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 122
FOXM1 transcription factor network 104
Angiopoietin receptor Tie2-mediated signaling 91
Syndecan-4-mediated signaling events 87
Endothelins 83
TCGA08_rtk_signaling 75
Thromboxane A2 receptor 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 122 9290 76 -0.078 0.1 1000 -1000 -0.007 -1000
FOXM1 transcription factor network 104 5349 51 -0.32 0.061 1000 -1000 -0.052 -1000
Angiopoietin receptor Tie2-mediated signaling 91 8014 88 -0.29 0.053 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 87 5850 67 -0.14 0.036 1000 -1000 -0.029 -1000
Endothelins 83 8043 96 -0.14 0.036 1000 -1000 -0.025 -1000
TCGA08_rtk_signaling 75 1957 26 -0.024 0.093 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 74 7780 105 -0.069 0.044 1000 -1000 -0.025 -1000
TCGA08_p53 73 512 7 -0.001 0.034 1000 -1000 -0.01 -1000
EGFR-dependent Endothelin signaling events 71 1491 21 -0.005 0.093 1000 -1000 -0.01 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 71 2364 33 -0.075 0.068 1000 -1000 -0.011 -1000
Effects of Botulinum toxin 68 1776 26 -0.007 0.052 1000 -1000 -0.011 -1000
PDGFR-alpha signaling pathway 67 2953 44 -0.093 0.036 1000 -1000 -0.021 -1000
Arf6 signaling events 65 4036 62 -0.005 0.092 1000 -1000 -0.007 -1000
Syndecan-3-mediated signaling events 65 2287 35 -0.071 0.08 1000 -1000 -0.028 -1000
Canonical Wnt signaling pathway 65 3341 51 -0.097 0.071 1000 -1000 -0.019 -1000
Wnt signaling 65 461 7 -0.006 0.037 1000 -1000 -0.002 -1000
HIF-2-alpha transcription factor network 64 2793 43 -0.074 0.047 1000 -1000 -0.039 -1000
S1P5 pathway 62 1069 17 -0.007 0.036 1000 -1000 -0.015 -1000
S1P4 pathway 62 1560 25 -0.012 0.043 1000 -1000 -0.007 -1000
TCGA08_retinoblastoma 61 495 8 -0.045 0.053 1000 -1000 -0.003 -1000
LPA receptor mediated events 58 5977 102 -0.13 0.039 1000 -1000 -0.057 -1000
Ras signaling in the CD4+ TCR pathway 58 995 17 -0.001 0.042 1000 -1000 -0.01 -1000
Nongenotropic Androgen signaling 55 2907 52 -0.087 0.06 1000 -1000 -0.017 -1000
Syndecan-1-mediated signaling events 54 1865 34 -0.004 0.035 1000 -1000 -0.018 -1000
IL2 signaling events mediated by STAT5 53 1168 22 -0.074 0.042 1000 -1000 -0.016 -1000
Syndecan-2-mediated signaling events 52 3590 69 -0.026 0.037 1000 -1000 -0.027 -1000
EPO signaling pathway 52 2881 55 -0.001 0.082 1000 -1000 -0.016 -1000
amb2 Integrin signaling 52 4340 82 -0.015 0.077 1000 -1000 -0.019 -1000
Glypican 2 network 51 206 4 0 0.007 1000 -1000 0 -1000
JNK signaling in the CD4+ TCR pathway 50 852 17 -0.14 0.063 1000 -1000 -0.01 -1000
IL23-mediated signaling events 50 3005 60 -0.064 0.15 1000 -1000 -0.035 -1000
Fc-epsilon receptor I signaling in mast cells 49 4835 97 -0.12 0.048 1000 -1000 -0.041 -1000
PLK2 and PLK4 events 48 146 3 -0.011 0.035 1000 -1000 -0.015 -1000
Osteopontin-mediated events 48 1831 38 -0.071 0.05 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 48 6101 125 -0.045 0.06 1000 -1000 -0.038 -1000
Ephrin B reverse signaling 45 2196 48 -0.067 0.066 1000 -1000 -0.043 -1000
FoxO family signaling 45 2923 64 -0.16 0.052 1000 -1000 -0.029 -1000
Presenilin action in Notch and Wnt signaling 44 2739 61 -0.079 0.08 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 44 2555 58 -0.065 0.038 1000 -1000 -0.025 -1000
FAS signaling pathway (CD95) 43 2061 47 -0.16 0.048 1000 -1000 -0.025 -1000
BCR signaling pathway 43 4320 99 -0.061 0.05 1000 -1000 -0.036 -1000
S1P3 pathway 43 1841 42 -0.018 0.036 1000 -1000 -0.009 -1000
Sphingosine 1-phosphate (S1P) pathway 42 1188 28 -0.012 0.036 1000 -1000 -0.015 -1000
Reelin signaling pathway 42 2388 56 -0.014 0.068 1000 -1000 -0.016 -1000
Regulation of nuclear SMAD2/3 signaling 41 5680 136 -0.21 0.19 1000 -1000 -0.042 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 41 2231 54 -0.034 0.082 1000 -1000 -0.027 -1000
Paxillin-dependent events mediated by a4b1 41 1485 36 -0.057 0.059 1000 -1000 -0.043 -1000
EPHB forward signaling 41 3545 85 -0.052 0.082 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 40 2663 65 -0.044 0.036 1000 -1000 -0.042 -1000
Noncanonical Wnt signaling pathway 40 1042 26 -0.039 0.037 1000 -1000 -0.047 -1000
BMP receptor signaling 40 3258 81 -0.031 0.058 1000 -1000 -0.011 -1000
IL1-mediated signaling events 40 2487 62 -0.045 0.074 1000 -1000 -0.035 -1000
IL12-mediated signaling events 39 3474 87 -0.11 0.094 1000 -1000 -0.016 -1000
Paxillin-independent events mediated by a4b1 and a4b7 39 1462 37 -0.034 0.083 1000 -1000 -0.014 -1000
Class I PI3K signaling events 39 2880 73 -0.053 0.062 1000 -1000 -0.017 -1000
Signaling events mediated by PTP1B 38 2913 76 -0.033 0.059 1000 -1000 -0.018 -1000
Glypican 1 network 38 1851 48 -0.038 0.051 1000 -1000 -0.033 -1000
S1P1 pathway 38 1395 36 -0.005 0.052 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 38 1655 43 -0.042 0.064 1000 -1000 -0.012 -1000
p38 MAPK signaling pathway 38 1704 44 0 0.043 1000 -1000 -0.013 -1000
PLK1 signaling events 37 3172 85 -0.048 0.051 1000 -1000 -0.017 -1000
mTOR signaling pathway 37 1989 53 -0.034 0.046 1000 -1000 -0.028 -1000
Stabilization and expansion of the E-cadherin adherens junction 37 2801 74 -0.12 0.079 1000 -1000 -0.048 -1000
Arf6 downstream pathway 36 1571 43 -0.026 0.051 1000 -1000 -0.024 -1000
Class I PI3K signaling events mediated by Akt 36 2460 68 -0.03 0.063 1000 -1000 -0.014 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 36 2503 68 -0.1 0.046 1000 -1000 -0.047 -1000
Neurotrophic factor-mediated Trk receptor signaling 36 4383 120 -0.035 0.087 1000 -1000 -0.028 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 35 3038 85 -0.12 0.12 1000 -1000 -0.04 -1000
Regulation of p38-alpha and p38-beta 35 1902 54 -0.002 0.047 1000 -1000 -0.01 -1000
IL6-mediated signaling events 35 2686 75 -0.076 0.11 1000 -1000 -0.032 -1000
IGF1 pathway 35 2002 57 -0.046 0.066 1000 -1000 -0.028 -1000
Plasma membrane estrogen receptor signaling 35 3063 86 -0.066 0.053 1000 -1000 -0.033 -1000
IFN-gamma pathway 34 2375 68 -0.041 0.064 1000 -1000 -0.035 -1000
Alternative NF-kappaB pathway 34 451 13 0 0.066 1000 -1000 0 -1000
TCR signaling in naïve CD8+ T cells 33 3113 93 -0.35 0.4 1000 -1000 -0.026 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 33 1509 45 -0.032 0.075 1000 -1000 -0.019 -1000
PDGFR-beta signaling pathway 33 3275 97 -0.055 0.068 1000 -1000 -0.04 -1000
a4b1 and a4b7 Integrin signaling 32 162 5 0.027 0.052 1000 -1000 0.033 -1000
Signaling events regulated by Ret tyrosine kinase 32 2699 82 -0.057 0.063 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 31 2039 65 -0.015 0.057 1000 -1000 -0.028 -1000
E-cadherin signaling in the nascent adherens junction 31 2356 76 -0.043 0.09 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 31 2423 78 -0.022 0.072 1000 -1000 -0.033 -1000
Caspase cascade in apoptosis 30 2258 74 -0.079 0.067 1000 -1000 -0.025 -1000
ErbB4 signaling events 30 2134 69 -0.071 0.062 1000 -1000 -0.018 -1000
Visual signal transduction: Cones 30 1157 38 -0.014 0.058 1000 -1000 -0.013 -1000
Regulation of Telomerase 30 3110 102 -0.027 0.077 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 29 3693 125 -0.022 0.087 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 29 1193 40 -0.049 0.05 1000 -1000 -0.049 -1000
Integrins in angiogenesis 29 2481 84 -0.044 0.071 1000 -1000 -0.021 -1000
Insulin Pathway 29 2201 74 -0.036 0.082 1000 -1000 -0.031 -1000
Signaling events mediated by PRL 29 1008 34 -0.034 0.047 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 28 654 23 -0.016 0.054 1000 -1000 -0.009 -1000
IL4-mediated signaling events 28 2619 91 -0.32 0.067 1000 -1000 -0.074 -1000
Aurora B signaling 28 1909 67 -0.032 0.062 1000 -1000 -0.02 -1000
Aurora A signaling 27 1656 60 -0.028 0.058 1000 -1000 -0.016 -1000
TRAIL signaling pathway 27 1332 48 -0.033 0.086 1000 -1000 -0.015 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 27 2242 83 -0.034 0.068 1000 -1000 -0.015 -1000
Signaling mediated by p38-gamma and p38-delta 27 417 15 -0.025 0.036 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 27 1581 58 -0.053 0.059 1000 -1000 -0.015 -1000
BARD1 signaling events 26 1513 57 -0.064 0.085 1000 -1000 -0.057 -1000
Nectin adhesion pathway 26 1698 63 -0.01 0.084 1000 -1000 -0.021 -1000
Glucocorticoid receptor regulatory network 25 2962 114 -0.13 0.064 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 24 762 31 -0.017 0.093 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class I 23 2469 104 -0.029 0.066 1000 -1000 -0.025 -1000
Coregulation of Androgen receptor activity 22 1727 76 -0.011 0.07 1000 -1000 -0.01 -1000
Insulin-mediated glucose transport 22 706 32 -0.016 0.041 1000 -1000 -0.016 -1000
IL27-mediated signaling events 22 1152 51 -0.015 0.064 1000 -1000 -0.042 -1000
E-cadherin signaling events 22 110 5 0.033 0.062 1000 -1000 0.033 -1000
Regulation of Androgen receptor activity 22 1583 70 -0.031 0.067 1000 -1000 -0.032 -1000
Ceramide signaling pathway 21 1660 76 -0.04 0.07 1000 -1000 -0.016 -1000
Signaling mediated by p38-alpha and p38-beta 20 893 44 -0.015 0.086 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class II 19 1461 75 -0.03 0.093 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 19 747 39 -0.069 0.036 1000 -1000 -0.017 -1000
RXR and RAR heterodimerization with other nuclear receptor 19 1025 52 -0.043 0.1 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 19 596 31 -0.021 0.036 1000 -1000 -0.014 -1000
Circadian rhythm pathway 18 402 22 -0.01 0.056 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 18 958 52 -0.014 0.09 1000 -1000 -0.019 -1000
ceramide signaling pathway 18 886 49 -0.014 0.053 1000 -1000 -0.012 -1000
Arf6 trafficking events 18 1315 71 -0.038 0.046 1000 -1000 -0.031 -1000
Arf1 pathway 18 1019 54 -0.075 0.044 1000 -1000 -0.013 -1000
Canonical NF-kappaB pathway 17 694 39 -0.033 0.065 1000 -1000 -0.019 -1000
VEGFR1 specific signals 17 971 56 -0.032 0.041 1000 -1000 -0.028 -1000
Sumoylation by RanBP2 regulates transcriptional repression 15 420 27 -0.032 0.077 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 15 315 20 -0.011 0.036 1000 -1000 -0.01 -1000
Nephrin/Neph1 signaling in the kidney podocyte 14 505 34 -0.054 0.096 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 13 609 46 0 0.094 1000 -1000 -0.025 -1000
Aurora C signaling 10 75 7 0 0.063 1000 -1000 -0.001 -1000
Class IB PI3K non-lipid kinase events 9 27 3 -0.036 0.036 1000 -1000 -0.033 -1000
LPA4-mediated signaling events 8 104 12 -0.017 0.018 1000 -1000 -0.012 -1000
Visual signal transduction: Rods 8 440 52 -0.033 0.084 1000 -1000 -0.009 -1000
Ephrin A reverse signaling 2 18 7 -0.019 0.048 1000 -1000 -0.009 -1000
Total 5102 287495 7203 -6.9 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 0.027 0.46 0.62 78 -0.74 86 164
HDAC7 -0.001 0.005 -10000 0 -0.049 3 3
HIF1A/ARNT/Cbp/p300/Src-1 -0.025 0.38 0.58 39 -0.69 73 112
SMAD4 0.033 0.014 0.079 10 -10000 0 10
ID2 0.048 0.47 0.63 98 -0.74 85 183
AP1 0.015 0.079 -10000 0 -0.17 71 71
ABCG2 0.014 0.46 0.62 88 -0.74 88 176
HIF1A 0.044 0.13 0.24 77 -0.15 63 140
TFF3 0.043 0.46 0.63 91 -0.74 84 175
GATA2 0.039 0.014 0.075 22 -0.079 2 24
AKT1 0.052 0.13 0.24 90 -0.18 44 134
response to hypoxia 0.011 0.088 0.17 81 -0.12 52 133
MCL1 0.055 0.47 0.62 105 -0.74 86 191
NDRG1 -0.001 0.45 0.62 69 -0.76 88 157
SERPINE1 -0.065 0.38 0.6 30 -0.76 81 111
FECH 0.044 0.46 0.63 91 -0.74 84 175
FURIN 0.051 0.47 0.63 99 -0.74 86 185
NCOA2 0.037 0.006 -10000 0 -10000 0 0
EP300 0.073 0.18 0.36 95 -0.3 28 123
HMOX1 -0.019 0.45 0.63 61 -0.77 87 148
BHLHE40 -0.054 0.4 0.55 73 -0.72 89 162
BHLHE41 -0.054 0.4 0.55 73 -0.72 89 162
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.07 0.18 0.35 46 -0.23 38 84
ENG 0.03 0.15 0.3 45 -0.25 17 62
JUN 0.035 0.013 -10000 0 -0.052 2 2
RORA 0.024 0.46 0.62 85 -0.74 87 172
ABCB1 -0.055 0.21 -10000 0 -0.83 29 29
TFRC 0.033 0.46 0.63 89 -0.75 85 174
CXCR4 0.016 0.46 0.63 79 -0.75 91 170
TF -0.078 0.4 0.63 41 -0.75 88 129
CITED2 0.014 0.45 0.61 84 -0.74 88 172
HIF1A/ARNT -0.073 0.44 0.67 16 -0.87 76 92
LDHA -0.066 0.28 -10000 0 -0.96 40 40
ETS1 0.059 0.47 0.63 105 -0.74 86 191
PGK1 0.048 0.48 0.62 101 -0.76 86 187
NOS2 -0.054 0.4 0.55 73 -0.72 89 162
ITGB2 0.006 0.46 0.62 78 -0.76 86 164
ALDOA 0.055 0.47 0.64 96 -0.74 86 182
Cbp/p300/CITED2 -0.021 0.45 0.6 67 -0.78 86 153
FOS 0.026 0.018 -10000 0 -0.043 1 1
HK2 0.058 0.48 0.62 109 -0.74 85 194
SP1 0.033 0.059 0.11 39 -0.15 40 79
GCK 0.1 0.24 0.55 61 -0.46 13 74
HK1 0.002 0.44 0.64 72 -0.74 84 156
NPM1 0.053 0.47 0.63 99 -0.74 84 183
EGLN1 0.05 0.47 0.62 98 -0.74 85 183
CREB1 0.032 0.034 -10000 0 -0.1 30 30
PGM1 0.052 0.47 0.63 99 -0.74 87 186
SMAD3 0.037 0.008 0.079 10 -10000 0 10
EDN1 0.057 0.21 0.47 26 -0.55 17 43
IGFBP1 -0.01 0.41 0.63 56 -0.74 76 132
VEGFA -0.016 0.34 0.48 78 -0.56 84 162
HIF1A/JAB1 0.045 0.1 0.2 58 -0.13 45 103
CP -0.033 0.44 0.61 62 -0.75 93 155
CXCL12 -0.033 0.41 0.62 45 -0.74 83 128
COPS5 0.036 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.052 0.14 5 -0.14 35 40
BNIP3 -0.005 0.44 0.64 71 -0.75 84 155
EGLN3 0.006 0.45 0.63 71 -0.74 85 156
CA9 -0.015 0.42 0.61 59 -0.74 83 142
TERT 0.051 0.47 0.63 100 -0.74 86 186
ENO1 0.049 0.47 0.63 101 -0.74 85 186
PFKL 0.055 0.47 0.62 108 -0.74 85 193
NCOA1 0.033 0.011 -10000 0 -10000 0 0
ADM -0.018 0.45 0.61 72 -0.76 91 163
ARNT 0.047 0.13 0.24 82 -0.14 67 149
HNF4A 0.038 0.01 0.083 10 -10000 0 10
ADFP -0.029 0.44 0.64 51 -0.76 86 137
SLC2A1 0.015 0.37 0.54 72 -0.6 79 151
LEP 0.009 0.42 0.63 68 -0.74 76 144
HIF1A/ARNT/Cbp/p300 -0.036 0.38 0.59 36 -0.69 77 113
EPO 0.021 0.31 0.55 50 -0.58 42 92
CREBBP 0.078 0.18 0.35 97 -0.27 27 124
HIF1A/ARNT/Cbp/p300/HDAC7 -0.041 0.37 0.55 37 -0.68 76 113
PFKFB3 0.009 0.45 0.65 75 -0.76 83 158
NT5E -0.026 0.44 0.63 61 -0.73 94 155
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 -0.087 0.66 1 33 -1.2 95 128
PLK1 0.061 0.16 0.64 16 -0.82 5 21
BIRC5 -0.062 0.44 0.65 15 -1.2 57 72
HSPA1B -0.088 0.65 0.96 35 -1.2 101 136
MAP2K1 0.045 0.1 0.25 56 -10000 0 56
BRCA2 -0.086 0.66 1 32 -1.2 93 125
FOXM1 -0.23 0.97 1.2 30 -1.9 101 131
XRCC1 -0.084 0.66 1 34 -1.2 94 128
FOXM1B/p19 -0.32 0.57 -10000 0 -1.4 99 99
Cyclin D1/CDK4 -0.11 0.59 0.86 28 -1.1 102 130
CDC2 -0.11 0.73 1.1 33 -1.3 102 135
TGFA -0.071 0.58 0.89 36 -1 98 134
SKP2 -0.089 0.66 1 33 -1.2 95 128
CCNE1 0.024 0.037 0.1 21 -0.034 114 135
CKS1B -0.097 0.68 1 33 -1.2 100 133
RB1 -0.073 0.37 0.49 16 -1 47 63
FOXM1C/SP1 -0.17 0.76 0.9 27 -1.5 102 129
AURKB 0.061 0.15 0.68 13 -0.97 2 15
CENPF -0.11 0.71 1.1 33 -1.2 109 142
CDK4 0.025 0.052 0.15 30 -10000 0 30
MYC -0.1 0.56 0.81 34 -1 103 137
CHEK2 0.037 0.092 0.23 50 -10000 0 50
ONECUT1 -0.089 0.63 0.93 35 -1.2 101 136
CDKN2A 0.003 0.018 -10000 0 -0.13 4 4
LAMA4 -0.092 0.66 0.97 35 -1.2 96 131
FOXM1B/HNF6 -0.16 0.77 0.96 32 -1.5 101 133
FOS -0.15 0.7 0.99 32 -1.2 123 155
SP1 0.034 0.019 0.072 3 -0.045 24 27
CDC25B -0.093 0.67 0.98 35 -1.2 99 134
response to radiation 0.023 0.067 0.15 72 -10000 0 72
CENPB -0.085 0.67 0.98 37 -1.2 96 133
CENPA -0.09 0.67 1 34 -1.2 95 129
NEK2 -0.079 0.67 1.1 33 -1.2 95 128
HIST1H2BA -0.088 0.65 0.96 35 -1.2 101 136
CCNA2 0.022 0.031 0.096 4 -0.034 79 83
EP300 0.033 0.011 -10000 0 -10000 0 0
CCNB1/CDK1 -0.19 0.84 1.1 29 -1.6 109 138
CCNB2 -0.11 0.69 1 35 -1.3 100 135
CCNB1 -0.12 0.74 1.1 34 -1.4 105 139
ETV5 -0.12 0.69 0.99 33 -1.2 117 150
ESR1 -0.09 0.65 0.99 32 -1.2 100 132
CCND1 -0.098 0.62 0.92 36 -1.1 101 137
GSK3A 0.037 0.084 0.2 54 -10000 0 54
Cyclin A-E1/CDK1-2 0.047 0.1 0.25 24 -0.16 42 66
CDK2 0.024 0.037 0.1 16 -0.034 120 136
G2/M transition of mitotic cell cycle 0.027 0.081 0.18 74 -10000 0 74
FOXM1B/Cbp/p300 -0.16 0.68 0.8 18 -1.4 101 119
GAS1 -0.092 0.67 1 36 -1.2 98 134
MMP2 -0.11 0.7 1 36 -1.2 109 145
RB1/FOXM1C -0.14 0.61 0.86 24 -1.2 100 124
CREBBP 0.036 0.005 -10000 0 0 8 8
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 -0.78 163 163
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.37 140 140
NCK1/Dok-R -0.14 0.35 -10000 0 -0.86 96 96
PIK3CA 0.031 0.013 -10000 0 0 80 80
mol:beta2-estradiol 0.032 0.098 0.23 96 -10000 0 96
RELA 0.036 0.005 -10000 0 0 9 9
SHC1 0.032 0.011 -10000 0 0 52 52
Rac/GDP 0.017 0.019 -10000 0 -0.13 5 5
F2 0.053 0.11 0.28 87 -0.09 64 151
TNIP2 0.036 0.006 -10000 0 0 13 13
NF kappa B/RelA -0.12 0.36 -10000 0 -0.83 96 96
FN1 0.035 0.009 -10000 0 0 29 29
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 -0.15 0.33 -10000 0 -0.82 96 96
GRB7 0.036 0.006 -10000 0 0 14 14
PAK1 0.036 0.006 -10000 0 0 15 15
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.86 96 96
CDKN1A -0.19 0.35 0.4 2 -0.65 175 177
ITGA5 0.033 0.011 -10000 0 0 56 56
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 0.37 4 -0.57 152 156
PLG -0.15 0.36 -10000 0 -0.89 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.37 -10000 0 -0.74 128 128
GRB2 0.035 0.007 -10000 0 0 17 17
PIK3R1 0.032 0.012 -10000 0 0 63 63
ANGPT2 -0.22 0.45 -10000 0 -0.86 142 142
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 -0.69 167 167
ANGPT4 0.023 0.028 -10000 0 -0.03 107 107
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 0.042 -10000 0 -0.14 20 20
FGF2 0.035 0.016 -10000 0 -0.012 43 43
STAT5A (dimer) -0.24 0.44 -10000 0 -0.8 177 177
mol:L-citrulline -0.12 0.32 0.37 4 -0.57 152 156
AGTR1 0.022 0.034 -10000 0 -0.038 112 112
MAPK14 -0.16 0.37 -10000 0 -0.9 96 96
Tie2/SHP2 -0.079 0.24 -10000 0 -0.81 35 35
TEK -0.087 0.25 -10000 0 -0.9 33 33
RPS6KB1 -0.2 0.37 -10000 0 -0.76 139 139
Angiotensin II/AT1 0.015 0.036 0.077 4 -0.056 89 93
Tie2/Ang1/GRB2 -0.14 0.38 -10000 0 -0.91 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 -0.16 0.36 -10000 0 -0.88 96 96
PI3K -0.24 0.44 -10000 0 -0.9 136 136
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 -0.69 164 164
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 -0.76 138 138
Tie2/Ang2 -0.29 0.5 -10000 0 -0.96 165 165
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 96 96
FOXO1 -0.22 0.39 -10000 0 -0.75 167 167
ELF1 0.028 0.036 0.11 4 -0.046 81 85
ELF2 -0.14 0.36 -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 -0.24 0.41 -10000 0 -0.8 167 167
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.17 0.32 0.39 3 -0.58 175 178
ETS1 -0.002 0.12 0.12 2 -0.25 93 95
PXN -0.17 0.31 0.36 1 -0.64 138 139
ITGB1 0.027 0.016 -10000 0 0 138 138
NOS3 -0.15 0.35 0.38 3 -0.64 150 153
RAC1 0.024 0.017 -10000 0 0 173 173
TNF -0.004 0.12 -10000 0 -0.25 92 92
MAPKKK cascade -0.15 0.35 -10000 0 -0.86 96 96
RASA1 0.034 0.009 -10000 0 0 32 32
Tie2/Ang1/Shc -0.15 0.37 -10000 0 -0.91 96 96
NCK1 0.035 0.008 -10000 0 0 27 27
vasculogenesis -0.1 0.29 0.35 5 -0.51 153 158
mol:Phosphatidic acid -0.15 0.35 -10000 0 -0.86 96 96
mol:Angiotensin II -0.004 0.013 -10000 0 -0.032 73 73
mol:NADP -0.12 0.32 0.37 4 -0.57 152 156
Rac1/GTP -0.18 0.34 -10000 0 -0.69 134 134
MMP2 -0.15 0.37 -10000 0 -0.9 96 96
Syndecan-4-mediated signaling events

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
PTK2 -0.031 0.16 -10000 0 -0.45 43 43
Syndecan-4/Syndesmos -0.14 0.28 -10000 0 -0.48 149 149
positive regulation of JNK cascade -0.13 0.26 -10000 0 -0.49 124 124
Syndecan-4/ADAM12 -0.13 0.29 -10000 0 -0.52 124 124
CCL5 0.033 0.011 -10000 0 0 53 53
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
DNM2 0.035 0.009 -10000 0 0 29 29
ITGA5 0.033 0.011 -10000 0 0 56 56
SDCBP 0.035 0.007 -10000 0 0 21 21
PLG 0.03 0.021 -10000 0 -0.047 17 17
ADAM12 0.024 0.017 -10000 0 0 168 168
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 -0.025 0.022 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.28 -10000 0 -0.48 149 149
Syndecan-4/CXCL12/CXCR4 -0.14 0.28 -10000 0 -0.53 122 122
Syndecan-4/Laminin alpha3 -0.13 0.29 -10000 0 -0.49 142 142
MDK 0.03 0.014 -10000 0 0 92 92
Syndecan-4/FZD7 -0.14 0.3 -10000 0 -0.5 152 152
Syndecan-4/Midkine -0.13 0.3 -10000 0 -0.49 154 154
FZD7 0.026 0.016 -10000 0 0 143 143
Syndecan-4/FGFR1/FGF -0.098 0.28 -10000 0 -0.47 136 136
THBS1 0.03 0.014 -10000 0 0 97 97
integrin-mediated signaling pathway -0.13 0.28 -10000 0 -0.47 153 153
positive regulation of MAPKKK cascade -0.13 0.26 -10000 0 -0.49 124 124
Syndecan-4/TACI -0.12 0.3 -10000 0 -0.48 149 149
CXCR4 0.029 0.015 -10000 0 0 103 103
cell adhesion -0.009 0.054 0.2 3 -0.25 17 20
Syndecan-4/Dynamin -0.12 0.29 -10000 0 -0.48 146 146
Syndecan-4/TSP1 -0.13 0.28 -10000 0 -0.5 135 135
Syndecan-4/GIPC -0.12 0.29 -10000 0 -0.48 146 146
Syndecan-4/RANTES -0.13 0.29 -10000 0 -0.49 144 144
ITGB1 0.027 0.016 -10000 0 0 138 138
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.033 0.011 -10000 0 0 48 48
RAC1 0.024 0.017 -10000 0 0 173 173
PRKCA 0.001 0.11 0.98 6 -10000 0 6
Syndecan-4/alpha-Actinin -0.14 0.3 -10000 0 -0.5 151 151
TFPI 0.029 0.015 -10000 0 0 103 103
F2 0.01 0.041 -10000 0 -0.045 168 168
alpha5/beta1 Integrin 0.029 0.042 -10000 0 -0.14 20 20
positive regulation of cell adhesion -0.13 0.27 -10000 0 -0.47 142 142
ACTN1 0.028 0.016 -10000 0 0 119 119
TNC 0.028 0.016 -10000 0 0 122 122
Syndecan-4/CXCL12 -0.14 0.28 -10000 0 -0.53 120 120
FGF6 0.035 0.008 -10000 0 0 27 27
RHOA 0.035 0.007 -10000 0 0 18 18
CXCL12 0.022 0.018 -10000 0 0 202 202
TNFRSF13B 0.036 0.005 -10000 0 0 8 8
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 -0.48 149 149
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.03 0.021 -10000 0 -0.045 27 27
cell migration -0.011 0.016 -10000 0 -10000 0 0
PRKCD 0.031 0.021 -10000 0 -0.044 24 24
vasculogenesis -0.13 0.27 -10000 0 -0.48 135 135
SDC4 -0.14 0.3 -10000 0 -0.51 148 148
Syndecan-4/Tenascin C -0.14 0.3 -10000 0 -0.5 153 153
Syndecan-4/PI-4-5-P2/PKC alpha -0.02 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.3 -10000 0 -0.49 146 146
MMP9 0.012 0.024 -10000 0 -0.043 37 37
Rac1/GTP -0.009 0.055 0.2 3 -0.26 17 20
cytoskeleton organization -0.13 0.27 -10000 0 -0.46 149 149
GIPC1 0.035 0.008 -10000 0 0 24 24
Syndecan-4/TFPI -0.13 0.29 -10000 0 -0.5 143 143
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.02 0.14 0.21 77 -0.26 85 162
PTK2B 0.036 0.006 -10000 0 0 16 16
mol:Ca2+ -0.1 0.25 0.4 1 -0.53 78 79
EDN1 0.005 0.092 0.14 9 -0.16 103 112
EDN3 0.033 0.011 -10000 0 0 52 52
EDN2 0.036 0.006 -10000 0 0 12 12
HRAS/GDP -0.016 0.17 0.3 18 -0.37 57 75
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0 0.12 0.2 17 -0.25 59 76
ADCY4 -0.035 0.097 0.14 39 -0.2 99 138
ADCY5 -0.035 0.097 0.14 39 -0.2 99 138
ADCY6 -0.007 0.13 0.22 41 -0.23 62 103
ADCY7 -0.014 0.13 0.21 39 -0.24 66 105
ADCY1 -0.002 0.11 0.21 26 -0.25 42 68
ADCY2 -0.007 0.13 0.21 46 -0.24 65 111
ADCY3 -0.035 0.097 0.14 39 -0.2 99 138
ADCY8 -0.011 0.12 0.22 38 -0.23 57 95
ADCY9 -0.009 0.13 0.22 43 -0.23 65 108
arachidonic acid secretion -0.08 0.26 0.32 26 -0.51 102 128
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.11 0.19 10 -0.25 47 57
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.009 -10000 0 0 32 32
ETA receptor/Endothelin-1/G12/GTP 0.004 0.12 -10000 0 -0.22 76 76
ETA receptor/Endothelin-1/Gs/GTP 0.005 0.12 -10000 0 -0.2 105 105
mol:GTP 0 0.006 0.026 3 -0.025 4 7
COL3A1 -0.074 0.15 0.18 9 -0.36 100 109
EDNRB 0.023 0.045 0.096 62 -0.082 48 110
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.017 0.14 0.21 76 -0.27 68 144
CYSLTR1 -0.034 0.12 0.19 41 -0.24 97 138
SLC9A1 -0.014 0.086 0.13 28 -0.16 107 135
mol:GDP -0.024 0.17 0.29 21 -0.38 57 78
SLC9A3 -0.12 0.29 -10000 0 -0.66 81 81
RAF1 -0.036 0.2 0.31 24 -0.41 83 107
JUN -0.14 0.33 0.5 1 -0.7 90 91
JAK2 -0.021 0.14 0.21 66 -0.25 86 152
mol:IP3 -0.004 0.12 0.22 19 -0.27 47 66
ETA receptor/Endothelin-1 -0.02 0.15 -10000 0 -0.27 113 113
PLCB1 0.033 0.013 -10000 0 -0.008 38 38
PLCB2 0.028 0.023 -10000 0 -0.022 80 80
ETA receptor/Endothelin-3 0.008 0.087 -10000 0 -0.14 104 104
FOS -0.094 0.35 0.41 15 -0.84 82 97
Gai/GDP -0.068 0.27 -10000 0 -0.73 66 66
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca ++ -0.02 0.17 0.25 55 -0.33 80 135
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.004 0.12 0.23 25 -0.29 47 72
GNAQ 0.027 0.026 -10000 0 -0.034 70 70
GNAZ 0.031 0.013 -10000 0 0 81 81
GNAL 0.036 0.006 -10000 0 0 13 13
Gs family/GDP -0.014 0.16 0.29 19 -0.35 56 75
ETA receptor/Endothelin-1/Gq/GTP -0.006 0.12 0.21 10 -0.27 57 67
MAPK14 -0.014 0.099 0.18 7 -0.25 44 51
TRPC6 -0.1 0.26 -10000 0 -0.56 77 77
GNAI2 0.034 0.01 -10000 0 0 43 43
GNAI3 0.036 0.006 -10000 0 0 15 15
GNAI1 0.018 0.018 -10000 0 0 263 263
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.1 0.18 15 -0.24 48 63
ETB receptor/Endothelin-2 0.017 0.071 -10000 0 -0.11 99 99
ETB receptor/Endothelin-3 0.016 0.069 -10000 0 -0.11 84 84
ETB receptor/Endothelin-1 0 0.1 0.18 26 -0.16 113 139
MAPK3 -0.077 0.32 0.39 18 -0.73 82 100
MAPK1 -0.091 0.34 0.4 16 -0.79 82 98
Rac1/GDP -0.012 0.15 0.31 15 -0.37 40 55
cAMP biosynthetic process 0.02 0.12 0.22 54 -0.21 46 100
MAPK8 -0.14 0.31 0.36 1 -0.58 138 139
SRC 0.036 0.006 -10000 0 0 14 14
ETB receptor/Endothelin-1/Gi/GTP -0.029 0.14 0.16 6 -0.34 59 65
p130Cas/CRK/Src/PYK2 -0.024 0.18 0.35 13 -0.47 43 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.015 0.15 0.31 13 -0.38 44 57
COL1A2 -0.052 0.17 0.22 2 -0.47 61 63
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.006 0.091 -10000 0 -0.14 115 115
mol:DAG -0.004 0.12 0.22 19 -0.27 47 66
MAP2K2 -0.052 0.26 0.34 36 -0.55 82 118
MAP2K1 -0.064 0.26 0.33 23 -0.58 84 107
EDNRA -0.008 0.1 0.14 6 -0.2 99 105
positive regulation of muscle contraction 0.033 0.15 0.22 150 -0.24 54 204
Gq family/GDP 0.002 0.16 0.3 6 -0.35 56 62
HRAS/GTP -0.016 0.16 0.27 26 -0.35 59 85
PRKCH -0.009 0.12 0.24 19 -0.29 44 63
RAC1 0.024 0.017 -10000 0 0 173 173
PRKCA -0.012 0.12 0.22 18 -0.28 49 67
PRKCB -0.008 0.12 0.21 19 -0.27 50 69
PRKCE -0.013 0.12 0.22 17 -0.29 48 65
PRKCD -0.007 0.12 0.25 24 -0.28 47 71
PRKCG -0.014 0.12 0.22 18 -0.29 50 68
regulation of vascular smooth muscle contraction -0.12 0.41 0.45 11 -1 82 93
PRKCQ -0.003 0.11 0.25 19 -0.3 32 51
PLA2G4A -0.09 0.28 0.32 25 -0.56 102 127
GNA14 0.027 0.026 -10000 0 -0.034 70 70
GNA15 0.03 0.019 -10000 0 -0.034 25 25
GNA12 0.023 0.018 -10000 0 0 193 193
GNA11 0.031 0.017 -10000 0 -0.035 16 16
Rac1/GTP 0.006 0.11 -10000 0 -0.22 70 70
MMP1 0.019 0.074 0.18 54 -10000 0 54
TCGA08_rtk_signaling

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
PDGFRA 0.025 0.017 -10000 0 0 167 167
HRAS 0.034 0.009 -10000 0 0 32 32
EGFR 0.009 0.016 -10000 0 0 381 381
AKT 0.09 0.12 0.24 125 -0.18 9 134
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.033 0.011 -10000 0 0 53 53
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.035 0.008 -10000 0 0 23 23
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.023 0.018 -10000 0 0 191 191
PIK3CA 0.031 0.013 -10000 0 0 80 80
PIK3CB 0.035 0.007 -10000 0 0 18 18
NRAS 0.032 0.012 -10000 0 0 63 63
PIK3CG 0.025 0.017 -10000 0 0 163 163
PIK3R3 0.036 0.006 -10000 0 0 15 15
PIK3R2 0.035 0.008 -10000 0 0 23 23
NF1 0.036 0.003 -10000 0 0 4 4
RAS -0.003 0.057 0.12 7 -0.13 50 57
ERBB2 0.036 0.004 -10000 0 0 5 5
proliferation/survival/translation -0.024 0.051 0.22 4 -0.19 15 19
PI3K 0.041 0.092 0.22 79 -0.15 12 91
PIK3R1 0.032 0.012 -10000 0 0 63 63
KRAS 0.034 0.009 -10000 0 0 35 35
FOXO 0.093 0.091 0.2 164 -10000 0 164
AKT2 0.035 0.008 -10000 0 0 28 28
PTEN 0.026 0.017 -10000 0 0 148 148
Thromboxane A2 receptor 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
TGM2 0.035 0.008 -10000 0 0 23 23
GNB1/GNG2 -0.046 0.078 -10000 0 -0.17 131 131
AKT1 -0.003 0.16 0.28 34 -0.31 35 69
EGF 0.035 0.008 -10000 0 0 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.015 0.07 0.27 21 -0.17 3 24
mol:Ca2+ -0.001 0.19 0.34 28 -0.27 122 150
LYN -0.015 0.07 0.28 18 -0.17 6 24
RhoA/GTP 0.002 0.084 0.16 28 -0.13 87 115
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.017 0.21 0.36 30 -0.32 124 154
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.035 0.008 -10000 0 0 26 26
TP alpha/Gq family/GDP/G beta5/gamma2 0.001 0.078 -10000 0 -0.25 30 30
G beta5/gamma2 -0.054 0.1 -10000 0 -0.23 128 128
PRKCH -0.016 0.21 0.36 25 -0.32 127 152
DNM1 0.035 0.008 -10000 0 0 26 26
TXA2/TP beta/beta Arrestin3 0.014 0.018 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.006 57 -0.002 2 59
PTGDR 0.035 0.008 -10000 0 0 26 26
G12 family/GTP -0.045 0.14 -10000 0 -0.29 93 93
ADRBK1 0.036 0.006 -10000 0 0 13 13
ADRBK2 0.035 0.009 -10000 0 0 29 29
RhoA/GTP/ROCK1 0.044 0.026 -10000 0 -0.12 10 10
mol:GDP -0.008 0.13 0.41 15 -0.28 17 32
mol:NADP 0.024 0.017 -10000 0 0 175 175
RAB11A 0.035 0.007 -10000 0 0 18 18
PRKG1 0.027 0.017 -10000 0 0 141 141
mol:IP3 -0.013 0.22 0.38 25 -0.34 125 150
cell morphogenesis 0.044 0.026 -10000 0 -0.12 10 10
PLCB2 -0.037 0.27 0.43 18 -0.45 125 143
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.013 0.072 0.26 23 -10000 0 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.018 0.06 0.25 14 -0.17 8 22
RHOA 0.035 0.007 -10000 0 0 18 18
PTGIR 0.034 0.009 -10000 0 0 33 33
PRKCB1 -0.017 0.22 0.37 25 -0.34 125 150
GNAQ 0.034 0.009 -10000 0 0 31 31
mol:L-citrulline 0.024 0.017 -10000 0 0 175 175
TXA2/TXA2-R family -0.048 0.28 0.41 23 -0.47 133 156
LCK -0.015 0.07 0.27 21 -10000 0 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.033 0.038 0.19 5 -10000 0 5
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 0.03 0.041 0.19 5 -0.15 1 6
MAPK14 -0.004 0.15 0.28 36 -0.22 120 156
TGM2/GTP -0.012 0.24 0.41 24 -0.38 114 138
MAPK11 -0.006 0.15 0.29 34 -0.22 122 156
ARHGEF1 0.011 0.12 0.22 46 -0.18 89 135
GNAI2 0.034 0.01 -10000 0 0 43 43
JNK cascade -0.021 0.22 0.38 25 -0.35 133 158
RAB11/GDP 0.034 0.01 -10000 0 -0.009 25 25
ICAM1 -0.005 0.18 0.32 38 -0.27 126 164
cAMP biosynthetic process -0.013 0.2 0.35 26 -0.32 109 135
Gq family/GTP/EBP50 0.013 0.051 0.24 7 -0.15 30 37
actin cytoskeleton reorganization 0.044 0.026 -10000 0 -0.12 10 10
SRC -0.018 0.062 0.25 16 -10000 0 16
GNB5 0.035 0.008 -10000 0 0 24 24
GNB1 0.035 0.007 -10000 0 0 20 20
EGF/EGFR -0.011 0.1 0.26 23 -0.23 40 63
VCAM1 -0.023 0.21 0.33 34 -0.33 135 169
TP beta/Gq family/GDP/G beta5/gamma2 0.001 0.078 -10000 0 -0.25 30 30
platelet activation -0.009 0.19 0.36 30 -0.28 120 150
PGI2/IP 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.015 0.02 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.004 0.069 -10000 0 -0.22 29 29
TXA2/TP beta/beta Arrestin2 0.004 0.047 -10000 0 -0.29 7 7
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 0.39 25 -0.38 126 151
EGFR 0.009 0.016 -10000 0 0 381 381
TXA2/TP alpha -0.029 0.26 0.42 19 -0.42 119 138
Gq family/GTP 0.009 0.048 0.2 12 -0.13 28 40
YES1 -0.014 0.071 0.28 19 -0.16 3 22
GNAI2/GTP 0.008 0.048 -10000 0 -0.14 2 2
PGD2/DP 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.01 -10000 0 0 37 37
FYN -0.015 0.072 0.28 19 -0.17 7 26
mol:NO 0.024 0.017 -10000 0 0 175 175
GNA15 0.033 0.012 -10000 0 0 57 57
PGK/cGMP 0.027 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.01 -10000 0 -0.009 25 25
TP alpha/TGM2/GDP/G beta/gamma 0.031 0.042 0.18 4 -0.15 1 5
NOS3 0.024 0.017 -10000 0 0 175 175
RAC1 0.024 0.017 -10000 0 0 173 173
PRKCA -0.015 0.21 0.35 26 -0.32 126 152
PRKCB -0.016 0.21 0.35 26 -0.32 131 157
PRKCE -0.018 0.21 0.36 26 -0.33 127 153
PRKCD -0.019 0.22 0.36 30 -0.35 129 159
PRKCG -0.022 0.22 0.37 25 -0.35 131 156
muscle contraction -0.042 0.26 0.4 24 -0.44 133 157
PRKCZ -0.016 0.2 0.35 27 -0.31 133 160
ARR3 0.037 0 -10000 0 -10000 0 0
TXA2/TP beta 0.036 0.039 0.19 4 -0.14 1 5
PRKCQ -0.026 0.2 0.35 27 -0.32 123 150
MAPKKK cascade -0.032 0.24 0.39 24 -0.4 125 149
SELE -0.01 0.18 0.32 30 -0.27 134 164
TP beta/GNAI2/GDP/G beta/gamma 0.026 0.053 0.19 4 -0.17 13 17
ROCK1 0.036 0.006 -10000 0 0 15 15
GNA14 0.034 0.009 -10000 0 0 30 30
chemotaxis -0.069 0.32 0.45 17 -0.56 135 152
GNA12 0.023 0.018 -10000 0 0 193 193
GNA13 0.035 0.007 -10000 0 0 19 19
GNA11 0.033 0.011 -10000 0 0 54 54
Rac1/GTP 0.017 0.02 -10000 0 -0.13 5 5
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 0 444 -10000 0 444
TP53 0.004 0.034 -10000 0 -0.22 9 9
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 0.023 0.3 3 -10000 0 3
MDM4 0.034 0.01 -10000 0 0 38 38
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 32 32
EGFR 0.009 0.016 -10000 0 0 381 381
EGF/EGFR 0.001 0.052 -10000 0 -0.11 64 64
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.057 -10000 0 -0.11 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.016 -10000 0 0 122 122
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 0.055 -10000 0 -0.12 61 61
mol:GDP 0.004 0.055 -10000 0 -0.11 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.033 0.011 -10000 0 0 53 53
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
HRAS/GTP -0.004 0.051 -10000 0 -0.11 67 67
SHC1 0.033 0.011 -10000 0 0 52 52
HRAS/GDP 0 0.057 -10000 0 -0.12 67 67
FRAP1 0.093 0.12 0.18 302 -0.18 4 306
EGF/EGFR dimer -0.005 0.056 -10000 0 -0.14 64 64
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 17 17
ETA receptor/Endothelin-1 0.023 0.059 -10000 0 -0.14 50 50
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 -10000 0 0 41 41
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.036 0.004 -10000 0 0 6 6
TCEB1 0.035 0.007 -10000 0 0 22 22
HIF1A/p53 -0.063 0.14 -10000 0 -0.27 139 139
HIF1A -0.057 0.12 0.16 1 -0.28 118 119
COPS5 0.036 0.006 -10000 0 0 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.059 -10000 0 -0.13 22 22
FIH (dimer) 0.025 0.017 -10000 0 0 156 156
CDKN2A 0.004 0.012 -10000 0 0 444 444
ARNT/IPAS 0.05 0.015 -10000 0 -10000 0 0
HIF1AN 0.025 0.017 -10000 0 0 156 156
GNB2L1 0.036 0.002 -10000 0 0 2 2
HIF1A/ARNT -0.061 0.14 -10000 0 -0.27 139 139
CUL2 0.026 0.017 -10000 0 0 153 153
OS9 0.031 0.013 -10000 0 0 73 73
RACK1/Elongin B/Elongin C 0.068 0.032 -10000 0 -0.13 10 10
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.075 0.13 -10000 0 -0.27 141 141
PHD1-3/OS9 0.063 0.064 -10000 0 -0.14 31 31
HIF1A/RACK1/Elongin B/Elongin C -0.043 0.15 -10000 0 -0.27 141 141
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 -0.063 0.14 -10000 0 -0.27 143 143
EGLN3 0.03 0.014 -10000 0 0 91 91
EGLN2 0.034 0.009 -10000 0 0 30 30
EGLN1 0.034 0.009 -10000 0 0 33 33
TP53 0.031 0.013 -10000 0 0 73 73
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.005 0.1 -10000 0 -0.61 12 12
ARNT 0.036 0.004 -10000 0 0 5 5
ARD1A 0.036 0.003 -10000 0 0 4 4
RBX1 0.033 0.01 -10000 0 0 45 45
HIF1A/p19ARF -0.064 0.12 -10000 0 -0.26 119 119
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 -0.007 0.006 0 180 -10000 0 180
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.04 0.04 -10000 0 -0.14 19 19
STXBP1 0.029 0.015 -10000 0 0 106 106
ACh/CHRNA1 0.026 0.053 0.095 40 -0.075 91 131
RAB3GAP2/RIMS1/UNC13B 0.052 0.05 -10000 0 -0.13 25 25
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 0.008 -10000 0 0 23 23
mol:ACh 0.016 0.063 0.093 145 -0.089 88 233
RAB3GAP2 0.035 0.009 -10000 0 0 29 29
STX1A/SNAP25/VAMP2 0.026 0.1 0.18 19 -0.16 76 95
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.026 0.053 0.095 40 -0.075 91 131
UNC13B 0.032 0.013 -10000 0 0 70 70
CHRNA1 0.035 0.007 -10000 0 0 18 18
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.012 0.041 0.096 9 -0.085 40 49
SNAP25 0.002 0.003 -10000 0 0 262 262
VAMP2 0.004 0.001 -10000 0 0 48 48
SYT1 0.018 0.018 -10000 0 0 262 262
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 0.026 0.1 0.18 19 -0.16 76 95
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.017 0.031 0.081 3 -0.056 51 54
PDGF/PDGFRA/CRKL 0.007 0.067 -10000 0 -0.14 68 68
positive regulation of JUN kinase activity 0.023 0.062 -10000 0 -0.11 69 69
CRKL 0.035 0.009 -10000 0 0 29 29
PDGF/PDGFRA/Caveolin-3 0.009 0.068 -10000 0 -0.14 68 68
AP1 -0.08 0.24 0.29 12 -0.59 77 89
mol:IP3 -0.015 0.046 0.095 25 -0.1 49 74
PLCG1 -0.015 0.046 0.095 25 -0.1 49 74
PDGF/PDGFRA/alphaV Integrin 0.004 0.075 -10000 0 -0.15 78 78
RAPGEF1 0.035 0.007 -10000 0 0 19 19
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca2+ -0.015 0.046 0.095 25 -0.1 49 74
CAV3 0.036 0.005 -10000 0 0 11 11
CAV1 0.016 0.018 -10000 0 0 290 290
SHC/Grb2/SOS1 0.028 0.064 -10000 0 -0.11 69 69
PDGF/PDGFRA/Shf -0.005 0.054 -10000 0 -0.1 96 96
FOS -0.093 0.22 0.42 1 -0.6 71 72
JUN -0.026 0.056 0.2 10 -0.2 16 26
oligodendrocyte development 0.003 0.075 -10000 0 -0.15 78 78
GRB2 0.035 0.007 -10000 0 0 17 17
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:DAG -0.015 0.046 0.095 25 -0.1 49 74
PDGF/PDGFRA 0.017 0.031 0.081 3 -0.056 51 54
actin cytoskeleton reorganization 0.007 0.065 -10000 0 -0.14 65 65
SRF -0.016 0.021 0.033 70 -10000 0 70
SHC1 0.033 0.011 -10000 0 0 52 52
PI3K 0.007 0.09 -10000 0 -0.15 108 108
PDGF/PDGFRA/Crk/C3G 0.027 0.071 -10000 0 -0.13 75 75
JAK1 -0.007 0.029 0.083 30 -10000 0 30
ELK1/SRF -0.02 0.083 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 0.027 0.034 -10000 0 -0.032 102 102
GO:0007205 -0.027 0.068 0.1 25 -0.19 55 80
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.023 0.062 -10000 0 -0.11 69 69
PDGF/PDGFRA/SHB 0.007 0.065 -10000 0 -0.14 65 65
PDGF/PDGFRA/Caveolin-1 -0.016 0.077 -10000 0 -0.17 87 87
ITGAV 0.034 0.009 -10000 0 0 31 31
ELK1 -0.032 0.066 0.13 7 -0.15 84 91
PIK3CA 0.031 0.013 -10000 0 0 80 80
PDGF/PDGFRA/Crk 0.006 0.072 -10000 0 -0.15 76 76
JAK-STAT cascade -0.007 0.029 0.082 30 -10000 0 30
cell proliferation -0.005 0.054 -10000 0 -0.1 96 96
Arf6 signaling events

