 27 27
PRKCA 0.001 0.06 0.16 26 -0.18 6 32
GRAP2 0.034 0.01 -10000 0 0 37 37
mol:IP3 0.003 0.055 -10000 0 -0.23 10 10
EntrezGene:6957 0.001 0.004 0.015 41 -10000 0 41
TCR/CD3/MHC I/CD8 0.018 0.05 0.15 12 -0.2 9 21
ORAI1 -0.34 0.49 -10000 0 -1.1 162 162
CSK 0.013 0.074 0.21 14 -0.3 12 26
B7 family/CD28 0.062 0.098 0.28 18 -0.28 11 29
CHUK 0.025 0.017 -10000 0 0 163 163
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.015 0.077 0.2 10 -0.33 12 22
PTPN6 0.008 0.08 0.22 14 -0.3 14 28
VAV1 0.018 0.077 0.2 26 -0.3 10 36
Monovalent TCR/CD3 0.022 0.017 0.1 9 -10000 0 9
CBL 0.036 0.005 -10000 0 0 8 8
LCK 0.006 0.093 0.24 14 -0.31 17 31
PAG1 0.015 0.074 0.2 14 -0.3 12 26
RAP1A 0.036 0.005 -10000 0 0 10 10
TCR/CD3/MHC I/CD8/LCK 0.015 0.079 0.21 11 -0.32 13 24
CD80 0.036 0.007 -10000 0 0 16 16
CD86 0.033 0.012 -10000 0 0 65 65
PDK1/CARD11/BCL10/MALT1 0.002 0.046 -10000 0 -0.15 26 26
HRAS 0.034 0.009 -10000 0 0 36 36
GO:0035030 0.012 0.075 0.21 20 -0.25 11 31
CD8A 0.001 0.004 0.015 41 -10000 0 41
CD8B 0.001 0.004 0.015 43 -10000 0 43
PTPRC 0.029 0.015 -10000 0 0 110 110
PDK1/PKC theta 0.007 0.092 0.23 24 -0.27 17 41
CSK/PAG1 0.011 0.072 0.21 13 -0.29 12 25
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.05 0.035 -10000 0 -0.15 13 13
GRAP2/SLP76 0.03 0.085 0.23 5 -0.3 14 19
STIM1 -0.071 0.11 1 1 -10000 0 1
RAS family/GTP 0.005 0.072 0.16 19 -0.18 30 49
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.019 0.066 0.17 10 -0.32 9 19
mol:DAG -0.02 0.038 -10000 0 -0.2 10 10
RAP1A/GDP 0.009 0.028 0.071 27 -0.052 16 43
PLCG1 0.034 0.01 -10000 0 0 37 37
CD247 0.001 0.004 0.014 41 -10000 0 41
cytotoxic T cell degranulation -0.13 0.3 -10000 0 -0.58 147 147
RAP1A/GTP 0.004 0.007 -10000 0 -0.054 4 4
mol:PI-3-4-5-P3 0.009 0.091 0.23 19 -0.26 21 40
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.069 0.18 1 -0.27 10 11
NRAS 0.032 0.012 -10000 0 0 63 63
ZAP70 0.037 0.002 -10000 0 0 2 2
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
LAT/GRAP2/SLP76/VAV1 0.011 0.068 0.2 4 -0.29 8 12
MALT1 0.034 0.009 -10000 0 0 34 34
TRAF6 0.036 0.005 -10000 0 0 10 10
CD8 heterodimer 0.003 0.008 0.028 44 -10000 0 44
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.028 -10000 0 -0.15 10 10
PRKCE 0.001 0.06 0.17 25 -0.18 6 31
PRKCQ 0.008 0.096 0.24 22 -0.29 17 39
LCP2 0.031 0.013 -10000 0 0 75 75
BCL10 0.035 0.007 -10000 0 0 19 19
regulation of survival gene product expression 0.005 0.077 0.19 21 -0.21 23 44
IKK complex 0 0.039 0.12 17 -0.089 3 20
RAS family/GDP -0.004 0.015 -10000 0 -0.041 38 38
MAP3K14 0.01 0.064 0.17 27 -0.17 17 44
PDPK1 0.005 0.08 0.2 21 -0.21 26 47
TCR/CD3/MHC I/CD8/Fyn 0.01 0.069 0.18 1 -0.34 9 10
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.008 0.059 -10000 0 -0.22 25 25
epithelial cell differentiation 0.064 0.052 -10000 0 -0.14 25 25
CYFIP2 0.031 0.013 -10000 0 0 76 76
ENAH -0.042 0.072 0.32 7 -0.27 7 14
EGFR 0.009 0.016 -10000 0 0 380 380
EPHA2 0.033 0.011 -10000 0 0 55 55
MYO6 -0.029 0.05 0.18 9 -0.22 13 22
CTNNB1 0.036 0.006 -10000 0 0 15 15
ABI1/Sra1/Nap1 0.029 0.065 -10000 0 -0.13 56 56
AQP5 -0.021 0.053 0.2 2 -0.29 10 12
CTNND1 0.035 0.009 -10000 0 0 31 31
mol:PI-4-5-P2 -0.031 0.045 0.17 7 -0.21 13 20
regulation of calcium-dependent cell-cell adhesion -0.028 0.044 0.18 8 -0.19 8 16
EGF 0.035 0.008 -10000 0 0 25 25
NCKAP1 0.037 0.002 -10000 0 0 2 2
AQP3 -0.035 0.076 -10000 0 -0.3 32 32
cortical microtubule organization 0.064 0.052 -10000 0 -0.14 25 25
GO:0000145 -0.03 0.041 0.16 7 -0.2 13 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.071 0.054 -10000 0 -0.14 25 25
MLLT4 0.034 0.009 -10000 0 0 34 34
ARF6/GDP -0.053 0.04 -10000 0 -0.22 13 13
ARF6 0.035 0.009 -10000 0 0 29 29
Ephrin A1/EPHA2/NCK1/GIT1 0.075 0.055 -10000 0 -0.13 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.031 0.087 0.16 1 -0.29 38 39
PVRL2 0.034 0.009 -10000 0 0 35 35
ZYX -0.022 0.045 0.18 6 -0.21 15 21
ARF6/GTP 0.079 0.061 -10000 0 -0.13 24 24
CDH1 0.034 0.01 -10000 0 0 37 37
EGFR/EGFR/EGF/EGF -0.001 0.06 -10000 0 -0.13 67 67
RhoA/GDP 0.064 0.057 -10000 0 -0.14 29 29
actin cytoskeleton organization -0.024 0.047 0.17 7 -0.23 12 19
IGF-1R heterotetramer 0.033 0.011 -10000 0 0 54 54
GIT1 0.037 0.003 -10000 0 0 3 3
IGF1R 0.033 0.011 -10000 0 0 54 54
IGF1 0.035 0.007 -10000 0 0 21 21
DIAPH1 -0.13 0.28 -10000 0 -0.58 50 50
Wnt receptor signaling pathway -0.064 0.052 0.14 25 -10000 0 25
RHOA 0.035 0.007 -10000 0 0 21 21
RhoA/GTP -0.054 0.042 -10000 0 -0.23 14 14
CTNNA1 0.035 0.007 -10000 0 0 18 18
VCL -0.024 0.048 0.17 7 -0.23 12 19
EFNA1 0.033 0.011 -10000 0 0 52 52
LPP -0.03 0.047 0.18 4 -0.24 13 17
Ephrin A1/EPHA2 0.046 0.063 -10000 0 -0.14 41 41
SEC6/SEC8 -0.044 0.029 -10000 0 -0.14 26 26
MGAT3 -0.028 0.045 0.18 8 -0.2 8 16
HGF/MET 0.037 0.048 -10000 0 -0.14 15 15
HGF 0.024 0.018 -10000 0 0 177 177
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.01 0.058 -10000 0 -0.21 28 28
actin cable formation -0.04 0.1 0.31 10 -0.32 27 37
KIAA1543 -0.025 0.037 0.16 7 -0.18 8 15
KIFC3 -0.031 0.042 0.19 5 -0.2 8 13
NCK1 0.035 0.008 -10000 0 0 27 27
EXOC3 0.037 0.003 -10000 0 0 4 4
ACTN1 -0.027 0.051 0.19 7 -0.22 16 23
NCK1/GIT1 0.05 0.024 -10000 0 -0.14 6 6
mol:GDP 0.064 0.052 -10000 0 -0.14 25 25
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.028 0.031 0.053 22 -0.13 25 47
PIP5K1C -0.031 0.046 0.18 7 -0.21 13 20
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.017 -10000 0 0 156 156
ROCK1 -0.035 0.086 0.35 11 -0.3 5 16
adherens junction assembly -0.024 0.072 0.22 6 -0.28 21 27
IGF-1R heterotetramer/IGF1 0.05 0.062 -10000 0 -0.15 37 37
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
MET 0.023 0.018 -10000 0 0 189 189
PLEKHA7 -0.028 0.031 0.053 22 -0.13 25 47
mol:GTP 0.072 0.053 -10000 0 -0.13 25 25
establishment of epithelial cell apical/basal polarity -0.039 0.039 0.12 12 -0.19 10 22
cortical actin cytoskeleton stabilization 0.008 0.059 -10000 0 -0.22 25 25
regulation of cell-cell adhesion -0.024 0.047 0.17 7 -0.23 12 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.01 0.058 -10000 0 -0.21 28 28
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.035 0.008 -10000 0 0 28 28
RAS family/GTP/Tiam1 -0.006 0.086 -10000 0 -0.2 63 63
NT3 (dimer)/TRKC 0.047 0.027 -10000 0 -0.14 6 6
NT3 (dimer)/TRKB 0.026 0.07 -10000 0 -0.13 74 74
SHC/Grb2/SOS1/GAB1/PI3K -0.008 0.095 -10000 0 -0.21 74 74
RAPGEF1 0.035 0.007 -10000 0 0 18 18
BDNF 0.032 0.012 -10000 0 0 66 66
PIK3CA 0.031 0.014 -10000 0 0 82 82
DYNLT1 0.034 0.01 -10000 0 0 45 45
NTRK1 0.036 0.007 -10000 0 0 17 17
NTRK2 0.027 0.016 -10000 0 0 138 138
NTRK3 0.034 0.009 -10000 0 0 35 35
NT-4/5 (dimer)/TRKB 0.013 0.059 -10000 0 -0.12 78 78
neuron apoptosis -0.008 0.12 0.32 39 -0.23 1 40
SHC 2-3/Grb2 0.007 0.13 0.24 1 -0.35 39 40
SHC1 0.033 0.011 -10000 0 0 52 52
SHC2 -0.01 0.12 -10000 0 -0.43 28 28
SHC3 -0.01 0.12 -10000 0 -0.42 28 28
STAT3 (dimer) 0.021 0.088 -10000 0 -0.29 37 37
NT3 (dimer)/TRKA 0.059 0.031 -10000 0 -10000 0 0
RIN/GDP 0.001 0.075 0.18 6 -0.22 28 34
GIPC1 0.035 0.008 -10000 0 0 24 24
KRAS 0.034 0.009 -10000 0 0 35 35
DNAJA3 -0.005 0.04 0.14 3 -0.16 3 6
RIN/GTP 0.011 0.036 -10000 0 -0.13 26 26
CCND1 -0.012 0.11 -10000 0 -0.5 26 26
MAGED1 0.035 0.008 -10000 0 0 26 26
PTPN11 0.036 0.005 -10000 0 0 11 11
RICS 0.033 0.011 -10000 0 0 47 47
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.04 0.032 -10000 0 -0.12 14 14
GRB2 0.035 0.007 -10000 0 0 18 18
NGF (dimer)/TRKA/MATK 0.046 0.014 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.048 0.019 -10000 0 -0.14 1 1
ELMO1 0.018 0.018 -10000 0 0 257 257
RhoG/GTP/ELMO1/DOCK1 0.008 0.045 -10000 0 -0.12 45 45
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.009 -10000 0 0 36 36
DOCK1 0.024 0.018 -10000 0 0 182 182
GAB2 0.033 0.011 -10000 0 0 48 48
RIT2 0.025 0.017 -10000 0 0 168 168
RIT1 0.032 0.012 -10000 0 0 62 62
FRS2 0.035 0.009 -10000 0 0 30 30
DNM1 0.035 0.008 -10000 0 0 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.01 0.047 0.16 2 -0.17 10 12
mol:GDP -0.002 0.1 0.21 11 -0.3 29 40
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.002 0.044 -10000 0 -0.13 44 44
RIT1/GDP 0.007 0.082 0.18 8 -0.21 31 39
TIAM1 0.033 0.011 -10000 0 0 46 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
BDNF (dimer)/TRKB 0.027 0.071 -10000 0 -0.13 72 72
KIDINS220/CRKL/C3G 0.05 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.052 -10000 0 -0.16 31 31
FRS2 family/SHP2 0.067 0.028 -10000 0 -0.13 6 6
SHC/GRB2/SOS1/GAB1 0.049 0.047 -10000 0 -0.12 25 25
RIT1/GTP 0.014 0.041 -10000 0 -0.13 36 36
NT3 (dimer) 0.035 0.008 -10000 0 0 25 25
RAP1/GDP -0.002 0.06 -10000 0 -0.18 29 29
KIDINS220/CRKL 0.035 0.008 -10000 0 0 28 28
BDNF (dimer) 0.032 0.012 -10000 0 0 66 66
ubiquitin-dependent protein catabolic process 0.043 0.017 -10000 0 -0.12 1 1
Schwann cell development -0.011 0.016 -10000 0 -0.055 38 38
EHD4 0.034 0.01 -10000 0 0 39 39
FRS2 family/GRB2/SOS1 0.062 0.029 -10000 0 -0.11 8 8
FRS2 family/SHP2/CRK family/C3G/GAB2 0.008 0.071 -10000 0 -0.25 20 20
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 10 10
CDC42/GTP 0.017 0.083 -10000 0 -0.15 78 78
ABL1 0.032 0.013 -10000 0 0 69 69
SH2B family/GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
Rap1/GTP 0.003 0.069 -10000 0 -0.21 27 27
STAT3 0.021 0.088 -10000 0 -0.29 37 37
axon guidance 0.004 0.072 -10000 0 -0.14 82 82
MAPK3 -0.008 0.053 0.18 35 -10000 0 35
MAPK1 -0.009 0.049 0.17 34 -10000 0 34
CDC42/GDP 0.009 0.08 0.17 11 -0.21 26 37
NTF3 0.035 0.008 -10000 0 0 25 25
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.025 -10000 0 -0.12 9 9
PI3K 0.018 0.076 -10000 0 -0.16 72 72
FRS3 0.037 0.002 -10000 0 0 2 2
FAIM 0.035 0.009 -10000 0 0 29 29
GAB1 0.033 0.011 -10000 0 0 55 55
RASGRF1 -0.004 0.042 0.18 4 -0.13 4 8
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.018 0.021 0.09 11 -0.13 2 13
RGS19 0.033 0.011 -10000 0 0 53 53
CDC42 0.035 0.008 -10000 0 0 26 26
RAS family/GTP 0.008 0.1 0.23 1 -0.38 22 23
Rac1/GDP 0.009 0.069 0.18 9 -0.22 20 29
NGF (dimer)/TRKA/GRIT 0.039 0.035 -10000 0 -0.12 21 21
neuron projection morphogenesis -0.035 0.24 -10000 0 -0.87 36 36
NGF (dimer)/TRKA/NEDD4-2 0.044 0.017 -10000 0 -0.12 1 1
MAP2K1 -0.011 0.06 0.18 19 -0.19 6 25
NGFR 0.032 0.013 -10000 0 0 71 71
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.042 -10000 0 -0.24 7 7
RAS family/GTP/PI3K -0.024 0.11 -10000 0 -0.21 99 99
FRS2 family/SHP2/GRB2/SOS1 0.076 0.04 -10000 0 -0.14 10 10
NRAS 0.032 0.012 -10000 0 0 63 63
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
PRKCI 0.035 0.008 -10000 0 0 27 27
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.017 -10000 0 0 162 162
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.087 -10000 0 -0.5 11 11
RASA1 0.035 0.009 -10000 0 0 30 30
TRKA/c-Abl 0.032 0.059 -10000 0 -0.14 48 48
SQSTM1 0.034 0.009 -10000 0 0 35 35
BDNF (dimer)/TRKB/GIPC 0.048 0.076 -10000 0 -0.12 67 67
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.035 -10000 0 -0.1 16 16
MATK 0.035 0.008 -10000 0 0 27 27
NEDD4L 0.034 0.01 -10000 0 0 45 45
RAS family/GDP -0.021 0.057 -10000 0 -0.16 52 52
NGF (dimer)/TRKA 0.01 0.04 0.15 4 -0.13 4 8
Rac1/GTP -0.014 0.055 -10000 0 -0.2 23 23
FRS2 family/SHP2/CRK family 0.087 0.057 -10000 0 -0.13 18 18
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.033 0.11 0.31 17 -0.3 21 38
PDGFB-D/PDGFRB/SLAP 0.017 0.075 -10000 0 -0.16 72 72
PDGFB-D/PDGFRB/APS/CBL 0.045 0.024 -10000 0 -0.12 8 8
AKT1 -0.024 0.093 0.26 15 -0.23 20 35
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.11 0.28 16 -0.32 21 37
PIK3CA 0.031 0.014 -10000 0 0 82 82
FGR 0.005 0.1 0.23 3 -0.46 15 18
mol:Ca2+ 0.017 0.1 0.27 12 -0.36 19 31
MYC 0.009 0.26 0.4 30 -0.67 53 83
SHC1 0.033 0.011 -10000 0 0 52 52
HRAS/GDP 0.015 0.07 0.18 36 -0.17 18 54
LRP1/PDGFRB/PDGFB 0.048 0.057 -10000 0 -0.14 32 32
GRB10 0.021 0.018 -10000 0 0 221 221
PTPN11 0.036 0.005 -10000 0 0 11 11
GO:0007205 0.016 0.1 0.27 12 -0.37 19 31
PTEN 0.025 0.017 -10000 0 0 166 166
GRB2 0.035 0.007 -10000 0 0 18 18
GRB7 0.036 0.006 -10000 0 0 15 15
PDGFB-D/PDGFRB/SHP2 0.047 0.035 -10000 0 -0.15 14 14
PDGFB-D/PDGFRB/GRB10 0.02 0.052 -10000 0 -0.15 32 32
cell cycle arrest 0.017 0.075 -10000 0 -0.16 72 72
HRAS 0.034 0.009 -10000 0 0 36 36
HIF1A -0.029 0.084 0.23 15 -0.24 18 33
GAB1 0.011 0.13 0.29 13 -0.37 30 43
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.01 0.13 0.31 18 -0.33 29 47
PDGFB-D/PDGFRB 0.054 0.054 -10000 0 -0.14 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.044 0.042 -10000 0 -0.15 21 21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.021 0.12 0.27 6 -0.29 34 40
positive regulation of MAPKKK cascade 0.047 0.035 -10000 0 -0.15 14 14
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.016 0.11 0.27 12 -0.37 19 31
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -0.01 27 27
PDGFB-D/PDGFRB/GRB7 0.05 0.024 -10000 0 -0.14 5 5
SHB 0.033 0.011 -10000 0 0 51 51
BLK 0.014 0.078 0.24 2 -0.43 7 9
PTPN2 0.034 0.016 0.07 1 -0.017 40 41
PDGFB-D/PDGFRB/SNX15 0.05 0.027 -10000 0 -0.14 8 8
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.001 0.16 0.31 16 -0.41 44 60
CBL 0.036 0.005 -10000 0 0 8 8
PDGFB-D/PDGFRB/DEP1 0.049 0.028 -10000 0 -0.14 8 8
LCK 0.017 0.063 0.24 2 -0.36 3 5
PDGFRB 0.031 0.022 0.078 1 -0.019 73 74
ACP1 0.035 0.007 -10000 0 0 18 18
HCK -0.042 0.18 -10000 0 -0.5 59 59
ABL1 0.007 0.12 0.25 20 -0.34 29 49
PDGFB-D/PDGFRB/CBL 0.011 0.13 0.33 7 -0.42 26 33
PTPN1 0.032 0.017 -10000 0 -0.011 65 65
SNX15 0.037 0.003 -10000 0 0 4 4
STAT3 0.034 0.01 -10000 0 0 37 37
STAT1 0.034 0.01 -10000 0 0 40 40
cell proliferation 0.017 0.24 0.38 34 -0.6 53 87
SLA 0.027 0.016 -10000 0 0 133 133
actin cytoskeleton reorganization -0.016 0.071 0.19 38 -0.2 7 45
SRC 0.014 0.047 -10000 0 -10000 0 0
PI3K -0.047 0.045 -10000 0 -0.17 36 36
PDGFB-D/PDGFRB/GRB7/SHC 0.061 0.038 -10000 0 -0.13 11 11
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.025 0.11 0.31 12 -0.33 21 33
LYN -0.035 0.16 -10000 0 -0.47 54 54
LRP1 0.032 0.013 -10000 0 0 70 70
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.036 0.004 -10000 0 0 5 5
STAT5A 0.036 0.004 -10000 0 0 5 5
NCK1-2/p130 Cas 0.064 0.067 -10000 0 -0.14 26 26
SPHK1 0.034 0.012 0.061 3 0 51 54
EDG1 0.035 0.011 0.061 3 0 45 48
mol:DAG 0.016 0.11 0.27 12 -0.37 19 31
PLCG1 0.016 0.11 0.29 10 -0.38 19 29
NHERF/PDGFRB 0.062 0.037 -10000 0 -0.13 12 12
YES1 -0.006 0.13 0.23 2 -0.55 23 25
cell migration 0.061 0.037 -10000 0 -0.13 12 12
SHC/Grb2/SOS1 0.066 0.062 -10000 0 -0.14 21 21
SLC9A3R2 0.036 0.005 -10000 0 0 8 8
SLC9A3R1 0.034 0.009 -10000 0 0 36 36
NHERF1-2/PDGFRB/PTEN 0.055 0.056 -10000 0 -0.11 13 13
FYN -0.052 0.19 0.23 1 -0.45 78 79
DOK1 -0.013 0.06 0.17 38 -0.13 1 39
HRAS/GTP 0.021 0.028 -10000 0 -0.13 16 16
PDGFB 0.034 0.01 -10000 0 0 38 38
RAC1 0.031 0.2 0.35 40 -0.43 50 90
PRKCD -0.009 0.063 0.18 39 -0.14 1 40
FER -0.011 0.063 0.18 37 -0.14 1 38
MAPKKK cascade -0.009 0.068 0.16 56 -0.18 5 61
RASA1 -0.01 0.064 0.18 37 -0.2 4 41
NCK1 0.035 0.008 -10000 0 0 27 27
NCK2 0.036 0.007 -10000 0 0 17 17
p62DOK/Csk -0.01 0.066 0.17 39 -0.2 3 42
PDGFB-D/PDGFRB/SHB 0.045 0.028 -10000 0 -0.14 6 6
chemotaxis 0.008 0.12 0.25 20 -0.33 29 49
STAT1-3-5/STAT1-3-5 0.06 0.073 -10000 0 -0.14 34 34
Bovine Papilomavirus E5/PDGFRB 0.02 0.026 -10000 0 -0.14 8 8
PTPRJ 0.036 0.005 -10000 0 0 11 11
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.032 0.012 -10000 0 0 59 59
GNB1/GNG2 0.029 0.034 -10000 0 -0.12 14 14
forebrain development 0.034 0.061 0.26 3 -0.36 3 6
GNAO1 0.031 0.014 -10000 0 0 87 87
SMO/beta Arrestin2 0.034 0.031 -10000 0 -0.14 4 4
SMO 0.025 0.018 -10000 0 0 170 170
ARRB2 0.035 0.008 -10000 0 0 25 25
GLI3/SPOP 0.002 0.11 0.22 1 -0.34 29 30
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.01 -10000 0 0 39 39
GNAI2 0.034 0.01 -10000 0 0 44 44
SIN3/HDAC complex 0.055 0.042 -10000 0 -0.13 17 17
GNAI1 0.018 0.018 -10000 0 0 261 261
XPO1 0.037 0.005 0.061 1 0 5 6
GLI1/Su(fu) 0.012 0.045 -10000 0 -0.26 6 6
SAP30 0.035 0.007 -10000 0 0 18 18
mol:GDP 0.025 0.018 -10000 0 0 170 170
MIM/GLI2A 0.041 0.014 0.12 11 -10000 0 11
IFT88 0.034 0.009 -10000 0 0 32 32
GNAI3 0.036 0.006 -10000 0 0 14 14
GLI2 0.001 0.088 -10000 0 -0.35 20 20
GLI3 -0.013 0.099 0.21 1 -0.33 28 29
CSNK1D 0.035 0.007 -10000 0 0 20 20
CSNK1E 0.032 0.013 -10000 0 0 68 68
SAP18 0.034 0.01 -10000 0 0 43 43
embryonic digit morphogenesis 0.034 0.009 -10000 0 0 32 32
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.011 0.087 -10000 0 -0.26 37 37
SIN3B 0.034 0.009 -10000 0 0 33 33
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.012 0.072 -10000 0 -0.28 23 23
GLI2/Su(fu) -0.003 0.072 -10000 0 -0.31 18 18
FOXA2 0.049 0.037 -10000 0 -0.49 1 1
neural tube patterning 0.034 0.061 0.26 3 -0.36 3 6
SPOP 0.035 0.008 -10000 0 0 23 23
Su(fu)/PIAS1 0.046 0.037 0.098 146 -0.088 8 154
GNB1 0.035 0.007 -10000 0 0 20 20
CSNK1G2 0.035 0.008 -10000 0 0 27 27
CSNK1G3 0.036 0.005 -10000 0 0 11 11
MTSS1 0.041 0.014 0.12 11 -10000 0 11
embryonic limb morphogenesis 0.034 0.061 0.26 3 -0.36 3 6
SUFU 0.002 0.01 -10000 0 -0.11 4 4
LGALS3 0.028 0.015 -10000 0 0 117 117
catabolic process 0.012 0.14 0.29 2 -0.45 29 31
GLI3A/CBP 0.045 0.009 -10000 0 -10000 0 0
KIF3A 0.033 0.011 -10000 0 0 53 53
GLI1 0.034 0.062 0.26 3 -0.36 3 6
RAB23 0.035 0.009 -10000 0 0 31 31
CSNK1A1 0.036 0.006 -10000 0 0 12 12
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.036 0.005 -10000 0 0 8 8
Su(fu)/Galectin3 0.037 0.04 0.098 118 -0.12 7 125
GNAZ 0.031 0.013 -10000 0 0 80 80
RBBP4 0.033 0.012 -10000 0 0 57 57
CSNK1G1 0.036 0.006 -10000 0 0 12 12
PIAS1 0.035 0.008 -10000 0 0 26 26
PRKACA 0.035 0.008 -10000 0 0 24 24
GLI2/SPOP 0.016 0.097 -10000 0 -0.32 25 25
STK36 0.001 0.003 0.022 4 -10000 0 4
Gi family/GNB1/GNG2/GDP -0.017 0.1 -10000 0 -0.35 30 30
PTCH1 0.033 0.057 0.25 3 -0.33 3 6
MIM/GLI1 0.057 0.068 0.35 2 -0.33 3 5
CREBBP 0.045 0.009 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.001 0.093 0.15 2 -0.29 31 33
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.036 0.007 -10000 0 0 17 17
PTK2 0.034 0.009 -10000 0 0 34 34
CRKL -0.018 0.044 0.097 27 -0.15 24 51
GRB2/SOS1/SHC 0.04 0.032 -10000 0 -0.12 14 14
HRAS 0.034 0.009 -10000 0 0 36 36
IRS1/Crk 0.019 0.048 -10000 0 -0.14 36 36
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.055 -10000 0 -0.15 28 28
AKT1 -0.034 0.075 0.16 26 -0.22 30 56
BAD -0.039 0.073 0.15 24 -0.23 29 53
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.045 0.099 28 -0.16 24 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.026 0.049 0.22 1 -0.15 29 30
RAF1 -0.034 0.15 -10000 0 -0.56 28 28
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.047 0.054 -10000 0 -0.14 30 30
YWHAZ 0.035 0.007 -10000 0 0 21 21
IGF-1R heterotetramer/IGF1/IRS1 0.033 0.049 -10000 0 -0.16 24 24
PIK3CA 0.031 0.014 -10000 0 0 82 82
RPS6KB1 -0.033 0.072 0.16 31 -0.2 23 54
GNB2L1 0.037 0.002 -10000 0 0 2 2
positive regulation of MAPKKK cascade -0.033 0.12 0.24 2 -0.44 28 30
PXN 0.036 0.004 -10000 0 0 7 7
PIK3R1 0.032 0.012 -10000 0 0 63 63
