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 127
FOXM1 transcription factor network 110
Angiopoietin receptor Tie2-mediated signaling 88
Endothelins 86
PDGFR-alpha signaling pathway 79
TCGA08_rtk_signaling 74
TCGA08_p53 73
Thromboxane A2 receptor signaling 72
HIF-2-alpha transcription factor network 72
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 72
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 127 9660 76 -0.081 0.1 1000 -1000 -0.006 -1000
FOXM1 transcription factor network 110 5635 51 -0.32 0.062 1000 -1000 -0.038 -1000
Angiopoietin receptor Tie2-mediated signaling 88 7822 88 -0.29 0.053 1000 -1000 -0.047 -1000
Endothelins 86 8305 96 -0.14 0.036 1000 -1000 -0.025 -1000
PDGFR-alpha signaling pathway 79 3482 44 -0.093 0.036 1000 -1000 -0.02 -1000
TCGA08_rtk_signaling 74 1944 26 -0.027 0.095 1000 -1000 -0.015 -1000
TCGA08_p53 73 515 7 -0.001 0.034 1000 -1000 -0.01 -1000
Thromboxane A2 receptor signaling 72 7617 105 -0.068 0.044 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 72 3108 43 -0.078 0.047 1000 -1000 -0.048 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 72 2386 33 -0.075 0.068 1000 -1000 -0.013 -1000
EGFR-dependent Endothelin signaling events 71 1500 21 -0.005 0.092 1000 -1000 -0.009 -1000
Effects of Botulinum toxin 70 1835 26 -0.007 0.053 1000 -1000 -0.011 -1000
Canonical Wnt signaling pathway 67 3418 51 -0.1 0.074 1000 -1000 -0.023 -1000
Syndecan-3-mediated signaling events 66 2316 35 -0.072 0.08 1000 -1000 -0.026 -1000
Wnt signaling 66 463 7 -0.006 0.037 1000 -1000 -0.001 -1000
Arf6 signaling events 65 4078 62 -0.005 0.093 1000 -1000 -0.003 -1000
Ras signaling in the CD4+ TCR pathway 65 1111 17 -0.001 0.043 1000 -1000 -0.002 -1000
LPA receptor mediated events 61 6232 102 -0.13 0.037 1000 -1000 -0.056 -1000
TCGA08_retinoblastoma 61 495 8 -0.046 0.056 1000 -1000 -0.002 -1000
Syndecan-4-mediated signaling events 60 4029 67 -0.14 0.036 1000 -1000 -0.03 -1000
S1P5 pathway 58 1000 17 -0.009 0.036 1000 -1000 -0.01 -1000
Nongenotropic Androgen signaling 58 3034 52 -0.084 0.058 1000 -1000 -0.02 -1000
S1P4 pathway 58 1474 25 -0.013 0.041 1000 -1000 -0.01 -1000
Syndecan-1-mediated signaling events 55 1889 34 -0.003 0.035 1000 -1000 -0.021 -1000
Fc-epsilon receptor I signaling in mast cells 55 5370 97 -0.13 0.048 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 53 906 17 -0.14 0.063 1000 -1000 -0.009 -1000
amb2 Integrin signaling 53 4352 82 -0.016 0.076 1000 -1000 -0.015 -1000
IL2 signaling events mediated by STAT5 53 1176 22 -0.072 0.042 1000 -1000 -0.019 -1000
Syndecan-2-mediated signaling events 52 3611 69 -0.026 0.037 1000 -1000 -0.024 -1000
EPO signaling pathway 52 2905 55 -0.001 0.082 1000 -1000 -0.011 -1000
IL23-mediated signaling events 52 3142 60 -0.064 0.15 1000 -1000 -0.024 -1000
Glypican 2 network 51 206 4 0 0.007 1000 -1000 0 -1000
Osteopontin-mediated events 50 1901 38 -0.074 0.05 1000 -1000 -0.016 -1000
PLK2 and PLK4 events 48 145 3 -0.011 0.035 1000 -1000 -0.014 -1000
Signaling events mediated by PTP1B 46 3561 76 -0.032 0.06 1000 -1000 -0.037 -1000
FoxO family signaling 46 2963 64 -0.17 0.053 1000 -1000 -0.035 -1000
BCR signaling pathway 46 4576 99 -0.06 0.05 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 46 1988 43 -0.039 0.064 1000 -1000 -0.016 -1000
Presenilin action in Notch and Wnt signaling 45 2799 61 -0.082 0.08 1000 -1000 -0.029 -1000
Ephrin B reverse signaling 44 2114 48 -0.065 0.068 1000 -1000 -0.048 -1000
IL2 signaling events mediated by PI3K 44 2596 58 -0.069 0.038 1000 -1000 -0.019 -1000
EPHB forward signaling 44 3751 85 -0.053 0.082 1000 -1000 -0.043 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 44 3030 68 -0.1 0.046 1000 -1000 -0.026 -1000
Regulation of nuclear SMAD2/3 signaling 43 5912 136 -0.21 0.2 1000 -1000 -0.045 -1000
Noncanonical Wnt signaling pathway 43 1120 26 -0.037 0.037 1000 -1000 -0.035 -1000
Arf6 downstream pathway 42 1838 43 -0.025 0.05 1000 -1000 -0.028 -1000
Reelin signaling pathway 42 2380 56 -0.014 0.067 1000 -1000 -0.017 -1000