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
CENTA1/KIF3B 0.014 0.035 -10000 0 -0.11 38 38
ARNO/beta Arrestin1-2 0.042 0.025 -10000 0 -0.094 7 7
EGFR 0.009 0.016 -10000 0 0 381 381
EPHA2 0.033 0.011 -10000 0 0 54 54
USP6 0.035 0.007 -10000 0 0 18 18
IQSEC1 0.035 0.007 -10000 0 0 19 19
EGFR/EGFR/EGF/EGF -0.005 0.056 -10000 0 -0.14 64 64
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
mol:GTP 0.002 0.012 -10000 0 -0.063 3 3
ARRB1 0.036 0.005 -10000 0 0 10 10
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.033 0.011 -10000 0 0 48 48
EGF 0.035 0.008 -10000 0 0 25 25
somatostatin receptor activity 0 0 0.001 155 0 6 161
ARAP2 0 0 0 129 0 2 131
mol:GDP 0.068 0.068 0.16 127 -0.16 4 131
mol:PI-3-4-5-P3 0 0 0 139 0 5 144
ITGA2B 0.036 0.004 -10000 0 0 5 5
ARF6 0.035 0.008 -10000 0 0 27 27
Ephrin A1/EPHA2/NCK1/GIT1 0.076 0.052 -10000 0 -0.12 24 24
ADAP1 0 0 0 61 0 1 62
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 0.083 0.087 0.19 138 -0.2 5 143
EGFR/EGFR/EGF/EGF/ARFGEP100 0.001 0.055 -10000 0 -0.12 62 62
ADRB2 0.034 0.01 -10000 0 0 42 42
receptor agonist activity 0 0 0 141 0 5 146
actin filament binding 0 0 0 142 0 7 149
SRC 0.036 0.006 -10000 0 0 14 14
ITGB3 0.036 0.003 -10000 0 0 4 4
GNAQ 0.035 0.009 -10000 0 0 31 31
EFA6/PI-4-5-P2 0.001 0.001 0.001 169 -0.001 4 173
ARF6/GDP 0.036 0.063 0.17 12 -0.22 11 23
ARF6/GDP/GULP/ACAP1 0.055 0.075 0.2 23 -0.2 3 26
alphaIIb/beta3 Integrin/paxillin/GIT1 0.092 0.012 -10000 0 -10000 0 0
ACAP1 0 0 0 58 -10000 0 58
ACAP2 0 0 0 70 0 3 73
LHCGR/beta Arrestin2 0.03 0.024 -10000 0 -0.14 7 7
EFNA1 0.033 0.011 -10000 0 0 50 50
HGF 0.024 0.017 -10000 0 0 177 177
CYTH3 0 0 0.001 148 -0.001 4 152
CYTH2 0 0.001 0.003 1 -0.003 6 7
NCK1 0.035 0.008 -10000 0 0 27 27
fibronectin binding 0 0 0 145 0 5 150
endosomal lumen acidification 0 0 0 145 0 6 151
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.024 0.017 -10000 0 0 168 168
GNAQ/ARNO 0.026 0.008 0.04 5 0 31 36
mol:Phosphatidic acid 0 0 0 70 0 3 73
PIP3-E 0.03 0.014 -10000 0 0 89 89
MET 0.023 0.018 -10000 0 0 191 191
GNA14 0.035 0.009 -10000 0 0 30 30
GNA15 0.033 0.012 -10000 0 0 57 57
GIT1 0.036 0.003 -10000 0 0 4 4
mol:PI-4-5-P2 0 0 0.001 152 -0.001 4 156
GNA11 0.033 0.011 -10000 0 0 54 54
LHCGR 0.037 0.003 -10000 0 0 3 3
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 0.043 -10000 0 -0.09 51 51
alphaIIb/beta3 Integrin 0.054 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.036 0.006 -9999 0 0 13 13
Syndecan-3/Src/Cortactin -0.025 0.18 -9999 0 -0.43 75 75
Syndecan-3/Neurocan -0.065 0.18 -9999 0 -0.48 78 78
POMC 0.036 0.006 -9999 0 0 14 14
EGFR 0.009 0.016 -9999 0 0 381 381
Syndecan-3/EGFR -0.057 0.16 -9999 0 -0.42 77 77
AGRP 0.036 0.005 -9999 0 0 9 9
NCSTN 0.035 0.008 -9999 0 0 28 28
PSENEN 0.035 0.008 -9999 0 0 28 28
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.035 0.006 -9999 0 0 16 16
APH1A 0.036 0.005 -9999 0 0 11 11
NCAN 0 0 -9999 0 -10000 0 0
long-term memory -0.033 0.2 -9999 0 -0.49 78 78
Syndecan-3/IL8 -0.056 0.18 -9999 0 -0.48 78 78
PSEN1 0.033 0.011 -9999 0 0 46 46
Src/Cortactin 0.051 0.015 -9999 0 -0.14 1 1
FYN 0.03 0.014 -9999 0 0 90 90
limb bud formation -0.066 0.18 -9999 0 -0.5 78 78
MC4R 0.035 0.007 -9999 0 0 20 20
SRC 0.036 0.006 -9999 0 0 14 14
PTN 0.021 0.018 -9999 0 0 209 209
FGFR/FGF/Syndecan-3 -0.067 0.19 -9999 0 -0.5 78 78
neuron projection morphogenesis -0.071 0.15 -9999 0 -0.43 73 73
Syndecan-3/AgRP -0.044 0.19 -9999 0 -0.49 78 78
Syndecan-3/AgRP/MC4R -0.025 0.19 -9999 0 -0.47 78 78
Fyn/Cortactin 0.029 0.061 -9999 0 -0.14 53 53
SDC3 -0.068 0.19 -9999 0 -0.51 78 78
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.055 0.18 -9999 0 -0.47 78 78
IL8 0.019 0.018 -9999 0 0 243 243
Syndecan-3/Fyn/Cortactin -0.034 0.21 -9999 0 -0.51 78 78
Syndecan-3/CASK -0.065 0.18 -9999 0 -0.48 78 78
alpha-MSH/MC4R 0.051 0.014 -9999 0 -10000 0 0
Gamma Secretase 0.08 0.069 -9999 0 -0.15 28 28
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.033 0.045 0.12 67 -0.039 84 151
AES 0.031 0.042 0.11 63 -0.036 80 143
FBXW11 0.035 0.008 -10000 0 0 25 25
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.026 -10000 0 -10000 0 0
SMAD4 0.032 0.012 -10000 0 0 58 58
DKK2 0.034 0.009 -10000 0 0 31 31
TLE1 0.031 0.041 0.11 64 -0.036 84 148
MACF1 0.033 0.011 -10000 0 0 49 49
CTNNB1 0.045 0.11 0.25 25 -0.36 14 39
WIF1 0.028 0.015 -10000 0 0 112 112
beta catenin/RanBP3 0.071 0.16 0.42 62 -0.35 9 71
KREMEN2 0.036 0.004 -10000 0 0 7 7
DKK1 0.017 0.018 -10000 0 0 271 271
beta catenin/beta TrCP1 0.06 0.11 0.26 22 -0.34 16 38
FZD1 0.024 0.017 -10000 0 0 173 173
AXIN2 -0.024 0.093 0.11 4 -0.24 67 71
AXIN1 0.037 0.001 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
Axin1/APC/GSK3/beta catenin 0.015 0.16 -10000 0 -0.6 29 29
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.13 0.25 13 -0.39 23 36
Axin1/APC/GSK3 0.005 0.09 0.23 5 -0.38 17 22
Axin1/APC/GSK3/beta catenin/Macf1 0.032 0.14 0.22 24 -0.34 39 63
HNF1A 0.006 0.03 0.071 74 -0.035 4 78
CTBP1 0.031 0.041 0.11 61 -0.037 83 144
MYC -0.097 0.4 0.74 14 -1.3 49 63
RANBP3 0.035 0.008 -10000 0 0 23 23
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 0.038 0.11 59 -0.036 68 127
TCF3 0.032 0.042 0.11 64 -0.036 83 147
WNT1/LRP6/FZD1/Axin1 0.059 0.046 -10000 0 -10000 0 0
Ran/GTP 0.026 0.016 -10000 0 -0.13 5 5
CtBP/CBP/TCF/TLE1/AES 0.035 0.19 0.46 65 -0.34 20 85
LEF1 0.033 0.044 0.11 71 -0.037 86 157
DVL1 0.01 0.098 -10000 0 -0.42 18 18
CSNK2A1 0.035 0.009 -10000 0 0 31 31
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.01 0.16 0.25 10 -0.48 32 42
DKK1/LRP6/Kremen 2 0.031 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 40 40
CSNK1A1 0.034 0.046 0.12 68 -0.038 86 154
NLK 0.026 0.023 -10000 0 -0.032 56 56
CCND1 -0.08 0.35 0.79 3 -1.3 38 41
WNT1 0.036 0.007 -10000 0 0 16 16
GSK3A 0.035 0.009 -10000 0 0 28 28
GSK3B 0.034 0.01 -10000 0 0 40 40
FRAT1 0.025 0.017 -10000 0 0 161 161
PPP2R5D 0.023 0.044 -10000 0 -0.24 8 8
APC 0.04 0.1 0.18 161 -10000 0 161
WNT1/LRP6/FZD1 0.001 0.049 -10000 0 -0.25 12 12
CREBBP 0.033 0.043 0.11 70 -0.036 86 156
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.006 0.089 -9999 0 -0.17 89 89
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 18 18
FZD3 0.029 0.015 -9999 0 0 110 110
WNT5A 0.029 0.015 -9999 0 0 99 99
WNT11 0.036 0.006 -9999 0 0 14 14
HIF-2-alpha transcription factor network

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.019 0.17 -10000 0 -0.66 31 31
oxygen homeostasis 0.004 0.02 0.044 66 -0.024 23 89
TCEB2 0.036 0.004 -10000 0 0 6 6
TCEB1 0.035 0.007 -10000 0 0 22 22
VHL/Elongin B/Elongin C/HIF2A 0.003 0.14 0.3 23 -0.24 45 68
EPO -0.04 0.2 0.4 17 -0.44 52 69
FIH (dimer) 0.016 0.038 0.11 18 -0.04 50 68
APEX1 0.016 0.043 0.1 8 -0.053 23 31
SERPINE1 -0.074 0.2 0.37 2 -0.47 76 78
FLT1 -0.012 0.16 -10000 0 -0.67 23 23
ADORA2A -0.037 0.24 0.44 35 -0.45 59 94
germ cell development -0.036 0.23 0.43 33 -0.42 69 102
SLC11A2 -0.034 0.24 0.45 34 -0.44 67 101
BHLHE40 -0.039 0.23 0.43 32 -0.43 69 101
HIF1AN 0.016 0.038 0.11 18 -0.04 50 68
HIF2A/ARNT/SIRT1 -0.016 0.16 0.35 25 -0.3 52 77
ETS1 0.047 0.032 0.12 15 -0.11 11 26
CITED2 -0.058 0.26 -10000 0 -0.8 51 51
KDR -0.001 0.16 -10000 0 -0.83 16 16
PGK1 -0.039 0.25 0.45 34 -0.45 75 109
SIRT1 0.024 0.017 -10000 0 0 171 171
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.028 0.27 0.48 12 -0.49 68 80
EPAS1 0 0.13 0.3 35 -0.26 39 74
SP1 0.041 0.011 0.11 8 -10000 0 8
ABCG2 -0.045 0.26 0.45 34 -0.46 82 116
EFNA1 -0.04 0.24 0.43 30 -0.45 70 100
FXN -0.039 0.23 0.43 35 -0.43 68 103
POU5F1 -0.039 0.23 0.43 32 -0.43 69 101
neuron apoptosis 0.027 0.26 0.48 68 -0.47 12 80
EP300 0.033 0.011 -10000 0 0 49 49
EGLN3 0.019 0.039 0.11 15 -0.041 49 64
EGLN2 0.022 0.041 0.11 19 -0.041 38 57
EGLN1 0.023 0.041 0.11 19 -0.04 59 78
VHL/Elongin B/Elongin C 0.045 0.023 -10000 0 -0.12 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.016 0.043 0.11 7 -0.053 25 32
SLC2A1 -0.051 0.23 0.43 27 -0.45 71 98
TWIST1 -0.064 0.21 0.41 15 -0.43 85 100
ELK1 0.038 0.035 0.11 29 -0.095 25 54
HIF2A/ARNT/Cbp/p300 0.001 0.19 0.38 31 -0.32 49 80
VEGFA -0.039 0.23 0.43 32 -0.43 69 101
CREBBP 0.036 0.005 -10000 0 0 8 8
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.006 0.1 0.19 87 -10000 0 87
GNAI2 0.034 0.01 -10000 0 0 43 43
S1P/S1P5/G12 0.009 0.03 -10000 0 -0.11 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
RhoA/GTP 0.007 0.11 -10000 0 -0.2 87 87
negative regulation of cAMP metabolic process -0.007 0.099 -10000 0 -0.21 80 80
GNAZ 0.031 0.013 -10000 0 0 81 81
GNAI3 0.036 0.006 -10000 0 0 15 15
GNA12 0.023 0.018 -10000 0 0 193 193
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.007 0.1 -10000 0 -0.21 80 80
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
RHOA 0.035 0.007 -10000 0 0 18 18
GNAI1 0.018 0.018 -10000 0 0 263 263
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
CDC42/GTP 0.007 0.1 -10000 0 -0.19 84 84
PLCG1 -0.011 0.097 0.12 5 -0.2 83 88
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 0 43 43
GNAI3 0.036 0.006 -10000 0 0 15 15
G12/G13 0.025 0.047 -10000 0 -0.14 28 28
cell migration 0.006 0.1 -10000 0 -0.19 84 84
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.012 0.098 0.12 4 -0.2 85 89
MAPK1 -0.006 0.094 0.12 5 -0.2 77 82
S1P/S1P5/Gi -0.007 0.1 -10000 0 -0.21 80 80
GNAI1 0.018 0.018 -10000 0 0 263 263
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.009 0.03 -10000 0 -0.11 28 28
RHOA 0.043 0.1 0.19 161 -0.18 3 164
S1P/S1P4/Gi -0.007 0.1 -10000 0 -0.21 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.031 0.013 -10000 0 0 81 81
S1P/S1P4/G12/G13 0.023 0.037 -10000 0 -0.1 28 28
GNA12 0.023 0.018 -10000 0 0 193 193
GNA13 0.035 0.007 -10000 0 0 19 19
CDC42 0.035 0.008 -10000 0 0 24 24
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.026 -10000 0 -0.052 56 56
CDKN2C -0.009 0.021 -10000 0 -0.035 121 121
CDKN2A 0.005 0.015 -10000 0 -0.043 1 1
CCND2 -0.001 0.018 0.11 6 -10000 0 6
RB1 -0.045 0.09 0.16 2 -0.18 139 141
CDK4 -0.001 0.02 0.13 6 -10000 0 6
CDK6 -0.001 0.02 0.13 6 -10000 0 6
G1/S progression 0.053 0.095 0.19 156 -0.16 2 158
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.006 0.057 -10000 0 -0.14 60 60
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.096 0.21 11 -0.21 39 50
AP1 -0.009 0.073 0.089 13 -0.14 89 102
mol:PIP3 -0.024 0.05 -10000 0 -0.13 77 77
AKT1 0.002 0.094 0.2 19 -0.24 27 46
PTK2B -0.002 0.058 0.13 3 -0.15 57 60
RHOA 0.022 0.078 0.17 26 -0.34 11 37
PIK3CB 0.035 0.007 -10000 0 0 18 18
mol:Ca2+ -0.009 0.04 0.19 5 -0.14 18 23
MAGI3 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 9 9
apoptosis 0.002 0.062 0.1 36 -0.16 53 89
HRAS/GDP 0.021 0.027 -10000 0 -0.13 15 15
positive regulation of microtubule depolymerization -0.02 0.074 0.17 11 -0.21 36 47
NF kappa B1 p50/RelA -0.021 0.066 0.08 51 -0.17 52 103
endothelial cell migration -0.017 0.097 -10000 0 -0.3 53 53
ADCY4 -0.004 0.091 0.14 13 -0.26 36 49
ADCY5 -0.004 0.091 0.14 13 -0.26 36 49
ADCY6 0.001 0.092 0.16 14 -0.25 37 51
ADCY7 -0.002 0.096 0.15 16 -0.25 42 58
ADCY1 -0.009 0.083 0.15 9 -0.26 34 43
ADCY2 -0.001 0.094 0.16 14 -0.25 40 54
ADCY3 -0.004 0.091 0.14 13 -0.26 36 49
ADCY8 -0.002 0.091 0.15 17 -0.25 38 55
ADCY9 0 0.091 0.16 15 -0.24 39 54
GSK3B -0.009 0.065 0.19 7 -0.19 25 32
arachidonic acid secretion -0.016 0.11 0.15 14 -0.24 66 80
GNG2 0 0.001 0.002 1 -0.003 8 9
TRIP6 -0.016 0.085 -10000 0 -0.25 57 57
GNAO1 0.003 0.057 0.12 24 -0.16 47 71
HRAS 0.034 0.009 -10000 0 0 32 32
NFKBIA -0.017 0.083 0.17 16 -0.22 37 53
GAB1 0.032 0.012 -10000 0 0 59 59
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.009 0.21 -10000 0 -0.8 31 31
JUN 0.034 0.01 -10000 0 0 40 40
LPA/LPA2/NHERF2 0.019 0.029 -10000 0 -0.061 53 53
TIAM1 -0.015 0.25 -10000 0 -0.98 31 31
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 -0.008 0.039 0.22 3 -0.14 19 22
PLCB3 0.006 0.035 0.2 5 -10000 0 5
FOS 0.025 0.017 -10000 0 0 158 158
positive regulation of mitosis -0.016 0.11 0.15 14 -0.24 66 80
LPA/LPA1-2-3 -0.008 0.04 -10000 0 -0.12 53 53
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.009 0.066 -10000 0 -0.28 9 9
GNAZ 0.003 0.063 0.12 28 -0.17 48 76
EGFR/PI3K-beta/Gab1 -0.02 0.054 -10000 0 -0.13 77 77
positive regulation of dendritic cell cytokine production -0.008 0.04 -10000 0 -0.12 53 53
LPA/LPA2/MAGI-3 -0.004 0.017 -10000 0 -0.052 53 53
ARHGEF1 0.039 0.12 0.19 153 -0.17 34 187
GNAI2 0.004 0.069 0.12 40 -0.17 53 93
GNAI3 0.007 0.063 0.12 39 -0.15 53 92
GNAI1 0.002 0.047 0.12 19 -0.16 29 48
LPA/LPA3 -0.006 0.021 -10000 0 -0.066 53 53
LPA/LPA2 -0.005 0.021 -10000 0 -0.065 53 53
LPA/LPA1 -0.012 0.054 -10000 0 -0.17 53 53
HB-EGF/EGFR -0.01 0.056 -10000 0 -0.14 66 66
HBEGF 0.011 0.046 0.092 116 -10000 0 116
mol:DAG -0.008 0.039 0.22 3 -0.14 19 22
cAMP biosynthetic process 0.003 0.11 0.18 33 -0.26 43 76
NFKB1 0.035 0.007 -10000 0 0 18 18
SRC 0.036 0.006 -10000 0 0 14 14
GNB1 0.035 0.007 -10000 0 0 20 20
LYN -0.023 0.095 0.17 19 -0.23 62 81
GNAQ 0.008 0.026 0.056 38 -0.058 55 93
LPAR2 0 0.001 -10000 0 -0.003 3 3
LPAR3 0 0.001 -10000 0 -0.002 1 1
LPAR1 -0.009 0.033 -10000 0 -0.1 53 53
IL8 -0.13 0.2 0.33 7 -0.39 157 164
PTK2 0.014 0.057 0.12 39 -0.14 50 89
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
CASP3 0.002 0.062 0.1 36 -0.16 53 89
EGFR 0.009 0.016 -10000 0 0 381 381
PLCG1 0.005 0.038 0.072 8 -0.1 35 43
PLD2 0.015 0.053 0.12 38 -0.12 52 90
G12/G13 0.018 0.062 -10000 0 -0.15 45 45
PI3K-beta -0.014 0.069 -10000 0 -0.24 28 28
cell migration -0.002 0.073 -10000 0 -0.25 29 29
SLC9A3R2 0.036 0.005 -10000 0 0 9 9
PXN 0.009 0.067 -10000 0 -0.29 9 9
HRAS/GTP -0.018 0.11 0.16 8 -0.25 66 74
RAC1 0.024 0.017 -10000 0 0 173 173
MMP9 0.017 0.018 -10000 0 0 267 267
PRKCE 0.036 0.003 -10000 0 0 4 4
PRKCD -0.005 0.054 0.18 14 -0.2 3 17
Gi(beta/gamma) -0.009 0.12 0.17 11 -0.26 60 71
mol:LPA -0.009 0.033 -10000 0 -0.1 53 53
TRIP6/p130 Cas/FAK1/Paxillin -0.008 0.081 -10000 0 -0.22 43 43
MAPKKK cascade -0.016 0.11 0.15 14 -0.24 66 80
contractile ring contraction involved in cytokinesis 0.021 0.08 0.18 21 -0.34 12 33
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.026 0.056 37 -0.058 55 92
GNA15 0.008 0.025 0.056 33 -0.057 51 84
GNA12 0.023 0.018 -10000 0 0 193 193
GNA13 0.035 0.007 -10000 0 0 19 19
MAPT -0.02 0.075 0.17 11 -0.21 37 48
GNA11 0.011 0.022 0.056 37 -0.057 34 71
Rac1/GTP -0.01 0.22 -10000 0 -0.85 31 31
MMP2 -0.017 0.097 -10000 0 -0.3 53 53
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.024 0.14 -10000 0 -0.37 21 21
MAP3K8 0.022 0.018 -10000 0 0 197 197
FOS 0.019 0.1 -10000 0 -0.36 13 13
PRKCA 0.029 0.025 -10000 0 -0.032 70 70
PTPN7 0.028 0.029 0.067 24 -0.037 72 96
HRAS 0.034 0.009 -10000 0 0 32 32
PRKCB 0 0.008 0.016 61 -0.013 76 137
NRAS 0.032 0.012 -10000 0 0 63 63
RAS family/GTP 0.042 0.065 -10000 0 -0.13 53 53
MAPK3 0.035 0.052 -10000 0 -0.33 2 2
MAP2K1 0.012 0.055 -10000 0 -0.22 12 12
ELK1 0.026 0.029 -10000 0 -0.04 80 80
BRAF 0.007 0.021 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.002 60 -0.004 77 137
MAPK1 0.008 0.13 -10000 0 -0.44 30 30
RAF1 -0.001 0.067 -10000 0 -0.34 17 17
KRAS 0.034 0.009 -10000 0 0 35 35
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 32 -10000 0 32
GNB1/GNG2 0.039 0.03 -10000 0 -0.1 20 20
regulation of S phase of mitotic cell cycle -0.004 0.081 -10000 0 -0.18 72 72
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.009 -10000 0 0 32 32
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 53 -10000 0 53
MAP2K1 -0.035 0.076 0.18 14 -0.18 67 81
T-DHT/AR 0.025 0.008 -10000 0 -0.023 6 6
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.003 12 -0.006 76 88
GNAI2 0.033 0.01 -10000 0 0 43 43
GNAI3 0.036 0.006 -10000 0 0 15 15
GNAI1 0.018 0.018 -10000 0 0 263 263
mol:GDP -0.02 0.036 -10000 0 -0.12 26 26
cell proliferation -0.059 0.18 0.29 9 -0.42 85 94
PIK3CA 0.031 0.013 -10000 0 0 80 80
FOS -0.087 0.28 0.38 3 -0.69 83 86
mol:Ca2+ -0.004 0.02 0.027 6 -0.053 59 65
MAPK3 -0.043 0.13 0.26 13 -0.3 78 91
MAPK1 -0.04 0.16 0.25 3 -0.49 37 40
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0 0.002 0.003 59 -0.004 74 133
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 74 133
HRAS/GTP 0.043 0.065 -10000 0 -0.093 78 78
actin cytoskeleton reorganization 0.019 0.054 -10000 0 -0.12 45 45
SRC 0.035 0.006 -10000 0 0 14 14
voltage-gated calcium channel activity 0 0.002 0.003 59 -0.004 74 133
PI3K 0.019 0.063 -10000 0 -0.13 73 73
apoptosis 0.048 0.19 0.43 84 -0.3 5 89
T-DHT/AR/PELP1 0.043 0.023 -10000 0 -0.1 9 9
HRAS/GDP 0.007 0.06 -10000 0 -0.15 28 28
CREB1 -0.068 0.19 0.3 5 -0.46 84 89
RAC1-CDC42/GTP 0.027 0.06 -10000 0 -0.12 45 45
AR 0.035 0.008 -10000 0 0 22 22
GNB1 0.035 0.007 -10000 0 0 20 20
RAF1 -0.026 0.068 0.19 14 -0.22 13 27
RAC1-CDC42/GDP 0.02 0.053 -10000 0 -0.17 13 13
T-DHT/AR/PELP1/Src 0.06 0.032 -10000 0 -0.086 13 13
MAP2K2 -0.038 0.069 0.16 8 -0.17 67 75
T-DHT/AR/PELP1/Src/PI3K -0.004 0.081 -10000 0 -0.19 72 72
GNAZ 0.031 0.013 -10000 0 0 81 81
SHBG 0.036 0.006 -10000 0 0 14 14
Gi family/GNB1/GNG2/GDP -0.038 0.17 -10000 0 -0.45 53 53
mol:T-DHT 0 0.001 0.002 1 -0.004 21 22
RAC1 0.024 0.017 -10000 0 0 173 173
GNRH1 -0.011 0.002 0 12 -0.017 1 13
Gi family/GTP -0.005 0.082 -10000 0 -0.19 62 62
CDC42 0.035 0.008 -10000 0 0 24 24
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.012 -10000 0 0 66 66
CCL5 0.033 0.011 -10000 0 0 53 53
SDCBP 0.035 0.007 -10000 0 0 21 21
FGFR/FGF2/Syndecan-1 0.014 0.1 0.21 24 -0.24 10 34
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 0.02 0.1 0.22 19 -0.25 11 30
Syndecan-1/Syntenin 0.025 0.11 0.23 25 -0.25 13 38
MAPK3 0.003 0.1 0.2 19 -0.23 18 37
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 66 66
keratinocyte migration 0.02 0.1 0.22 19 -0.24 11 30
Syndecan-1/RANTES 0.019 0.1 0.23 18 -0.25 10 28
Syndecan-1/CD147 0.023 0.11 0.24 14 -0.24 18 32
Syndecan-1/Syntenin/PIP2 0.022 0.1 0.21 25 -0.24 13 38
LAMA5 0.032 0.012 -10000 0 0 65 65
positive regulation of cell-cell adhesion 0.022 0.1 0.21 25 -0.23 13 38
MMP7 0.027 0.016 -10000 0 0 137 137
HGF 0.024 0.017 -10000 0 0 177 177
Syndecan-1/CASK -0.001 0.085 0.15 5 -0.24 10 15
Syndecan-1/HGF/MET 0.024 0.089 0.24 9 -0.25 5 14
regulation of cell adhesion -0.004 0.11 0.24 27 -0.25 14 41
HPSE 0.032 0.012 -10000 0 0 59 59
positive regulation of cell migration 0.014 0.1 0.21 24 -0.24 10 34
SDC1 0.01 0.095 0.17 36 -0.25 9 45
Syndecan-1/Collagen 0.014 0.1 0.21 24 -0.24 10 34
PPIB 0.034 0.01 -10000 0 0 39 39
MET 0.023 0.018 -10000 0 0 191 191
PRKACA 0.035 0.008 -10000 0 0 25 25
MMP9 0.017 0.018 -10000 0 0 267 267
MAPK1 0.003 0.098 0.2 18 -0.24 18 36
homophilic cell adhesion 0.016 0.1 0.21 29 -0.25 9 38
MMP1 0.031 0.013 -10000 0 0 71 71
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.014 -10000 0 -0.005 56 56
ELF1 0.042 0.016 -10000 0 -10000 0 0
CCNA2 0.028 0.015 -10000 0 0 117 117
PIK3CA 0.03 0.015 -10000 0 -0.002 87 87
JAK3 0.034 0.012 -10000 0 -0.009 31 31
PIK3R1 0.032 0.014 -10000 0 -0.002 68 68
JAK1 0.033 0.012 -10000 0 -0.003 46 46
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.02 0.18 0.24 2 -0.53 39 41
SHC1 0.032 0.014 -10000 0 -0.004 60 60
SP1 -0.011 0.12 -10000 0 -0.27 89 89
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 0.034 0.011 -10000 0 -0.006 30 30
G1/S transition of mitotic cell cycle -0.069 0.27 0.27 10 -0.58 95 105
PTPN11 0.035 0.01 -10000 0 -0.012 18 18
CCND2 -0.074 0.19 -10000 0 -0.49 89 89
LCK 0.035 0.01 -10000 0 -0.009 24 24
GRB2 0.035 0.01 -10000 0 -0.009 24 24
IL2 0.035 0.009 -10000 0 -0.012 17 17
CDK6 0.024 0.017 -10000 0 0 176 176
CCND3 -0.026 0.2 0.38 2 -0.74 27 29
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.014 0.061 0.14 1 -0.13 69 70
EPHB2 0.034 0.01 -10000 0 0 42 42
Syndecan-2/TACI 0.017 0.055 0.14 1 -0.12 66 67
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.022 0.073 -10000 0 -0.12 83 83
HRAS 0.034 0.009 -10000 0 0 32 32
Syndecan-2/CASK -0.009 0.041 -10000 0 -0.11 69 69
ITGA5 0.033 0.011 -10000 0 0 56 56
BAX -0.009 0.073 -10000 0 -0.9 3 3
EPB41 0.036 0.005 -10000 0 0 9 9
positive regulation of cell-cell adhesion 0.013 0.054 -10000 0 -0.11 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 0 246 246
Syndecan-2/MMP2 0.009 0.062 0.14 1 -0.14 65 66
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.019 0.054 -10000 0 -0.14 42 42
dendrite morphogenesis 0.015 0.054 0.14 1 -0.12 62 63
Syndecan-2/GM-CSF 0.017 0.055 0.14 1 -0.12 64 65
determination of left/right symmetry 0.007 0.024 0.085 5 -0.24 4 9
Syndecan-2/PKC delta 0.016 0.054 0.14 1 -0.12 62 63
GNB2L1 0.036 0.002 -10000 0 0 2 2
MAPK3 -0.023 0.051 0.11 34 -0.12 20 54
MAPK1 -0.02 0.05 0.12 31 -0.13 18 49
Syndecan-2/RACK1 0.03 0.063 0.14 3 -0.11 77 80
NF1 0.036 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.024 0.085 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 0.063 0.14 1 -0.11 92 93
Syndecan-2/Kininogen 0.016 0.054 0.14 1 -0.12 63 64
ITGB1 0.027 0.016 -10000 0 0 138 138
SRC -0.026 0.051 0.17 11 -0.19 8 19
Syndecan-2/CASK/Protein 4.1 0.015 0.05 -10000 0 -0.1 68 68
extracellular matrix organization 0.014 0.051 -10000 0 -0.12 57 57
actin cytoskeleton reorganization 0.014 0.061 0.14 1 -0.13 69 70
Syndecan-2/Caveolin-2/Ras 0.007 0.067 0.15 2 -0.13 75 77
Syndecan-2/Laminin alpha3 0.016 0.052 0.14 1 -0.12 60 61
Syndecan-2/RasGAP 0.037 0.078 -10000 0 -0.12 89 89
alpha5/beta1 Integrin 0.029 0.042 -10000 0 -0.14 20 20
PRKCD 0.034 0.01 -10000 0 0 40 40
Syndecan-2 dimer 0.015 0.054 0.14 1 -0.12 62 63
GO:0007205 0.001 0.011 -10000 0 -0.12 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.014 0.067 0.19 1 -0.13 75 76
RHOA 0.035 0.007 -10000 0 0 18 18
SDCBP 0.035 0.007 -10000 0 0 21 21
TNFRSF13B 0.036 0.005 -10000 0 0 8 8
RASA1 0.034 0.009 -10000 0 0 32 32
alpha2/beta1 Integrin 0.019 0.054 -10000 0 -0.14 42 42
Syndecan-2/Synbindin 0.016 0.059 0.14 1 -0.13 67 68
TGFB1 0.032 0.012 -10000 0 0 66 66
CASP3 -0.016 0.052 0.11 32 -0.2 4 36
FN1 0.035 0.009 -10000 0 0 29 29
Syndecan-2/IL8 -0.003 0.069 -10000 0 -0.17 61 61
SDC2 0.007 0.024 0.085 5 -0.24 4 9
KNG1 0.035 0.008 -10000 0 0 28 28
Syndecan-2/Neurofibromin 0.017 0.056 0.14 1 -0.12 68 69
TRAPPC4 0.036 0.006 -10000 0 0 15 15
CSF2 0.036 0.005 -10000 0 0 10 10
Syndecan-2/TGFB1 0.015 0.051 -10000 0 -0.12 57 57
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.055 -10000 0 -0.11 73 73
Syndecan-2/Ezrin 0.014 0.053 -10000 0 -0.11 70 70
PRKACA -0.021 0.051 0.12 35 -0.18 3 38
angiogenesis -0.003 0.068 -10000 0 -0.17 61 61
MMP2 0.029 0.015 -10000 0 0 108 108
IL8 0.019 0.018 -10000 0 0 243 243
calcineurin-NFAT signaling pathway 0.017 0.055 0.14 1 -0.12 66 67
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.047 0.082 0.37 1 -10000 0 1
CRKL 0.043 0.09 0.16 146 -10000 0 146
mol:DAG 0.016 0.063 0.21 2 -0.19 28 30
HRAS 0.043 0.1 0.23 61 -0.19 2 63
MAPK8 0.012 0.076 0.16 83 -0.13 7 90
RAP1A 0.049 0.093 0.16 186 -10000 0 186
GAB1 0.04 0.087 0.16 161 -10000 0 161
MAPK14 0.034 0.1 0.17 153 -0.13 8 161
EPO 0.027 0.02 -10000 0 -0.032 2 2
PLCG1 0.016 0.063 0.21 2 -0.19 28 30
EPOR/TRPC2/IP3 Receptors 0.041 0.013 -10000 0 -0.032 2 2
RAPGEF1 0.035 0.007 -10000 0 0 19 19
EPO/EPOR (dimer)/SOCS3 0.051 0.038 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.06 0.072 0.21 28 -10000 0 28
EPO/EPOR (dimer) 0.039 0.03 -10000 0 -10000 0 0
IRS2 0.038 0.088 0.16 130 -0.16 4 134
STAT1 0.02 0.066 0.23 4 -0.21 12 16
STAT5B 0.019 0.066 0.23 3 -0.19 29 32
cell proliferation 0.008 0.075 0.16 84 -0.12 7 91
GAB1/SHIP/PIK3R1/SHP2/SHC 0.037 0.064 0.16 3 -0.18 6 9
TEC 0.049 0.093 0.16 160 -10000 0 160
SOCS3 0.036 0.004 -10000 0 0 7 7
STAT1 (dimer) 0.02 0.065 0.23 4 -0.22 8 12
JAK2 0.037 0.018 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
EPO/EPOR (dimer)/JAK2 0.047 0.053 0.22 11 -10000 0 11
EPO/EPOR 0.039 0.03 -10000 0 -10000 0 0
LYN 0.032 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.036 0.085 0.2 37 -10000 0 37
elevation of cytosolic calcium ion concentration 0.041 0.013 -10000 0 -0.032 2 2
SHC1 0.033 0.011 -10000 0 0 52 52
EPO/EPOR (dimer)/LYN 0.04 0.059 -10000 0 -0.13 29 29
mol:IP3 0.016 0.063 0.21 2 -0.19 28 30
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.023 0.093 0.16 135 -0.17 11 146
SH2B3 -0.001 0.006 0.026 8 -10000 0 8
NFKB1 0.034 0.1 0.17 149 -0.14 8 157
EPO/EPOR (dimer)/JAK2/SOCS3 0.015 0.015 -10000 0 -10000 0 0
PTPN6 0.049 0.094 0.17 167 -10000 0 167
TEC/VAV2/GRB2 0.082 0.071 0.23 33 -10000 0 33
EPOR 0.041 0.013 -10000 0 -0.032 2 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.06 0.072 0.21 28 -10000 0 28
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.032 0.012 -10000 0 0 63 63
CRKL/CBL/C3G 0.08 0.067 0.22 28 -10000 0 28
VAV2 0.047 0.091 0.16 154 -10000 0 154
CBL 0.049 0.093 0.16 186 -10000 0 186
SHC/Grb2/SOS1 0.021 0.035 -10000 0 -0.1 4 4
STAT5A 0.019 0.065 0.25 2 -0.19 28 30
GRB2 0.035 0.007 -10000 0 0 17 17
STAT5 (dimer) 0.034 0.073 0.27 5 -0.22 2 7
LYN/PLCgamma2 0.026 0.07 -10000 0 -0.17 53 53
PTPN11 0.036 0.005 -10000 0 0 11 11
BTK 0.046 0.093 0.16 182 -10000 0 182
BCL2 0.047 0.082 0.31 1 -10000 0 1
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.029 0.085 -10000 0 -0.14 87 87
alphaM/beta2 Integrin/GPIbA 0.049 0.069 -10000 0 -0.12 59 59
alphaM/beta2 Integrin/proMMP-9 -0.008 0.09 -10000 0 -0.13 145 145
PLAUR 0.03 0.014 -10000 0 0 89 89
HMGB1 0.038 0.015 0.082 1 -10000 0 1
alphaM/beta2 Integrin/Talin 0.038 0.071 -10000 0 -0.13 56 56
AGER 0.041 0.01 0.08 2 -10000 0 2
RAP1A 0.036 0.005 -10000 0 0 11 11
SELPLG 0.036 0.004 -10000 0 0 6 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.074 0.084 -10000 0 -0.12 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.017 0.018 -10000 0 0 267 267
CYR61 0.025 0.017 -10000 0 0 166 166
TLN1 0.029 0.015 -10000 0 0 102 102
Rap1/GTP 0.028 0.072 -10000 0 -0.22 17 17
RHOA 0.035 0.007 -10000 0 0 18 18
P-selectin oligomer 0.036 0.006 -10000 0 0 14 14
MYH2 0.025 0.071 0.18 3 -0.28 8 11
MST1R 0.035 0.007 -10000 0 0 21 21
leukocyte activation during inflammatory response 0.056 0.064 -10000 0 -0.1 54 54
APOB 0.036 0.006 -10000 0 0 14 14
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 0 108 108
JAM3 0.033 0.011 -10000 0 0 51 51
GP1BA 0.036 0.005 -10000 0 0 10 10
alphaM/beta2 Integrin/CTGF 0.021 0.085 -10000 0 -0.13 101 101
alphaM/beta2 Integrin 0.024 0.072 0.17 1 -0.24 15 16
JAM3 homodimer 0.033 0.011 -10000 0 0 51 51
ICAM2 0.034 0.009 -10000 0 0 31 31
ICAM1 0.031 0.014 -10000 0 0 84 84
phagocytosis triggered by activation of immune response cell surface activating receptor 0.025 0.075 0.17 1 -0.24 16 17
cell adhesion 0.048 0.068 -10000 0 -0.12 59 59
NFKB1 -0.002 0.078 0.21 20 -10000 0 20
THY1 0.031 0.013 -10000 0 0 79 79
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 0.038 0.1 -10000 0 -0.14 100 100
IL6 -0.015 0.039 -10000 0 -10000 0 0
ITGB2 0.033 0.019 0.077 1 -10000 0 1
elevation of cytosolic calcium ion concentration 0.03 0.085 -10000 0 -0.14 67 67
alphaM/beta2 Integrin/JAM2/JAM3 0.049 0.1 -10000 0 -0.15 91 91
JAM2 0.033 0.012 -10000 0 0 57 57
alphaM/beta2 Integrin/ICAM1 0.077 0.076 -10000 0 -0.12 45 45
alphaM/beta2 Integrin/uPA/Plg 0.041 0.08 -10000 0 -0.12 62 62
RhoA/GTP 0.029 0.073 0.17 11 -0.24 14 25
positive regulation of phagocytosis 0.017 0.1 0.21 1 -0.23 56 57
Ron/MSP 0.051 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.087 -10000 0 -0.14 67 67
alphaM/beta2 Integrin/uPAR 0.038 0.076 -10000 0 -0.13 63 63
PLAU 0.019 0.018 -10000 0 0 237 237
PLAT 0.027 0.016 -10000 0 0 128 128
actin filament polymerization 0.027 0.073 0.21 6 -0.27 8 14
MST1 0.035 0.008 -10000 0 0 25 25
alphaM/beta2 Integrin/lipoprotein(a) 0.062 0.068 -10000 0 -0.1 54 54
TNF 0.006 0.088 0.21 17 -10000 0 17
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.019 0.073 -10000 0 -0.14 65 65
fibrinolysis 0.039 0.079 -10000 0 -0.12 62 62
HCK 0.027 0.016 -10000 0 0 128 128
dendritic cell antigen processing and presentation 0.025 0.075 0.17 1 -0.24 16 17
VTN 0.036 0.004 -10000 0 0 6 6
alphaM/beta2 Integrin/CYR61 0.011 0.092 -10000 0 -0.14 120 120
LPA 0.034 0.009 -10000 0 0 33 33
LRP1 0.031 0.013 -10000 0 0 71 71
cell migration 0.001 0.11 0.15 36 -0.14 149 185
FN1 0.035 0.009 -10000 0 0 29 29
alphaM/beta2 Integrin/Thy1 0.031 0.084 -10000 0 -0.13 90 90
MPO 0.036 0.004 -10000 0 0 5 5
KNG1 0.035 0.008 -10000 0 0 28 28
RAP1/GDP 0.024 0.007 -10000 0 -0.11 1 1
ROCK1 0.025 0.073 0.19 2 -0.27 11 13
ELA2 0.034 0.009 -10000 0 0 32 32
PLG 0.034 0.01 -10000 0 0 37 37
CTGF 0.026 0.016 -10000 0 0 141 141
alphaM/beta2 Integrin/Hck 0.031 0.092 -10000 0 -0.18 72 72
ITGAM 0.042 0.01 0.08 2 -10000 0 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.072 -10000 0 -0.12 54 54
HP 0.027 0.016 -10000 0 0 136 136
leukocyte adhesion 0.023 0.12 -10000 0 -0.21 65 65
SELP 0.036 0.006 -10000 0 0 14 14
Glypican 2 network

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
MDK 0.03 0.014 -9999 0 0 92 92
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.007 0.05 -9999 0 -0.13 57 57
neuron projection morphogenesis 0.007 0.05 -9999 0 -0.13 57 57
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.069 0.057 -10000 0 -0.12 32 32
MAP4K1 0.035 0.008 -10000 0 0 26 26
MAP3K8 0.022 0.018 -10000 0 0 196 196
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.035 0.009 -10000 0 0 29 29
MAP3K1 0 0.054 0.13 1 -0.16 32 33
JUN -0.14 0.24 -10000 0 -0.51 138 138
MAP3K7 0 0.052 -10000 0 -0.17 30 30
GRAP2 0.034 0.009 -10000 0 0 35 35
CRK 0.035 0.008 -10000 0 0 23 23
MAP2K4 -0.016 0.071 -10000 0 -0.25 20 20
LAT 0.036 0.005 -10000 0 0 10 10
LCP2 0.031 0.013 -10000 0 0 77 77
MAPK8 -0.13 0.25 -10000 0 -0.54 138 138
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.01 0.056 -10000 0 -0.16 33 33
LAT/GRAP2/SLP76/HPK1/HIP-55 0.063 0.054 -10000 0 -0.11 32 32
IL23-mediated signaling events