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
HRAS/GTP 0.016 0.054 -10000 0 -0.14 43 43
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.067 0.057 -10000 0 -0.12 34 34
IGF-1R heterotetramer 0.036 0.014 -10000 0 -0.034 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.049 0.06 -10000 0 -0.14 36 36
Crk/p130 Cas/Paxillin 0.038 0.055 0.22 1 -0.14 36 37
IGF1R 0.036 0.014 -10000 0 -0.034 1 1
IGF1 0.034 0.025 -10000 0 -0.058 30 30
IRS2/Crk -0.03 0.058 0.1 19 -0.19 31 50
PI3K 0.04 0.088 -10000 0 -0.14 77 77
apoptosis 0.038 0.076 0.22 30 -0.17 21 51
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
PRKCD 0.005 0.063 0.17 8 -0.21 24 32
RAF1/14-3-3 E -0.012 0.13 -10000 0 -0.48 29 29
BAD/14-3-3 -0.04 0.08 0.18 13 -0.23 30 43
PRKCZ -0.027 0.07 0.16 31 -0.2 23 54
Crk/p130 Cas/Paxillin/FAK1 -0.046 0.073 0.13 25 -0.22 30 55
PTPN1 0.034 0.01 -10000 0 0 43 43
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.007 0.06 -10000 0 -0.22 25 25
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.038 0.071 -10000 0 -0.14 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.028 0.051 0.13 3 -0.14 35 38
GRB10 0.021 0.018 -10000 0 0 221 221
PTPN11 -0.018 0.045 0.099 28 -0.15 24 52
IRS1 0.01 0.041 0.12 3 -0.16 24 27
IRS2 -0.02 0.049 0.1 20 -0.2 24 44
IGF-1R heterotetramer/IGF1 0.04 0.051 -10000 0 -0.17 24 24
GRB2 0.035 0.007 -10000 0 0 18 18
PDPK1 -0.026 0.077 0.17 29 -0.21 22 51
YWHAE 0.035 0.008 -10000 0 0 27 27
PRKD1 -0.003 0.065 0.15 1 -0.24 28 29
SHC1 0.033 0.011 -10000 0 0 52 52
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.052 0.038 -10000 0 -0.1 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.039 0.17 -10000 0 -0.52 41 41
AKT1 -0.052 0.23 -10000 0 -0.62 59 59
PIK3CA 0.031 0.014 -10000 0 0 82 82
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.046 0.24 -10000 0 -0.63 59 59
mol:Ca2+ 0.006 0.051 -10000 0 -0.25 3 3
IGF1R 0.033 0.011 -10000 0 0 54 54
E2/ER alpha (dimer)/Striatin 0.046 0.012 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 52 52
apoptosis 0.051 0.22 0.59 61 -10000 0 61
RhoA/GTP -0.043 0.037 -10000 0 -0.13 54 54
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.013 0.15 0.18 8 -0.39 46 54
regulation of stress fiber formation 0.038 0.06 0.18 22 -0.14 26 48
E2/ERA-ERB (dimer) 0.045 0.015 -10000 0 -10000 0 0
KRAS 0.034 0.009 -10000 0 0 35 35
G13/GTP 0.043 0.014 -10000 0 -10000 0 0
pseudopodium formation -0.038 0.06 0.14 26 -0.18 22 48
E2/ER alpha (dimer)/PELP1 0.044 0.023 -10000 0 -0.12 7 7
GRB2 0.035 0.007 -10000 0 0 18 18
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.031 0.014 -10000 0 0 87 87
HRAS 0.034 0.009 -10000 0 0 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.013 0.16 0.22 1 -0.42 49 50
E2/ER beta (dimer) 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.003 0.058 0.13 3 -0.19 26 29
mol:NADP -0.013 0.16 0.22 1 -0.42 49 50
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.007 0.05 0.17 18 -0.34 1 19
IGF-1R heterotetramer 0.033 0.011 -10000 0 0 54 54
PLCB1 0.01 0.04 -10000 0 -0.34 1 1
PLCB2 0.009 0.04 -10000 0 -0.34 1 1
IGF1 0.035 0.007 -10000 0 0 21 21
mol:L-citrulline -0.013 0.16 0.22 1 -0.42 49 50
RHOA 0.035 0.007 -10000 0 0 21 21
Gai/GDP -0.067 0.24 -10000 0 -0.64 70 70
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.035 0.009 -10000 0 0 31 31
GNAQ 0.035 0.009 -10000 0 0 30 30
ESR1 0.035 0.009 -10000 0 0 31 31
Gq family/GDP/Gbeta gamma -0.002 0.15 -10000 0 -0.48 37 37
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.14 -10000 0 -0.69 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.004 0.16 0.25 8 -0.39 46 54
GNAZ 0.031 0.013 -10000 0 0 80 80
E2/ER alpha (dimer) 0.026 0.007 -10000 0 -10000 0 0
STRN 0.037 0.003 -10000 0 0 4 4
GNAL 0.036 0.006 -10000 0 0 14 14
PELP1 0.036 0.007 -10000 0 0 17 17
MAPK11 -0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
GNAI1 0.018 0.018 -10000 0 0 261 261
HBEGF -0.011 0.18 0.33 26 -0.47 42 68
cAMP biosynthetic process 0.037 0.016 -10000 0 -10000 0 0
SRC -0.039 0.16 0.2 9 -0.47 45 54
PI3K 0.018 0.076 -10000 0 -0.16 72 72
GNB1 0.035 0.007 -10000 0 0 20 20
G13/GDP/Gbeta gamma 0.021 0.069 -10000 0 -0.17 34 34
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.12 -10000 0 -0.34 41 41
Gs family/GTP 0.047 0.02 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.065 -10000 0 -0.13 54 54
vasodilation -0.011 0.16 0.22 1 -0.4 49 50
mol:DAG 0.007 0.05 0.17 18 -0.34 1 19
Gs family/GDP/Gbeta gamma 0.003 0.062 -10000 0 -0.18 34 34
MSN -0.042 0.061 0.14 23 -0.2 22 45
Gq family/GTP 0.023 0.042 -10000 0 -0.35 1 1
mol:PI-3-4-5-P3 -0.044 0.22 -10000 0 -0.61 59 59
NRAS 0.032 0.012 -10000 0 0 63 63
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.011 0.16 0.4 49 -0.22 1 50
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
RhoA/GDP 0.017 0.068 -10000 0 -0.19 29 29
NOS3 -0.015 0.17 0.22 1 -0.44 49 50
GNA11 0.033 0.011 -10000 0 0 51 51
MAPKKK cascade 0.002 0.15 0.26 1 -0.46 37 38
E2/ER alpha (dimer)/PELP1/Src 0 0.16 0.24 18 -0.41 45 63
ruffle organization -0.038 0.06 0.14 26 -0.18 22 48
ROCK2 -0.033 0.064 0.16 29 -0.2 14 43
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GNA13 0.035 0.007 -10000 0 0 20 20
MMP9 -0.023 0.17 0.36 9 -0.43 50 59
MMP2 -0.023 0.17 0.25 11 -0.46 45 56
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.1 -10000 0 -0.26 27 27
mol:DAG -0.012 0.089 0.18 4 -0.25 26 30
PLCG1 -0.013 0.091 0.18 4 -0.26 26 30
YES1 -0.017 0.086 -10000 0 -0.28 21 21
FZD3 0.029 0.015 -10000 0 0 109 109
FZD6 0.027 0.016 -10000 0 0 130 130
G protein 0.002 0.11 0.2 25 -0.28 26 51
MAP3K7 -0.035 0.075 0.14 6 -0.23 31 37
mol:Ca2+ -0.012 0.087 0.18 4 -0.24 26 30
mol:IP3 -0.012 0.089 0.18 4 -0.25 26 30
NLK -0.037 0.25 -10000 0 -0.77 52 52
GNB1 0.035 0.007 -10000 0 0 20 20
CAMK2A -0.03 0.077 0.16 5 -0.24 26 31
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
Noncanonical Wnts/FZD -0.006 0.089 -10000 0 -0.29 16 16
CSNK1A1 0.036 0.006 -10000 0 0 12 12
GNAS -0.016 0.081 -10000 0 -0.28 17 17
GO:0007205 -0.019 0.084 0.18 4 -0.26 26 30
WNT6 0.037 0.002 -10000 0 0 1 1
WNT4 0.035 0.007 -10000 0 0 20 20
NFAT1/CK1 alpha -0.005 0.099 0.22 5 -0.28 24 29
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.03 0.015 -10000 0 0 99 99
WNT11 0.036 0.006 -10000 0 0 15 15
CDC42 -0.026 0.083 0.17 5 -0.27 23 28
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.034 -10000 0 -0.14 8 8
CRKL 0.048 0.11 0.28 7 -0.4 16 23
mol:PIP3 0 0.054 -10000 0 -0.85 1 1
AKT1 -0.013 0.054 -10000 0 -0.76 1 1
PTK2B 0.036 0.006 -10000 0 0 16 16
RAPGEF1 0.045 0.1 0.28 12 -0.38 16 28
RANBP10 0.036 0.005 -10000 0 0 8 8
PIK3CA 0.031 0.014 -10000 0 0 82 82
HGF/MET/SHIP2 0.043 0.038 -10000 0 -0.13 2 2
MAP3K5 0.044 0.11 0.27 8 -0.36 18 26
HGF/MET/CIN85/CBL/ENDOPHILINS 0.041 0.035 -10000 0 -10000 0 0
AP1 0.033 0.08 0.15 99 -0.15 46 145
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 52 52
apoptosis -0.12 0.36 -10000 0 -0.78 113 113
STAT3 (dimer) 0.012 0.057 -10000 0 -0.27 10 10
GAB1/CRKL/SHP2/PI3K 0.064 0.12 0.29 3 -0.38 20 23
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.064 0.11 0.28 4 -0.39 16 20
PTPN11 0.036 0.005 -10000 0 0 11 11
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.034 0.01 -10000 0 0 37 37
PTEN 0.025 0.017 -10000 0 0 166 166
ELK1 0.11 0.18 0.36 169 -10000 0 169
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.032 0.16 1 -0.14 12 13
PAK1 -0.017 0.053 -10000 0 -0.72 1 1
HGF/MET/RANBP10 0.043 0.037 -10000 0 -10000 0 0
HRAS 0.012 0.081 -10000 0 -0.47 10 10
DOCK1 0.036 0.1 0.26 9 -0.39 16 25
GAB1 0.046 0.1 -10000 0 -0.41 16 16
CRK 0.048 0.11 0.28 4 -0.4 16 20
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.066 -10000 0 -0.42 9 9
JUN 0.034 0.01 -10000 0 0 41 41
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.018 -10000 0 -0.12 1 1
PIK3R1 0.032 0.012 -10000 0 0 63 63
cell morphogenesis 0.031 0.11 0.26 31 -0.31 14 45
GRB2/SHC 0.074 0.064 0.17 105 -0.12 2 107
FOS 0.025 0.017 -10000 0 0 162 162
GLMN 0.003 0.012 0.069 2 -0.17 2 4
cell motility 0.11 0.18 0.36 169 -10000 0 169
HGF/MET/MUC20 0.029 0.024 -10000 0 -10000 0 0
cell migration 0.073 0.063 0.17 105 -0.12 2 107
GRB2 0.035 0.007 -10000 0 0 18 18
CBL 0.036 0.005 -10000 0 0 8 8
MET/RANBP10 0.034 0.027 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.046 -10000 0 -0.27 5 5
MET/MUC20 0.017 0.013 -10000 0 -10000 0 0
RAP1B 0.044 0.1 0.27 13 -0.36 16 29
RAP1A 0.039 0.1 0.29 11 -0.36 15 26
HGF/MET/RANBP9 0.041 0.041 -10000 0 -0.12 7 7
RAF1 0.038 0.1 0.28 2 -0.44 13 15
STAT3 0.009 0.054 -10000 0 -0.29 9 9
cell proliferation 0.037 0.078 0.24 14 -0.27 8 22
RPS6KB1 0.013 0.018 0.13 1 -10000 0 1
MAPK3 0.08 0.16 0.42 14 -10000 0 14
MAPK1 0.11 0.21 0.51 66 -10000 0 66
RANBP9 0.036 0.006 -10000 0 0 16 16
MAPK8 -0.046 0.16 0.25 3 -0.33 77 80
SRC 0.007 0.043 -10000 0 -0.29 4 4
PI3K 0.058 0.074 0.17 89 -0.16 7 96
MET/Glomulin 0.015 0.028 -10000 0 -0.088 22 22
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.028 0.099 0.29 1 -0.42 14 15
MET 0.023 0.018 -10000 0 0 189 189
MAP4K1 0.053 0.11 0.29 5 -0.36 18 23
PTK2 0.034 0.009 -10000 0 0 34 34
MAP2K2 0.037 0.1 0.3 13 -0.4 13 26
BAD -0.02 0.053 -10000 0 -0.72 1 1
MAP2K4 0.037 0.1 0.26 12 -0.34 18 30
SHP2/GRB2/SOS1/GAB1 0.021 0.077 -10000 0 -0.34 17 17
INPPL1 0.036 0.006 -10000 0 0 13 13
PXN 0.036 0.004 -10000 0 0 7 7
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.001 0.018 0.076 13 -0.12 1 14
PLCgamma1/PKC 0.024 0.014 -10000 0 -0.13 3 3
HGF 0.024 0.018 -10000 0 0 177 177
RASA1 0.035 0.009 -10000 0 0 30 30
NCK1 0.035 0.008 -10000 0 0 27 27
PTPRJ 0.036 0.005 -10000 0 0 11 11
NCK/PLCgamma1 0.079 0.058 0.17 110 -0.097 7 117
PDPK1 -0.004 0.055 -10000 0 -0.79 1 1
HGF/MET/SHIP 0.029 0.024 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.036 0.028 -9999 0 -0.14 2 2
FBXW11 0.035 0.007 -9999 0 0 22 22
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 22 22
CHUK 0.025 0.017 -9999 0 0 163 163
NF kappa B2 p100/RelB 0.065 0.063 -9999 0 -0.12 10 10
NFKB1 0.035 0.007 -9999 0 0 18 18
MAP3K14 0.036 0.006 -9999 0 0 13 13
NF kappa B1 p50/RelB 0.048 0.024 -9999 0 -0.14 5 5
RELB 0.034 0.009 -9999 0 0 32 32
NFKB2 0.026 0.017 -9999 0 0 155 155
NF kappa B2 p52/RelB 0.033 0.023 -9999 0 -10000 0 0
regulation of B cell activation 0.033 0.023 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.017 -9999 0 0 142 142
ITGB7 0.036 0.006 -9999 0 0 14 14
ITGA4 0.036 0.006 -9999 0 0 13 13
alpha4/beta7 Integrin 0.052 0.012 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.039 0.025 -9999 0 -9999 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.016 0.11 0.24 16 -0.37 22 38
CRKL 0.02 0.1 0.22 14 -0.39 22 36
HRAS 0.032 0.1 0.25 8 -0.32 22 30
mol:PIP3 0.058 0.12 0.28 36 -0.32 24 60
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.036 0.004 -10000 0 0 7 7
GAB1 0.025 0.11 0.23 13 -0.4 22 35
FOXO3 0.054 0.16 0.3 39 -0.35 41 80
AKT1 0.055 0.17 0.32 38 -0.37 41 79
BAD 0.047 0.16 0.31 35 -0.36 42 77
megakaryocyte differentiation 0.025 0.1 0.23 12 -0.39 20 32
GSK3B 0.048 0.17 0.32 39 -0.37 43 82
RAF1 0.022 0.091 0.24 14 -0.27 23 37
SHC1 0.033 0.011 -10000 0 0 52 52
STAT3 0.018 0.1 0.22 6 -0.4 22 28
STAT1 0.016 0.2 -10000 0 -0.87 21 21
HRAS/SPRED1 0.024 0.089 0.22 8 -0.27 23 31
cell proliferation 0.009 0.094 0.23 4 -0.38 22 26
PIK3CA 0.031 0.014 -10000 0 0 82 82
TEC 0.036 0.004 -10000 0 0 6 6
RPS6KB1 0.056 0.12 0.26 28 -0.37 21 49
HRAS/SPRED2 0.043 0.099 0.25 11 -0.27 22 33
LYN/TEC/p62DOK 0.066 0.12 0.27 1 -0.4 22 23
MAPK3 0.02 0.087 0.25 21 -0.21 22 43
STAP1 0.025 0.1 0.22 7 -0.39 22 29
GRAP2 0.034 0.01 -10000 0 0 37 37
JAK2 0.015 0.17 -10000 0 -0.74 21 21
STAT1 (dimer) 0.02 0.2 -10000 0 -0.85 21 21
mol:Gleevec -0.002 0.006 -10000 0 -0.023 1 1
GRB2/SOCS1/VAV1 0.073 0.12 0.28 1 -0.38 22 23
actin filament polymerization 0.027 0.1 0.22 7 -0.38 22 29
LYN 0.031 0.013 -10000 0 0 74 74
STAP1/STAT5A (dimer) 0.024 0.14 0.28 3 -0.54 21 24
PIK3R1 0.033 0.012 -10000 0 0 63 63
CBL/CRKL/GRB2 0.053 0.11 0.27 5 -0.38 21 26
PI3K 0.063 0.14 0.3 23 -0.36 23 46
PTEN 0.025 0.017 -10000 0 0 166 166
SCF/KIT/EPO/EPOR 0.023 0.22 -10000 0 -1 21 21
MAPK8 0.008 0.095 0.24 3 -0.39 22 25
STAT3 (dimer) 0.02 0.1 0.23 8 -0.39 22 30
positive regulation of transcription 0.02 0.078 0.23 22 -0.18 18 40
mol:GDP 0.041 0.098 0.22 4 -0.33 22 26
PIK3C2B 0.025 0.1 0.24 11 -0.39 22 33
CBL/CRKL 0.041 0.11 0.25 8 -0.38 21 29
FER 0.023 0.1 0.24 7 -0.39 22 29
SH2B3 0.025 0.1 0.22 7 -0.39 22 29
PDPK1 0.051 0.12 0.28 33 -0.3 24 57
SNAI2 0.026 0.11 0.23 12 -0.4 21 33
positive regulation of cell proliferation 0.028 0.17 0.32 3 -0.66 21 24
KITLG 0.039 0.021 -10000 0 -0.051 20 20
cell motility 0.028 0.17 0.32 3 -0.66 21 24
PTPN6 0.023 0.025 -10000 0 -0.033 68 68
EPOR 0.048 0.085 -10000 0 -0.5 2 2
STAT5A (dimer) 0.032 0.14 0.29 5 -0.54 21 26
SOCS1 0.036 0.005 -10000 0 0 9 9
cell migration -0.022 0.1 0.38 22 -0.24 7 29
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.026 0.022 -10000 0 -0.036 14 14
VAV1 0.034 0.009 -10000 0 0 33 33
GRB10 0.011 0.088 0.3 4 -0.36 19 23
PTPN11 0.027 0.022 -10000 0 -0.027 67 67
SCF/KIT 0.029 0.11 0.23 9 -0.41 22 31
GO:0007205 -0.002 0.007 0.021 17 -0.023 1 18
MAP2K1 0.012 0.082 0.22 13 -0.22 26 39
CBL 0.036 0.005 -10000 0 0 8 8
KIT 0.005 0.24 -10000 0 -1.1 22 22
MAP2K2 0.017 0.092 0.29 20 -0.22 23 43
SHC/Grb2/SOS1 0.053 0.11 0.24 2 -0.36 22 24
STAT5A 0.033 0.14 0.29 5 -0.56 21 26
GRB2 0.035 0.007 -10000 0 0 18 18
response to radiation 0.027 0.11 0.23 13 -0.4 21 34
SHC/GRAP2 0.043 0.031 -10000 0 -0.14 8 8
PTPRO 0.024 0.1 0.24 12 -0.4 20 32
SH2B2 0.025 0.1 0.22 7 -0.39 22 29
DOK1 0.037 0.002 -10000 0 0 2 2
MATK 0.019 0.1 0.22 5 -0.39 22 27
CREBBP 0.052 0.045 0.14 5 -0.12 21 26
BCL2 0.039 0.14 -10000 0 -0.76 9 9
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.051 0.39 0.77 2 -1 26 28
STAT6 (cleaved dimer) -0.068 0.35 -10000 0 -0.89 37 37
IGHG1 -0.013 0.26 0.44 20 -0.8 22 42
IGHG3 -0.067 0.36 0.63 1 -0.88 39 40
AKT1 -0.024 0.27 0.52 5 -0.71 32 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.016 0.19 0.46 6 -0.54 8 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.008 0.26 0.5 5 -0.74 20 25
THY1 -0.13 0.5 0.79 2 -1.2 67 69
MYB 0.033 0.011 -10000 0 0 55 55
HMGA1 0.036 0.005 -10000 0 0 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3 0 0.26 0.52 13 -0.58 16 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.007 0.25 0.5 4 -0.77 17 21
SP1 0.029 0.076 0.12 95 -0.14 69 164
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.045 -10000 0 -0.079 1 1
STAT6 (dimer)/ETS1 -0.054 0.37 0.59 1 -0.94 31 32
SOCS1 -0.04 0.3 0.5 6 -0.66 35 41
SOCS3 -0.004 0.22 -10000 0 -0.69 2 2
FCER2 -0.028 0.32 0.66 1 -0.76 18 19
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.064 0.38 0.72 1 -1 26 27
GRB2 0.035 0.007 -10000 0 0 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.003 0.22 0.45 11 -0.58 18 29
T cell proliferation -0.071 0.38 0.64 3 -0.95 36 39
IL4R/JAK1 -0.072 0.38 0.67 1 -0.97 34 35
EGR2 -0.12 0.5 0.73 1 -1.2 58 59
JAK2 0.019 0.066 0.16 18 -10000 0 18
JAK3 0.034 0.016 -10000 0 -0.042 4 4
PIK3R1 0.032 0.012 -10000 0 0 63 63
JAK1 0.027 0.04 0.11 8 -10000 0 8
COL1A2 -0.11 0.48 0.54 2 -1.2 76 78
CCL26 -0.063 0.38 0.69 2 -0.91 38 40
IL4R -0.059 0.41 0.78 4 -1.1 27 31
PTPN6 0.015 0.037 -10000 0 -0.059 6 6
IL13RA2 -0.32 0.66 0.77 3 -1.1 177 180
IL13RA1 0.024 0.067 0.16 18 -10000 0 18
IRF4 0.047 0.11 -10000 0 -10000 0 0
ARG1 0.005 0.21 0.51 4 -0.77 10 14
CBL -0.008 0.24 0.48 6 -0.56 17 23
GTF3A 0.048 0.035 0.12 70 -0.15 3 73
PIK3CA 0.031 0.014 -10000 0 0 82 82
IL13RA1/JAK2 0.026 0.1 0.24 10 -0.16 23 33
IRF4/BCL6 0.042 0.11 -10000 0 -10000 0 0
CD40LG 0.041 0.004 0.14 1 -10000 0 1
MAPK14 -0.006 0.24 0.49 6 -0.57 13 19
mitosis -0.019 0.26 0.51 5 -0.66 32 37
STAT6 -0.069 0.43 0.79 6 -1.1 33 39
SPI1 0.038 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.25 0.48 6 -0.65 31 37
STAT6 (dimer) -0.068 0.43 0.79 6 -1.1 33 39
STAT6 (dimer)/PARP14 -0.083 0.38 -10000 0 -0.97 36 36
mast cell activation -0.002 0.016 -10000 0 -0.041 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.007 0.21 0.48 5 -0.54 8 13
FRAP1 -0.023 0.27 0.52 5 -0.7 32 37
LTA -0.066 0.38 0.72 1 -1 24 25
FES 0.036 0.006 -10000 0 0 15 15
T-helper 1 cell differentiation 0.063 0.43 1 33 -0.79 6 39
CCL11 -0.068 0.36 -10000 0 -0.98 25 25
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.01 0.22 0.51 5 -0.56 6 11
IL2RG 0.034 0.016 -10000 0 -0.044 1 1
IL10 -0.051 0.39 0.72 3 -1 22 25
IRS1 0.033 0.011 -10000 0 0 51 51
IRS2 0.03 0.014 -10000 0 0 94 94
IL4 0.027 0.17 0.58 1 -0.84 5 6
IL5 -0.065 0.38 0.72 1 -1 26 27
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.058 0.39 0.67 11 -0.92 37 48
COL1A1 0.016 0.26 0.61 5 -1 8 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.076 0.38 -10000 0 -1.1 27 27
IL2R gamma/JAK3 0.054 0.019 -10000 0 -10000 0 0
TFF3 -0.06 0.38 0.72 1 -1 26 27
ALOX15 -0.066 0.38 0.72 1 -1 26 27
MYBL1 0.03 0.014 -10000 0 0 96 96
T-helper 2 cell differentiation -0.046 0.34 0.64 4 -0.78 35 39
SHC1 0.033 0.011 -10000 0 0 52 52
CEBPB 0.034 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.017 0.26 0.52 5 -0.75 21 26
mol:PI-3-4-5-P3 -0.023 0.27 0.52 5 -0.7 32 37
PI3K -0.028 0.28 0.52 5 -0.75 32 37
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.005 0.047 -10000 0 -0.088 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.004 0.22 0.44 11 -0.57 22 33
ITGB3 -0.066 0.38 0.72 1 -1 26 27
PIGR -0.054 0.38 0.72 2 -1 24 26
IGHE -0.003 0.079 0.18 39 -0.18 13 52
MAPKKK cascade 0.005 0.21 0.44 11 -0.56 22 33
BCL6 0.031 0.013 -10000 0 0 71 71
OPRM1 -0.065 0.38 0.72 1 -1 22 23
RETNLB -0.063 0.38 0.69 2 -0.91 38 40
SELP -0.062 0.38 0.8 2 -1 27 29
AICDA -0.064 0.36 -10000 0 -0.99 23 23
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.036 0.005 -10000 0 0 11 11
Caspase 8 (4 units) -0.01 0.097 -10000 0 -0.24 25 25
NEF 0.002 0 -10000 0 -10000 0 0
NFKBIA 0.038 0.019 0.078 64 -10000 0 64
BIRC3 -0.025 0.029 0.18 2 -0.2 2 4
CYCS -0.004 0.079 0.18 47 -0.24 9 56
RIPK1 0.035 0.007 -10000 0 0 20 20
CD247 0.002 0 -10000 0 -10000 0 0
MAP2K7 -0.01 0.1 -10000 0 -0.38 8 8
protein ubiquitination 0.012 0.065 0.21 3 -0.25 7 10
CRADD 0.036 0.005 -10000 0 0 11 11
DAXX 0.036 0.004 -10000 0 0 6 6
FAS 0.02 0.018 -10000 0 0 239 239
BID -0.003 0.057 0.12 1 -0.17 43 44
NF-kappa-B/RelA/I kappa B alpha 0.076 0.055 -10000 0 -0.14 17 17
TRADD 0.036 0.005 -10000 0 0 10 10
MAP3K5 0.03 0.014 -10000 0 0 90 90
CFLAR 0.036 0.005 -10000 0 0 8 8
FADD 0.036 0.006 -10000 0 0 12 12
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.076 0.055 -10000 0 -0.14 17 17
MAPK8 -0.006 0.093 -10000 0 -0.36 8 8
APAF1 0.037 0.003 -10000 0 0 3 3
TRAF1 0.035 0.008 -10000 0 0 24 24
TRAF2 0.036 0.006 -10000 0 0 16 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.061 -10000 0 -0.17 47 47
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.029 0.077 -10000 0 -0.28 11 11
CHUK 0.013 0.067 0.21 3 -0.27 7 10
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.04 0.084 -10000 0 -0.12 61 61
TCRz/NEF 0.007 0.001 -10000 0 -10000 0 0
TNF 0.037 0.003 -10000 0 0 4 4