Signaling events mediated by VEGFR1 and VEGFR2 42 5289 125 -0.045 0.06 1000 -1000 -0.041 -1000
ErbB2/ErbB3 signaling events 41 2691 65 -0.044 0.036 1000 -1000 -0.039 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 41 2250 54 -0.037 0.079 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 41 1504 36 -0.053 0.052 1000 -1000 -0.045 -1000
Sphingosine 1-phosphate (S1P) pathway 40 1135 28 -0.011 0.036 1000 -1000 -0.014 -1000
BMP receptor signaling 40 3313 81 -0.033 0.054 1000 -1000 -0.007 -1000
mTOR signaling pathway 40 2142 53 -0.031 0.046 1000 -1000 -0.021 -1000
IL6-mediated signaling events 40 3003 75 -0.076 0.11 1000 -1000 -0.024 -1000
Class I PI3K signaling events 40 2980 73 -0.05 0.068 1000 -1000 -0.019 -1000
IL12-mediated signaling events 39 3415 87 -0.11 0.095 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 39 1472 37 -0.034 0.082 1000 -1000 -0.012 -1000
IL1-mediated signaling events 39 2467 62 -0.046 0.074 1000 -1000 -0.039 -1000
p38 MAPK signaling pathway 39 1721 44 0 0.044 1000 -1000 -0.01 -1000
Glypican 1 network 38 1866 48 -0.032 0.052 1000 -1000 -0.033 -1000
PLK1 signaling events 38 3261 85 -0.05 0.054 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 38 1810 47 -0.17 0.048 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 38 2828 74 -0.13 0.079 1000 -1000 -0.046 -1000
Class I PI3K signaling events mediated by Akt 37 2558 68 -0.029 0.064 1000 -1000 -0.014 -1000
S1P1 pathway 37 1342 36 -0.004 0.055 1000 -1000 -0.018 -1000
PDGFR-beta signaling pathway 37 3614 97 -0.052 0.066 1000 -1000 -0.041 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 36 3104 85 -0.12 0.11 1000 -1000 -0.018 -1000
IFN-gamma pathway 36 2508 68 -0.04 0.064 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 36 1947 54 0 0.047 1000 -1000 -0.014 -1000
IGF1 pathway 36 2070 57 -0.046 0.067 1000 -1000 -0.029 -1000
Neurotrophic factor-mediated Trk receptor signaling 36 4379 120 -0.035 0.087 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 35 2330 65 -0.017 0.057 1000 -1000 -0.02 -1000
TCR signaling in naïve CD8+ T cells 35 3296 93 -0.34 0.39 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 34 171 5 0.026 0.052 1000 -1000 0.032 -1000
Signaling events regulated by Ret tyrosine kinase 34 2833 82 -0.058 0.062 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 34 449 13 0 0.065 1000 -1000 0 -1000
Plasma membrane estrogen receptor signaling 33 2884 86 -0.067 0.052 1000 -1000 -0.033 -1000
IL4-mediated signaling events 32 2992 91 -0.32 0.063 1000 -1000 -0.054 -1000
E-cadherin signaling in the nascent adherens junction 32 2436 76 -0.041 0.091 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 32 2511 78 -0.022 0.073 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 31 1829 58 -0.054 0.059 1000 -1000 -0.016 -1000
Caspase cascade in apoptosis 30 2261 74 -0.08 0.066 1000 -1000 -0.032 -1000
ErbB4 signaling events 30 2099 69 -0.07 0.064 1000 -1000 -0.027 -1000
Aurora A signaling 30 1800 60 -0.028 0.058 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class III 30 1208 40 -0.048 0.048 1000 -1000 -0.046 -1000
Signaling mediated by p38-gamma and p38-delta 30 451 15 -0.025 0.036 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 30 1362 45 -0.034 0.076 1000 -1000 -0.028 -1000
Insulin Pathway 30 2238 74 -0.034 0.084 1000 -1000 -0.032 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 29 673 23 -0.018 0.054 1000 -1000 -0.007 -1000
p75(NTR)-mediated signaling 29 3668 125 -0.023 0.088 1000 -1000 -0.039 -1000
Integrins in angiogenesis 29 2514 84 -0.046 0.071 1000 -1000 -0.02 -1000
Regulation of Telomerase 29 3005 102 -0.028 0.076 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 29 1016 34 -0.036 0.047 1000 -1000 -0.027 -1000
Aurora B signaling 29 1961 67 -0.033 0.063 1000 -1000 -0.014 -1000
Visual signal transduction: Cones 28 1093 38 -0.014 0.059 1000 -1000 -0.011 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 28 2387 83 -0.036 0.068 1000 -1000 -0.014 -1000
S1P3 pathway 28 1211 42 -0.02 0.037 1000 -1000 -0.022 -1000
TRAIL signaling pathway 27 1320 48 -0.034 0.087 1000 -1000 -0.015 -1000