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
CCL2 -0.064 0.6 0.74 36 -1 127 163
IL23A 0.089 0.37 0.78 20 -0.95 23 43
NF kappa B1 p50/RelA/I kappa B alpha 0.08 0.34 0.62 22 -0.84 25 47
positive regulation of T cell mediated cytotoxicity 0.088 0.4 0.77 36 -0.94 25 61
ITGA3 0.088 0.36 0.74 23 -0.91 21 44
IL17F 0.034 0.27 0.51 33 -0.59 28 61
IL12B 0.061 0.079 0.2 70 -0.075 2 72
STAT1 (dimer) 0.07 0.36 0.65 32 -0.91 25 57
CD4 0.071 0.42 0.75 29 -1.1 31 60
IL23 0.096 0.36 0.73 18 -0.93 22 40
IL23R 0.067 0.14 0.28 93 -0.15 11 104
IL1B 0.083 0.4 0.75 30 -1.1 26 56
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.097 0.36 0.7 30 -0.88 19 49
TYK2 0.043 0.059 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 0.059 0.15 53 -10000 0 53
PIK3CA 0.031 0.013 -10000 0 0 80 80
IL12Rbeta1/TYK2 0.055 0.074 0.19 38 -0.13 11 49
IL23R/JAK2 0.1 0.16 0.38 75 -0.19 16 91
positive regulation of chronic inflammatory response 0.088 0.4 0.77 36 -0.94 25 61
natural killer cell activation -0.005 0.011 -10000 0 -0.031 39 39
JAK2 0.056 0.079 0.2 68 -10000 0 68
PIK3R1 0.032 0.012 -10000 0 0 63 63
NFKB1 0.039 0.009 0.066 2 0 18 20
RELA 0.039 0.008 0.066 2 0 9 11
positive regulation of dendritic cell antigen processing and presentation 0.098 0.35 0.71 20 -0.89 22 42
ALOX12B 0.085 0.36 0.69 30 -0.87 21 51
CXCL1 0.095 0.37 0.73 39 -0.85 24 63
T cell proliferation 0.088 0.4 0.77 36 -0.94 25 61
NFKBIA 0.036 0.014 0.066 2 0 57 59
IL17A 0.058 0.24 0.46 51 -0.46 29 80
PI3K 0.046 0.35 0.64 22 -0.86 27 49
IFNG 0.019 0.033 0.098 28 -0.081 6 34
STAT3 (dimer) 0.048 0.35 0.61 27 -0.84 27 54
IL18R1 0.035 0.008 -10000 0 -0.032 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 0.094 0.27 0.55 51 -0.51 22 73
IL18/IL18R 0.062 0.035 -10000 0 -0.12 7 7
macrophage activation -0.002 0.016 0.038 1 -0.043 15 16
TNF 0.091 0.36 0.76 20 -0.95 18 38
STAT3/STAT4 0.068 0.36 0.62 25 -0.88 27 52
STAT4 (dimer) 0.07 0.36 0.63 30 -0.89 27 57
IL18 0.031 0.013 -10000 0 -0.03 1 1
IL19 0.098 0.36 0.75 19 -0.88 19 38
STAT5A (dimer) 0.083 0.37 0.64 35 -0.88 27 62
STAT1 0.034 0.01 -10000 0 0 40 40
SOCS3 0.036 0.004 -10000 0 0 7 7
CXCL9 0.099 0.37 0.73 33 -0.87 21 54
MPO 0.086 0.36 0.69 30 -0.86 22 52
positive regulation of humoral immune response 0.088 0.4 0.77 36 -0.94 25 61
IL23/IL23R/JAK2/TYK2 0.086 0.4 0.77 36 -0.98 24 60
IL6 0.15 0.37 0.74 44 -0.89 18 62
STAT5A 0.036 0.004 -10000 0 0 5 5
IL2 0.022 0.03 -10000 0 -0.036 102 102
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.031 39 39
CD3E 0.086 0.36 0.7 26 -0.89 19 45
keratinocyte proliferation 0.088 0.4 0.77 36 -0.94 25 61
NOS2 0.087 0.36 0.68 37 -0.82 27 64
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.012 -10000 0 0 63 63
LAT2 -0.016 0.094 0.16 1 -0.28 46 47
AP1 -0.058 0.18 -10000 0 -0.39 68 68
mol:PIP3 0.021 0.14 0.28 30 -0.3 34 64
IKBKB 0.011 0.094 0.2 31 -0.19 35 66
AKT1 -0.055 0.1 0.26 9 -0.29 33 42
IKBKG 0.01 0.093 0.2 31 -0.19 35 66
MS4A2 0.039 0.008 0.066 4 0 5 9
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.013 -10000 0 0 80 80
MAP3K1 -0.023 0.12 0.25 6 -0.31 49 55
mol:Ca2+ 0.023 0.12 0.24 34 -0.24 34 68
LYN 0.03 0.015 -10000 0 -0.034 6 6
CBLB -0.023 0.11 0.16 2 -0.28 66 68
SHC1 0.033 0.011 -10000 0 0 52 52
RasGAP/p62DOK 0.048 0.052 -10000 0 -0.12 36 36
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 0.071 0.26 13 -0.17 11 24
PTPN13 -0.036 0.19 -10000 0 -0.6 38 38
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 6 -0.32 34 40
SYK 0.03 0.015 -10000 0 -0.034 6 6
GRB2 0.036 0.007 -10000 0 0 17 17
LAT/PLCgamma1/GRB2/SLP76/GADs 0.009 0.11 0.21 3 -0.28 50 53
LAT -0.021 0.11 0.18 3 -0.28 65 68
PAK2 -0.022 0.13 0.23 6 -0.33 50 56
NFATC2 -0.013 0.013 -10000 0 -0.043 69 69
HRAS -0.02 0.14 0.22 4 -0.35 52 56
GAB2 0.033 0.011 -10000 0 0 47 47
PLA2G1B -0.005 0.19 -10000 0 -0.92 20 20
Fc epsilon R1 0.042 0.067 -10000 0 -0.11 72 72
Antigen/IgE/Fc epsilon R1 0.044 0.06 -10000 0 -0.093 72 72
mol:GDP -0.013 0.14 0.22 2 -0.36 48 50
JUN 0.034 0.01 -10000 0 0 40 40
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 0 158 158
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.015 0.12 -10000 0 -0.29 68 68
CHUK 0.012 0.091 0.2 33 -0.19 32 65
KLRG1 -0.018 0.099 0.14 2 -0.28 47 49
VAV1 -0.021 0.11 0.16 4 -0.28 59 63
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.024 0.11 0.16 2 -0.28 68 70
negative regulation of mast cell degranulation -0.021 0.092 0.12 1 -0.25 51 52
BTK -0.012 0.13 -10000 0 -0.38 44 44
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.027 0.11 -10000 0 -0.18 134 134
GAB2/PI3K/SHP2 -0.068 0.073 -10000 0 -0.2 80 80
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.003 0.072 -10000 0 -0.19 57 57
RAF1 -0.007 0.2 -10000 0 -0.97 20 20
Fc epsilon R1/FcgammaRIIB/SHIP 0.024 0.095 -10000 0 -0.13 129 129
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 0.082 -10000 0 -0.11 99 99
MAPK3 -0.004 0.19 -10000 0 -0.9 20 20
MAPK1 -0.013 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 -0.56 143 143
DUSP1 0.031 0.013 -10000 0 0 77 77
NF-kappa-B/RelA 0.018 0.066 0.14 27 -0.13 35 62
actin cytoskeleton reorganization -0.027 0.19 -10000 0 -0.6 36 36
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.01 0.15 0.23 8 -0.35 53 61
FER -0.022 0.12 0.16 3 -0.28 68 71
RELA 0.036 0.005 -10000 0 0 9 9
ITK 0.001 0.04 -10000 0 -0.26 4 4
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.007 0.14 0.25 8 -0.35 43 51
cytokine secretion 0.01 0.045 0.091 21 -0.094 37 58
SPHK1 -0.02 0.12 0.15 4 -0.28 66 70
PTK2 -0.03 0.2 -10000 0 -0.64 36 36
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.025 0.12 0.28 3 -0.28 48 51
EDG1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG 0.003 0.15 0.26 30 -0.33 42 72
MAP2K2 -0.005 0.2 -10000 0 -0.92 20 20
MAP2K1 -0.017 0.19 -10000 0 -0.92 20 20
MAP2K7 0.035 0.008 -10000 0 0 24 24
KLRG1/SHP2 0.001 0.097 0.2 8 -0.25 46 54
MAP2K4 0.025 0.14 -10000 0 -0.9 11 11
Fc epsilon R1/FcgammaRIIB 0.026 0.1 -10000 0 -0.14 129 129
mol:Choline -0.031 0.07 0.26 13 -0.17 11 24
SHC/Grb2/SOS1 0.011 0.13 0.2 1 -0.28 62 63
FYN 0.03 0.014 -10000 0 0 90 90
DOK1 0.036 0.002 -10000 0 0 2 2
PXN -0.03 0.19 -10000 0 -0.59 36 36
HCLS1 -0.025 0.13 0.16 6 -0.32 65 71
PRKCB 0.013 0.12 0.23 32 -0.24 38 70
FCGR2B 0.021 0.018 -10000 0 0 222 222
IGHE -0.001 0.004 0.023 1 -10000 0 1
KLRG1/SHIP -0.022 0.094 0.12 1 -0.26 51 52
LCP2 0.031 0.013 -10000 0 0 77 77
PLA2G4A -0.016 0.12 0.16 10 -0.3 59 69
RASA1 0.034 0.009 -10000 0 0 32 32
mol:Phosphatidic acid -0.031 0.07 0.26 13 -0.17 11 24
IKK complex 0.008 0.079 0.19 27 -0.16 20 47
WIPF1 0 0 -10000 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.031 0.014 -10000 0 0 83 83
PLK4 0.035 0.007 -10000 0 0 20 20
regulation of centriole replication -0.011 0.032 0.092 43 -9999 0 43
Osteopontin-mediated 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
IKK alpha homodimer 0.002 0.077 0.2 2 -0.19 36 38
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.12 0.25 1 -0.32 43 44
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.081 -10000 0 -0.16 74 74
AP1 -0.011 0.14 0.28 6 -0.28 75 81
ILK -0.031 0.072 0.2 2 -0.23 33 35
bone resorption -0.039 0.083 0.18 7 -0.24 35 42
PTK2B 0.035 0.006 -10000 0 0 16 16
PYK2/p130Cas 0.045 0.09 -10000 0 -0.16 59 59
ITGAV 0.031 0.026 -10000 0 -0.056 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.02 0.068 -10000 0 -0.14 73 73
alphaV/beta3 Integrin/Osteopontin 0.05 0.092 -10000 0 -0.16 72 72
MAP3K1 -0.03 0.063 0.22 1 -0.2 27 28
JUN 0.034 0.01 -10000 0 0 40 40
MAPK3 -0.031 0.085 0.18 6 -0.24 40 46
MAPK1 -0.029 0.086 0.17 12 -0.25 38 50
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.027 0.059 0.23 1 -0.2 26 27
ITGB3 0.032 0.026 -10000 0 -0.055 39 39
NFKBIA -0.038 0.11 0.18 5 -0.32 44 49
FOS 0.026 0.017 -10000 0 0 158 158
CD44 0.029 0.015 -10000 0 0 110 110
CHUK 0.025 0.017 -10000 0 0 163 163
PLAU -0.071 0.25 -10000 0 -0.97 32 32
NF kappa B1 p50/RelA -0.001 0.12 -10000 0 -0.34 36 36
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 9 9
alphaV beta3 Integrin 0.04 0.058 -10000 0 -0.13 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.032 0.065 0.19 2 -0.23 29 31
VAV3 -0.024 0.072 0.18 3 -0.22 33 36
MAP3K14 -0.028 0.074 0.17 5 -0.23 24 29
ROCK2 0.035 0.007 -10000 0 0 21 21
SPP1 0.03 0.026 -10000 0 -0.058 29 29
RAC1 0.024 0.017 -10000 0 0 173 173
Rac1/GTP -0.021 0.07 0.17 1 -0.22 28 29
MMP2 -0.061 0.12 -10000 0 -0.32 61 61
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.044 0.042 -10000 0 -0.14 24 24
AKT1 -0.017 0.17 0.27 20 -0.41 48 68
PTK2B -0.001 0.11 0.2 57 -0.3 19 76
VEGFR2 homodimer/Frs2 0.026 0.082 0.18 5 -0.31 17 22
CAV1 0.016 0.018 -10000 0 0 290 290
CALM1 0.033 0.011 -10000 0 0 54 54
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.022 0.085 0.18 2 -0.27 22 24
endothelial cell proliferation 0.011 0.14 0.28 30 -0.38 29 59
mol:Ca2+ 0.006 0.13 0.21 88 -0.24 47 135
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.017 0.087 0.2 2 -0.27 23 25
RP11-342D11.1 -0.005 0.1 0.17 69 -0.23 46 115
CDH5 0.03 0.014 -10000 0 0 92 92
VEGFA homodimer 0.036 0.034 -10000 0 -0.098 13 13
SHC1 0.033 0.011 -10000 0 0 52 52
SHC2 0.032 0.012 -10000 0 0 64 64
HRAS/GDP 0.005 0.09 -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 3 -0.37 16 19
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.022 0.086 0.18 2 -0.28 22 24
VEGFR1 homodimer 0.034 0.009 -10000 0 0 33 33
SHC/GRB2/SOS1 0.036 0.1 -10000 0 -0.23 47 47
GRB10 -0.011 0.11 0.2 39 -0.32 34 73
PTPN11 0.036 0.005 -10000 0 0 11 11
GRB2 0.035 0.007 -10000 0 0 17 17
PAK1 0.036 0.006 -10000 0 0 15 15
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.037 0.12 0.22 2 -0.27 38 40
HRAS 0.034 0.009 -10000 0 0 32 32
VEGF/Rho/ROCK1/Integrin Complex 0.012 0.1 0.18 5 -0.32 30 35
HIF1A 0.033 0.01 -10000 0 0 44 44
FRS2 0.034 0.009 -10000 0 0 30 30
oxygen and reactive oxygen species metabolic process 0.016 0.085 0.19 2 -0.27 23 25
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.036 0.006 -10000 0 0 12 12
Nck/Pak 0.049 0.023 -10000 0 -0.14 5 5
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.01 0.1 0.18 2 -0.28 33 35
mol:GDP 0.017 0.093 -10000 0 -0.23 47 47
mol:NADP 0.032 0.12 0.32 19 -0.34 14 33
eNOS/Hsp90 0.029 0.12 0.3 19 -0.32 15 34
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.006 0.13 0.22 88 -0.24 47 135
HIF1A/ARNT 0.046 0.031 -10000 0 -0.14 11 11
SHB 0.033 0.011 -10000 0 0 51 51
VEGFA -0.003 0.013 -10000 0 -0.039 52 52
VEGFC 0.033 0.011 -10000 0 0 51 51
FAK1/Vinculin 0.012 0.12 0.26 13 -0.44 19 32
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 18 18
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.037 0.1 0.2 5 -0.27 27 32
PTPN6 0.033 0.011 -10000 0 0 51 51
EPAS1 0.032 0.062 -10000 0 -0.22 17 17
mol:L-citrulline 0.032 0.12 0.32 19 -0.34 14 33
ITGAV 0.034 0.009 -10000 0 0 31 31
PIK3CA 0.031 0.013 -10000 0 0 80 80
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.039 0.094 0.2 5 -0.26 25 30
VEGFR2 homodimer/VEGFA homodimer 0.012 0.097 -10000 0 -0.23 56 56
VEGFR2/3 heterodimer 0.026 0.084 0.18 5 -0.31 18 23
VEGFB 0.036 0.005 -10000 0 0 8 8
MAPK11 0.009 0.13 0.27 42 -0.33 21 63
VEGFR2 homodimer -0.006 0.081 0.17 4 -0.38 15 19
FLT1 0.034 0.009 -10000 0 0 33 33
NEDD4 0.029 0.033 0.088 9 -0.056 54 63
MAPK3 0.012 0.12 0.27 44 -0.3 20 64
MAPK1 0.01 0.13 0.27 45 -0.28 23 68
VEGFA145/NRP2 0.023 0.022 -10000 0 -0.045 7 7
VEGFR1/2 heterodimer 0.024 0.083 0.18 4 -0.31 18 22
KDR -0.006 0.082 0.17 4 -0.38 15 19
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.098 0.2 12 -0.23 47 59
SRC 0.036 0.006 -10000 0 0 14 14
platelet activating factor biosynthetic process 0.012 0.13 0.26 47 -0.3 21 68
PI3K -0.001 0.14 0.24 28 -0.34 44 72
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.021 0.086 0.18 2 -0.27 22 24
FES 0.007 0.13 0.22 89 -0.31 21 110
GAB1 0.012 0.12 0.24 17 -0.36 26 43
VEGFR2 homodimer/VEGFA homodimer/Src 0.021 0.086 0.17 1 -0.28 22 23
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 5 5
eNOS/Caveolin-1 0.009 0.095 0.29 4 -0.37 12 16
VEGFR2 homodimer/VEGFA homodimer/Yes 0.018 0.09 0.18 1 -0.3 22 23
PI3K/GAB1 -0.003 0.16 0.26 25 -0.39 48 73
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.06 0.097 0.23 3 -0.25 21 24
PRKACA 0.035 0.008 -10000 0 0 25 25
VEGFR2/3 heterodimer/VEGFC homodimer 0.038 0.08 0.2 1 -0.28 16 17
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.007 0.13 0.22 86 -0.32 20 106
actin cytoskeleton reorganization 0.022 0.086 0.18 2 -0.27 22 24
PTK2 0.009 0.13 0.25 22 -0.44 21 43
EDG1 0 0.14 0.22 78 -0.34 30 108
mol:DAG 0.006 0.13 0.22 88 -0.24 47 135
CaM/Ca2+ 0.02 0.12 0.22 50 -0.23 49 99
MAP2K3 0 0.12 0.22 65 -0.31 19 84
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.046 0.14 0.23 102 -0.3 43 145
PLCG1 0.006 0.13 0.22 88 -0.24 47 135
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.035 0.091 0.2 4 -0.27 21 25
IQGAP1 0.033 0.011 -10000 0 0 51 51
YES1 0.034 0.01 -10000 0 0 41 41
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.021 0.089 0.18 2 -0.28 24 26
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.019 0.086 0.18 2 -0.27 22 24
cell migration 0.007 0.14 0.26 22 -0.38 34 56
mol:PI-3-4-5-P3 0.001 0.14 0.24 28 -0.32 44 72
FYN 0.03 0.014 -10000 0 0 90 90
VEGFB/NRP1 0.006 0.12 0.2 88 -0.31 19 107
mol:NO 0.032 0.12 0.32 19 -0.34 14 33
PXN 0.036 0.004 -10000 0 0 7 7
HRAS/GTP -0.045 0.069 -10000 0 -0.24 46 46
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.006 0.097 -10000 0 -0.3 43 43
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.036 0.003 -10000 0 0 4 4
NOS3 0.031 0.13 0.33 17 -0.38 14 31
VEGFR2 homodimer/VEGFA homodimer/Sck 0.015 0.093 -10000 0 -0.27 29 29
RAC1 0.024 0.017 -10000 0 0 173 173
PRKCA 0 0.12 0.22 69 -0.29 23 92
PRKCB 0.004 0.12 0.22 67 -0.22 47 114
VCL 0.025 0.017 -10000 0 0 154 154
VEGFA165/NRP1 -0.025 0.082 0.12 39 -0.23 47 86
VEGFR1/2 heterodimer/VEGFA homodimer 0.02 0.086 0.18 2 -0.28 21 23
VEGFA165/NRP2 0.023 0.022 -10000 0 -0.045 7 7
MAPKKK cascade -0.031 0.091 0.17 8 -0.32 33 41
NRP2 0.036 0.005 -10000 0 0 8 8
VEGFC homodimer 0.033 0.011 -10000 0 0 51 51
NCK1 0.035 0.008 -10000 0 0 27 27
ROCK1 0.036 0.006 -10000 0 0 15 15
FAK1/Paxillin 0.027 0.13 0.26 17 -0.42 21 38
MAP3K13 0.007 0.13 0.22 87 -0.31 21 108
PDPK1 -0.017 0.13 0.22 38 -0.33 34 72
Ephrin B reverse 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
EFNB2 0.028 0.015 -10000 0 0 116 116
EPHB2 0.034 0.011 -10000 0 0 42 42
EFNB1 -0.017 0.02 0.084 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.047 0.053 -10000 0 -0.14 8 8
Ephrin B2/EPHB1-2 0.031 0.056 -10000 0 -0.1 52 52
neuron projection morphogenesis 0.032 0.041 -10000 0 -0.14 8 8
Ephrin B1/EPHB1-2/Tiam1 0.057 0.049 -10000 0 -0.11 16 16
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 -10000 0 -0.52 52 52
YES1 -0.055 0.24 -10000 0 -0.75 52 52
Ephrin B1/EPHB1-2/NCK2 0.061 0.044 -10000 0 -0.1 19 19
PI3K -0.02 0.19 -10000 0 -0.56 51 51
mol:GDP 0.055 0.048 -10000 0 -0.11 20 20
ITGA2B 0.036 0.004 -10000 0 0 5 5
endothelial cell proliferation 0.015 0.047 -10000 0 -0.11 46 46
FYN -0.067 0.24 -10000 0 -0.77 52 52
MAP3K7 -0.051 0.16 0.22 1 -0.54 51 52
FGR -0.051 0.23 -10000 0 -0.73 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 0.008 -10000 0 0 23 23
cell adhesion -0.032 0.17 -10000 0 -0.53 51 51
LYN -0.062 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 -0.048 0.18 -10000 0 -0.57 51 51
SRC -0.05 0.23 -10000 0 -0.72 52 52
ITGB3 0.036 0.003 -10000 0 0 4 4
EPHB1 0.03 0.015 -10000 0 0 95 95
EPHB4 0.025 0.017 -10000 0 0 166 166
RAC1 0.024 0.017 -10000 0 0 173 173
Ephrin B2/EPHB4 0.016 0.047 -10000 0 -0.11 46 46
alphaIIb/beta3 Integrin 0.054 0.006 -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 -0.059 0.043 0.1 20 -10000 0 20
MAPK8 -0.056 0.15 -10000 0 -0.49 52 52
Ephrin B1/EPHB1-2/RGS3 0.066 0.035 -10000 0 -0.11 6 6
endothelial cell migration 0.01 0.17 0.19 127 -0.45 43 170
NCK2 0.035 0.007 -10000 0 0 17 17
PTPN13 0.034 0.013 -10000 0 0 60 60
regulation of focal adhesion formation -0.059 0.043 0.1 20 -10000 0 20
chemotaxis -0.064 0.034 0.11 6 -10000 0 6
PIK3CA 0.031 0.013 -10000 0 0 80 80
Rac1/GTP 0.04 0.047 -10000 0 -0.14 8 8
angiogenesis -0.047 0.18 -10000 0 -0.57 51 51
LCK -0.049 0.23 -10000 0 -0.72 51 51
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.001 0.047 -10000 0 -10000 0 0
PLK1 -0.059 0.2 -10000 0 -0.68 19 19
CDKN1B -0.11 0.21 0.4 4 -0.37 136 140
FOXO3 -0.065 0.22 0.33 5 -0.49 81 86
KAT2B -0.001 0.021 0.047 17 -0.041 76 93
FOXO1/SIRT1 0.014 0.048 -10000 0 -0.22 8 8
CAT -0.075 0.26 -10000 0 -1.1 19 19
CTNNB1 0.036 0.006 -10000 0 0 15 15
AKT1 0.021 0.042 -10000 0 -0.062 62 62
FOXO1 0.004 0.051 0.22 1 -0.24 8 9
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 0.2 0.26 15 -0.44 62 77
response to oxidative stress 0 0.023 0.052 13 -0.047 42 55
FOXO3A/SIRT1 -0.06 0.21 -10000 0 -0.47 85 85
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 0.02 0.054 0.2 1 -0.23 8 9
mol:GDP 0 0.023 0.052 13 -0.047 42 55
RAN 0.034 0.011 -10000 0 -0.015 20 20
GADD45A -0.15 0.33 0.47 1 -0.86 69 70
YWHAQ 0.036 0.005 -10000 0 0 9 9
FOXO1/14-3-3 family 0.005 0.15 -10000 0 -0.52 21 21
MST1 0.022 0.043 0.11 1 -0.06 86 87
CSNK1D 0.035 0.007 -10000 0 0 20 20
CSNK1E 0.032 0.012 -10000 0 0 67 67
FOXO4/14-3-3 family -0.003 0.15 -10000 0 -0.55 21 21
YWHAB 0.035 0.008 -10000 0 0 24 24
MAPK8 0.024 0.076 0.18 76 -0.14 12 88
MAPK9 0.052 0.097 0.19 151 -0.14 17 168
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 0.39 6 -0.75 101 107
RBL2 -0.072 0.28 -10000 0 -0.93 36 36
RAL/GDP 0.018 0.049 -10000 0 -0.14 20 20
CHUK 0.012 0.038 -10000 0 -0.059 73 73
Ran/GTP 0.019 0.025 -10000 0 -0.12 6 6
CSNK1G2 0.034 0.009 -10000 0 0 30 30
RAL/GTP 0.017 0.051 0.14 2 -0.12 22 24
CSNK1G1 0.036 0.006 -10000 0 0 14 14
FASLG 0.022 0.041 -10000 0 -0.59 1 1
SKP2 0.035 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 93 94
CCNB1 -0.16 0.42 0.49 1 -1.1 83 84
FOXO1-3a-4/beta catenin -0.039 0.21 0.37 10 -0.4 78 88
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.054 0.2 1 -0.23 8 9
CSNK1A1 0.036 0.006 -10000 0 0 14 14
SGK1 -0.001 0.021 0.047 17 -0.041 76 93
CSNK1G3 0.036 0.006 -10000 0 0 13 13
Ran/GTP/Exportin 1 0.039 0.036 -10000 0 -0.14 7 7
ZFAND5 -0.019 0.16 0.24 15 -0.36 60 75
SFN 0.031 0.013 -10000 0 0 78 78
CDK2 0.036 0.012 -10000 0 -0.031 3 3
FOXO3A/14-3-3 -0.012 0.16 -10000 0 -0.48 29 29
CREBBP 0.038 0.008 -10000 0 -0.031 3 3
FBXO32 -0.059 0.2 0.32 1 -0.44 81 82
BCL6 -0.093 0.32 -10000 0 -1 46 46
RALB 0.033 0.013 -10000 0 -0.015 32 32
RALA 0.023 0.018 -10000 0 -0.001 184 184
YWHAH 0.031 0.013 -10000 0 0 73 73
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.032 0.17 -10000 0 -0.46 66 66
HDAC1 0.027 0.034 0.093 16 -0.039 84 100
AES 0.033 0.013 0.069 9 -0.004 46 55
FBXW11 0.035 0.008 -10000 0 0 25 25
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -10000 0 0
TLE1 0.034 0.013 0.068 8 -0.007 36 44
AP1 -0.01 0.073 -10000 0 -0.2 55 55
NCSTN 0.035 0.008 -10000 0 0 28 28
ADAM10 0.033 0.012 -10000 0 0 56 56
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.011 0.12 -10000 0 -0.45 14 14
NICD/RBPSUH -0.035 0.17 -10000 0 -0.46 66 66
WIF1 0.028 0.015 -10000 0 0 112 112
NOTCH1 -0.031 0.18 -10000 0 -0.49 64 64
PSENEN 0.035 0.008 -10000 0 0 28 28
KREMEN2 0.036 0.004 -10000 0 0 7 7
DKK1 0.017 0.018 -10000 0 0 271 271
beta catenin/beta TrCP1 0.062 0.091 0.23 18 -0.32 7 25
APH1B 0.035 0.006 -10000 0 0 16 16
APH1A 0.036 0.005 -10000 0 0 11 11
AXIN1 0.013 0.065 0.25 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.012 0.072 0.17 49 -0.18 19 68
PSEN1 0.033 0.011 -10000 0 0 46 46
FOS 0.025 0.017 -10000 0 0 158 158
JUN 0.034 0.01 -10000 0 0 40 40
MAP3K7 0.032 0.018 0.063 7 -0.011 61 68
CTNNB1 0.048 0.088 0.22 24 -0.32 5 29
MAPK3 0.036 0.004 -10000 0 0 6 6
DKK2/LRP6/Kremen 2 0.064 0.027 -10000 0 -0.12 1 1
HNF1A 0 0.006 0.031 10 -10000 0 10
CTBP1 0.034 0.013 0.07 7 -0.007 34 41
MYC -0.079 0.37 -10000 0 -1.2 50 50
NKD1 0 0.003 -10000 0 -10000 0 0
FZD1 0.024 0.017 -10000 0 0 173 173
NOTCH1 precursor/Deltex homolog 1 -0.035 0.17 -10000 0 -0.46 66 66
apoptosis -0.01 0.073 -10000 0 -0.2 56 56
Delta 1/NOTCHprecursor -0.035 0.17 -10000 0 -0.46 66 66
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.025 0.036 -10000 0 -10000 0 0
Gamma Secretase 0.08 0.07 -10000 0 -0.15 28 28
APC -0.023 0.17 0.23 4 -0.58 34 38
DVL1 0.019 0.096 -10000 0 -0.42 17 17
CSNK2A1 0.034 0.009 -10000 0 0 31 31
MAP3K7IP1 0.032 0.018 0.063 8 -0.012 55 63
DKK1/LRP6/Kremen 2 0.031 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 40 40
CSNK1A1 0.036 0.006 -10000 0 0 14 14
NLK 0.011 0.051 0.13 1 -0.21 20 21
CCND1 -0.047 0.34 -10000 0 -1.2 41 41
WNT1 0.035 0.006 -10000 0 0 16 16
Axin1/APC/beta catenin 0.012 0.13 0.24 1 -0.42 30 31
DKK2 0.034 0.009 -10000 0 0 31 31
NOTCH1 precursor/DVL1 -0.009 0.19 -10000 0 -0.47 63 63
GSK3B 0.034 0.01 -10000 0 0 40 40
FRAT1 0.025 0.017 -10000 0 0 161 161
NOTCH/Deltex homolog 1 -0.032 0.17 -10000 0 -0.46 66 66
PPP2R5D 0.027 0.037 -10000 0 -0.25 4 4
MAPK1 0.033 0.01 -10000 0 0 45 45
WNT1/LRP6/FZD1 0.057 0.046 -10000 0 -10000 0 0
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.032 0.021 0.07 5 -0.019 62 67
IL2 signaling events mediated by PI3K

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
BCL2L1 0.004 0.093 -10000 0 -0.53 1 1
UGCG -0.027 0.19 -10000 0 -0.74 31 31
AKT1/mTOR/p70S6K/Hsp90/TERT -0.006 0.13 0.26 9 -0.31 55 64
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.026 0.19 -10000 0 -0.72 31 31
mol:DAG -0.007 0.032 0.17 15 -10000 0 15
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.18 0.3 5 -0.42 62 67
FRAP1 -0.034 0.2 0.3 9 -0.47 62 71
FOXO3 -0.033 0.2 0.3 8 -0.46 64 72
AKT1 -0.039 0.21 0.31 7 -0.5 64 71
GAB2 0.03 0.019 -10000 0 -0.012 80 80
SMPD1 0.003 0.09 -10000 0 -0.49 14 14
SGMS1 -0.003 0.034 0.076 11 -0.072 65 76
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 0.045 0.083 6 -0.13 73 79
CALM1 0.033 0.011 -10000 0 0 54 54
cell proliferation -0.032 0.19 0.27 12 -0.39 69 81
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.077 -10000 0 -0.16 73 73
RPS6KB1 0.029 0.027 -10000 0 -10000 0 0
mol:sphingomyelin -0.007 0.032 0.17 15 -10000 0 15
natural killer cell activation 0 0.003 0.007 25 -0.01 44 69
JAK3 0.034 0.016 -10000 0 -0.028 22 22
PIK3R1 0.031 0.019 -10000 0 -0.029 24 24
JAK1 0.032 0.019 -10000 0 -0.028 29 29
NFKB1 0.035 0.007 -10000 0 0 18 18
MYC -0.065 0.29 0.45 7 -0.83 56 63
MYB 0.034 0.041 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.16 0.26 7 -0.38 54 61
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.16 0.27 8 -0.37 54 62
Rac1/GDP 0.004 0.05 0.1 14 -0.13 46 60
T cell proliferation -0.023 0.15 0.26 8 -0.35 53 61
SHC1 0.029 0.019 -10000 0 -0.011 85 85
RAC1 0.024 0.017 -10000 0 0 173 173
positive regulation of cyclin-dependent protein kinase activity 0.005 0.012 0.057 24 -10000 0 24
PRKCZ -0.025 0.15 0.26 8 -0.36 54 62
NF kappa B1 p50/RelA -0.011 0.19 0.31 8 -0.42 62 70
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.094 -10000 0 -0.32 18 18
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 9 9
IL2RA 0.021 0.021 -10000 0 -0.004 198 198
IL2RB 0.032 0.018 -10000 0 -0.028 22 22
TERT 0.036 0.006 -10000 0 0 14 14
E2F1 0.036 0.031 -10000 0 -10000 0 0
SOS1 0 0.003 0.008 27 -0.009 44 71
RPS6 0.031 0.013 -10000 0 0 81 81
mol:cAMP -0.003 0.007 -10000 0 -0.031 25 25
PTPN11 0.032 0.018 -10000 0 -0.023 47 47
IL2RG 0.034 0.017 -10000 0 -0.03 24 24
actin cytoskeleton organization -0.023 0.15 0.26 8 -0.35 53 61
GRB2 0.033 0.016 -10000 0 -0.017 42 42
IL2 0.035 0.016 -10000 0 -0.03 24 24
PIK3CA 0.03 0.02 -10000 0 -0.029 26 26
Rac1/GTP 0.026 0.064 0.16 5 -0.12 46 51
LCK 0.034 0.017 -10000 0 -0.03 25 25
BCL2 -0.02 0.16 0.31 2 -0.43 37 39
FAS signaling pathway (CD95)

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
SPTAN1 -0.017 0.056 0.22 8 -0.21 21 29
RFC1 -0.02 0.048 0.18 2 -0.21 25 27
PRKDC -0.016 0.055 0.19 7 -0.21 23 30
RIPK1 0.027 0.021 -10000 0 -0.023 73 73
CASP7 -0.16 0.28 -10000 0 -0.57 162 162
FASLG/FAS/FADD/FAF1 -0.012 0.083 0.16 27 -0.17 48 75
MAP2K4 -0.043 0.14 0.21 2 -0.31 42 44
mol:ceramide 0.004 0.089 0.18 5 -0.23 19 24
GSN -0.008 0.058 0.19 11 -0.22 19 30
FASLG/FAS/FADD/FAF1/Caspase 8 -0.011 0.093 0.18 12 -0.23 28 40
FAS 0.021 0.02 -10000 0 0 238 238
BID -0.031 0.033 -10000 0 -0.13 21 21
MAP3K1 -0.1 0.19 -10000 0 -0.36 166 166
MAP3K7 0.035 0.01 -10000 0 0 41 41
RB1 -0.017 0.045 0.23 1 -0.21 23 24
CFLAR 0.029 0.021 -10000 0 -0.027 59 59
HGF/MET 0.034 0.049 -10000 0 -0.12 22 22
ARHGDIB -0.016 0.055 0.22 6 -0.22 21 27
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 0.1 -10000 0 -0.63 10 10
MAPK8 -0.033 0.13 0.24 1 -0.34 22 23
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 0.052 -10000 0 -0.12 27 27
CFLAR/RIP1 0.048 0.02 -10000 0 -0.064 9 9
FAIM3 0.033 0.009 -10000 0 0 36 36
FAF1 0.038 0.012 -10000 0 -10000 0 0
PARP1 -0.019 0.048 0.22 1 -0.21 26 27
DFFB -0.016 0.046 0.22 2 -0.21 23 25
CHUK 0.015 0.096 -10000 0 -0.6 10 10
FASLG 0.039 0.008 -10000 0 -10000 0 0
FAS/FADD 0.021 0.053 -10000 0 -0.14 34 34
HGF 0.024 0.017 -10000 0 0 177 177
LMNA -0.02 0.049 0.2 5 -0.19 25 30
CASP6 -0.017 0.047 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 0.084 3 -10000 0 3
IL6 0.02 0.13 -10000 0 -0.61 6 6
MET 0.023 0.018 -10000 0 0 191 191
ICAD/CAD -0.021 0.049 0.25 4 -0.2 23 27
FASLG/FAS/FADD/FAF1/Caspase 10 0.004 0.09 0.18 5 -0.24 19 24
activation of caspase activity by cytochrome c -0.031 0.033 -10000 0 -0.13 16 16
PAK2 -0.015 0.049 0.14 2 -0.2 25 27
BCL2 0.035 0.007 -10000 0 0 20 20
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.003 0.12 0.26 3 -0.32 29 32
IKBKB 0.017 0.078 0.26 4 -0.25 10 14
AKT1 0.001 0.083 0.22 27 -0.18 13 40
IKBKG 0.009 0.07 0.23 1 -0.24 11 12
CALM1 -0.029 0.12 0.21 3 -0.35 46 49
PIK3CA 0.031 0.013 -10000 0 0 80 80
MAP3K1 0.027 0.13 0.29 7 -0.36 23 30
MAP3K7 0.034 0.01 -10000 0 0 41 41
mol:Ca2+ -0.027 0.13 0.22 4 -0.37 45 49
DOK1 0.036 0.002 -10000 0 0 2 2
AP-1 -0.009 0.092 0.19 11 -0.22 38 49
LYN 0.031 0.013 -10000 0 0 74 74
BLNK 0.019 0.018 -10000 0 0 243 243
SHC1 0.033 0.011 -10000 0 0 52 52
BCR complex 0.05 0.015 -10000 0 -10000 0 0
CD22 -0.016 0.092 -10000 0 -0.29 35 35
CAMK2G -0.018 0.12 0.21 4 -0.34 43 47
CSNK2A1 0.034 0.009 -10000 0 0 31 31
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.036 0.054 -10000 0 -0.2 24 24
GO:0007205 -0.028 0.14 0.22 4 -0.38 45 49
SYK 0.031 0.013 -10000 0 0 76 76
ELK1 -0.033 0.13 0.21 4 -0.36 45 49
NFATC1 -0.017 0.092 0.25 4 -0.27 28 32
B-cell antigen/BCR complex 0.05 0.015 -10000 0 -10000 0 0
PAG1/CSK 0.023 0.022 -10000 0 -0.13 10 10
NFKBIB 0.02 0.042 0.14 1 -0.13 19 20
HRAS -0.028 0.12 0.18 7 -0.32 47 54
NFKBIA 0.02 0.039 0.14 1 -0.12 16 17
NF-kappa-B/RelA/I kappa B beta 0.025 0.038 0.14 1 -0.1 19 20
RasGAP/Csk 0.045 0.096 -10000 0 -0.12 113 113
mol:GDP -0.026 0.13 0.22 4 -0.36 45 49
PTEN 0.026 0.017 -10000 0 0 148 148
CD79B 0.036 0.005 -10000 0 0 10 10
NF-kappa-B/RelA/I kappa B alpha 0.025 0.036 0.14 1 -0.099 14 15
GRB2 0.035 0.007 -10000 0 0 17 17
PI3K/BCAP/CD19 -0.038 0.16 0.38 1 -0.43 45 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 -0.026 0.13 0.23 4 -0.38 44 48
CSK 0.035 0.007 -10000 0 0 21 21
FOS -0.031 0.13 0.2 7 -0.35 46 53
CHUK -0.061 0.14 0.23 1 -0.26 124 125
IBTK 0.034 0.009 -10000 0 0 30 30
CARD11/BCL10/MALT1/TAK1 -0.003 0.13 0.23 1 -0.34 39 40
PTPN6 -0.021 0.094 0.18 7 -0.31 32 39
RELA 0.036 0.005 -10000 0 0 9 9
BCL2A1 0.017 0.034 0.095 12 -0.089 21 33
VAV2 -0.014 0.1 -10000 0 -0.32 31 31
ubiquitin-dependent protein catabolic process 0.021 0.042 0.14 1 -0.13 19 20
BTK 0.019 0.012 -10000 0 -10000 0 0
CD19 -0.016 0.093 -10000 0 -0.29 36 36
MAP4K1 0.035 0.008 -10000 0 0 26 26
CD72 0.033 0.011 -10000 0 0 55 55
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.12 0.26 8 -0.31 23 31
SH3BP5 0.033 0.011 -10000 0 0 51 51
PIK3AP1 -0.023 0.14 0.23 4 -0.4 42 46
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.036 0.18 -10000 0 -0.49 55 55
RAF1 -0.033 0.11 0.19 5 -0.32 42 47
RasGAP/p62DOK/SHIP 0.037 0.084 -10000 0 -0.11 112 112
CD79A 0.034 0.009 -10000 0 0 34 34
re-entry into mitotic cell cycle -0.01 0.092 0.18 11 -0.22 38 49
RASA1 0.034 0.009 -10000 0 0 32 32
MAPK3 -0.038 0.096 0.18 3 -0.3 37 40
MAPK1 -0.037 0.099 0.19 4 -0.3 39 43
CD72/SHP1 -0.002 0.1 0.26 7 -0.29 36 43
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 0.022 0.12 0.28 7 -0.32 22 29
actin cytoskeleton organization 0.034 0.11 0.26 15 -0.3 18 33
NF-kappa-B/RelA 0.042 0.087 0.26 1 -0.24 23 24
Calcineurin -0.009 0.13 0.24 2 -0.32 43 45
PI3K -0.031 0.085 -10000 0 -0.27 34 34
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.14 0.24 4 -0.41 40 44
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.015 0.15 -10000 0 -0.62 8 8
DAPP1 -0.004 0.15 -10000 0 -0.7 8 8
cytokine secretion -0.015 0.088 0.25 4 -0.25 28 32
mol:DAG -0.026 0.13 0.23 4 -0.38 44 48
PLCG2 0.032 0.012 -10000 0 0 63 63
MAP2K1 -0.036 0.1 0.18 4 -0.32 39 43
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.074 -10000 0 -0.12 96 96
mol:PI-3-4-5-P3 -0.018 0.07 0.18 18 -0.22 15 33
ETS1 -0.029 0.11 0.21 5 -0.33 38 43
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.091 -10000 0 -0.15 60 60
B-cell antigen/BCR complex/LYN -0.011 0.098 -10000 0 -0.3 38 38
MALT1 0.034 0.009 -10000 0 0 32 32
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.031 0.12 0.27 13 -0.31 18 31
B-cell antigen/BCR complex/LYN/SYK 0.023 0.11 -10000 0 -0.28 33 33
CARD11 -0.027 0.13 0.22 4 -0.36 45 49
FCGR2B 0.021 0.018 -10000 0 0 222 222
PPP3CA 0.034 0.01 -10000 0 0 38 38
BCL10 0.035 0.007 -10000 0 0 20 20
IKK complex 0.003 0.043 0.12 5 -0.12 9 14
PTPRC 0.029 0.015 -10000 0 0 110 110
PDPK1 -0.015 0.056 0.16 17 -0.17 9 26
PPP3CB 0.025 0.017 -10000 0 0 157 157
PPP3CC 0.036 0.006 -10000 0 0 13 13
POU2F2 0.015 0.03 0.09 2 -0.08 23 25
S1P3 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
PDGFRB 0.035 0.008 -10000 0 0 27 27
mol:S1P 0.001 0.001 0.017 4 -10000 0 4
S1P1/S1P/Gi -0.018 0.11 -10000 0 -0.23 78 78
GNAO1 0.031 0.014 -10000 0 0 87 87
S1P/S1P3/G12/G13 0.024 0.038 -10000 0 -0.1 28 28
AKT1 -0.012 0.16 -10000 0 -0.5 44 44
AKT3 0.01 0.077 -10000 0 -0.37 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.008 -10000 0 0 27 27
GNAI2 0.034 0.011 -10000 0 -10000 0 0
GNAI3 0.036 0.007 -10000 0 0 15 15
GNAI1 0.018 0.019 -10000 0 0 263 263
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 0.033 0.01 -10000 0 0 45 45
mol:Ca2+ -0.001 0.1 0.19 1 -0.26 47 48
MAPK3 -0.008 0.098 0.17 1 -0.24 52 53
MAPK1 -0.003 0.094 0.17 1 -0.24 42 43
JAK2 -0.011 0.11 0.19 5 -0.31 43 48
CXCR4 -0.006 0.099 0.14 4 -0.25 49 53
FLT1 0.036 0.01 0.069 1 -10000 0 1
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
SRC -0.007 0.098 0.17 1 -0.25 48 49
S1P/S1P3/Gi 0 0.1 0.19 1 -0.26 46 47
RAC1 0.024 0.017 -10000 0 0 173 173
RhoA/GTP 0.012 0.11 0.18 1 -0.27 40 41
VEGFA 0.002 0.002 0.032 3 -10000 0 3
S1P/S1P2/Gi -0.004 0.099 0.16 1 -0.2 78 79
VEGFR1 homodimer/VEGFA homodimer 0.029 0.01 0.11 3 -10000 0 3
RHOA 0.035 0.007 -10000 0 0 18 18
S1P/S1P3/Gq 0.015 0.04 -10000 0 -0.15 26 26
GNAQ 0.034 0.009 -10000 0 0 31 31
GNAZ 0.031 0.014 -10000 0 0 81 81
G12/G13 0.025 0.047 -10000 0 -0.14 28 28
GNA14 0.034 0.009 -10000 0 0 30 30
GNA15 0.033 0.012 -10000 0 0 57 57
GNA12 0.023 0.018 -10000 0 0 193 193
GNA13 0.035 0.007 -10000 0 0 19 19
GNA11 0.033 0.011 -10000 0 0 54 54
Rac1/GTP 0.001 0.092 -10000 0 -0.29 27 27
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.009 -10000 0 0 34 34
SPHK1 0.033 0.011 -10000 0 0 50 50
GNAI2 0.034 0.01 -10000 0 0 43 43
mol:S1P 0.018 0.015 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
mol:Sphinganine-1-P -0.012 0.032 0.092 42 -10000 0 42
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.028 0.046 -10000 0 -0.16 4 4
GNAI3 0.036 0.006 -10000 0 0 15 15
G12/G13 0.025 0.047 -10000 0 -0.14 28 28
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.033 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 0 263 263
S1P/S1P5/G12 0.016 0.037 -10000 0 -0.16 4 4
S1P/S1P3/Gq 0.025 0.042 -10000 0 -0.25 8 8
S1P/S1P4/Gi -0.003 0.11 0.13 7 -0.22 74 81
GNAQ 0.034 0.009 -10000 0 0 31 31
GNAZ 0.031 0.013 -10000 0 0 81 81
GNA14 0.034 0.009 -10000 0 0 30 30
GNA15 0.033 0.012 -10000 0 0 57 57
GNA12 0.023 0.018 -10000 0 0 193 193
GNA13 0.035 0.007 -10000 0 0 19 19
GNA11 0.033 0.011 -10000 0 0 54 54
ABCC1 0.035 0.007 -10000 0 0 19 19
Reelin signaling pathway

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
CDK5R1/CDK5 0.028 0.041 -10000 0 -0.14 18 18
VLDLR 0.027 0.016 -10000 0 0 135 135
CRKL 0.035 0.009 -10000 0 0 29 29
LRPAP1 0.035 0.007 -10000 0 0 18 18
FYN 0.03 0.014 -10000 0 0 90 90
ITGA3 0.033 0.011 -10000 0 0 56 56
RELN/VLDLR/Fyn 0.018 0.06 -10000 0 -0.13 51 51
MAPK8IP1/MKK7/MAP3K11/JNK1 0.068 0.06 -10000 0 -0.11 4 4
AKT1 -0.014 0.069 -10000 0 -0.2 49 49
MAP2K7 0.035 0.008 -10000 0 0 24 24
RAPGEF1 0.035 0.007 -10000 0 0 19 19
DAB1 0.036 0.005 -10000 0 0 9 9
RELN/LRP8/DAB1 0.041 0.036 -10000 0 -0.11 3 3
LRPAP1/LRP8 0.045 0.036 -10000 0 -0.15 14 14
RELN/LRP8/DAB1/Fyn 0.041 0.059 -10000 0 -0.12 33 33
DAB1/alpha3/beta1 Integrin 0.029 0.058 -10000 0 -0.12 21 21
long-term memory 0.042 0.064 -10000 0 -0.12 31 31
DAB1/LIS1 0.048 0.072 -10000 0 -0.13 30 30
DAB1/CRLK/C3G 0.038 0.058 -10000 0 -0.12 23 23
PIK3CA 0.031 0.013 -10000 0 0 80 80
DAB1/NCK2 0.049 0.072 -10000 0 -0.13 28 28
ARHGEF2 0.035 0.007 -10000 0 0 20 20
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.035 0.006 -10000 0 0 16 16
CDK5R1 0.035 0.008 -10000 0 0 24 24
RELN 0.023 0.018 -10000 0 0 188 188
PIK3R1 0.032 0.012 -10000 0 0 63 63
RELN/LRP8/Fyn 0.029 0.056 -10000 0 -0.13 34 34
GRIN2A/RELN/LRP8/DAB1/Fyn 0.051 0.071 -10000 0 -0.12 33 33
MAPK8 0.027 0.016 -10000 0 0 138 138
RELN/VLDLR/DAB1 0.03 0.044 -10000 0 -0.11 19 19
ITGB1 0.027 0.016 -10000 0 0 138 138
MAP1B 0.023 0.083 0.16 107 -0.21 3 110
RELN/LRP8 0.039 0.044 -10000 0 -0.13 11 11
GRIN2B/RELN/LRP8/DAB1/Fyn 0.051 0.07 -10000 0 -0.12 31 31
PI3K 0.019 0.075 -10000 0 -0.16 73 73
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.027 -10000 0 -0.14 1 1
RAP1A 0.032 0.11 0.25 41 -0.19 1 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 0.007 -10000 0 0 22 22
NCK2 0.035 0.007 -10000 0 0 17 17
neuron differentiation 0.009 0.064 -10000 0 -0.22 14 14
neuron adhesion 0.033 0.11 0.24 47 -10000 0 47
LRP8 0.034 0.009 -10000 0 0 35 35
GSK3B -0.009 0.079 0.18 1 -0.21 45 46
RELN/VLDLR/DAB1/Fyn 0.031 0.064 -10000 0 -0.11 51 51
MAP3K11 0.036 0.005 -10000 0 0 10 10
RELN/VLDLR/DAB1/P13K -0.008 0.074 -10000 0 -0.19 55 55
CDK5 0.023 0.018 -10000 0 0 192 192
MAPT -0.013 0.067 0.72 1 -10000 0 1
neuron migration 0 0.12 0.21 70 -0.28 33 103
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.009 0.064 -10000 0 -0.22 14 14
RELN/VLDLR 0.044 0.06 -10000 0 -0.12 26 26
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 93 93
HSPA8 0.036 0.009 -10000 0 0 24 24
SMAD3/SMAD4/ER alpha 0.044 0.087 0.23 9 -0.14 34 43
AKT1 0.029 0.021 -10000 0 -0.029 39 39
GSC 0.002 0.028 0.11 11 -0.064 3 14
NKX2-5 0.033 0.017 0.07 8 -0.06 12 20
muscle cell differentiation -0.017 0.13 0.31 49 -10000 0 49
SMAD2-3/SMAD4/SP1 0.051 0.14 0.33 5 -0.23 57 62
SMAD4 0.022 0.054 0.14 1 -0.12 33 34
CBFB 0.035 0.006 -10000 0 0 16 16
SAP18 0.034 0.01 -10000 0 0 41 41
Cbp/p300/MSG1 0.011 0.086 -10000 0 -0.12 121 121
SMAD3/SMAD4/VDR 0.045 0.12 -10000 0 -0.2 33 33
MYC 0.029 0.014 -10000 0 -10000 0 0
CDKN2B -0.21 0.19 -10000 0 -0.49 51 51
AP1 -0.001 0.099 0.24 1 -0.23 48 49
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.011 0.13 -10000 0 -0.36 39 39
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.002 0.081 -10000 0 -0.27 31 31
SP3 0.035 0.016 0.08 11 -0.054 10 21
CREB1 0.036 0.004 -10000 0 0 7 7
FOXH1 0.035 0.016 0.073 9 -0.06 12 21
SMAD3/SMAD4/GR 0.04 0.091 0.26 1 -0.16 29 30
GATA3 0.027 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.091 -10000 0 -0.28 31 31
MEF2C/TIF2 -0.019 0.074 0.3 7 -0.23 15 22
endothelial cell migration 0.19 0.5 1.2 104 -10000 0 104
MAX 0.026 0.043 0.084 87 -0.053 89 176
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 56 56
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 26 26
NR3C1 0.027 0.043 0.085 86 -0.053 90 176
VDR 0.035 0.007 -10000 0 0 18 18
CDKN1A -0.11 0.36 0.39 1 -1.1 59 60
KAT2B -0.003 0.008 -10000 0 -0.024 11 11
SMAD2/SMAD2/SMAD4/FOXH1 0.049 0.077 0.2 2 -0.16 37 39
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 -1.2 104 104
SMAD3/SMAD4/ATF2 0.041 0.086 0.21 1 -0.15 45 46
SMAD3/SMAD4/ATF3 0.021 0.1 -10000 0 -0.17 75 75
SAP30 0.035 0.007 -10000 0 0 20 20
Cbp/p300/PIAS3 0.041 0.073 -10000 0 -0.094 92 92
JUN -0.014 0.097 0.19 7 -0.25 42 49
SMAD3/SMAD4/IRF7 0.044 0.09 -10000 0 -0.16 35 35
TFE3 0.016 0.059 0.11 8 -0.095 101 109
COL1A2 -0.045 0.21 -10000 0 -0.64 53 53
mesenchymal cell differentiation -0.041 0.086 0.16 34 -10000 0 34
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.035 0.008 -10000 0 0 28 28
FOS 0.02 0.03 0.12 2 -0.047 39 41
SMAD3/SMAD4/Max 0.041 0.087 0.26 1 -0.15 30 31
Cbp/p300/SNIP1 0.044 0.056 -10000 0 -0.12 9 9
ZBTB17 0.035 0.006 -10000 0 -10000 0 0
LAMC1 -0.033 0.098 0.16 6 -0.3 38 44
TGIF2/HDAC complex/SMAD3/SMAD4 0.04 0.084 0.21 1 -0.15 47 48
IRF7 0.034 0.01 -10000 0 -10000 0 0
ESR1 0.037 0.039 0.12 67 -0.026 59 126
HNF4A 0.035 0.007 -10000 0 0 20 20
MEF2C -0.028 0.068 0.3 7 -0.23 19 26
SMAD2-3/SMAD4 0.043 0.095 0.24 1 -0.19 31 32
Cbp/p300/Src-1 0.031 0.075 -10000 0 -0.14 43 43
IGHV3OR16-13 0.005 0.056 -10000 0 -0.48 6 6
TGIF2/HDAC complex 0.035 0.008 -10000 0 0 28 28
CREBBP 0.022 0.034 -10000 0 -0.045 101 101
SKIL 0.036 0.006 -10000 0 0 13 13
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.032 0.013 -10000 0 0 67 67
SNIP1 0.037 0.007 -10000 0 0 12 12
GCN5L2 0.022 0.034 -10000 0 -0.04 114 114
SMAD3/SMAD4/TFE3 0.031 0.12 0.28 4 -0.22 52 56
MSG1/HSC70 0.009 0.079 -10000 0 -0.14 100 100
SMAD2 0.035 0.017 0.089 2 -0.048 11 13
SMAD3 0.019 0.058 0.14 1 -0.12 43 44
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.073 -10000 0 -0.18 43 43
SMAD2/SMAD2/SMAD4 -0.012 0.07 0.18 8 -0.2 40 48
NCOR1 0.035 0.008 -10000 0 0 26 26
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA1 0.033 0.011 -10000 0 0 50 50
MYOD/E2A 0.051 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.059 0.14 0.34 5 -0.23 48 53
IFNB1 -0.005 0.057 0.2 2 -0.19 4 6
SMAD3/SMAD4/MEF2C 0.027 0.092 0.27 3 -0.24 18 21
CITED1 0.026 0.017 -10000 0 0 151 151
SMAD2-3/SMAD4/ARC105 0.042 0.085 0.22 2 -0.17 31 33
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.007 0.1 -10000 0 -0.33 29 29
RUNX1-3/PEBPB2 0.066 0.023 -10000 0 -10000 0 0
SMAD7 -0.04 0.18 0.28 2 -0.44 55 57
MYC/MIZ-1 0.028 0.057 -10000 0 -0.14 47 47
SMAD3/SMAD4 -0.08 0.23 -10000 0 -0.47 110 110
IL10 -0.007 0.061 0.19 8 -0.18 3 11
PIASy/HDAC complex 0.028 0.031 0.068 28 -0.031 89 117
PIAS3 0.023 0.029 -10000 0 -0.031 107 107
CDK2 0.021 0.032 -10000 0 -0.03 129 129
IL5 -0.008 0.063 0.2 5 -0.2 2 7
CDK4 0.021 0.031 -10000 0 -0.046 73 73
PIAS4 0.028 0.031 0.068 28 -0.031 89 117
ATF3 0.028 0.016 -10000 0 0 125 125
SMAD3/SMAD4/SP1 0.03 0.14 0.27 9 -0.24 62 71
FOXG1 0.001 0.007 0.023 22 -10000 0 22
FOXO3 -0.009 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 0.068 0.3 7 -0.22 19 26
CEBPB 0.032 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.025 0.073 0.18 2 -0.14 50 52
MYOD1 0.036 0.004 -10000 0 0 7 7
SMAD3/SMAD4/HNF4 0.04 0.085 0.21 1 -0.15 46 47
SMAD3/SMAD4/GATA3 0.033 0.085 -10000 0 -0.17 22 22
SnoN/SIN3/HDAC complex/NCoR1 0.036 0.006 -10000 0 0 13 13
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.069 0.093 -10000 0 -0.15 16 16
SMAD3/SMAD4/SP1-3 0.047 0.14 0.34 3 -0.24 54 57
MED15 0 0 -10000 0 -10000 0 0
SP1 0.014 0.075 0.12 18 -0.12 107 125
SIN3B 0.035 0.009 -10000 0 0 29 29
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.07 0.084 0.24 2 -0.16 37 39
ITGB5 -0.031 0.1 0.23 3 -0.27 32 35
TGIF/SIN3/HDAC complex/CtBP -0.009 0.096 -10000 0 -0.3 32 32
SMAD3/SMAD4/AR 0.041 0.085 0.21 1 -0.15 49 50
AR 0.035 0.007 -10000 0 0 22 22
negative regulation of cell growth -0.016 0.12 0.18 1 -0.29 63 64
SMAD3/SMAD4/MYOD 0.042 0.086 0.21 1 -0.15 50 51
E2F5 0.036 0.005 -10000 0 0 8 8
E2F4 0.036 0.006 -10000 0 0 12 12
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.062 0.097 0.24 1 -0.18 30 31
SMAD2-3/SMAD4/FOXO1-3a-4 -0.006 0.097 -10000 0 -0.3 32 32
TFDP1 0.033 0.011 -10000 0 0 53 53
SMAD3/SMAD4/AP1 0.024 0.12 0.26 1 -0.24 44 45
SMAD3/SMAD4/RUNX2 0.041 0.086 -10000 0 -0.16 34 34
TGIF2 0.035 0.008 -10000 0 0 28 28
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.005 -10000 0 0 11 11
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.01 -10000 0 0 45 45
VLDLR 0.027 0.016 -10000 0 0 135 135
LRPAP1 0.035 0.007 -10000 0 0 18 18
NUDC 0.035 0.008 -10000 0 0 27 27
RELN/LRP8 0.039 0.044 -10000 0 -0.13 11 11
CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 13 13
KATNA1 0.033 0.01 -10000 0 0 44 44
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.037 0.1 0.19 139 -0.21 6 145
IQGAP1/CaM 0.031 0.058 -10000 0 -0.15 44 44
DAB1 0.036 0.005 -10000 0 0 9 9
IQGAP1 0.033 0.011 -10000 0 0 51 51
PLA2G7 0.033 0.011 -10000 0 0 53 53
CALM1 0.033 0.011 -10000 0 0 54 54
DYNLT1 0.033 0.01 -10000 0 0 44 44
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 24 24
LIS1/Poliovirus Protein 3A -0.023 0.028 -10000 0 -0.14 24 24
CDK5R2 0.035 0.006 -10000 0 0 16 16
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.031 0.048 -10000 0 -0.12 19 19
YWHAE 0.035 0.008 -10000 0 0 27 27
NDEL1/14-3-3 E 0.064 0.17 0.32 136 -0.27 17 153
MAP1B -0.014 0.067 -10000 0 -0.2 51 51
RAC1 -0.003 0.051 -10000 0 -0.26 12 12
p35/CDK5 -0.025 0.056 0.2 7 -0.21 12 19
RELN 0.023 0.018 -10000 0 0 188 188
PAFAH/LIS1 0.022 0.039 -10000 0 -0.15 21 21
LIS1/CLIP170 -0.023 0.028 -10000 0 -0.14 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.034 0.078 0.14 8 -0.27 26 34
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.014 0.087 0.17 1 -0.23 52 53
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.056 0.16 0.3 135 -0.27 15 150
LIS1/IQGAP1 0.014 0.058 -10000 0 -0.15 50 50
RHOA -0.005 0.065 -10000 0 -0.27 19 19
PAFAH1B1 -0.021 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.013 -10000 0 0 76 76
PAFAH1B2 0.036 0.004 -10000 0 0 7 7
MAP1B/LIS1/Dynein heavy chain 0.007 0.078 -10000 0 -0.2 54 54
NDEL1/Katanin 60/Dynein heavy chain 0.082 0.15 0.33 109 -0.26 22 131
LRP8 0.034 0.009 -10000 0 0 35 35
NDEL1/Katanin 60 0.056 0.16 0.31 126 -0.27 18 144
P39/CDK5 -0.025 0.056 0.2 7 -0.21 12 19
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.052 -10000 0 -0.19 26 26
CDK5 -0.014 0.045 0.19 8 -0.22 6 14
PPP2R5D 0.036 0.004 -10000 0 0 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.019 0.023 -10000 0 -0.12 24 24
CSNK2A1 0.034 0.009 -10000 0 0 31 31
RELN/VLDLR/DAB1/LIS1 0.033 0.059 -10000 0 -0.13 33 33
RELN/VLDLR 0.044 0.06 -10000 0 -0.12 26 26
CDC42 -0.002 0.045 -10000 0 -0.2 15 15
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.035 0.009 -10000 0 0 29 29
Rac1/GDP 0.024 0.021 -10000 0 -0.025 10 10
DOCK1 0.024 0.017 -10000 0 0 175 175
ITGA4 0.036 0.006 -10000 0 0 13 13
RAC1 0.024 0.017 -10000 0 0 173 173
alpha4/beta7 Integrin 0.052 0.011 -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 0.034 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.052 0.017 -10000 0 -10000 0 0
lamellipodium assembly -0.046 0.14 -10000 0 -0.36 73 73
PIK3CA 0.031 0.013 -10000 0 0 80 80
PI3K 0.019 0.075 -10000 0 -0.16 73 73
ARF6 0.035 0.008 -10000 0 0 27 27
TLN1 0.029 0.015 -10000 0 0 102 102
PXN -0.021 0.01 0.092 3 -10000 0 3
PIK3R1 0.032 0.012 -10000 0 0 63 63
ARF6/GTP 0.049 0.048 -10000 0 -0.11 1 1
cell adhesion 0.049 0.047 -10000 0 -0.11 13 13
CRKL/CBL 0.051 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.039 0.026 -10000 0 -10000 0 0
ITGB1 0.027 0.016 -10000 0 0 138 138
ITGB7 0.036 0.005 -10000 0 0 11 11
ARF6/GDP 0.035 0.015 -10000 0 -0.025 14 14
alpha4/beta1 Integrin/Paxillin/VCAM1 0.016 0.079 -10000 0 -0.11 116 116
p130Cas/Crk/Dock1 0.028 0.035 -10000 0 -0.11 17 17
VCAM1 0.022 0.018 -10000 0 0 196 196
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.048 -10000 0 -0.12 13 13
alpha4/beta1 Integrin/Paxillin/GIT1 0.059 0.04 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.057 0.039 -10000 0 -10000 0 0
CBL 0.036 0.004 -10000 0 0 7 7
PRKACA 0.035 0.008 -10000 0 0 25 25
GIT1 0.036 0.003 -10000 0 0 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.048 -10000 0 -0.12 13 13
Rac1/GTP -0.052 0.16 -10000 0 -0.4 73 73
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.014 -10000 0 -10000 0 0
cell-cell adhesion 0.03 0.04 0.19 13 -10000 0 13
Ephrin B/EPHB2/RasGAP 0.058 0.09 -10000 0 -0.13 73 73
ITSN1 0.035 0.007 -10000 0 0 21 21
PIK3CA 0.031 0.013 -10000 0 0 80 80
SHC1 0.033 0.011 -10000 0 0 52 52
Ephrin B1/EPHB3 0.044 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.039 0.025 -10000 0 -0.12 6 6
HRAS/GDP 0.004 0.081 0.17 1 -0.22 37 38
Ephrin B/EPHB1/GRB7 0.067 0.075 -10000 0 -0.12 46 46
Endophilin/SYNJ1 -0.027 0.056 0.19 14 -0.18 2 16
KRAS 0.034 0.009 -10000 0 0 35 35
Ephrin B/EPHB1/Src 0.065 0.077 -10000 0 -0.12 53 53
endothelial cell migration 0.02 0.073 -10000 0 -0.14 63 63
GRB2 0.035 0.007 -10000 0 0 17 17
GRB7 0.036 0.006 -10000 0 0 14 14
PAK1 -0.028 0.061 0.18 19 -10000 0 19
HRAS 0.034 0.009 -10000 0 0 32 32
RRAS -0.026 0.056 0.2 10 -0.18 9 19
DNM1 0.035 0.008 -10000 0 0 26 26
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.019 0.065 0.18 20 -0.18 11 31
lamellipodium assembly -0.03 0.04 -10000 0 -0.19 13 13
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.008 0.072 -10000 0 -0.29 14 14
PIK3R1 0.032 0.012 -10000 0 0 63 63
EPHB2 0.034 0.01 -10000 0 0 42 42
EPHB3 0.033 0.011 -10000 0 0 52 52
EPHB1 0.03 0.014 -10000 0 0 95 95
EPHB4 0.025 0.017 -10000 0 0 166 166
mol:GDP 0.019 0.12 0.2 96 -0.24 34 130
Ephrin B/EPHB2 0.051 0.068 -10000 0 -0.11 65 65
Ephrin B/EPHB3 0.05 0.068 -10000 0 -0.11 64 64
JNK cascade -0.005 0.07 0.23 23 -0.19 4 27
Ephrin B/EPHB1 0.051 0.066 -10000 0 -0.11 54 54
RAP1/GDP 0.028 0.12 0.2 101 -0.22 35 136
EFNB2 0.028 0.015 -10000 0 0 116 116
EFNB3 0.035 0.009 -10000 0 0 29 29
EFNB1 0.037 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.03 0.058 -10000 0 -0.11 52 52
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 11 11
CDC42/GTP 0.043 0.083 -10000 0 -0.19 33 33
Rap1/GTP -0.044 0.052 0.052 8 -0.2 22 30
axon guidance 0.044 0.014 -10000 0 -10000 0 0
MAPK3 -0.009 0.071 0.18 3 -0.27 16 19
MAPK1 -0.009 0.074 0.18 2 -0.27 20 22
Rac1/GDP -0.008 0.093 0.25 19 -0.24 31 50
actin cytoskeleton reorganization -0.039 0.06 -10000 0 -0.2 39 39
CDC42/GDP 0.036 0.13 0.22 109 -0.23 35 144
PI3K 0.024 0.076 -10000 0 -0.14 63 63
EFNA5 0.036 0.004 -10000 0 0 6 6
Ephrin B2/EPHB4 0.016 0.047 -10000 0 -0.11 46 46
Ephrin B/EPHB2/Intersectin/N-WASP 0.001 0.06 -10000 0 -0.3 6 6
CDC42 0.035 0.008 -10000 0 0 24 24
RAS family/GTP -0.052 0.06 -10000 0 -0.24 24 24
PTK2 -0.015 0.08 0.53 9 -0.2 15 24
MAP4K4 -0.005 0.071 0.23 23 -0.19 4 27
SRC 0.036 0.006 -10000 0 0 14 14
KALRN 0.035 0.008 -10000 0 0 23 23
Intersectin/N-WASP 0.032 0.033 -10000 0 -0.14 7 7
neuron projection morphogenesis 0.064 0.17 0.33 124 -0.22 13 137
MAP2K1 -0.001 0.071 0.2 1 -0.27 17 18
WASL 0.024 0.017 -10000 0 0 172 172
Ephrin B1/EPHB1-2/NCK1 0.082 0.038 -10000 0 -0.12 9 9
cell migration -0.015 0.087 0.2 2 -0.29 19 21
NRAS 0.032 0.012 -10000 0 0 63 63
SYNJ1 -0.027 0.057 0.19 14 -0.18 2 16
PXN 0.036 0.004 -10000 0 0 7 7
TF -0.022 0.051 0.19 6 -0.18 21 27
HRAS/GTP 0.034 0.079 -10000 0 -0.2 21 21
Ephrin B1/EPHB1-2 0.052 0.035 -10000 0 -0.11 6 6
cell adhesion mediated by integrin 0.019 0.046 0.15 4 -0.27 4 8
RAC1 0.024 0.017 -10000 0 0 173 173
mol:GTP 0.042 0.077 -10000 0 -0.13 59 59
RAC1-CDC42/GTP -0.03 0.046 -10000 0 -0.2 14 14
RASA1 0.034 0.009 -10000 0 0 32 32
RAC1-CDC42/GDP 0.011 0.095 0.25 17 -0.24 32 49
ruffle organization 0.074 0.17 0.31 141 -0.25 6 147
NCK1 0.035 0.008 -10000 0 0 27 27
receptor internalization -0.031 0.053 0.18 14 -0.18 2 16
Ephrin B/EPHB2/KALRN 0.064 0.079 -10000 0 -0.12 62 62
ROCK1 -0.01 0.045 0.18 17 -10000 0 17
RAS family/GDP -0.042 0.063 -10000 0 -0.21 41 41
Rac1/GTP -0.028 0.045 -10000 0 -0.2 13 13
Ephrin B/EPHB1/Src/Paxillin 0.009 0.065 -10000 0 -0.22 6 6
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.015 0.013 0.085 5 -10000 0 5
RAS family/GTP 0.013 0.11 0.22 1 -0.18 73 74
NFATC4 -0.021 0.067 0.17 20 -0.18 5 25
ERBB2IP 0.034 0.011 -10000 0 -0.001 42 42
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.029 0.077 0.17 9 -0.18 19 28
JUN -0.004 0.087 0.21 6 -0.36 7 13
HRAS 0.034 0.009 -10000 0 0 32 32
DOCK7 -0.036 0.068 0.15 11 -0.16 71 82
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.08 0.21 14 -0.13 85 99
AKT1 -0.01 0.008 0.013 30 -10000 0 30
BAD -0.015 0.014 0.085 7 -10000 0 7
MAPK10 0.007 0.072 0.16 42 -0.15 13 55
mol:GTP 0 0.001 -10000 0 -0.005 24 24
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.083 0.2 7 -0.19 19 26
RAF1 -0.019 0.1 0.25 10 -0.24 33 43
ErbB2/ErbB3/neuregulin 2 0.002 0.073 0.2 17 -0.13 91 108
STAT3 -0.023 0.24 -10000 0 -0.9 35 35
cell migration -0.005 0.071 0.19 20 -0.18 15 35
mol:PI-3-4-5-P3 -0.001 0.002 0.004 14 -0.005 4 18
cell proliferation -0.041 0.24 0.44 3 -0.58 58 61
FOS -0.032 0.2 0.37 6 -0.42 90 96
NRAS 0.032 0.012 -10000 0 0 63 63
mol:Ca2+ -0.029 0.077 0.17 9 -0.18 19 28
MAPK3 -0.019 0.18 0.4 3 -0.48 38 41
MAPK1 -0.044 0.22 0.4 3 -0.57 50 53
JAK2 -0.027 0.078 0.17 19 -0.18 19 38
NF2 0.01 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.005 0.08 0.15 13 -0.16 88 101
NRG1 0.036 0.005 -10000 0 0 9 9
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
MAPK8 -0.014 0.087 0.19 4 -0.22 49 53
MAPK9 0.014 0.076 0.16 57 -0.14 5 62
ERBB2 -0.016 0.068 0.26 29 -10000 0 29
ERBB3 0.018 0.018 -10000 0 0 256 256
SHC1 0.033 0.011 -10000 0 0 52 52
RAC1 0.024 0.017 -10000 0 0 173 173
apoptosis 0.012 0.03 0.2 10 -0.07 4 14
STAT3 (dimer) -0.021 0.24 -10000 0 -0.88 35 35
RNF41 -0.02 0.019 0.076 10 -0.12 2 12
FRAP1 -0.015 0.012 0.084 5 -10000 0 5
RAC1-CDC42/GTP -0.022 0.044 -10000 0 -0.13 48 48
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.008 -10000 0 -10000 0 0
CHRNA1 -0.007 0.15 0.35 5 -0.36 42 47
myelination -0.033 0.072 0.22 9 -0.2 4 13
PPP3CB -0.02 0.067 0.16 18 -0.18 14 32
KRAS 0.034 0.009 -10000 0 0 35 35
RAC1-CDC42/GDP 0.021 0.074 0.22 1 -0.16 45 46
NRG2 0.036 0.005 -10000 0 0 10 10
mol:GDP -0.005 0.08 0.15 13 -0.16 88 101
SOS1 0 0.001 -10000 0 -0.004 5 5
MAP2K2 -0.028 0.1 0.22 11 -0.24 38 49
SRC 0.036 0.006 -10000 0 0 14 14
mol:cAMP -0.001 0.001 0.003 2 -0.004 1 3
PTPN11 -0.031 0.083 0.17 21 -0.18 19 40
MAP2K1 -0.038 0.2 0.38 2 -0.57 35 37
heart morphogenesis -0.029 0.077 0.17 9 -0.18 19 28
RAS family/GDP 0.021 0.11 0.24 1 -0.18 76 77
GRB2 0.035 0.007 -10000 0 0 17 17
PRKACA 0.018 0.009 -10000 0 -10000 0 0
CHRNE 0.001 0.025 0.075 2 -0.12 7 9
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.008 -10000 0 -0.013 30 30
nervous system development -0.029 0.077 0.17 9 -0.18 19 28
CDC42 0.035 0.008 -10000 0 0 24 24
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.099 -10000 0 -0.25 27 27
mol:DAG -0.012 0.09 0.18 4 -0.25 27 31
PLCG1 -0.013 0.092 0.18 4 -0.25 27 31
YES1 -0.016 0.084 0.14 1 -0.28 20 21
FZD3 0.029 0.015 -10000 0 0 110 110
FZD6 0.027 0.016 -10000 0 0 130 130
G protein 0.003 0.1 0.2 23 -0.27 25 48
MAP3K7 -0.036 0.074 0.15 4 -0.23 31 35
mol:Ca2+ -0.012 0.088 0.18 4 -0.24 27 31
mol:IP3 -0.012 0.09 0.18 4 -0.25 27 31
NLK -0.039 0.25 -10000 0 -0.78 52 52
GNB1 0.035 0.007 -10000 0 0 20 20
CAMK2A -0.031 0.078 0.17 4 -0.24 27 31
MAP3K7IP1 0.034 0.009 -10000 0 0 35 35
Noncanonical Wnts/FZD -0.006 0.089 -10000 0 -0.17 89 89
CSNK1A1 0.036 0.006 -10000 0 0 14 14
GNAS -0.014 0.08 0.14 2 -0.17 83 85
GO:0007205 -0.02 0.085 0.18 4 -0.25 27 31
WNT6 0.037 0.002 -10000 0 0 1 1
WNT4 0.035 0.007 -10000 0 0 18 18
NFAT1/CK1 alpha -0.005 0.098 0.22 5 -0.26 27 32
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.029 0.015 -10000 0 0 99 99
WNT11 0.036 0.006 -10000 0 0 14 14
CDC42 -0.025 0.082 0.17 5 -0.27 21 26
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.063 0.064 -9999 0 -0.12 12 12
SMAD6-7/SMURF1 0.044 0.038 -9999 0 -0.12 2 2
NOG 0 0 -9999 0 -10000 0 0
SMAD9 -0.024 0.15 -9999 0 -0.44 54 54
SMAD4 0.032 0.012 -9999 0 0 58 58
SMAD5 -0.029 0.098 -9999 0 -0.3 45 45
BMP7/USAG1 0.033 0.027 -9999 0 -10000 0 0
SMAD5/SKI -0.021 0.11 -9999 0 -0.31 43 43
SMAD1 -0.031 0.15 -9999 0 -0.4 50 50
BMP2 0.029 0.015 -9999 0 0 107 107
SMAD1/SMAD1/SMAD4 -0.01 0.13 -9999 0 -0.36 42 42
BMPR1A 0.025 0.017 -9999 0 0 167 167
BMPR1B 0.036 0.006 -9999 0 0 14 14
BMPR1A-1B/BAMBI 0.02 0.06 -9999 0 -0.13 50 50
AHSG 0.035 0.009 -9999 0 0 29 29
CER1 0.031 0.013 -9999 0 0 71 71
BMP2-4/CER1 0.039 0.055 -9999 0 -0.12 35 35
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.01 0.078 -9999 0 -0.24 31 31
BMP2-4 (homodimer) 0.029 0.051 -9999 0 -0.14 35 35
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.058 0.052 -9999 0 -0.12 12 12
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.025 0.017 -9999 0 0 167 167
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.021 0.07 -9999 0 -0.17 58 58
BMP2-4/USAG1 0.033 0.046 -9999 0 -0.12 16 16
SMAD6/SMURF1/SMAD5 -0.012 0.09 -9999 0 -0.29 33 33
SOSTDC1 0.023 0.018 -9999 0 0 184 184
BMP7/BMPR2/BMPR1A-1B 0.058 0.053 -9999 0 -0.12 14 14
SKI 0.037 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.035 0.008 -9999 0 0 24 24
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 41 41
BMP2-4/CHRD 0.043 0.054 -9999 0 -0.12 34 34
SMAD5/SMAD5/SMAD4 -0.022 0.11 -9999 0 -0.31 43 43
MAPK1 0.033 0.01 -9999 0 0 45 45
TAK1/TAB family 0.019 0.083 -9999 0 -0.21 18 18
BMP7 (homodimer) 0.034 0.01 -9999 0 0 39 39
NUP214 0.035 0.007 -9999 0 0 18 18
BMP6/FETUA 0.049 0.016 -9999 0 -10000 0 0
SMAD1/SKI -0.015 0.15 -9999 0 -0.38 52 52
SMAD6 0.036 0.005 -9999 0 0 11 11
CTDSP2 0.033 0.012 -9999 0 0 57 57
BMP2-4/FETUA 0.042 0.055 -9999 0 -0.12 35 35
MAP3K7IP1 0.034 0.009 -9999 0 0 35 35
GREM1 0.032 0.012 -9999 0 0 64 64
BMPR2 (homodimer) 0.036 0.006 -9999 0 0 12 12
GADD34/PP1CA 0.052 0.053 -9999 0 -0.13 31 31
BMPR1A-1B (homodimer) 0.034 0.032 -9999 0 -0.14 6 6
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.018 0.15 -9999 0 -0.39 53 53
SMAD6-7/SMURF1/SMAD1 0.004 0.14 -9999 0 -0.38 42 42
SMAD6/SMURF1 0.025 0.017 -9999 0 0 167 167
BAMBI 0.018 0.018 -9999 0 0 255 255
SMURF2 0.035 0.007 -9999 0 0 20 20
BMP2-4/CHRDL1 0.028 0.043 -9999 0 -0.11 35 35
BMP2-4/GREM1 0.039 0.054 -9999 0 -0.12 33 33
SMAD7 0.033 0.01 -9999 0 0 44 44
SMAD8A/SMAD8A/SMAD4 -0.012 0.15 -9999 0 -0.41 58 58
SMAD1/SMAD6 -0.015 0.14 -9999 0 -0.38 43 43
TAK1/SMAD6 0.032 0.034 -9999 0 -0.14 8 8
BMP7 0.034 0.01 -9999 0 0 39 39
BMP6 0.035 0.008 -9999 0 0 24 24
MAP3K7IP2 0.033 0.011 -9999 0 0 46 46
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.003 0.055 -9999 0 -0.22 16 16
PPM1A 0.034 0.009 -9999 0 0 30 30
SMAD1/SMURF2 -0.017 0.15 -9999 0 -0.39 51 51
SMAD7/SMURF1 0.033 0.029 -9999 0 -0.14 2 2
CTDSPL 0.036 0.006 -9999 0 0 12 12
PPP1CA 0.035 0.007 -9999 0 0 20 20
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.035 0.006 -9999 0 0 16 16
PPP1R15A 0.033 0.011 -9999 0 0 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.016 0.072 -9999 0 -0.21 32 32
CHRD 0.035 0.007 -9999 0 0 22 22
BMPR2 0.036 0.006 -9999 0 0 12 12
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.02 0.071 -9999 0 -0.18 53 53
BMP4 0.033 0.011 -9999 0 0 49 49
FST 0.033 0.011 -9999 0 0 48 48
BMP2-4/NOG 0.028 0.043 -9999 0 -0.11 35 35
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.05 0.061 -9999 0 -0.12 9 9
IL1-mediated signaling events