FASLG 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.042 0.016 0.079 72 -10000 0 72
TNFR1A/BAG4/TNF-alpha 0.053 0.056 -10000 0 -0.13 41 41
CASP6 0.005 0.11 -10000 0 -0.56 7 7
CASP7 -0.034 0.14 0.27 13 -0.3 41 54
RELA 0.043 0.015 0.079 74 -10000 0 74
CASP2 0.025 0.017 -10000 0 0 164 164
CASP3 -0.001 0.11 0.26 11 -0.32 15 26
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
TNFR1A/BAG4 0.035 0.055 -10000 0 -0.14 42 42
CASP8 0.036 0.006 -10000 0 0 13 13
CASP9 0.034 0.009 -10000 0 0 34 34
MAP3K14 0.024 0.077 0.19 2 -0.28 8 10
APAF-1/Caspase 9 -0.011 0.084 0.17 9 -0.22 14 23
BCL2 -0.016 0.091 -10000 0 -0.34 7 7
Caspase cascade in apoptosis

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
TOP1 -0.008 0.087 -10000 0 -0.26 35 35
ACTA1 -0.036 0.09 0.16 1 -0.28 37 38
NUMA1 -0.002 0.084 -10000 0 -0.32 18 18
SPTAN1 -0.044 0.091 0.2 5 -0.27 42 47
LIMK1 0.011 0.11 0.19 75 -0.32 15 90
BIRC3 0.031 0.014 -10000 0 0 82 82
BIRC2 0.036 0.006 -10000 0 0 12 12
BAX 0.034 0.01 -10000 0 0 43 43
CASP10 -0.008 0.032 0.083 47 -10000 0 47
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.09 -10000 0 -0.29 31 31
DIABLO 0.036 0.004 -10000 0 0 6 6
apoptotic nuclear changes -0.043 0.09 0.2 5 -0.27 42 47
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.036 0.005 -10000 0 0 11 11
GSN -0.037 0.096 0.2 5 -0.29 36 41
MADD 0.036 0.006 -10000 0 0 15 15
TFAP2A 0.045 0.054 -10000 0 -0.44 5 5
BID -0.001 0.04 0.11 2 -0.19 18 20
MAP3K1 -0.002 0.051 -10000 0 -0.39 5 5
TRADD 0.036 0.005 -10000 0 0 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.05 0.018 -10000 0 -0.14 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.041 0.098 0.2 12 -0.28 40 52
CASP9 0.034 0.009 -10000 0 0 34 34
DNA repair 0.034 0.071 0.2 40 -10000 0 40
neuron apoptosis 0.017 0.11 -10000 0 -0.61 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.024 0.088 -10000 0 -0.32 26 26
APAF1 0.037 0.003 -10000 0 0 3 3
CASP6 0.026 0.11 -10000 0 -0.84 6 6
TRAF2 0.036 0.006 -10000 0 0 16 16
ICAD/CAD -0.046 0.084 0.21 1 -0.3 30 31
CASP7 -0.079 0.11 -10000 0 -0.23 144 144
KRT18 0.026 0.054 -10000 0 -0.45 5 5
apoptosis -0.033 0.092 -10000 0 -0.33 22 22
DFFA -0.042 0.086 0.17 1 -0.29 33 34
DFFB -0.04 0.085 -10000 0 -0.28 34 34
PARP1 -0.034 0.071 -10000 0 -0.21 40 40
actin filament polymerization -0.017 0.1 0.3 15 -0.18 75 90
TNF 0.037 0.003 -10000 0 0 4 4
CYCS 0.015 0.039 0.18 3 -0.24 3 6
SATB1 0.018 0.11 -10000 0 -0.73 6 6
SLK -0.025 0.084 -10000 0 -0.28 34 34
p15 BID/BAX 0.002 0.061 0.15 2 -0.16 44 46
CASP2 0.06 0.1 0.22 127 -0.26 7 134
JNK cascade 0.002 0.051 0.38 5 -10000 0 5
CASP3 -0.039 0.09 -10000 0 -0.29 37 37
LMNB2 0.062 0.092 0.24 8 -0.37 4 12
RIPK1 0.035 0.007 -10000 0 0 20 20
CASP4 0.03 0.014 -10000 0 0 94 94
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.16 6 6
negative regulation of DNA binding 0.045 0.054 -10000 0 -0.43 5 5
stress fiber formation -0.036 0.084 -10000 0 -0.28 34 34
GZMB -0.005 0.033 0.093 47 -10000 0 47
CASP1 -0.01 0.066 -10000 0 -0.2 54 54
LMNB1 0.043 0.13 0.24 10 -0.32 26 36
APP 0.017 0.11 -10000 0 -0.62 15 15
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.011 0.002 0 13 -10000 0 13
VIM -0.033 0.095 -10000 0 -0.32 27 27
LMNA 0.065 0.09 0.24 13 -0.35 4 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.018 0.058 0.16 1 -0.27 9 10
LRDD 0.035 0.007 -10000 0 0 21 21
SREBF1 -0.042 0.087 0.18 1 -0.3 31 32
APAF-1/Caspase 9 0.014 0.1 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.002 0.083 -10000 0 -0.31 18 18
CFL2 0.017 0.11 0.18 75 -0.31 15 90
GAS2 -0.033 0.091 0.19 3 -0.29 32 35
positive regulation of apoptosis 0.061 0.1 0.23 21 -0.38 7 28
PRF1 0.023 0.018 -10000 0 0 190 190
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.003 0.1 -10000 0 -0.39 30 30
Crk/p130 Cas/Paxillin -0.057 0.094 -10000 0 -0.2 117 117
JUN -0.016 0.048 -10000 0 -0.25 10 10
HRAS 0.034 0.009 -10000 0 0 36 36
RET51/GFRalpha1/GDNF/GRB10 0.037 0.06 -10000 0 -0.12 28 28
RAP1A 0.036 0.005 -10000 0 0 10 10
FRS2 0.035 0.009 -10000 0 0 30 30
RAP1A/GDP 0.026 0.008 -10000 0 -0.13 1 1
RET51/GFRalpha1/GDNF/DOK1 0.062 0.047 -10000 0 -10000 0 0
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
RET9/GFRalpha1/GDNF/Enigma 0.048 0.033 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
RAP1A/GTP 0.056 0.048 -10000 0 -0.11 1 1
GRB7 0.036 0.006 -10000 0 0 15 15
RET51/GFRalpha1/GDNF 0.061 0.047 -10000 0 -10000 0 0
MAPKKK cascade -0.007 0.075 -10000 0 -0.19 14 14
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.039 0.046 -10000 0 -0.11 23 23
lamellipodium assembly -0.027 0.083 -10000 0 -0.2 60 60
RET51/GFRalpha1/GDNF/SHC 0.058 0.051 -10000 0 -0.12 8 8
PIK3CA 0.031 0.014 -10000 0 0 82 82
RET9/GFRalpha1/GDNF/SHC 0.041 0.039 -10000 0 -0.11 8 8
RET9/GFRalpha1/GDNF/Shank3 0.032 0.022 -10000 0 -10000 0 0
MAPK3 -0.026 0.035 0.2 7 -10000 0 7
DOK1 0.037 0.002 -10000 0 0 2 2
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 7 7
neurite development -0.021 0.039 0.23 4 -0.21 8 12
DOK5 0.029 0.015 -10000 0 0 110 110
GFRA1 0.025 0.017 -10000 0 0 162 162
MAPK8 0 0.044 -10000 0 -0.26 5 5
HRAS/GTP 0.021 0.094 -10000 0 -0.18 11 11
tube development 0.026 0.028 0.2 3 -0.099 8 11
MAPK1 -0.025 0.035 0.2 7 -10000 0 7
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.012 0.064 -10000 0 -0.22 15 15
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
SRC 0.034 0.009 -10000 0 0 34 34
PDLIM7 0.036 0.005 -10000 0 0 9 9
RET51/GFRalpha1/GDNF/Dok6 0.057 0.043 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 52 52
RET51/GFRalpha1/GDNF/Dok4 0.062 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.037 0.073 -10000 0 -0.11 67 67
PRKCA 0.036 0.004 -10000 0 0 6 6
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
CREB1 -0.033 0.097 -10000 0 -0.19 121 121
PIK3R1 0.032 0.012 -10000 0 0 63 63
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.011 0.066 -10000 0 -0.17 30 30
RET51/GFRalpha1/GDNF/Grb7 0.062 0.047 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.027 0.016 -10000 0 0 135 135
DOK4 0.036 0.006 -10000 0 0 13 13
JNK cascade -0.017 0.048 -10000 0 -0.24 12 12
RET9/GFRalpha1/GDNF/FRS2 0.046 0.034 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.035 0.009 -10000 0 0 30 30
NCK1 0.035 0.008 -10000 0 0 27 27
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.01 0.039 -10000 0 -0.18 18 18
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.026 0.093 -10000 0 -0.19 112 112
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.034 0.099 -10000 0 -0.19 115 115
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.009 0.048 -10000 0 -0.18 17 17
PI3K -0.058 0.13 0.19 1 -0.26 110 111
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.039 0.038 -10000 0 -0.1 8 8
GRB10 0.021 0.018 -10000 0 0 221 221
activation of MAPKK activity 0.011 0.051 -10000 0 -0.28 12 12
RET51/GFRalpha1/GDNF/FRS2 0.06 0.047 -10000 0 -10000 0 0
GAB1 0.033 0.011 -10000 0 0 55 55
IRS1 0.033 0.011 -10000 0 0 51 51
IRS2 0.03 0.014 -10000 0 0 94 94
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.01 0.056 -10000 0 -0.18 26 26
RET51/GFRalpha1/GDNF/PKC alpha 0.062 0.047 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 18 18
PRKACA 0.035 0.008 -10000 0 0 24 24
GDNF 0.036 0.004 -10000 0 0 6 6
RAC1 0.025 0.017 -10000 0 0 162 162
RET51/GFRalpha1/GDNF/IRS1 0.055 0.057 -10000 0 -0.11 22 22
Rac1/GTP -0.029 0.098 -10000 0 -0.26 39 39
RET9/GFRalpha1/GDNF 0.034 0.023 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.037 0.026 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.008 0.071 -10000 0 -0.3 21 21
KLHL20 0.049 0.094 0.23 42 -0.19 16 58
CYFIP2 0.031 0.013 -10000 0 0 76 76
Rac1/GDP 0.008 0.061 0.19 3 -0.25 14 17
ENAH 0.007 0.074 -10000 0 -0.32 20 20
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 29 0 5 34
RAP1A 0.036 0.005 -10000 0 0 10 10
CTNNB1 0.036 0.006 -10000 0 0 15 15
CDC42/GTP -0.023 0.057 0.12 25 -0.2 21 46
ABI1/Sra1/Nap1 -0.015 0.034 -10000 0 -0.13 29 29
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.084 0.039 -10000 0 -0.13 8 8
RAPGEF1 0 0.078 0.21 1 -0.28 19 20
CTNND1 0.035 0.009 -10000 0 0 31 31
regulation of calcium-dependent cell-cell adhesion 0.021 0.075 -10000 0 -0.3 22 22
CRK 0.007 0.08 0.19 3 -0.29 20 23
E-cadherin/gamma catenin/alpha catenin 0.062 0.035 -10000 0 -0.13 8 8
alphaE/beta7 Integrin 0.049 0.026 -10000 0 -0.14 7 7
IQGAP1 0.033 0.011 -10000 0 0 48 48
NCKAP1 0.037 0.002 -10000 0 0 2 2
Rap1/GTP/I-afadin 0.043 0.015 -10000 0 -0.1 1 1
DLG1 0.008 0.075 -10000 0 -0.3 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.034 0.044 -10000 0 -0.18 29 29
MLLT4 0.034 0.009 -10000 0 0 34 34
ARF6/GTP/NME1/Tiam1 0.036 0.033 -10000 0 -0.1 23 23
PI3K -0.041 0.058 0.06 1 -0.23 29 30
ARF6 0.035 0.009 -10000 0 0 29 29
mol:Ca2+ 0 0 0.001 68 0 27 95
E-cadherin/gamma catenin 0.048 0.018 -10000 0 -10000 0 0
TIAM1 0.034 0.011 -10000 0 0 46 46
E-cadherin(dimer)/Ca2+ 0.072 0.054 -10000 0 -0.14 25 25
AKT1 -0.02 0.056 0.14 9 -0.18 24 33
PIK3R1 0.032 0.012 -10000 0 0 63 63
CDH1 0.034 0.01 -10000 0 0 37 37
RhoA/GDP 0.017 0.074 0.2 4 -0.25 16 20
actin cytoskeleton organization 0.041 0.076 0.17 71 -0.14 15 86
CDC42/GDP 0.016 0.072 0.2 4 -0.25 14 18
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.049 -10000 0 -0.2 23 23
ITGB7 0.036 0.006 -10000 0 0 14 14
RAC1 0.025 0.017 -10000 0 0 162 162
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.077 0.058 -10000 0 -0.15 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin 0.056 0.031 -10000 0 -0.11 10 10
mol:GDP 0 0.076 0.2 5 -0.28 14 19
CDC42/GTP/IQGAP1 0.035 0.042 -10000 0 -0.12 33 33
JUP 0.033 0.011 -10000 0 0 51 51
p120 catenin/RhoA/GDP 0.031 0.082 0.22 5 -0.25 18 23
RAC1/GTP/IQGAP1 0.024 0.043 -10000 0 -0.12 30 30
PIP5K1C/AP1M1 0.02 0.03 -10000 0 -0.13 18 18
RHOA 0.035 0.007 -10000 0 0 21 21
CDC42 0.035 0.008 -10000 0 0 26 26
CTNNA1 0.036 0.007 -10000 0 0 18 18
positive regulation of S phase of mitotic cell cycle 0.015 0.048 0.12 17 -0.12 29 46
NME1 0 0 -10000 0 0 31 31
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.009 0.073 -10000 0 -0.3 20 20
regulation of cell-cell adhesion -0.027 0.04 -10000 0 -0.17 25 25
WASF2 -0.008 0.018 -10000 0 -0.073 29 29
Rap1/GTP -0.019 0.067 0.15 32 -0.22 22 54
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.091 0.051 -10000 0 -0.13 12 12
CCND1 0.017 0.057 0.14 17 -0.15 29 46
VAV2 0.023 0.11 -10000 0 -0.52 10 10
RAP1/GDP -0.006 0.069 0.16 29 -0.25 15 44
adherens junction assembly 0.009 0.071 -10000 0 -0.3 20 20
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.017 -10000 0 0 156 156
PIP5K1C 0.033 0.011 -10000 0 0 47 47
regulation of heterotypic cell-cell adhesion 0.069 0.047 0.2 3 -0.14 13 16
E-cadherin/beta catenin 0.007 0.02 -10000 0 -0.094 7 7
mol:GTP 0 0 0.001 62 0 31 93
SRC 0.007 0.07 -10000 0 -0.29 21 21
PIK3CA 0.031 0.014 -10000 0 0 82 82
Rac1/GTP -0.008 0.07 0.19 1 -0.29 18 19
E-cadherin/beta catenin/alpha catenin 0.064 0.036 -10000 0 -0.14 10 10
ITGAE 0.035 0.007 -10000 0 0 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.077 -10000 0 -0.3 22 22
ErbB4 signaling events

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.022 0.13 -10000 0 -0.63 18 18
epithelial cell differentiation -0.006 0.14 -10000 0 -0.65 18 18
ITCH 0.03 0.031 0.11 1 -0.11 21 22
WWP1 -0.021 0.22 -10000 0 -1.1 18 18
FYN 0.03 0.014 -10000 0 0 88 88
EGFR 0.009 0.016 -10000 0 0 380 380
PRL 0.036 0.006 -10000 0 0 15 15
neuron projection morphogenesis -0.026 0.11 0.25 6 -0.51 19 25
PTPRZ1 0.023 0.018 -10000 0 0 197 197
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.055 0.12 -10000 0 -0.54 18 18
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.11 -10000 0 -0.57 18 18
ADAM17 0.03 0.031 -10000 0 -0.1 22 22
ErbB4/ErbB4 0 0.14 -10000 0 -0.69 18 18
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.009 0.12 -10000 0 -0.62 18 18
NCOR1 0.035 0.008 -10000 0 0 27 27
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.12 -10000 0 -0.58 18 18
GRIN2B -0.026 0.11 0.23 2 -0.55 18 20
ErbB4/ErbB2/betacellulin 0.026 0.12 -10000 0 -0.55 18 18
STAT1 0.034 0.01 -10000 0 0 40 40
HBEGF 0.035 0.007 -10000 0 0 21 21
PRLR 0.036 0.004 -10000 0 0 6 6
E4ICDs/ETO2 0.022 0.13 -10000 0 -0.63 18 18
axon guidance -0.029 0.16 -10000 0 -0.79 18 18
NEDD4 0.029 0.031 0.11 1 -0.11 20 21
Prolactin receptor/Prolactin receptor/Prolactin 0.052 0.011 -10000 0 -10000 0 0
CBFA2T3 0.035 0.008 -10000 0 0 28 28
ErbB4/ErbB2/HBEGF 0.025 0.11 -10000 0 -0.55 18 18
MAPK3 -0.018 0.11 0.27 4 -0.52 18 22
STAT1 (dimer) 0.02 0.13 -10000 0 -0.63 18 18
MAPK1 -0.021 0.11 0.27 4 -0.53 18 22
JAK2 0.031 0.014 -10000 0 0 82 82
ErbB4/ErbB2/neuregulin 1 beta 0.005 0.11 -10000 0 -0.55 18 18
NRG1 -0.022 0.02 0.092 4 -0.084 18 22
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.036 0.004 -10000 0 0 7 7
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.029 0.16 -10000 0 -0.79 18 18
neural crest cell migration 0.005 0.11 -10000 0 -0.54 18 18
ERBB2 -0.022 0.023 0.1 7 -0.084 18 25
WWOX/E4ICDs 0.023 0.13 -10000 0 -0.63 18 18
SHC1 0.033 0.011 -10000 0 0 52 52
ErbB4/EGFR/neuregulin 4 -0.014 0.096 -10000 0 -0.46 18 18
apoptosis -0.006 0.12 0.58 18 -10000 0 18
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.023 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB2/epiregulin 0.024 0.12 -10000 0 -0.55 18 18
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.064 0.13 -10000 0 -0.57 18 18
MDM2 -0.002 0.13 0.26 12 -0.6 18 30
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.019 0.1 -10000 0 -0.51 18 18
STAT5A -0.035 0.15 -10000 0 -0.76 18 18
ErbB4/EGFR/neuregulin 1 beta -0.003 0.087 -10000 0 -0.42 18 18
DLG4 0.036 0.006 -10000 0 0 12 12
GRB2/SHC 0.043 0.037 -10000 0 -0.15 14 14
E4ICDs/TAB2/NCoR1 0.031 0.13 -10000 0 -0.62 18 18
STAT5A (dimer) 0.002 0.16 -10000 0 -0.72 18 18
MAP3K7IP2 0.033 0.011 -10000 0 0 48 48
STAT5B (dimer) -0.016 0.16 0.29 1 -0.76 18 19
LRIG1 0.031 0.014 -10000 0 0 85 85
EREG 0.035 0.008 -10000 0 0 23 23
BTC 0.036 0.005 -10000 0 0 11 11
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.03 0.16 -10000 0 -0.8 18 18
ERBB4 0 0.14 -10000 0 -0.69 18 18
STAT5B 0.036 0.004 -10000 0 0 5 5
YAP1 -0.07 0.2 -10000 0 -0.49 92 92
GRB2 0.035 0.007 -10000 0 0 18 18
ErbB4/ErbB2/neuregulin 4 0.002 0.11 -10000 0 -0.55 18 18
glial cell differentiation -0.03 0.13 0.62 18 -10000 0 18
WWOX 0.036 0.006 -10000 0 0 15 15
cell proliferation -0.012 0.11 0.26 1 -0.57 18 19
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.023 0.058 0.16 1 -0.19 27 28
BIRC5 0.029 0.015 -10000 0 0 111 111
NFKBIA -0.008 0.042 0.21 3 -0.18 16 19
CPEB1 0.033 0.012 -10000 0 0 56 56
AKT1 -0.006 0.033 0.24 1 -0.18 7 8
NDEL1 0.035 0.007 -10000 0 0 20 20
Aurora A/BRCA1 0.023 0.043 0.14 1 -0.15 23 24
NDEL1/TACC3 0.036 0.058 0.16 1 -0.14 37 38
GADD45A 0.031 0.013 -10000 0 0 77 77
GSK3B 0.035 0.015 0.089 25 0 39 64
PAK1/Aurora A 0.029 0.05 0.16 1 -0.16 25 26
MDM2 0.034 0.01 -10000 0 0 45 45
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.012 0.026 0.093 25 -10000 0 25
TP53 0.002 0.073 -10000 0 -0.24 35 35
DLG7 -0.004 0.042 0.1 39 -0.18 13 52
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.033 0.012 -10000 0 0 57 57
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.038 0.061 0.17 1 -0.16 37 38
G2/M transition of mitotic cell cycle 0.023 0.043 -10000 0 -0.15 23 23
AURKA 0.006 0.05 0.13 24 -0.21 19 43
AURKB 0.008 0.034 -10000 0 -0.14 26 26
CDC25B -0.001 0.075 -10000 0 -0.28 28 28
G2/M transition checkpoint 0.001 0.036 0.088 1 -0.14 24 25
mRNA polyadenylation 0.015 0.051 -10000 0 -0.13 46 46
Aurora A/CPEB 0.016 0.052 0.14 1 -0.13 46 47
Aurora A/TACC1/TRAP/chTOG 0.051 0.082 -10000 0 -0.16 52 52
BRCA1 0.036 0.006 -10000 0 0 12 12
centrosome duplication 0.029 0.049 0.16 1 -0.16 25 26
regulation of centrosome cycle 0.035 0.057 0.15 1 -0.14 37 38
spindle assembly 0.049 0.081 -10000 0 -0.16 52 52
TDRD7 0.034 0.01 -10000 0 0 39 39
Aurora A/RasGAP/Survivin 0.039 0.074 -10000 0 -0.14 60 60
CENPA 0.002 0.063 -10000 0 -0.26 24 24
Aurora A/PP2A 0.03 0.05 0.16 1 -0.16 25 26
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.007 0.052 -10000 0 -0.21 18 18
negative regulation of DNA binding 0.002 0.073 -10000 0 -0.24 36 36
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.041 0.046 -10000 0 -0.14 27 27
RASA1 0.035 0.009 -10000 0 0 30 30
Ajuba/Aurora A 0.001 0.036 0.089 1 -0.14 24 25
mitotic prometaphase -0.004 0.01 0.068 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.05 0.13 24 -0.21 19 43
TACC1 0.035 0.008 -10000 0 0 23 23
TACC3 0.033 0.012 -10000 0 0 57 57
Aurora A/Antizyme1 0.023 0.044 0.14 1 -0.15 24 25
Aurora A/RasGAP 0.027 0.06 0.16 1 -0.22 23 24
OAZ1 0.035 0.009 -10000 0 0 30 30
RAN 0.036 0.005 -10000 0 0 10 10
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.036 0.015 0.088 27 0 24 51
GIT1 0.037 0.003 -10000 0 0 3 3
GIT1/beta-PIX/PAK1 0.058 0.047 -10000 0 -0.13 26 26
Importin alpha/Importin beta/TPX2 -0.012 0.026 0.093 25 -10000 0 25
PPP2R5D 0.036 0.004 -10000 0 0 5 5
Aurora A/TPX2 -0.028 0.056 0.096 4 -0.23 21 25
PAK1 0.036 0.006 -10000 0 0 16 16
CKAP5 0.034 0.01 -10000 0 0 37 37
Signaling events mediated by HDAC Class III

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.033 0.011 -10000 0 0 50 50
HDAC4 0.035 0.009 -10000 0 0 30 30
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.003 0.04 -10000 0 -0.13 45 45
CDKN1A -0.039 0.12 -10000 0 -0.46 37 37
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.034 0.01 -10000 0 0 43 43
FOXO3 0.001 0.033 0.25 7 -10000 0 7
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.023 -10000 0 -0.18 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.034 0.01 -10000 0 0 40 40
TAT 0.036 0.006 -10000 0 0 12 12
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.001 -10000 0 -10000 0 0
PPARGC1A 0.031 0.013 -10000 0 0 79 79
FHL2 0.028 0.016 -10000 0 0 126 126
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.046 0.16 32 -0.15 5 37
HIST2H4A 0.003 0.04 0.13 45 -10000 0 45
SIRT1/FOXO3a 0.027 0.04 0.15 37 -10000 0 37
SIRT1 0.033 0.047 0.18 40 -10000 0 40
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.056 0.17 26 -0.13 16 42
SIRT1/Histone H1b 0.029 0.045 0.17 4 -0.15 6 10
apoptosis -0.048 0.052 0.12 10 -0.17 28 38
SIRT1/PGC1A 0.03 0.044 0.15 28 -0.12 13 41
p53/SIRT1 0.043 0.091 0.33 36 -0.15 20 56
SIRT1/FOXO4 0.025 0.043 0.15 30 -0.14 11 41
FOXO1/FHL2/SIRT1 0.022 0.042 0.14 22 -0.1 21 43
HIST1H1E 0.013 0.023 -10000 0 -0.18 6 6
SIRT1/p300 0.037 0.05 0.16 30 -0.14 11 41
muscle cell differentiation 0.004 0.037 0.12 4 -0.11 40 44
TP53 0.04 0.046 0.18 42 -10000 0 42
KU70/SIRT1/BAX 0.049 0.052 0.17 28 -0.12 10 38
CREBBP 0.036 0.005 -10000 0 0 9 9
MEF2D 0.036 0.006 -10000 0 0 12 12
HIV-1 Tat/SIRT1 0.039 0.045 0.16 31 -0.15 4 35
ACSS2 0.003 0.04 0.13 45 -10000 0 45
SIRT1/PCAF/MYOD -0.004 0.038 0.12 40 -0.12 4 44
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.011 0.027 0.086 36 -10000 0 36
SNTA1 0.032 0.013 -10000 0 0 71 71
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.017 0.037 0.083 52 -0.13 12 64
MAPK12 -0.01 0.031 0.2 4 -0.17 9 13