BARD1 signaling events 26 1532 57 -0.064 0.085 1000 -1000 -0.058 -1000
Glucocorticoid receptor regulatory network 26 3014 114 -0.12 0.064 1000 -1000 -0.043 -1000
Coregulation of Androgen receptor activity 24 1833 76 -0.011 0.07 1000 -1000 -0.01 -1000
Insulin-mediated glucose transport 24 797 32 -0.016 0.042 1000 -1000 -0.015 -1000
Nectin adhesion pathway 24 1563 63 -0.01 0.083 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class I 23 2428 104 -0.029 0.066 1000 -1000 -0.027 -1000
Regulation of Androgen receptor activity 23 1649 70 -0.032 0.067 1000 -1000 -0.021 -1000
RXR and RAR heterodimerization with other nuclear receptor 22 1144 52 -0.044 0.1 1000 -1000 -0.019 -1000
IL27-mediated signaling events 22 1161 51 -0.016 0.063 1000 -1000 -0.03 -1000
Ceramide signaling pathway 21 1620 76 -0.04 0.07 1000 -1000 -0.015 -1000
E-cadherin signaling events 21 109 5 0.033 0.063 1000 -1000 0.032 -1000
Atypical NF-kappaB pathway 20 650 31 -0.021 0.037 1000 -1000 -0.014 -1000
Calcium signaling in the CD4+ TCR pathway 20 648 31 -0.021 0.09 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 19 1481 75 -0.03 0.093 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 19 762 39 -0.068 0.036 1000 -1000 -0.01 -1000
Signaling mediated by p38-alpha and p38-beta 19 836 44 -0.015 0.084 1000 -1000 -0.018 -1000
Arf6 trafficking events 19 1407 71 -0.038 0.046 1000 -1000 -0.034 -1000
VEGFR1 specific signals 19 1085 56 -0.032 0.042 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 18 720 39 -0.033 0.065 1000 -1000 -0.017 -1000
Circadian rhythm pathway 18 409 22 -0.01 0.056 1000 -1000 -0.025 -1000
ceramide signaling pathway 18 882 49 -0.015 0.053 1000 -1000 -0.015 -1000
Arf1 pathway 18 1023 54 -0.075 0.044 1000 -1000 -0.012 -1000
Nephrin/Neph1 signaling in the kidney podocyte 17 579 34 -0.054 0.095 1000 -1000 -0.04 -1000
Signaling events mediated by the Hedgehog family 17 923 52 -0.015 0.09 1000 -1000 -0.02 -1000
Rapid glucocorticoid signaling 16 322 20 -0.011 0.036 1000 -1000 -0.01 -1000
Sumoylation by RanBP2 regulates transcriptional repression 15 412 27 -0.033 0.077 1000 -1000 -0.029 -1000
FOXA2 and FOXA3 transcription factor networks 11 544 46 0 0.1 1000 -1000 -0.044 -1000
Aurora C signaling 10 75 7 0 0.063 1000 -1000 -0.006 -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 99 12 -0.017 0.017 1000 -1000 -0.012 -1000
Visual signal transduction: Rods 8 427 52 -0.034 0.085 1000 -1000 -0.01 -1000
Ephrin A reverse signaling 2 17 7 -0.019 0.048 1000 -1000 -0.011 -1000
Total 5195 292535 7203 -7 8.6 131000 -131000 -3 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.027 0.46 0.62 84 -0.76 87 171
HDAC7 -0.001 0.005 -10000 0 -0.051 3 3
HIF1A/ARNT/Cbp/p300/Src-1 -0.029 0.39 0.59 36 -0.69 78 114
SMAD4 0.033 0.014 0.08 10 -10000 0 10
ID2 0.046 0.48 0.62 105 -0.76 85 190
AP1 0.013 0.083 -10000 0 -0.18 73 73
ABCG2 0.013 0.47 0.63 89 -0.76 89 178
HIF1A 0.044 0.13 0.23 83 -0.15 68 151
TFF3 0.04 0.47 0.63 94 -0.74 86 180
GATA2 0.038 0.014 0.076 22 -0.077 2 24
AKT1 0.052 0.14 0.25 90 -0.19 43 133
response to hypoxia 0.012 0.09 0.17 85 -0.12 51 136
MCL1 0.052 0.48 0.63 106 -0.75 87 193
NDRG1 -0.003 0.46 0.62 69 -0.76 90 159
SERPINE1 -0.068 0.39 0.58 36 -0.78 80 116
FECH 0.042 0.47 0.63 93 -0.74 86 179
FURIN 0.052 0.48 0.63 102 -0.75 86 188
NCOA2 0.037 0.006 -10000 0 -10000 0 0
EP300 0.073 0.18 0.36 96 -0.31 29 125
HMOX1 -0.022 0.46 0.63 64 -0.79 87 151
BHLHE40 -0.056 0.41 0.55 74 -0.72 91 165
BHLHE41 -0.056 0.41 0.55 74 -0.72 91 165
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.07 0.18 0.36 47 -0.23 37 84
ENG 0.03 0.15 0.3 51 -0.25 19 70
JUN 0.035 0.013 -10000 0 -0.002 43 43
RORA 0.024 0.47 0.62 86 -0.75 88 174
ABCB1 -0.057 0.22 -10000 0 -0.84 29 29
TFRC 0.03 0.47 0.62 97 -0.74 90 187
CXCR4 0.012 0.47 0.62 84 -0.76 92 176
TF -0.081 0.41 0.64 40 -0.75 92 132
CITED2 0.011 0.46 0.61 85 -0.75 89 174
HIF1A/ARNT -0.077 0.45 0.66 20 -0.87 78 98
LDHA -0.066 0.28 -10000 0 -0.97 40 40
ETS1 0.056 0.48 0.64 102 -0.75 87 189
PGK1 0.045 0.48 0.63 101 -0.77 87 188
NOS2 -0.056 0.41 0.55 74 -0.72 91 165