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
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 46 46
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 0.036 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 0.092 94 -10000 0 94
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.05 -10000 0 -0.13 28 28
IL1R2 0.03 0.014 -10000 0 0 90 90
IL1R1 0.036 0.006 -10000 0 0 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.015 0.1 -10000 0 -0.31 34 34
TOLLIP 0.034 0.009 -10000 0 0 30 30
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.004 -10000 0 0 7 7
TAK1/TAB1/TAB2 0.056 0.047 -10000 0 -0.14 19 19
IKK complex/ELKS -0.045 0.096 -10000 0 -0.26 16 16
JUN -0.039 0.041 0.19 1 -0.21 9 10
MAP3K7 0.034 0.01 -10000 0 0 41 41
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.032 0.11 -10000 0 -0.14 111 111
IL1 alpha/IL1R1/IL1RAP/MYD88 0.065 0.069 -10000 0 -0.13 50 50
PIK3R1 0.032 0.012 -10000 0 0 63 63
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.074 0.075 -10000 0 -0.12 49 49
IL1 beta fragment/IL1R1/IL1RAP 0.026 0.081 0.16 8 -0.14 83 91
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.033 0.036 0.16 3 -0.2 7 10
IRAK1 -0.018 0.01 -10000 0 -0.11 5 5
IL1RN/IL1R1 0.053 0.01 -10000 0 -10000 0 0
IRAK4 0.035 0.007 -10000 0 0 18 18
PRKCI 0.035 0.008 -10000 0 0 26 26
TRAF6 0.036 0.005 -10000 0 0 10 10
PI3K 0.019 0.075 -10000 0 -0.16 73 73
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.12 -10000 0 -0.27 64 64
CHUK 0.025 0.017 -10000 0 0 163 163
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.026 0.081 0.16 8 -0.14 83 91
IL1 beta/IL1R2 0.017 0.071 -10000 0 -0.14 71 71
IRAK/TRAF6/TAK1/TAB1/TAB2 0.059 0.067 -10000 0 -0.14 34 34
NF kappa B1 p50/RelA 0.016 0.098 -10000 0 -0.15 106 106
IRAK3 0.035 0.008 -10000 0 0 27 27
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.038 0.082 -10000 0 -0.13 81 81
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.076 -10000 0 -0.19 51 51
IL1 alpha/IL1R1/IL1RAP 0.049 0.053 -10000 0 -0.12 33 33
RELA 0.036 0.005 -10000 0 0 9 9
MAP3K7IP1 0.034 0.009 -10000 0 0 35 35
SQSTM1 0.034 0.009 -10000 0 0 35 35
MYD88 0.034 0.009 -10000 0 0 36 36
IRAK/TRAF6/MEKK3 0.049 0.038 -10000 0 -0.12 22 22
IL1RAP 0.03 0.014 -10000 0 0 94 94
UBE2N 0.036 0.006 -10000 0 0 13 13
IRAK/TRAF6 -0.039 0.062 0.062 69 -0.19 24 93
CASP1 0.029 0.015 -10000 0 0 108 108
IL1RN/IL1R2 0.045 0.021 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.038 0.096 -10000 0 -0.15 91 91
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.1 -10000 0 -0.3 38 38
PIK3CA 0.031 0.013 -10000 0 0 80 80
IL1RN 0.036 0.004 -10000 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.065 0.059 -10000 0 -0.14 22 22
MAP2K6 -0.038 0.035 0.18 3 -0.2 7 10
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.041 0.087 0.23 22 -0.2 8 30
TBX21 0.067 0.2 0.51 12 -0.52 9 21
B2M 0.035 0.008 -10000 0 0 27 27
TYK2 0.036 0.039 0.12 14 -0.05 28 42
IL12RB1 0.037 0.04 0.11 19 -0.051 31 50
GADD45B 0.058 0.29 0.51 18 -0.99 24 42
IL12RB2 0.04 0.04 0.12 20 -0.051 23 43
GADD45G 0.089 0.18 0.48 19 -0.49 5 24
natural killer cell activation 0.012 0.024 0.055 73 -0.032 22 95
RELB 0.034 0.009 -10000 0 0 32 32
RELA 0.036 0.005 -10000 0 0 9 9
IL18 0.034 0.022 0.088 2 -0.043 17 19
IL2RA 0.024 0.017 -10000 0 0 172 172
IFNG 0.034 0.009 -10000 0 0 30 30
STAT3 (dimer) 0.072 0.22 0.43 34 -0.5 28 62
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 45 45
FASLG 0.071 0.2 0.52 12 -0.52 9 21
NF kappa B2 p52/RelB 0.05 0.18 0.41 15 -0.45 18 33
CD4 0.025 0.026 -10000 0 -0.04 55 55
SOCS1 0.036 0.005 -10000 0 0 8 8
EntrezGene:6955 -0.001 0.01 -10000 0 -0.025 59 59
CD3D 0.025 0.028 -10000 0 -0.042 64 64
CD3E 0.028 0.027 -10000 0 -0.04 67 67
CD3G 0.027 0.028 -10000 0 -0.042 67 67
IL12Rbeta2/JAK2 0.055 0.059 0.18 19 -10000 0 19
CCL3 0.07 0.2 0.44 30 -0.45 20 50
CCL4 0.039 0.33 0.56 16 -1 31 47
HLA-A 0.036 0.006 -10000 0 0 13 13
IL18/IL18R 0.094 0.061 0.21 36 -0.097 22 58
NOS2 0.072 0.19 0.42 37 -0.4 23 60
IL12/IL12R/TYK2/JAK2/SPHK2 0.038 0.086 0.22 26 -0.19 13 39
IL1R1 0.069 0.2 0.55 11 -0.52 8 19
IL4 0.004 0.048 -10000 0 -0.073 82 82
JAK2 0.033 0.038 0.11 13 -0.051 23 36
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 45 45
TCR/CD3/MHC I/CD8 0.006 0.044 0.11 1 -0.17 15 16
RAB7A 0.09 0.2 0.44 30 -0.51 24 54
lysosomal transport 0.09 0.2 0.42 35 -0.49 24 59
FOS -0.11 0.48 0.5 10 -1.1 94 104
STAT4 (dimer) 0.084 0.2 0.43 37 -0.45 24 61
STAT5A (dimer) 0.077 0.19 0.42 13 -0.45 19 32
GZMA 0.067 0.2 0.55 12 -0.52 9 21
GZMB 0.066 0.2 0.57 11 -0.52 9 20
HLX 0 0 -10000 0 -10000 0 0
LCK 0.061 0.2 0.45 27 -0.46 20 47
TCR/CD3/MHC II/CD4 -0.023 0.12 0.16 22 -0.25 81 103
IL2/IL2R 0.063 0.044 -10000 0 -10000 0 0
MAPK14 0.092 0.23 0.47 29 -0.6 23 52
CCR5 0.075 0.17 0.39 40 -0.37 22 62
IL1B 0.029 0.037 0.11 9 -0.05 26 35
STAT6 0.052 0.098 0.28 22 -0.4 3 25
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 0.025 0.017 -10000 0 0 158 158
IL12B 0.04 0.04 0.12 20 -0.051 25 45
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 -0.04 0.087 0.2 8 -0.23 22 30
IL2RB 0.033 0.011 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.2 0.43 37 -0.42 24 61
IL2RG 0.035 0.008 -10000 0 0 24 24
IL12 0.061 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 45 45
IL2 0.036 0.005 -10000 0 0 10 10
SPHK2 0.034 0.009 -10000 0 0 34 34
FRAP1 0.035 0.007 -10000 0 0 17 17
IL12A 0.038 0.04 0.12 16 -0.051 32 48
IL12/IL12R/TYK2/JAK2 0.062 0.21 0.48 30 -0.48 20 50
MAP2K3 0.086 0.23 0.46 30 -0.59 25 55
RIPK2 0.036 0.006 -10000 0 0 14 14
MAP2K6 0.089 0.22 0.46 30 -0.55 25 55
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.021 0.027 -10000 0 -0.044 48 48
IL18RAP 0.038 0.02 0.083 3 -0.041 22 25
IL12Rbeta1/TYK2 0.049 0.062 0.18 7 -0.15 14 21
EOMES -0.018 0.038 0.075 2 -0.098 49 51
STAT1 (dimer) 0.086 0.19 0.43 25 -0.43 11 36
T cell proliferation 0.074 0.18 0.39 37 -0.38 26 63
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.039 0.02 0.083 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 0.043 0.17 0.33 2 -0.45 28 30
ATF2 0.084 0.21 0.44 28 -0.57 23 51
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.002 0.038 -10000 0 -10000 0 0
CRKL 0.035 0.009 -10000 0 0 29 29
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
DOCK1 0.024 0.017 -10000 0 0 175 175
ITGA4 0.036 0.006 -10000 0 0 13 13
alpha4/beta7 Integrin/MAdCAM1 0.083 0.035 -10000 0 -0.12 5 5
EPO 0.025 0.017 -10000 0 0 166 166
alpha4/beta7 Integrin 0.052 0.011 -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) 0.035 0.026 -10000 0 -10000 0 0
lamellipodium assembly -0.015 0.1 -10000 0 -0.37 20 20
PIK3CA 0.031 0.013 -10000 0 0 80 80
PI3K 0.019 0.075 -10000 0 -0.16 73 73
ARF6 0.035 0.008 -10000 0 0 27 27
JAK2 0.01 0.03 -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 0.034 0.009 -10000 0 0 32 32
cell adhesion 0.08 0.034 -10000 0 -0.12 5 5
CRKL/CBL 0.051 0.014 -10000 0 -10000 0 0
ITGB1 0.027 0.016 -10000 0 0 138 138
SRC -0.034 0.058 0.19 4 -10000 0 4
ITGB7 0.036 0.005 -10000 0 0 11 11
RAC1 0.024 0.017 -10000 0 0 173 173
alpha4/beta1 Integrin/VCAM1 0.003 0.077 -10000 0 -0.12 126 126
p130Cas/Crk/Dock1 -0.031 0.063 0.2 4 -0.2 7 11
VCAM1 0.022 0.018 -10000 0 0 196 196
RHOA 0.035 0.007 -10000 0 0 18 18
alpha4/beta1 Integrin/Paxillin/GIT1 0.067 0.043 -10000 0 -10000 0 0
BCAR1 -0.033 0.051 0.18 4 -10000 0 4
EPOR 0.035 0.008 -10000 0 0 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.036 0.004 -10000 0 0 7 7
GIT1 0.036 0.003 -10000 0 0 4 4
Rac1/GTP -0.016 0.1 -10000 0 -0.4 19 19
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.023 0.053 0.17 14 -0.22 9 23
DAPP1 -0.027 0.12 -10000 0 -0.3 66 66
Src family/SYK family/BLNK-LAT/BTK-ITK -0.048 0.19 0.25 2 -0.48 59 61
mol:DAG -0.015 0.087 0.2 13 -0.21 43 56
HRAS 0.034 0.02 0.068 1 -0.032 27 28
RAP1A 0.038 0.013 0.063 4 -0.017 20 24
ARF5/GDP -0.002 0.095 -10000 0 -0.31 32 32
PLCG2 0.032 0.012 -10000 0 0 63 63
PLCG1 0.035 0.007 -10000 0 0 19 19
ARF5 0.024 0.017 -10000 0 0 175 175
mol:GTP -0.025 0.052 0.16 16 -0.2 9 25
ARF1/GTP -0.02 0.045 0.12 14 -0.2 11 25
RHOA 0.035 0.007 -10000 0 0 18 18
YES1 0.034 0.01 -10000 0 0 41 41
RAP1A/GTP -0.025 0.051 0.16 15 -0.19 9 24
ADAP1 -0.026 0.046 0.14 13 -0.19 9 22
ARAP3 -0.025 0.051 0.16 16 -0.19 9 25
INPPL1 0.036 0.006 -10000 0 0 12 12
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.033 0.011 -10000 0 0 48 48
ARHGEF7 0.032 0.012 -10000 0 0 59 59
ARF1 0.035 0.008 -10000 0 0 24 24
NRAS 0.034 0.018 0.068 1 -0.033 12 13
FYN 0.03 0.014 -10000 0 0 90 90
ARF6 0.035 0.008 -10000 0 0 27 27
FGR 0.033 0.011 -10000 0 0 54 54
mol:Ca2+ 0.003 0.058 0.14 35 -0.12 18 53
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.033 0.011 -10000 0 0 46 46
ZAP70 0.036 0.002 -10000 0 0 2 2
mol:IP3 -0.009 0.068 0.18 29 -0.16 21 50
LYN 0.031 0.013 -10000 0 0 74 74
ARF1/GDP 0.007 0.11 -10000 0 -0.33 36 36
RhoA/GDP 0.023 0.089 0.19 11 -0.21 30 41
PDK1/Src/Hsp90 0.047 0.01 -10000 0 -10000 0 0
BLNK 0.019 0.018 -10000 0 0 243 243
actin cytoskeleton reorganization 0.007 0.1 0.2 24 -0.29 25 49
SRC 0.036 0.006 -10000 0 0 14 14
PLEKHA2 -0.012 0.024 0.085 29 -10000 0 29
RAC1 0.024 0.017 -10000 0 0 173 173
PTEN 0.026 0.022 -10000 0 -0.035 16 16
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.028 0.052 0.16 15 -0.2 9 24
RhoA/GTP -0.028 0.058 0.18 17 -0.21 10 27
Src family/SYK family/BLNK-LAT -0.053 0.16 -10000 0 -0.35 85 85
BLK 0.035 0.007 -10000 0 0 17 17
PDPK1 0.036 0.004 -10000 0 0 7 7
CYTH1 -0.026 0.046 0.14 13 -0.19 9 22
HCK 0.027 0.016 -10000 0 0 128 128
CYTH3 -0.026 0.046 0.14 13 -0.19 9 22
CYTH2 -0.026 0.046 0.14 13 -0.19 9 22
KRAS 0.034 0.021 0.075 2 -0.032 31 33
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.003 0.031 0.21 3 -0.16 1 4
SGK1 0 0.03 0.21 2 -0.15 2 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.11 -10000 0 -0.33 37 37
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.031 0.013 -10000 0 0 76 76
ARF6/GDP -0.028 0.066 0.18 13 -0.22 26 39
mol:PI-3-4-5-P3 -0.026 0.049 0.15 13 -0.2 9 22
ARAP3/RAP1A/GTP -0.025 0.051 0.16 15 -0.2 9 24
VAV1 0.034 0.009 -10000 0 0 35 35
mol:PI-3-4-P2 -0.011 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.062 0.092 0.21 102 -0.14 42 144
PLEKHA1 -0.008 0.022 0.085 23 -10000 0 23
Rac1/GDP -0.002 0.098 -10000 0 -0.31 33 33
LAT 0.036 0.005 -10000 0 0 10 10
Rac1/GTP -0.005 0.15 -10000 0 -0.46 35 35
ITK -0.029 0.049 0.15 14 -0.19 9 23
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.026 0.11 0.23 11 -0.28 50 61
LCK 0.035 0.007 -10000 0 0 17 17
BTK -0.027 0.052 0.15 17 -0.19 9 26
Signaling events mediated by PTP1B