CCND1 -0.019 0.1 -10000 0 -0.37 40 40
p38 gamma/SNTA1 -0.01 0.038 0.2 4 -0.16 10 14
MAP2K3 0.036 0.005 -10000 0 0 10 10
PKN1 0.033 0.011 -10000 0 0 48 48
G2/M transition checkpoint -0.01 0.03 0.2 4 -0.17 9 13
MAP2K6 -0.005 0.036 0.24 5 -0.18 10 15
MAPT -0.025 0.077 0.16 5 -0.2 74 79
MAPK13 -0.014 0.03 0.093 36 -10000 0 36
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.032 -10000 0 -0.2 11 11
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.024 -10000 0 -0.13 10 10
alphaV beta3 Integrin 0.06 0.049 -10000 0 -0.13 27 27
PTK2 0.011 0.09 0.24 10 -0.29 20 30
IGF1R 0.033 0.011 -10000 0 0 54 54
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.036 0.007 -10000 0 0 17 17
SRC 0.034 0.009 -10000 0 0 34 34
CDKN1B 0 0.093 -10000 0 -0.32 38 38
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.01 0.073 -10000 0 -0.29 25 25
ROCK1 0.036 0.006 -10000 0 0 15 15
AKT1 -0.003 0.07 0.2 1 -0.31 22 23
PTK2B -0.003 0.073 0.18 50 -0.19 4 54
alphaV/beta3 Integrin/JAM-A 0.071 0.047 0.18 7 -0.12 20 27
CBL 0.036 0.005 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.062 0.044 -10000 0 -0.13 24 24
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.069 0.068 -10000 0 -0.14 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.057 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Syndecan-1 0.055 0.043 -10000 0 -0.13 16 16
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.05 0.084 -10000 0 -0.15 68 68
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
alphaV/beta3 Integrin/Osteopontin 0.047 0.071 -10000 0 -0.14 59 59
RPS6KB1 -0.046 0.064 0.24 3 -0.21 19 22
TLN1 0.029 0.015 -10000 0 0 101 101
MAPK3 0.001 0.086 -10000 0 -0.34 26 26
GPR124 0.035 0.008 -10000 0 0 24 24
MAPK1 -0.002 0.088 -10000 0 -0.35 25 25
PXN 0.036 0.004 -10000 0 0 7 7
PIK3R1 0.032 0.012 -10000 0 0 63 63
alphaV/beta3 Integrin/Tumstatin 0.064 0.044 -10000 0 -0.13 24 24
cell adhesion 0.049 0.053 -10000 0 -0.16 26 26
ANGPTL3 0.036 0.005 -10000 0 0 9 9
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.029 -10000 0 -0.12 9 9
IGF-1R heterotetramer 0.033 0.011 -10000 0 0 54 54
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
TGFBR2 0.035 0.009 -10000 0 0 29 29
ITGB3 0.037 0.003 -10000 0 0 4 4
IGF1 0.035 0.007 -10000 0 0 21 21
RAC1 0.025 0.017 -10000 0 0 162 162
regulation of cell-matrix adhesion 0.059 0.045 -10000 0 -0.13 24 24
apoptosis 0.034 0.009 -10000 0 0 31 31
CD47 0.035 0.008 -10000 0 0 24 24
alphaV/beta3 Integrin/CD47 0.06 0.048 -10000 0 -0.13 26 26
VCL 0.026 0.017 -10000 0 0 151 151
alphaV/beta3 Integrin/Del1 0.063 0.044 -10000 0 -0.13 24 24
CSF1 0.036 0.004 -10000 0 0 7 7
PIK3C2A 0.01 0.018 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.026 0.042 -10000 0 -0.12 29 29
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.051 -10000 0 -0.13 28 28
FAK1/Vinculin 0.014 0.077 0.24 7 -0.25 20 27
alphaV beta3/Integrin/ppsTEM5 0.06 0.045 -10000 0 -0.13 24 24
RHOA 0.035 0.007 -10000 0 0 21 21
VTN 0.036 0.004 -10000 0 0 5 5
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.035 0.008 -10000 0 0 25 25
F11R -0.012 0.033 0.093 44 -10000 0 44
alphaV/beta3 Integrin/Lactadherin 0.061 0.046 -10000 0 -0.13 24 24
alphaV/beta3 Integrin/TGFBR2 0.059 0.047 -10000 0 -0.13 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.06 0.04 -10000 0 -0.11 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.047 0.05 -10000 0 -0.12 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.035 0.009 -10000 0 0 30 30
alphaV/beta3 Integrin/Pyk2 0.064 0.062 0.19 45 -0.12 28 73
SDC1 0.031 0.014 -10000 0 0 82 82
VAV3 -0.026 0.03 0.18 2 -0.19 5 7
PTPN11 0.036 0.005 -10000 0 0 11 11
IRS1 0.033 0.011 -10000 0 0 51 51
FAK1/Paxillin 0.028 0.084 0.23 10 -0.25 20 30
cell migration -0.003 0.07 0.22 8 -0.25 15 23
ITGAV 0.035 0.009 -10000 0 0 31 31
PI3K 0.055 0.087 -10000 0 -0.14 67 67
SPP1 0.033 0.011 -10000 0 0 54 54
KDR 0.029 0.015 -10000 0 0 103 103
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.035 0.009 -10000 0 0 31 31
COL4A3 0.037 0 -10000 0 -10000 0 0
angiogenesis -0.001 0.094 -10000 0 -0.38 25 25
Rac1/GTP -0.026 0.035 0.18 1 -0.18 6 7
EDIL3 0.037 0.003 -10000 0 0 4 4
cell proliferation 0.058 0.047 -10000 0 -0.12 27 27
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.031 0.049 -10000 0 -0.11 21 21
TC10/GTP 0.027 0.048 -10000 0 -0.12 21 21
Insulin Receptor/Insulin/IRS1/Shp2 0.076 0.059 -10000 0 -0.13 27 27
HRAS 0.034 0.009 -10000 0 0 36 36
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.032 0.013 -10000 0 0 70 70
FOXO3 -0.009 0.016 0.02 7 -0.056 33 40
AKT1 -0.025 0.088 0.23 16 -0.22 24 40
INSR 0.033 0.022 0.075 20 -0.039 34 54
Insulin Receptor/Insulin 0.055 0.063 0.23 3 -0.14 34 37
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.018 -10000 0 0 221 221
SORBS1 0.026 0.017 -10000 0 0 156 156
CRK 0.035 0.008 -10000 0 0 23 23
PTPN1 -0.023 0.048 0.15 16 -0.25 8 24
CAV1 -0.011 0.037 0.17 6 -0.19 8 14
CBL/APS/CAP/Crk-II/C3G 0.049 0.054 -10000 0 -0.11 14 14
Insulin Receptor/Insulin/IRS1/NCK2 0.074 0.064 -10000 0 -0.14 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.079 -10000 0 -0.13 76 76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.025 0.074 -10000 0 -0.31 14 14
RPS6KB1 -0.031 0.081 0.2 17 -0.21 25 42
PARD6A 0.035 0.007 -10000 0 0 19 19
CBL 0.036 0.005 -10000 0 0 8 8
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.021 0.019 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.033 0.086 0.18 21 -0.22 27 48
HRAS/GTP -0.034 0.035 0.034 18 -0.13 41 59
Insulin Receptor 0.033 0.022 0.075 20 -0.039 34 54
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.084 0.069 -10000 0 -0.13 32 32
PRKCI 0.025 0.088 -10000 0 -0.41 17 17
Insulin Receptor/Insulin/GRB14/PDK1 0.015 0.068 -10000 0 -0.14 71 71
SHC1 0.033 0.011 -10000 0 0 52 52
negative regulation of MAPKKK cascade 0.03 0.056 -10000 0 -10000 0 0
PI3K 0.047 0.087 -10000 0 -0.14 76 76
NCK2 0.036 0.007 -10000 0 0 17 17
RHOQ 0.036 0.006 -10000 0 0 16 16
mol:H2O2 -0.004 0.006 0.031 1 -0.034 8 9
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
AKT2 -0.026 0.08 0.22 15 -0.2 12 27
PRKCZ 0.003 0.077 -10000 0 -0.39 17 17
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.014 0.05 0.16 21 -0.15 4 25
F2RL2 0.036 0.004 -10000 0 0 6 6
TRIP10 0.034 0.009 -10000 0 0 35 35
Insulin Receptor/Insulin/Shc 0.059 0.038 -10000 0 -0.12 9 9
TC10/GTP/CIP4/Exocyst 0.042 0.03 -10000 0 -0.12 14 14
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.048 -10000 0 -0.13 14 14
RAPGEF1 0.035 0.007 -10000 0 0 18 18
RASA1 0.035 0.009 -10000 0 0 30 30
NCK1 0.035 0.008 -10000 0 0 27 27
CBL/APS/CAP/Crk-II 0.044 0.041 -10000 0 -0.11 14 14
TC10/GDP 0.023 0.025 -10000 0 -0.13 12 12
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.066 -10000 0 -0.14 30 30
INPP5D -0.018 0.03 0.064 24 -0.11 21 45
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.006 0.005 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 11 11
IRS1 0.033 0.011 -10000 0 0 51 51
p62DOK/RasGAP 0.03 0.057 -10000 0 -10000 0 0
INS 0.035 0.024 0.097 9 -0.039 33 42
mol:PI-3-4-P2 -0.018 0.029 0.064 24 -0.11 21 45
GRB2 0.035 0.007 -10000 0 0 18 18
EIF4EBP1 -0.034 0.079 0.2 13 -0.22 24 37
PTPRA 0.032 0.017 0.075 1 -0.052 7 8
PIK3CA 0.031 0.014 -10000 0 0 82 82
TC10/GTP/CIP4 0.042 0.03 -10000 0 -0.12 14 14
PDPK1 0.036 0.005 -10000 0 0 8 8
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.015 0.054 0.14 1 -0.16 32 33
Insulin Receptor/Insulin/IRS1 0.056 0.047 -10000 0 -0.12 22 22
Insulin Receptor/Insulin/IRS3 0.048 0.033 -10000 0 -0.07 7 7
Par3/Par6 0.074 0.041 -10000 0 -0.11 16 16
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.033 0.012 -10000 0 0 57 57
mol:Halofuginone -0.002 0.03 -10000 0 -0.17 15 15
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.026 0.15 -10000 0 -0.42 57 57
PRL-3/alpha Tubulin 0.018 0.033 -10000 0 -0.13 21 21
mol:Ca2+ -0.017 0.044 0.26 11 -10000 0 11
AGT 0.029 0.015 -10000 0 0 109 109
CCNA2 -0.025 0.12 -10000 0 -0.6 14 14
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.059 0.12 4 -0.33 15 19
CDK2/Cyclin E1 -0.003 0.15 -10000 0 -0.37 59 59
MAPK3 -0.013 0.03 0.093 37 -10000 0 37
PRL-2 /Rab GGTase beta 0.047 0.035 -10000 0 -0.16 12 12
MAPK1 -0.01 0.032 0.093 42 -10000 0 42
PTP4A1 -0.023 0.1 -10000 0 -0.62 14 14
PTP4A3 0.031 0.013 -10000 0 0 75 75
PTP4A2 0.036 0.006 -10000 0 0 16 16
ITGB1 -0.009 0.026 0.093 27 -10000 0 27
SRC 0.034 0.009 -10000 0 0 34 34
RAC1 -0.004 0.091 -10000 0 -0.39 22 22
Rab GGTase beta/Rab GGTase alpha 0.045 0.032 -10000 0 -0.14 11 11
PRL-1/ATF-5 -0.029 0.11 0.3 2 -0.57 15 17
RABGGTA 0.034 0.01 -10000 0 0 41 41
BCAR1 -0.009 0.055 0.25 21 -10000 0 21
RHOC -0.008 0.12 -10000 0 -0.39 37 37
RHOA -0.009 0.13 -10000 0 -0.44 35 35
cell motility -0.003 0.13 0.26 1 -0.4 33 34
PRL-1/alpha Tubulin -0.036 0.1 -10000 0 -0.56 15 15
PRL-3/alpha1 Integrin 0.018 0.033 -10000 0 -0.13 21 21
ROCK1 -0.002 0.13 0.26 1 -0.36 41 42
RABGGTB 0.035 0.008 -10000 0 0 25 25
CDK2 0.034 0.01 -10000 0 0 40 40
mitosis -0.023 0.1 -10000 0 -0.61 14 14
ATF5 0.034 0.009 -10000 0 0 34 34
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.033 0.012 -10000 0 0 59 59
SMAD2 -0.018 0.066 0.17 2 -0.21 35 37
SMAD3 0.003 0.06 -10000 0 -0.34 8 8
SMAD3/SMAD4 -0.009 0.17 -10000 0 -0.5 44 44
SMAD4/Ubc9/PIASy 0.054 0.054 -10000 0 -0.13 35 35
SMAD2/SMAD2/SMAD4 0.025 0.1 -10000 0 -0.25 29 29
PPM1A 0.035 0.009 -10000 0 0 31 31
CALM1 0.033 0.012 -10000 0 0 57 57
SMAD2/SMAD4 -0.001 0.069 -10000 0 -0.2 35 35
MAP3K1 0.035 0.007 -10000 0 0 20 20
TRAP-1/SMAD4 0.036 0.054 -10000 0 -0.14 40 40
MAPK3 0.037 0.003 -10000 0 0 4 4
MAPK1 0.034 0.01 -10000 0 0 44 44
NUP214 0.035 0.007 -10000 0 0 18 18
CTDSP1 0.036 0.006 -10000 0 0 15 15
CTDSP2 0.033 0.012 -10000 0 0 58 58
CTDSPL 0.036 0.006 -10000 0 0 13 13
KPNB1 0.035 0.008 -10000 0 0 23 23
TGFBRAP1 0.036 0.005 -10000 0 0 10 10
UBE2I 0.036 0.004 -10000 0 0 6 6
NUP153 0.035 0.009 -10000 0 0 30 30
KPNA2 0.034 0.01 -10000 0 0 40 40
PIAS4 0.035 0.008 -10000 0 0 24 24
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.05 0.024 -10000 0 -0.14 6 6
Necdin/E2F1 -0.017 0.085 -10000 0 -0.14 148 148
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.073 0.048 -10000 0 -0.12 23 23
NGF (dimer)/p75(NTR)/BEX1 0.01 0.064 -10000 0 -0.12 95 95
NT-4/5 (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
IKBKB 0.037 0.003 -10000 0 0 4 4
AKT1 -0.016 0.078 0.2 25 -0.2 23 48
IKBKG 0.037 0 -10000 0 -10000 0 0
BDNF 0.032 0.012 -10000 0 0 66 66
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.009 -10000 0 -10000 0 0
FURIN 0.036 0.005 -10000 0 0 10 10
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.034 -10000 0 -0.13 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.022 0.069 -10000 0 -0.16 50 50
proBDNF (dimer) 0.032 0.012 -10000 0 0 66 66
NTRK1 0.036 0.007 -10000 0 0 17 17
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.005 0.11 0.28 1 -0.36 29 30
IRAK1 0.035 0.007 -10000 0 0 19 19
SHC1 -0.003 0.036 0.092 61 -10000 0 61
ARHGDIA 0.035 0.007 -10000 0 0 18 18
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
Gamma Secretase 0.08 0.072 -10000 0 -0.16 28 28
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.039 0.059 -10000 0 -0.11 54 54
MAGEH1 0.032 0.013 -10000 0 0 70 70
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.004 0.076 -10000 0 -0.11 147 147
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.16 6 6
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.035 0.008 -10000 0 0 26 26
APP 0.035 0.007 -10000 0 0 20 20
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.009 -10000 0 0 36 36
RhoA/GDP/RHOGDI 0.05 0.03 0.18 1 -0.1 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.003 0.054 0.22 7 -10000 0 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.017 0.056 -10000 0 -0.18 32 32
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.019 -10000 0 -0.12 1 1
NCSTN 0.035 0.009 -10000 0 0 29 29
mol:GTP 0.031 0.041 -10000 0 -0.12 29 29
PSENEN 0.035 0.009 -10000 0 0 31 31
mol:ceramide -0.007 0.044 0.19 7 -10000 0 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.054 -10000 0 -0.27 10 10
p75(NTR)/beta APP 0.043 0.032 -10000 0 -0.14 9 9
BEX1 0.028 0.015 -10000 0 0 115 115
mol:GDP -0.008 0.003 -10000 0 -10000 0 0
NGF (dimer) 0.046 0.034 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.04 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
RAC1/GTP 0.025 0.024 -10000 0 -0.097 5 5
MYD88 0.034 0.009 -10000 0 0 36 36
CHUK 0.025 0.017 -10000 0 0 163 163
NGF (dimer)/p75(NTR)/PKA 0.032 0.041 -10000 0 -0.12 29 29
RHOB 0.031 0.013 -10000 0 0 74 74
RHOA 0.035 0.007 -10000 0 0 21 21
MAGE-G1/E2F1 0.025 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.035 0.008 -10000 0 0 25 25
TP53 -0.015 0.063 0.22 7 -0.21 6 13
PRDM4 -0.007 0.045 0.19 7 -10000 0 7
BDNF (dimer) 0.08 0.035 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
SORT1 0.036 0.006 -10000 0 0 14 14
activation of caspase activity 0.066 0.046 -10000 0 -0.12 23 23
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.031 -10000 0 -0.11 5 5
RHOC 0.035 0.007 -10000 0 0 19 19
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.012 0.1 0.2 31 -0.31 16 47
DIABLO 0.036 0.004 -10000 0 0 6 6
SMPD2 -0.007 0.044 0.19 7 -10000 0 7
APH1B 0.036 0.006 -10000 0 0 15 15
APH1A 0.036 0.006 -10000 0 0 12 12
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.023 -10000 0 -0.12 4 4
PSEN1 0.033 0.011 -10000 0 0 47 47
APAF-1/Pro-Caspase 9 0.05 0.018 -10000 0 -0.14 2 2
NT3 (dimer)/p75(NTR) 0.044 0.021 -10000 0 -10000 0 0
MAPK8 0.001 0.076 0.2 17 -0.27 8 25
MAPK9 0.025 0.086 0.2 35 -0.26 8 43
APAF1 0.037 0.003 -10000 0 0 3 3
NTF3 0.035 0.008 -10000 0 0 25 25
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.018 0.018 -10000 0 0 259 259
RAC1/GDP 0.017 0.02 -10000 0 -0.13 5 5
RhoA-B-C/GDP 0.049 0.074 -10000 0 -0.15 54 54
p75 CTF/Sortilin/TRAF6/NRIF 0.076 0.056 -10000 0 -0.12 32 32
RhoA-B-C/GTP 0.031 0.041 -10000 0 -0.12 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.088 0.058 -10000 0 -0.12 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.086 0.029 -10000 0 -0.12 2 2
PRKACB 0.033 0.011 -10000 0 0 48 48
proBDNF (dimer)/p75 ECD 0.047 0.019 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.031 0.014 -10000 0 0 82 82
BIRC2 0.036 0.006 -10000 0 0 12 12
neuron projection morphogenesis -0.016 0.071 0.14 26 -0.16 29 55
BAD 0.008 0.089 0.21 15 -0.28 14 29
RIPK2 0.036 0.006 -10000 0 0 14 14
NGFR 0.032 0.013 -10000 0 0 71 71
CYCS -0.012 0.041 0.2 4 -0.19 3 7
ADAM17 0.036 0.006 -10000 0 0 13 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.057 0.03 -10000 0 -0.11 3 3
BCL2L11 0.008 0.089 0.21 14 -0.28 13 27
BDNF (dimer)/p75(NTR) 0.042 0.023 -10000 0 -10000 0 0
PI3K 0.028 0.068 -10000 0 -0.12 70 70
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.021 -10000 0 -0.1 4 4
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
PRKCI 0.035 0.008 -10000 0 0 27 27
NGF (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.05 0.048 -10000 0 -0.12 27 27
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.025 0.017 -10000 0 0 162 162
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.009 -10000 0 0 36 36
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.032 0.035 0.14 16 -0.15 2 18
SQSTM1 0.034 0.009 -10000 0 0 35 35
NGFRAP1 0.036 0.006 -10000 0 0 13 13
CASP3 0.008 0.087 0.2 15 -0.26 16 31
E2F1 0.034 0.009 -10000 0 0 36 36
CASP9 0.034 0.009 -10000 0 0 34 34
IKK complex 0.038 0.068 -10000 0 -0.24 10 10
NGF (dimer)/TRKA 0.026 0.005 -10000 0 -10000 0 0
MMP7 0.027 0.016 -10000 0 0 138 138
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.051 -10000 0 -0.11 31 31
MMP3 0.035 0.007 -10000 0 0 21 21
APAF-1/Caspase 9 -0.023 0.04 -10000 0 -0.21 6 6
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.026 0.16 -10000 0 -0.52 15 15
RAD9A 0.036 0.005 -10000 0 0 9 9
AP1 0.009 0.083 -10000 0 -0.18 72 72
IFNAR2 0.033 0.021 -10000 0 -0.035 37 37
AKT1 0.013 0.056 -10000 0 -0.26 19 19
ER alpha/Oestrogen 0.024 0.014 -10000 0 -0.024 3 3
NFX1/SIN3/HDAC complex -0.006 0.085 -10000 0 -0.27 33 33
EGF 0.033 0.016 -10000 0 -0.032 21 21
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.053 -10000 0 -0.17 22 22
TERT/c-Abl 0.033 0.16 -10000 0 -0.51 19 19
SAP18 0.034 0.01 -10000 0 0 43 43
MRN complex 0.069 0.024 -10000 0 -0.13 4 4
WT1 0.033 0.021 -10000 0 -0.035 37 37
WRN 0.035 0.009 -10000 0 0 29 29
SP1 0.034 0.023 -10000 0 -0.043 37 37
SP3 0.034 0.016 -10000 0 -0.031 26 26
TERF2IP 0.034 0.01 -10000 0 0 39 39
Telomerase/Nucleolin 0.04 0.16 -10000 0 -0.49 19 19
Mad/Max 0.047 0.028 -10000 0 -10000 0 0
TERT 0.023 0.16 -10000 0 -0.56 11 11
CCND1 -0.016 0.29 -10000 0 -0.95 40 40
MAX 0.032 0.018 -10000 0 -0.03 30 30
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 57 57
TERF2 0.028 0.011 0.084 6 -10000 0 6
PTGES3 0.036 0.006 -10000 0 0 15 15
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.048 0.1 -10000 0 -0.42 13 13
CDKN1B -0.028 0.084 0.1 35 -0.32 30 65
RAD1 0.035 0.007 -10000 0 0 18 18
XRCC5 0.036 0.005 -10000 0 0 9 9
XRCC6 0.034 0.01 -10000 0 0 40 40
SAP30 0.036 0.007 -10000 0 0 18 18
TRF2/PARP2 0.032 0.058 -10000 0 -0.14 47 47
UBE3A 0.035 0.012 -10000 0 -0.023 19 19
JUN 0.032 0.016 -10000 0 -0.03 18 18
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.025 0.021 -10000 0 -0.13 4 4
FOS 0.024 0.02 -10000 0 -0.03 16 16
IFN-gamma/IRF1 0.033 0.07 -10000 0 -0.19 39 39
PARP2 0.035 0.008 -10000 0 0 23 23
BLM 0.029 0.015 -10000 0 0 107 107
Telomerase 0.016 0.055 -10000 0 -0.32 9 9
IRF1 0.025 0.04 0.093 1 -0.097 39 40
ESR1 0.035 0.009 -10000 0 0 31 31
KU/TER 0.047 0.029 -10000 0 -0.14 9 9
ATM/TRF2 0.044 0.028 -10000 0 -0.1 9 9
ubiquitin-dependent protein catabolic process 0.003 0.083 -10000 0 -0.28 26 26
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.002 0.085 -10000 0 -0.28 26 26
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.03 0.024 -10000 0 -0.042 34 34
ATM 0.022 0.038 0.13 38 -0.18 5 43
SMAD3 -0.014 0.028 0.091 28 -10000 0 28
ABL1 0.032 0.013 -10000 0 0 69 69
MXD1 0.034 0.016 -10000 0 -0.03 30 30
MRE11A 0.036 0.005 -10000 0 0 8 8
HUS1 0.025 0.017 -10000 0 0 165 165
RPS6KB1 0.036 0.005 -10000 0 0 9 9
TERT/NF kappa B1/14-3-3 0.041 0.17 -10000 0 -0.53 18 18
NR2F2 0.022 0.023 -10000 0 -0.03 52 52
MAPK3 -0.017 0.017 0.094 2 -10000 0 2
MAPK1 -0.014 0.022 0.097 10 -10000 0 10
TGFB1/TGF beta receptor Type II 0.032 0.012 -10000 0 0 66 66
NFKB1 0.035 0.007 -10000 0 0 18 18
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.022 0.038 0.13 38 -0.18 5 43
NBN 0.036 0.006 -10000 0 0 13 13
EGFR 0.009 0.016 -10000 0 0 381 381
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.057 -10000 0 -0.14 64 64
MYC 0.028 0.019 -10000 0 -0.029 20 20
IL2 0.034 0.023 -10000 0 -0.043 37 37
KU 0.047 0.029 -10000 0 -0.14 9 9
RAD50 0.036 0.006 -10000 0 0 12 12
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.032 0.012 -10000 0 0 66 66
TRF2/BLM 0.01 0.08 -10000 0 -0.15 94 94
FRAP1 0.036 0.006 -10000 0 0 16 16
KU/TERT 0.049 0.16 -10000 0 -0.51 16 16
SP1/HDAC2 0.042 0.047 -10000 0 -0.14 14 14