ITGB2 0.003 0.46 0.61 86 -0.77 90 176
ALDOA 0.054 0.48 0.64 100 -0.76 86 186
Cbp/p300/CITED2 -0.023 0.46 0.61 67 -0.8 86 153
FOS 0.026 0.018 -10000 0 0 163 163
HK2 0.055 0.48 0.63 104 -0.75 87 191
SP1 0.033 0.059 0.11 38 -0.15 40 78
GCK 0.1 0.24 0.56 59 -0.48 11 70
HK1 -0.001 0.45 0.63 78 -0.75 86 164
NPM1 0.05 0.48 0.63 100 -0.76 84 184
EGLN1 0.047 0.47 0.63 97 -0.75 85 182
CREB1 0.032 0.034 -10000 0 -0.1 30 30
PGM1 0.049 0.48 0.64 100 -0.75 87 187
SMAD3 0.037 0.008 0.08 10 -10000 0 10
EDN1 0.053 0.22 0.47 28 -0.54 20 48
IGFBP1 -0.011 0.42 0.64 57 -0.76 74 131
VEGFA -0.014 0.34 0.49 82 -0.57 87 169
HIF1A/JAB1 0.043 0.1 0.21 43 -0.19 17 60
CP -0.036 0.45 0.61 65 -0.76 93 158
CXCL12 -0.039 0.41 0.62 47 -0.76 83 130
COPS5 0.037 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.053 0.14 5 -0.14 35 40
BNIP3 -0.008 0.45 0.65 70 -0.76 84 154
EGLN3 0.004 0.45 0.62 75 -0.75 86 161
CA9 -0.017 0.43 0.6 64 -0.75 84 148
TERT 0.048 0.48 0.63 101 -0.75 86 187
ENO1 0.045 0.48 0.64 98 -0.76 85 183
PFKL 0.053 0.48 0.64 102 -0.76 85 187
NCOA1 0.033 0.011 -10000 0 0 49 49
ADM -0.021 0.46 0.62 72 -0.76 95 167
ARNT 0.048 0.13 0.24 84 -0.14 65 149
HNF4A 0.037 0.012 0.084 6 -10000 0 6
ADFP -0.03 0.44 0.63 56 -0.76 90 146
SLC2A1 0.013 0.37 0.54 75 -0.6 84 159
LEP 0.006 0.43 0.64 68 -0.76 74 142
HIF1A/ARNT/Cbp/p300 -0.04 0.39 0.6 35 -0.7 80 115
EPO 0.02 0.31 0.56 50 -0.61 37 87
CREBBP 0.078 0.18 0.36 100 -0.27 29 129
HIF1A/ARNT/Cbp/p300/HDAC7 -0.044 0.38 0.56 35 -0.68 80 115
PFKFB3 0.006 0.46 0.65 76 -0.77 84 160
NT5E -0.03 0.44 0.64 59 -0.74 94 153
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.089 0.66 1 34 -1.2 103 137
PLK1 0.062 0.16 0.61 19 -0.71 7 26
BIRC5 -0.065 0.44 0.7 13 -1.2 59 72
HSPA1B -0.09 0.66 0.94 39 -1.2 103 142
MAP2K1 0.046 0.1 0.25 56 -10000 0 56
BRCA2 -0.087 0.66 1 34 -1.2 103 137
FOXM1 -0.24 0.99 1.2 35 -1.9 103 138
XRCC1 -0.086 0.67 1 35 -1.2 98 133
FOXM1B/p19 -0.32 0.57 -10000 0 -1.4 101 101
Cyclin D1/CDK4 -0.11 0.6 0.87 29 -1.1 105 134
CDC2 -0.11 0.74 1.1 37 -1.3 106 143
TGFA -0.072 0.58 0.86 41 -1 102 143
SKP2 -0.09 0.66 1 33 -1.2 98 131
CCNE1 0.024 0.037 0.1 21 -0.034 114 135
CKS1B -0.096 0.69 1 35 -1.2 103 138
RB1 -0.073 0.37 0.5 16 -1 49 65
FOXM1C/SP1 -0.17 0.76 0.89 29 -1.5 104 133
AURKB 0.059 0.16 0.64 16 -0.95 4 20
CENPF -0.11 0.71 1.1 35 -1.2 112 147
CDK4 0.025 0.052 0.15 31 -10000 0 31
MYC -0.11 0.57 0.81 36 -1 108 144
CHEK2 0.037 0.094 0.23 51 -10000 0 51
ONECUT1 -0.091 0.64 0.9 40 -1.2 104 144
CDKN2A 0.003 0.018 -10000 0 -0.14 4 4
LAMA4 -0.094 0.66 0.98 36 -1.2 105 141
FOXM1B/HNF6 -0.17 0.78 0.94 36 -1.5 104 140
FOS -0.15 0.7 0.99 33 -1.2 132 165
SP1 0.034 0.019 0.07 5 -0.028 39 44
CDC25B -0.086 0.69 1 38 -1.2 106 144
response to radiation 0.024 0.068 0.15 73 -10000 0 73
CENPB -0.077 0.68 1 39 -1.2 99 138
CENPA -0.091 0.67 1 35 -1.2 99 134
NEK2 -0.081 0.67 1.1 34 -1.2 101 135
HIST1H2BA -0.09 0.66 0.94 39 -1.2 103 142
CCNA2 0.022 0.031 0.094 5 -0.034 77 82
EP300 0.033 0.011 -10000 0 0 50 50
CCNB1/CDK1 -0.19 0.85 1.1 29 -1.6 111 140
CCNB2 -0.11 0.7 1 38 -1.3 108 146
CCNB1 -0.12 0.75 1.1 36 -1.3 110 146
ETV5 -0.12 0.69 1 34 -1.2 122 156
ESR1 -0.092 0.66 1 32 -1.2 99 131
CCND1 -0.097 0.62 0.9 39 -1.1 105 144
GSK3A 0.037 0.085 0.21 49 -10000 0 49
Cyclin A-E1/CDK1-2 0.048 0.1 0.26 24 -0.16 43 67
CDK2 0.024 0.037 0.1 17 -0.034 118 135
G2/M transition of mitotic cell cycle 0.028 0.083 0.18 74 -10000 0 74
FOXM1B/Cbp/p300 -0.17 0.69 0.8 19 -1.4 103 122
GAS1 -0.093 0.68 1 36 -1.2 107 143
MMP2 -0.12 0.7 1 37 -1.2 115 152
RB1/FOXM1C -0.14 0.62 0.86 25 -1.2 103 128
CREBBP 0.036 0.005 -10000 0 0 9 9
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 -0.82 141 141
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.38 131 131
NCK1/Dok-R -0.14 0.35 -10000 0 -0.86 96 96
PIK3CA 0.031 0.014 -10000 0 0 82 82
mol:beta2-estradiol 0.031 0.098 0.23 96 -10000 0 96
RELA 0.036 0.004 -10000 0 0 7 7
SHC1 0.032 0.011 -10000 0 0 52 52
Rac/GDP 0.017 0.02 -10000 0 -0.13 5 5
F2 0.053 0.11 0.28 87 -0.091 64 151
TNIP2 0.036 0.006 -10000 0 0 12 12
NF kappa B/RelA -0.11 0.36 -10000 0 -0.83 96 96