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
PDGFRB 0.035 0.008 -10000 0 0 27 27
Jak2/Leptin Receptor -0.003 0.14 -10000 0 -0.32 55 55
PTP1B/AKT1 0 0.11 -10000 0 -0.27 43 43
FYN 0.03 0.014 -10000 0 0 90 90
p210 bcr-abl/PTP1B -0.01 0.11 0.17 3 -0.27 44 47
EGFR 0.009 0.016 -10000 0 -0.031 3 3
EGF/EGFR -0.033 0.09 -10000 0 -0.28 38 38
CSF1 0.036 0.005 -10000 0 0 8 8
AKT1 0.033 0.011 -10000 0 0 53 53
INSR 0.035 0.009 -10000 0 -0.001 26 26
PTP1B/N-cadherin -0.005 0.12 0.18 1 -0.28 52 53
Insulin Receptor/Insulin 0.02 0.11 -10000 0 -0.26 32 32
HCK 0.027 0.016 -10000 0 0 128 128
CRK 0.035 0.008 -10000 0 0 23 23
TYK2 -0.009 0.12 0.3 19 -0.29 41 60
EGF 0.027 0.024 -10000 0 -0.031 66 66
YES1 0.034 0.01 -10000 0 0 41 41
CAV1 0.007 0.14 0.21 33 -0.3 48 81
TXN 0.035 0.011 -10000 0 0 40 40
PTP1B/IRS1/GRB2 0.006 0.12 0.2 1 -0.28 45 46
cell migration 0.01 0.11 0.27 44 -0.17 3 47
STAT3 0.034 0.01 -10000 0 0 37 37
PRLR 0.038 0.004 -10000 0 -10000 0 0
ITGA2B 0.036 0.004 -10000 0 0 5 5
CSF1R 0.027 0.016 -10000 0 0 131 131
Prolactin Receptor/Prolactin 0.057 0.012 -10000 0 -10000 0 0
FGR 0.033 0.011 -10000 0 0 54 54
PTP1B/p130 Cas -0.012 0.1 0.16 1 -0.26 45 46
Crk/p130 Cas -0.001 0.11 0.17 1 -0.26 48 49
DOK1 -0.008 0.1 0.18 4 -0.29 33 37
JAK2 -0.014 0.13 -10000 0 -0.34 55 55
Jak2/Leptin Receptor/Leptin -0.014 0.12 -10000 0 -0.31 34 34
PIK3R1 0.032 0.012 -10000 0 0 63 63
PTPN1 -0.01 0.11 0.17 3 -0.27 44 47
LYN 0.031 0.013 -10000 0 0 74 74
CDH2 0.033 0.011 -10000 0 0 55 55
SRC 0.014 0.099 -10000 0 -0.45 18 18
ITGB3 0.036 0.003 -10000 0 0 4 4
CAT1/PTP1B -0.01 0.17 0.23 19 -0.36 65 84
CAPN1 0.036 0.006 -10000 0 -0.004 8 8
CSK 0.035 0.007 -10000 0 0 21 21
PI3K 0.011 0.13 -10000 0 -0.29 43 43
mol:H2O2 0.004 0.005 0.029 6 -10000 0 6
STAT3 (dimer) -0.012 0.11 -10000 0 -0.28 35 35
negative regulation of transcription -0.014 0.13 -10000 0 -0.33 55 55
FCGR2A 0.028 0.015 -10000 0 0 114 114
FER 0.036 0.008 -10000 0 -0.002 15 15
alphaIIb/beta3 Integrin 0.053 0.006 -10000 0 -10000 0 0
BLK 0.035 0.007 -10000 0 0 17 17
Insulin Receptor/Insulin/Shc 0.059 0.036 -10000 0 -0.13 8 8
RHOA 0.035 0.007 -10000 0 0 18 18
LEPR 0.035 0.007 -10000 0 0 20 20
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.035 0.007 -10000 0 0 17 17
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.006 0.15 0.2 5 -0.35 58 63
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 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.056 0.046 -10000 0 -0.12 23 23
CSF1/CSF1R -0.002 0.13 -10000 0 -0.28 50 50
Ras protein signal transduction -0.01 0.069 0.57 5 -10000 0 5
IRS1 0.033 0.011 -10000 0 0 52 52
INS 0.036 0.007 -10000 0 -0.002 15 15
LEP 0.024 0.017 -10000 0 0 173 173
STAT5B -0.004 0.11 0.17 2 -0.28 32 34
STAT5A -0.004 0.11 0.17 4 -0.28 33 37
GRB2 0.035 0.007 -10000 0 0 17 17
PDGFB-D/PDGFRB 0.001 0.12 0.18 1 -0.27 44 45
CSN2 0.013 0.041 -10000 0 -10000 0 0
PIK3CA 0.031 0.013 -10000 0 0 80 80
LAT -0.028 0.18 -10000 0 -0.47 64 64
YBX1 0.038 0.042 -10000 0 -0.29 8 8
LCK 0.035 0.007 -10000 0 0 17 17
SHC1 0.033 0.011 -10000 0 0 52 52
NOX4 0.034 0.015 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.056 -10000 0 -0.13 36 36
fibroblast growth factor receptor signaling pathway 0.051 0.055 -10000 0 -0.13 36 36
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.033 0.011 -10000 0 0 52 52
GPC1/SLIT2 0.032 0.044 -10000 0 -0.14 23 23
SMAD2 -0.023 0.048 0.18 11 -0.2 3 14
GPC1/PrPc/Cu2+ 0.026 0.058 -10000 0 -0.14 52 52
GPC1/Laminin alpha1 0.015 0.04 -10000 0 -0.13 35 35
TDGF1 0.035 0.007 -10000 0 0 18 18
CRIPTO/GPC1 0.038 0.047 -10000 0 -0.14 29 29
APP/GPC1 0.034 0.058 -10000 0 -0.16 38 38
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.023 0.033 0.089 22 -0.12 22 44
FLT1 0.034 0.009 -10000 0 0 33 33
GPC1/TGFB/TGFBR1/TGFBR2 0.051 0.053 -10000 0 -0.12 34 34
SERPINC1 0.036 0.005 -10000 0 0 11 11
FYN -0.018 0.029 0.089 23 -0.12 8 31
FGR -0.022 0.033 0.089 23 -0.12 21 44
positive regulation of MAPKKK cascade -0.038 0.12 0.2 10 -0.3 62 72
SLIT2 0.029 0.015 -10000 0 0 103 103
GPC1/NRG 0.037 0.05 -10000 0 -0.14 35 35
NRG1 0.036 0.005 -10000 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.032 0.043 -10000 0 -0.12 35 35
LYN -0.022 0.033 0.089 22 -0.12 23 45
mol:Spermine -0.01 0.004 -10000 0 -10000 0 0
cell growth 0.051 0.055 -10000 0 -0.13 36 36
BMP signaling pathway -0.032 0.012 0 64 -10000 0 64
SRC -0.025 0.034 0.089 23 -0.12 28 51
TGFBR1 0.035 0.007 -10000 0 0 17 17
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.018 0.018 -10000 0 0 262 262
GPC1 0.032 0.012 -10000 0 0 64 64
TGFBR1 (dimer) 0.035 0.007 -10000 0 0 17 17
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.025 0.034 0.089 24 -0.12 27 51
HCK -0.018 0.03 0.089 19 -0.12 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 33 33
TGFBR2 0.035 0.009 -10000 0 0 29 29
cell death 0.034 0.057 -10000 0 -0.16 38 38
ATIII/GPC1 0.037 0.049 -10000 0 -0.14 33 33
PLA2G2A/GPC1 -0.005 0.074 -10000 0 -0.15 93 93
LCK -0.024 0.034 0.089 24 -0.12 25 49
neuron differentiation 0.037 0.05 -10000 0 -0.14 35 35
PrPc/Cu2+ 0.016 0.038 -10000 0 -0.13 31 31
APP 0.035 0.007 -10000 0 0 21 21
TGFBR2 (dimer) 0.034 0.009 -10000 0 0 29 29
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.051 -10000 0 -0.18 28 28
PDGFRB 0.036 0.009 -10000 0 -0.001 28 28
SPHK1 0.017 0.04 -10000 0 -0.76 1 1
mol:S1P 0.019 0.042 -10000 0 -0.68 1 1
S1P1/S1P/Gi -0.001 0.14 0.23 19 -0.42 33 52
GNAO1 0.032 0.015 0.063 1 0 87 88
PDGFB-D/PDGFRB/PLCgamma1 0.027 0.14 0.25 22 -0.37 31 53
PLCG1 -0.005 0.13 0.22 21 -0.42 29 50
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.036 0.009 -10000 0 -0.001 28 28
GNAI2 0.036 0.012 -10000 0 0 43 43
GNAI3 0.037 0.007 -10000 0 0 15 15
GNAI1 0.018 0.019 -10000 0 0 263 263
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.007 0.073 0.12 5 -0.27 27 32
S1P1/S1P 0.024 0.077 0.22 3 -0.28 17 20
negative regulation of cAMP metabolic process 0 0.14 0.23 20 -0.41 33 53
MAPK3 0.002 0.14 0.27 22 -0.44 26 48
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
KDR 0.027 0.034 0.093 1 -0.13 18 19
PLCB2 0.036 0.089 0.22 19 -0.26 17 36
RAC1 0.024 0.017 -10000 0 0 173 173
RhoA/GTP 0.018 0.066 -10000 0 -0.24 18 18
receptor internalization 0.023 0.073 0.21 3 -0.26 17 20
PTGS2 0.032 0.15 0.34 10 -0.44 20 30
Rac1/GTP 0.009 0.057 -10000 0 -0.27 12 12
RHOA 0.035 0.007 -10000 0 0 18 18
VEGFA -0.001 0.021 -10000 0 -0.098 23 23
negative regulation of T cell proliferation 0 0.14 0.23 20 -0.41 33 53
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.015 -10000 0 0 81 81
MAPK1 0.003 0.14 0.26 22 -0.46 24 46
S1P1/S1P/PDGFB-D/PDGFRB 0.052 0.1 0.25 12 -0.29 20 32
ABCC1 0.036 0.008 -10000 0 0 19 19
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.019 0.11 0.22 2 -0.37 28 30
adherens junction organization -0.001 0.076 0.18 1 -0.31 19 20
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.11 0.22 15 -0.31 20 35
FMN1 0.008 0.063 0.18 1 -0.27 15 16
mol:IP3 -0.008 0.079 0.14 5 -0.25 32 37
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.013 0.067 0.19 1 -0.28 15 16
CTNNB1 0.035 0.006 -10000 0 0 15 15
AKT1 -0.006 0.088 0.14 2 -0.31 26 28
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.027 0.067 -10000 0 -0.48 4 4
CTNND1 0.035 0.009 -10000 0 0 32 32
mol:PI-4-5-P2 0.003 0.067 0.17 3 -0.27 17 20
VASP 0.002 0.062 0.18 1 -0.27 15 16
ZYX 0.006 0.057 0.16 1 -0.32 9 10
JUB 0.008 0.063 0.18 1 -0.27 15 16
EGFR(dimer) 0.001 0.065 -10000 0 -0.32 13 13
E-cadherin/beta catenin-gamma catenin 0.064 0.029 -10000 0 -0.12 3 3
mol:PI-3-4-5-P3 0.02 0.093 -10000 0 -0.29 25 25
PIK3CA 0.03 0.015 -10000 0 -0.002 84 84
PI3K 0.02 0.095 -10000 0 -0.29 25 25
FYN -0.042 0.13 0.25 1 -0.33 64 65
mol:Ca2+ -0.008 0.078 0.14 5 -0.24 32 37
JUP 0.033 0.011 -10000 0 0 51 51
PIK3R1 0.031 0.015 -10000 0 -0.004 72 72
mol:DAG -0.008 0.079 0.14 5 -0.25 32 37
CDH1 0.034 0.01 -10000 0 0 38 38
RhoA/GDP 0.062 0.13 0.24 28 -0.3 20 48
establishment of polarity of embryonic epithelium 0.002 0.062 0.18 1 -0.27 15 16
SRC 0.036 0.006 -10000 0 0 14 14
RAC1 0.024 0.017 -10000 0 0 173 173
RHOA 0.035 0.007 -10000 0 0 18 18
EGFR 0.009 0.016 -10000 0 0 381 381
CASR -0.024 0.075 0.14 17 -0.27 25 42
RhoA/GTP 0.009 0.086 -10000 0 -0.26 27 27
AKT2 -0.005 0.08 0.15 1 -0.28 25 26
actin cable formation -0.002 0.061 0.17 1 -0.26 16 17
apoptosis 0.01 0.098 0.33 29 -0.21 4 33
CTNNA1 0.035 0.008 -10000 0 -0.001 21 21
mol:GDP -0.021 0.074 0.19 4 -0.31 20 24
PIP5K1A 0.003 0.067 0.17 3 -0.27 17 20
PLCG1 -0.008 0.081 0.14 5 -0.26 32 37
Rac1/GTP -0.004 0.069 -10000 0 -0.32 13 13
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
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 0.012 0.05 -10000 0 -0.12 46 46
TRAF2/ASK1 0.032 0.043 -10000 0 -0.12 35 35
ATM 0.034 0.009 -10000 0 0 35 35
MAP2K3 0.014 0.099 0.24 1 -0.31 24 25
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.09 0.27 1 -0.28 23 24
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 67 67
TXN 0.007 0.002 -10000 0 0 40 40
CALM1 0.033 0.011 -10000 0 0 54 54
GADD45A 0.031 0.013 -10000 0 0 75 75
GADD45B 0.03 0.014 -10000 0 0 89 89
MAP3K1 0.035 0.007 -10000 0 0 20 20
MAP3K6 0.035 0.007 -10000 0 0 20 20
MAP3K7 0.034 0.01 -10000 0 0 41 41
MAP3K4 0.032 0.012 -10000 0 0 66 66
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.053 -10000 0 -0.14 38 38
TAK1/TAB family 0.009 0.054 -10000 0 -0.31 11 11
RAC1/OSM/MEKK3 0.03 0.026 -10000 0 -0.1 5 5
TRAF2 0.036 0.006 -10000 0 0 15 15
RAC1/OSM/MEKK3/MKK3 0.012 0.075 -10000 0 -0.27 21 21
TRAF6 0.009 0.033 -10000 0 -0.2 12 12
RAC1 0.024 0.017 -10000 0 0 173 173
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.017 0.018 -10000 0 0 272 272
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.009 0.054 -10000 0 -0.13 53 53
MAPK11 0.033 0.011 -10000 0 0 49 49
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.011 0.066 -10000 0 -0.13 66 66
OSM/MEKK3 0.027 0.003 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 0 35 35
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 35 35
MAPK14 0.036 0.004 -10000 0 0 6 6
MAP3K7IP2 0.033 0.011 -10000 0 0 46 46
MAP3K5 0.03 0.014 -10000 0 0 90 90
MAP3K10 0.035 0.008 -10000 0 0 28 28
MAP3K3 0.036 0.004 -10000 0 0 7 7
TRX/ASK1 0.022 0.037 -10000 0 -0.16 16 16
GADD45/MTK1/MTK1 0.043 0.075 -10000 0 -0.13 64 64
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.009 0.026 1 -0.034 16 17
BUB1B -0.023 0.084 0.12 22 -0.22 64 86
PLK1 0.004 0.023 0.083 17 -0.071 3 20
PLK1S1 0.002 0.014 0.049 21 -0.039 2 23
KIF2A 0.004 0.021 0.076 15 -0.064 3 18
regulation of mitotic centrosome separation 0.005 0.023 0.083 17 -0.071 3 20
GOLGA2 0.035 0.008 -10000 0 0 28 28
Hec1/SPC24 -0.004 0.01 -10000 0 -0.055 5 5
WEE1 -0.032 0.13 -10000 0 -0.46 36 36
cytokinesis -0.021 0.11 0.16 9 -0.3 57 66
PP2A-alpha B56 0.051 0.087 -10000 0 -0.51 9 9
AURKA 0.002 0.016 0.056 21 -0.04 2 23
PICH/PLK1 -0.034 0.073 0.071 9 -0.18 87 96
CENPE 0.003 0.047 0.12 50 -0.1 12 62
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization 0.004 0.02 0.074 16 -0.063 3 19
PPP2CA 0.035 0.007 -10000 0 0 21 21
FZR1 0.035 0.008 -10000 0 0 28 28
TPX2 -0.025 0.089 0.11 2 -0.22 84 86
PAK1 0.036 0.006 -10000 0 0 15 15
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.008 -10000 0 0 25 25
CLSPN 0.01 0.025 -10000 0 -0.2 5 5
GORASP1 0.034 0.009 -10000 0 0 33 33
metaphase 0.001 0.003 0.015 11 -0.011 1 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.014 0.049 21 -0.039 2 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 0.023 0.083 17 -0.071 3 20
ODF2 0.035 0.009 -10000 0 0 29 29
BUB1 0.02 0.074 -10000 0 -0.57 7 7
TPT1 -0.002 0.05 -10000 0 -0.18 34 34
CDC25C 0.011 0.03 -10000 0 -0.22 7 7
CDC25B 0.012 0.032 -10000 0 -0.029 175 175
SGOL1 0.001 0.009 0.034 16 -0.026 1 17
RHOA 0.035 0.007 -10000 0 0 18 18
CCNB1/CDK1 -0.02 0.12 -10000 0 -0.23 98 98
CDC14B -0.011 0.004 0.01 6 -10000 0 6
CDC20 0.028 0.016 -10000 0 0 125 125
PLK1/PBIP1 -0.015 0.036 0.069 6 -0.089 77 83
mitosis -0.001 0.003 0.011 11 -10000 0 11
FBXO5 -0.017 0.061 0.12 17 -0.16 54 71
CDC2 0.015 0.023 -10000 0 -0.03 42 42
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.059 -10000 0 -0.26 23 23
ERCC6L -0.045 0.1 -10000 0 -0.22 93 93
NLP/gamma Tubulin 0.001 0.027 0.075 11 -0.1 21 32
microtubule cytoskeleton organization -0.002 0.05 -10000 0 -0.18 34 34
G2/M transition DNA damage checkpoint -0.001 0.002 0.01 5 -10000 0 5
PPP1R12A 0.035 0.008 -10000 0 0 24 24
interphase -0.001 0.002 0.01 5 -10000 0 5
PLK1/PRC1-2 0.007 0.075 0.13 1 -0.14 87 88
GRASP65/GM130/RAB1/GTP/PLK1 0.046 0.053 -10000 0 -0.12 29 29
RAB1A 0.035 0.007 -10000 0 0 18 18
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.002 0.018 0.066 18 -0.051 1 19
mitotic prometaphase -0.001 0.005 0.02 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process -0.048 0.1 0.18 1 -0.27 42 43
microtubule-based process 0.019 0.024 0.099 5 -0.064 3 8
Golgi organization 0.005 0.023 0.083 17 -0.071 3 20
Cohesin/SA2 0.02 0.033 0.096 6 -0.094 21 27
PPP1CB/MYPT1 0.046 0.036 -10000 0 -0.15 14 14
KIF20A 0.029 0.015 -10000 0 0 109 109
APC/C/CDC20 0.019 0.024 0.11 5 -0.061 1 6
PPP2R1A 0.032 0.012 -10000 0 0 61 61
chromosome segregation -0.015 0.035 0.068 6 -0.088 77 83
PRC1 0.028 0.016 -10000 0 0 123 123
ECT2 0.001 0.059 0.15 46 -0.11 24 70
C13orf34 0.003 0.019 0.07 17 -0.056 2 19
NUDC 0.001 0.059 -10000 0 -0.26 23 23
regulation of attachment of spindle microtubules to kinetochore -0.023 0.083 0.11 24 -0.21 64 88
spindle assembly 0.002 0.025 0.085 15 -0.078 13 28
spindle stabilization 0.002 0.014 0.048 21 -0.044 1 22
APC/C/HCDH1 0.024 0.026 0.089 1 -0.12 15 16
MKLP2/PLK1 0.019 0.024 0.099 5 -0.064 3 8
CCNB1 0.014 0.028 -10000 0 -0.028 116 116
PPP1CB 0.036 0.006 -10000 0 0 15 15
BTRC 0.025 0.017 -10000 0 0 155 155
ROCK2 0.016 0.029 -10000 0 -0.21 3 3
TUBG1 0.002 0.05 -10000 0 -0.22 22 22
G2/M transition of mitotic cell cycle -0.047 0.1 0.14 18 -0.23 92 110
MLF1IP -0.009 0.006 0.01 1 -10000 0 1
INCENP 0.036 0.005 -10000 0 0 8 8
mTOR signaling 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
GBL 0.036 0.006 -10000 0 0 15 15
MKNK1 0.034 0.009 -10000 0 0 34 34
mol:PIP3 -0.018 0.057 0.094 7 -0.23 22 29
FRAP1 0.03 0.1 0.28 2 -0.48 12 14
AKT1 0.007 0.1 0.17 95 -0.26 30 125
INSR 0.035 0.008 -10000 0 0 25 25
Insulin Receptor/Insulin 0.046 0.013 -10000 0 -10000 0 0
mol:GTP 0.032 0.11 0.2 58 -0.26 30 88
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.005 0.047 -10000 0 -0.19 15 15
TSC2 0.035 0.008 -10000 0 0 28 28
RHEB/GDP 0.002 0.076 0.14 1 -0.22 35 36
TSC1 0.034 0.01 -10000 0 0 40 40
Insulin Receptor/IRS1 0.022 0.061 -10000 0 -0.25 23 23
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.023 0.071 0.16 1 -0.22 14 15
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.036 0.085 0.26 10 -0.32 4 14
MAP3K5 -0.026 0.084 0.16 1 -0.22 73 74
PIK3R1 0.033 0.012 -10000 0 0 63 63
apoptosis -0.026 0.084 0.16 1 -0.22 73 74
mol:LY294002 0 0 0.001 4 -0.001 18 22
EIF4B 0.029 0.082 0.24 11 -0.31 5 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.072 0.24 7 -0.28 4 11
eIF4E/eIF4G1/eIF4A1 0.009 0.075 -10000 0 -0.3 15 15
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.082 -10000 0 -0.22 34 34
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.06 0.2 8 -0.21 10 18
FKBP1A 0.034 0.01 -10000 0 0 44 44
RHEB/GTP 0.014 0.086 0.23 5 -0.23 29 34
mol:Amino Acids 0 0 0.001 4 -0.001 18 22
FKBP12/Rapamycin 0.022 0.023 -10000 0 -0.13 10 10
PDPK1 -0.021 0.061 0.16 15 -0.23 20 35
EIF4E 0.034 0.01 -10000 0 0 38 38
ASK1/PP5C -0.034 0.24 -10000 0 -0.56 79 79
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0.11 -10000 0 -0.33 32 32
TSC1/TSC2 0.035 0.12 0.21 58 -0.28 30 88
tumor necrosis factor receptor activity 0 0 0.001 18 -0.001 4 22
RPS6 0.031 0.013 -10000 0 0 81 81
PPP5C 0.034 0.01 -10000 0 0 39 39
EIF4G1 0.033 0.011 -10000 0 0 49 49
IRS1 0.001 0.058 -10000 0 -0.26 23 23
INS 0.036 0.006 -10000 0 0 14 14
PTEN 0.026 0.017 -10000 0 0 148 148
PDK2 -0.021 0.061 0.16 15 -0.23 19 34
EIF4EBP1 -0.02 0.25 -10000 0 -1.1 24 24
PIK3CA 0.031 0.014 -10000 0 0 80 80
PPP2R5D 0.025 0.097 0.27 3 -0.44 12 15
peptide biosynthetic process -0.02 0.017 0.18 3 -10000 0 3
RHEB 0.024 0.017 -10000 0 0 173 173
EIF4A1 0.035 0.007 -10000 0 0 17 17
mol:Rapamycin 0 0.001 0.004 16 -0.003 14 30
EEF2 -0.021 0.017 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.004 0.24 -10000 0 -1.1 24 24
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.01 0.057 -10000 0 -0.2 28 28
epithelial cell differentiation 0.063 0.051 -10000 0 -0.14 25 25
CYFIP2 0.031 0.013 -10000 0 0 78 78
ENAH -0.041 0.07 0.24 12 -0.25 9 21
EGFR 0.009 0.016 -10000 0 0 381 381
EPHA2 0.033 0.011 -10000 0 0 54 54
MYO6 -0.029 0.049 0.18 9 -0.21 13 22
CTNNB1 0.036 0.006 -10000 0 0 15 15
ABI1/Sra1/Nap1 0.031 0.063 -10000 0 -0.12 58 58
AQP5 -0.02 0.051 0.21 2 -0.28 9 11
CTNND1 0.034 0.009 -10000 0 0 32 32
mol:PI-4-5-P2 -0.031 0.044 0.18 6 -0.2 13 19
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 0.036 0.002 -10000 0 0 2 2
AQP3 -0.035 0.075 -10000 0 -0.3 32 32
cortical microtubule organization 0.063 0.051 -10000 0 -0.14 25 25
GO:0000145 -0.03 0.04 0.16 6 -0.19 13 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.07 0.054 -10000 0 -0.14 25 25
MLLT4 0.034 0.009 -10000 0 0 36 36
ARF6/GDP -0.052 0.039 -10000 0 -0.22 12 12
ARF6 0.035 0.008 -10000 0 0 27 27
Ephrin A1/EPHA2/NCK1/GIT1 0.076 0.052 -10000 0 -0.12 24 24
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.029 0.079 0.16 1 -0.28 33 34
PVRL2 0.034 0.009 -10000 0 0 35 35
ZYX -0.021 0.046 0.18 6 -0.21 15 21
ARF6/GTP 0.079 0.059 -10000 0 -0.12 23 23
CDH1 0.034 0.01 -10000 0 0 38 38
EGFR/EGFR/EGF/EGF -0.001 0.059 -10000 0 -0.13 66 66
RhoA/GDP 0.063 0.056 -10000 0 -0.14 29 29
actin cytoskeleton organization -0.024 0.045 0.17 6 -0.22 12 18
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 57 57
GIT1 0.036 0.003 -10000 0 0 4 4
IGF1R 0.033 0.012 -10000 0 0 57 57
IGF1 0.035 0.008 -10000 0 0 23 23
DIAPH1 -0.12 0.27 -10000 0 -0.52 130 130
Wnt receptor signaling pathway -0.063 0.051 0.14 25 -10000 0 25
RHOA 0.035 0.007 -10000 0 0 18 18
RhoA/GTP -0.053 0.041 -10000 0 -0.21 16 16
CTNNA1 0.035 0.007 -10000 0 0 20 20
VCL -0.024 0.046 0.17 6 -0.23 12 18
EFNA1 0.033 0.011 -10000 0 0 50 50
LPP -0.03 0.045 0.18 4 -0.22 13 17
Ephrin A1/EPHA2 0.046 0.062 -10000 0 -0.14 40 40
SEC6/SEC8 -0.044 0.028 -10000 0 -0.14 25 25
MGAT3 -0.028 0.044 0.19 8 -0.19 8 16
HGF/MET 0.036 0.05 -10000 0 -0.14 16 16
HGF 0.024 0.017 -10000 0 0 177 177
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.01 0.057 -10000 0 -0.21 28 28
actin cable formation -0.039 0.1 0.32 9 -0.3 33 42
KIAA1543 -0.025 0.036 0.16 7 -0.18 8 15
KIFC3 -0.031 0.042 0.19 5 -0.19 8 13
NCK1 0.035 0.008 -10000 0 0 27 27
EXOC3 0.036 0.003 -10000 0 0 4 4
ACTN1 -0.026 0.049 0.19 7 -0.21 16 23
NCK1/GIT1 0.05 0.022 -10000 0 -0.14 5 5
mol:GDP 0.063 0.051 -10000 0 -0.14 25 25
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.028 0.03 0.053 22 -0.13 25 47
PIP5K1C -0.031 0.045 0.18 6 -0.21 13 19
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.017 -10000 0 0 152 152
ROCK1 -0.034 0.085 0.28 17 -0.29 5 22
adherens junction assembly -0.023 0.073 0.23 6 -0.33 14 20
IGF-1R heterotetramer/IGF1 0.048 0.062 -10000 0 -0.14 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 0 191 191
PLEKHA7 -0.028 0.03 0.053 22 -0.13 25 47
mol:GTP 0.073 0.051 -10000 0 -0.12 24 24
establishment of epithelial cell apical/basal polarity -0.038 0.039 0.12 13 -0.18 10 23
cortical actin cytoskeleton stabilization 0.01 0.057 -10000 0 -0.2 28 28
regulation of cell-cell adhesion -0.024 0.045 0.17 6 -0.22 12 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.01 0.057 -10000 0 -0.21 28 28
Arf6 downstream 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
PLAUR -0.013 0.19 -10000 0 -0.83 23 23
regulation of axonogenesis 0.003 0.064 0.25 22 -10000 0 22
myoblast fusion -0.015 0.093 0.35 27 -10000 0 27
mol:GTP 0.015 0.065 -10000 0 -0.18 44 44
regulation of calcium-dependent cell-cell adhesion -0.026 0.073 0.17 41 -10000 0 41
ARF1/GTP 0.035 0.061 -10000 0 -0.14 46 46
mol:GM1 0.003 0.047 -10000 0 -0.13 45 45
mol:Choline -0.015 0.041 0.085 3 -0.13 40 43
lamellipodium assembly -0.009 0.1 -10000 0 -0.37 33 33
MAPK3 0.012 0.081 -10000 0 -0.29 25 25
ARF6/GTP/NME1/Tiam1 0.027 0.074 -10000 0 -0.18 41 41
ARF1 0.035 0.008 -10000 0 0 24 24
ARF6/GDP 0.015 0.093 -10000 0 -0.35 27 27
ARF1/GDP 0.013 0.1 -10000 0 -0.29 43 43
ARF6 0.039 0.042 -10000 0 -0.13 25 25
RAB11A 0.035 0.007 -10000 0 0 18 18
TIAM1 0.029 0.022 -10000 0 -0.044 32 32
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.082 -10000 0 -0.31 24 24
actin filament bundle formation -0.019 0.11 0.29 47 -10000 0 47
KALRN 0.006 0.069 0.13 2 -0.26 28 30
RAB11FIP3/RAB11A 0.047 0.034 -10000 0 -0.16 12 12
RhoA/GDP 0.02 0.11 -10000 0 -0.29 47 47
NME1 -0.001 0.008 -10000 0 -0.03 24 24
Rac1/GDP 0.013 0.089 -10000 0 -0.3 29 29
substrate adhesion-dependent cell spreading 0.015 0.065 -10000 0 -0.18 44 44
cortical actin cytoskeleton organization -0.009 0.1 -10000 0 -0.37 33 33
RAC1 0.024 0.017 -10000 0 0 173 173
liver development 0.015 0.065 -10000 0 -0.18 44 44
ARF6/GTP 0.015 0.065 -10000 0 -0.18 44 44
RhoA/GTP 0.034 0.063 -10000 0 -0.15 50 50
mol:GDP -0.005 0.1 0.17 2 -0.3 44 46
ARF6/GTP/RAB11FIP3/RAB11A 0.051 0.068 -10000 0 -0.14 45 45
RHOA 0.035 0.007 -10000 0 0 18 18
PLD1 0.012 0.051 -10000 0 -0.14 44 44
RAB11FIP3 0.036 0.006 -10000 0 0 15 15
tube morphogenesis -0.009 0.1 -10000 0 -0.37 33 33
ruffle organization -0.003 0.064 -10000 0 -0.25 22 22
regulation of epithelial cell migration 0.015 0.065 -10000 0 -0.18 44 44
PLD2 0.012 0.052 -10000 0 -0.14 46 46
PIP5K1A -0.003 0.064 -10000 0 -0.25 22 22
mol:Phosphatidic acid -0.015 0.041 0.085 3 -0.13 40 43
Rac1/GTP -0.009 0.1 -10000 0 -0.37 33 33
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 -0.018 0.021 0.092 16 -10000 0 16
BAD/BCL-XL/YWHAZ 0.048 0.034 -10000 0 -0.12 12 12
CDKN1B -0.024 0.12 -10000 0 -0.33 57 57
CDKN1A -0.024 0.12 -10000 0 -0.33 58 58
FRAP1 0.035 0.007 -10000 0 0 17 17
PRKDC 0.033 0.01 -10000 0 0 44 44
FOXO3 -0.019 0.11 -10000 0 -0.31 59 59
AKT1 -0.019 0.12 -10000 0 -0.33 58 58
BAD 0.036 0.006 -10000 0 0 14 14
AKT3 0.014 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.019 0.11 -10000 0 -0.31 59 59
AKT1/ASK1 -0.009 0.12 -10000 0 -0.32 58 58
BAD/YWHAZ 0.063 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 58 -10000 0 58
TSC1 -0.025 0.12 0.2 1 -0.33 57 58
YWHAZ 0.035 0.007 -10000 0 0 21 21
AKT1/RAF1 -0.002 0.13 -10000 0 -0.34 60 60
EP300 0.033 0.011 -10000 0 0 49 49
mol:GDP -0.019 0.12 -10000 0 -0.32 58 58
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.027 0.12 -10000 0 -0.33 60 60
YWHAQ 0.036 0.005 -10000 0 0 9 9
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 31 31
negative regulation of cell cycle 0.005 0.11 0.4 20 -10000 0 20
YWHAH 0.031 0.013 -10000 0 0 73 73
AKT1S1 -0.019 0.11 -10000 0 -0.31 59 59
CASP9 -0.021 0.11 0.2 3 -0.32 57 60
YWHAB 0.035 0.008 -10000 0 0 24 24
p27Kip1/KPNA1 -0.008 0.13 0.27 3 -0.32 58 61
GBL 0.036 0.006 -10000 0 0 15 15
PDK1/Src/Hsp90 0.047 0.01 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
SRC 0.036 0.006 -10000 0 0 14 14
AKT2/p21CIP1 -0.025 0.11 0.23 1 -0.29 57 58
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.067 -10000 0 -0.44 7 7
CHUK -0.021 0.1 -10000 0 -0.33 46 46
BAD/BCL-XL 0.004 0.12 -10000 0 -0.32 56 56
mTORC2 0.06 0.031 -10000 0 -0.12 8 8
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.007 0.13 -10000 0 -0.46 24 24
PDPK1 0.036 0.004 -10000 0 0 7 7
MDM2 -0.017 0.12 0.2 11 -0.32 57 68
MAPKKK cascade 0.002 0.13 0.33 60 -10000 0 60
MDM2/Cbp/p300 0.015 0.13 0.27 1 -0.31 58 59
TSC1/TSC2 -0.03 0.13 0.26 8 -0.34 60 68
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.12 0.26 1 -0.3 58 59
glucose import -0.008 0.022 0.2 3 -10000 0 3
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.082 -10000 0 -0.33 9 9
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.022 0.2 3 -10000 0 3
GSK3A -0.019 0.11 0.23 9 -0.32 54 63
FOXO1 -0.019 0.11 -10000 0 -0.31 59 59
GSK3B -0.024 0.12 0.2 1 -0.34 58 59
SFN 0.031 0.013 -10000 0 0 78 78
G1/S transition of mitotic cell cycle -0.028 0.12 0.25 8 -0.33 59 67
p27Kip1/14-3-3 family 0.008 0.11 -10000 0 -0.53 13 13
PRKACA 0.035 0.008 -10000 0 0 25 25
KPNA1 0.035 0.008 -10000 0 0 27 27
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.024 0.017 -10000 0 0 173 173
CREBBP 0.036 0.005 -10000 0 0 8 8
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.042 0.01 -10000 0 -0.042 1 1
NFATC2 0.014 0.15 0.27 5 -0.37 38 43
NFATC3 0.017 0.13 0.28 21 -0.24 68 89
CD40LG -0.016 0.33 0.49 41 -0.72 63 104
ITCH 0.035 0.046 0.19 8 -10000 0 8
CBLB 0.036 0.048 0.19 11 -10000 0 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.051 0.26 0.38 13 -0.64 52 65
JUNB 0.031 0.014 -10000 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.027 -10000 0 -0.13 6 6
T cell anergy 0.016 0.067 0.26 10 -0.25 1 11
TLE4 0.01 0.11 -10000 0 -0.32 21 21
Jun/NFAT1-c-4/p21SNFT -0.017 0.33 -10000 0 -0.74 68 68
AP-1/NFAT1-c-4 -0.033 0.35 -10000 0 -0.81 59 59
IKZF1 0.006 0.099 0.17 6 -0.24 37 43
T-helper 2 cell differentiation -0.085 0.23 -10000 0 -0.67 35 35
AP-1/NFAT1 0.017 0.14 0.28 17 -0.29 44 61
CALM1 0.046 0.024 0.13 2 -10000 0 2
EGR2 -0.08 0.41 0.51 10 -1 65 75
EGR3 -0.059 0.42 0.51 10 -1.1 58 68
NFAT1/FOXP3 0.038 0.12 0.26 3 -0.28 27 30
EGR1 0.029 0.015 0.07 1 -10000 0 1
JUN 0.032 0.041 0.11 35 -0.052 11 46
EGR4 0.037 0.004 0.07 1 -10000 0 1
mol:Ca2+ 0.005 0.003 -10000 0 -10000 0 0
GBP3 0.006 0.099 0.17 6 -0.24 37 43
FOSL1 0.033 0.011 -10000 0 0 55 55
NFAT1-c-4/MAF/IRF4 0.009 0.33 -10000 0 -0.74 69 69
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 -0.009 0.33 -10000 0 -0.74 70 70
CTLA4 0.009 0.092 0.18 1 -0.26 21 22
NFAT1-c-4 (dimer)/EGR1 -0.03 0.34 -10000 0 -0.79 70 70
NFAT1-c-4 (dimer)/EGR4 -0.001 0.33 -10000 0 -0.75 69 69
FOS 0.023 0.038 0.11 19 -0.049 9 28
IFNG -0.009 0.13 -10000 0 -0.45 10 10
T cell activation -0.013 0.21 -10000 0 -0.56 26 26
MAF 0.034 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 0.008 0.28 0.61 68 -0.46 16 84
TNF -0.04 0.31 0.42 6 -0.72 69 75
FASLG -0.1 0.46 -10000 0 -1.1 73 73
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 0.42 1 -0.37 23 24
NFAT1-c-4/ICER1 -0.033 0.32 -10000 0 -0.74 70 70
GATA3 0.027 0.018 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.004 0.14 -10000 0 -0.44 10 10
IL2RA -0.06 0.25 0.36 4 -0.63 55 59
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.007 0.11 -10000 0 -0.36 24 24
E2F1 0.037 0.051 -10000 0 -0.25 13 13
PPARG 0.035 0.008 -10000 0 -10000 0 0
SLC3A2 0.008 0.12 0.24 2 -0.38 26 28
IRF4 0.037 0.002 -10000 0 -10000 0 0
PTGS2 -0.071 0.28 0.45 1 -0.71 62 63
CSF2 -0.016 0.33 0.49 40 -0.72 62 102
JunB/Fra1/NFAT1-c-4 -0.014 0.31 -10000 0 -0.72 68 68
IL4 -0.089 0.24 -10000 0 -0.7 34 34
IL5 -0.016 0.33 0.49 41 -0.72 62 103
IL2 -0.013 0.22 -10000 0 -0.57 25 25
IL3 0.007 0.088 -10000 0 -0.58 7 7
RNF128 0.014 0.022 0.17 1 -10000 0 1
NFATC1 -0.008 0.28 0.46 15 -0.61 68 83
CDK4 -0.011 0.27 0.55 28 -1 14 42
PTPRK -0.001 0.14 -10000 0 -0.43 34 34
IL8 -0.1 0.29 0.48 5 -0.76 60 65
POU2F1 0.039 0.008 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.035 0.009 -10000 0 0 29 29
RAS family/GTP/Tiam1 -0.006 0.085 -10000 0 -0.2 62 62
NT3 (dimer)/TRKC 0.046 0.026 -10000 0 -0.14 6 6
NT3 (dimer)/TRKB 0.026 0.069 -10000 0 -0.12 73 73
SHC/Grb2/SOS1/GAB1/PI3K -0.008 0.095 -10000 0 -0.21 75 75
RAPGEF1 0.035 0.007 -10000 0 0 19 19
BDNF 0.032 0.012 -10000 0 0 67 67
PIK3CA 0.031 0.013 -10000 0 0 80 80
DYNLT1 0.033 0.01 -10000 0 0 44 44
NTRK1 0.035 0.006 -10000 0 0 16 16
NTRK2 0.026 0.016 -10000 0 0 142 142
NTRK3 0.034 0.01 -10000 0 0 38 38
NT-4/5 (dimer)/TRKB 0.013 0.058 -10000 0 -0.12 77 77
neuron apoptosis -0.007 0.12 0.32 42 -0.23 1 43
SHC 2-3/Grb2 0.007 0.13 0.24 1 -0.34 42 43
SHC1 0.033 0.011 -10000 0 0 52 52
SHC2 -0.012 0.12 -10000 0 -0.43 29 29
SHC3 -0.012 0.12 -10000 0 -0.41 31 31
STAT3 (dimer) 0.022 0.087 -10000 0 -0.28 36 36
NT3 (dimer)/TRKA 0.059 0.03 -10000 0 -10000 0 0
RIN/GDP 0.001 0.074 0.18 5 -0.22 25 30
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 0.035 -10000 0 -0.13 26 26
CCND1 -0.011 0.11 -10000 0 -0.49 25 25
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 46 46
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.04 0.031 -10000 0 -0.12 14 14
GRB2 0.035 0.007 -10000 0 0 17 17
NGF (dimer)/TRKA/MATK 0.045 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 0.046 -10000 0 -0.12 46 46
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.009 -10000 0 0 32 32
DOCK1 0.024 0.017 -10000 0 0 175 175
GAB2 0.033 0.011 -10000 0 0 47 47
RIT2 0.024 0.017 -10000 0 0 170 170
RIT1 0.032 0.012 -10000 0 0 60 60
FRS2 0.034 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 0.009 0.048 0.16 2 -0.17 12 14
mol:GDP -0.001 0.1 0.22 6 -0.32 24 30
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.002 0.043 -10000 0 -0.13 45 45
RIT1/GDP 0.008 0.081 0.19 6 -0.23 22 28
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 0.069 -10000 0 -0.12 70 70
KIDINS220/CRKL/C3G 0.05 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.051 -10000 0 -0.15 31 31
FRS2 family/SHP2 0.067 0.028 -10000 0 -0.12 6 6
SHC/GRB2/SOS1/GAB1 0.048 0.046 -10000 0 -0.11 25 25
RIT1/GTP 0.015 0.04 -10000 0 -0.13 35 35
NT3 (dimer) 0.035 0.008 -10000 0 0 23 23
RAP1/GDP -0.002 0.06 -10000 0 -0.18 27 27
KIDINS220/CRKL 0.034 0.009 -10000 0 0 29 29
BDNF (dimer) 0.032 0.012 -10000 0 0 67 67
ubiquitin-dependent protein catabolic process 0.043 0.017 -10000 0 -0.11 1 1
Schwann cell development -0.01 0.016 -10000 0 -0.056 33 33
EHD4 0.034 0.01 -10000 0 0 41 41
FRS2 family/GRB2/SOS1 0.062 0.029 -10000 0 -0.11 8 8
FRS2 family/SHP2/CRK family/C3G/GAB2 0.008 0.07 -10000 0 -0.25 20 20
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 11 11
CDC42/GTP 0.019 0.081 -10000 0 -0.14 73 73
ABL1 0.032 0.013 -10000 0 0 70 70
SH2B family/GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
Rap1/GTP 0.003 0.068 -10000 0 -0.24 12 12
STAT3 0.022 0.087 -10000 0 -0.28 36 36
axon guidance 0.005 0.07 -10000 0 -0.14 79 79
MAPK3 -0.007 0.055 0.17 43 -10000 0 43
MAPK1 -0.008 0.05 0.17 35 -10000 0 35
CDC42/GDP 0.011 0.08 0.18 10 -0.22 22 32
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.025 -10000 0 -0.12 9 9
PI3K 0.019 0.075 -10000 0 -0.16 73 73
FRS3 0.036 0.002 -10000 0 0 2 2
FAIM 0.034 0.009 -10000 0 0 30 30
GAB1 0.032 0.012 -10000 0 0 59 59
RASGRF1 -0.006 0.039 0.14 2 -0.13 4 6
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.018 0.02 0.089 10 -0.12 2 12
RGS19 0.033 0.011 -10000 0 0 51 51
CDC42 0.035 0.008 -10000 0 0 24 24
RAS family/GTP 0.009 0.1 0.23 1 -0.38 22 23
Rac1/GDP 0.009 0.068 0.18 7 -0.23 17 24
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 0.043 0.017 -10000 0 -0.12 1 1
MAP2K1 -0.011 0.058 0.18 17 -0.19 6 23
NGFR 0.031 0.013 -10000 0 0 71 71
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.043 -10000 0 -0.22 9 9
RAS family/GTP/PI3K -0.023 0.1 -10000 0 -0.21 99 99
FRS2 family/SHP2/GRB2/SOS1 0.076 0.039 -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 26 26
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.017 -10000 0 0 173 173
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.086 -10000 0 -0.48 12 12
RASA1 0.034 0.009 -10000 0 0 32 32
TRKA/c-Abl 0.032 0.058 -10000 0 -0.14 48 48
SQSTM1 0.034 0.009 -10000 0 0 35 35
BDNF (dimer)/TRKB/GIPC 0.049 0.074 -10000 0 -0.12 66 66
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.033 -10000 0 -0.1 14 14
MATK 0.034 0.009 -10000 0 0 30 30
NEDD4L 0.033 0.01 -10000 0 0 44 44
RAS family/GDP -0.02 0.056 -10000 0 -0.16 48 48
NGF (dimer)/TRKA 0.009 0.04 0.15 4 -0.13 4 8
Rac1/GTP -0.014 0.055 -10000 0 -0.21 23 23
FRS2 family/SHP2/CRK family 0.087 0.056 -10000 0 -0.12 17 17
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.03 0.035 -10000 0 -0.14 9 9
CRKL 0.042 0.11 0.28 6 -0.4 21 27
mol:PIP3 -0.009 0.1 -10000 0 -0.79 7 7
AKT1 -0.02 0.092 0.25 1 -0.7 7 8
PTK2B 0.035 0.006 -10000 0 0 16 16
RAPGEF1 0.04 0.11 0.29 10 -0.38 21 31
RANBP10 0.036 0.005 -10000 0 0 10 10
PIK3CA 0.031 0.013 -10000 0 0 80 80
HGF/MET/SHIP2 0.042 0.038 -10000 0 -0.12 2 2
MAP3K5 0.04 0.11 0.27 8 -0.36 23 31
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.035 -10000 0 -10000 0 0
AP1 0.035 0.079 0.14 105 -0.14 46 151
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 -0.79 109 109
STAT3 (dimer) 0.011 0.059 -10000 0 -0.28 11 11
GAB1/CRKL/SHP2/PI3K 0.058 0.13 0.31 2 -0.39 22 24
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.059 0.12 0.29 3 -0.39 21 24
PTPN11 0.036 0.005 -10000 0 0 11 11
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.035 0.007 -10000 0 0 19 19
PTEN 0.026 0.017 -10000 0 0 148 148
ELK1 0.12 0.18 0.35 181 -10000 0 181
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.034 0.16 1 -0.16 7 8
PAK1 -0.024 0.088 -10000 0 -0.68 7 7
HGF/MET/RANBP10 0.042 0.037 -10000 0 -10000 0 0
HRAS 0.011 0.083 -10000 0 -0.47 11 11
DOCK1 0.031 0.11 0.26 8 -0.39 20 28
GAB1 0.045 0.12 -10000 0 -0.41 21 21
CRK 0.043 0.11 0.29 3 -0.4 21 24
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.069 -10000 0 -0.42 10 10
JUN 0.034 0.01 -10000 0 0 40 40
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.01 0.017 -10000 0 -0.12 1 1
PIK3R1 0.032 0.012 -10000 0 0 63 63
cell morphogenesis 0.024 0.11 0.28 22 -0.32 14 36
GRB2/SHC 0.077 0.065 0.17 115 -0.12 2 117
FOS 0.025 0.017 -10000 0 0 158 158
GLMN 0.004 0.004 0.068 2 -10000 0 2
cell motility 0.12 0.18 0.35 181 -10000 0 181
HGF/MET/MUC20 0.029 0.024 -10000 0 -10000 0 0
cell migration 0.075 0.063 0.17 115 -0.12 2 117
GRB2 0.035 0.007 -10000 0 0 17 17
CBL 0.036 0.004 -10000 0 0 7 7
MET/RANBP10 0.033 0.026 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.048 -10000 0 -0.19 20 20
MET/MUC20 0.017 0.013 -10000 0 -10000 0 0
RAP1B 0.039 0.11 0.28 10 -0.36 21 31
RAP1A 0.034 0.11 0.29 9 -0.35 21 30
HGF/MET/RANBP9 0.04 0.042 -10000 0 -0.12 8 8
RAF1 0.038 0.1 0.28 2 -0.45 13 15
STAT3 0.009 0.058 -10000 0 -0.29 11 11
cell proliferation 0.039 0.081 0.23 16 -0.28 9 25
RPS6KB1 0.014 0.018 -10000 0 -10000 0 0
MAPK3 0.084 0.17 0.38 38 -10000 0 38
MAPK1 0.12 0.22 0.52 68 -10000 0 68
RANBP9 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.048 0.16 0.26 2 -0.34 74 76
SRC 0.007 0.046 -10000 0 -0.18 19 19
PI3K 0.061 0.074 0.17 97 -0.15 10 107
MET/Glomulin 0.016 0.026 -10000 0 -0.087 17 17
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.029 0.1 0.27 2 -0.43 14 16
MET 0.023 0.018 -10000 0 0 191 191
MAP4K1 0.048 0.11 0.3 4 -0.37 22 26
PTK2 0.034 0.009 -10000 0 0 32 32
MAP2K2 0.038 0.11 0.3 14 -0.42 12 26
BAD -0.027 0.088 -10000 0 -0.63 8 8
MAP2K4 0.033 0.11 0.27 10 -0.34 23 33
SHP2/GRB2/SOS1/GAB1 0.016 0.085 -10000 0 -0.33 22 22
INPPL1 0.036 0.006 -10000 0 0 12 12
PXN 0.036 0.004 -10000 0 0 7 7
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.001 0.018 0.081 3 -0.12 1 4
PLCgamma1/PKC 0.025 0.013 -10000 0 -0.13 3 3
HGF 0.024 0.017 -10000 0 0 177 177
RASA1 0.034 0.009 -10000 0 0 32 32
NCK1 0.035 0.008 -10000 0 0 27 27
PTPRJ 0.036 0.005 -10000 0 0 11 11
NCK/PLCgamma1 0.083 0.059 0.17 120 -0.12 1 121
PDPK1 -0.012 0.096 0.29 1 -0.74 7 8
HGF/MET/SHIP 0.029 0.024 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.035 0.007 -10000 0 0 19 19
RAC1-CDC42/GTP/PAK family 0.002 0.048 -10000 0 -0.14 41 41
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.034 0.01 -10000 0 0 41 41
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 0.004 -10000 0 0 7 7
FYN 0.03 0.014 -10000 0 0 90 90
MAP3K12 0.036 0.005 -10000 0 0 9 9
FGR 0.033 0.011 -10000 0 0 54 54
p38 alpha/TAB1 0.018 0.11 0.19 3 -0.26 38 41
PRKG1 0.026 0.016 -10000 0 0 141 141
DUSP8 0.034 0.01 -10000 0 0 39 39
PGK/cGMP/p38 alpha 0.004 0.098 0.17 1 -0.25 38 39
apoptosis 0.017 0.1 0.18 3 -0.25 38 41
RAL/GTP 0.026 0.038 -10000 0 -0.12 20 20
LYN 0.031 0.013 -10000 0 0 74 74
DUSP1 0.031 0.013 -10000 0 0 77 77
PAK1 0.036 0.006 -10000 0 0 15 15
SRC 0.036 0.006 -10000 0 0 14 14
RAC1/OSM/MEKK3/MKK3 0.044 0.037 -10000 0 -0.11 5 5
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.024 0.017 -10000 0 0 173 173
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 0.03 0.028 -10000 0 -0.12 5 5
MAPK11 -0.002 0.13 0.21 3 -0.32 44 47
BLK 0.035 0.007 -10000 0 0 17 17
HCK 0.027 0.016 -10000 0 0 128 128
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 48 48
TRAF6/MEKK3 0.045 0.01 -10000 0 -0.1 1 1
MAP3K7IP1 0.034 0.009 -10000 0 0 35 35
MAPK14 0.009 0.11 0.18 4 -0.27 40 44
positive regulation of innate immune response 0.001 0.14 0.23 3 -0.34 47 50
LCK 0.035 0.007 -10000 0 0 17 17
p38alpha-beta/MKP7 -0.001 0.14 0.21 4 -0.33 47 51
p38alpha-beta/MKP5 0.014 0.14 0.24 3 -0.34 40 43
PGK/cGMP 0.02 0.012 -10000 0 -10000 0 0
PAK2 0.035 0.007 -10000 0 0 20 20
p38alpha-beta/MKP1 0.005 0.14 0.24 3 -0.34 47 50
CDC42 0.035 0.008 -10000 0 0 24 24
RALB 0.035 0.007 -10000 0 0 17 17
RALA 0.024 0.018 -10000 0 0 180 180
PAK3 0.027 0.016 -10000 0 0 139 139
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.064 0.26 0.62 9 -0.77 17 26
CRP 0.06 0.26 0.61 9 -0.76 17 26
cell cycle arrest 0.052 0.29 0.53 17 -0.75 30 47
TIMP1 0.005 0.36 0.55 15 -0.8 68 83
IL6ST 0.028 0.033 0.09 1 -0.048 36 37
Rac1/GDP 0.039 0.11 0.3 16 -0.3 11 27
AP1 0.012 0.2 0.31 2 -0.55 39 41
GAB2 0.034 0.012 -10000 0 -0.041 1 1
TNFSF11 0.058 0.26 0.57 8 -0.77 17 25
HSP90B1 0.001 0.22 0.3 3 -0.84 30 33
GAB1 0.033 0.013 -10000 0 -0.042 1 1
MAPK14 0.029 0.065 -10000 0 -0.3 3 3
AKT1 -0.013 0.17 -10000 0 -0.58 29 29
FOXO1 -0.014 0.16 -10000 0 -0.52 33 33
MAP2K6 0.028 0.07 -10000 0 -0.28 6 6
mol:GTP 0 0.004 -10000 0 -0.022 1 1
MAP2K4 0.033 0.14 0.34 24 -0.37 14 38
MITF 0.032 0.083 0.22 11 -0.29 9 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.033 0.011 -10000 0 0 46 46
A2M -0.076 0.34 -10000 0 -1.2 44 44
CEBPB 0.032 0.013 -10000 0 0 71 71
GRB2/SOS1/GAB family/SHP2 0.021 0.13 0.26 3 -0.48 24 27
STAT3 0.042 0.3 0.54 16 -0.8 30 46
STAT1 0.021 0.065 -10000 0 -0.72 3 3
CEBPD 0.024 0.33 0.54 11 -0.9 42 53
PIK3CA 0.031 0.014 -10000 0 -0.041 1 1
PI3K 0.019 0.075 -10000 0 -0.15 74 74
JUN 0.034 0.01 -10000 0 0 40 40
PIAS3/MITF 0.077 0.11 0.27 22 -0.3 9 31
MAPK11 0.026 0.064 -10000 0 -0.3 3 3
STAT3 (dimer)/FOXO1 -0.021 0.26 0.44 9 -0.63 49 58
GRB2/SOS1/GAB family 0.043 0.12 0.23 2 -0.31 30 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.004 0.1 0.18 10 -0.29 35 45
GRB2 0.036 0.008 -10000 0 -0.042 1 1
JAK2 0.031 0.014 -10000 0 0 83 83
LBP 0.064 0.25 0.52 18 -0.64 24 42
PIK3R1 0.032 0.013 -10000 0 -0.042 1 1
JAK1 0.03 0.026 -10000 0 -0.042 45 45
MYC 0.014 0.36 0.6 10 -0.88 56 66
FGG 0.058 0.26 0.57 8 -0.77 17 25
macrophage differentiation 0.052 0.29 0.53 17 -0.75 30 47
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.074 -10000 0 -0.19 5 5
JUNB 0.053 0.29 0.52 23 -0.87 25 48
FOS 0.025 0.017 -10000 0 0 158 158
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.083 0.22 13 -0.29 10 23
STAT1/PIAS1 0.071 0.12 0.28 20 -0.37 6 26
GRB2/SOS1/GAB family/SHP2/PI3K -0.001 0.17 -10000 0 -0.5 35 35
STAT3 (dimer) 0.044 0.29 0.54 16 -0.79 30 46
PRKCD 0.11 0.22 0.41 95 -0.44 20 115
IL6R 0.03 0.027 -10000 0 -0.041 57 57
SOCS3 0.059 0.086 0.42 3 -10000 0 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.045 0.087 0.18 1 -0.17 43 44
Rac1/GTP 0.033 0.11 0.31 10 -0.33 11 21
HCK 0.027 0.016 -10000 0 0 128 128
MAPKKK cascade 0.011 0.19 0.34 2 -0.59 35 37
bone resorption 0.06 0.25 0.56 9 -0.72 17 26
IRF1 0.053 0.29 0.55 16 -0.88 23 39
mol:GDP 0.031 0.09 0.24 14 -0.29 9 23
SOS1 0.001 0.004 0.025 10 -0.022 1 11
VAV1 0.03 0.09 0.24 15 -0.29 9 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.02 0.075 -10000 0 -0.33 12 12
PTPN11 0.015 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 0.074 -10000 0 -0.15 40 40
gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.063 -10000 0 -0.12 33 33
IL6 0.015 0.027 -10000 0 -0.045 13 13
PIAS3 0.036 0.006 -10000 0 0 14 14
PTPRE 0.01 0.03 -10000 0 -0.058 31 31
PIAS1 0.035 0.008 -10000 0 0 27 27
RAC1 0.024 0.018 -10000 0 0 174 174
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.018 0.052 0.17 6 -0.22 6 12
LMO4 0.029 0.033 0.09 1 -0.047 44 45
STAT3 (dimer)/PIAS3 0.015 0.26 0.47 5 -0.73 31 36
MCL1 -0.014 0.16 -10000 0 -0.85 11 11
IGF1 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
NCK2 0.035 0.007 -10000 0 0 17 17
PTK2 0.034 0.009 -10000 0 0 32 32
CRKL -0.017 0.044 0.097 27 -0.15 24 51
GRB2/SOS1/SHC 0.04 0.031 -10000 0 -0.12 14 14
HRAS 0.034 0.009 -10000 0 0 32 32
IRS1/Crk 0.018 0.047 -10000 0 -0.14 35 35
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.055 -10000 0 -0.14 29 29
AKT1 -0.034 0.075 0.15 28 -0.22 30 58
BAD -0.038 0.072 0.15 25 -0.22 29 54
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.045 0.1 28 -0.16 24 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.025 0.048 0.16 1 -0.14 29 30
RAF1 -0.032 0.14 -10000 0 -0.56 27 27
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.046 0.054 0.17 1 -0.14 30 31
YWHAZ 0.035 0.007 -10000 0 0 21 21
IGF-1R heterotetramer/IGF1/IRS1 0.033 0.049 0.17 1 -0.16 24 25
PIK3CA 0.031 0.013 -10000 0 0 80 80
RPS6KB1 -0.033 0.071 0.16 31 -0.2 22 53
GNB2L1 0.036 0.002 -10000 0 0 2 2
positive regulation of MAPKKK cascade -0.033 0.12 0.23 3 -0.43 27 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 0.015 0.054 -10000 0 -0.14 43 43
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.066 0.057 -10000 0 -0.12 34 34
IGF-1R heterotetramer 0.036 0.014 0.092 1 -0.034 1 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.048 0.06 0.18 1 -0.14 35 36
Crk/p130 Cas/Paxillin 0.038 0.056 0.2 3 -0.13 35 38
IGF1R 0.036 0.014 0.092 1 -0.034 1 2
IGF1 0.033 0.026 0.092 1 -0.055 33 34
IRS2/Crk -0.03 0.057 0.1 18 -0.18 32 50
PI3K 0.039 0.087 0.2 1 -0.14 78 79
apoptosis 0.037 0.076 0.23 23 -0.18 12 35
HRAS/GDP 0.021 0.027 -10000 0 -0.13 15 15
PRKCD 0.004 0.064 0.17 8 -0.21 24 32
RAF1/14-3-3 E -0.012 0.13 -10000 0 -0.48 27 27
BAD/14-3-3 -0.039 0.08 0.19 12 -0.24 23 35
PRKCZ -0.027 0.07 0.15 32 -0.2 22 54
Crk/p130 Cas/Paxillin/FAK1 -0.046 0.072 0.13 26 -0.22 29 55
PTPN1 0.034 0.009 -10000 0 0 30 30
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.006 0.06 -10000 0 -0.22 25 25
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.038 0.07 -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 0.027 0.051 0.13 5 -0.14 35 40
GRB10 0.021 0.018 -10000 0 0 220 220
PTPN11 -0.018 0.045 0.1 28 -0.15 24 52
IRS1 0.01 0.042 0.12 5 -0.16 24 29
IRS2 -0.019 0.049 0.1 20 -0.19 24 44
IGF-1R heterotetramer/IGF1 0.039 0.051 0.15 1 -0.17 24 25
GRB2 0.035 0.007 -10000 0 0 17 17
PDPK1 -0.026 0.076 0.17 31 -0.2 22 53
YWHAE 0.035 0.008 -10000 0 0 27 27
PRKD1 -0.002 0.064 0.2 1 -0.24 25 26
SHC1 0.033 0.011 -10000 0 0 52 52
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.053 0.036 -10000 0 -0.097 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.17 -10000 0 -0.5 44 44
AKT1 -0.053 0.23 -10000 0 -0.62 61 61
PIK3CA 0.031 0.013 -10000 0 0 80 80
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.046 0.24 -10000 0 -0.64 59 59
mol:Ca2+ 0.001 0.044 0.17 4 -0.25 3 7
IGF1R 0.033 0.012 -10000 0 0 57 57
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 0.052 0.22 0.58 63 -10000 0 63
RhoA/GTP -0.041 0.038 -10000 0 -0.13 48 48
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.012 0.15 0.18 4 -0.36 54 58
regulation of stress fiber formation 0.038 0.058 0.18 20 -0.14 23 43
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 0.013 -10000 0 -10000 0 0
pseudopodium formation -0.038 0.058 0.14 23 -0.18 20 43
E2/ER alpha (dimer)/PELP1 0.044 0.023 -10000 0 -0.11 7 7
GRB2 0.035 0.007 -10000 0 0 17 17
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.009 -10000 0 0 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.16 -10000 0 -0.4 54 54
E2/ER beta (dimer) 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.004 0.057 0.13 2 -0.19 27 29
mol:NADP -0.012 0.16 -10000 0 -0.4 54 54
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.002 0.042 0.17 4 -0.33 1 5
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 57 57
PLCB1 0.01 0.04 -10000 0 -0.33 1 1
PLCB2 0.008 0.04 -10000 0 -0.33 1 1
IGF1 0.035 0.008 -10000 0 0 23 23
mol:L-citrulline -0.012 0.16 -10000 0 -0.4 54 54
RHOA 0.035 0.007 -10000 0 0 18 18
Gai/GDP -0.066 0.24 -10000 0 -0.64 69 69
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.034 0.009 -10000 0 0 31 31
GNAQ 0.034 0.009 -10000 0 0 31 31
ESR1 0.035 0.009 -10000 0 0 29 29
Gq family/GDP/Gbeta gamma -0.003 0.15 -10000 0 -0.51 32 32
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.14 -10000 0 -0.68 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.001 0.16 0.25 2 -0.38 49 51
GNAZ 0.031 0.013 -10000 0 0 81 81
E2/ER alpha (dimer) 0.026 0.006 -10000 0 -10000 0 0
STRN 0.036 0.003 -10000 0 0 3 3
GNAL 0.036 0.006 -10000 0 0 13 13
PELP1 0.035 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 43 43
GNAI3 0.036 0.006 -10000 0 0 15 15
GNAI1 0.018 0.018 -10000 0 0 263 263
HBEGF -0.02 0.18 0.31 10 -0.44 48 58
cAMP biosynthetic process 0.037 0.015 -10000 0 -10000 0 0
SRC -0.041 0.16 0.2 5 -0.47 45 50
PI3K 0.019 0.075 -10000 0 -0.16 73 73
GNB1 0.035 0.007 -10000 0 0 20 20
G13/GDP/Gbeta gamma 0.022 0.068 -10000 0 -0.17 34 34
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.025 0.12 -10000 0 -0.3 57 57
Gs family/GTP 0.047 0.019 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.063 -10000 0 -0.13 52 52
vasodilation -0.01 0.16 -10000 0 -0.38 54 54
mol:DAG 0.002 0.042 0.17 4 -0.33 1 5
Gs family/GDP/Gbeta gamma 0.004 0.062 -10000 0 -0.18 34 34
MSN -0.039 0.057 0.14 20 -0.19 21 41
Gq family/GTP 0.022 0.043 -10000 0 -0.34 1 1
mol:PI-3-4-5-P3 -0.045 0.23 -10000 0 -0.6 63 63
NRAS 0.032 0.012 -10000 0 0 63 63
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.01 0.16 0.38 54 -10000 0 54
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
RhoA/GDP 0.018 0.067 -10000 0 -0.19 29 29
NOS3 -0.014 0.17 -10000 0 -0.44 49 49
GNA11 0.033 0.011 -10000 0 0 54 54
MAPKKK cascade 0 0.15 -10000 0 -0.47 37 37
E2/ER alpha (dimer)/PELP1/Src -0.003 0.16 0.23 6 -0.38 54 60
ruffle organization -0.038 0.058 0.14 23 -0.18 20 43
ROCK2 -0.034 0.061 0.16 25 -0.19 12 37
GNA14 0.034 0.009 -10000 0 0 30 30
GNA15 0.033 0.012 -10000 0 0 57 57
GNA13 0.035 0.007 -10000 0 0 19 19
MMP9 -0.025 0.17 0.37 4 -0.43 51 55
MMP2 -0.025 0.17 0.22 12 -0.46 47 59
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.073 -10000 0 -0.12 39 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.035 0.009 -10000 0 0 29 29
STAT1 (dimer)/Cbp/p300 0.022 0.083 0.27 5 -0.22 17 22
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.062 -10000 0 -0.14 39 39
antigen processing and presentation of peptide antigen via MHC class I -0.025 0.079 0.12 5 -0.19 55 60
CaM/Ca2+ 0.046 0.078 -10000 0 -0.14 33 33
RAP1A 0.036 0.005 -10000 0 0 11 11
STAT1 (dimer)/SHP2 -0.022 0.059 0.16 17 -0.18 9 26
AKT1 -0.033 0.084 0.27 5 -0.23 32 37
MAP2K1 -0.028 0.056 0.15 17 -0.2 8 25
MAP3K11 -0.022 0.059 0.16 23 -0.18 7 30
IFNGR1 0.031 0.019 -10000 0 -0.036 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.028 0.12 -10000 0 -0.35 43 43
Rap1/GTP -0.039 0.036 -10000 0 -0.16 7 7
CRKL/C3G 0.05 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.064 0.076 -10000 0 -0.13 35 35
CEBPB -0.009 0.12 0.35 3 -0.42 22 25
STAT3 0.034 0.01 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.061 0.089 -10000 0 -0.74 3 3
STAT1 -0.024 0.06 0.17 19 -0.18 9 28
CALM1 0.033 0.011 -10000 0 0 54 54
IFN-gamma (dimer) 0.03 0.021 -10000 0 -0.037 38 38
PIK3CA 0.031 0.013 -10000 0 0 80 80
STAT1 (dimer)/PIAS1 -0.025 0.07 0.18 20 -0.21 15 35
CEBPB/PTGES2/Cbp/p300 0.008 0.09 -10000 0 -0.29 23 23
mol:Ca2+ 0.046 0.07 -10000 0 -0.12 39 39
MAPK3 0.006 0.079 0.34 1 -0.68 2 3
STAT1 (dimer) -0.027 0.11 0.19 7 -0.26 54 61
MAPK1 -0.041 0.2 0.34 1 -0.75 35 36
JAK2 0.027 0.022 -10000 0 -0.037 34 34
PIK3R1 0.032 0.012 -10000 0 0 63 63
JAK1 0.033 0.017 -10000 0 -0.036 17 17
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.001 0.096 0.3 4 -0.4 12 16
SMAD7 -0.009 0.06 0.16 22 -0.15 14 36
CBL/CRKL/C3G 0.018 0.071 0.27 4 -0.19 4 8
PI3K 0.026 0.094 -10000 0 -0.18 39 39
IFNG 0.03 0.021 -10000 0 -0.037 38 38
apoptosis 0.012 0.086 0.31 3 -0.41 8 11
CAMK2G 0.024 0.018 -10000 0 0 179 179
STAT3 (dimer) 0.034 0.01 -10000 0 0 37 37
CAMK2A 0.036 0.005 -10000 0 0 10 10
CAMK2B 0.017 0.018 -10000 0 0 272 272
FRAP1 -0.039 0.077 0.23 5 -0.22 32 37
PRKCD -0.032 0.08 0.29 5 -0.21 25 30
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.025 0.079 0.12 5 -0.19 55 60
PTPN2 0.035 0.007 -10000 0 0 18 18
EP300 0.034 0.011 -10000 0 0 49 49
IRF1 -0.035 0.058 0.21 3 -0.28 12 15
STAT1 (dimer)/PIASy -0.025 0.065 0.24 6 -0.19 7 13
SOCS1 0.019 0.083 -10000 0 -1 3 3
mol:GDP -0.021 0.066 0.17 21 -0.18 4 25
CASP1 -0.019 0.073 0.18 15 -0.16 62 77
PTGES2 0.035 0.007 -10000 0 0 20 20
IRF9 -0.002 0.044 0.12 16 -0.13 19 35
mol:PI-3-4-5-P3 0.013 0.082 -10000 0 -0.15 72 72
RAP1/GDP -0.031 0.052 0.11 15 -0.18 5 20
CBL -0.022 0.058 0.16 21 -0.18 6 27
MAP3K1 -0.023 0.056 0.15 19 -0.18 6 25
PIAS1 0.035 0.008 -10000 0 0 27 27
PIAS4 0.035 0.008 -10000 0 0 27 27
antigen processing and presentation of peptide antigen via MHC class II -0.025 0.079 0.12 5 -0.19 55 60
PTPN11 -0.016 0.059 0.16 25 -0.18 6 31
CREBBP 0.037 0.005 -10000 0 0 8 8
RAPGEF1 0.035 0.007 -10000 0 0 19 19
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.036 0.028 -9999 0 -0.14 2 2
FBXW11 0.035 0.008 -9999 0 0 25 25
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.008 -9999 0 0 25 25
CHUK 0.025 0.017 -9999 0 0 163 163
NF kappa B2 p100/RelB 0.066 0.059 -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 0.025 0.017 -9999 0 0 158 158
NF kappa B2 p52/RelB 0.033 0.023 -9999 0 -10000 0 0
regulation of B cell activation 0.032 0.023 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.027 0.073 0.2 18 -0.27 9 27
FYN -0.011 0.1 0.23 10 -0.31 31 41
LAT/GRAP2/SLP76 0.02 0.072 0.22 4 -0.29 10 14
IKBKB 0.036 0.003 -10000 0 0 4 4
AKT1 0.005 0.083 0.21 16 -0.24 21 37
B2M 0.036 0.01 -10000 0 -10000 0 0
IKBKG -0.003 0.034 0.094 13 -0.097 10 23
MAP3K8 0.022 0.018 -10000 0 0 196 196
mol:Ca2+ -0.01 0.01 0.088 1 -0.038 2 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 0.25 16 -0.28 25 41
TRPV6 0.4 0.59 1.2 168 -10000 0 168
CD28 0.037 0.001 -10000 0 -10000 0 0
SHC1 0.018 0.077 0.2 27 -0.32 9 36
receptor internalization 0.018 0.06 0.17 8 -0.29 8 16
PRF1 -0.14 0.31 -10000 0 -0.61 145 145
KRAS 0.034 0.009 -10000 0 0 35 35
GRB2 0.035 0.007 -10000 0 0 17 17
COT/AKT1 0.006 0.063 0.19 5 -0.21 18 23
LAT 0.012 0.072 0.21 13 -0.31 10 23
EntrezGene:6955 0.001 0.004 0.014 41 -10000 0 41
CD3D 0.035 0.011 -10000 0 -10000 0 0
CD3E 0.038 0.007 -10000 0 -10000 0 0
CD3G 0.037 0.008 -10000 0 -10000 0 0
RASGRP2 0.006 0.02 0.074 3 -0.14 6 9
RASGRP1 -0.024 0.13 0.23 25 -0.24 93 118
HLA-A 0.037 0.007 -10000 0 -10000 0 0
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 0.009 0.053 0.13 36 -0.1 18 54
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.037 -10000 0 -0.12 26 26
PRKCA -0.001 0.057 0.18 19 -0.19 5 24
GRAP2 0.034 0.009 -10000 0 0 35 35
mol:IP3 0.002 0.053 -10000 0 -0.24 8 8
EntrezGene:6957 0.001 0.004 0.014 41 -10000 0 41
TCR/CD3/MHC I/CD8 0.018 0.048 0.15 11 -0.22 5 16
ORAI1 -0.35 0.5 0.38 5 -1.1 168 173
CSK 0.013 0.072 0.21 14 -0.3 11 25
B7 family/CD28 0.062 0.096 0.27 19 -0.32 7 26
CHUK 0.025 0.017 -10000 0 0 163 163
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.015 0.074 0.2 9 -0.32 11 20
PTPN6 0.008 0.076 0.22 12 -0.31 12 24
VAV1 0.018 0.076 0.21 25 -0.31 9 34
Monovalent TCR/CD3 0.022 0.017 0.11 1 -10000 0 1
CBL 0.036 0.004 -10000 0 0 7 7
LCK 0.006 0.09 0.24 12 -0.31 15 27
PAG1 0.015 0.071 0.21 10 -0.3 11 21
RAP1A 0.036 0.005 -10000 0 0 11 11
TCR/CD3/MHC I/CD8/LCK 0.014 0.075 0.21 9 -0.31 12 21
CD80 0.036 0.007 -10000 0 0 16 16
CD86 0.032 0.012 -10000 0 0 64 64
PDK1/CARD11/BCL10/MALT1 0.002 0.046 -10000 0 -0.14 25 25
HRAS 0.034 0.009 -10000 0 0 32 32
GO:0035030 0.011 0.073 0.2 21 -0.26 8 29
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 0.006 0.09 0.23 22 -0.28 15 37
CSK/PAG1 0.011 0.071 0.21 13 -0.29 11 24
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.049 0.035 -10000 0 -0.14 13 13
GRAP2/SLP76 0.029 0.083 0.24 5 -0.32 11 16
STIM1 -0.06 0.18 1.2 7 -10000 0 7
RAS family/GTP 0.004 0.072 0.16 21 -0.18 29 50
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.019 0.062 0.18 8 -0.3 8 16
mol:DAG -0.02 0.036 -10000 0 -0.22 8 8
RAP1A/GDP 0.009 0.027 0.071 26 -0.051 15 41
PLCG1 0.035 0.007 -10000 0 0 19 19
CD247 0.001 0.004 0.014 41 -10000 0 41
cytotoxic T cell degranulation -0.14 0.3 -10000 0 -0.59 145 145
RAP1A/GTP 0.003 0.008 -10000 0 -0.053 6 6
mol:PI-3-4-5-P3 0.009 0.09 0.24 17 -0.26 20 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.011 0.067 0.2 2 -0.29 8 10
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 0.01 0.066 0.21 4 -0.3 7 11
MALT1 0.034 0.009 -10000 0 0 32 32
TRAF6 0.036 0.005 -10000 0 0 10 10
CD8 heterodimer 0.003 0.008 0.027 43 -10000 0 43
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.026 -10000 0 -0.16 8 8
PRKCE -0.001 0.057 0.18 19 -0.19 5 24
PRKCQ 0.008 0.094 0.25 20 -0.3 15 35
LCP2 0.031 0.013 -10000 0 0 77 77
BCL10 0.035 0.007 -10000 0 0 20 20
regulation of survival gene product expression 0.005 0.076 0.2 17 -0.22 18 35
IKK complex -0.002 0.038 0.13 13 -0.098 2 15
RAS family/GDP -0.004 0.015 -10000 0 -0.04 37 37
MAP3K14 0.009 0.063 0.18 24 -0.17 18 42
PDPK1 0.005 0.079 0.21 18 -0.23 19 37
TCR/CD3/MHC I/CD8/Fyn 0.01 0.068 0.18 1 -0.36 7 8
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.036 0.005 -10000 0 0 11 11
Caspase 8 (4 units) -0.009 0.096 -10000 0 -0.24 24 24
NEF 0.002 0 -10000 0 -10000 0 0
NFKBIA 0.038 0.019 0.077 64 -10000 0 64
BIRC3 -0.025 0.029 0.18 2 -0.2 2 4
CYCS -0.003 0.083 0.18 51 -0.26 10 61
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 -0.36 11 11
protein ubiquitination 0.013 0.065 0.21 3 -0.27 6 9
CRADD 0.036 0.006 -10000 0 0 12 12
DAXX 0.036 0.004 -10000 0 0 6 6
FAS 0.019 0.018 -10000 0 0 238 238
BID -0.002 0.056 0.12 1 -0.17 42 43
NF-kappa-B/RelA/I kappa B alpha 0.075 0.054 -10000 0 -0.13 17 17
TRADD 0.036 0.005 -10000 0 0 11 11
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 0.075 0.055 -10000 0 -0.13 17 17
MAPK8 -0.007 0.093 -10000 0 -0.35 10 10
APAF1 0.036 0.003 -10000 0 0 4 4
TRAF1 0.035 0.008 -10000 0 0 23 23
TRAF2 0.036 0.006 -10000 0 0 15 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.003 0.06 -10000 0 -0.17 45 45
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.031 0.075 -10000 0 -0.27 12 12
CHUK 0.013 0.066 0.21 3 -0.29 6 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.041 0.082 -10000 0 -0.12 58 58
TCRz/NEF 0.007 0.001 -10000 0 -10000 0 0
TNF 0.036 0.003 -10000 0 0 4 4
FASLG 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.042 0.016 0.078 72 -10000 0 72
TNFR1A/BAG4/TNF-alpha 0.053 0.056 -10000 0 -0.12 41 41
CASP6 0.006 0.11 -10000 0 -0.57 7 7
CASP7 -0.032 0.14 0.27 11 -0.31 30 41
RELA 0.043 0.016 0.078 74 -10000 0 74
CASP2 0.024 0.017 -10000 0 0 169 169
CASP3 0 0.11 0.26 10 -0.33 15 25
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
TNFR1A/BAG4 0.035 0.054 -10000 0 -0.14 42 42
CASP8 0.036 0.006 -10000 0 0 13 13
CASP9 0.034 0.009 -10000 0 0 33 33
MAP3K14 0.026 0.076 0.19 2 -0.27 10 12
APAF-1/Caspase 9 -0.009 0.085 0.14 53 -0.23 15 68
BCL2 -0.015 0.09 0.27 1 -0.32 9 10
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.028 0.11 0.32 9 -0.3 22 31
PDGFB-D/PDGFRB/SLAP 0.018 0.072 -10000 0 -0.15 71 71
PDGFB-D/PDGFRB/APS/CBL 0.045 0.022 -10000 0 -0.12 7 7
AKT1 -0.026 0.089 0.27 12 -0.24 15 27
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.1 0.29 9 -0.32 22 31
PIK3CA 0.031 0.013 -10000 0 0 80 80
FGR 0.006 0.1 0.26 4 -0.5 13 17
mol:Ca2+ 0.011 0.1 0.25 9 -0.37 20 29
MYC 0.01 0.26 0.4 21 -0.68 50 71
SHC1 0.033 0.011 -10000 0 0 52 52
HRAS/GDP 0.012 0.066 0.17 26 -0.18 12 38
LRP1/PDGFRB/PDGFB 0.048 0.055 -10000 0 -0.13 32 32
GRB10 0.021 0.018 -10000 0 0 220 220
PTPN11 0.036 0.005 -10000 0 0 11 11
GO:0007205 0.011 0.1 0.25 9 -0.37 20 29
PTEN 0.026 0.017 -10000 0 0 148 148
GRB2 0.035 0.007 -10000 0 0 17 17
GRB7 0.036 0.006 -10000 0 0 14 14
PDGFB-D/PDGFRB/SHP2 0.047 0.033 -10000 0 -0.14 13 13
PDGFB-D/PDGFRB/GRB10 0.021 0.049 -10000 0 -0.14 30 30
cell cycle arrest 0.017 0.072 -10000 0 -0.15 71 71
HRAS 0.034 0.009 -10000 0 0 32 32
HIF1A -0.03 0.081 0.24 13 -0.25 12 25
GAB1 0.006 0.12 0.27 10 -0.36 31 41
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.005 0.12 0.3 14 -0.32 30 44
PDGFB-D/PDGFRB 0.056 0.053 0.19 1 -0.14 14 15
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.044 0.04 -10000 0 -0.14 20 20
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.025 0.12 0.29 8 -0.28 38 46
positive regulation of MAPKKK cascade 0.047 0.033 -10000 0 -0.14 13 13
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.011 0.1 0.25 9 -0.38 20 29
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -0.009 29 29
PDGFB-D/PDGFRB/GRB7 0.05 0.022 -10000 0 -0.14 4 4
SHB 0.033 0.011 -10000 0 0 51 51
BLK 0.012 0.077 0.36 1 -0.46 6 7
PTPN2 0.032 0.018 -10000 0 -0.019 49 49
PDGFB-D/PDGFRB/SNX15 0.049 0.025 -10000 0 -0.14 7 7
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.006 0.15 0.29 13 -0.41 43 56
CBL 0.036 0.004 -10000 0 0 7 7
PDGFB-D/PDGFRB/DEP1 0.049 0.026 -10000 0 -0.14 7 7
LCK 0.017 0.06 0.26 4 -0.35 2 6
PDGFRB 0.031 0.021 0.064 2 -0.019 71 73
ACP1 0.035 0.007 -10000 0 0 18 18
HCK -0.043 0.18 0.22 1 -0.5 61 62
ABL1 0.002 0.11 0.25 10 -0.34 29 39
PDGFB-D/PDGFRB/CBL 0.006 0.13 0.28 7 -0.43 27 34
PTPN1 0.032 0.018 -10000 0 -0.015 60 60
SNX15 0.036 0.004 -10000 0 0 6 6
STAT3 0.034 0.01 -10000 0 0 37 37
STAT1 0.034 0.01 -10000 0 0 40 40
cell proliferation 0.018 0.24 0.38 24 -0.6 51 75
SLA 0.027 0.016 -10000 0 0 134 134
actin cytoskeleton reorganization -0.018 0.067 0.2 30 -0.19 7 37
SRC 0.017 0.052 0.29 2 -10000 0 2
PI3K -0.047 0.044 -10000 0 -0.17 35 35
PDGFB-D/PDGFRB/GRB7/SHC 0.061 0.037 -10000 0 -0.12 10 10
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.019 0.1 0.29 9 -0.33 22 31
LYN -0.035 0.16 0.22 2 -0.47 53 55
LRP1 0.031 0.013 -10000 0 0 71 71
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 0.066 0.065 -10000 0 -0.14 25 25
SPHK1 0.033 0.011 0.058 1 0 50 51
EDG1 0.034 0.011 0.058 1 0 45 46
mol:DAG 0.011 0.1 0.25 9 -0.38 20 29
PLCG1 0.011 0.1 0.26 9 -0.38 20 29
NHERF/PDGFRB 0.062 0.036 -10000 0 -0.12 11 11
YES1 -0.009 0.13 0.23 2 -0.52 25 27
cell migration 0.061 0.036 -10000 0 -0.12 11 11
SHC/Grb2/SOS1 0.068 0.061 -10000 0 -0.13 20 20
SLC9A3R2 0.036 0.005 -10000 0 0 9 9
SLC9A3R1 0.034 0.01 -10000 0 0 37 37
NHERF1-2/PDGFRB/PTEN 0.06 0.052 -10000 0 -0.11 13 13
FYN -0.055 0.19 0.22 1 -0.45 81 82
DOK1 -0.017 0.053 0.17 27 -10000 0 27
HRAS/GTP 0.021 0.027 -10000 0 -0.13 15 15
PDGFB 0.034 0.01 -10000 0 0 37 37
RAC1 0.031 0.19 0.32 39 -0.43 48 87
PRKCD -0.015 0.053 0.17 27 -0.13 3 30
FER -0.016 0.054 0.17 26 -0.13 2 28
MAPKKK cascade -0.014 0.061 0.15 44 -0.18 5 49
RASA1 -0.015 0.055 0.17 27 -0.19 4 31
NCK1 0.035 0.008 -10000 0 0 27 27
NCK2 0.035 0.007 -10000 0 0 17 17
p62DOK/Csk -0.014 0.063 0.18 31 -0.2 3 34
PDGFB-D/PDGFRB/SHB 0.045 0.027 -10000 0 -0.14 5 5
chemotaxis 0.002 0.11 0.25 11 -0.33 29 40
STAT1-3-5/STAT1-3-5 0.062 0.072 -10000 0 -0.15 21 21
Bovine Papilomavirus E5/PDGFRB 0.02 0.024 -10000 0 -0.14 7 7
PTPRJ 0.036 0.005 -10000 0 0 11 11
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 0.016 -9999 0 0 138 138
ITGB7 0.036 0.005 -9999 0 0 11 11
ITGA4 0.036 0.006 -9999 0 0 13 13
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.039 0.025 -9999 0 -9999 0 0
Signaling events regulated by Ret tyrosine kinase