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.022 0.14 -10000 0 -0.46 19 19
Smad3/Myc 0.01 0.052 -10000 0 -0.13 50 50
911 complex 0.047 0.039 -10000 0 -0.13 4 4
IFNG 0.027 0.04 0.093 1 -0.094 43 44
Telomerase/PinX1 0.022 0.14 -10000 0 -0.46 19 19
Telomerase/AKT1/mTOR/p70S6K 0.022 0.094 0.22 1 -0.43 11 12
SIN3B 0.035 0.009 -10000 0 0 33 33
YWHAE 0.035 0.008 -10000 0 0 27 27
Telomerase/EST1B 0.022 0.14 -10000 0 -0.46 19 19
response to DNA damage stimulus 0.009 0.018 -10000 0 -0.084 11 11
MRN complex/TRF2/Rap1 0.076 0.073 -10000 0 -0.14 41 41
TRF2/WRN 0.035 0.046 -10000 0 -0.12 40 40
Telomerase/hnRNP C1/C2 0.022 0.14 -10000 0 -0.46 19 19
E2F1 0.032 0.021 -10000 0 -0.035 35 35
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.036 0.007 -10000 0 0 17 17
DKC1 0.035 0.007 -10000 0 0 18 18
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.001 0.013 -10000 0 -0.092 9 9
STMN1 -0.015 0.028 0.092 30 -10000 0 30
Aurora B/RasGAP/Survivin 0.034 0.076 -10000 0 -0.14 73 73
Chromosomal passenger complex/Cul3 protein complex -0.033 0.079 -10000 0 -0.2 66 66
BIRC5 0.029 0.015 -10000 0 0 111 111
DES 0.025 0.093 -10000 0 -0.64 9 9
Aurora C/Aurora B/INCENP 0.062 0.022 -10000 0 -10000 0 0
Aurora B/TACC1 0.042 0.026 -10000 0 -0.12 9 9
Aurora B/PP2A 0.05 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.001 0.05 -10000 0 -0.19 28 28
mitotic metaphase/anaphase transition -0.001 0.003 0.009 21 -0.009 1 22
NDC80 -0.01 0.006 0.014 3 -10000 0 3
Cul3 protein complex 0.027 0.033 -10000 0 -0.14 8 8
KIF2C -0.019 0.12 -10000 0 -0.47 32 32
PEBP1 -0.001 0.003 0.009 17 -0.008 15 32
KIF20A 0.029 0.015 -10000 0 0 110 110
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.04 0.045 -10000 0 -0.15 25 25
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.002 0.08 -10000 0 -0.48 9 9
PSMA3 0.034 0.01 -10000 0 0 37 37
G2/M transition of mitotic cell cycle -0.001 0.002 0.008 13 -0.006 3 16
H3F3B 0.009 0.032 -10000 0 -0.2 11 11
AURKB 0.032 0.015 -10000 0 -0.009 55 55
AURKC 0.036 0.006 -10000 0 0 15 15
CDCA8 0.032 0.013 -10000 0 -0.003 59 59
cytokinesis -0.026 0.15 0.19 6 -0.41 53 59
Aurora B/Septin1 -0.015 0.14 0.19 4 -0.38 54 58
AURKA -0.001 0.002 0.008 13 -0.006 3 16
INCENP 0.034 0.014 0.058 3 -0.024 26 29
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.036 0.006 0.059 1 0 11 12
hSgo1/Aurora B/Survivin 0.021 0.051 -10000 0 -0.11 58 58
EVI5 0.036 0.007 -10000 0 0 17 17
RhoA/GTP 0.011 0.13 -10000 0 -0.32 54 54
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.005 0.079 0.13 1 -0.28 33 34
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.045 0.03 -10000 0 -0.15 8 8
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.048 0.026 -10000 0 -0.15 6 6
RHOA 0.035 0.007 -10000 0 0 21 21
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 0.005 0.067 -10000 0 -0.3 19 19
RASA1 0.035 0.009 -10000 0 0 30 30
KLHL9 0.021 0.018 -10000 0 0 214 214
mitotic prometaphase -0.001 0.003 0.009 17 -0.008 15 32
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.03 -10000 0 -0.15 8 8
PPP1CC 0.036 0.005 -10000 0 0 9 9
Centraspindlin 0.001 0.13 -10000 0 -0.34 53 53
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
NSUN2 0.002 0.042 -10000 0 -0.29 9 9
MYLK -0.015 0.07 -10000 0 -0.2 63 63
KIF23 0.028 0.018 -10000 0 -0.006 102 102
VIM -0.013 0.02 0.089 12 -10000 0 12
RACGAP1 0.031 0.016 -10000 0 -0.003 88 88
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.003 0.065 -10000 0 -0.28 23 23
Chromosomal passenger complex -0.016 0.1 0.14 5 -0.25 61 66
Chromosomal passenger complex/EVI5 0.061 0.087 -10000 0 -0.15 57 57
TACC1 0.035 0.008 -10000 0 0 23 23
PPP2R5D 0.036 0.004 -10000 0 0 5 5
CUL3 0.037 0.002 -10000 0 0 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.033 0.011 -10000 0 0 48 48
NFATC1 0.004 0.1 -10000 0 -0.4 22 22
NFATC2 -0.035 0.084 -10000 0 -0.16 119 119
NFATC3 0.01 0.02 -10000 0 -0.1 14 14
YWHAE 0.035 0.008 -10000 0 0 27 27
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.076 0.16 3 -0.23 24 27
Exportin 1/Ran/NUP214 0.068 0.03 -10000 0 -0.16 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.019 0.091 -10000 0 -0.22 21 21
BCL2/BAX 0.047 0.024 -10000 0 -0.14 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.027 -10000 0 -0.13 14 14
CaM/Ca2+ 0.021 0.027 -10000 0 -0.13 14 14
BAX 0.034 0.01 -10000 0 0 43 43
MAPK14 0.036 0.004 -10000 0 0 5 5
BAD 0.036 0.006 -10000 0 0 13 13
CABIN1/MEF2D 0.006 0.082 -10000 0 -0.22 23 23
Calcineurin A alpha-beta B1/BCL2 0.035 0.007 -10000 0 0 20 20
FKBP8 0.035 0.009 -10000 0 0 31 31
activation-induced cell death of T cells -0.006 0.081 0.22 23 -10000 0 23
KPNB1 0.035 0.008 -10000 0 0 23 23
KPNA2 0.034 0.01 -10000 0 0 40 40
XPO1 0.036 0.004 -10000 0 0 5 5
SFN 0.031 0.013 -10000 0 0 80 80
MAP3K8 0.022 0.018 -10000 0 0 198 198
NFAT4/CK1 alpha 0.024 0.044 0.17 1 -0.16 17 18
MEF2D/NFAT1/Cbp/p300 0.01 0.11 0.23 1 -0.21 36 37
CABIN1 -0.008 0.076 0.16 3 -0.23 24 27
CALM1 0.033 0.012 -10000 0 0 57 57
RAN 0.036 0.005 -10000 0 0 10 10
MAP3K1 0.035 0.007 -10000 0 0 20 20
CAMK4 0.036 0.005 -10000 0 0 8 8
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.037 0.003 -10000 0 0 4 4
YWHAH 0.032 0.013 -10000 0 0 73 73
Calcineurin A alpha-beta B1/AKAP79/PKA 0.049 0.016 -10000 0 -10000 0 0
YWHAB 0.034 0.01 -10000 0 0 41 41
MAPK8 0.027 0.016 -10000 0 0 141 141
MAPK9 0.036 0.006 -10000 0 0 13 13
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.032 0.012 -10000 0 0 63 63
NFAT1-c-4/YWHAQ 0.001 0.11 -10000 0 -0.38 20 20
PRKCH 0.034 0.01 -10000 0 0 42 42
CABIN1/Cbp/p300 0.047 0.028 -10000 0 -0.14 7 7
CASP3 0.034 0.009 -10000 0 0 32 32
PIM1 0.036 0.005 -10000 0 0 8 8
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.02 -10000 0 -0.11 10 10
apoptosis 0.019 0.035 -10000 0 -0.17 11 11
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.097 -10000 0 -0.31 27 27
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.037 0.003 -10000 0 0 3 3
JNK2/NFAT4 0.026 0.036 -10000 0 -0.12 20 20
BAD/BCL-XL 0.046 0.027 -10000 0 -0.14 6 6
PRKCD 0.034 0.01 -10000 0 0 40 40
NUP214 0.035 0.007 -10000 0 0 18 18
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.036 0.004 -10000 0 0 6 6
PRKCG 0.037 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.017 -10000 0 0 165 165
FKBP38/BCL2 0.049 0.016 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 0 50 50
PRKCB1 0.031 0.014 -10000 0 0 83 83
CSNK2A1 0.033 0.011 -10000 0 0 51 51
NFATc/JNK1 0.01 0.1 -10000 0 -0.38 22 22
CaM/Ca2+/FKBP38 0.039 0.031 -10000 0 -0.12 14 14
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 10 10
CSNK1A1 -0.016 0.022 0.088 12 -0.12 10 22
CaM/Ca2+/CAMK IV 0.041 0.03 -10000 0 -0.12 13 13
NFATc/ERK1 0.022 0.1 -10000 0 -0.38 22 22
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.018 0.093 -10000 0 -0.24 15 15
NR4A1 -0.024 0.08 0.16 9 -0.2 27 36
GSK3B 0.034 0.01 -10000 0 0 39 39
positive T cell selection 0.01 0.02 -10000 0 -0.1 14 14
NFAT1/CK1 alpha -0.021 0.071 -10000 0 -0.18 45 45
RCH1/ KPNB1 0.035 0.059 -10000 0 -0.15 44 44
YWHAQ 0.036 0.005 -10000 0 0 8 8
PRKACA 0.035 0.008 -10000 0 0 24 24
AKAP5 0.034 0.009 -10000 0 0 32 32
MEF2D 0.036 0.006 -10000 0 0 12 12
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.035 0.007 -10000 0 0 21 21
NFATc/p38 alpha 0.021 0.1 -10000 0 -0.38 22 22
CREBBP 0.036 0.005 -10000 0 0 9 9
BCL2 0.035 0.007 -10000 0 0 20 20
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.044 0.039 -10000 0 -0.14 18 18
ATM 0.034 0.01 -10000 0 0 37 37
UBE2D3 0.036 0.006 -10000 0 0 12 12
PRKDC 0.034 0.01 -10000 0 0 45 45
ATR 0.035 0.008 -10000 0 0 25 25
UBE2L3 0.034 0.009 -10000 0 0 32 32
FANCD2 0.008 0.036 -10000 0 -0.2 14 14
protein ubiquitination 0.077 0.056 -10000 0 -0.13 22 22
XRCC5 0.036 0.005 -10000 0 0 9 9
XRCC6 0.034 0.01 -10000 0 0 40 40
M/R/N Complex 0.069 0.024 -10000 0 -0.13 4 4
MRE11A 0.036 0.005 -10000 0 0 8 8
DNA-PK 0.056 0.05 -10000 0 -0.14 23 23
FA complex/FANCD2/Ubiquitin 0.002 0.085 -10000 0 -0.28 27 27
FANCF 0.035 0.008 -10000 0 0 26 26
BRCA1 0.036 0.006 -10000 0 0 12 12
CCNE1 0.033 0.012 -10000 0 0 57 57
CDK2/Cyclin E1 0.045 0.023 -10000 0 -0.14 2 2
FANCG 0.031 0.014 -10000 0 0 86 86
BRCA1/BACH1/BARD1 0.046 0.038 -10000 0 -0.14 19 19
FANCE 0.037 0.003 -10000 0 0 4 4
FANCC 0.036 0.006 -10000 0 0 15 15
NBN 0.036 0.006 -10000 0 0 13 13
FANCA 0.036 0.007 -10000 0 0 17 17
DNA repair -0.013 0.085 0.21 11 -0.26 25 36
BRCA1/BARD1/ubiquitin 0.046 0.038 -10000 0 -0.14 19 19
BARD1/DNA-PK 0.069 0.066 -10000 0 -0.14 36 36
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.039 0.14 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.064 -10000 0 -0.22 27 27
BRCA1/BACH1/BARD1/TopBP1 0.051 0.062 -10000 0 -0.14 46 46
BRCA1/BARD1/P53 0.066 0.069 -10000 0 -0.13 47 47
BARD1/CSTF1/BRCA1 0.061 0.042 -10000 0 -0.13 18 18
BRCA1/BACH1 0.036 0.006 -10000 0 0 12 12
BARD1 0.035 0.007 -10000 0 0 21 21
PCNA 0.032 0.012 -10000 0 0 62 62
BRCA1/BARD1/UbcH5C 0.063 0.043 -10000 0 -0.14 20 20
BRCA1/BARD1/UbcH7 0.059 0.048 -10000 0 -0.13 24 24
BRCA1/BARD1/RAD51/PCNA 0.069 0.062 -10000 0 -0.13 33 33
BARD1/DNA-PK/P53 0.067 0.084 -10000 0 -0.14 58 58
BRCA1/BARD1/Ubiquitin 0.046 0.038 -10000 0 -0.14 19 19
BRCA1/BARD1/CTIP 0.04 0.059 -10000 0 -0.14 44 44
FA complex 0.013 0.058 -10000 0 -0.18 32 32
BARD1/EWS 0.043 0.039 -10000 0 -0.14 19 19
RBBP8 -0.013 0.029 0.093 34 -10000 0 34
TP53 0.032 0.013 -10000 0 0 73 73
TOPBP1 0.033 0.011 -10000 0 0 51 51
G1/S transition of mitotic cell cycle -0.064 0.068 0.13 47 -10000 0 47
BRCA1/BARD1 0.085 0.06 -10000 0 -0.13 22 22
CSTF1 0.034 0.009 -10000 0 0 34 34
BARD1/EWS-Fli1 0.021 0.031 -10000 0 -0.13 19 19
CDK2 0.034 0.01 -10000 0 0 40 40
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.007 -10000 0 0 22 22
RAD50 0.036 0.006 -10000 0 0 12 12
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.046 0.038 -10000 0 -0.14 19 19
EWSR1 0.034 0.009 -10000 0 0 34 34
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.029 0.015 -10000 0 0 109 109
positive regulation of NF-kappaB transcription factor activity 0.035 0.046 -10000 0 -0.14 25 25
MAP2K4 0.015 0.06 0.21 2 -0.29 8 10
IKBKB 0.037 0.003 -10000 0 0 4 4
TNFRSF10B 0.035 0.008 -10000 0 0 25 25
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.014 0.028 -10000 0 -0.11 20 20
IKBKG 0.037 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.036 0.006 -10000 0 0 12 12
TRAIL/TRAILR2 0.035 0.045 -10000 0 -0.14 24 24
TRAIL/TRAILR3 0.035 0.046 -10000 0 -0.14 25 25
TRAIL/TRAILR1 0.015 0.036 -10000 0 -0.13 26 26
TRAIL/TRAILR4 0.035 0.046 -10000 0 -0.14 25 25
TRAIL/TRAILR1/DAP3/GTP 0.029 0.04 -10000 0 -0.11 33 33
IKK complex -0.033 0.12 -10000 0 -0.22 133 133
RIPK1 0.035 0.007 -10000 0 0 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.023 0.025 -10000 0 -0.13 12 12
MAPK3 -0.005 0.039 0.093 68 -10000 0 68
MAP3K1 0.022 0.055 -10000 0 -0.3 6 6
TRAILR4 (trimer) 0.036 0.006 -10000 0 0 12 12
TRADD 0.036 0.005 -10000 0 0 10 10
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.018 0.049 -10000 0 -0.17 23 23
CFLAR 0.036 0.005 -10000 0 0 8 8
MAPK1 -0.004 0.039 0.093 68 -10000 0 68
TRAIL/TRAILR1/FADD/TRADD/RIP 0.07 0.048 -10000 0 -0.11 25 25
mol:ceramide 0.014 0.028 -10000 0 -0.11 20 20
FADD 0.036 0.006 -10000 0 0 12 12
MAPK8 0.007 0.047 0.19 1 -0.28 6 7
TRAF2 0.036 0.006 -10000 0 0 16 16
TRAILR3 (trimer) 0.036 0.006 -10000 0 0 14 14
CHUK 0.025 0.017 -10000 0 0 163 163
TRAIL/TRAILR1/FADD 0.033 0.039 -10000 0 -0.12 25 25
DAP3 0.035 0.008 -10000 0 0 23 23
CASP10 -0.004 0.052 0.14 16 -0.17 22 38
JNK cascade 0.035 0.046 -10000 0 -0.14 25 25
TRAIL (trimer) 0.029 0.015 -10000 0 0 109 109
TNFRSF10C 0.036 0.006 -10000 0 0 14 14
TRAIL/TRAILR1/DAP3/GTP/FADD 0.042 0.047 -10000 0 -0.11 32 32
TRAIL/TRAILR2/FADD 0.05 0.048 -10000 0 -0.12 23 23
cell death 0.014 0.028 -10000 0 -0.11 20 20
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.024 0.05 -10000 0 -0.25 4 4
TRAILR2 (trimer) 0.035 0.008 -10000 0 0 25 25
CASP8 0.016 0.023 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.087 0.057 -10000 0 -0.12 22 22
Retinoic acid receptors-mediated signaling

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC3 0.036 0.004 -10000 0 0 7 7
VDR 0.035 0.007 -10000 0 0 21 21
Cbp/p300/PCAF 0.042 0.024 -10000 0 -0.12 7 7
EP300 0.033 0.011 -10000 0 0 50 50
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.049 -10000 0 -0.21 8 8
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.004 -10000 0 0 5 5
AKT1 0.007 0.08 0.2 4 -0.23 11 15
RAR alpha/9cRA/Cyclin H -0.027 0.13 -10000 0 -0.3 37 37
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.056 -10000 0 -0.2 21 21
CDC2 0.018 0.02 -10000 0 -0.001 248 248
response to UV -0.001 0.007 -10000 0 -0.026 33 33
RAR alpha/Jnk1 0.022 0.028 0.16 1 -10000 0 1
NCOR2 0.037 0.002 -10000 0 0 2 2
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.028 0.15 -10000 0 -0.54 33 33
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA3 0.034 0.01 -10000 0 0 41 41
NCOA1 0.033 0.011 -10000 0 0 49 49
VDR/VDR/DNA 0.035 0.007 -10000 0 0 21 21
RARG 0.032 0.017 -10000 0 -0.023 44 44
RAR gamma1/9cRA 0.046 0.013 -10000 0 -10000 0 0
MAPK3 0.032 0.018 -10000 0 -0.032 37 37
MAPK1 0.034 0.01 -10000 0 0 44 44
MAPK8 0.024 0.022 -10000 0 -0.045 21 21
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.022 0.12 -10000 0 -0.36 33 33
RARA 0.006 0.037 -10000 0 -0.2 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.041 -10000 0 -0.18 10 10
PRKCA 0.031 0.027 0.077 2 -0.072 32 34
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.03 0.16 -10000 0 -0.62 33 33
RXRG 0.019 0.028 -10000 0 -10000 0 0
RXRA -0.013 0.082 -10000 0 -0.3 24 24
RXRB 0.019 0.026 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RBP1 0.027 0.017 -10000 0 0 142 142
CRBP1/9-cic-RA -0.004 0.061 -10000 0 -0.13 90 90
RARB 0.032 0.021 -10000 0 -0.046 33 33
PRKCG 0.032 0.027 -10000 0 -0.071 33 33
MNAT1 0.034 0.01 -10000 0 0 38 38
RAR alpha/RXRs -0.015 0.13 -10000 0 -0.41 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.006 0.09 -10000 0 -0.3 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.057 -10000 0 -0.19 13 13
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.03 0.16 -10000 0 -0.62 33 33
positive regulation of DNA binding -0.031 0.12 -10000 0 -0.28 37 37
NRIP1 -0.054 0.27 -10000 0 -1.1 33 33
RXRs/RARs -0.008 0.12 -10000 0 -0.41 33 33
RXRs/RXRs/DNA/9cRA -0.034 0.11 -10000 0 -0.36 33 33
PRKACA 0.035 0.008 -10000 0 0 24 24
CDK7 0.035 0.008 -10000 0 0 24 24
TFIIH 0.06 0.051 -10000 0 -0.17 19 19
RAR alpha/9cRA 0.022 0.088 -10000 0 -0.18 23 23
CCNH 0.036 0.006 -10000 0 0 16 16
CREBBP 0.036 0.005 -10000 0 0 9 9
RAR gamma2/9cRA 0.056 0.051 -10000 0 -0.15 19 19
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.041 0.01 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.009 0.061 -10000 0 -0.12 88 88
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.036 0.004 -10000 0 0 7 7
RGS9-1/Gbeta5/R9AP 0.046 0.015 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.047 0.012 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.036 0.005 -10000 0 0 8 8
Cone Metarhodopsin II/X-Arrestin 0.027 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.056 0.18 2 -10000 0 2
Cone PDE6 0.053 0.048 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.016 0.065 -10000 0 -0.11 87 87
GNAT2/GDP 0.059 0.021 -10000 0 -0.1 1 1
GNB5 0.035 0.008 -10000 0 0 23 23
mol:GMP (4 units) -0.011 0.033 0.18 13 -10000 0 13
Cone Transducin 0.045 0.011 -10000 0 -10000 0 0
SLC24A2 0.03 0.015 -10000 0 0 100 100
GNB3/GNGT2 0.026 0.005 -10000 0 -10000 0 0
GNB3 0.035 0.007 -10000 0 0 20 20
GNAT2/GTP 0.027 0.003 -10000 0 -10000 0 0
CNGA3 0.022 0.018 -10000 0 0 199 199
ARR3 0.037 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.01 0.062 -10000 0 -0.12 88 88
mol:Pi 0.045 0.015 -10000 0 -0.12 1 1
Cone CNG Channel 0.026 0.076 -10000 0 -0.11 84 84
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.03 0.015 -10000 0 0 100 100
RGS9 0.035 0.007 -10000 0 0 18 18
PDE6C 0.026 0.017 -10000 0 0 155 155
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.035 0.008 -10000 0 0 23 23
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.018 0.091 -10000 0 -0.24 38 38
CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
AKT1 0.033 0.011 -10000 0 0 54 54
AKT2 0.035 0.008 -10000 0 0 28 28
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.002 0.089 0.17 2 -0.25 37 39
YWHAZ 0.035 0.007 -10000 0 0 21 21
CALM1 0.033 0.012 -10000 0 0 57 57
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.016 0.021 0.093 16 -10000 0 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.032 0.013 -10000 0 0 73 73
YWHAB 0.034 0.01 -10000 0 0 41 41
SNARE/Synip 0.021 0.018 -10000 0 -0.11 8 8
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.034 0.009 -10000 0 0 34 34
PRKCI 0.035 0.008 -10000 0 0 27 27
AS160/CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
RHOQ 0.036 0.006 -10000 0 0 16 16
GYS1 0.001 0.039 0.13 11 -0.21 6 17
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.034 0.009 -10000 0 0 35 35
TC10/GTP/CIP4/Exocyst 0.042 0.03 -10000 0 -0.12 14 14
AS160/14-3-3 -0.005 0.098 -10000 0 -0.41 18 18
VAMP2 0.033 0.011 -10000 0 0 49 49
SLC2A4 -0.004 0.096 0.18 1 -0.28 37 38
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.004 0.077 -10000 0 -0.3 27 27
SFN 0.031 0.013 -10000 0 0 80 80
LNPEP 0.036 0.005 -10000 0 0 8 8
YWHAE 0.035 0.008 -10000 0 0 27 27
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.035 0.008 -10000 0 0 26 26
alphaV beta3 Integrin 0.044 0.043 -10000 0 -0.14 24 24
PTK2 0.012 0.11 -10000 0 -0.29 43 43
positive regulation of JNK cascade 0.021 0.09 -10000 0 -0.29 17 17
CDC42/GDP 0.036 0.12 -10000 0 -0.37 21 21
Rac1/GDP 0.029 0.099 -10000 0 -0.35 14 14
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 10 10
CTNNB1 0.036 0.006 -10000 0 0 15 15
CDC42/GTP 0.029 0.11 -10000 0 -0.35 17 17
nectin-3/I-afadin 0.044 0.027 -10000 0 -0.14 5 5
RAPGEF1 0.005 0.12 -10000 0 -0.35 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.005 0.12 -10000 0 -0.39 34 34
PDGFB-D/PDGFRB 0.035 0.008 -10000 0 0 26 26
TLN1 -0.006 0.058 0.16 21 -0.23 13 34
Rap1/GTP -0.001 0.083 -10000 0 -0.27 35 35
IQGAP1 0.033 0.011 -10000 0 0 48 48
Rap1/GTP/I-afadin 0.043 0.015 -10000 0 -0.1 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.027 -10000 0 -0.14 5 5
PVR 0.035 0.009 -10000 0 0 31 31
Necl-5(dimer) 0.035 0.009 -10000 0 0 31 31
mol:GDP 0.021 0.13 -10000 0 -0.41 31 31
MLLT4 0.034 0.009 -10000 0 0 34 34
PIK3CA 0.031 0.014 -10000 0 0 82 82
PI3K 0.057 0.09 -10000 0 -0.14 72 72
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.05 0.015 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.02 0.077 -10000 0 -0.28 12 12
PVRL1 0.036 0.005 -10000 0 0 8 8
PVRL3 0.032 0.012 -10000 0 0 60 60
PVRL2 0.034 0.009 -10000 0 0 35 35
PIK3R1 0.032 0.012 -10000 0 0 63 63
CDH1 0.034 0.01 -10000 0 0 37 37
CLDN1 0.034 0.009 -10000 0 0 36 36
JAM-A/CLDN1 0.074 0.045 -10000 0 -0.12 8 8
SRC 0.012 0.13 -10000 0 -0.41 35 35
ITGB3 0.037 0.003 -10000 0 0 4 4
nectin-1(dimer)/I-afadin/I-afadin 0.05 0.015 -10000 0 -10000 0 0
FARP2 0.026 0.14 -10000 0 -0.48 15 15