FN1 0.035 0.009 -10000 0 0 30 30
PLD2 -0.15 0.36 -10000 0 -0.89 96 96
PTPN11 0.036 0.005 -10000 0 0 11 11
GRB14 0.032 0.013 -10000 0 0 70 70
ELK1 -0.14 0.33 -10000 0 -0.82 96 96
GRB7 0.036 0.006 -10000 0 0 15 15
PAK1 0.036 0.006 -10000 0 0 16 16
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.86 96 96
CDKN1A -0.19 0.36 -10000 0 -0.66 166 166
ITGA5 0.033 0.012 -10000 0 0 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.36 -10000 0 -0.86 96 96
CRK 0.035 0.008 -10000 0 0 23 23
mol:NO -0.12 0.32 0.38 3 -0.59 138 141
PLG -0.15 0.36 -10000 0 -0.89 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.75 124 124
GRB2 0.035 0.007 -10000 0 0 18 18
PIK3R1 0.032 0.012 -10000 0 0 63 63
ANGPT2 -0.22 0.45 -10000 0 -1 109 109
BMX -0.15 0.36 -10000 0 -0.89 96 96
ANGPT1 -0.16 0.42 -10000 0 -1 95 95
tube development -0.21 0.36 -10000 0 -0.7 165 165
ANGPT4 0.022 0.029 -10000 0 -0.025 128 128
response to hypoxia -0.013 0.026 -10000 0 -0.063 96 96
Tie2/Ang1/GRB14 -0.14 0.37 -10000 0 -0.9 96 96
alpha5/beta1 Integrin 0.028 0.043 -10000 0 -0.14 21 21
FGF2 0.034 0.017 -10000 0 -0.014 49 49
STAT5A (dimer) -0.24 0.44 -10000 0 -0.81 176 176
mol:L-citrulline -0.12 0.32 0.38 3 -0.59 138 141
AGTR1 0.022 0.034 -10000 0 -0.048 92 92
MAPK14 -0.16 0.37 -10000 0 -0.9 96 96
Tie2/SHP2 -0.079 0.24 -10000 0 -0.84 32 32
TEK -0.085 0.25 -10000 0 -0.96 29 29
RPS6KB1 -0.2 0.37 -10000 0 -0.77 136 136
Angiotensin II/AT1 0.014 0.036 0.085 1 -0.057 88 89
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -0.9 96 96
MAPK3 -0.15 0.34 -10000 0 -0.84 96 96
MAPK1 -0.15 0.34 -10000 0 -0.84 96 96
Tie2/Ang1/GRB7 -0.14 0.38 -10000 0 -0.91 96 96
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.15 0.36 -10000 0 -0.88 96 96
PI3K -0.24 0.44 -10000 0 -0.9 136 136
FES -0.16 0.37 -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 -0.73 144 144
STAT5A 0.036 0.004 -10000 0 0 5 5
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.37 -10000 0 -0.77 136 136
Tie2/Ang2 -0.29 0.5 -10000 0 -0.97 163 163
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 96 96
FOXO1 -0.22 0.39 -10000 0 -0.74 168 168
ELF1 0.028 0.036 0.11 4 -0.046 81 85
ELF2 -0.14 0.35 -10000 0 -0.87 96 96
mol:Choline -0.15 0.35 -10000 0 -0.86 96 96
cell migration -0.066 0.097 -10000 0 -0.21 137 137
FYN -0.24 0.41 -10000 0 -0.81 164 164
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.17 0.32 0.39 3 -0.59 170 173
ETS1 -0.002 0.12 -10000 0 -0.25 93 93
PXN -0.17 0.31 -10000 0 -0.65 134 134
ITGB1 0.026 0.017 -10000 0 0 144 144
NOS3 -0.15 0.35 0.4 1 -0.67 137 138
RAC1 0.025 0.017 -10000 0 0 163 163
TNF -0.003 0.12 -10000 0 -0.25 92 92
MAPKKK cascade -0.15 0.35 -10000 0 -0.86 96 96
RASA1 0.035 0.009 -10000 0 0 30 30
Tie2/Ang1/Shc -0.15 0.37 -10000 0 -0.91 96 96
NCK1 0.035 0.008 -10000 0 0 27 27
vasculogenesis -0.1 0.29 0.36 4 -0.52 147 151
mol:Phosphatidic acid -0.15 0.35 -10000 0 -0.86 96 96
mol:Angiotensin II -0.004 0.013 0.023 2 -0.032 75 77
mol:NADP -0.12 0.32 0.38 3 -0.59 138 141
Rac1/GTP -0.18 0.34 -10000 0 -0.7 132 132
MMP2 -0.15 0.36 -10000 0 -0.9 96 96
Endothelins

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.022 0.15 0.21 78 -0.27 88 166
PTK2B 0.036 0.006 -10000 0 0 16 16
mol:Ca2+ -0.1 0.25 0.39 2 -0.53 74 76
EDN1 0.004 0.093 0.15 7 -0.16 100 107
EDN3 0.033 0.011 -10000 0 0 52 52
EDN2 0.036 0.006 -10000 0 0 12 12
HRAS/GDP -0.014 0.17 0.31 16 -0.38 55 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.003 0.12 0.2 18 -0.26 55 73
ADCY4 -0.036 0.099 0.14 40 -0.2 98 138
ADCY5 -0.036 0.099 0.14 40 -0.2 98 138
ADCY6 -0.009 0.13 0.19 94 -0.24 63 157
ADCY7 -0.015 0.13 0.19 84 -0.24 68 152
ADCY1 -0.001 0.11 0.18 70 -0.25 40 110
ADCY2 -0.008 0.13 0.19 93 -0.24 65 158
ADCY3 -0.036 0.099 0.14 40 -0.2 98 138
ADCY8 -0.012 0.13 0.19 86 -0.24 57 143
ADCY9 -0.011 0.13 0.19 92 -0.24 66 158
arachidonic acid secretion -0.079 0.26 0.32 28 -0.5 107 135
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.11 0.18 13 -0.26 46 59
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.01 -10000 0 0 36 36
ETA receptor/Endothelin-1/G12/GTP 0.004 0.12 -10000 0 -0.23 71 71