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.096 -10000 0 -0.39 27 27
Crk/p130 Cas/Paxillin -0.056 0.092 -10000 0 -0.19 118 118
JUN -0.016 0.047 -10000 0 -0.25 11 11
HRAS 0.034 0.009 -10000 0 0 32 32
RET51/GFRalpha1/GDNF/GRB10 0.037 0.058 -10000 0 -0.12 27 27
RAP1A 0.036 0.005 -10000 0 0 11 11
FRS2 0.034 0.009 -10000 0 0 30 30
RAP1A/GDP 0.026 0.008 -10000 0 -0.13 1 1
RET51/GFRalpha1/GDNF/DOK1 0.063 0.044 -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 0.047 0.033 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 18 18
RAP1A/GTP 0.055 0.047 -10000 0 -0.11 1 1
GRB7 0.036 0.006 -10000 0 0 14 14
RET51/GFRalpha1/GDNF 0.063 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.004 0.073 -10000 0 -0.18 14 14
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.038 0.045 -10000 0 -0.1 23 23
lamellipodium assembly -0.027 0.082 -10000 0 -0.2 59 59
RET51/GFRalpha1/GDNF/SHC 0.059 0.049 -10000 0 -0.12 8 8
PIK3CA 0.031 0.013 -10000 0 0 80 80
RET9/GFRalpha1/GDNF/SHC 0.04 0.039 -10000 0 -0.11 8 8
RET9/GFRalpha1/GDNF/Shank3 0.032 0.022 -10000 0 -10000 0 0
MAPK3 -0.025 0.037 0.2 9 -10000 0 9
DOK1 0.036 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 0.041 0.2 7 -0.21 9 16
DOK5 0.029 0.015 -10000 0 0 100 100
GFRA1 0.025 0.017 -10000 0 0 161 161
MAPK8 0 0.045 -10000 0 -0.18 19 19
HRAS/GTP 0.023 0.091 -10000 0 -0.12 109 109
tube development 0.025 0.025 0.2 1 -0.096 8 9
MAPK1 -0.023 0.038 0.19 10 -10000 0 10
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.013 0.063 -10000 0 -0.22 14 14
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
SRC 0.036 0.006 -10000 0 0 14 14
PDLIM7 0.036 0.005 -10000 0 0 11 11
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 0.063 0.044 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.039 0.071 -10000 0 -0.11 65 65
PRKCA 0.036 0.004 -10000 0 0 6 6
HRAS/GDP 0.021 0.027 -10000 0 -0.13 15 15
CREB1 -0.031 0.095 -10000 0 -0.19 115 115
PIK3R1 0.032 0.012 -10000 0 0 63 63
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.011 0.064 -10000 0 -0.17 28 28
RET51/GFRalpha1/GDNF/Grb7 0.063 0.044 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.028 0.016 -10000 0 0 126 126
DOK4 0.035 0.006 -10000 0 0 16 16
JNK cascade -0.016 0.047 -10000 0 -0.23 13 13
RET9/GFRalpha1/GDNF/FRS2 0.045 0.034 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.034 0.009 -10000 0 0 32 32
NCK1 0.035 0.008 -10000 0 0 27 27
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.011 0.038 -10000 0 -0.17 17 17
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.091 -10000 0 -0.19 105 105
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.096 -10000 0 -0.19 121 121
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.048 -10000 0 -0.18 17 17
PI3K -0.057 0.13 -10000 0 -0.26 105 105
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.042 0.035 -10000 0 -0.096 8 8
GRB10 0.021 0.018 -10000 0 0 220 220
activation of MAPKK activity 0.01 0.049 -10000 0 -0.28 11 11
RET51/GFRalpha1/GDNF/FRS2 0.06 0.045 -10000 0 -10000 0 0
GAB1 0.032 0.012 -10000 0 0 59 59
IRS1 0.033 0.011 -10000 0 0 52 52
IRS2 0.03 0.014 -10000 0 0 96 96
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.008 0.056 -10000 0 -0.17 26 26
RET51/GFRalpha1/GDNF/PKC alpha 0.063 0.044 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 17 17
PRKACA 0.035 0.008 -10000 0 0 25 25
GDNF 0.036 0.004 -10000 0 0 6 6
RAC1 0.024 0.017 -10000 0 0 173 173
RET51/GFRalpha1/GDNF/IRS1 0.056 0.056 -10000 0 -0.11 22 22
Rac1/GTP -0.029 0.097 -10000 0 -0.23 59 59
RET9/GFRalpha1/GDNF 0.033 0.023 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.037 0.025 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.032 0.012 -10000 0 0 67 67
GNB1/GNG2 0.028 0.034 -10000 0 -0.11 14 14
forebrain development 0.034 0.063 0.25 4 -0.42 3 7
GNAO1 0.03 0.014 -10000 0 0 87 87
SMO/beta Arrestin2 0.033 0.031 -10000 0 -0.14 4 4
SMO 0.024 0.018 -10000 0 -10000 0 0
ARRB2 0.035 0.008 -10000 0 0 26 26
GLI3/SPOP 0.002 0.11 0.27 1 -0.32 32 33
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.01 -10000 0 0 40 40
GNAI2 0.034 0.01 -10000 0 0 43 43
SIN3/HDAC complex 0.055 0.041 -10000 0 -0.12 17 17
GNAI1 0.018 0.018 -10000 0 0 263 263
XPO1 0.037 0.005 -10000 0 -10000 0 0
GLI1/Su(fu) 0.012 0.047 -10000 0 -0.3 5 5
SAP30 0.035 0.007 -10000 0 0 20 20
mol:GDP 0.024 0.018 -10000 0 -10000 0 0
MIM/GLI2A 0.041 0.013 0.12 11 -10000 0 11
IFT88 0.035 0.008 -10000 0 0 28 28
GNAI3 0.036 0.006 -10000 0 0 15 15
GLI2 0.001 0.089 -10000 0 -0.34 21 21
GLI3 -0.013 0.1 0.27 1 -0.32 30 31
CSNK1D 0.035 0.007 -10000 0 0 20 20
CSNK1E 0.032 0.012 -10000 0 0 67 67
SAP18 0.034 0.01 -10000 0 0 41 41
embryonic digit morphogenesis 0.035 0.008 -10000 0 0 28 28
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.01 0.088 -10000 0 -0.2 69 69
SIN3B 0.034 0.009 -10000 0 0 29 29
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.012 0.072 -10000 0 -0.26 26 26
GLI2/Su(fu) -0.003 0.072 -10000 0 -0.31 17 17
FOXA2 0.05 0.041 -10000 0 -0.49 1 1
neural tube patterning 0.034 0.063 0.25 4 -0.42 3 7
SPOP 0.035 0.008 -10000 0 0 23 23
Su(fu)/PIAS1 0.047 0.038 0.098 151 -0.083 9 160
GNB1 0.035 0.007 -10000 0 0 20 20
CSNK1G2 0.034 0.009 -10000 0 0 30 30
CSNK1G3 0.036 0.006 -10000 0 0 13 13
MTSS1 0.041 0.013 0.12 11 -10000 0 11
embryonic limb morphogenesis 0.034 0.063 0.25 4 -0.42 3 7
SUFU 0.002 0.01 -10000 0 -0.11 4 4
LGALS3 0.028 0.015 -10000 0 0 114 114
catabolic process 0.012 0.14 0.31 2 -0.44 31 33
GLI3A/CBP 0.044 0.008 -10000 0 -10000 0 0
KIF3A 0.033 0.011 -10000 0 0 55 55
GLI1 0.034 0.064 0.25 4 -0.43 3 7
RAB23 0.034 0.009 -10000 0 0 31 31
CSNK1A1 0.036 0.006 -10000 0 0 14 14
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.036 0.005 -10000 0 0 8 8
Su(fu)/Galectin3 0.038 0.04 0.098 123 -0.11 8 131
GNAZ 0.031 0.013 -10000 0 0 81 81
RBBP4 0.033 0.011 -10000 0 0 56 56
CSNK1G1 0.036 0.006 -10000 0 0 14 14
PIAS1 0.035 0.008 -10000 0 0 27 27
PRKACA 0.035 0.008 -10000 0 0 25 25
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 -0.015 0.1 -10000 0 -0.36 30 30
PTCH1 0.033 0.059 0.23 4 -0.38 3 7
MIM/GLI1 0.057 0.069 0.35 2 -0.39 3 5
CREBBP 0.044 0.008 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.002 0.091 0.16 2 -0.24 44 46
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.007 0.071 -10000 0 -0.29 22 22
KLHL20 0.048 0.09 0.2 58 -0.19 16 74
CYFIP2 0.031 0.013 -10000 0 0 78 78
Rac1/GDP 0.007 0.061 0.2 1 -0.29 10 11
ENAH 0.007 0.074 -10000 0 -0.31 21 21
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 62 0 12 74
RAP1A 0.036 0.005 -10000 0 0 11 11
CTNNB1 0.036 0.006 -10000 0 0 15 15
CDC42/GTP -0.026 0.052 0.12 13 -0.21 18 31
ABI1/Sra1/Nap1 -0.014 0.033 -10000 0 -0.14 27 27
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.084 0.036 -10000 0 -0.13 8 8
RAPGEF1 -0.006 0.074 -10000 0 -0.29 18 18
CTNND1 0.034 0.009 -10000 0 0 32 32
regulation of calcium-dependent cell-cell adhesion 0.02 0.076 -10000 0 -0.29 23 23
CRK 0 0.076 0.2 1 -0.29 22 23
E-cadherin/gamma catenin/alpha catenin 0.061 0.035 -10000 0 -0.12 8 8
alphaE/beta7 Integrin 0.049 0.025 -10000 0 -0.14 7 7
IQGAP1 0.033 0.011 -10000 0 0 51 51
NCKAP1 0.036 0.002 -10000 0 0 2 2
Rap1/GTP/I-afadin 0.043 0.015 -10000 0 -0.1 1 1
DLG1 0.007 0.075 -10000 0 -0.3 23 23
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.044 -10000 0 -0.18 30 30
MLLT4 0.034 0.009 -10000 0 0 36 36
ARF6/GTP/NME1/Tiam1 0.036 0.033 -10000 0 -0.1 23 23
PI3K -0.043 0.058 0.059 2 -0.23 30 32
ARF6 0.035 0.008 -10000 0 0 27 27
mol:Ca2+ 0 0 0.001 69 0 28 97
E-cadherin/gamma catenin 0.048 0.018 -10000 0 -10000 0 0
TIAM1 0.033 0.011 -10000 0 0 46 46
E-cadherin(dimer)/Ca2+ 0.07 0.054 -10000 0 -0.14 25 25
AKT1 -0.023 0.052 0.13 7 -0.18 24 31
PIK3R1 0.032 0.012 -10000 0 0 63 63
CDH1 0.034 0.01 -10000 0 0 38 38
RhoA/GDP 0.011 0.07 0.19 2 -0.27 12 14
actin cytoskeleton organization 0.04 0.072 0.17 62 -0.14 16 78
CDC42/GDP 0.011 0.068 0.19 2 -0.26 11 13
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.049 -10000 0 -0.2 23 23
ITGB7 0.036 0.005 -10000 0 0 11 11
RAC1 0.024 0.017 -10000 0 0 173 173
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.077 0.057 -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 -0.006 0.071 0.19 2 -0.3 12 14
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 0.026 0.077 0.21 1 -0.26 15 16
RAC1/GTP/IQGAP1 0.023 0.042 -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 18 18
CDC42 0.035 0.008 -10000 0 0 24 24
CTNNA1 0.035 0.007 -10000 0 0 20 20
positive regulation of S phase of mitotic cell cycle 0.014 0.045 0.11 8 -0.13 26 34
NME1 0 0 -10000 0 0 32 32
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.008 0.072 -10000 0 -0.3 20 20
regulation of cell-cell adhesion -0.028 0.04 -10000 0 -0.17 25 25
WASF2 -0.008 0.018 -10000 0 -0.074 27 27
Rap1/GTP -0.023 0.061 0.15 19 -0.25 16 35
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.09 0.051 -10000 0 -0.13 13 13
CCND1 0.016 0.054 0.13 8 -0.16 26 34
VAV2 0.019 0.1 -10000 0 -0.54 8 8
RAP1/GDP -0.011 0.064 0.16 17 -0.25 15 32
adherens junction assembly 0.009 0.071 -10000 0 -0.29 20 20
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.017 -10000 0 0 152 152
PIP5K1C 0.033 0.011 -10000 0 0 50 50
regulation of heterotypic cell-cell adhesion 0.068 0.047 0.2 3 -0.13 14 17
E-cadherin/beta catenin 0.006 0.02 -10000 0 -0.097 5 5
mol:GTP 0 0 0.001 64 0 32 96
SRC 0.006 0.073 -10000 0 -0.29 23 23
PIK3CA 0.031 0.013 -10000 0 0 80 80
Rac1/GTP -0.007 0.07 0.18 1 -0.28 21 22
E-cadherin/beta catenin/alpha catenin 0.064 0.036 -10000 0 -0.13 10 10
ITGAE 0.035 0.007 -10000 0 0 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.077 -10000 0 -0.3 23 23
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.016 0.11 0.27 11 -0.38 21 32
CRKL 0.019 0.1 0.23 9 -0.4 21 30
HRAS 0.034 0.1 0.25 9 -0.33 21 30
mol:PIP3 0.052 0.12 0.29 27 -0.35 20 47
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.036 0.004 -10000 0 0 6 6
GAB1 0.025 0.11 0.24 11 -0.4 22 33
FOXO3 0.053 0.16 0.32 28 -0.36 38 66
AKT1 0.054 0.17 0.33 27 -0.39 38 65
BAD 0.047 0.16 0.32 27 -0.37 39 66
megakaryocyte differentiation 0.025 0.1 0.24 10 -0.39 19 29
GSK3B 0.047 0.17 0.33 29 -0.39 39 68
RAF1 0.023 0.091 0.24 13 -0.28 22 35
SHC1 0.033 0.011 -10000 0 0 52 52
STAT3 0.018 0.1 0.22 5 -0.4 22 27
STAT1 0.015 0.2 -10000 0 -0.87 21 21
HRAS/SPRED1 0.025 0.09 0.22 9 -0.27 22 31
cell proliferation 0.01 0.095 0.23 4 -0.38 22 26
PIK3CA 0.031 0.013 -10000 0 0 80 80
TEC 0.036 0.005 -10000 0 0 8 8
RPS6KB1 0.055 0.12 0.27 19 -0.37 21 40
HRAS/SPRED2 0.044 0.1 0.25 12 -0.28 21 33
LYN/TEC/p62DOK 0.065 0.12 -10000 0 -0.4 21 21
MAPK3 0.02 0.088 0.24 25 -0.22 18 43
STAP1 0.026 0.1 0.23 5 -0.39 22 27
GRAP2 0.034 0.009 -10000 0 0 35 35
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 0.072 0.11 -10000 0 -0.39 21 21
actin filament polymerization 0.027 0.1 0.23 5 -0.38 22 27
LYN 0.031 0.013 -10000 0 0 74 74
STAP1/STAT5A (dimer) 0.024 0.14 0.29 1 -0.54 21 22
PIK3R1 0.032 0.012 -10000 0 0 63 63
CBL/CRKL/GRB2 0.053 0.11 0.28 3 -0.38 21 24
PI3K 0.061 0.13 0.3 15 -0.37 21 36
PTEN 0.026 0.017 -10000 0 0 148 148
SCF/KIT/EPO/EPOR 0.022 0.22 -10000 0 -1 21 21
MAPK8 0.009 0.095 0.23 3 -0.39 22 25
STAT3 (dimer) 0.02 0.1 0.24 7 -0.39 22 29
positive regulation of transcription 0.021 0.078 0.22 27 -0.18 18 45
mol:GDP 0.041 0.098 0.24 1 -0.34 21 22
PIK3C2B 0.025 0.1 0.24 11 -0.39 22 33
CBL/CRKL 0.041 0.11 0.27 4 -0.38 21 25
FER 0.023 0.1 0.24 6 -0.39 22 28
SH2B3 0.026 0.1 0.23 5 -0.39 22 27
PDPK1 0.046 0.12 0.28 28 -0.33 21 49
SNAI2 0.026 0.11 0.23 11 -0.4 21 32
positive regulation of cell proliferation 0.027 0.17 -10000 0 -0.66 21 21
KITLG 0.038 0.021 -10000 0 -0.051 20 20
cell motility 0.027 0.17 -10000 0 -0.66 21 21
PTPN6 0.023 0.025 -10000 0 -0.033 67 67
EPOR 0.048 0.083 -10000 0 -10000 0 0
STAT5A (dimer) 0.032 0.14 -10000 0 -0.54 21 21
SOCS1 0.036 0.005 -10000 0 0 8 8
cell migration -0.022 0.1 0.38 22 -0.25 7 29
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.025 0.022 -10000 0 -0.036 15 15
VAV1 0.034 0.009 -10000 0 0 35 35
GRB10 0.011 0.087 0.3 4 -0.4 13 17
PTPN11 0.027 0.022 -10000 0 -0.032 56 56
SCF/KIT 0.03 0.11 0.24 5 -0.41 22 27
GO:0007205 -0.002 0.007 0.021 19 -0.022 2 21
MAP2K1 0.013 0.081 0.22 12 -0.23 22 34
CBL 0.036 0.004 -10000 0 0 7 7
KIT 0.006 0.24 -10000 0 -1.1 21 21
MAP2K2 0.018 0.093 0.28 24 -0.23 20 44
SHC/Grb2/SOS1 0.052 0.11 -10000 0 -0.36 21 21
STAT5A 0.032 0.14 -10000 0 -0.56 21 21
GRB2 0.035 0.007 -10000 0 0 17 17
response to radiation 0.027 0.11 0.23 12 -0.39 21 33
SHC/GRAP2 0.043 0.03 -10000 0 -0.14 8 8
PTPRO 0.024 0.1 0.24 10 -0.4 19 29
SH2B2 0.026 0.1 0.23 5 -0.39 22 27
DOK1 0.036 0.002 -10000 0 0 2 2
MATK 0.019 0.1 0.23 4 -0.39 22 26
CREBBP 0.051 0.045 0.14 3 -0.12 21 24
BCL2 0.04 0.13 -10000 0 -0.87 6 6
Caspase cascade in apoptosis

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
TOP1 -0.007 0.088 -10000 0 -0.34 12 12
ACTA1 -0.037 0.092 -10000 0 -0.31 32 32
NUMA1 -0.002 0.085 -10000 0 -0.31 20 20
SPTAN1 -0.044 0.092 0.2 5 -0.29 37 42
LIMK1 0.011 0.11 0.19 79 -0.34 16 95
BIRC3 0.031 0.013 -10000 0 0 81 81
BIRC2 0.036 0.005 -10000 0 0 11 11
BAX 0.033 0.01 -10000 0 0 44 44
CASP10 -0.008 0.031 0.082 47 -10000 0 47
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.092 -10000 0 -0.29 30 30
DIABLO 0.036 0.004 -10000 0 0 6 6
apoptotic nuclear changes -0.044 0.092 0.2 5 -0.29 37 42
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.036 0.006 -10000 0 0 12 12
GSN -0.038 0.098 0.2 5 -0.32 33 38
MADD 0.036 0.006 -10000 0 0 15 15
TFAP2A 0.045 0.055 -10000 0 -0.44 5 5
BID 0 0.039 0.11 5 -0.19 16 21
MAP3K1 -0.003 0.051 -10000 0 -0.39 5 5
TRADD 0.036 0.005 -10000 0 0 11 11
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 -0.042 0.099 0.2 12 -0.31 35 47
CASP9 0.034 0.009 -10000 0 0 33 33
DNA repair 0.034 0.071 0.28 18 -10000 0 18
neuron apoptosis 0.017 0.12 -10000 0 -0.62 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.025 0.088 -10000 0 -0.31 28 28
APAF1 0.036 0.003 -10000 0 0 4 4
CASP6 0.027 0.11 -10000 0 -0.84 6 6
TRAF2 0.036 0.006 -10000 0 0 15 15
ICAD/CAD -0.047 0.084 0.22 1 -0.3 32 33
CASP7 -0.079 0.11 -10000 0 -0.24 141 141
KRT18 0.027 0.051 -10000 0 -0.46 4 4
apoptosis -0.033 0.092 -10000 0 -0.34 19 19
DFFA -0.043 0.087 0.17 1 -0.3 33 34
DFFB -0.042 0.085 -10000 0 -0.3 31 31
PARP1 -0.035 0.071 -10000 0 -0.28 18 18
actin filament polymerization -0.017 0.11 0.32 16 -0.18 79 95
TNF 0.036 0.003 -10000 0 0 4 4
CYCS 0.016 0.039 0.18 3 -0.24 3 6
SATB1 0.018 0.11 -10000 0 -0.73 6 6
SLK -0.026 0.085 -10000 0 -0.29 33 33
p15 BID/BAX 0.002 0.06 0.15 2 -0.16 44 46
CASP2 0.062 0.1 0.22 131 -0.26 5 136
JNK cascade 0.003 0.051 0.38 5 -10000 0 5
CASP3 -0.04 0.092 -10000 0 -0.31 34 34
LMNB2 0.062 0.092 0.22 14 -0.36 4 18
RIPK1 0.035 0.007 -10000 0 0 20 20
CASP4 0.03 0.014 -10000 0 0 92 92
Mammalian IAPs/DIABLO 0.058 0.034 -10000 0 -0.15 6 6
negative regulation of DNA binding 0.045 0.054 -10000 0 -0.43 5 5
stress fiber formation -0.036 0.085 -10000 0 -0.29 33 33
GZMB -0.005 0.033 0.092 47 -10000 0 47
CASP1 -0.011 0.066 -10000 0 -0.2 55 55
LMNB1 0.044 0.13 0.24 8 -0.39 15 23
APP 0.017 0.12 -10000 0 -0.63 15 15
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
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 0.22 1 -0.34 23 24
LMNA 0.067 0.088 0.23 13 -0.36 2 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.018 0.056 0.16 1 -0.23 11 12
LRDD 0.035 0.007 -10000 0 0 20 20
SREBF1 -0.043 0.088 0.18 1 -0.3 34 35
APAF-1/Caspase 9 0.014 0.1 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.002 0.084 -10000 0 -0.3 20 20
CFL2 0.017 0.11 0.18 78 -0.32 16 94
GAS2 -0.033 0.092 0.2 2 -0.3 32 34
positive regulation of apoptosis 0.062 0.1 0.23 21 -0.4 6 27
PRF1 0.023 0.018 -10000 0 0 192 192
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.02 0.13 -10000 0 -0.63 18 18
epithelial cell differentiation -0.008 0.14 -10000 0 -0.65 18 18
ITCH 0.031 0.031 0.11 1 -0.1 22 23
WWP1 -0.021 0.22 -10000 0 -1.1 18 18
FYN 0.03 0.014 -10000 0 0 90 90
EGFR 0.009 0.016 -10000 0 0 381 381
PRL 0.036 0.006 -10000 0 0 15 15
neuron projection morphogenesis -0.028 0.11 0.24 6 -0.5 19 25
PTPRZ1 0.022 0.018 -10000 0 0 201 201
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.054 0.12 -10000 0 -0.54 18 18
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.003 0.11 -10000 0 -0.57 18 18
ADAM17 0.031 0.031 -10000 0 -0.096 24 24
ErbB4/ErbB4 0.001 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 26 26
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.016 0.12 -10000 0 -0.58 18 18
GRIN2B -0.028 0.11 0.21 3 -0.55 18 21
ErbB4/ErbB2/betacellulin 0.024 0.12 -10000 0 -0.55 18 18
STAT1 0.034 0.01 -10000 0 0 40 40
HBEGF 0.035 0.008 -10000 0 0 23 23
PRLR 0.036 0.004 -10000 0 0 6 6
E4ICDs/ETO2 0.02 0.13 -10000 0 -0.63 18 18
axon guidance -0.032 0.16 -10000 0 -0.78 18 18
NEDD4 0.029 0.031 0.11 1 -0.11 21 22
Prolactin receptor/Prolactin receptor/Prolactin 0.052 0.011 -10000 0 -10000 0 0
CBFA2T3 0.034 0.009 -10000 0 0 30 30
ErbB4/ErbB2/HBEGF 0.023 0.11 -10000 0 -0.55 18 18
MAPK3 -0.021 0.11 0.26 5 -0.52 18 23
STAT1 (dimer) 0.019 0.13 -10000 0 -0.63 18 18
MAPK1 -0.023 0.11 0.26 5 -0.52 19 24
JAK2 0.031 0.014 -10000 0 0 83 83
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.11 0.21 1 -0.55 18 19
NRG1 -0.022 0.021 0.089 5 -0.083 18 23
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.036 0.005 -10000 0 0 10 10
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.032 0.16 -10000 0 -0.78 18 18
neural crest cell migration 0.003 0.11 0.21 1 -0.54 18 19
ERBB2 -0.021 0.023 0.098 8 -0.083 18 26
WWOX/E4ICDs 0.022 0.13 -10000 0 -0.62 18 18
SHC1 0.033 0.011 -10000 0 0 52 52
ErbB4/EGFR/neuregulin 4 -0.015 0.099 -10000 0 -0.48 18 18
apoptosis -0.004 0.12 0.58 18 -10000 0 18
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.021 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB2/epiregulin 0.023 0.11 -10000 0 -0.55 18 18
ErbB4/ErbB4/betacellulin/betacellulin 0.022 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.062 0.13 -10000 0 -0.57 18 18
MDM2 0 0.13 0.27 13 -0.6 18 31
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.02 0.1 -10000 0 -0.51 18 18
STAT5A -0.037 0.15 -10000 0 -0.76 18 18
ErbB4/EGFR/neuregulin 1 beta -0.005 0.089 -10000 0 -0.43 18 18
DLG4 0.036 0.005 -10000 0 0 11 11
GRB2/SHC 0.043 0.037 -10000 0 -0.15 14 14
E4ICDs/TAB2/NCoR1 0.029 0.13 -10000 0 -0.62 18 18
STAT5A (dimer) -0.001 0.16 -10000 0 -0.72 18 18
MAP3K7IP2 0.033 0.011 -10000 0 0 46 46
STAT5B (dimer) -0.017 0.16 0.28 1 -0.76 18 19
LRIG1 0.03 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 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.032 0.16 -10000 0 -0.79 18 18
ERBB4 0.001 0.14 -10000 0 -0.69 18 18
STAT5B 0.036 0.004 -10000 0 0 5 5
YAP1 -0.071 0.2 -10000 0 -0.49 93 93
GRB2 0.035 0.007 -10000 0 0 17 17
ErbB4/ErbB2/neuregulin 4 0.001 0.11 -10000 0 -0.55 18 18
glial cell differentiation -0.029 0.13 0.62 18 -10000 0 18
WWOX 0.035 0.007 -10000 0 0 17 17
cell proliferation -0.014 0.11 -10000 0 -0.57 18 18
Visual signal transduction: Cones

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
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 + 0.01 0.06 -10000 0 -0.11 88 88
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.036 0.005 -10000 0 0 8 8
RGS9-1/Gbeta5/R9AP 0.045 0.015 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.046 0.012 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.036 0.005 -10000 0 0 9 9
Cone Metarhodopsin II/X-Arrestin 0.027 0 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.056 0.092 75 -0.11 71 146
Cone PDE6 0.053 0.047 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.017 0.064 -10000 0 -0.11 87 87
GNAT2/GDP 0.058 0.02 -10000 0 -0.1 1 1
GNB5 0.035 0.008 -10000 0 0 24 24
mol:GMP (4 units) -0.011 0.032 0.18 12 -10000 0 12
Cone Transducin 0.045 0.01 -10000 0 -10000 0 0
SLC24A2 0.029 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 18 18
GNAT2/GTP 0.027 0.003 -10000 0 -10000 0 0
CNGA3 0.022 0.018 -10000 0 0 197 197
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 0.061 -10000 0 -0.12 88 88
mol:Pi 0.045 0.015 -10000 0 -0.11 1 1
Cone CNG Channel 0.026 0.075 -10000 0 -0.11 81 81
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.029 0.015 -10000 0 0 100 100
RGS9 0.035 0.007 -10000 0 0 17 17
PDE6C 0.025 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
Regulation of Telomerase

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
Telomerase catalytic core complex 0.028 0.15 -10000 0 -0.46 26 26
RAD9A 0.036 0.005 -10000 0 0 11 11
AP1 0.011 0.079 -10000 0 -0.17 70 70
IFNAR2 0.033 0.02 -10000 0 -0.035 36 36
AKT1 0.013 0.056 -10000 0 -0.25 19 19
ER alpha/Oestrogen 0.024 0.014 -10000 0 -0.023 13 13
NFX1/SIN3/HDAC complex -0.005 0.082 -10000 0 -0.26 32 32
EGF 0.033 0.016 -10000 0 -0.014 45 45
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.052 -10000 0 -0.16 20 20
TERT/c-Abl 0.035 0.16 -10000 0 -0.46 28 28
SAP18 0.034 0.01 -10000 0 0 41 41
MRN complex 0.069 0.024 -10000 0 -0.12 4 4
WT1 0.033 0.02 -10000 0 -0.035 36 36
WRN 0.035 0.009 -10000 0 0 29 29
SP1 0.033 0.023 -10000 0 -0.043 38 38
SP3 0.033 0.016 -10000 0 -0.03 25 25
TERF2IP 0.034 0.01 -10000 0 0 37 37
Telomerase/Nucleolin 0.04 0.16 -10000 0 -0.44 30 30
Mad/Max 0.047 0.028 -10000 0 -10000 0 0
TERT 0.024 0.16 -10000 0 -0.47 26 26
CCND1 -0.013 0.29 -10000 0 -0.95 39 39
MAX 0.032 0.018 -10000 0 -0.03 29 29
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 56 56
TERF2 0.027 0.011 0.085 4 -10000 0 4
PTGES3 0.036 0.006 -10000 0 0 14 14
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.048 0.1 -10000 0 -0.4 14 14
CDKN1B -0.027 0.082 0.099 35 -0.34 26 61
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 39 39
SAP30 0.035 0.007 -10000 0 0 20 20
TRF2/PARP2 0.033 0.056 -10000 0 -0.14 45 45
UBE3A 0.035 0.011 -10000 0 -0.023 17 17
JUN 0.032 0.016 -10000 0 -0.03 17 17
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.025 0.02 -10000 0 -0.13 4 4
FOS 0.024 0.02 -10000 0 -0.03 15 15
IFN-gamma/IRF1 0.034 0.069 -10000 0 -0.18 38 38
PARP2 0.035 0.007 -10000 0 0 21 21
BLM 0.029 0.015 -10000 0 0 107 107
Telomerase 0.016 0.055 -10000 0 -0.32 9 9
IRF1 0.025 0.039 -10000 0 -0.11 31 31
ESR1 0.035 0.009 -10000 0 0 29 29
KU/TER 0.047 0.029 -10000 0 -0.14 9 9
ATM/TRF2 0.044 0.027 -10000 0 -0.11 7 7
ubiquitin-dependent protein catabolic process 0.003 0.079 0.14 1 -0.26 27 28
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.003 0.081 -10000 0 -0.27 27 27
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.029 0.023 -10000 0 -0.041 33 33
ATM 0.022 0.038 0.13 38 -0.18 5 43
SMAD3 -0.014 0.028 0.09 28 -10000 0 28
ABL1 0.032 0.013 -10000 0 0 70 70
MXD1 0.034 0.016 -10000 0 -0.03 29 29
MRE11A 0.036 0.004 -10000 0 0 7 7
HUS1 0.025 0.017 -10000 0 0 166 166
RPS6KB1 0.036 0.005 -10000 0 0 9 9
TERT/NF kappa B1/14-3-3 0.043 0.17 -10000 0 -0.49 23 23
NR2F2 0.022 0.023 -10000 0 -0.03 52 52
MAPK3 -0.017 0.017 0.093 2 -10000 0 2
MAPK1 -0.014 0.022 0.095 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 14 14
EGFR 0.009 0.016 -10000 0 0 382 382
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.056 -10000 0 -0.14 64 64
MYC 0.028 0.019 -10000 0 -0.029 21 21
IL2 0.034 0.023 -10000 0 -0.043 36 36
KU 0.047 0.029 -10000 0 -0.14 9 9
RAD50 0.036 0.006 -10000 0 0 13 13
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.032 0.012 -10000 0 0 66 66
TRF2/BLM 0.01 0.077 -10000 0 -0.15 92 92
FRAP1 0.035 0.007 -10000 0 0 17 17
KU/TERT 0.05 0.16 -10000 0 -0.44 29 29
SP1/HDAC2 0.042 0.045 -10000 0 -0.085 38 38
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.025 0.14 -10000 0 -0.42 30 30
Smad3/Myc 0.013 0.048 -10000 0 -0.12 39 39
911 complex 0.046 0.039 -10000 0 -0.12 5 5
IFNG 0.027 0.04 -10000 0 -0.1 38 38
Telomerase/PinX1 0.025 0.14 -10000 0 -0.42 30 30
Telomerase/AKT1/mTOR/p70S6K 0.022 0.093 0.22 1 -0.43 11 12
SIN3B 0.035 0.009 -10000 0 0 29 29
YWHAE 0.035 0.008 -10000 0 0 27 27
Telomerase/EST1B 0.025 0.14 -10000 0 -0.42 30 30
response to DNA damage stimulus 0.009 0.017 -10000 0 -0.08 9 9
MRN complex/TRF2/Rap1 0.077 0.071 -10000 0 -0.14 39 39
TRF2/WRN 0.034 0.045 -10000 0 -0.11 40 40
Telomerase/hnRNP C1/C2 0.025 0.14 -10000 0 -0.42 30 30
E2F1 0.033 0.02 -10000 0 -0.035 35 35
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 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
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.05 0.023 -10000 0 -0.14 6 6
Necdin/E2F1 -0.018 0.085 -10000 0 -0.14 156 156
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.073 0.047 -10000 0 -0.12 23 23
NGF (dimer)/p75(NTR)/BEX1 0.011 0.063 -10000 0 -0.12 95 95
NT-4/5 (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
IKBKB 0.036 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 67 67
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.009 -10000 0 -10000 0 0
FURIN 0.036 0.006 -10000 0 0 12 12
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.034 -10000 0 -0.12 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.023 0.067 -10000 0 -0.15 50 50
proBDNF (dimer) 0.032 0.012 -10000 0 0 67 67
NTRK1 0.035 0.006 -10000 0 0 16 16
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.004 0.11 0.26 2 -0.36 29 31
IRAK1 0.035 0.007 -10000 0 0 19 19
SHC1 -0.003 0.035 0.091 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 0.069 -10000 0 -0.15 28 28
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.039 0.058 -10000 0 -0.11 54 54
MAGEH1 0.032 0.013 -10000 0 0 70 70
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.003 0.075 -10000 0 -0.11 146 146
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.15 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 21 21
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 0.029 0.18 1 -0.1 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.004 0.054 0.22 8 -10000 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.056 -10000 0 -0.18 32 32
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.041 0.019 -10000 0 -0.12 1 1
NCSTN 0.035 0.008 -10000 0 0 28 28
mol:GTP 0.031 0.04 -10000 0 -0.11 29 29
PSENEN 0.035 0.008 -10000 0 0 28 28
mol:ceramide -0.007 0.044 0.19 8 -10000 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.014 0.052 -10000 0 -0.18 26 26
p75(NTR)/beta APP 0.042 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 0.039 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
RAC1/GTP 0.024 0.024 -10000 0 -0.095 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 0.031 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 18 18
MAGE-G1/E2F1 0.026 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.035 0.008 -10000 0 0 23 23
TP53 -0.014 0.064 0.22 8 -0.2 6 14
PRDM4 -0.006 0.046 0.19 8 -10000 0 8
BDNF (dimer) 0.08 0.032 -10000 0 -10000 0 0
PIK3CA 0.031 0.013 -10000 0 0 80 80
SORT1 0.036 0.006 -10000 0 0 15 15
activation of caspase activity 0.066 0.045 -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 20 20
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.016 0.1 0.2 32 -0.31 16 48
DIABLO 0.036 0.004 -10000 0 0 6 6
SMPD2 -0.007 0.044 0.19 8 -10000 0 8
APH1B 0.035 0.006 -10000 0 0 16 16
APH1A 0.036 0.005 -10000 0 0 11 11
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.023 -10000 0 -0.12 4 4
PSEN1 0.033 0.011 -10000 0 0 46 46
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 0.004 0.077 0.2 18 -0.26 9 27
MAPK9 0.028 0.088 0.2 37 -0.27 8 45
APAF1 0.036 0.003 -10000 0 0 4 4
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.018 0.018 -10000 0 0 258 258
RAC1/GDP 0.017 0.019 -10000 0 -0.13 5 5
RhoA-B-C/GDP 0.049 0.073 -10000 0 -0.14 53 53
p75 CTF/Sortilin/TRAF6/NRIF 0.076 0.055 -10000 0 -0.12 32 32
RhoA-B-C/GTP 0.031 0.04 -10000 0 -0.11 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.087 0.058 -10000 0 -0.12 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.085 0.029 -10000 0 -0.12 2 2
PRKACB 0.033 0.011 -10000 0 0 50 50
proBDNF (dimer)/p75 ECD 0.046 0.019 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.031 0.013 -10000 0 0 81 81
BIRC2 0.036 0.005 -10000 0 0 11 11
neuron projection morphogenesis -0.016 0.07 0.14 27 -0.16 29 56
BAD 0.012 0.091 0.2 22 -0.28 15 37
RIPK2 0.036 0.006 -10000 0 0 14 14
NGFR 0.031 0.013 -10000 0 0 71 71
CYCS -0.012 0.042 0.19 5 -0.19 3 8
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 0.012 0.091 0.2 22 -0.28 14 36
BDNF (dimer)/p75(NTR) 0.041 0.023 -10000 0 -10000 0 0
PI3K 0.028 0.068 -10000 0 -0.12 71 71
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 26 26
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 0.047 -10000 0 -0.12 27 27
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.024 0.017 -10000 0 0 173 173
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.01 -10000 0 0 37 37
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.031 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 0.012 0.09 0.19 22 -0.27 16 38
E2F1 0.035 0.007 -10000 0 0 17 17
CASP9 0.034 0.009 -10000 0 0 33 33
IKK complex 0.037 0.067 -10000 0 -0.25 9 9
NGF (dimer)/TRKA 0.026 0.005 -10000 0 -10000 0 0
MMP7 0.027 0.016 -10000 0 0 137 137
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 20 20
APAF-1/Caspase 9 -0.022 0.041 -10000 0 -0.2 7 7
Signaling events mediated by HDAC Class III