RAC1 0.025 0.017 -10000 0 0 162 162
CTNNA1 0.035 0.007 -10000 0 0 18 18
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.035 -10000 0 -0.12 5 5
nectin-1/I-afadin 0.05 0.015 -10000 0 -10000 0 0
nectin-2/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.024 0.043 -10000 0 -0.12 30 30
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.059 0.034 -10000 0 -0.12 5 5
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.042 -10000 0 -0.12 33 33
F11R 0.033 0.011 -10000 0 0 52 52
positive regulation of filopodium formation 0.021 0.09 -10000 0 -0.29 17 17
alphaV/beta3 Integrin/Talin 0.03 0.087 0.21 31 -0.2 29 60
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
PIP5K1C -0.01 0.041 0.09 4 -0.21 15 19
VAV2 0.025 0.14 -10000 0 -0.45 19 19
RAP1/GDP 0.026 0.11 -10000 0 -0.31 35 35
ITGAV 0.035 0.009 -10000 0 0 31 31
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.056 0.038 -10000 0 -0.14 7 7
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.027 -10000 0 -0.14 5 5
Rac1/GTP 0.026 0.093 -10000 0 -0.34 12 12
PTPRM 0.008 0.045 -10000 0 -0.23 16 16
E-cadherin/beta catenin/alpha catenin 0.083 0.059 -10000 0 -0.13 13 13
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 0 26 26
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.024 0.1 -10000 0 -0.48 17 17
SMARCC2 0.034 0.01 -10000 0 0 44 44
SMARCC1 0.034 0.009 -10000 0 0 33 33
TBX21 0.032 0.055 0.34 1 -10000 0 1
SUMO2 0.033 0.019 -10000 0 -0.03 35 35
STAT1 (dimer) 0.036 0.039 0.11 22 -0.17 14 36
FKBP4 0.034 0.009 -10000 0 0 34 34
FKBP5 0.028 0.016 -10000 0 0 118 118
GR alpha/HSP90/FKBP51/HSP90 -0.025 0.065 -10000 0 -0.18 11 11
PRL 0.039 0.058 0.54 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.042 0.12 -10000 0 -0.32 2 2
RELA 0.015 0.11 0.18 32 -0.16 127 159
FGG -0.049 0.1 -10000 0 -0.32 2 2
GR beta/TIF2 -0.024 0.076 -10000 0 -0.22 2 2
IFNG 0.036 0.083 0.36 1 -10000 0 1
apoptosis -0.021 0.2 0.45 21 -0.51 31 52
CREB1 0.043 0.01 -10000 0 -10000 0 0
histone acetylation 0.022 0.055 0.22 1 -0.24 1 2
BGLAP 0.04 0.062 -10000 0 -10000 0 0
GR/PKAc 0.021 0.092 -10000 0 -0.19 19 19
NF kappa B1 p50/RelA 0.03 0.18 0.3 30 -0.26 120 150
SMARCD1 0.035 0.007 -10000 0 0 20 20
MDM2 -0.008 0.036 -10000 0 -10000 0 0
GATA3 0.031 0.021 -10000 0 -10000 0 0
AKT1 0.029 0.03 0.16 8 -0.091 18 26
CSF2 0.006 0.032 -10000 0 -10000 0 0
GSK3B 0.032 0.02 -10000 0 -0.03 32 32
NR1I3 -0.014 0.18 0.46 15 -0.5 18 33
CSN2 -0.046 0.089 -10000 0 -0.29 2 2
BRG1/BAF155/BAF170/BAF60A 0.064 0.074 -10000 0 -0.17 38 38
NFATC1 0.041 0.008 -10000 0 -10000 0 0
POU2F1 0.04 0.012 -10000 0 -10000 0 0
CDKN1A -0.12 0.41 -10000 0 -1.2 59 59
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 0.029 26 -10000 0 26
SFN 0.031 0.013 -10000 0 0 80 80
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.01 0.068 -10000 0 -0.16 7 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.07 0.28 0.47 9 -0.67 71 80
JUN 0.024 0.053 0.33 4 -10000 0 4
IL4 0.036 0.053 -10000 0 -10000 0 0
CDK5R1 0.035 0.009 -10000 0 0 25 25
PRKACA 0.035 0.008 -10000 0 0 24 24
cortisol/GR alpha (monomer)/AP-1 -0.049 0.053 -10000 0 -0.23 12 12
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.004 0.074 -10000 0 -0.16 18 18
cortisol/GR alpha (monomer) -0.057 0.12 -10000 0 -0.37 2 2
NCOA2 0.036 0.006 -10000 0 0 12 12
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.039 0.031 0.18 6 -10000 0 6
AP-1/NFAT1-c-4 0.048 0.077 0.41 3 -10000 0 3
AFP 0.024 0.067 -10000 0 -10000 0 0
SUV420H1 0.033 0.011 -10000 0 0 50 50
IRF1 -0.029 0.13 -10000 0 -0.66 15 15
TP53 -0.013 0.17 -10000 0 -0.49 56 56
PPP5C 0.034 0.01 -10000 0 0 40 40
KRT17 0.04 0.082 0.45 1 -10000 0 1
KRT14 0.031 0.067 -10000 0 -10000 0 0
TBP 0.043 0.018 -10000 0 -10000 0 0
CREBBP 0.029 0.018 -10000 0 -0.094 10 10
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.011 -10000 0 -10000 0 0
AP-1 0.048 0.077 0.41 3 -10000 0 3
MAPK14 0.034 0.018 -10000 0 -0.03 32 32
MAPK10 0.029 0.021 -10000 0 -0.03 27 27
MAPK11 0.03 0.021 -10000 0 -0.03 32 32
KRT5 0.04 0.08 0.45 1 -10000 0 1
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.033 0.018 0.077 1 -0.067 9 10
STAT1 0.036 0.039 0.11 22 -0.17 14 36
CGA 0.036 0.055 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.034 0.071 -10000 0 -0.36 8 8
MAPK3 0.034 0.02 0.077 1 -0.03 38 39
MAPK1 0.031 0.02 -10000 0 -0.03 31 31
ICAM1 0.03 0.14 0.33 22 -10000 0 22
NFKB1 0.016 0.11 0.18 30 -0.16 122 152
MAPK8 0.034 0.059 0.27 3 -10000 0 3
MAPK9 0.033 0.019 -10000 0 -0.03 31 31
cortisol/GR alpha (dimer) -0.024 0.2 0.46 20 -0.53 33 53
BAX -0.033 0.18 -10000 0 -0.9 9 9
POMC 0.032 0.074 0.48 1 -10000 0 1
EP300 0.026 0.019 -10000 0 -0.094 10 10
cortisol/GR alpha (dimer)/p53 -0.071 0.13 -10000 0 -0.42 18 18
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.069 0.24 31 -10000 0 31
SGK1 -0.017 0.06 -10000 0 -0.24 14 14
IL13 0.028 0.064 -10000 0 -10000 0 0
IL6 0.031 0.13 0.34 19 -10000 0 19
PRKACG 0.036 0.005 -10000 0 0 10 10
IL5 0.021 0.072 0.41 1 -10000 0 1
IL2 0.041 0.077 0.36 1 -10000 0 1
CDK5 0.024 0.018 -10000 0 0 184 184
PRKACB 0.033 0.011 -10000 0 0 48 48
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.11 0.4 0.34 17 -0.79 126 143
CDK5R1/CDK5 0.03 0.042 -10000 0 -0.14 17 17
NF kappa B1 p50/RelA/PKAc 0.056 0.17 0.3 28 -0.21 111 139
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.038 0.11 -10000 0 -0.38 1 1
SMARCA4 0.032 0.012 -10000 0 0 62 62
chromatin remodeling -0.038 0.11 -10000 0 -0.4 23 23
NF kappa B1 p50/RelA/Cbp 0.046 0.16 0.3 17 -0.22 114 131
JUN (dimer) 0.024 0.053 0.33 4 -10000 0 4
YWHAH 0.032 0.013 -10000 0 0 73 73
VIPR1 0.035 0.065 0.38 5 -10000 0 5
NR3C1 -0.04 0.086 -10000 0 -0.35 1 1
NR4A1 0.039 0.009 -10000 0 -10000 0 0
TIF2/SUV420H1 0.036 0.055 -10000 0 -0.14 42 42
MAPKKK cascade -0.021 0.2 0.45 21 -0.51 31 52
cortisol/GR alpha (dimer)/Src-1 -0.049 0.12 -10000 0 -0.37 3 3
PBX1 0.04 0.01 -10000 0 -10000 0 0
POU1F1 0.041 0.011 -10000 0 -10000 0 0
SELE 0.027 0.13 0.34 2 -10000 0 2
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.038 0.11 -10000 0 -0.41 23 23
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.038 0.11 -10000 0 -0.38 1 1
mol:cortisol -0.035 0.061 -10000 0 -0.2 1 1
MMP1 0.037 0.073 0.36 1 -0.49 3 4
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.003 0.038 0.098 26 -0.11 10 36
NFATC2 -0.001 0.027 0.083 16 -0.098 12 28
NFATC3 -0.003 0.038 0.098 26 -0.11 12 38
CD40LG 0.01 0.11 0.29 35 -0.24 3 38
PTGS2 -0.021 0.068 0.26 5 -0.24 3 8
JUNB 0.031 0.014 -10000 0 0 84 84
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.028 -10000 0 -0.12 13 13
CaM/Ca2+ 0.026 0.028 -10000 0 -0.12 13 13
CALM1 0.035 0.014 -10000 0 -10000 0 0
JUN 0.037 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.021 0.02 -10000 0 -0.11 10 10
FOSL1 0.033 0.011 -10000 0 0 53 53
CREM 0.026 0.016 -10000 0 0 145 145
Jun/NFAT1-c-4/p21SNFT 0.056 0.071 0.26 13 -0.18 4 17
FOS 0.027 0.019 -10000 0 -10000 0 0
IFNG 0.009 0.11 0.36 15 -0.24 3 18
AP-1/NFAT1-c-4 0.09 0.12 0.36 7 -0.27 3 10
FASLG 0.009 0.11 0.29 34 -0.24 3 37
NFAT1-c-4/ICER1 0.04 0.051 0.21 11 -10000 0 11
IL2RA 0.001 0.086 0.26 18 -0.24 2 20
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 10 10
CSF2 0.009 0.11 0.29 35 -0.24 3 38
JunB/Fra1/NFAT1-c-4 0.055 0.059 0.22 6 -0.19 1 7
IL4 0.009 0.11 0.29 35 -0.24 3 38
IL2 0.013 0.086 -10000 0 -0.84 5 5
IL3 0.033 0.075 -10000 0 -0.6 6 6
FKBP1A 0.032 0.012 -10000 0 0 63 63
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.039 0.008 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.035 0.01 -10000 0 -10000 0 0
SVIL 0.024 0.018 -10000 0 -10000 0 0
ZNF318 0.035 0.005 -10000 0 -0.045 1 1
JMJD2C 0.036 0.013 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.053 0.041 -10000 0 -0.08 32 32
CARM1 0.035 0.008 -10000 0 0 28 28
PRDX1 0.035 0.007 -10000 0 0 20 20
PELP1 0.035 0.007 -10000 0 0 17 17
CTNNB1 0.036 0.006 -10000 0 -10000 0 0
AKT1 0.032 0.012 -10000 0 -0.001 55 55
PTK2B 0.036 0.007 -10000 0 -10000 0 0
MED1 0 0 -10000 0 -10000 0 0
MAK 0.033 0.009 -10000 0 -0.045 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.022 0.018 -10000 0 -10000 0 0
GSN 0.032 0.013 -10000 0 -10000 0 0
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA6 0.033 0.012 -10000 0 -10000 0 0
DNA-PK 0.055 0.05 -10000 0 -0.14 23 23
NCOA4 0.026 0.017 -10000 0 0 146 146
PIAS3 0.036 0.006 -10000 0 -10000 0 0
cell proliferation 0.023 0.045 -10000 0 -0.44 4 4
XRCC5 0.036 0.005 -10000 0 0 9 9
UBE3A 0.038 0.003 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.032 0.033 0.12 1 -0.071 33 34
FHL2 0.018 0.2 -10000 0 -0.69 33 33
RANBP9 0.036 0.007 -10000 0 -10000 0 0
JMJD1A 0.044 0.012 -10000 0 -10000 0 0
CDK6 0.024 0.017 -10000 0 0 177 177
TGFB1I1 0.033 0.012 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.034 0.057 -10000 0 -0.1 54 54
XRCC6 0.034 0.01 -10000 0 0 40 40
T-DHT/AR 0.049 0.06 0.22 1 -0.13 33 34
CTDSP1 0.036 0.006 -10000 0 0 15 15
CTDSP2 0.032 0.012 -10000 0 -0.04 1 1
BRCA1 0.037 0.006 -10000 0 -10000 0 0
TCF4 0.032 0.012 -10000 0 -0.036 1 1
CDKN2A 0.004 0.012 -10000 0 0 449 449
SRF 0.04 0.056 0.11 90 -0.15 33 123
NKX3-1 0.026 0.07 -10000 0 -0.3 15 15
KLK3 0.016 0.046 -10000 0 -10000 0 0
TMF1 0.036 0.007 -10000 0 0 18 18
HNRNPA1 -0.001 0 -10000 0 -10000 0 0
AOF2 0.034 0.011 -10000 0 -10000 0 0
APPL1 -0.011 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.051 0.041 -10000 0 -0.08 33 33
AR 0.036 0.031 -10000 0 -0.069 33 33
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 -0.001 0 -10000 0 -10000 0 0
PAWR 0.036 0.006 -10000 0 0 13 13
PRKDC 0.033 0.01 -10000 0 0 45 45
PA2G4 0.034 0.008 -10000 0 -0.001 22 22
UBE2I 0.036 0.004 -10000 0 0 6 6
T-DHT/AR/Cyclin D3/CDK11 p58 0.045 0.044 0.14 1 -0.078 46 47
RPS6KA3 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.039 0.046 -10000 0 -0.087 21 21
LATS2 -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.046 0.043 0.14 1 -0.08 39 40
Cyclin D3/CDK11 p58 0.022 0.028 -10000 0 -0.13 16 16
VAV3 0.029 0.015 -10000 0 -10000 0 0
KLK2 0.026 0.055 -10000 0 -0.32 10 10
CASP8 0.036 0.006 -10000 0 0 13 13
T-DHT/AR/TIF2/CARM1 0.07 0.046 -10000 0 -0.11 1 1
TMPRSS2 0.026 0.071 -10000 0 -0.3 15 15
CCND1 0.029 0.015 -10000 0 -10000 0 0
PIAS1 0.036 0.008 -10000 0 -10000 0 0
mol:T-DHT 0.004 0.017 0.052 1 -0.049 33 34
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.036 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.037 0.041 -10000 0 -0.08 17 17
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.017 0.052 1 -0.049 33 34
CCND3 0.035 0.008 -10000 0 0 25 25
TGIF1 -0.001 0 -10000 0 -10000 0 0
FKBP4 0.035 0.009 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.054 0.094 -10000 0 -0.2 46 46
Ran/GTP/Exportin 1/HDAC1 -0.029 0.022 -10000 0 -0.11 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.11 -10000 0 -0.26 52 52
SUMO1 0.037 0.003 -10000 0 0 4 4
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.034 -10000 0 -0.15 21 21
FKBP3 0.034 0.009 -10000 0 0 35 35
Histones 0.035 0.076 -10000 0 -0.24 22 22
YY1/LSF 0.015 0.064 -10000 0 -0.22 19 19
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
I kappa B alpha/HDAC3 0 0.078 -10000 0 -0.2 52 52
I kappa B alpha/HDAC1 0.008 0.097 -10000 0 -0.22 62 62
SAP18 0.034 0.01 -10000 0 0 43 43
RELA -0.003 0.081 0.19 1 -0.28 18 19
HDAC1/Smad7 0.043 0.041 -10000 0 -0.13 6 6
RANGAP1 0.033 0.011 -10000 0 0 46 46
HDAC3/TR2 0.027 0.071 -10000 0 -0.26 20 20
NuRD/MBD3 Complex -0.01 0.11 -10000 0 -0.34 37 37
NF kappa B1 p50/RelA 0.012 0.088 -10000 0 -0.29 18 18
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.035 0.008 -10000 0 0 23 23
GATA1 0.037 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.11 -10000 0 -0.34 35 35
RBBP7 0.036 0.005 -10000 0 0 8 8
NPC 0.018 0.021 -10000 0 -0.09 18 18
RBBP4 0.033 0.012 -10000 0 0 57 57
MAX 0.034 0.009 -10000 0 0 32 32
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 22 22
NFKBIA -0.001 0.082 -10000 0 -0.32 27 27
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.09 -10000 0 -0.29 29 29
SIN3 complex 0.055 0.042 -10000 0 -0.13 17 17
SMURF1 0.025 0.017 -10000 0 0 165 165
CHD3 0.036 0.006 -10000 0 0 13 13
SAP30 0.035 0.007 -10000 0 0 18 18
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.035 0.008 -10000 0 0 27 27
YY1/HDAC3 -0.002 0.078 -10000 0 -0.24 31 31
YY1/HDAC2 0.014 0.061 -10000 0 -0.21 19 19
YY1/HDAC1 0.016 0.063 -10000 0 -0.22 19 19
NuRD/MBD2 Complex (MeCP1) -0.003 0.095 -10000 0 -0.28 34 34
PPARG 0.002 0.078 -10000 0 -0.26 22 22
HDAC8/hEST1B 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.036 0.004 -10000 0 0 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 22 22
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
HDAC3/SMRT (N-CoR2) 0.027 0.071 -10000 0 -0.26 20 20
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.043 0.04 -10000 0 -0.13 6 6
CREBBP 0.036 0.005 -10000 0 0 9 9
NuRD/MBD3/MBD3L2 Complex -0.005 0.11 -10000 0 -0.33 34 34
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC3 0.006 0.064 -10000 0 -0.3 16 16
HDAC2 0.033 0.012 -10000 0 0 59 59
YY1 0.01 0.028 -10000 0 -0.21 7 7
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.034 0.01 -10000 0 0 45 45
NCOR2 0.037 0.002 -10000 0 0 2 2
MXD1 0.037 0.003 -10000 0 0 3 3
STAT3 0.006 0.06 -10000 0 -0.22 33 33
NFKB1 0.035 0.007 -10000 0 0 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 24 24
YY1/LSF/HDAC1 0.029 0.072 -10000 0 -0.22 19 19
YY1/SAP30/HDAC1 0.031 0.07 -10000 0 -0.21 19 19
EP300 0.033 0.011 -10000 0 0 50 50
STAT3 (dimer non-phopshorylated) 0.006 0.06 -10000 0 -0.22 33 33
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.082 -10000 0 -0.32 27 27
histone deacetylation -0.004 0.095 -10000 0 -0.28 35 35
STAT3 (dimer non-phopshorylated)/HDAC3 0 0.094 -10000 0 -0.31 29 29
nuclear export -0.023 0.005 -10000 0 -10000 0 0
PRKACA 0.035 0.008 -10000 0 0 24 24
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.033 0.011 -10000 0 0 55 55
GATA2/HDAC3 0.026 0.07 -10000 0 -0.26 20 20
GATA1/HDAC1 0.051 0.023 -10000 0 -0.14 6 6
GATA1/HDAC3 0.027 0.071 -10000 0 -0.26 20 20
CHD4 0.034 0.01 -10000 0 0 37 37
TNF-alpha/TNFR1A 0.035 0.056 -10000 0 -0.14 43 43
SIN3/HDAC complex/Mad/Max -0.004 0.085 -10000 0 -0.29 26 26
NuRD Complex -0.003 0.11 -10000 0 -0.34 34 34
positive regulation of chromatin silencing 0.033 0.074 -10000 0 -0.24 22 22
SIN3B 0.034 0.009 -10000 0 0 33 33
MTA2 0.036 0.004 -10000 0 0 5 5
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.036 0.004 -10000 0 0 5 5
SUMO1/HDAC1 0.036 0.056 -10000 0 -0.22 6 6
HDAC complex 0.066 0.073 -10000 0 -0.15 42 42
GATA1/Fog1 0.027 0 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.054 0.05 -10000 0 -0.14 22 22
TNF 0.037 0.003 -10000 0 0 4 4
negative regulation of cell growth -0.004 0.085 -10000 0 -0.28 27 27
NuRD/MBD2/PRMT5 Complex -0.003 0.095 -10000 0 -0.28 34 34
Ran/GTP/Exportin 1 0.036 0.059 -10000 0 -0.16 21 21
NF kappa B/RelA/I kappa B alpha -0.005 0.093 -10000 0 -0.25 52 52
SIN3/HDAC complex/NCoR1 -0.003 0.093 -10000 0 -0.32 26 26
TFCP2 0.035 0.008 -10000 0 0 25 25
NR2C1 0.037 0.003 -10000 0 0 4 4
MBD3 0.034 0.01 -10000 0 0 40 40
MBD2 0.036 0.007 -10000 0 0 17 17
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.012 -10000 0 0 66 66
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.002 0.068 0.41 4 -10000 0 4
IL27/IL27R/JAK1 0.041 0.062 -10000 0 -10000 0 0
TBX21 -0.015 0.092 0.35 18 -10000 0 18
IL12B 0.037 0.004 -10000 0 0 6 6
IL12A -0.011 0.002 0.002 14 -10000 0 14
IL6ST 0.034 0.011 -10000 0 -0.033 1 1
IL27RA/JAK1 0.027 0.046 -10000 0 -10000 0 0
IL27 -0.001 0.004 -10000 0 -10000 0 0
TYK2 0.034 0.011 -10000 0 -0.033 1 1
T-helper cell lineage commitment 0.063 0.083 0.18 149 -0.13 7 156
T-helper 2 cell differentiation 0.002 0.068 0.41 4 -10000 0 4
T cell proliferation during immune response 0.002 0.068 0.41 4 -10000 0 4
MAPKKK cascade -0.002 0.068 -10000 0 -0.41 4 4
STAT3 0.034 0.01 -10000 0 0 37 37
STAT2 0.036 0.006 -10000 0 0 13 13
STAT1 0.034 0.01 -10000 0 0 40 40
IL12RB1 0.035 0.008 -10000 0 0 26 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.016 0.09 0.35 17 -10000 0 17
IL27/IL27R/JAK2/TYK2 -0.002 0.068 -10000 0 -0.41 4 4
positive regulation of T cell mediated cytotoxicity -0.002 0.068 -10000 0 -0.41 4 4
STAT1 (dimer) 0.048 0.081 -10000 0 -10000 0 0
JAK2 0.03 0.014 -10000 0 -0.032 1 1
JAK1 0.034 0.01 -10000 0 0 40 40
STAT2 (dimer) 0.015 0.099 -10000 0 -0.35 10 10
T cell proliferation 0.003 0.061 -10000 0 -0.32 4 4
IL12/IL12R/TYK2/JAK2 0.011 0.18 -10000 0 -0.77 24 24
IL17A 0.061 0.081 0.18 142 -0.13 8 150
mast cell activation 0.002 0.068 0.41 4 -10000 0 4
IFNG 0.003 0.029 -10000 0 -0.088 24 24
T cell differentiation -0.001 0.003 -10000 0 -0.017 9 9
STAT3 (dimer) 0.011 0.11 -10000 0 -0.38 13 13
STAT5A (dimer) 0.015 0.1 -10000 0 -0.34 11 11
STAT4 (dimer) 0.014 0.098 -10000 0 -0.37 7 7
STAT4 0.035 0.009 -10000 0 0 29 29
T cell activation -0.005 0.005 -10000 0 -0.086 1 1
IL27R/JAK2/TYK2 0.038 0.063 -10000 0 -10000 0 0
GATA3 0.007 0.092 0.67 9 -10000 0 9
IL18 -0.01 0.004 0 74 -10000 0 74
positive regulation of mast cell cytokine production 0.011 0.11 -10000 0 -0.37 13 13
IL27/EBI3 0.025 0.011 -10000 0 -10000 0 0
IL27RA 0.002 0.027 -10000 0 -10000 0 0
IL6 0.02 0.018 -10000 0 0 235 235
STAT5A 0.036 0.004 -10000 0 0 5 5
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.028 -10000 0 -10000 0 0
IL1B -0.009 0.005 0 101 -10000 0 101
EBI3 0.034 0.011 -10000 0 -0.033 1 1
TNF -0.011 0.001 0 4 -10000 0 4
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.011 0.002 0.001 22 -10000 0 22
SMARCC1 -0.005 0.12 -10000 0 -1.2 4 4
REL 0.036 0.004 -10000 0 -0.011 3 3
HDAC7 -0.03 0.057 0.18 4 -0.22 19 23
JUN 0.034 0.01 -10000 0 0 41 41
EP300 0.033 0.011 -10000 0 0 50 50
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.017 0.019 0.09 4 -10000 0 4
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR 0.019 0.079 0.25 2 -0.22 19 21
MAP2K6 0.035 0.012 -10000 0 -0.035 11 11
BRM/BAF57 0.047 0.024 -10000 0 -0.14 3 3
MAP2K4 0.034 0.014 -10000 0 -0.034 13 13
SMARCA2 0.032 0.013 -10000 0 0 69 69
PDE9A -0.014 0.2 -10000 0 -0.79 29 29
NCOA2 0.036 0.006 -10000 0 0 12 12
CEBPA 0.028 0.016 -10000 0 0 121 121
EHMT2 0.037 0.002 -10000 0 0 1 1
cell proliferation -0.019 0.093 0.26 7 -0.32 15 22
NR0B1 0.03 0.014 -10000 0 0 88 88
EGR1 0.029 0.015 -10000 0 0 107 107
RXRs/9cRA 0.066 0.02 -10000 0 -0.11 1 1
AR/RACK1/Src -0.013 0.063 0.18 14 -0.22 2 16
AR/GR 0.003 0.061 0.16 1 -0.2 25 26
GNB2L1 0.037 0.002 -10000 0 0 2 2
PKN1 0.033 0.011 -10000 0 0 48 48
RCHY1 0.036 0.006 -10000 0 0 16 16
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.011 0.02 0.095 6 -10000 0 6
T-DHT/AR/TIF2/CARM1 0.015 0.057 0.21 5 -0.19 5 10
SRC -0.02 0.037 0.17 11 -10000 0 11
NR3C1 0.035 0.007 -10000 0 0 22 22
KLK3 -0.003 0.074 0.37 2 -10000 0 2
APPBP2 0.034 0.015 -10000 0 -0.033 16 16
TRIM24 0.024 0.018 -10000 0 0 181 181
T-DHT/AR/TIP60 -0.024 0.029 0.082 2 -0.15 10 12
TMPRSS2 0.017 0.084 -10000 0 -0.55 8 8
RXRG 0.036 0.006 -10000 0 0 14 14
mol:9cRA 0 0 0.002 1 -10000 0 1
RXRA 0.035 0.008 -10000 0 0 22 22
RXRB 0.037 0.002 -10000 0 0 1 1