ETA receptor/Endothelin-1/Gs/GTP 0.004 0.12 -10000 0 -0.21 104 104
mol:GTP 0 0.007 0.026 3 -0.025 4 7
COL3A1 -0.077 0.16 0.19 9 -0.37 102 111
EDNRB 0.023 0.045 0.098 61 -0.084 47 108
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.018 0.14 0.21 76 -0.29 64 140
CYSLTR1 -0.036 0.12 0.19 42 -0.25 96 138
SLC9A1 -0.014 0.087 0.13 28 -0.18 69 97
mol:GDP -0.022 0.17 0.3 20 -0.39 54 74
SLC9A3 -0.12 0.28 -10000 0 -0.65 80 80
RAF1 -0.034 0.2 0.29 31 -0.41 84 115
JUN -0.14 0.33 0.48 1 -0.71 88 89
JAK2 -0.022 0.14 0.21 68 -0.26 86 154
mol:IP3 -0.001 0.12 0.23 16 -0.28 41 57
ETA receptor/Endothelin-1 -0.022 0.15 -10000 0 -0.28 108 108
PLCB1 0.032 0.014 -10000 0 -0.004 58 58
PLCB2 0.029 0.023 -10000 0 -0.023 78 78
ETA receptor/Endothelin-3 0.006 0.09 -10000 0 -0.15 105 105
FOS -0.094 0.35 0.36 31 -0.82 85 116
Gai/GDP -0.069 0.27 -10000 0 -0.73 67 67
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca ++ -0.018 0.18 0.26 57 -0.34 75 132
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.001 0.13 0.24 23 -0.3 40 63
GNAQ 0.027 0.026 -10000 0 -0.034 70 70
GNAZ 0.031 0.013 -10000 0 0 80 80
GNAL 0.036 0.006 -10000 0 0 13 13
Gs family/GDP -0.011 0.16 0.28 19 -0.36 54 73
ETA receptor/Endothelin-1/Gq/GTP -0.005 0.13 0.2 14 -0.28 56 70
MAPK14 -0.011 0.1 0.17 9 -0.25 46 55
TRPC6 -0.11 0.25 0.4 1 -0.56 72 73
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
GNAI1 0.018 0.018 -10000 0 0 262 262
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.1 0.18 19 -0.25 48 67
ETB receptor/Endothelin-2 0.017 0.071 -10000 0 -0.11 101 101
ETB receptor/Endothelin-3 0.015 0.07 -10000 0 -0.11 95 95
ETB receptor/Endothelin-1 -0.001 0.1 0.18 26 -0.17 103 129
MAPK3 -0.076 0.32 0.35 29 -0.72 85 114
MAPK1 -0.09 0.34 0.35 30 -0.76 88 118
Rac1/GDP -0.009 0.15 0.3 16 -0.38 38 54
cAMP biosynthetic process 0.018 0.12 0.21 65 -0.22 46 111
MAPK8 -0.14 0.3 0.35 3 -0.56 139 142
SRC 0.034 0.009 -10000 0 0 34 34
ETB receptor/Endothelin-1/Gi/GTP -0.03 0.14 0.16 5 -0.35 57 62
p130Cas/CRK/Src/PYK2 -0.019 0.18 0.35 13 -0.48 43 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.013 0.15 0.31 13 -0.38 42 55
COL1A2 -0.051 0.17 0.22 2 -0.48 59 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.005 0.093 -10000 0 -0.15 117 117
mol:DAG -0.001 0.12 0.23 16 -0.28 41 57
MAP2K2 -0.052 0.26 0.33 37 -0.55 85 122
MAP2K1 -0.063 0.26 0.31 31 -0.57 88 119
EDNRA -0.011 0.11 0.15 2 -0.2 104 106
positive regulation of muscle contraction 0.027 0.15 0.22 147 -0.28 41 188
Gq family/GDP 0.006 0.16 0.31 5 -0.36 52 57
HRAS/GTP -0.014 0.16 0.28 24 -0.35 58 82
PRKCH -0.006 0.12 0.24 18 -0.3 39 57
RAC1 0.025 0.017 -10000 0 0 163 163
PRKCA -0.009 0.12 0.22 19 -0.3 43 62
PRKCB -0.003 0.12 0.22 19 -0.29 45 64
PRKCE -0.01 0.12 0.21 18 -0.3 45 63
PRKCD -0.004 0.13 0.26 24 -0.29 43 67
PRKCG -0.011 0.12 0.22 18 -0.3 47 65
regulation of vascular smooth muscle contraction -0.12 0.42 0.41 20 -1 84 104
PRKCQ -0.003 0.11 0.25 20 -0.3 32 52
PLA2G4A -0.089 0.28 0.33 27 -0.54 107 134
GNA14 0.027 0.026 -10000 0 -0.034 70 70
GNA15 0.03 0.019 -10000 0 -0.035 24 24
GNA12 0.023 0.018 -10000 0 0 189 189
GNA11 0.032 0.017 -10000 0 -0.036 16 16
Rac1/GTP 0.007 0.12 -10000 0 -0.23 65 65
MMP1 0.02 0.075 0.19 32 -10000 0 32
PDGFR-alpha signaling pathway

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
PDGFRA 0.017 0.032 0.082 4 -0.014 219 223
PDGF/PDGFRA/CRKL 0.007 0.069 -10000 0 -0.12 95 95
positive regulation of JUN kinase activity 0.024 0.063 -10000 0 -0.12 69 69
CRKL 0.035 0.008 -10000 0 0 28 28
PDGF/PDGFRA/Caveolin-3 0.009 0.069 -10000 0 -0.11 107 107
AP1 -0.079 0.24 0.3 12 -0.59 77 89
mol:IP3 -0.015 0.047 0.093 27 -0.1 55 82
PLCG1 -0.015 0.047 0.095 26 -0.1 55 81
PDGF/PDGFRA/alphaV Integrin 0.003 0.077 -10000 0 -0.16 78 78
RAPGEF1 0.035 0.007 -10000 0 0 18 18
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca2+ -0.015 0.047 0.093 27 -0.1 55 82
CAV3 0.036 0.005 -10000 0 0 11 11
CAV1 0.016 0.018 -10000 0 0 288 288
SHC/Grb2/SOS1 0.028 0.065 -10000 0 -0.12 69 69
PDGF/PDGFRA/Shf -0.005 0.055 -10000 0 -0.09 121 121
FOS -0.093 0.22 0.26 5 -0.6 72 77