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
EP300 0.033 0.011 -10000 0 0 49 49
HDAC4 0.035 0.009 -10000 0 0 29 29
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.003 0.041 -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 0.033 0.01 -10000 0 0 44 44
FOXO3 0 0.031 0.25 6 -10000 0 6
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.022 -10000 0 -0.18 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.034 0.01 -10000 0 0 39 39
TAT 0.036 0.005 -10000 0 0 11 11
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 0.04 0.044 0.16 32 -0.14 3 35
HIST2H4A 0.003 0.041 0.13 45 -10000 0 45
SIRT1/FOXO3a 0.026 0.039 0.15 38 -10000 0 38
SIRT1 0.032 0.046 0.18 39 -10000 0 39
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.048 0.055 0.17 25 -0.12 14 39
SIRT1/Histone H1b 0.029 0.044 0.18 2 -0.16 5 7
apoptosis -0.049 0.05 0.12 7 -0.17 27 34
SIRT1/PGC1A 0.031 0.042 0.14 27 -0.11 11 38
p53/SIRT1 0.043 0.089 0.33 36 -0.15 18 54
SIRT1/FOXO4 0.026 0.042 0.15 30 -0.14 9 39
FOXO1/FHL2/SIRT1 0.023 0.04 0.13 25 -0.091 20 45
HIST1H1E 0.013 0.023 -10000 0 -0.18 6 6
SIRT1/p300 0.038 0.048 0.16 32 -0.14 8 40
muscle cell differentiation 0.003 0.036 0.12 2 -0.11 39 41
TP53 0.041 0.046 0.18 43 -10000 0 43
KU70/SIRT1/BAX 0.05 0.05 0.17 27 -0.12 7 34
CREBBP 0.036 0.005 -10000 0 0 8 8
MEF2D 0.036 0.005 -10000 0 0 11 11
HIV-1 Tat/SIRT1 0.039 0.043 0.15 37 -0.14 2 39
ACSS2 0.003 0.041 0.13 45 -10000 0 45
SIRT1/PCAF/MYOD -0.003 0.036 0.12 39 -0.12 2 41
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 0.059 0.048 -10000 0 -0.13 27 27
PTK2 0.006 0.088 0.24 7 -0.29 21 28
IGF1R 0.033 0.012 -10000 0 0 57 57
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.035 0.007 -10000 0 0 19 19
SRC 0.036 0.006 -10000 0 0 14 14
CDKN1B 0 0.094 -10000 0 -0.31 39 39
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.01 0.072 -10000 0 -0.29 25 25
ROCK1 0.036 0.006 -10000 0 0 15 15
AKT1 -0.004 0.07 0.2 1 -0.3 23 24
PTK2B -0.004 0.072 0.18 48 -0.19 4 52
alphaV/beta3 Integrin/JAM-A 0.071 0.048 -10000 0 -0.12 21 21
CBL 0.036 0.004 -10000 0 0 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.062 0.044 -10000 0 -0.12 24 24
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.068 0.067 -10000 0 -0.13 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.057 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Syndecan-1 0.055 0.043 -10000 0 -0.12 16 16
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.049 0.083 -10000 0 -0.15 66 66
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.013 -10000 0 0 80 80
alphaV/beta3 Integrin/Osteopontin 0.047 0.07 -10000 0 -0.14 57 57
RPS6KB1 -0.044 0.066 0.23 4 -0.28 4 8
TLN1 0.029 0.015 -10000 0 0 102 102
MAPK3 0.002 0.086 -10000 0 -0.33 26 26
GPR124 0.035 0.008 -10000 0 0 24 24
MAPK1 -0.002 0.087 -10000 0 -0.34 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 0.063 0.043 -10000 0 -0.12 24 24
cell adhesion 0.048 0.052 -10000 0 -0.16 25 25
ANGPTL3 0.036 0.005 -10000 0 0 10 10
VEGFR2 homodimer/VEGFA homodimer/Src 0.036 0.029 -10000 0 -0.12 10 10
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 57 57
Rac1/GDP 0.017 0.019 -10000 0 -0.13 5 5
TGFBR2 0.035 0.009 -10000 0 0 29 29
ITGB3 0.036 0.003 -10000 0 0 4 4
IGF1 0.035 0.008 -10000 0 0 23 23
RAC1 0.024 0.017 -10000 0 0 173 173
regulation of cell-matrix adhesion 0.059 0.045 -10000 0 -0.12 24 24
apoptosis 0.034 0.009 -10000 0 0 31 31
CD47 0.035 0.008 -10000 0 0 23 23
alphaV/beta3 Integrin/CD47 0.06 0.047 -10000 0 -0.13 25 25
VCL 0.025 0.017 -10000 0 0 154 154
alphaV/beta3 Integrin/Del1 0.063 0.043 -10000 0 -0.12 24 24
CSF1 0.036 0.005 -10000 0 0 8 8
PIK3C2A 0.01 0.018 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.026 0.041 -10000 0 -0.12 29 29
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.05 -10000 0 -0.12 28 28
FAK1/Vinculin 0.013 0.076 0.25 6 -0.26 16 22
alphaV beta3/Integrin/ppsTEM5 0.06 0.045 -10000 0 -0.12 24 24
RHOA 0.035 0.007 -10000 0 0 18 18
VTN 0.036 0.004 -10000 0 0 6 6
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.035 0.008 -10000 0 0 25 25
F11R -0.012 0.032 0.092 44 -10000 0 44
alphaV/beta3 Integrin/Lactadherin 0.061 0.045 -10000 0 -0.13 24 24
alphaV/beta3 Integrin/TGFBR2 0.059 0.047 -10000 0 -0.12 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.04 -10000 0 -0.11 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.046 0.049 -10000 0 -0.11 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.035 0.009 -10000 0 0 29 29
alphaV/beta3 Integrin/Pyk2 0.063 0.061 0.19 43 -0.12 28 71
SDC1 0.031 0.014 -10000 0 0 83 83
VAV3 -0.026 0.029 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 52 52
FAK1/Paxillin 0.024 0.081 0.24 7 -0.24 21 28
cell migration -0.004 0.07 0.23 6 -0.25 16 22
ITGAV 0.034 0.009 -10000 0 0 31 31
PI3K 0.054 0.086 -10000 0 -0.14 54 54
SPP1 0.033 0.011 -10000 0 0 54 54
KDR 0.029 0.015 -10000 0 0 101 101
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.009 -10000 0 0 31 31
COL4A3 0.037 0 -10000 0 -10000 0 0
angiogenesis 0 0.094 -10000 0 -0.37 25 25
Rac1/GTP -0.025 0.035 0.18 2 -0.18 6 8
EDIL3 0.036 0.004 -10000 0 0 5 5
cell proliferation 0.058 0.046 -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 23 23
TC10/GTP 0.027 0.047 -10000 0 -0.12 20 20
Insulin Receptor/Insulin/IRS1/Shp2 0.074 0.059 -10000 0 -0.13 29 29
HRAS 0.034 0.009 -10000 0 0 32 32
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.032 0.013 -10000 0 0 70 70
FOXO3 -0.01 0.016 0.021 2 -0.055 33 35
AKT1 -0.025 0.087 0.22 16 -0.21 24 40
INSR 0.032 0.021 -10000 0 -0.039 34 34
Insulin Receptor/Insulin 0.058 0.063 0.22 7 -0.14 34 41
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.018 -10000 0 0 220 220
SORBS1 0.025 0.017 -10000 0 0 154 154
CRK 0.035 0.008 -10000 0 0 23 23
PTPN1 -0.024 0.047 0.14 17 -0.25 8 25
CAV1 -0.012 0.037 0.16 6 -0.19 8 14
CBL/APS/CAP/Crk-II/C3G 0.05 0.053 -10000 0 -0.11 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.072 0.063 -10000 0 -0.14 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.079 -10000 0 -0.13 82 82
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.021 0.068 -10000 0 -0.36 8 8
RPS6KB1 -0.032 0.081 0.2 16 -0.2 25 41
PARD6A 0.035 0.007 -10000 0 0 20 20
CBL 0.036 0.004 -10000 0 0 7 7
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.021 0.018 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.035 0.085 0.17 22 -0.22 27 49
HRAS/GTP -0.036 0.033 -10000 0 -0.12 43 43
Insulin Receptor 0.031 0.021 -10000 0 -0.039 34 34
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.082 0.068 -10000 0 -0.13 34 34
PRKCI 0.023 0.091 -10000 0 -0.4 19 19
Insulin Receptor/Insulin/GRB14/PDK1 0.014 0.068 -10000 0 -0.13 77 77
SHC1 0.033 0.011 -10000 0 0 52 52
negative regulation of MAPKKK cascade 0.029 0.055 -10000 0 -0.21 1 1
PI3K 0.045 0.086 -10000 0 -0.13 82 82
NCK2 0.035 0.007 -10000 0 0 17 17
RHOQ 0.035 0.007 -10000 0 0 17 17
mol:H2O2 -0.004 0.006 -10000 0 -0.034 8 8
HRAS/GDP 0.021 0.027 -10000 0 -0.13 15 15
AKT2 -0.028 0.078 0.21 14 -0.19 14 28
PRKCZ 0.002 0.079 -10000 0 -0.39 18 18
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.016 0.051 0.16 24 -0.14 5 29
F2RL2 0.036 0.004 -10000 0 0 7 7
TRIP10 0.034 0.009 -10000 0 0 36 36
Insulin Receptor/Insulin/Shc 0.057 0.037 -10000 0 -0.12 8 8
TC10/GTP/CIP4/Exocyst 0.041 0.029 -10000 0 -0.12 14 14
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.072 0.046 -10000 0 -0.13 14 14
RAPGEF1 0.035 0.007 -10000 0 0 19 19
RASA1 0.034 0.009 -10000 0 0 32 32
NCK1 0.035 0.008 -10000 0 0 27 27
CBL/APS/CAP/Crk-II 0.044 0.041 -10000 0 -0.11 13 13
TC10/GDP 0.023 0.024 -10000 0 -0.13 12 12
Insulin Receptor/Insulin/SHC/GRB10 0.043 0.065 -10000 0 -0.13 30 30
INPP5D -0.02 0.027 0.061 23 -0.11 23 46
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 52 52
p62DOK/RasGAP 0.029 0.056 -10000 0 -0.21 1 1
INS 0.034 0.022 0.097 7 -0.039 34 41
mol:PI-3-4-P2 -0.02 0.027 0.061 23 -0.11 23 46
GRB2 0.035 0.007 -10000 0 0 17 17
EIF4EBP1 -0.034 0.079 0.2 13 -0.21 24 37
PTPRA 0.034 0.016 -10000 0 -0.052 7 7
PIK3CA 0.031 0.013 -10000 0 0 80 80
TC10/GTP/CIP4 0.041 0.029 -10000 0 -0.12 14 14
PDPK1 0.036 0.004 -10000 0 0 7 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.014 0.052 -10000 0 -0.16 34 34
Insulin Receptor/Insulin/IRS1 0.053 0.046 -10000 0 -0.12 23 23
Insulin Receptor/Insulin/IRS3 0.046 0.031 -10000 0 -0.069 8 8
Par3/Par6 0.073 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 0.032 0.012 -10000 0 0 58 58
mol:Halofuginone -0.001 0.029 -10000 0 -0.17 14 14
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.028 0.15 -10000 0 -0.41 59 59
PRL-3/alpha Tubulin 0.018 0.032 -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 0 108 108
CCNA2 -0.03 0.1 -10000 0 -0.58 13 13
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.002 0.056 0.11 4 -0.32 14 18
CDK2/Cyclin E1 -0.005 0.15 -10000 0 -0.37 59 59
MAPK3 -0.013 0.03 0.092 37 -10000 0 37
PRL-2 /Rab GGTase beta 0.047 0.035 -10000 0 -0.16 12 12
MAPK1 -0.01 0.032 0.092 42 -10000 0 42
PTP4A1 -0.022 0.099 -10000 0 -0.6 13 13
PTP4A3 0.031 0.013 -10000 0 0 73 73
PTP4A2 0.035 0.006 -10000 0 0 16 16
ITGB1 -0.009 0.026 0.092 27 -10000 0 27
SRC 0.036 0.006 -10000 0 0 14 14
RAC1 -0.001 0.085 -10000 0 -0.39 20 20
Rab GGTase beta/Rab GGTase alpha 0.045 0.032 -10000 0 -0.14 11 11
PRL-1/ATF-5 -0.033 0.1 -10000 0 -0.54 14 14
RABGGTA 0.034 0.01 -10000 0 0 41 41
BCAR1 -0.009 0.055 0.25 21 -10000 0 21
RHOC -0.007 0.12 -10000 0 -0.36 44 44
RHOA -0.008 0.13 -10000 0 -0.44 34 34
cell motility -0.005 0.12 -10000 0 -0.37 39 39
PRL-1/alpha Tubulin -0.034 0.095 -10000 0 -0.55 14 14
PRL-3/alpha1 Integrin 0.018 0.032 -10000 0 -0.13 21 21
ROCK1 -0.004 0.12 -10000 0 -0.37 39 39
RABGGTB 0.035 0.008 -10000 0 0 26 26
CDK2 0.034 0.01 -10000 0 0 40 40
mitosis -0.021 0.098 -10000 0 -0.59 13 13
ATF5 0.034 0.009 -10000 0 0 36 36
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 0.032 0.012 -10000 0 0 58 58
SMAD2 -0.016 0.06 0.17 2 -0.24 19 21
SMAD3 0.005 0.054 -10000 0 -0.32 6 6
SMAD3/SMAD4 -0.01 0.17 -10000 0 -0.49 45 45
SMAD4/Ubc9/PIASy 0.054 0.052 -10000 0 -0.12 34 34
SMAD2/SMAD2/SMAD4 0.027 0.1 -10000 0 -0.25 28 28
PPM1A 0.034 0.009 -10000 0 0 30 30
CALM1 0.033 0.011 -10000 0 0 54 54
SMAD2/SMAD4 0 0.066 -10000 0 -0.21 29 29
MAP3K1 0.035 0.007 -10000 0 0 20 20
TRAP-1/SMAD4 0.036 0.053 -10000 0 -0.14 40 40
MAPK3 0.036 0.004 -10000 0 0 6 6
MAPK1 0.033 0.01 -10000 0 0 45 45
NUP214 0.035 0.007 -10000 0 0 18 18
CTDSP1 0.035 0.006 -10000 0 0 16 16
CTDSP2 0.033 0.012 -10000 0 0 57 57
CTDSPL 0.036 0.006 -10000 0 0 12 12
KPNB1 0.035 0.007 -10000 0 0 22 22
TGFBRAP1 0.036 0.005 -10000 0 0 10 10
UBE2I 0.036 0.004 -10000 0 0 6 6
NUP153 0.034 0.009 -10000 0 0 31 31
KPNA2 0.034 0.01 -10000 0 0 39 39
PIAS4 0.035 0.008 -10000 0 0 27 27
IL4-mediated signaling events

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
BCL2L1 -0.058 0.38 0.83 1 -1.1 21 22
STAT6 (cleaved dimer) -0.07 0.35 -10000 0 -0.94 31 31
IGHG1 -0.015 0.26 0.43 20 -0.8 22 42
IGHG3 -0.068 0.36 0.63 1 -0.95 29 30
AKT1 -0.026 0.27 0.52 4 -0.74 29 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.014 0.19 0.47 4 -0.57 7 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.01 0.26 0.53 2 -0.78 18 20
THY1 -0.13 0.5 0.78 2 -1.2 62 64
MYB 0.032 0.012 -10000 0 0 58 58
HMGA1 0.036 0.005 -10000 0 0 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.003 0.26 0.54 8 -0.61 13 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.009 0.25 0.51 2 -0.81 15 17
SP1 0.029 0.076 0.12 95 -0.14 71 166
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.045 -10000 0 -0.078 1 1
STAT6 (dimer)/ETS1 -0.056 0.37 -10000 0 -0.96 28 28
SOCS1 -0.041 0.3 0.52 2 -0.68 29 31
SOCS3 -0.006 0.22 -10000 0 -0.65 3 3
FCER2 -0.03 0.32 0.65 1 -0.79 16 17
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.065 0.38 0.72 1 -1.1 21 22
GRB2 0.035 0.007 -10000 0 0 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.002 0.22 0.49 4 -0.61 15 19
T cell proliferation -0.073 0.38 0.66 1 -1 26 27
IL4R/JAK1 -0.073 0.38 0.66 1 -1 28 29
EGR2 -0.12 0.5 0.72 1 -1.3 51 52
JAK2 0.019 0.066 0.15 18 -10000 0 18
JAK3 0.035 0.016 -10000 0 -0.037 10 10
PIK3R1 0.032 0.012 -10000 0 0 63 63
JAK1 0.026 0.039 0.11 7 -10000 0 7
COL1A2 -0.11 0.48 0.49 6 -1.2 76 82
CCL26 -0.064 0.38 0.72 1 -0.98 29 30
IL4R -0.061 0.41 0.8 3 -1.1 22 25
PTPN6 0.015 0.037 -10000 0 -0.06 4 4
IL13RA2 -0.32 0.66 0.76 3 -1.1 174 177
IL13RA1 0.023 0.067 0.15 18 -10000 0 18
IRF4 0.046 0.11 -10000 0 -10000 0 0
ARG1 -0.003 0.22 0.49 6 -0.89 10 16
CBL -0.01 0.24 0.49 4 -0.58 14 18
GTF3A 0.048 0.034 0.12 70 -0.15 3 73
PIK3CA 0.031 0.013 -10000 0 0 80 80
IL13RA1/JAK2 0.025 0.1 0.23 13 -0.17 10 23
IRF4/BCL6 0.042 0.11 -10000 0 -10000 0 0
CD40LG 0.041 0.004 0.14 1 -10000 0 1
MAPK14 -0.007 0.24 0.5 3 -0.59 11 14
mitosis -0.021 0.26 0.51 5 -0.69 29 34
STAT6 -0.07 0.43 0.82 4 -1.1 27 31
SPI1 0.037 0.013 0.1 2 -10000 0 2
RPS6KB1 -0.025 0.26 0.48 6 -0.67 29 35
STAT6 (dimer) -0.07 0.43 0.82 4 -1.1 27 31
STAT6 (dimer)/PARP14 -0.084 0.38 -10000 0 -1 28 28
mast cell activation -0.002 0.016 -10000 0 -0.041 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.005 0.22 0.5 2 -0.61 5 7
FRAP1 -0.026 0.27 0.52 4 -0.73 29 33
LTA -0.068 0.38 0.72 1 -1.1 21 22
FES 0.035 0.007 -10000 0 0 17 17
T-helper 1 cell differentiation 0.067 0.42 1.1 27 -0.82 4 31
CCL11 -0.069 0.36 -10000 0 -1 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.009 0.22 0.51 4 -0.61 5 9
IL2RG 0.034 0.016 -10000 0 -0.035 7 7
IL10 -0.052 0.39 0.71 3 -1 22 25
IRS1 0.033 0.011 -10000 0 0 52 52
IRS2 0.03 0.014 -10000 0 0 96 96
IL4 0.022 0.18 0.57 1 -0.88 7 8
IL5 -0.067 0.38 0.72 1 -1.1 21 22
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.06 0.39 0.69 7 -0.92 37 44
COL1A1 0.017 0.26 0.6 6 -1.1 7 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.077 0.38 -10000 0 -1.1 22 22
IL2R gamma/JAK3 0.054 0.019 -10000 0 -10000 0 0
TFF3 -0.062 0.38 0.72 1 -1 21 22
ALOX15 -0.067 0.38 0.72 1 -1.1 21 22
MYBL1 0.03 0.014 -10000 0 0 97 97
T-helper 2 cell differentiation -0.048 0.34 0.63 4 -0.83 29 33
SHC1 0.033 0.011 -10000 0 0 52 52
CEBPB 0.035 0.015 0.1 4 -10000 0 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.019 0.26 0.53 4 -0.82 17 21
mol:PI-3-4-5-P3 -0.025 0.27 0.52 4 -0.73 29 33
PI3K -0.03 0.29 0.52 4 -0.79 28 32
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.004 0.047 -10000 0 -0.088 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.002 0.22 0.44 9 -0.58 21 30
ITGB3 -0.067 0.38 0.72 1 -1.1 21 22
PIGR -0.055 0.38 0.71 2 -1.1 21 23
IGHE -0.007 0.079 0.18 37 -0.18 16 53
MAPKKK cascade 0.003 0.21 0.44 9 -0.57 21 30
BCL6 0.031 0.012 -10000 0 -10000 0 0
OPRM1 -0.067 0.38 0.72 1 -1.1 21 22
RETNLB -0.064 0.38 0.72 1 -0.98 29 30
SELP -0.063 0.38 0.79 2 -1.1 21 23
AICDA -0.066 0.36 -10000 0 -1 20 20
Aurora B signaling

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
Condensin I complex 0.001 0.011 -10000 0 -0.09 7 7
STMN1 -0.015 0.027 0.091 30 -10000 0 30
Aurora B/RasGAP/Survivin 0.034 0.074 -10000 0 -0.14 71 71
Chromosomal passenger complex/Cul3 protein complex -0.032 0.076 -10000 0 -0.19 64 64
BIRC5 0.029 0.015 -10000 0 0 108 108
DES 0.028 0.078 -10000 0 -0.6 7 7
Aurora C/Aurora B/INCENP 0.062 0.022 -10000 0 -10000 0 0
Aurora B/TACC1 0.042 0.026 -10000 0 -0.11 9 9
Aurora B/PP2A 0.05 0.015 -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 20 -0.009 1 21
NDC80 -0.01 0.007 0.014 3 -10000 0 3
Cul3 protein complex 0.026 0.032 -10000 0 -0.14 8 8
KIF2C -0.018 0.12 -10000 0 -0.43 35 35
PEBP1 -0.001 0.003 0.009 18 -0.008 11 29
KIF20A 0.028 0.015 -10000 0 0 109 109
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.04 0.044 -10000 0 -0.14 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 0.072 -10000 0 -0.46 7 7
PSMA3 0.034 0.009 -10000 0 0 35 35
G2/M transition of mitotic cell cycle -0.001 0.002 0.008 10 -0.006 3 13
H3F3B 0.009 0.032 -10000 0 -0.2 11 11
AURKB 0.032 0.015 -10000 0 -0.009 54 54
AURKC 0.036 0.006 -10000 0 0 15 15
CDCA8 0.032 0.013 -10000 0 -0.003 58 58
cytokinesis -0.024 0.14 0.18 7 -0.42 49 56
Aurora B/Septin1 -0.013 0.14 0.19 4 -0.39 49 53
AURKA -0.001 0.002 0.008 10 -0.006 3 13
INCENP 0.034 0.014 0.058 1 -0.022 28 29
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.036 0.006 0.058 1 0 11 12
hSgo1/Aurora B/Survivin 0.022 0.05 -10000 0 -0.11 56 56
EVI5 0.035 0.007 -10000 0 0 18 18
RhoA/GTP 0.012 0.13 -10000 0 -0.32 52 52
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.004 0.075 0.12 2 -0.27 31 33
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.045 0.029 -10000 0 -0.14 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 18 18
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 0.006 0.065 -10000 0 -0.3 18 18
RASA1 0.034 0.009 -10000 0 0 32 32
KLHL9 0.021 0.018 -10000 0 0 213 213
mitotic prometaphase -0.001 0.003 0.009 18 -0.008 11 29
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.029 -10000 0 -0.14 8 8
PPP1CC 0.036 0.005 -10000 0 0 9 9
Centraspindlin 0.002 0.13 -10000 0 -0.34 51 51
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
NSUN2 0.003 0.037 -10000 0 -0.28 7 7
MYLK -0.015 0.07 -10000 0 -0.2 64 64
KIF23 0.028 0.018 -10000 0 -0.006 103 103
VIM -0.013 0.019 0.088 12 -10000 0 12
RACGAP1 0.03 0.016 -10000 0 -0.003 86 86
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.062 -10000 0 -0.28 21 21
Chromosomal passenger complex -0.015 0.096 0.13 4 -0.25 59 63
Chromosomal passenger complex/EVI5 0.062 0.085 -10000 0 -0.15 55 55
TACC1 0.035 0.008 -10000 0 0 23 23
PPP2R5D 0.036 0.004 -10000 0 0 5 5
CUL3 0.036 0.002 -10000 0 0 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A 0.023 0.057 0.16 1 -0.2 26 27
BIRC5 0.029 0.015 -10000 0 0 108 108
NFKBIA -0.008 0.042 0.14 8 -0.18 16 24
CPEB1 0.033 0.012 -10000 0 0 57 57
AKT1 -0.006 0.033 0.17 2 -0.18 7 9
NDEL1 0.035 0.007 -10000 0 0 18 18
Aurora A/BRCA1 0.023 0.043 0.14 1 -0.15 23 24
NDEL1/TACC3 0.036 0.057 0.16 1 -0.18 21 22
GADD45A 0.031 0.013 -10000 0 0 75 75
GSK3B 0.035 0.016 0.089 25 0 40 65
PAK1/Aurora A 0.029 0.05 0.16 1 -0.16 24 25
MDM2 0.033 0.011 -10000 0 0 46 46
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.012 0.026 0.092 26 -10000 0 26
TP53 0.004 0.07 -10000 0 -0.23 33 33
DLG7 -0.004 0.043 0.19 2 -0.18 13 15
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.012 -10000 0 0 59 59
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.038 0.061 0.17 1 -0.18 24 25
G2/M transition of mitotic cell cycle 0.023 0.042 -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 0.074 0.12 1 -0.28 28 29
G2/M transition checkpoint 0.001 0.036 0.088 1 -0.14 23 24
mRNA polyadenylation 0.015 0.051 -10000 0 -0.13 46 46
Aurora A/CPEB 0.015 0.051 0.14 1 -0.13 46 47
Aurora A/TACC1/TRAP/chTOG 0.051 0.081 -10000 0 -0.21 29 29
BRCA1 0.036 0.006 -10000 0 0 12 12
centrosome duplication 0.029 0.049 0.16 1 -0.16 24 25
regulation of centrosome cycle 0.035 0.056 0.15 1 -0.18 21 22
spindle assembly 0.049 0.08 -10000 0 -0.2 29 29
TDRD7 0.034 0.01 -10000 0 0 40 40
Aurora A/RasGAP/Survivin 0.04 0.073 -10000 0 -0.18 25 25
CENPA 0.002 0.064 -10000 0 -0.26 25 25
Aurora A/PP2A 0.029 0.05 0.16 1 -0.16 24 25
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 0.04 0.045 -10000 0 -0.14 27 27
RASA1 0.034 0.009 -10000 0 0 32 32
Ajuba/Aurora A 0.001 0.036 0.089 1 -0.14 23 24
mitotic prometaphase -0.004 0.009 0.068 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.049 0.13 24 -0.21 19 43
TACC1 0.035 0.008 -10000 0 0 23 23
TACC3 0.032 0.012 -10000 0 0 59 59
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 0.034 0.009 -10000 0 0 34 34
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 -10000 0 27
GIT1 0.036 0.003 -10000 0 0 4 4
GIT1/beta-PIX/PAK1 0.058 0.047 -10000 0 -0.12 26 26
Importin alpha/Importin beta/TPX2 -0.012 0.026 0.092 26 -10000 0 26
PPP2R5D 0.036 0.004 -10000 0 0 5 5
Aurora A/TPX2 -0.028 0.055 0.096 4 -0.22 21 25
PAK1 0.036 0.006 -10000 0 0 15 15
CKAP5 0.034 0.01 -10000 0 0 37 37
TRAIL signaling pathway

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
TNFSF10 0.029 0.015 -10000 0 0 109 109
positive regulation of NF-kappaB transcription factor activity 0.035 0.045 -10000 0 -0.14 25 25
MAP2K4 0.015 0.059 0.21 2 -0.27 8 10
IKBKB 0.036 0.003 -10000 0 0 4 4
TNFRSF10B 0.035 0.008 -10000 0 0 26 26
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.014 0.028 -10000 0 -0.1 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 0.034 0.044 -10000 0 -0.14 24 24
TRAIL/TRAILR3 0.035 0.045 -10000 0 -0.14 25 25
TRAIL/TRAILR1 0.015 0.035 -10000 0 -0.13 26 26
TRAIL/TRAILR4 0.035 0.045 -10000 0 -0.14 25 25
TRAIL/TRAILR1/DAP3/GTP 0.028 0.04 -10000 0 -0.1 34 34
IKK complex -0.033 0.12 -10000 0 -0.22 132 132
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 0.024 -10000 0 -0.13 12 12
MAPK3 -0.005 0.039 0.092 68 -10000 0 68
MAP3K1 0.022 0.055 -10000 0 -0.28 7 7
TRAILR4 (trimer) 0.036 0.006 -10000 0 0 12 12
TRADD 0.036 0.005 -10000 0 0 11 11
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 0.092 68 -10000 0 68
TRAIL/TRAILR1/FADD/TRADD/RIP 0.07 0.047 -10000 0 -0.1 25 25
mol:ceramide 0.014 0.028 -10000 0 -0.1 20 20
FADD 0.036 0.006 -10000 0 0 12 12
MAPK8 0.008 0.04 0.19 1 -0.24 4 5
TRAF2 0.036 0.006 -10000 0 0 15 15
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 0.038 -10000 0 -0.11 25 25
DAP3 0.035 0.007 -10000 0 0 22 22
CASP10 -0.004 0.051 0.14 15 -0.16 22 37
JNK cascade 0.035 0.045 -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 33 33
TRAIL/TRAILR2/FADD 0.05 0.048 -10000 0 -0.12 23 23
cell death 0.014 0.028 -10000 0 -0.1 20 20
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.024 0.05 -10000 0 -0.17 20 20
TRAILR2 (trimer) 0.035 0.008 -10000 0 0 26 26
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 0.086 0.057 -10000 0 -0.11 23 23
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.034 0.009 -10000 0 0 32 32
NFATC1 0.004 0.1 0.23 1 -0.4 22 23
NFATC2 -0.034 0.082 -10000 0 -0.16 115 115
NFATC3 0.01 0.019 -10000 0 -0.1 13 13
YWHAE 0.035 0.008 -10000 0 0 27 27
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.075 0.16 2 -0.23 22 24
Exportin 1/Ran/NUP214 0.068 0.029 -10000 0 -0.15 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.02 0.089 -10000 0 -0.24 12 12
BCL2/BAX 0.047 0.023 -10000 0 -0.14 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.026 -10000 0 -0.13 13 13
CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 13 13
BAX 0.033 0.01 -10000 0 0 44 44
MAPK14 0.036 0.004 -10000 0 0 6 6
BAD 0.036 0.006 -10000 0 0 14 14
CABIN1/MEF2D 0.007 0.081 -10000 0 -0.22 21 21
Calcineurin A alpha-beta B1/BCL2 0.035 0.007 -10000 0 0 20 20
FKBP8 0.035 0.009 -10000 0 0 29 29
activation-induced cell death of T cells -0.007 0.08 0.22 21 -10000 0 21
KPNB1 0.035 0.007 -10000 0 0 22 22
KPNA2 0.034 0.01 -10000 0 0 39 39
XPO1 0.036 0.004 -10000 0 0 5 5
SFN 0.031 0.013 -10000 0 0 78 78
MAP3K8 0.022 0.018 -10000 0 0 196 196
NFAT4/CK1 alpha 0.025 0.042 0.17 1 -0.16 16 17
MEF2D/NFAT1/Cbp/p300 0.011 0.11 0.23 1 -0.21 36 37
CABIN1 -0.007 0.075 0.16 2 -0.24 22 24
CALM1 0.033 0.011 -10000 0 0 54 54
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 9 9
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.036 0.004 -10000 0 0 6 6
YWHAH 0.031 0.013 -10000 0 0 73 73
Calcineurin A alpha-beta B1/AKAP79/PKA 0.049 0.016 -10000 0 -10000 0 0
YWHAB 0.035 0.008 -10000 0 0 24 24
MAPK8 0.027 0.016 -10000 0 0 138 138
MAPK9 0.036 0.006 -10000 0 0 15 15
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.033 0.01 -10000 0 0 44 44
NFAT1-c-4/YWHAQ 0.001 0.1 -10000 0 -0.37 20 20
PRKCH 0.034 0.01 -10000 0 0 43 43
CABIN1/Cbp/p300 0.047 0.028 -10000 0 -0.14 7 7
CASP3 0.034 0.009 -10000 0 0 31 31
PIM1 0.036 0.005 -10000 0 0 8 8
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.019 -10000 0 -0.11 10 10
apoptosis 0.02 0.035 -10000 0 -0.21 6 6
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.095 -10000 0 -0.32 24 24
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.036 0.003 -10000 0 0 4 4
JNK2/NFAT4 0.026 0.036 -10000 0 -0.12 20 20
BAD/BCL-XL 0.048 0.025 -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 0 158 158
FKBP38/BCL2 0.049 0.016 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 0 49 49
PRKCB1 0.031 0.013 -10000 0 0 82 82
CSNK2A1 0.034 0.009 -10000 0 0 31 31
NFATc/JNK1 0.013 0.099 0.24 1 -0.39 21 22
CaM/Ca2+/FKBP38 0.04 0.03 -10000 0 -0.11 13 13
FKBP12/FK506 0.022 0.023 -10000 0 -0.13 10 10
CSNK1A1 -0.016 0.021 0.087 12 -0.11 9 21
CaM/Ca2+/CAMK IV 0.041 0.029 -10000 0 -0.11 13 13
NFATc/ERK1 0.022 0.1 0.24 1 -0.38 22 23
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.019 0.091 -10000 0 -0.24 15 15
NR4A1 -0.024 0.079 0.18 2 -0.2 27 29
GSK3B 0.034 0.01 -10000 0 0 40 40
positive T cell selection 0.01 0.019 -10000 0 -0.1 13 13
NFAT1/CK1 alpha -0.019 0.069 -10000 0 -0.18 42 42
RCH1/ KPNB1 0.036 0.057 -10000 0 -0.15 43 43
YWHAQ 0.036 0.005 -10000 0 0 9 9
PRKACA 0.035 0.008 -10000 0 0 25 25
AKAP5 0.034 0.009 -10000 0 0 31 31
MEF2D 0.036 0.005 -10000 0 0 11 11
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.035 0.007 -10000 0 0 21 21
NFATc/p38 alpha 0.022 0.1 0.24 1 -0.38 22 23
CREBBP 0.036 0.005 -10000 0 0 8 8
BCL2 0.035 0.007 -10000 0 0 20 20
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.026 0.084 36 -10000 0 36
SNTA1 0.033 0.011 -10000 0 0 55 55
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.014 0.033 0.082 52 -10000 0 52
MAPK12 -0.011 0.029 0.2 3 -0.17 9 12
CCND1 -0.019 0.1 -10000 0 -0.37 39 39
p38 gamma/SNTA1 -0.01 0.038 0.2 3 -0.16 10 13
MAP2K3 0.036 0.005 -10000 0 0 10 10
PKN1 0.033 0.011 -10000 0 0 48 48
G2/M transition checkpoint -0.011 0.029 0.2 3 -0.17 9 12
MAP2K6 -0.005 0.034 0.21 5 -0.18 10 15
MAPT -0.025 0.077 0.16 5 -0.2 73 78
MAPK13 -0.014 0.03 0.092 36 -10000 0 36
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.031 -10000 0 -0.2 11 11
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 0.005 -10000 0 0 8 8
VDR 0.035 0.007 -10000 0 0 18 18
Cbp/p300/PCAF 0.042 0.024 -10000 0 -0.12 7 7
EP300 0.033 0.011 -10000 0 0 49 49
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.05 -10000 0 -0.2 5 5
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.004 -10000 0 0 6 6
AKT1 0.008 0.078 0.21 1 -0.22 10 11
RAR alpha/9cRA/Cyclin H -0.024 0.12 -10000 0 -0.3 35 35
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.055 -10000 0 -0.2 20 20
CDC2 0.019 0.02 -10000 0 -0.001 241 241
response to UV -0.001 0.007 -10000 0 -0.026 33 33
RAR alpha/Jnk1 0.023 0.028 0.16 1 -10000 0 1
NCOR2 0.036 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 0.035 0.008 -10000 0 0 27 27
NCOA1 0.033 0.011 -10000 0 0 50 50
VDR/VDR/DNA 0.035 0.007 -10000 0 0 18 18
RARG 0.032 0.017 -10000 0 -0.025 41 41
RAR gamma1/9cRA 0.046 0.012 -10000 0 -10000 0 0
MAPK3 0.032 0.018 -10000 0 -0.03 39 39
MAPK1 0.033 0.01 -10000 0 0 45 45
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 -0.02 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 0.006 0.038 -10000 0 -0.16 8 8
PRKCA 0.031 0.027 0.075 4 -0.072 32 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.029 0.16 -10000 0 -0.61 33 33
RXRG 0.019 0.028 -10000 0 -10000 0 0
RXRA -0.011 0.082 0.15 4 -0.3 24 28
RXRB 0.019 0.026 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RBP1 0.026 0.016 -10000 0 0 141 141
CRBP1/9-cic-RA -0.004 0.06 -10000 0 -0.13 90 90
RARB 0.032 0.021 -10000 0 -0.046 32 32
PRKCG 0.031 0.027 -10000 0 -0.071 33 33
MNAT1 0.034 0.01 -10000 0 0 38 38
RAR alpha/RXRs -0.013 0.13 -10000 0 -0.42 24 24
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.006 0.089 -10000 0 -0.32 18 18
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.056 -10000 0 -0.18 11 11
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.029 0.16 -10000 0 -0.61 33 33
positive regulation of DNA binding -0.028 0.12 -10000 0 -0.28 36 36
NRIP1 -0.053 0.27 -10000 0 -1.1 33 33
RXRs/RARs -0.007 0.12 -10000 0 -0.41 33 33
RXRs/RXRs/DNA/9cRA -0.032 0.11 -10000 0 -0.36 33 33
PRKACA 0.035 0.008 -10000 0 0 25 25
CDK7 0.035 0.008 -10000 0 0 24 24
TFIIH 0.059 0.049 -10000 0 -0.16 19 19
RAR alpha/9cRA 0.022 0.087 -10000 0 -0.17 22 22
CCNH 0.035 0.007 -10000 0 0 18 18
CREBBP 0.036 0.005 -10000 0 0 8 8
RAR gamma2/9cRA 0.056 0.049 -10000 0 -0.14 18 18
BARD1 signaling events

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
BARD1/CSTF1 0.044 0.037 -10000 0 -0.14 17 17
ATM 0.034 0.009 -10000 0 0 35 35
UBE2D3 0.036 0.006 -10000 0 0 12 12
PRKDC 0.033 0.01 -10000 0 0 44 44
ATR 0.035 0.008 -10000 0 0 25 25
UBE2L3 0.034 0.009 -10000 0 0 33 33
FANCD2 0.008 0.035 -10000 0 -0.2 14 14
protein ubiquitination 0.077 0.055 -10000 0 -0.13 21 21
XRCC5 0.036 0.005 -10000 0 0 9 9
XRCC6 0.034 0.01 -10000 0 0 39 39
M/R/N Complex 0.069 0.024 -10000 0 -0.12 4 4
MRE11A 0.036 0.004 -10000 0 0 7 7
DNA-PK 0.057 0.049 -10000 0 -0.14 22 22
FA complex/FANCD2/Ubiquitin 0.002 0.087 -10000 0 -0.29 27 27
FANCF 0.035 0.008 -10000 0 0 27 27
BRCA1 0.036 0.006 -10000 0 0 12 12
CCNE1 0.032 0.012 -10000 0 0 58 58
CDK2/Cyclin E1 0.045 0.023 -10000 0 -0.14 2 2
FANCG 0.03 0.014 -10000 0 0 85 85
BRCA1/BACH1/BARD1 0.046 0.037 -10000 0 -0.14 18 18
FANCE 0.036 0.003 -10000 0 0 4 4
FANCC 0.035 0.007 -10000 0 0 17 17
NBN 0.036 0.006 -10000 0 0 14 14
FANCA 0.035 0.007 -10000 0 0 17 17
DNA repair -0.018 0.081 0.22 7 -0.29 17 24
BRCA1/BARD1/ubiquitin 0.046 0.037 -10000 0 -0.14 18 18
BARD1/DNA-PK 0.07 0.064 -10000 0 -0.14 34 34
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.037 0.14 17 -10000 0 17
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.063 -10000 0 -0.22 26 26
BRCA1/BACH1/BARD1/TopBP1 0.051 0.061 -10000 0 -0.13 45 45
BRCA1/BARD1/P53 0.067 0.067 -10000 0 -0.13 46 46
BARD1/CSTF1/BRCA1 0.062 0.04 -10000 0 -0.12 17 17
BRCA1/BACH1 0.036 0.006 -10000 0 0 12 12
BARD1 0.035 0.007 -10000 0 0 20 20
PCNA 0.034 0.01 -10000 0 0 41 41
BRCA1/BARD1/UbcH5C 0.064 0.042 -10000 0 -0.13 19 19
BRCA1/BARD1/UbcH7 0.059 0.046 -10000 0 -0.13 23 23
BRCA1/BARD1/RAD51/PCNA 0.072 0.06 -10000 0 -0.13 34 34
BARD1/DNA-PK/P53 0.068 0.083 -10000 0 -0.13 57 57
BRCA1/BARD1/Ubiquitin 0.046 0.037 -10000 0 -0.14 18 18
BRCA1/BARD1/CTIP 0.04 0.058 -10000 0 -0.13 44 44
FA complex 0.012 0.059 -10000 0 -0.18 34 34
BARD1/EWS 0.044 0.038 -10000 0 -0.14 18 18
RBBP8 -0.013 0.029 0.092 34 -10000 0 34
TP53 0.031 0.013 -10000 0 0 73 73
TOPBP1 0.033 0.011 -10000 0 0 52 52
G1/S transition of mitotic cell cycle -0.064 0.066 0.13 46 -10000 0 46
BRCA1/BARD1 0.085 0.058 -10000 0 -0.13 21 21
CSTF1 0.034 0.009 -10000 0 0 30 30
BARD1/EWS-Fli1 0.021 0.029 -10000 0 -0.13 18 18
CDK2 0.034 0.01 -10000 0 0 40 40
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.008 -10000 0 0 25 25
RAD50 0.036 0.006 -10000 0 0 13 13
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.046 0.037 -10000 0 -0.14 18 18
EWSR1 0.034 0.009 -10000 0 0 33 33
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.035 0.008 -10000 0 0 27 27
alphaV beta3 Integrin 0.044 0.042 -10000 0 -0.14 24 24
PTK2 0.012 0.11 -10000 0 -0.32 28 28
positive regulation of JNK cascade 0.021 0.09 -10000 0 -0.26 35 35
CDC42/GDP 0.036 0.12 -10000 0 -0.34 37 37
Rac1/GDP 0.028 0.099 -10000 0 -0.33 17 17
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 11 11
CTNNB1 0.036 0.006 -10000 0 0 15 15
CDC42/GTP 0.029 0.11 -10000 0 -0.31 33 33
nectin-3/I-afadin 0.043 0.027 -10000 0 -0.14 5 5
RAPGEF1 0.005 0.12 -10000 0 -0.35 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.005 0.13 -10000 0 -0.38 41 41
PDGFB-D/PDGFRB 0.035 0.008 -10000 0 0 27 27
TLN1 -0.006 0.058 0.16 21 -0.23 13 34
Rap1/GTP -0.002 0.085 -10000 0 -0.27 40 40
IQGAP1 0.033 0.011 -10000 0 0 51 51
Rap1/GTP/I-afadin 0.042 0.015 -10000 0 -0.1 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.043 0.027 -10000 0 -0.14 5 5
PVR 0.034 0.009 -10000 0 0 32 32
Necl-5(dimer) 0.034 0.009 -10000 0 0 32 32
mol:GDP 0.021 0.14 -10000 0 -0.4 38 38
MLLT4 0.034 0.009 -10000 0 0 36 36
PIK3CA 0.031 0.013 -10000 0 0 80 80
PI3K 0.057 0.088 -10000 0 -0.13 71 71
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 0.019 0.078 -10000 0 -0.28 16 16
PVRL1 0.036 0.004 -10000 0 0 7 7
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 38 38
CLDN1 0.034 0.009 -10000 0 0 36 36
JAM-A/CLDN1 0.074 0.045 -10000 0 -0.11 9 9
SRC 0.012 0.14 -10000 0 -0.41 41 41
ITGB3 0.036 0.003 -10000 0 0 4 4
nectin-1(dimer)/I-afadin/I-afadin 0.05 0.015 -10000 0 -10000 0 0
FARP2 0.027 0.13 -10000 0 -0.43 21 21
RAC1 0.024 0.017 -10000 0 0 173 173
CTNNA1 0.035 0.007 -10000 0 0 20 20
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 0.023 0.042 -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 -0.26 35 35
alphaV/beta3 Integrin/Talin 0.031 0.087 0.21 32 -0.21 25 57
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 0.04 0.089 4 -0.22 14 18
VAV2 0.025 0.14 -10000 0 -0.45 22 22
RAP1/GDP 0.026 0.11 -10000 0 -0.31 38 38
ITGAV 0.034 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 -0.13 7 7
nectin-3(dimer)/I-afadin/I-afadin 0.043 0.027 -10000 0 -0.14 5 5
Rac1/GTP 0.024 0.094 -10000 0 -0.33 16 16
PTPRM 0.008 0.045 -10000 0 -0.22 16 16
E-cadherin/beta catenin/alpha catenin 0.084 0.057 -10000 0 -0.12 12 12
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 0 24 24
Glucocorticoid receptor regulatory network

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
PCK2 -0.023 0.1 0.23 2 -0.47 16 18
SMARCC2 0.033 0.01 -10000 0 0 44 44
SMARCC1 0.034 0.009 -10000 0 0 32 32
TBX21 0.031 0.055 0.34 1 -10000 0 1
SUMO2 0.034 0.019 0.071 1 -0.03 33 34
STAT1 (dimer) 0.036 0.038 0.11 19 -0.17 13 32
FKBP4 0.034 0.009 -10000 0 0 34 34
FKBP5 0.028 0.015 -10000 0 0 117 117
GR alpha/HSP90/FKBP51/HSP90 -0.024 0.064 -10000 0 -0.18 10 10
PRL 0.04 0.058 0.54 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.042 0.12 -10000 0 -0.32 1 1
RELA 0.015 0.11 0.18 32 -0.16 125 157
FGG -0.049 0.1 -10000 0 -0.32 2 2
GR beta/TIF2 -0.025 0.075 -10000 0 -0.22 2 2
IFNG 0.037 0.081 -10000 0 -10000 0 0
apoptosis -0.017 0.2 0.44 26 -0.5 36 62
CREB1 0.043 0.01 -10000 0 -10000 0 0
histone acetylation 0.022 0.054 0.22 1 -0.24 1 2
BGLAP 0.04 0.061 -10000 0 -10000 0 0
GR/PKAc 0.021 0.091 -10000 0 -0.2 11 11
NF kappa B1 p50/RelA 0.03 0.18 0.3 30 -0.26 118 148
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 0.029 0.16 7 -0.09 17 24
CSF2 0.006 0.032 -10000 0 -10000 0 0
GSK3B 0.032 0.02 0.071 1 -0.03 30 31
NR1I3 -0.012 0.18 0.45 18 -0.5 19 37
CSN2 -0.046 0.089 0.26 2 -0.29 2 4
BRG1/BAF155/BAF170/BAF60A 0.064 0.073 -10000 0 -0.16 38 38
NFATC1 0.04 0.01 -10000 0 -10000 0 0
POU2F1 0.04 0.012 -10000 0 -10000 0 0
CDKN1A -0.13 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 27 -10000 0 27
SFN 0.031 0.013 -10000 0 0 78 78
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.011 0.068 -10000 0 -0.15 7 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.066 0.27 0.43 18 -0.66 71 89
JUN 0.024 0.053 0.35 3 -10000 0 3
IL4 0.035 0.053 -10000 0 -10000 0 0
CDK5R1 0.035 0.009 -10000 0 0 24 24
PRKACA 0.035 0.008 -10000 0 0 25 25
cortisol/GR alpha (monomer)/AP-1 -0.047 0.051 -10000 0 -0.22 10 10
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.005 0.073 -10000 0 -0.16 17 17
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 0.17 7 -10000 0 7
AP-1/NFAT1-c-4 0.048 0.075 0.44 2 -10000 0 2
AFP 0.025 0.066 -10000 0 -10000 0 0
SUV420H1 0.033 0.011 -10000 0 0 51 51
IRF1 -0.027 0.12 -10000 0 -0.64 14 14
TP53 -0.016 0.17 -10000 0 -0.49 57 57
PPP5C 0.034 0.01 -10000 0 0 39 39
KRT17 0.041 0.08 0.45 1 -10000 0 1
KRT14 0.031 0.067 -10000 0 -10000 0 0
TBP 0.042 0.018 -10000 0 -10000 0 0
CREBBP 0.029 0.018 -10000 0 -0.093 10 10
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.031 0.012 -10000 0 -10000 0 0
AP-1 0.048 0.075 0.44 2 -10000 0 2
MAPK14 0.034 0.019 -10000 0 -0.03 32 32
MAPK10 0.029 0.02 0.073 1 -0.031 25 26
MAPK11 0.031 0.02 0.071 1 -0.03 31 32
KRT5 0.041 0.078 0.45 1 -10000 0 1
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.033 0.018 0.092 2 -0.066 9 11
STAT1 0.036 0.038 0.11 19 -0.17 13 32
CGA 0.036 0.056 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.033 0.067 -10000 0 -0.35 6 6
MAPK3 0.034 0.019 0.075 2 -0.03 35 37
MAPK1 0.031 0.02 -10000 0 -0.03 30 30
ICAM1 0.029 0.14 0.34 15 -10000 0 15
NFKB1 0.016 0.11 0.17 30 -0.16 121 151
MAPK8 0.034 0.058 0.28 2 -10000 0 2
MAPK9 0.033 0.019 -10000 0 -0.03 30 30
cortisol/GR alpha (dimer) -0.021 0.2 0.44 25 -0.52 36 61
BAX -0.033 0.18 -10000 0 -0.86 10 10
POMC 0.032 0.074 0.48 1 -10000 0 1
EP300 0.026 0.019 -10000 0 -0.093 10 10
cortisol/GR alpha (dimer)/p53 -0.071 0.13 -10000 0 -0.42 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.069 0.24 31 -10000 0 31
SGK1 -0.016 0.06 -10000 0 -0.25 12 12
IL13 0.029 0.063 -10000 0 -10000 0 0
IL6 0.03 0.13 0.34 17 -10000 0 17
PRKACG 0.036 0.005 -10000 0 0 11 11
IL5 0.021 0.071 0.43 1 -10000 0 1
IL2 0.042 0.075 -10000 0 -10000 0 0
CDK5 0.023 0.018 -10000 0 0 192 192
PRKACB 0.033 0.011 -10000 0 0 50 50
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.11 0.4 0.34 16 -0.79 125 141
CDK5R1/CDK5 0.028 0.042 -10000 0 -0.14 18 18
NF kappa B1 p50/RelA/PKAc 0.055 0.16 0.3 28 -0.21 108 136
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.038 0.1 -10000 0 -0.37 1 1
SMARCA4 0.032 0.012 -10000 0 0 63 63
chromatin remodeling -0.037 0.11 -10000 0 -0.37 28 28
NF kappa B1 p50/RelA/Cbp 0.046 0.16 0.3 21 -0.22 112 133
JUN (dimer) 0.024 0.053 0.35 3 -10000 0 3
YWHAH 0.031 0.013 -10000 0 0 73 73
VIPR1 0.034 0.065 0.38 5 -10000 0 5
NR3C1 -0.04 0.085 -10000 0 -0.34 1 1
NR4A1 0.039 0.008 -10000 0 -10000 0 0
TIF2/SUV420H1 0.036 0.054 -10000 0 -0.14 42 42
MAPKKK cascade -0.017 0.2 0.44 26 -0.5 36 62
cortisol/GR alpha (dimer)/Src-1 -0.05 0.12 -10000 0 -0.36 3 3
PBX1 0.04 0.011 -10000 0 -10000 0 0
POU1F1 0.041 0.011 -10000 0 -10000 0 0
SELE 0.026 0.13 0.34 2 -10000 0 2
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.037 0.11 -10000 0 -0.37 28 28
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.038 0.1 -10000 0 -0.37 1 1
mol:cortisol -0.034 0.061 -10000 0 -10000 0 0
MMP1 0.038 0.072 0.35 1 -0.49 3 4
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.003 0.036 0.096 25 -0.1 9 34
NFATC2 -0.001 0.027 0.078 19 -0.096 10 29
NFATC3 -0.003 0.038 0.093 30 -0.1 10 40
CD40LG 0.015 0.12 0.29 41 -0.24 1 42
PTGS2 -0.017 0.073 0.28 7 -0.24 1 8
JUNB 0.031 0.014 -10000 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.026 0.083 1 -0.12 12 13
CaM/Ca2+ 0.026 0.026 0.083 1 -0.12 12 13
CALM1 0.035 0.013 0.07 1 -10000 0 1
JUN 0.036 0.012 0.07 1 -10000 0 1
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.02 -10000 0 -0.11 10 10
FOSL1 0.033 0.011 -10000 0 0 55 55
CREM 0.026 0.016 -10000 0 0 142 142
Jun/NFAT1-c-4/p21SNFT 0.057 0.069 0.26 12 -0.18 3 15
FOS 0.027 0.019 0.07 1 -10000 0 1
IFNG 0.014 0.11 0.3 36 -10000 0 36
AP-1/NFAT1-c-4 0.093 0.11 0.35 10 -0.26 1 11
FASLG 0.014 0.12 0.29 39 -0.24 1 40
NFAT1-c-4/ICER1 0.041 0.052 0.21 10 -10000 0 10
IL2RA 0.005 0.088 0.26 19 -0.24 1 20
FKBP12/FK506 0.022 0.023 -10000 0 -0.13 10 10
CSF2 0.015 0.12 0.29 40 -0.24 1 41
JunB/Fra1/NFAT1-c-4 0.057 0.061 0.22 9 -0.18 1 10
IL4 0.015 0.12 0.29 39 -10000 0 39
IL2 0.012 0.087 -10000 0 -0.84 5 5
IL3 0.03 0.085 -10000 0 -0.58 9 9
FKBP1A 0.033 0.01 -10000 0 0 44 44
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
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.053 0.093 -10000 0 -0.19 54 54
Ran/GTP/Exportin 1/HDAC1 -0.029 0.022 -10000 0 -0.11 26 26
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.11 -10000 0 -0.25 53 53
SUMO1 0.036 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 33 33
Histones 0.034 0.072 -10000 0 -0.22 23 23
YY1/LSF 0.016 0.062 -10000 0 -0.22 18 18
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
I kappa B alpha/HDAC3 0.001 0.076 -10000 0 -0.2 51 51
I kappa B alpha/HDAC1 0.008 0.097 -10000 0 -0.22 63 63
SAP18 0.034 0.01 -10000 0 0 41 41
RELA -0.002 0.076 0.19 1 -0.26 16 17
HDAC1/Smad7 0.042 0.041 -10000 0 -0.12 6 6
RANGAP1 0.033 0.01 -10000 0 0 45 45
HDAC3/TR2 0.027 0.07 -10000 0 -0.25 21 21
NuRD/MBD3 Complex -0.009 0.11 -10000 0 -0.34 36 36
NF kappa B1 p50/RelA 0.011 0.088 -10000 0 -0.29 18 18
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.035 0.007 -10000 0 0 18 18
GATA1 0.037 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.007 0.11 -10000 0 -0.33 35 35
RBBP7 0.036 0.005 -10000 0 0 8 8
NPC 0.017 0.02 -10000 0 -0.087 18 18
RBBP4 0.033 0.011 -10000 0 0 56 56
MAX 0.034 0.009 -10000 0 0 32 32
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.008 -10000 0 0 25 25
NFKBIA 0.002 0.078 -10000 0 -0.32 23 23
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.006 0.087 -10000 0 -0.29 29 29
SIN3 complex 0.056 0.041 -10000 0 -0.12 17 17
SMURF1 0.025 0.017 -10000 0 0 167 167
CHD3 0.036 0.005 -10000 0 0 11 11
SAP30 0.035 0.007 -10000 0 0 20 20
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.035 0.008 -10000 0 0 26 26
YY1/HDAC3 0 0.074 -10000 0 -0.24 29 29
YY1/HDAC2 0.016 0.056 -10000 0 -0.2 17 17
YY1/HDAC1 0.017 0.061 -10000 0 -0.22 18 18
NuRD/MBD2 Complex (MeCP1) -0.002 0.091 -10000 0 -0.28 33 33
PPARG 0.002 0.077 -10000 0 -0.21 52 52
HDAC8/hEST1B 0.023 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 0.008 -10000 0 0 25 25
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
HDAC3/SMRT (N-CoR2) 0.026 0.07 -10000 0 -0.25 21 21
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.04 -10000 0 -0.12 6 6
CREBBP 0.036 0.005 -10000 0 0 8 8
NuRD/MBD3/MBD3L2 Complex -0.003 0.1 -10000 0 -0.32 34 34
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC3 0.009 0.057 -10000 0 -0.15 45 45
HDAC2 0.032 0.012 -10000 0 0 67 67
YY1 0.01 0.028 -10000 0 -0.21 7 7
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.033 0.01 -10000 0 0 44 44
NCOR2 0.036 0.002 -10000 0 0 2 2
MXD1 0.036 0.003 -10000 0 0 3 3
STAT3 0.006 0.06 -10000 0 -0.21 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 25 25
YY1/LSF/HDAC1 0.03 0.07 -10000 0 -0.21 18 18
YY1/SAP30/HDAC1 0.032 0.068 -10000 0 -0.2 18 18
EP300 0.033 0.011 -10000 0 0 49 49
STAT3 (dimer non-phopshorylated) 0.006 0.06 -10000 0 -0.21 33 33
proteasomal ubiquitin-dependent protein catabolic process 0.002 0.077 -10000 0 -0.32 23 23
histone deacetylation -0.003 0.092 -10000 0 -0.27 35 35
STAT3 (dimer non-phopshorylated)/HDAC3 0 0.092 -10000 0 -0.31 27 27
nuclear export -0.023 0.005 -10000 0 -10000 0 0
PRKACA 0.035 0.008 -10000 0 0 25 25
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.033 0.011 -10000 0 0 53 53
GATA2/HDAC3 0.026 0.069 -10000 0 -0.24 21 21
GATA1/HDAC1 0.05 0.024 -10000 0 -0.14 7 7
GATA1/HDAC3 0.027 0.07 -10000 0 -0.25 21 21
CHD4 0.034 0.01 -10000 0 0 37 37
TNF-alpha/TNFR1A 0.035 0.055 -10000 0 -0.14 43 43
SIN3/HDAC complex/Mad/Max -0.004 0.085 -10000 0 -0.26 33 33
NuRD Complex -0.002 0.1 0.16 1 -0.33 33 34
positive regulation of chromatin silencing 0.032 0.071 -10000 0 -0.21 23 23
SIN3B 0.035 0.009 -10000 0 0 29 29
MTA2 0.036 0.004 -10000 0 0 6 6
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.036 0.004 -10000 0 0 5 5
SUMO1/HDAC1 0.036 0.055 -10000 0 -0.22 6 6
HDAC complex 0.066 0.069 -10000 0 -0.14 40 40
GATA1/Fog1 0.027 0 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.054 0.046 -10000 0 -0.13 20 20
TNF 0.036 0.003 -10000 0 0 4 4
negative regulation of cell growth -0.004 0.085 -10000 0 -0.26 34 34
NuRD/MBD2/PRMT5 Complex -0.002 0.091 -10000 0 -0.28 33 33
Ran/GTP/Exportin 1 0.036 0.059 -10000 0 -0.16 21 21
NF kappa B/RelA/I kappa B alpha -0.006 0.093 -10000 0 -0.25 53 53
SIN3/HDAC complex/NCoR1 -0.003 0.088 -10000 0 -0.31 25 25
TFCP2 0.035 0.008 -10000 0 0 25 25
NR2C1 0.036 0.004 -10000 0 0 5 5
MBD3 0.034 0.01 -10000 0 0 43 43
MBD2 0.035 0.007 -10000 0 0 17 17
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 -0.044 1 1
JMJD2C 0.036 0.014 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.052 0.041 -10000 0 -0.079 32 32
CARM1 0.035 0.009 -10000 0 0 29 29
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 0.011 -10000 0 -0.001 54 54
PTK2B 0.036 0.007 -10000 0 -10000 0 0
MED1 0 0 -10000 0 -10000 0 0
MAK 0.033 0.008 -10000 0 -0.044 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 0.034 0.01 -10000 0 -10000 0 0
DNA-PK 0.055 0.049 -10000 0 -0.14 22 22
NCOA4 0.027 0.016 -10000 0 0 139 139
PIAS3 0.036 0.006 -10000 0 -10000 0 0
cell proliferation 0.022 0.049 -10000 0 -0.43 5 5
XRCC5 0.036 0.005 -10000 0 0 9 9
UBE3A 0.037 0.003 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.031 0.033 0.12 1 -0.071 33 34
FHL2 0.018 0.2 -10000 0 -0.68 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 0 176 176
TGFB1I1 0.033 0.012 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.034 0.056 -10000 0 -0.1 53 53
XRCC6 0.033 0.01 -10000 0 0 39 39
T-DHT/AR 0.048 0.059 0.22 1 -0.13 33 34
CTDSP1 0.036 0.006 -10000 0 0 16 16
CTDSP2 0.031 0.012 -10000 0 -0.042 1 1
BRCA1 0.036 0.006 -10000 0 -10000 0 0
TCF4 0.031 0.012 -10000 0 -0.038 1 1
CDKN2A 0.004 0.012 -10000 0 0 444 444
SRF 0.04 0.055 0.11 90 -0.15 33 123
NKX3-1 0.025 0.07 -10000 0 -0.3 15 15
KLK3 0.016 0.046 -10000 0 -10000 0 0
TMF1 0.035 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 0.05 0.041 -10000 0 -0.08 33 33
AR 0.035 0.03 -10000 0 -0.068 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 15 15
PRKDC 0.033 0.01 -10000 0 0 44 44
PA2G4 0.034 0.007 -10000 0 -0.034 1 1
UBE2I 0.036 0.004 -10000 0 0 6 6
T-DHT/AR/Cyclin D3/CDK11 p58 0.045 0.044 0.13 1 -0.078 42 43
RPS6KA3 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.039 0.046 -10000 0 -0.086 21 21
LATS2 -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.046 0.043 -10000 0 -0.079 39 39
Cyclin D3/CDK11 p58 0.021 0.028 -10000 0 -0.13 16 16
VAV3 0.029 0.015 -10000 0 -10000 0 0
KLK2 0.026 0.051 -10000 0 -0.32 8 8
CASP8 0.035 0.006 -10000 0 0 13 13
T-DHT/AR/TIF2/CARM1 0.07 0.046 -10000 0 -0.11 1 1
TMPRSS2 0.025 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 0.051 1 -0.049 33 34
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.036 0.009 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.036 0.04 -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 0.051 1 -0.049 33 34
CCND3 0.035 0.008 -10000 0 0 26 26
TGIF1 -0.001 0 -10000 0 -10000 0 0
FKBP4 0.035 0.009 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.027 0.078 -10000 0 -0.24 22 22
CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 13 13
AKT1 0.033 0.011 -10000 0 0 53 53
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 0.006 0.075 0.17 2 -0.26 22 24
YWHAZ 0.035 0.007 -10000 0 0 21 21
CALM1 0.033 0.011 -10000 0 0 54 54
YWHAQ 0.036 0.005 -10000 0 0 9 9
TBC1D4 -0.016 0.021 0.092 16 -10000 0 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.013 -10000 0 0 73 73
YWHAB 0.035 0.008 -10000 0 0 24 24
SNARE/Synip 0.021 0.017 -10000 0 -0.11 8 8
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.036 0.006 -10000 0 0 15 15
PRKCI 0.035 0.008 -10000 0 0 26 26
AS160/CaM/Ca2+ 0.021 0.026 -10000 0 -0.13 13 13
RHOQ 0.035 0.007 -10000 0 0 17 17
GYS1 0.002 0.041 0.24 4 -0.21 6 10
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.034 0.009 -10000 0 0 36 36
TC10/GTP/CIP4/Exocyst 0.041 0.029 -10000 0 -0.12 14 14
AS160/14-3-3 -0.005 0.098 -10000 0 -0.4 19 19
VAMP2 0.033 0.011 -10000 0 0 48 48
SLC2A4 0.005 0.081 0.18 1 -0.29 22 23
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.004 0.076 -10000 0 -0.3 27 27
SFN 0.031 0.013 -10000 0 0 78 78
LNPEP 0.036 0.005 -10000 0 0 8 8
YWHAE 0.035 0.008 -10000 0 0 27 27
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 0.001 0.067 0.5 2 -10000 0 2
IL27/IL27R/JAK1 0.04 0.062 -10000 0 -10000 0 0
TBX21 -0.014 0.093 0.34 19 -10000 0 19
IL12B 0.037 0.005 -10000 0 0 9 9
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 0.048 -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 0.064 0.083 0.18 153 -0.18 2 155
T-helper 2 cell differentiation 0.001 0.067 0.5 2 -10000 0 2
T cell proliferation during immune response 0.001 0.067 0.5 2 -10000 0 2
MAPKKK cascade -0.001 0.067 -10000 0 -0.5 2 2
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 23 23
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.015 0.091 0.34 18 -10000 0 18
IL27/IL27R/JAK2/TYK2 -0.002 0.067 -10000 0 -0.51 2 2
positive regulation of T cell mediated cytotoxicity -0.001 0.067 -10000 0 -0.5 2 2
STAT1 (dimer) 0.048 0.08 -10000 0 -10000 0 0
JAK2 0.03 0.014 -10000 0 -0.032 1 1
JAK1 0.033 0.01 -10000 0 0 41 41
STAT2 (dimer) 0.015 0.099 -10000 0 -0.37 6 6
T cell proliferation 0.003 0.061 -10000 0 -0.32 3 3
IL12/IL12R/TYK2/JAK2 0.006 0.18 -10000 0 -0.76 26 26
IL17A 0.062 0.082 0.18 146 -0.18 2 148
mast cell activation 0.001 0.067 0.5 2 -10000 0 2
IFNG 0.003 0.029 -10000 0 -0.093 12 12
T cell differentiation -0.001 0.003 -10000 0 -0.017 9 9
STAT3 (dimer) 0.011 0.11 -10000 0 -0.39 11 11
STAT5A (dimer) 0.016 0.1 -10000 0 -0.36 7 7
STAT4 (dimer) 0.015 0.098 -10000 0 -0.37 6 6
STAT4 0.035 0.009 -10000 0 0 29 29
T cell activation -0.005 0.005 -10000 0 -0.085 1 1
IL27R/JAK2/TYK2 0.039 0.062 -10000 0 -10000 0 0
GATA3 0.007 0.092 0.67 9 -10000 0 9
IL18 -0.01 0.004 0 72 -10000 0 72
positive regulation of mast cell cytokine production 0.011 0.11 -10000 0 -0.38 11 11
IL27/EBI3 0.025 0.011 -10000 0 -10000 0 0
IL27RA 0.001 0.025 -10000 0 -10000 0 0
IL6 0.019 0.018 -10000 0 0 238 238
STAT5A 0.036 0.004 -10000 0 0 5 5
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.031 0.35 1 -10000 0 1
IL1B -0.009 0.005 0 101 -10000 0 101
EBI3 0.034 0.012 -10000 0 -0.033 1 1
TNF -0.011 0.001 0 4 -10000 0 4
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.062 0.03 -9999 0 -0.12 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 38 38
Regulation of Androgen receptor activity