CARM1 0.035 0.008 -10000 0 0 28 28
NR2C2 0.036 0.005 -10000 0 0 8 8
KLK2 -0.002 0.046 0.2 2 -0.24 2 4
AR -0.004 0.045 0.15 6 -0.2 17 23
SENP1 0 0 0.003 1 -10000 0 1
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.011 -10000 0 -0.001 46 46
SRY 0.036 0.004 -10000 0 -0.038 1 1
GATA2 0.035 0.008 -10000 0 0 23 23
MYST2 0.034 0.01 -10000 0 0 37 37
HOXB13 0.037 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.015 0.065 0.19 17 -0.23 2 19
positive regulation of transcription 0.035 0.008 -10000 0 0 23 23
DNAJA1 0.032 0.017 -10000 0 -0.033 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.037 -10000 0 -0.26 8 8
NCOA1 0.037 0.034 0.15 2 -0.27 4 6
SPDEF 0.037 0.003 -10000 0 0 4 4
T-DHT/AR/TIF2 -0.032 0.085 0.19 2 -0.25 40 42
T-DHT/AR/Hsp90 -0.023 0.029 0.082 2 -0.15 10 12
GSK3B 0.034 0.01 -10000 0 0 39 39
NR2C1 0.036 0.003 -10000 0 0 4 4
mol:T-DHT -0.018 0.035 0.17 9 -0.12 4 13
SIRT1 0.024 0.017 -10000 0 0 172 172
ZMIZ2 -0.001 0.001 -10000 0 -0.019 1 1
POU2F1 0.037 0.035 0.12 13 -0.11 22 35
T-DHT/AR/DAX-1 -0.021 0.038 0.2 2 -0.18 3 5
CREBBP 0.036 0.005 -10000 0 0 9 9
SMARCE1 0.037 0.004 -10000 0 0 7 7
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.007 0.034 0.093 48 -10000 0 48
MAP4K4 0.003 0.053 -10000 0 -0.21 11 11
BAG4 0.036 0.005 -10000 0 0 11 11
PKC zeta/ceramide 0.004 0.048 -10000 0 -0.23 12 12
NFKBIA 0.033 0.012 -10000 0 0 57 57
BIRC3 0.031 0.014 -10000 0 0 82 82
BAX 0.002 0.075 -10000 0 -0.32 23 23
RIPK1 0.035 0.007 -10000 0 0 20 20
AKT1 -0.012 0.04 0.47 2 -10000 0 2
BAD -0.003 0.048 -10000 0 -0.24 11 11
SMPD1 -0.003 0.054 0.13 3 -0.19 23 26
RB1 -0.003 0.048 0.21 1 -0.23 12 13
FADD/Caspase 8 0.015 0.051 -10000 0 -0.26 4 4
MAP2K4 -0.006 0.052 0.18 6 -0.23 12 18
NSMAF 0.035 0.009 -10000 0 0 29 29
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.052 0.2 7 -0.24 11 18
EGF 0.035 0.008 -10000 0 0 25 25
mol:ceramide 0.005 0.052 -10000 0 -0.24 12 12
MADD 0.036 0.006 -10000 0 0 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.007 0.035 0.093 51 -10000 0 51
ASAH1 0.036 0.007 -10000 0 0 17 17
negative regulation of cell cycle -0.002 0.048 0.2 1 -0.23 12 13
cell proliferation 0.02 0.054 0.2 2 -0.24 4 6
BID 0.004 0.15 -10000 0 -0.58 26 26
MAP3K1 0 0.051 0.14 2 -0.24 12 14
EIF2A -0.009 0.05 0.2 5 -0.22 13 18
TRADD 0.036 0.005 -10000 0 0 10 10
CRADD 0.036 0.005 -10000 0 0 11 11
MAPK3 -0.006 0.049 0.18 11 -0.25 4 15
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.063 0.18 10 -0.22 21 31
Cathepsin D/ceramide 0.021 0.056 -10000 0 -0.24 12 12
FADD 0.009 0.047 -10000 0 -0.22 5 5
KSR1 -0.003 0.048 -10000 0 -0.24 12 12
MAPK8 -0.039 0.095 0.18 1 -0.19 115 116
PRKRA -0.005 0.052 0.23 2 -0.23 13 15
PDGFA 0.027 0.016 -10000 0 0 134 134
TRAF2 0.036 0.006 -10000 0 0 16 16
IGF1 0.035 0.007 -10000 0 0 21 21
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.005 0.051 -10000 0 -0.24 12 12
CTSD 0.033 0.012 -10000 0 0 56 56
regulation of nitric oxide biosynthetic process 0.05 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.022 0.058 0.22 2 -0.26 4 6
PRKCD 0.034 0.01 -10000 0 0 40 40
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.007 0.035 0.093 51 -10000 0 51
RelA/NF kappa B1 0.05 0.025 -10000 0 -0.14 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.036 0.006 -10000 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.054 -10000 0 -0.24 7 7
TNFR1A/BAG4/TNF-alpha 0.053 0.056 -10000 0 -0.13 41 41
mol:Sphingosine-1-phosphate -0.007 0.034 0.093 48 -10000 0 48
MAP2K1 -0.016 0.051 0.18 7 -0.23 11 18
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
CYCS 0.024 0.062 0.14 22 -0.19 9 31
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
NFKB1 0.035 0.007 -10000 0 0 18 18
TNFR1A/BAG4 0.035 0.055 -10000 0 -0.14 42 42
EIF2AK2 -0.01 0.053 0.21 5 -0.22 13 18
TNF-alpha/TNFR1A/FAN 0.047 0.067 -10000 0 -0.14 55 55
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.049 -10000 0 -0.31 2 2
MAP2K2 -0.008 0.052 0.18 19 -0.32 2 21
SMPD3 0.006 0.056 0.16 1 -0.27 9 10
TNF 0.037 0.003 -10000 0 0 4 4
PKC zeta/PAR4 0.026 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.006 0.044 0.13 7 -0.15 14 21
NF kappa B1/RelA/I kappa B alpha 0.07 0.048 -10000 0 -0.12 20 20
AIFM1 -0.003 0.049 0.14 2 -0.19 18 20
BCL2 0.035 0.007 -10000 0 0 20 20
E-cadherin signaling events

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.063 0.03 -9999 0 -0.13 3 3
E-cadherin/beta catenin 0.048 0.022 -9999 0 -0.14 3 3
CTNNB1 0.036 0.006 -9999 0 0 15 15
JUP 0.033 0.011 -9999 0 0 51 51
CDH1 0.034 0.01 -9999 0 0 37 37
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.009 0.14 0.32 18 -1 8 26
VDR 0.035 0.007 -10000 0 0 21 21
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.012 0.099 0.25 2 -0.28 38 40
RXRs/LXRs/DNA/Oxysterols 0.004 0.14 0.31 2 -0.42 41 43
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0 0.016 0.047 3 -0.049 43 46
RARs/THRs/DNA/Src-1 0.016 0.054 -10000 0 -0.16 41 41
RXRs/NUR77 0.079 0.065 -10000 0 -0.14 8 8
RXRs/PPAR 0.019 0.048 -10000 0 -0.19 4 4
NCOR2 0.037 0.002 -10000 0 0 2 2
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.081 0.024 -10000 0 -10000 0 0
RARA 0.037 0.003 -10000 0 0 3 3
NCOA1 0.033 0.011 -10000 0 0 49 49
VDR/VDR/DNA 0.035 0.007 -10000 0 0 21 21
RARs/RARs/DNA/9cRA 0.056 0.033 -10000 0 -10000 0 0
RARG 0.036 0.005 -10000 0 0 11 11
RPS6KB1 -0.004 0.087 0.51 8 -0.4 8 16
RARs/THRs/DNA/SMRT 0.03 0.025 -10000 0 -0.18 5 5
THRA 0.036 0.006 -10000 0 0 12 12
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.058 0.074 0.29 3 -0.16 39 42
NR1H4 0.036 0.004 -10000 0 0 6 6
RXRs/LXRs/DNA 0.085 0.1 0.31 2 -0.22 37 39
NR1H2 0.029 0.031 0.091 2 -0.062 46 48
NR1H3 0.03 0.033 0.092 2 -0.069 44 46
RXRs/VDR/DNA/Vit D3 0.071 0.061 0.21 1 -0.11 32 33
NR4A1 0.036 0.006 -10000 0 0 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.04 0.13 1 -0.14 5 6
RXRG 0.03 0.03 0.09 1 -0.06 46 47
RXR alpha/CCPG 0.023 0.021 -10000 0 -0.057 9 9
RXRA 0.03 0.03 0.09 1 -0.061 44 45
RXRB 0.031 0.033 -10000 0 -0.067 48 48
THRB 0.036 0.004 -10000 0 0 7 7
PPARG 0.035 0.008 -10000 0 0 26 26
PPARD 0.037 0.002 -10000 0 0 1 1
TNF -0.002 0.13 -10000 0 -0.55 11 11
mol:Oxysterols 0 0.015 0.047 3 -0.044 44 47
cholesterol transport 0.005 0.14 0.31 2 -0.41 41 43
PPARA 0.034 0.01 -10000 0 0 43 43
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.036 0.005 -10000 0 0 10 10
RXRs/NUR77/BCL2 0.02 0.031 -10000 0 -0.16 1 1
SREBF1 -0.01 0.17 -10000 0 -0.79 15 15
RXRs/RXRs/DNA/9cRA 0.058 0.074 0.28 3 -0.16 39 42
ABCA1 -0.044 0.26 0.35 2 -0.85 45 47
RARs/THRs 0.1 0.027 -10000 0 -0.12 1 1
RXRs/FXR 0.08 0.065 0.22 1 -0.13 10 11
BCL2 0.035 0.007 -10000 0 0 20 20
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.036 0.006 -10000 0 0 12 12
CLTC 0.011 0.088 -10000 0 -0.31 29 29
calcium ion-dependent exocytosis 0.017 0.064 0.13 1 -0.2 20 21
Dynamin 2/GTP 0.026 0.011 0.081 1 -0.1 1 2
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.003 0.079 -10000 0 -0.28 29 29
CPE -0.015 0.009 -10000 0 -0.12 1 1
CTNNB1 0.036 0.006 -10000 0 0 15 15
membrane fusion 0.02 0.063 -10000 0 -0.16 31 31
CTNND1 -0.019 0.011 0.087 1 -0.18 1 2
DNM2 0.035 0.008 -10000 0 0 27 27
mol:PI-4-5-P2 0.011 0.065 0.15 8 -0.2 23 31
TSHR -0.016 0.009 0.092 1 -0.12 1 2
INS 0.01 0.086 -10000 0 -0.44 16 16
BIN1 0.031 0.013 -10000 0 0 76 76
mol:Choline 0.02 0.063 -10000 0 -0.16 31 31
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.005 -10000 0 -0.11 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.009 -10000 0 0 29 29
mol:Ca2+ 0.026 0.011 0.08 1 -0.1 1 2
JUP 0.012 0.069 -10000 0 -0.26 23 23
ASAP2/amphiphysin II 0.028 0.046 -10000 0 -0.11 48 48
ARF6/GTP 0.025 0.009 -10000 0 -0.13 1 1
CDH1 0.009 0.072 -10000 0 -0.26 26 26
clathrin-independent pinocytosis 0.025 0.009 -10000 0 -0.13 1 1
MAPK8IP3 0.036 0.004 -10000 0 0 7 7
positive regulation of endocytosis 0.025 0.009 -10000 0 -0.13 1 1
EXOC2 0.036 0.006 -10000 0 0 15 15
substrate adhesion-dependent cell spreading 0.004 0.053 -10000 0 -0.31 5 5
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.034 0.01 -10000 0 0 37 37
regulation of calcium-dependent cell-cell adhesion -0.038 0.077 0.26 25 -10000 0 25
positive regulation of phagocytosis -0.015 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.046 0.015 -10000 0 -0.12 1 1
ACAP1 0.021 0.061 -10000 0 -0.21 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.004 0.055 -10000 0 -0.27 14 14
clathrin heavy chain/ACAP1 0.016 0.083 0.2 8 -0.23 30 38
JIP4/KLC1 0.036 0.036 -10000 0 -0.11 26 26
EXOC1 0.033 0.011 -10000 0 0 50 50
exocyst 0.003 0.052 -10000 0 -0.31 5 5
RALA/GTP 0.013 0.029 -10000 0 -0.13 16 16
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.039 -10000 0 -0.12 26 26
receptor recycling 0.025 0.009 -10000 0 -0.13 1 1
CTNNA1 -0.02 0.011 0.087 1 -0.18 1 2
NME1 -0.009 0.005 -10000 0 -0.11 1 1
clathrin coat assembly 0.011 0.088 -10000 0 -0.3 30 30
IL2RA 0.007 0.066 -10000 0 -0.33 14 14
VAMP3 -0.015 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.031 0.082 -10000 0 -0.22 30 30
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0 0.038 -10000 0 -0.19 14 14
PLD2 0 0.038 -10000 0 -0.14 30 30
EXOC5 0.031 0.014 -10000 0 0 87 87
PIP5K1C 0.009 0.061 0.12 3 -0.2 20 23
SDC1 0.013 0.073 -10000 0 -0.26 26 26
ARF6/GDP 0.026 0.006 -10000 0 0 29 29
EXOC7 0.036 0.005 -10000 0 0 11 11
E-cadherin/beta catenin 0.04 0.08 -10000 0 -0.27 24 24
mol:Phosphatidic acid 0.02 0.063 -10000 0 -0.16 31 31
endocytosis -0.026 0.045 0.11 48 -10000 0 48
SCAMP2 0.035 0.009 -10000 0 0 29 29
ADRB2 0.01 0.087 0.23 1 -0.3 28 29
EXOC3 0.037 0.003 -10000 0 0 4 4
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.01 0.09 1 -0.1 1 2
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.004 0.084 -10000 0 -0.3 29 29
RALA 0.024 0.018 -10000 0 0 182 182
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.084 0.22 1 -0.26 30 31
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.061 0.039 -10000 0 -0.12 20 20
HDAC3 0.036 0.004 -10000 0 0 7 7
Ran/GTP/Exportin 1/HDAC4 -0.03 0.023 -10000 0 -0.11 35 35
GATA1/HDAC4 0.047 0.035 -10000 0 -0.14 15 15
GATA1/HDAC5 0.053 0.012 -10000 0 -0.14 1 1
GATA2/HDAC5 0.05 0.016 -10000 0 -0.14 1 1
HDAC5/BCL6/BCoR 0.052 0.051 -10000 0 -0.13 28 28
HDAC9 0.022 0.018 -10000 0 0 206 206
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.029 -10000 0 -0.12 15 15
HDAC4/ANKRA2 0.044 0.041 -10000 0 -0.15 20 20
HDAC5/YWHAB 0.047 0.029 -10000 0 -0.16 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.034 -10000 0 -0.15 21 21
GATA2 0.035 0.008 -10000 0 0 23 23
HDAC4/RFXANK 0.038 0.05 -10000 0 -0.15 30 30
BCOR 0.034 0.009 -10000 0 0 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.036 0.006 -10000 0 0 14 14
GNB1/GNG2 0.021 0.031 -10000 0 -0.13 20 20
Histones 0.023 0.066 -10000 0 -0.17 38 38
ADRBK1 0.036 0.005 -10000 0 0 10 10
HDAC4 0.035 0.009 -10000 0 0 30 30
XPO1 0.036 0.004 -10000 0 0 5 5
HDAC5/ANKRA2 0.05 0.025 -10000 0 -0.14 7 7
HDAC4/Ubc9 0.046 0.035 -10000 0 -0.14 15 15
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.047 0.031 -10000 0 -0.14 11 11
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.037 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.044 0.039 -10000 0 -0.14 18 18
CAMK4 0.036 0.005 -10000 0 0 8 8
Tubulin/HDAC6 0.037 0.044 -10000 0 -0.12 38 38
SUMO1 0.037 0.003 -10000 0 0 4 4
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.034 0.01 -10000 0 0 41 41
GATA1 0.037 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
NR3C1 0.035 0.007 -10000 0 0 22 22
SUMO1/HDAC4 0.033 0.058 -10000 0 -0.23 6 6
SRF 0.037 0.002 -10000 0 0 1 1
HDAC4/YWHAB 0.041 0.043 -10000 0 -0.16 20 20
Tubulin 0.015 0.042 -10000 0 -0.13 38 38
HDAC4/14-3-3 E 0.042 0.045 -10000 0 -0.15 24 24
GNB1 0.035 0.007 -10000 0 0 20 20
RANGAP1 0.033 0.011 -10000 0 0 46 46
BCL6/BCoR 0.036 0.047 -10000 0 -0.14 28 28
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.038 -10000 0 -0.13 16 16
HDAC4/SRF 0.066 0.036 -10000 0 -0.13 14 14
HDAC4/ER alpha 0.044 0.036 -10000 0 -0.14 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.023 0.066 -10000 0 -0.17 38 38
cell motility 0.036 0.044 -10000 0 -0.12 38 38
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.036 0.004 -10000 0 0 6 6
HDAC7/HDAC3 0.027 0.008 -10000 0 -0.13 1 1
BCL6 0.032 0.013 -10000 0 0 71 71
HDAC4/CaMK II delta B 0.035 0.009 -10000 0 0 30 30
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 0.035 0.009 -10000 0 0 31 31
HDAC6/HDAC11 0.054 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.059 -10000 0 -0.16 21 21
NPC 0.018 0.021 -10000 0 -0.09 18 18
MEF2C 0.035 0.008 -10000 0 0 28 28
RAN 0.036 0.005 -10000 0 0 10 10
HDAC4/MEF2C 0.093 0.055 -10000 0 -0.12 26 26
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.037 0.002 -10000 0 0 2 2
TUBB2A 0.034 0.01 -10000 0 0 45 45
HDAC11 0.036 0.005 -10000 0 0 8 8
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 24 24
ANKRA2 0.036 0.006 -10000 0 0 13 13
RFXANK 0.034 0.01 -10000 0 0 44 44
nuclear import -0.028 0.059 0.21 26 -10000 0 26
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.036 0.007 -10000 0 0 17 17
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0 -10000 0 -10000 0 0
monocyte activation -0.068 0.16 -10000 0 -0.34 135 135
MAP2K2 0.019 0.039 -10000 0 -0.59 2 2
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.002 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -10000 0 0
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B 0 0.04 0.081 71 -0.076 57 128
Channel 0.023 0.004 -10000 0 -10000 0 0
NLRP1 -0.001 0 -10000 0 -10000 0 0
CALM1 0.033 0.012 -10000 0 0 57 57
negative regulation of phagocytosis -0.02 0.12 -10000 0 -0.41 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0 -10000 0 -10000 0 0
MAPK3 -0.009 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.003 -10000 0 -10000 0 0
PGR -0.009 0.002 -10000 0 -10000 0 0
PA/Cellular Receptors 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.002 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
macrophage activation -0.012 0.011 0.068 8 -10000 0 8
TNF 0.037 0.003 -10000 0 0 4 4
VCAM1 -0.068 0.16 -10000 0 -0.34 134 134
platelet activation -0.02 0.12 -10000 0 -0.41 44 44
MAPKKK cascade 0.003 0.02 0.065 3 -0.069 29 32
IL18 -0.005 0.036 0.086 40 -0.076 60 100
negative regulation of macrophage activation -0.002 0 -10000 0 -10000 0 0
LEF -0.002 0 -10000 0 -10000 0 0
CASP1 0.003 0.004 0.025 13 -10000 0 13
mol:cAMP -0.02 0.12 -10000 0 -0.41 44 44
necrosis -0.002 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.05 0.018 -10000 0 -0.14 2 2
FBXW11 0.035 0.007 -10000 0 0 22 22
NF kappa B1 p50/c-Rel 0.033 0.018 -10000 0 -0.13 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.07 0.21 1 -0.26 14 15
NFKBIA 0.005 0.059 -10000 0 -0.18 28 28
MAPK14 0.036 0.004 -10000 0 0 5 5
NF kappa B1 p105/p50 0.029 0.031 -10000 0 -0.13 16 16
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
REL 0.037 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.019 -10000 0 -0.13 5 5
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.021 -10000 0 -0.13 7 7
PIK3CA 0.031 0.014 -10000 0 0 82 82
NF kappa B1 p50 dimer -0.02 0.029 0.18 7 -0.14 5 12
PIK3R1 0.032 0.012 -10000 0 0 63 63
NFKB1 -0.021 0.011 0.093 4 -10000 0 4
RELA 0.036 0.004 -10000 0 0 7 7
positive regulation of anti-apoptosis 0.015 0.041 0.14 2 -0.18 4 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.027 0.073 0.18 2 -0.26 15 17
SRC 0.034 0.009 -10000 0 0 34 34
PI3K 0.018 0.076 -10000 0 -0.16 72 72
NF kappa B1 p50/RelA 0.015 0.041 0.14 2 -0.18 4 6
IKBKB 0.037 0.003 -10000 0 0 4 4
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 22 22
SYK 0.031 0.013 -10000 0 0 74 74
I kappa B alpha/PIK3R1 0.018 0.073 0.22 1 -0.24 24 25
cell death 0.026 0.071 0.18 2 -0.25 15 17
NF kappa B1 p105/c-Rel 0.033 0.018 -10000 0 -0.13 5 5
LCK 0.035 0.007 -10000 0 0 18 18
BCL3 0.035 0.009 -10000 0 0 31 31
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.035 0.14 28 -0.18 3 31
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.009 0.046 0.12 2 -0.18 9 11
AP2 0.021 0.028 -10000 0 -0.13 15 15
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.029 0.036 -10000 0 -0.12 14 14
CLTB 0.036 0.005 -10000 0 0 9 9
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0.03 -10000 0 -0.18 10 10
CD4 0.031 0.013 -10000 0 0 74 74
CLTA 0.034 0.01 -10000 0 0 41 41
mol:GTP -0.003 0.002 0.006 1 -0.019 6 7
ARFGAP1 -0.011 0.003 0 43 -10000 0 43
mol:PI-4-5-P2 0.008 0.019 0.1 11 -10000 0 11
ARF1/GTP 0.019 0.018 -10000 0 -0.1 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.031 -10000 0 -0.18 9 9
mol:Choline 0.008 0.019 0.11 11 -10000 0 11
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.035 0.008 -10000 0 0 24 24
DDEF1 0.006 0.018 0.1 9 -10000 0 9
ARF1/GDP 0.006 0.012 -10000 0 -0.086 4 4
AP2M1 0.034 0.01 -10000 0 0 40 40
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.017 0.067 1 -0.12 8 9
Rac/GTP 0.017 0.02 -10000 0 -0.097 8 8
ARF1/GTP/GGA3/ARF-GAP1 0.041 0.025 -10000 0 -0.11 8 8
ARFIP2 0.032 0.015 -10000 0 -0.038 13 13
COPA 0.036 0.006 -10000 0 0 14 14
RAC1 0.025 0.017 -10000 0 0 162 162
ARF1/GTP/coatomer protein complex 0.005 0.043 -10000 0 -0.18 10 10
ARF1/GTP/ARHGAP10 0.021 0.016 -10000 0 -0.12 6 6
GGA3 0.036 0.005 -10000 0 0 8 8
ARF1/GTP/Membrin 0.028 0.025 -10000 0 -0.24 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.006 0.034 -10000 0 -0.18 10 10
ARF1/GDP/Membrin 0.031 0.028 -10000 0 -0.27 3 3
Arfaptin 2/Rac/GDP 0.028 0.035 -10000 0 -0.12 15 15
CYTH2 -0.003 0.002 0.006 1 -0.019 6 7
ARF1/GTP/GGA3 0.044 0.021 -10000 0 -0.12 6 6
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.02 -10000 0 -0.13 5 5
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.004 0.058 -10000 0 -0.18 32 32
PLD2 0.008 0.019 0.11 11 -10000 0 11
ARF-GAP1/v-SNARE -0.011 0.003 0 43 -10000 0 43
PIP5K1A 0.008 0.019 0.1 11 -10000 0 11
ARF1/GTP/Membrin/GBF1/p115 0.002 0.036 -10000 0 -0.1 10 10
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.019 0.11 11 -10000 0 11
KDEL Receptor/Ligand/ARF-GAP1 -0.011 0.003 0 43 -10000 0 43
GOSR2 0.015 0.023 -10000 0 -0.32 2 2
USO1 0.002 0.006 0.03 17 -0.031 4 21
GBF1 -0.073 0.15 -10000 0 -0.31 139 139
ARF1/GTP/Arfaptin 2 0.042 0.034 -10000 0 -0.12 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.046 -10000 0 -0.13 35 35
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.033 0.021 0.078 8 -0.059 18 26
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.08 -10000 0 -0.25 19 19
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.011 -10000 0 -0.13 2 2
NFKBIA -0.033 0.047 0.2 1 -0.28 14 15
BIRC2 0.036 0.006 -10000 0 0 12 12
IKBKB 0.037 0.003 -10000 0 0 4 4
RIPK2 0.036 0.006 -10000 0 0 14 14
IKBKG 0.02 0.047 -10000 0 -0.25 10 10
IKK complex/A20 0.059 0.074 -10000 0 -0.26 9 9
NEMO/A20/RIP2 0.036 0.006 -10000 0 0 14 14
XPO1 0.036 0.004 -10000 0 0 5 5
NEMO/ATM 0.039 0.056 -10000 0 -0.26 11 11
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
Exportin 1/RanGTP 0.047 0.023 -10000 0 -0.15 6 6
IKK complex/ELKS 0.028 0.053 -10000 0 -0.24 9 9
BCL10/MALT1/TRAF6 0.063 0.035 -10000 0 -0.13 10 10