JUN -0.026 0.058 0.21 10 -0.2 18 28
oligodendrocyte development 0.003 0.077 -10000 0 -0.16 78 78
GRB2 0.035 0.007 -10000 0 0 18 18
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:DAG -0.015 0.047 0.093 27 -0.1 55 82
PDGF/PDGFRA 0.017 0.032 0.082 4 -0.014 219 223
actin cytoskeleton reorganization 0.006 0.067 -10000 0 -0.14 66 66
SRF -0.015 0.021 0.034 56 -10000 0 56
SHC1 0.033 0.011 -10000 0 0 52 52
PI3K 0.007 0.091 -10000 0 -0.15 107 107
PDGF/PDGFRA/Crk/C3G 0.027 0.073 -10000 0 -0.13 76 76
JAK1 -0.006 0.03 0.082 33 -10000 0 33
ELK1/SRF -0.02 0.084 0.14 67 -0.16 59 126
SHB 0.033 0.011 -10000 0 0 51 51
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.034 0.078 2 -0.032 101 103
GO:0007205 -0.028 0.071 0.11 25 -0.2 55 80
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.063 -10000 0 -0.12 69 69
PDGF/PDGFRA/SHB 0.006 0.067 -10000 0 -0.14 66 66
PDGF/PDGFRA/Caveolin-1 -0.015 0.078 -10000 0 -0.16 98 98
ITGAV 0.035 0.009 -10000 0 0 31 31
ELK1 -0.033 0.069 0.089 26 -0.15 96 122
PIK3CA 0.031 0.014 -10000 0 0 82 82
PDGF/PDGFRA/Crk 0.005 0.074 -10000 0 -0.15 77 77
JAK-STAT cascade -0.006 0.03 0.082 33 -10000 0 33
cell proliferation -0.005 0.055 -10000 0 -0.09 121 121
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 0 166 166
HRAS 0.034 0.009 -10000 0 0 36 36
EGFR 0.009 0.016 -10000 0 0 379 379
AKT 0.092 0.12 0.25 128 -0.18 12 140
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.033 0.011 -10000 0 0 54 54
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.035 0.007 -10000 0 0 20 20
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.023 0.018 -10000 0 0 190 190
PIK3CA 0.031 0.014 -10000 0 0 82 82
PIK3CB 0.036 0.007 -10000 0 0 17 17
NRAS 0.032 0.012 -10000 0 0 63 63
PIK3CG 0.025 0.017 -10000 0 0 164 164
PIK3R3 0.036 0.006 -10000 0 0 15 15
PIK3R2 0.035 0.008 -10000 0 0 26 26
NF1 0.036 0.003 -10000 0 0 4 4
RAS -0.003 0.054 0.14 3 -0.24 11 14
ERBB2 0.036 0.004 -10000 0 0 6 6
proliferation/survival/translation -0.027 0.052 0.22 4 -0.2 11 15
PI3K 0.041 0.093 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 34 34
FOXO 0.095 0.093 0.2 169 -10000 0 169
AKT2 0.035 0.008 -10000 0 0 28 28
PTEN 0.025 0.017 -10000 0 0 168 168
TCGA08_p53

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
CDKN2A -0.001 0.004 0 448 -10000 0 448
TP53 0.004 0.033 -10000 0 -0.22 8 8
Senescence 0.004 0.035 -10000 0 -0.22 10 10
Apoptosis 0.004 0.035 -10000 0 -0.22 10 10
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.019 0.3 2 -10000 0 2
MDM4 0.034 0.01 -10000 0 0 37 37
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.034 0.01 -10000 0 0 41 41
GNB1/GNG2 -0.046 0.077 -10000 0 -0.17 133 133
AKT1 -0.003 0.16 0.27 34 -0.28 47 81
EGF 0.035 0.008 -10000 0 0 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.016 0.067 0.27 19 -0.17 3 22
mol:Ca2+ 0 0.19 0.35 25 -0.27 116 141
LYN -0.016 0.07 0.28 18 -0.17 6 24
RhoA/GTP 0 0.083 0.16 26 -0.13 89 115
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.016 0.2 0.36 27 -0.32 126 153
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.035 0.008 -10000 0 0 25 25
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.076 -10000 0 -0.24 32 32
G beta5/gamma2 -0.054 0.1 -10000 0 -0.23 129 129
PRKCH -0.016 0.2 0.36 23 -0.32 127 150
DNM1 0.035 0.008 -10000 0 0 26 26
TXA2/TP beta/beta Arrestin3 0.015 0.018 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.005 56 -0.002 4 60
PTGDR 0.035 0.008 -10000 0 0 28 28
G12 family/GTP -0.044 0.14 -10000 0 -0.29 93 93
ADRBK1 0.036 0.005 -10000 0 0 10 10
ADRBK2 0.035 0.009 -10000 0 0 29 29
RhoA/GTP/ROCK1 0.044 0.027 -10000 0 -0.13 10 10
mol:GDP -0.008 0.13 0.41 15 -0.27 21 36
mol:NADP 0.025 0.017 -10000 0 0 168 168
RAB11A 0.036 0.006 -10000 0 0 16 16
PRKG1 0.026 0.017 -10000 0 0 147 147
mol:IP3 -0.012 0.22 0.38 23 -0.34 124 147
cell morphogenesis 0.044 0.027 -10000 0 -0.13 10 10
PLCB2 -0.036 0.27 0.43 15 -0.45 124 139
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.014 0.069 0.27 20 -10000 0 20
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.02 0.054 0.24 10 -0.17 8 18