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
HDAC1 -0.011 0.002 0.012 1 -10000 0 1
SMARCC1 -0.005 0.12 -10000 0 -1.2 4 4
REL 0.036 0.004 -10000 0 -0.007 4 4
HDAC7 -0.029 0.057 0.17 5 -0.21 19 24
JUN 0.034 0.01 -10000 0 0 40 40
EP300 0.033 0.011 -10000 0 0 49 49
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.017 0.019 0.089 4 -10000 0 4
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR 0.02 0.078 0.25 2 -0.22 19 21
MAP2K6 0.035 0.013 -10000 0 -0.034 14 14
BRM/BAF57 0.047 0.024 -10000 0 -0.14 3 3
MAP2K4 0.034 0.014 -10000 0 -0.033 16 16
SMARCA2 0.032 0.013 -10000 0 0 67 67
PDE9A -0.013 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 -0.022 0.086 0.31 2 -0.31 14 16
NR0B1 0.03 0.014 -10000 0 0 88 88
EGR1 0.029 0.015 -10000 0 0 107 107
RXRs/9cRA 0.067 0.019 -10000 0 -0.11 1 1
AR/RACK1/Src -0.02 0.052 0.19 1 -0.22 2 3
AR/GR 0.003 0.06 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 0.035 0.006 -10000 0 0 16 16
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.012 0.02 0.087 7 -10000 0 7
T-DHT/AR/TIF2/CARM1 0.016 0.055 0.21 3 -0.2 3 6
SRC -0.021 0.034 0.17 7 -10000 0 7
NR3C1 0.035 0.008 -10000 0 0 24 24
KLK3 -0.003 0.073 0.32 1 -0.36 3 4
APPBP2 0.034 0.015 -10000 0 -0.033 16 16
TRIM24 0.023 0.018 -10000 0 0 186 186
T-DHT/AR/TIP60 -0.023 0.028 0.081 2 -0.15 8 10
TMPRSS2 0.016 0.085 -10000 0 -0.55 8 8
RXRG 0.036 0.006 -10000 0 0 13 13
mol:9cRA 0 0 0.002 1 -10000 0 1
RXRA 0.035 0.007 -10000 0 0 19 19
RXRB 0.037 0.002 -10000 0 0 1 1
CARM1 0.035 0.009 -10000 0 0 29 29
NR2C2 0.036 0.005 -10000 0 0 8 8
KLK2 -0.006 0.041 -10000 0 -0.25 1 1
AR -0.004 0.043 0.14 4 -0.2 17 21
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -0.001 47 47
SRY 0.036 0.004 -10000 0 -0.009 4 4
GATA2 0.035 0.007 -10000 0 0 18 18
MYST2 0.034 0.01 -10000 0 0 37 37
HOXB13 0.037 0.003 -10000 0 0 4 4
T-DHT/AR/RACK1/Src -0.022 0.053 0.18 8 -0.23 2 10
positive regulation of transcription 0.035 0.007 -10000 0 0 18 18
DNAJA1 0.031 0.017 -10000 0 -0.033 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.037 -10000 0 -0.26 8 8
NCOA1 0.038 0.023 0.13 4 -0.18 2 6
SPDEF 0.037 0.004 -10000 0 0 5 5
T-DHT/AR/TIF2 -0.031 0.084 0.18 2 -0.25 40 42
T-DHT/AR/Hsp90 -0.023 0.028 0.081 2 -0.15 9 11
GSK3B 0.034 0.01 -10000 0 0 40 40
NR2C1 0.036 0.004 -10000 0 0 5 5
mol:T-DHT -0.019 0.031 0.15 7 -0.12 3 10
SIRT1 0.024 0.017 -10000 0 0 171 171
ZMIZ2 -0.001 0.001 -10000 0 -0.016 1 1
POU2F1 0.037 0.035 0.12 13 -0.11 22 35
T-DHT/AR/DAX-1 -0.021 0.036 0.17 1 -0.19 2 3
CREBBP 0.036 0.005 -10000 0 0 8 8
SMARCE1 0.037 0.004 -10000 0 0 6 6
Ceramide signaling pathway

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
SPHK2 -0.008 0.033 0.092 47 -10000 0 47
MAP4K4 0.004 0.051 -10000 0 -0.21 9 9
BAG4 0.036 0.005 -10000 0 0 11 11
PKC zeta/ceramide 0.003 0.05 -10000 0 -0.23 14 14
NFKBIA 0.033 0.012 -10000 0 0 57 57
BIRC3 0.031 0.013 -10000 0 0 81 81
BAX 0.001 0.078 -10000 0 -0.33 23 23
RIPK1 0.035 0.007 -10000 0 0 20 20
AKT1 -0.012 0.04 0.47 2 -10000 0 2
BAD -0.004 0.05 -10000 0 -0.24 13 13
SMPD1 -0.003 0.052 0.13 3 -0.2 17 20
RB1 -0.004 0.051 0.21 1 -0.24 14 15
FADD/Caspase 8 0.014 0.05 -10000 0 -0.24 5 5
MAP2K4 -0.007 0.054 0.18 4 -0.23 14 18
NSMAF 0.035 0.009 -10000 0 0 29 29
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.054 0.2 7 -0.24 13 20
EGF 0.035 0.008 -10000 0 0 25 25
mol:ceramide 0.004 0.054 -10000 0 -0.25 14 14
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 0.034 0.092 51 -10000 0 51
ASAH1 0.035 0.007 -10000 0 0 17 17
negative regulation of cell cycle -0.003 0.051 0.2 1 -0.24 14 15
cell proliferation 0.019 0.056 0.2 2 -0.22 6 8
BID 0.004 0.15 -10000 0 -0.59 26 26
MAP3K1 -0.001 0.053 0.14 2 -0.24 14 16
EIF2A -0.01 0.052 0.2 5 -0.22 14 19
TRADD 0.036 0.005 -10000 0 0 11 11
CRADD 0.036 0.006 -10000 0 0 12 12
MAPK3 -0.006 0.051 0.18 11 -0.23 6 17
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.064 0.18 10 -0.22 22 32
Cathepsin D/ceramide 0.019 0.059 -10000 0 -0.24 14 14
FADD 0.009 0.045 -10000 0 -0.23 3 3
KSR1 -0.004 0.051 -10000 0 -0.24 14 14
MAPK8 -0.04 0.095 0.18 1 -0.19 111 112
PRKRA -0.006 0.054 0.23 2 -0.23 15 17
PDGFA 0.027 0.016 -10000 0 0 134 134
TRAF2 0.036 0.006 -10000 0 0 15 15
IGF1 0.035 0.008 -10000 0 0 23 23
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.004 0.054 -10000 0 -0.24 14 14
CTSD 0.033 0.011 -10000 0 0 55 55
regulation of nitric oxide biosynthetic process 0.049 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.021 0.06 0.21 2 -0.24 6 8
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 0.034 0.092 51 -10000 0 51
RelA/NF kappa B1 0.049 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 15 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.054 -10000 0 -0.24 6 6
TNFR1A/BAG4/TNF-alpha 0.053 0.056 -10000 0 -0.12 41 41
mol:Sphingosine-1-phosphate -0.008 0.033 0.092 47 -10000 0 47
MAP2K1 -0.016 0.053 0.18 8 -0.23 13 21
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 9 9
CYCS 0.024 0.064 0.14 12 -0.21 9 21
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
NFKB1 0.035 0.007 -10000 0 0 18 18
TNFR1A/BAG4 0.035 0.054 -10000 0 -0.14 42 42
EIF2AK2 -0.011 0.055 0.21 5 -0.23 14 19
TNF-alpha/TNFR1A/FAN 0.047 0.066 -10000 0 -0.13 54 54
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.033 0.051 -10000 0 -0.26 5 5
MAP2K2 -0.008 0.053 0.18 20 -0.22 5 25
SMPD3 0.006 0.056 0.16 1 -0.28 9 10
TNF 0.036 0.003 -10000 0 0 4 4
PKC zeta/PAR4 0.026 0.005 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.005 0.045 0.13 7 -0.15 16 23
NF kappa B1/RelA/I kappa B alpha 0.07 0.047 -10000 0 -0.12 20 20
AIFM1 -0.004 0.052 0.14 2 -0.2 18 20
BCL2 0.035 0.007 -10000 0 0 20 20
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.047 0.064 -10000 0 -10000 0 0
MKNK1 0.034 0.009 -10000 0 0 34 34
MAPK14 0.047 0.036 0.16 3 -0.082 20 23
ATF2/c-Jun 0.002 0.091 -10000 0 -0.32 30 30
MAPK11 0.044 0.038 0.16 3 -0.082 20 23
MITF 0.032 0.048 0.17 7 -0.2 7 14
MAPKAPK5 0.034 0.038 0.18 3 -10000 0 3
KRT8 0.036 0.039 0.17 9 -10000 0 9
MAPKAPK3 0.035 0.007 -10000 0 0 19 19
MAPKAPK2 0.034 0.01 -10000 0 0 43 43
p38alpha-beta/CK2 0.063 0.055 0.23 3 -10000 0 3
CEBPB 0.024 0.069 0.17 17 -0.21 27 44
SLC9A1 0.032 0.04 0.16 1 -0.26 2 3
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.032 0.054 0.26 4 -0.26 2 6
p38alpha-beta/MNK1 0.066 0.067 0.21 1 -0.14 17 18
JUN -0.002 0.088 -10000 0 -0.32 29 29
PPARGC1A 0.032 0.056 0.2 4 -0.21 13 17
USF1 0.028 0.037 0.18 3 -10000 0 3
RAB5/GDP/GDI1 0.014 0.076 -10000 0 -0.22 26 26
NOS2 0.028 0.037 0.18 3 -10000 0 3
DDIT3 0.029 0.061 0.17 8 -0.19 20 28
RAB5A 0.034 0.009 -10000 0 0 32 32
HSPB1 0.086 0.13 0.28 144 -0.15 3 147
p38alpha-beta/HBP1 0.053 0.057 0.22 2 -10000 0 2
CREB1 0.024 0.069 0.22 1 -0.18 34 35
RAB5/GDP 0.019 0.034 -10000 0 -0.13 24 24
EIF4E -0.015 0.056 0.2 8 -0.2 6 14
RPS6KA4 0.034 0.038 0.18 3 -10000 0 3
PLA2G4A -0.014 0.052 0.2 4 -0.19 11 15
GDI1 0.025 0.059 0.18 3 -0.23 17 20
TP53 0.01 0.05 0.17 10 -10000 0 10
RPS6KA5 0.035 0.04 0.18 5 -0.19 1 6
ESR1 0.032 0.037 0.19 2 -10000 0 2
HBP1 0.025 0.017 -10000 0 0 163 163
MEF2C 0.032 0.048 0.22 1 -0.22 7 8
MEF2A 0.031 0.046 0.18 4 -0.21 6 10
EIF4EBP1 0.021 0.073 0.22 1 -0.34 3 4
KRT19 0.036 0.039 0.18 7 -10000 0 7
ELK4 0.031 0.036 0.16 2 -10000 0 2
ATF6 0.033 0.037 -10000 0 -10000 0 0
ATF1 0.019 0.072 0.22 1 -0.26 3 4
p38alpha-beta/MAPKAPK2 0.07 0.055 0.21 2 -10000 0 2
p38alpha-beta/MAPKAPK3 0.073 0.056 0.22 3 -0.13 2 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.038 -10000 0 -0.11 20 20
HDAC3 0.036 0.005 -10000 0 0 8 8
Ran/GTP/Exportin 1/HDAC4 -0.03 0.022 -10000 0 -0.1 35 35
GATA1/HDAC4 0.047 0.034 -10000 0 -0.14 15 15
GATA1/HDAC5 0.053 0.012 -10000 0 -0.14 1 1
GATA2/HDAC5 0.051 0.016 -10000 0 -0.14 1 1
HDAC5/BCL6/BCoR 0.052 0.051 -10000 0 -0.13 28 28
HDAC9 0.021 0.018 -10000 0 0 210 210
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.028 -10000 0 -0.12 14 14
HDAC4/ANKRA2 0.044 0.04 -10000 0 -0.14 20 20
HDAC5/YWHAB 0.048 0.028 -10000 0 -0.16 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.034 -10000 0 -0.15 21 21
GATA2 0.035 0.007 -10000 0 0 18 18
HDAC4/RFXANK 0.038 0.049 -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 -0.16 39 39
ADRBK1 0.036 0.006 -10000 0 0 13 13
HDAC4 0.035 0.009 -10000 0 0 29 29
XPO1 0.036 0.004 -10000 0 0 5 5
HDAC5/ANKRA2 0.049 0.025 -10000 0 -0.14 7 7
HDAC4/Ubc9 0.046 0.034 -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 0.038 -10000 0 -0.14 18 18
CAMK4 0.036 0.005 -10000 0 0 9 9
Tubulin/HDAC6 0.036 0.043 -10000 0 -0.12 38 38
SUMO1 0.036 0.003 -10000 0 0 4 4
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.035 0.008 -10000 0 0 24 24
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 0.008 -10000 0 0 24 24
SUMO1/HDAC4 0.033 0.058 -10000 0 -0.23 6 6
SRF 0.037 0.002 -10000 0 0 1 1
HDAC4/YWHAB 0.043 0.042 -10000 0 -0.15 20 20
Tubulin 0.015 0.042 -10000 0 -0.13 38 38
HDAC4/14-3-3 E 0.042 0.044 -10000 0 -0.14 24 24
GNB1 0.035 0.007 -10000 0 0 20 20
RANGAP1 0.033 0.01 -10000 0 0 45 45
BCL6/BCoR 0.036 0.047 -10000 0 -0.14 28 28
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.036 -10000 0 -0.12 15 15
HDAC4/SRF 0.065 0.035 -10000 0 -0.12 14 14
HDAC4/ER alpha 0.044 0.035 -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 -0.16 39 39
cell motility 0.036 0.043 -10000 0 -0.11 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 0.003 -10000 0 -10000 0 0
BCL6 0.032 0.013 -10000 0 0 69 69
HDAC4/CaMK II delta B 0.034 0.009 -10000 0 0 29 29
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 0.035 0.009 -10000 0 0 29 29
HDAC6/HDAC11 0.054 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.059 -10000 0 -0.16 21 21
NPC 0.017 0.02 -10000 0 -0.087 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 0.054 -10000 0 -0.12 25 25
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.036 0.002 -10000 0 0 2 2
TUBB2A 0.033 0.011 -10000 0 0 47 47
HDAC11 0.036 0.004 -10000 0 0 7 7
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 25 25
ANKRA2 0.036 0.006 -10000 0 0 14 14
RFXANK 0.034 0.01 -10000 0 0 42 42
nuclear import -0.029 0.058 0.21 26 -10000 0 26
Cellular roles of Anthrax toxin

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
ANTXR1 0.035 0.006 -10000 0 0 16 16
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 -0.069 0.16 -10000 0 -0.34 135 135
MAP2K2 0.018 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 0.041 0.082 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 0.011 -10000 0 0 54 54
negative regulation of phagocytosis -0.018 0.12 -10000 0 -0.41 41 41
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 0.067 7 -10000 0 7
TNF 0.036 0.003 -10000 0 0 4 4
VCAM1 -0.069 0.16 -10000 0 -0.34 134 134
platelet activation -0.018 0.12 -10000 0 -0.41 41 41
MAPKKK cascade 0.003 0.02 0.064 3 -0.07 30 33
IL18 -0.005 0.035 0.084 39 -0.076 60 99
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 12 -10000 0 12
mol:cAMP -0.018 0.12 -10000 0 -0.41 41 41
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
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.008 0.14 0.32 19 -1 8 27
VDR 0.035 0.007 -10000 0 0 18 18
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.013 0.098 0.25 2 -0.28 38 40
RXRs/LXRs/DNA/Oxysterols 0.005 0.14 0.3 2 -0.4 45 47
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0 0.016 0.046 3 -0.049 43 46
RARs/THRs/DNA/Src-1 0.016 0.053 -10000 0 -0.21 5 5
RXRs/NUR77 0.079 0.064 -10000 0 -0.13 10 10
RXRs/PPAR 0.02 0.047 -10000 0 -0.19 5 5
NCOR2 0.036 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 0.082 0.022 -10000 0 -10000 0 0
RARA 0.036 0.003 -10000 0 0 3 3
NCOA1 0.033 0.011 -10000 0 0 50 50
VDR/VDR/DNA 0.035 0.007 -10000 0 0 18 18
RARs/RARs/DNA/9cRA 0.056 0.032 -10000 0 -10000 0 0
RARG 0.036 0.005 -10000 0 0 8 8
RPS6KB1 -0.004 0.087 0.51 8 -0.4 8 16
RARs/THRs/DNA/SMRT 0.03 0.024 -10000 0 -0.17 5 5
THRA 0.036 0.005 -10000 0 0 11 11
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 0.084 0.1 0.31 2 -0.22 36 38
NR1H2 0.029 0.031 0.09 2 -0.062 45 47
NR1H3 0.03 0.033 0.091 1 -0.069 44 45
RXRs/VDR/DNA/Vit D3 0.072 0.061 -10000 0 -0.13 8 8
NR4A1 0.036 0.006 -10000 0 0 12 12
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.039 -10000 0 -0.14 6 6
RXRG 0.03 0.03 0.089 1 -0.06 46 47
RXR alpha/CCPG 0.023 0.021 -10000 0 -0.055 10 10
RXRA 0.03 0.03 0.089 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 -0.001 0.13 -10000 0 -0.53 12 12
mol:Oxysterols 0 0.015 0.046 3 -0.042 49 52
cholesterol transport 0.005 0.14 0.3 2 -0.4 45 47
PPARA 0.033 0.01 -10000 0 0 44 44
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 0.029 -10000 0 -0.16 1 1
SREBF1 -0.01 0.17 0.34 2 -0.75 16 18
RXRs/RXRs/DNA/9cRA 0.058 0.074 0.28 3 -0.16 39 42
ABCA1 -0.043 0.26 0.34 2 -0.84 45 47
RARs/THRs 0.1 0.024 -10000 0 -0.12 1 1
RXRs/FXR 0.08 0.065 -10000 0 -0.12 32 32
BCL2 0.035 0.007 -10000 0 0 20 20
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 0.049 0.019 -10000 0 -0.14 2 2
FBXW11 0.035 0.008 -10000 0 0 25 25
NF kappa B1 p50/c-Rel 0.033 0.018 -10000 0 -0.12 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.067 -10000 0 -0.26 13 13
NFKBIA 0.002 0.056 -10000 0 -0.3 8 8
MAPK14 0.036 0.004 -10000 0 0 6 6
NF kappa B1 p105/p50 0.028 0.03 -10000 0 -0.13 16 16
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
REL 0.036 0.003 -10000 0 0 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.019 -10000 0 -0.12 5 5
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.02 -10000 0 -0.12 7 7
PIK3CA 0.031 0.013 -10000 0 0 80 80
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 0.092 4 -10000 0 4
RELA 0.036 0.005 -10000 0 0 9 9
positive regulation of anti-apoptosis 0.013 0.038 0.14 2 -0.16 4 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.071 -10000 0 -0.25 15 15
SRC 0.036 0.006 -10000 0 0 14 14
PI3K 0.019 0.075 -10000 0 -0.16 73 73
NF kappa B1 p50/RelA 0.013 0.038 0.14 2 -0.13 22 24
IKBKB 0.036 0.003 -10000 0 0 4 4
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.008 -10000 0 0 25 25
SYK 0.031 0.013 -10000 0 0 76 76
I kappa B alpha/PIK3R1 0.014 0.07 -10000 0 -0.24 23 23
cell death 0.022 0.069 -10000 0 -0.24 15 15
NF kappa B1 p105/c-Rel 0.033 0.018 -10000 0 -0.12 5 5
LCK 0.035 0.007 -10000 0 0 17 17
BCL3 0.034 0.009 -10000 0 0 34 34
Circadian rhythm 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
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 0.056 -10000 0 -0.13 49 49
ATR 0.035 0.008 -10000 0 0 25 25
NR1D1 0.014 0.065 -10000 0 -10000 0 0
ARNTL 0.032 0.02 -10000 0 -0.069 8 8
TIMELESS 0 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 -0.13 1 11
CHEK1 0.033 0.011 -10000 0 0 49 49
mol:HEME 0.01 0.027 0.13 1 -0.13 10 11
PER1 0.033 0.011 -10000 0 0 51 51
BMAL/CLOCK/NPAS2 0.056 0.075 0.23 1 -0.14 50 51
BMAL1/CLOCK 0.01 0.12 -10000 0 -0.53 16 16
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 0.13 1 -0.13 10 11
PER1/TIMELESS 0.022 0.16 -10000 0 -1 10 10
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.007 -10000 0 0 19 19
Signaling events mediated by the Hedgehog family

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
TGFB2 0.034 0.032 -10000 0 -10000 0 0
IHH 0.051 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 0.014 0.027 -10000 0 -0.11 15 15
LRPAP1 0.035 0.007 -10000 0 0 18 18
dorsoventral neural tube patterning -0.014 0.026 0.11 15 -10000 0 15
SMO/beta Arrestin2 0.09 0.065 0.26 14 -10000 0 14
SMO 0.025 0.031 0.19 1 -10000 0 1
AKT1 -0.009 0.13 -10000 0 -0.44 29 29
ARRB2 0.035 0.008 -10000 0 0 26 26
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.036 0.006 -10000 0 0 13 13
heart looping 0.026 0.033 0.22 3 -10000 0 3
STIL 0.053 0.094 0.19 154 -10000 0 154
DHH N/PTCH2 0.027 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.016 0.02 0.11 21 -10000 0 21
PIK3CA 0.031 0.013 -10000 0 0 80 80
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 0.047 -10000 0 -10000 0 0
IHH N/Hhip 0.033 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 20 20
PI3K 0.019 0.075 -10000 0 -0.16 73 73
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.03 0.014 -10000 0 0 87 87
somite specification 0.026 0.033 0.22 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.017 0.023 0.16 1 -10000 0 1
SHH Np/Cholesterol/PTCH2 0.02 0.016 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.02 0.016 -10000 0 -10000 0 0
SHH -0.014 0.012 0.092 1 -10000 0 1
catabolic process 0.02 0.025 0.14 22 -10000 0 22
SMO/Vitamin D3 0.023 0.04 0.19 19 -10000 0 19
SHH Np/Cholesterol/Hhip -0.01 0.008 -10000 0 -10000 0 0
LRP2 0.036 0.006 -10000 0 0 13 13
receptor-mediated endocytosis 0.022 0.038 0.17 19 -10000 0 19
SHH Np/Cholesterol/BOC -0.01 0.008 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.02 0.016 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.01 0.008 -10000 0 -10000 0 0
mol:Vitamin D3 0.079 0.089 0.2 173 -10000 0 173
IHH N/PTCH2 0.061 0.011 -10000 0 -10000 0 0
CDON 0.036 0.005 -10000 0 0 8 8
IHH N/PTCH1 0.046 0.028 0.17 21 -10000 0 21
Megalin/LRPAP1 0.048 0.029 -10000 0 -0.14 10 10
PTCH2 0.036 0.005 -10000 0 0 8 8
SHH Np/Cholesterol 0.011 0.009 -10000 0 -10000 0 0
PTCH1 0.02 0.025 0.14 22 -10000 0 22
HHIP 0 0 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 0.005 0.081 -10000 0 -0.29 17 17
BAG4 0.036 0.005 -10000 0 0 11 11
BAD -0.004 0.033 0.11 1 -0.14 10 11
NFKBIA 0.033 0.012 -10000 0 0 57 57
BIRC3 0.031 0.013 -10000 0 0 81 81
BAX 0.002 0.045 0.18 17 -0.13 10 27
EnzymeConsortium:3.1.4.12 0.004 0.021 0.061 2 -0.078 9 11
IKBKB -0.005 0.08 -10000 0 -0.29 15 15
MAP2K2 -0.007 0.054 0.17 28 -0.16 7 35
MAP2K1 -0.014 0.04 0.17 6 -0.16 9 15
SMPD1 0.003 0.029 0.1 1 -0.12 13 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.012 0.076 -10000 0 -0.32 8 8
MAP2K4 -0.007 0.034 0.15 3 -0.14 5 8
protein ubiquitination -0.006 0.08 -10000 0 -0.31 13 13
EnzymeConsortium:2.7.1.37 -0.013 0.048 0.17 9 -0.17 7 16
response to UV 0 0 0.002 12 -0.002 1 13
RAF1 -0.01 0.038 0.17 6 -0.14 10 16
CRADD 0.036 0.006 -10000 0 0 12 12
mol:ceramide 0.003 0.032 0.11 1 -0.13 10 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0.039 0.033 -10000 0 -0.11 18 18
MADD 0.035 0.006 -10000 0 0 15 15
MAP3K1 -0.002 0.033 0.15 2 -0.14 7 9
TRADD 0.036 0.005 -10000 0 0 11 11
RELA/p50 0.036 0.005 -10000 0 0 9 9
MAPK3 -0.006 0.048 0.16 14 -0.16 5 19
MAPK1 -0.012 0.057 0.17 9 -0.2 14 23
p50/RELA/I-kappa-B-alpha 0.043 0.038 -10000 0 -0.14 18 18
FADD 0.009 0.073 -10000 0 -0.29 8 8
KSR1 -0.004 0.031 0.11 1 -0.15 6 7
MAPK8 -0.01 0.029 0.16 2 -0.15 3 5
TRAF2 0.036 0.006 -10000 0 0 15 15
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.008 0.074 -10000 0 -0.3 13 13
TNF R/SODD 0.035 0.054 -10000 0 -0.14 42 42
TNF 0.036 0.003 -10000 0 0 4 4
CYCS 0.017 0.052 0.15 22 -0.14 9 31
IKBKG -0.006 0.078 -10000 0 -0.29 16 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.015 0.083 -10000 0 -0.34 10 10
RELA 0.036 0.005 -10000 0 0 9 9
RIPK1 0.035 0.007 -10000 0 0 20 20
AIFM1 -0.004 0.039 0.12 14 -0.14 11 25
TNF/TNF R/SODD 0.053 0.055 -10000 0 -0.12 41 41
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.036 0.079 -10000 0 -0.55 8 8
NSMAF 0.008 0.082 0.21 5 -0.3 15 20
response to hydrogen peroxide 0 0 0.002 12 -0.002 1 13
BCL2 0.035 0.007 -10000 0 0 20 20
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.036 0.005 -10000 0 0 11 11
CLTC 0.013 0.087 -10000 0 -0.32 24 24
calcium ion-dependent exocytosis 0.017 0.067 0.13 1 -0.22 18 19
Dynamin 2/GTP 0.026 0.011 -10000 0 -0.1 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.004 0.079 -10000 0 -0.28 27 27
CPE -0.015 0.009 -10000 0 -0.11 1 1
CTNNB1 0.036 0.006 -10000 0 0 15 15
membrane fusion 0.019 0.066 -10000 0 -0.17 31 31
CTNND1 -0.019 0.011 0.086 1 -0.18 1 2
DNM2 0.035 0.009 -10000 0 0 29 29
mol:PI-4-5-P2 0.011 0.066 0.16 2 -0.22 18 20
TSHR -0.016 0.009 0.091 1 -0.11 1 2
INS 0.012 0.081 -10000 0 -0.44 14 14
BIN1 0.031 0.013 -10000 0 0 77 77
mol:Choline 0.019 0.066 -10000 0 -0.17 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 0.008 -10000 0 0 27 27
mol:Ca2+ 0.025 0.011 -10000 0 -0.1 1 1
JUP 0.012 0.069 -10000 0 -0.27 21 21
ASAP2/amphiphysin II 0.028 0.045 -10000 0 -0.1 48 48
ARF6/GTP 0.025 0.009 -10000 0 -0.13 1 1
CDH1 0.009 0.071 -10000 0 -0.26 24 24
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 0.005 0.052 -10000 0 -0.3 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 0.076 0.27 21 -10000 0 21
positive regulation of phagocytosis -0.015 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.046 0.014 -10000 0 -0.12 1 1
ACAP1 0.02 0.063 -10000 0 -0.22 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.004 0.062 -10000 0 -0.3 14 14
clathrin heavy chain/ACAP1 0.017 0.084 0.2 9 -0.32 10 19
JIP4/KLC1 0.036 0.035 -10000 0 -0.1 26 26
EXOC1 0.033 0.011 -10000 0 0 50 50
exocyst 0.003 0.051 -10000 0 -0.31 5 5
RALA/GTP 0.013 0.03 -10000 0 -0.13 17 17
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.038 -10000 0 -0.12 26 26
receptor recycling 0.025 0.009 -10000 0 -0.13 1 1
CTNNA1 -0.019 0.011 0.086 1 -0.18 1 2
NME1 -0.009 0.005 -10000 0 -0.11 1 1
clathrin coat assembly 0.012 0.087 -10000 0 -0.32 24 24
IL2RA 0.007 0.067 -10000 0 -0.32 14 14
VAMP3 -0.015 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.032 0.082 -10000 0 -0.3 10 10
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.001 0.043 -10000 0 -0.21 15 15
PLD2 -0.001 0.043 -10000 0 -0.21 15 15
EXOC5 0.03 0.014 -10000 0 0 85 85
PIP5K1C 0.009 0.062 -10000 0 -0.23 15 15
SDC1 0.014 0.073 -10000 0 -0.26 24 24
ARF6/GDP 0.026 0.006 -10000 0 0 27 27
EXOC7 0.036 0.005 -10000 0 0 10 10
E-cadherin/beta catenin 0.041 0.079 -10000 0 -0.28 21 21
mol:Phosphatidic acid 0.019 0.066 -10000 0 -0.17 31 31
endocytosis -0.027 0.044 0.1 48 -10000 0 48
SCAMP2 0.034 0.009 -10000 0 0 31 31
ADRB2 0.011 0.086 0.23 1 -0.32 21 22
EXOC3 0.036 0.003 -10000 0 0 4 4
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.01 0.089 1 -0.1 1 2
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.005 0.083 -10000 0 -0.32 21 21
RALA 0.024 0.018 -10000 0 0 180 180
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.084 0.22 1 -0.28 23 24
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.009 0.034 0.14 28 -0.22 2 30
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.009 0.046 0.12 2 -0.19 7 9
AP2 0.021 0.027 -10000 0 -0.13 15 15
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.027 0.036 -10000 0 -0.12 15 15
CLTB 0.036 0.005 -10000 0 0 11 11
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.031 -10000 0 -0.18 10 10
CD4 0.031 0.013 -10000 0 0 72 72
CLTA 0.034 0.01 -10000 0 0 42 42
mol:GTP -0.003 0.002 -10000 0 -0.019 6 6
ARFGAP1 -0.011 0.003 0 41 -10000 0 41
mol:PI-4-5-P2 0.008 0.019 0.1 11 -10000 0 11
ARF1/GTP 0.019 0.017 -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 0.11 8 -10000 0 8
ARF1/GDP 0.007 0.011 -10000 0 -0.086 3 3
AP2M1 0.034 0.01 -10000 0 0 37 37
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.017 0.066 1 -0.11 9 10
Rac/GTP 0.016 0.02 -10000 0 -0.14 5 5
ARF1/GTP/GGA3/ARF-GAP1 0.041 0.025 -10000 0 -0.1 8 8
ARFIP2 0.032 0.014 -10000 0 -0.038 13 13
COPA 0.036 0.006 -10000 0 0 13 13
RAC1 0.024 0.017 -10000 0 0 173 173
ARF1/GTP/coatomer protein complex 0.005 0.044 -10000 0 -0.19 10 10
ARF1/GTP/ARHGAP10 0.021 0.015 -10000 0 -0.11 6 6
GGA3 0.036 0.004 -10000 0 0 7 7
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 0.005 0.036 -10000 0 -0.18 12 12
ARF1/GDP/Membrin 0.031 0.028 -10000 0 -0.27 3 3
Arfaptin 2/Rac/GDP 0.027 0.035 -10000 0 -0.12 15 15
CYTH2 -0.003 0.002 -10000 0 -0.019 6 6
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 0.019 -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 -0.19 31 31
PLD2 0.008 0.019 0.11 11 -10000 0 11
ARF-GAP1/v-SNARE -0.011 0.003 0 41 -10000 0 41
PIP5K1A 0.008 0.019 0.1 11 -10000 0 11
ARF1/GTP/Membrin/GBF1/p115 0.002 0.036 -10000 0 -0.11 8 8
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 41 -10000 0 41
GOSR2 0.015 0.023 -10000 0 -0.31 2 2
USO1 0.002 0.006 0.036 10 -0.03 4 14
GBF1 -0.075 0.15 -10000 0 -0.31 140 140
ARF1/GTP/Arfaptin 2 0.041 0.033 -10000 0 -0.12 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.031 0.046 -10000 0 -0.12 35 35
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.033 0.02 0.077 8 -0.076 13 21
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.079 -10000 0 -0.25 18 18
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.011 -10000 0 -0.13 2 2
NFKBIA -0.033 0.046 0.2 1 -0.28 14 15
BIRC2 0.036 0.005 -10000 0 0 11 11
IKBKB 0.036 0.003 -10000 0 0 4 4
RIPK2 0.036 0.006 -10000 0 0 14 14
IKBKG 0.021 0.046 -10000 0 -0.25 9 9
IKK complex/A20 0.06 0.072 -10000 0 -0.26 8 8
NEMO/A20/RIP2 0.036 0.006 -10000 0 0 14 14
XPO1 0.036 0.004 -10000 0 0 5 5
NEMO/ATM 0.04 0.054 -10000 0 -0.29 7 7
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 0.022 -10000 0 -0.14 6 6
IKK complex/ELKS 0.029 0.052 -10000 0 -0.25 7 7
BCL10/MALT1/TRAF6 0.063 0.034 -10000 0 -0.12 10 10
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.034 0.02 0.077 9 -0.073 13 22
RELA 0.034 0.02 0.077 9 -0.072 15 24
MALT1 0.034 0.009 -10000 0 0 32 32
cIAP1/UbcH5C 0.05 0.027 -10000 0 -0.18 6 6
ATM 0.034 0.009 -10000 0 0 35 35
TNF/TNFR1A 0.035 0.055 -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 0.036 0.003 -10000 0 0 4 4
NF kappa B1 p50/RelA 0.065 0.06 -10000 0 -0.17 27 27
BCL10 0.035 0.007 -10000 0 0 20 20
proteasomal ubiquitin-dependent protein catabolic process -0.033 0.046 0.2 1 -0.27 14 15
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.021 0.077 8 -0.076 13 21
TNFRSF1A 0.032 0.012 -10000 0 0 64 64
IKK complex 0.041 0.06 -10000 0 -0.26 7 7
CYLD 0.036 0.006 -10000 0 0 15 15
IKK complex/PKC alpha 0.051 0.066 -10000 0 -0.26 7 7
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.027 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.014 0.016 -10000 0 -10000 0 0
mol:DAG -0.019 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 0.04 0.19 1 -10000 0 1
HIF1A 0.04 0.013 -10000 0 -10000 0 0
GAB1 0.032 0.012 -10000 0 0 59 59
AKT1 -0.032 0.087 0.2 7 -0.3 24 31
PLCG1 -0.019 0.032 0.19 1 -10000 0 1
NOS3 0.008 0.066 -10000 0 -0.32 6 6
CBL 0.036 0.004 -10000 0 0 7 7
mol:NO 0.013 0.072 -10000 0 -0.31 6 6
FLT1 0.016 0.008 -10000 0 -10000 0 0
PGF 0.031 0.013 -10000 0 0 71 71
VEGFR1 homodimer/NRP2/VEGFR121 0.03 0.025 -10000 0 -10000 0 0
CALM1 0.033 0.011 -10000 0 0 54 54
PIK3CA 0.031 0.013 -10000 0 0 80 80
eNOS/Hsp90 0.001 0.068 -10000 0 -0.3 6 6
endothelial cell proliferation -0.006 0.048 -10000 0 -0.31 3 3
mol:Ca2+ -0.019 0.032 0.19 1 -10000 0 1
MAPK3 -0.027 0.033 -10000 0 -10000 0 0
MAPK1 -0.027 0.035 0.15 2 -10000 0 2
PIK3R1 0.032 0.012 -10000 0 0 63 63
PLGF homodimer 0.031 0.013 -10000 0 0 71 71
PRKACA 0.035 0.008 -10000 0 0 25 25
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.018 -10000 0 0 290 290
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 -0.028 0.045 0.21 1 -10000 0 1
PI3K 0.037 0.077 -10000 0 -0.2 15 15
PRKCA -0.024 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 0.005 -10000 0 0 8 8
mol:IP3 -0.019 0.032 0.19 1 -10000 0 1
RASA1 -0.026 0.026 0.19 1 -10000 0 1
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 0.005 -10000 0 0 8 8
NCK1 0.035 0.008 -10000 0 0 27 27
eNOS/Caveolin-1 0.002 0.069 -10000 0 -0.32 7 7
PTPN11 0.036 0.005 -10000 0 0 11 11
mol:PI-3-4-5-P3 0.035 0.076 -10000 0 -0.2 15 15
mol:L-citrulline 0.013 0.072 -10000 0 -0.31 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.043 -10000 0 -0.19 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.028 -10000 0 -0.19 1 1
CD2AP 0.034 0.01 -10000 0 0 41 41
PI3K/GAB1 0.041 0.087 -10000 0 -0.19 22 22
PDPK1 -0.03 0.066 0.24 4 -0.26 2 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.029 -10000 0 -0.19 1 1
mol:NADP 0.013 0.072 -10000 0 -0.31 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.042 -10000 0 -0.18 3 3
VEGFR1 homodimer/NRP2 0.032 0.028 -10000 0 -10000 0 0
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 -0.032 0.03 -10000 0 -0.15 20 20
MDM2/SUMO1 0.034 0.053 -10000 0 -0.21 6 6
HDAC4 0.035 0.009 -10000 0 0 29 29
Ran/GTP/Exportin 1/HDAC1 -0.031 0.03 -10000 0 -0.14 26 26
SUMO1 0.036 0.003 -10000 0 0 4 4
NPC/RanGAP1/SUMO1 0.005 0.034 -10000 0 -0.15 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.008 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 25 25
SUMO1/HDAC4 0.033 0.058 -10000 0 -0.23 6 6
SUMO1/HDAC1 0.036 0.055 -10000 0 -0.22 6 6
RANGAP1 0.033 0.01 -10000 0 0 45 45
MDM2/SUMO1/SUMO1 0.077 0.047 -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 0.033 0.011 -10000 0 0 46 46
UBE2I 0.036 0.004 -10000 0 0 6 6
Ran/GTP/Exportin 1 0.013 0.051 0.2 1 -0.26 5 6
NPC 0.017 0.02 -10000 0 -0.087 18 18
PIAS2 0.035 0.007 -10000 0 0 18 18
PIAS1 0.035 0.008 -10000 0 0 27 27
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 -0.095 20 20
MAPK9 0.007 0.001 -9999 0 0 15 15
adrenocorticotropin secretion -0.011 0.002 0 17 -10000 0 17
GNB1/GNG2 0.02 0.025 -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 6 6
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 13 13
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.035 0.007 -9999 0 0 17 17
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.003 -9999 0 0 138 138
MAPK11 0.007 0.002 -9999 0 0 49 49
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 -10000 0 -0.041 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.054 0.018 -10000 0 -10000 0 0
PLCG1 0.035 0.007 -10000 0 0 19 19
ARRB2 0.035 0.008 -10000 0 0 26 26
WASL 0.024 0.017 -10000 0 0 172 172
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 0.015 0.036 -10000 0 -0.23 5 5
FYN -0.008 0.046 0.18 24 -10000 0 24
mol:Ca2+ 0.086 0.037 0.19 1 -0.12 3 4
mol:DAG 0.087 0.037 0.2 1 -0.12 3 4
NPHS2 0.039 0.008 -10000 0 -0.041 1 1
mol:IP3 0.087 0.037 0.2 1 -0.12 3 4
regulation of endocytosis 0.052 0.05 -10000 0 -0.13 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.07 0.028 0.18 1 -10000 0 1
establishment of cell polarity 0.054 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.096 0.058 -10000 0 -0.14 16 16
Nephrin/NEPH1/beta Arrestin2 0.055 0.051 -10000 0 -0.13 4 4
NPHS1 0.039 0.01 0.077 6 -10000 0 6
Nephrin/NEPH1/podocin 0.053 0.044 0.21 1 -0.1 1 2
TJP1 0.034 0.01 -10000 0 0 38 38
NCK1 0.035 0.008 -10000 0 0 27 27
NCK2 0.035 0.007 -10000 0 0 17 17
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.089 0.038 0.2 1 -0.12 3 4
CD2AP 0.034 0.01 -10000 0 0 41 41
Nephrin/NEPH1/podocin/GRB2 0.087 0.043 0.2 1 -0.12 7 8
GRB2 0.035 0.007 -10000 0 0 17 17
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.049 0.18 25 -10000 0 25
cytoskeleton organization -0.009 0.036 0.21 5 -0.22 3 8
Nephrin/NEPH1 0.046 0.016 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.064 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 0.032 0.19 0.53 1 -0.66 20 21
PCK1 0.048 0.12 0.52 3 -0.53 4 7
HNF4A 0.048 0.16 0.69 1 -0.71 6 7
KCNJ11 0.057 0.18 0.47 4 -0.57 18 22
AKT1 0.057 0.13 0.37 1 -0.35 20 21
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.07 0.19 0.56 3 -0.57 17 20
NKX2-1 0.025 0.11 0.28 3 -0.32 16 19
ACADM 0.041 0.18 0.49 2 -0.66 14 16
TAT 0.045 0.13 0.5 2 -0.6 6 8
CEBPB 0.034 0.015 0.12 1 -10000 0 1
CEBPA 0.031 0.018 -10000 0 -10000 0 0
TTR 0.02 0.18 0.64 2 -0.64 12 14
PKLR 0.046 0.17 0.47 4 -0.63 9 13
APOA1 0.064 0.2 0.63 3 -0.84 7 10
CPT1C 0.045 0.16 0.44 4 -0.53 17 21
ALAS1 0.025 0.24 -10000 0 -1.2 15 15
TFRC 0.014 0.29 0.52 5 -0.96 35 40
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 0.11 1 -10000 0 1
CPT1A 0.043 0.16 0.53 1 -0.63 9 10
HMGCS1 0.047 0.17 0.56 2 -0.58 12 14
NR3C1 0.046 0.02 -10000 0 -10000 0 0
CPT1B 0.043 0.16 0.49 2 -0.58 12 14
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.036 0.005 -10000 0 -10000 0 0
GCK 0.094 0.19 0.5 14 -0.56 11 25
CREB1 0.043 0.013 0.11 14 -10000 0 14
IGFBP1 0.058 0.13 0.62 1 -0.63 5 6
PDX1 0.047 0.11 0.33 4 -0.31 12 16
UCP2 0.012 0.24 0.5 3 -0.68 43 46
ALDOB 0.057 0.18 0.49 3 -0.61 14 17
AFP 0.015 0.032 0.27 2 -10000 0 2
BDH1 0.033 0.19 0.53 1 -0.68 19 20
HADH 0.057 0.18 0.47 4 -0.57 18 22
F2 0.063 0.2 0.78 1 -0.84 7 8
HNF1A 0.006 0.005 0.11 1 -10000 0 1
G6PC 0.006 0.083 0.42 1 -10000 0 1
SLC2A2 0.055 0.13 0.44 1 -0.43 5 6
INS 0.025 0.042 0.19 14 -0.095 34 48
FOXA1 0.014 0.013 0.15 2 -10000 0 2
FOXA3 0.019 0.056 0.2 5 -0.18 24 29
FOXA2 0.091 0.22 0.65 3 -0.65 18 21
ABCC8 0.056 0.18 0.51 2 -0.62 13 15
ALB 0.016 0.032 0.3 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 0.005 -9999 0 0 8 8
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 0.005 0.064 -9999 0 -0.39 13 13
AURKB 0.034 0.01 -9999 0 0 39 39
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 9 -9999 0 9
PI3K Class IB/PDE3B 0.036 0.005 -9999 0 0 9 9
PDE3B 0.036 0.005 -9999 0 0 9 9
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 4 -9999 0 4
ADCY5 -0.009 0.001 0 4 -9999 0 4
ADCY6 -0.017 0.006 0.085 1 -9999 0 1
ADCY7 -0.014 0.018 0.085 15 -9999 0 15
ADCY1 -0.012 0.009 -10000 0 -9999 0 0
ADCY2 -0.017 0.007 0.085 2 -9999 0 2
ADCY3 -0.009 0.001 0 4 -9999 0 4
ADCY8 -0.007 0.032 0.085 54 -9999 0 54
PRKCE -0.011 0.001 0 4 -9999 0 4
ADCY9 -0.017 0.009 0.085 4 -9999 0 4
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.018 0.043 0.17 12 -9999 0 12
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 0.006 -10000 0 0 12 12
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 0.008 -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 12 12
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.068 0.024 -10000 0 -10000 0 0
mol:Na + 0.043 0.016 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.045 0.015 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.054 0.018 -10000 0 -10000 0 0
CNGB1 0.035 0.007 -10000 0 0 17 17
RDH5 0.035 0.007 -10000 0 0 19 19
SAG 0.036 0.005 -10000 0 0 8 8
mol:Ca2+ -0.033 0.031 0.18 9 -10000 0 9
Na + (4 Units) 0.04 0.018 -10000 0 -10000 0 0
RGS9 0.035 0.007 -10000 0 0 17 17
GNB1/GNGT1 0.031 0.038 -10000 0 -0.14 13 13
GNAT1/GDP 0.058 0.02 -10000 0 -0.1 1 1
GUCY2D 0.036 0.006 -10000 0 0 12 12
GNGT1 0.024 0.017 -10000 0 0 172 172
GUCY2F 0.037 0 -10000 0 -10000 0 0
GNB5 0.035 0.008 -10000 0 0 24 24
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 0.006 -10000 0 0 12 12
CNGA1 0.036 0.005 -10000 0 0 11 11
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 0.009 0.029 -10000 0 -0.15 14 14
GCAP Family/Ca ++ 0.023 0.001 -10000 0 -10000 0 0
PDE6A/B 0.053 0.009 -10000 0 -10000 0 0
mol:Pi 0.045 0.015 -10000 0 -0.11 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.041 0.041 -10000 0 -0.11 13 13
PDE6B 0.036 0.004 -10000 0 0 5 5
PDE6A 0.036 0.005 -10000 0 0 9 9
PDE6G 0.036 0.003 -10000 0 0 3 3
RHO 0.036 0.006 -10000 0 0 14 14
PDE6 0.084 0.027 -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 6 6
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/1269528/2.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/1282577/1.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.

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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)
Meta

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