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.033 0.02 0.078 9 -0.056 18 27
RELA 0.034 0.021 0.078 9 -0.058 20 29
MALT1 0.034 0.009 -10000 0 0 34 34
cIAP1/UbcH5C 0.05 0.027 -10000 0 -0.18 6 6
ATM 0.034 0.01 -10000 0 0 37 37
TNF/TNFR1A 0.035 0.056 -10000 0 -0.14 43 43
TRAF6 0.036 0.005 -10000 0 0 10 10
PRKCA 0.036 0.004 -10000 0 0 6 6
CHUK 0.025 0.017 -10000 0 0 163 163
UBE2D3 0.036 0.006 -10000 0 0 12 12
TNF 0.037 0.003 -10000 0 0 4 4
NF kappa B1 p50/RelA 0.066 0.06 -10000 0 -0.17 27 27
BCL10 0.035 0.007 -10000 0 0 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.033 0.047 0.2 1 -0.28 14 15
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.021 0.078 8 -0.059 18 26
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
IKK complex 0.04 0.062 -10000 0 -0.25 9 9
CYLD 0.036 0.006 -10000 0 0 15 15
IKK complex/PKC alpha 0.05 0.068 -10000 0 -0.26 7 7
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.03 0.15 -10000 0 -0.99 10 10
CLOCK 0.033 0.019 -10000 0 -0.067 10 10
TIMELESS/CRY2 0.024 0.16 -10000 0 -1 10 10
DEC1/BMAL1 0.033 0.057 -10000 0 -0.14 42 42
ATR 0.035 0.008 -10000 0 0 25 25
NR1D1 0.014 0.066 -10000 0 -0.36 9 9
ARNTL 0.032 0.02 -10000 0 -0.069 8 8
TIMELESS 0.001 0.16 -10000 0 -1.1 10 10
NPAS2 0.037 0.017 -10000 0 -0.067 10 10
CRY2 0.035 0.007 -10000 0 0 21 21
mol:CO -0.01 0.027 0.13 10 -0.087 4 14
CHEK1 0.033 0.011 -10000 0 0 50 50
mol:HEME 0.01 0.027 0.087 4 -0.13 10 14
PER1 0.033 0.011 -10000 0 0 53 53
BMAL/CLOCK/NPAS2 0.056 0.076 0.23 1 -0.14 51 52
BMAL1/CLOCK 0.011 0.12 -10000 0 -0.51 18 18
S phase of mitotic cell cycle 0.03 0.15 -10000 0 -0.99 10 10
TIMELESS/CHEK1/ATR 0.03 0.16 -10000 0 -1 10 10
mol:NADPH 0.01 0.027 0.087 4 -0.13 10 14
PER1/TIMELESS 0.022 0.16 -10000 0 -1 10 10
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.036 0.006 -10000 0 0 16 16
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 0.047 0.065 -10000 0 -10000 0 0
MKNK1 0.034 0.009 -10000 0 0 35 35
MAPK14 0.047 0.037 0.16 3 -0.083 22 25
ATF2/c-Jun -0.001 0.094 -10000 0 -0.32 32 32
MAPK11 0.043 0.039 0.16 3 -0.083 22 25
MITF 0.031 0.049 0.22 1 -0.2 7 8
MAPKAPK5 0.034 0.039 0.22 1 -10000 0 1
KRT8 0.035 0.039 0.21 2 -10000 0 2
MAPKAPK3 0.035 0.007 -10000 0 0 19 19
MAPKAPK2 0.034 0.01 -10000 0 0 43 43
p38alpha-beta/CK2 0.062 0.056 0.23 3 -10000 0 3
CEBPB 0.024 0.069 0.17 16 -0.21 26 42
SLC9A1 0.032 0.041 -10000 0 -0.26 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.031 0.055 0.26 4 -0.26 2 6
p38alpha-beta/MNK1 0.064 0.069 0.21 1 -0.14 20 21
JUN -0.004 0.092 -10000 0 -0.33 31 31
PPARGC1A 0.032 0.057 0.23 2 -0.21 13 15
USF1 0.028 0.037 0.18 3 -10000 0 3
RAB5/GDP/GDI1 0.012 0.077 -10000 0 -0.22 26 26
NOS2 0.028 0.037 0.18 3 -10000 0 3
DDIT3 0.029 0.062 0.22 1 -0.2 20 21
RAB5A 0.034 0.009 -10000 0 0 32 32
HSPB1 0.084 0.13 0.28 142 -0.15 3 145
p38alpha-beta/HBP1 0.053 0.058 0.23 2 -10000 0 2
CREB1 0.023 0.07 0.23 1 -0.23 2 3
RAB5/GDP 0.019 0.034 -10000 0 -0.13 24 24
EIF4E -0.015 0.057 0.21 7 -0.2 6 13
RPS6KA4 0.034 0.039 0.19 2 -10000 0 2
PLA2G4A -0.015 0.053 0.2 4 -0.19 11 15
GDI1 0.024 0.059 0.22 1 -0.23 17 18
TP53 0.01 0.051 0.17 10 -10000 0 10
RPS6KA5 0.034 0.041 0.18 4 -0.19 1 5
ESR1 0.032 0.038 0.22 1 -10000 0 1
HBP1 0.025 0.017 -10000 0 0 164 164
MEF2C 0.031 0.049 0.18 4 -0.22 7 11
MEF2A 0.031 0.047 0.22 1 -0.21 6 7
EIF4EBP1 0.02 0.075 0.23 1 -0.34 3 4
KRT19 0.035 0.04 0.21 2 -10000 0 2
ELK4 0.031 0.037 -10000 0 -10000 0 0
ATF6 0.033 0.037 -10000 0 -10000 0 0
ATF1 0.018 0.072 0.23 1 -0.3 2 3
p38alpha-beta/MAPKAPK2 0.07 0.056 0.22 2 -10000 0 2
p38alpha-beta/MAPKAPK3 0.072 0.058 0.22 3 -0.14 2 5
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.033 0.028 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.014 0.016 -10000 0 -10000 0 0
mol:DAG -0.018 0.032 0.19 1 -10000 0 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.017 -10000 0 -10000 0 0
CaM/Ca2+ -0.023 0.041 0.16 3 -0.2 3 6
HIF1A 0.04 0.013 -10000 0 -10000 0 0
GAB1 0.033 0.011 -10000 0 0 55 55
AKT1 -0.031 0.088 0.2 7 -0.32 23 30
PLCG1 -0.018 0.032 0.19 1 -10000 0 1
NOS3 0.007 0.067 0.2 1 -0.3 8 9
CBL 0.036 0.005 -10000 0 0 8 8
mol:NO 0.014 0.076 0.22 2 -0.3 7 9
FLT1 0.016 0.008 -10000 0 -10000 0 0
PGF 0.031 0.013 -10000 0 0 74 74
VEGFR1 homodimer/NRP2/VEGFR121 0.03 0.025 -10000 0 -10000 0 0
CALM1 0.033 0.012 -10000 0 0 57 57
PIK3CA 0.031 0.014 -10000 0 0 82 82
eNOS/Hsp90 -0.001 0.069 -10000 0 -0.29 7 7
endothelial cell proliferation -0.002 0.052 0.2 4 -0.25 3 7
mol:Ca2+ -0.018 0.032 0.19 1 -10000 0 1
MAPK3 -0.027 0.033 0.15 3 -10000 0 3
MAPK1 -0.027 0.033 0.15 1 -0.19 1 2
PIK3R1 0.032 0.012 -10000 0 0 63 63
PLGF homodimer 0.031 0.013 -10000 0 0 74 74
PRKACA 0.035 0.008 -10000 0 0 24 24
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.018 -10000 0 0 288 288
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.014 0.016 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.025 0.048 0.22 1 -10000 0 1
PI3K 0.036 0.078 -10000 0 -0.2 15 15
PRKCA -0.023 0.031 0.17 1 -10000 0 1
PRKCB -0.017 0.029 0.17 1 -10000 0 1
VEGFR1 homodimer/PLGF homodimer 0.03 0.029 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.036 0.004 -10000 0 0 7 7
mol:IP3 -0.018 0.032 0.19 1 -10000 0 1
RASA1 -0.026 0.027 0.19 1 -0.2 5 6
NRP2 0.036 0.005 -10000 0 0 8 8
VEGFR1 homodimer 0.016 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.036 0.004 -10000 0 0 7 7
NCK1 0.035 0.008 -10000 0 0 27 27
eNOS/Caveolin-1 0.001 0.071 -10000 0 -0.28 16 16
PTPN11 0.036 0.005 -10000 0 0 11 11
mol:PI-3-4-5-P3 0.035 0.077 -10000 0 -0.2 15 15
mol:L-citrulline 0.014 0.076 0.22 2 -0.3 7 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.04 0.044 -10000 0 -0.19 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.029 -10000 0 -0.2 1 1
CD2AP 0.034 0.01 -10000 0 0 40 40
PI3K/GAB1 0.042 0.088 -10000 0 -0.2 21 21
PDPK1 -0.029 0.067 0.24 4 -0.27 2 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.029 -10000 0 -0.2 1 1
mol:NADP 0.014 0.076 0.22 2 -0.3 7 9
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.043 -10000 0 -0.19 3 3
VEGFR1 homodimer/NRP2 0.032 0.028 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 0.035 0.032 -10000 0 -10000 0 0
IHH 0.052 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 0.014 0.027 -10000 0 -0.11 15 15
LRPAP1 0.036 0.007 -10000 0 0 17 17
dorsoventral neural tube patterning -0.014 0.027 0.11 15 -10000 0 15
SMO/beta Arrestin2 0.09 0.064 0.26 13 -10000 0 13
SMO 0.025 0.031 0.19 1 -10000 0 1
AKT1 -0.008 0.13 -10000 0 -0.45 29 29
ARRB2 0.035 0.008 -10000 0 0 25 25
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.036 0.005 -10000 0 0 10 10
heart looping 0.026 0.033 0.22 3 -10000 0 3
STIL 0.05 0.093 0.19 145 -10000 0 145
DHH N/PTCH2 0.027 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.017 0.021 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.038 0.048 -10000 0 -10000 0 0
determination of left/right symmetry 0.026 0.033 0.22 3 -10000 0 3
PIK3R1 0.032 0.012 -10000 0 0 63 63
skeletal system development 0.038 0.048 -10000 0 -10000 0 0
IHH N/Hhip 0.034 0.008 -10000 0 -10000 0 0
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.026 0.033 0.22 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.035 0.007 -10000 0 0 18 18
PI3K 0.018 0.076 -10000 0 -0.16 72 72
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.031 0.014 -10000 0 0 86 86
somite specification 0.026 0.033 0.22 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.017 0.024 0.17 1 -10000 0 1
SHH Np/Cholesterol/PTCH2 0.021 0.016 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.02 0.016 -10000 0 -10000 0 0
SHH -0.015 0.012 0.093 1 -10000 0 1
catabolic process 0.02 0.026 0.14 22 -10000 0 22
SMO/Vitamin D3 0.022 0.038 0.19 15 -10000 0 15
SHH Np/Cholesterol/Hhip -0.01 0.008 -10000 0 -10000 0 0
LRP2 0.036 0.006 -10000 0 0 12 12
receptor-mediated endocytosis 0.023 0.039 0.28 3 -10000 0 3
SHH Np/Cholesterol/BOC -0.01 0.008 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.021 0.016 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.01 0.008 -10000 0 -10000 0 0
mol:Vitamin D3 0.076 0.087 0.2 164 -10000 0 164
IHH N/PTCH2 0.061 0.011 -10000 0 -10000 0 0
CDON 0.036 0.004 -10000 0 0 7 7
IHH N/PTCH1 0.046 0.028 0.17 21 -10000 0 21
Megalin/LRPAP1 0.049 0.029 -10000 0 -0.14 10 10
PTCH2 0.036 0.005 -10000 0 0 8 8
SHH Np/Cholesterol 0.012 0.009 -10000 0 -10000 0 0
PTCH1 0.02 0.026 0.14 22 -10000 0 22
HHIP 0 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.083 -10000 0 -0.3 18 18
BAG4 0.036 0.005 -10000 0 0 11 11
BAD -0.004 0.033 0.1 3 -0.14 11 14
NFKBIA 0.033 0.012 -10000 0 0 57 57
BIRC3 0.031 0.014 -10000 0 0 82 82
BAX 0.001 0.044 0.19 13 -0.14 9 22
EnzymeConsortium:3.1.4.12 0.004 0.021 0.061 2 -0.085 8 10
IKBKB -0.005 0.082 0.2 3 -0.3 16 19
MAP2K2 -0.009 0.052 0.17 24 -0.16 6 30
MAP2K1 -0.015 0.039 0.17 5 -0.17 6 11
SMPD1 0.002 0.029 0.11 1 -0.12 15 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.012 0.078 -10000 0 -0.33 9 9
MAP2K4 -0.007 0.036 0.16 4 -0.15 5 9
protein ubiquitination -0.007 0.082 -10000 0 -0.31 15 15
EnzymeConsortium:2.7.1.37 -0.014 0.047 0.18 8 -0.17 7 15
response to UV 0 0 0.002 8 -0.002 2 10
RAF1 -0.01 0.038 0.17 6 -0.15 10 16
CRADD 0.036 0.005 -10000 0 0 11 11
mol:ceramide 0.003 0.032 0.11 1 -0.13 12 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.033 -10000 0 -0.12 18 18
MADD 0.036 0.006 -10000 0 0 15 15
MAP3K1 -0.002 0.033 0.15 2 -0.14 8 10
TRADD 0.036 0.005 -10000 0 0 10 10
RELA/p50 0.036 0.004 -10000 0 0 7 7
MAPK3 -0.007 0.046 0.18 9 -0.17 5 14
MAPK1 -0.013 0.056 0.18 8 -0.2 13 21
p50/RELA/I-kappa-B-alpha 0.043 0.039 -10000 0 -0.14 18 18
FADD 0.009 0.075 -10000 0 -0.32 8 8
KSR1 -0.004 0.031 0.11 1 -0.14 8 9
MAPK8 -0.009 0.031 0.16 3 -0.15 3 6
TRAF2 0.036 0.006 -10000 0 0 16 16
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.009 0.077 -10000 0 -0.31 14 14
TNF R/SODD 0.035 0.055 -10000 0 -0.14 42 42
TNF 0.036 0.003 -10000 0 0 4 4
CYCS 0.016 0.052 0.14 21 -0.15 7 28
IKBKG -0.006 0.08 -10000 0 -0.3 16 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.015 0.085 -10000 0 -0.35 11 11
RELA 0.036 0.004 -10000 0 0 7 7
RIPK1 0.035 0.007 -10000 0 0 20 20
AIFM1 -0.005 0.039 0.12 13 -0.14 12 25
TNF/TNF R/SODD 0.053 0.056 -10000 0 -0.13 41 41
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.038 0.071 -10000 0 -0.57 6 6
NSMAF 0.007 0.084 0.21 5 -0.31 16 21
response to hydrogen peroxide 0 0 0.002 8 -0.002 2 10
BCL2 0.035 0.007 -10000 0 0 20 20
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.007 -10000 0 0 21 21
Ran/GTP/Exportin 1/HDAC4 -0.033 0.031 -10000 0 -0.13 35 35
MDM2/SUMO1 0.034 0.053 -10000 0 -0.21 6 6
HDAC4 0.035 0.009 -10000 0 0 30 30
Ran/GTP/Exportin 1/HDAC1 -0.031 0.03 -10000 0 -0.14 25 25
SUMO1 0.037 0.003 -10000 0 0 4 4
NPC/RanGAP1/SUMO1 0.005 0.035 -10000 0 -0.15 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.009 0.041 -10000 0 -0.16 21 21
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 24 24
SUMO1/HDAC4 0.033 0.058 -10000 0 -0.23 6 6
SUMO1/HDAC1 0.036 0.056 -10000 0 -0.22 6 6
RANGAP1 0.033 0.011 -10000 0 0 46 46
MDM2/SUMO1/SUMO1 0.077 0.048 -10000 0 -0.12 17 17
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.007 0.034 -10000 0 -0.15 21 21
Ran/GTP 0.019 0.05 -10000 0 -0.15 21 21
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.01 -10000 0 0 45 45
UBE2I 0.036 0.004 -10000 0 0 6 6
Ran/GTP/Exportin 1 0.013 0.052 0.2 1 -0.16 21 22
NPC 0.018 0.021 -10000 0 -0.09 18 18
PIAS2 0.035 0.007 -10000 0 0 19 19
PIAS1 0.035 0.008 -10000 0 0 26 26
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.037 0.028 -9999 0 -0.097 20 20
MAPK9 0.008 0.001 -9999 0 0 13 13
adrenocorticotropin secretion -0.011 0.002 0 17 -10000 0 17
GNB1/GNG2 0.02 0.026 -9999 0 -0.11 20 20
GNB1 0.035 0.007 -9999 0 0 20 20
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.008 0.001 -9999 0 0 5 5
Gs family/GTP 0.023 0.004 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.003 0 -9999 0 -10000 0 0
GNAL 0.036 0.006 -9999 0 0 14 14
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.036 0.007 -9999 0 0 17 17
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.003 -9999 0 0 141 141
MAPK11 0.007 0.002 -9999 0 0 53 53
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.054 0.018 -10000 0 -10000 0 0
KIRREL 0.038 0.01 0.075 1 -0.041 1 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.054 0.018 -10000 0 -10000 0 0
PLCG1 0.034 0.01 -10000 0 0 37 37
ARRB2 0.035 0.008 -10000 0 0 25 25
WASL 0.025 0.017 -10000 0 0 166 166
Nephrin/NEPH1/podocin/CD2AP 0.084 0.05 0.2 1 -0.12 17 18
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.037 -10000 0 -0.22 6 6
FYN -0.008 0.046 0.18 24 -10000 0 24
mol:Ca2+ 0.082 0.039 0.19 1 -0.13 3 4
mol:DAG 0.084 0.04 0.2 1 -0.13 3 4
NPHS2 0.039 0.008 -10000 0 -0.041 1 1
mol:IP3 0.084 0.04 0.2 1 -0.13 3 4
regulation of endocytosis 0.052 0.051 -10000 0 -0.14 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.069 0.027 0.18 1 -10000 0 1
establishment of cell polarity 0.054 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.095 0.059 -10000 0 -0.14 17 17
Nephrin/NEPH1/beta Arrestin2 0.055 0.052 -10000 0 -0.14 4 4
NPHS1 0.039 0.01 0.077 6 -10000 0 6
Nephrin/NEPH1/podocin 0.052 0.045 0.21 1 -0.11 1 2
TJP1 0.034 0.009 -10000 0 0 34 34
NCK1 0.035 0.008 -10000 0 0 27 27
NCK2 0.036 0.007 -10000 0 0 17 17
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.085 0.041 0.2 1 -0.13 3 4
CD2AP 0.034 0.01 -10000 0 0 40 40
Nephrin/NEPH1/podocin/GRB2 0.087 0.043 0.2 1 -0.13 7 8
GRB2 0.035 0.007 -10000 0 0 18 18
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.051 0.18 26 -10000 0 26
cytoskeleton organization -0.01 0.036 0.22 5 -0.2 3 8
Nephrin/NEPH1 0.046 0.016 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.065 0.038 -10000 0 -0.14 9 9
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL 0.041 0.2 0.47 3 -0.64 22 25
PCK1 0.044 0.12 0.43 2 -0.67 2 4
HNF4A 0.052 0.17 0.64 5 -0.71 6 11
KCNJ11 0.067 0.18 0.48 4 -0.58 17 21
AKT1 0.058 0.13 0.44 1 -0.36 21 22
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.08 0.19 0.56 3 -0.58 16 19
NKX2-1 0.03 0.11 0.28 3 -0.31 19 22
ACADM 0.05 0.18 0.53 2 -0.66 13 15
TAT 0.051 0.13 0.53 2 -0.64 5 7
CEBPB 0.033 0.015 0.12 1 -10000 0 1
CEBPA 0.031 0.018 -10000 0 -10000 0 0
TTR 0.032 0.19 0.6 4 -0.61 14 18
PKLR 0.056 0.17 0.46 6 -0.55 16 22
APOA1 0.078 0.22 0.65 5 -0.78 9 14
CPT1C 0.055 0.17 0.47 4 -0.54 16 20
ALAS1 0.031 0.24 -10000 0 -1.2 15 15
TFRC 0.021 0.3 0.51 6 -0.95 36 42
FOXF1 0.031 0.013 -10000 0 -10000 0 0
NF1 0.034 0.036 -10000 0 -0.17 15 15
HNF1A (dimer) 0.006 0.005 0.12 1 -10000 0 1
CPT1A 0.052 0.17 0.61 1 -0.58 13 14
HMGCS1 0.057 0.17 0.46 8 -0.57 13 21
NR3C1 0.047 0.02 -10000 0 -10000 0 0
CPT1B 0.053 0.17 0.49 3 -0.64 9 12
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.036 0.006 -10000 0 -10000 0 0
GCK 0.093 0.19 0.5 19 -0.55 11 30
CREB1 0.044 0.013 0.15 1 -10000 0 1
IGFBP1 0.053 0.13 -10000 0 -0.58 6 6
PDX1 0.053 0.11 0.33 4 -0.31 12 16
UCP2 0.023 0.25 0.49 5 -0.66 47 52
ALDOB 0.066 0.19 0.5 3 -0.6 15 18
AFP 0.015 0.033 0.28 2 -10000 0 2
BDH1 0.044 0.2 0.46 4 -0.64 22 26
HADH 0.067 0.18 0.48 4 -0.58 17 21
F2 0.076 0.21 0.78 2 -0.81 8 10
HNF1A 0.006 0.005 0.11 1 -10000 0 1
G6PC 0.009 0.082 0.43 1 -10000 0 1
SLC2A2 0.063 0.13 0.45 1 -0.43 6 7
INS 0.025 0.043 0.19 14 -0.096 34 48
FOXA1 0.014 0.013 0.15 2 -10000 0 2
FOXA3 0.019 0.057 0.2 5 -0.19 23 28
FOXA2 0.1 0.23 0.63 3 -0.66 17 20
ABCC8 0.067 0.19 0.48 4 -0.59 16 20
ALB 0.016 0.033 0.31 1 -10000 0 1
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.036 0.004 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.063 0.022 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.006 0.064 -9999 0 -0.39 13 13
AURKB 0.034 0.01 -9999 0 0 41 41
AURKC 0.036 0.006 -9999 0 0 15 15
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.036 0.005 0 10 -9999 0 10
PI3K Class IB/PDE3B 0.036 0.005 -9999 0 0 10 10
PDE3B 0.036 0.005 -9999 0 0 10 10
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0.001 0 3 -9999 0 3
ADCY5 -0.009 0.001 0 3 -9999 0 3
ADCY6 -0.017 0.006 0.086 1 -9999 0 1
ADCY7 -0.014 0.018 0.086 15 -9999 0 15
ADCY1 -0.012 0.009 -10000 0 -9999 0 0
ADCY2 -0.017 0.007 0.086 2 -9999 0 2
ADCY3 -0.009 0.001 0 3 -9999 0 3
ADCY8 -0.006 0.032 0.086 54 -9999 0 54
PRKCE -0.012 0.001 0 3 -9999 0 3
ADCY9 -0.017 0.009 0.086 4 -9999 0 4
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.017 0.043 0.17 11 -9999 0 11
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.036 0.005 -10000 0 0 11 11
GNAT1/GTP 0.026 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.047 0.01 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.048 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.036 0.006 -10000 0 0 13 13
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.069 0.024 -10000 0 -10000 0 0
mol:Na + 0.044 0.015 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.046 0.015 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.055 0.018 -10000 0 -10000 0 0
CNGB1 0.036 0.006 -10000 0 0 14 14
RDH5 0.035 0.007 -10000 0 0 19 19
SAG 0.036 0.005 -10000 0 0 10 10
mol:Ca2+ -0.034 0.026 0.16 8 -10000 0 8
Na + (4 Units) 0.041 0.018 -10000 0 -10000 0 0
RGS9 0.035 0.007 -10000 0 0 18 18
GNB1/GNGT1 0.031 0.038 -10000 0 -0.14 13 13
GNAT1/GDP 0.058 0.022 -10000 0 -0.1 1 1
GUCY2D 0.036 0.006 -10000 0 0 12 12
GNGT1 0.025 0.017 -10000 0 0 170 170
GUCY2F 0.037 0 -10000 0 -10000 0 0
GNB5 0.035 0.008 -10000 0 0 23 23
mol:GMP (4 units) 0.029 0.007 -10000 0 -10000 0 0
mol:11-cis-retinal 0.035 0.007 -10000 0 0 19 19
mol:cGMP 0.029 0.006 -10000 0 -10000 0 0
GNB1 0.035 0.007 -10000 0 0 20 20
Rhodopsin 0.051 0.013 -10000 0 -10000 0 0
SLC24A1 0.036 0.005 -10000 0 0 11 11
CNGA1 0.036 0.005 -10000 0 0 9 9
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.046 0.007 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.01 0.03 -10000 0 -0.15 14 14
GCAP Family/Ca ++ 0.024 0.001 -10000 0 -10000 0 0
PDE6A/B 0.053 0.008 -10000 0 -10000 0 0
mol:Pi 0.045 0.015 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.041 0.042 -10000 0 -0.11 13 13
PDE6B 0.036 0.004 -10000 0 0 5 5
PDE6A 0.036 0.004 -10000 0 0 7 7
PDE6G 0.037 0.003 -10000 0 0 3 3
RHO 0.036 0.006 -10000 0 0 13 13
PDE6 0.085 0.026 -10000 0 -0.11 1 1
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.047 0.002 -10000 0 -10000 0 0
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.037 0.002 -10000 0 0 1 1
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.048 0.008 -10000 0 -9999 0 0
EFNA5 0.036 0.004 -10000 0 0 5 5
FYN -0.019 0.016 0.18 2 -9999 0 2
neuron projection morphogenesis 0.048 0.008 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.048 0.008 -10000 0 -9999 0 0
EPHA5 0.036 0.005 -10000 0 0 10 10
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1668895/2.GDAC_MergeDataFiles.Finished/GBM.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/GBM/1676621/1.GetReducedSegments.Finished/GBM.RS.tsv

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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