RHOA 0.035 0.007 -10000 0 0 21 21
PTGIR 0.035 0.009 -10000 0 0 31 31
PRKCB1 -0.017 0.22 0.37 22 -0.34 125 147
GNAQ 0.035 0.009 -10000 0 0 30 30
mol:L-citrulline 0.025 0.017 -10000 0 0 168 168
TXA2/TXA2-R family -0.048 0.28 0.42 20 -0.47 133 153
LCK -0.016 0.067 0.27 18 -10000 0 18
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.032 0.039 0.19 3 -0.13 1 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.02 0.14 -10000 0 -0.46 45 45
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.041 0.19 3 -0.14 2 5
MAPK14 -0.004 0.15 0.29 34 -0.22 122 156
TGM2/GTP -0.015 0.24 0.41 22 -0.38 95 117
MAPK11 -0.006 0.15 0.29 31 -0.22 123 154
ARHGEF1 0.01 0.12 0.22 50 -0.18 89 139
GNAI2 0.034 0.01 -10000 0 0 44 44
JNK cascade -0.021 0.22 0.38 23 -0.35 133 156
RAB11/GDP 0.034 0.009 -10000 0 -0.008 21 21
ICAM1 -0.004 0.18 0.32 34 -0.27 125 159
cAMP biosynthetic process -0.013 0.2 0.35 23 -0.32 96 119
Gq family/GTP/EBP50 0.013 0.054 0.24 7 -0.16 31 38
actin cytoskeleton reorganization 0.044 0.027 -10000 0 -0.13 10 10
SRC -0.02 0.055 0.24 13 -10000 0 13
GNB5 0.035 0.007 -10000 0 0 22 22
GNB1 0.035 0.007 -10000 0 0 20 20
EGF/EGFR -0.009 0.11 0.28 21 -0.23 41 62
VCAM1 -0.023 0.21 0.32 35 -0.33 135 170
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.076 -10000 0 -0.24 32 32
platelet activation -0.009 0.19 0.35 29 -0.28 119 148
PGI2/IP 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.014 0.024 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.006 0.067 -10000 0 -0.21 30 30
TXA2/TP beta/beta Arrestin2 0.004 0.049 -10000 0 -0.26 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.02 -10000 0 -10000 0 0
mol:DAG -0.021 0.24 0.39 22 -0.38 128 150
EGFR 0.009 0.016 -10000 0 0 379 379
TXA2/TP alpha -0.028 0.26 0.43 16 -0.43 97 113
Gq family/GTP 0.009 0.047 0.2 10 -0.13 28 38
YES1 -0.015 0.07 0.27 19 -0.17 3 22
GNAI2/GTP 0.007 0.048 -10000 0 -0.13 2 2
PGD2/DP 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.009 -10000 0 0 36 36
FYN -0.017 0.07 0.27 18 -0.17 7 25
mol:NO 0.025 0.017 -10000 0 0 168 168
GNA15 0.033 0.011 -10000 0 0 51 51
PGK/cGMP 0.027 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.01 -10000 0 -0.006 26 26
TP alpha/TGM2/GDP/G beta/gamma 0.029 0.042 0.18 2 -0.13 1 3
NOS3 0.025 0.017 -10000 0 0 168 168
RAC1 0.025 0.017 -10000 0 0 163 163
PRKCA -0.014 0.2 0.36 23 -0.32 126 149
PRKCB -0.015 0.21 0.36 23 -0.32 130 153
PRKCE -0.017 0.21 0.36 23 -0.33 126 149
PRKCD -0.019 0.22 0.36 28 -0.35 128 156
PRKCG -0.022 0.22 0.37 22 -0.35 132 154
muscle contraction -0.041 0.26 0.41 20 -0.44 134 154
PRKCZ -0.016 0.2 0.36 24 -0.31 133 157
ARR3 0.037 0 -10000 0 -10000 0 0
TXA2/TP beta 0.036 0.038 0.19 2 -0.14 1 3
PRKCQ -0.026 0.2 0.36 23 -0.32 122 145
MAPKKK cascade -0.031 0.24 0.39 21 -0.4 125 146
SELE -0.01 0.18 0.33 27 -0.27 133 160
TP beta/GNAI2/GDP/G beta/gamma 0.025 0.053 0.19 2 -0.16 14 16
ROCK1 0.036 0.006 -10000 0 0 15 15
GNA14 0.035 0.009 -10000 0 0 29 29
chemotaxis -0.068 0.32 0.46 15 -0.56 135 150
GNA12 0.023 0.018 -10000 0 0 189 189
GNA13 0.035 0.007 -10000 0 0 20 20
GNA11 0.033 0.011 -10000 0 0 51 51
Rac1/GTP 0.017 0.02 -10000 0 -0.14 5 5
HIF-2-alpha transcription factor network

Figure 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
MMP14 -0.02 0.17 -10000 0 -0.66 31 31
oxygen homeostasis 0.004 0.021 0.045 65 -0.024 27 92
TCEB2 0.036 0.004 -10000 0 0 7 7
TCEB1 0.035 0.007 -10000 0 0 22 22
VHL/Elongin B/Elongin C/HIF2A 0.002 0.14 0.3 23 -0.23 55 78
EPO -0.043 0.2 0.4 17 -0.42 63 80
FIH (dimer) 0.015 0.039 0.11 17 -0.04 58 75
APEX1 0.016 0.043 0.11 8 -0.049 46 54
SERPINE1 -0.078 0.2 0.38 2 -0.46 83 85
FLT1 -0.012 0.16 -10000 0 -0.64 27 27
ADORA2A -0.038 0.24 0.44 35 -0.42 77 112
germ cell development -0.038 0.23 0.43 33 -0.41 80 113
SLC11A2 -0.036 0.25 0.46 34 -0.43 77 111
BHLHE40 -0.041 0.24 0.44 32 -0.42 81 113
HIF1AN 0.015 0.039 0.11 17 -0.04 58 75
HIF2A/ARNT/SIRT1 -0.018 0.17 0.35 25 -0.29 62 87
ETS1 0.047 0.033 0.12 43 -0.11 11 54
CITED2 -0.055 0.26 -10000 0 -0.81 49 49
KDR -0.002 0.16 -10000 0 -0.83 16 16
PGK1 -0.041 0.26 0.46 34 -0.45 81 115
SIRT1 0.024 0.017 -10000 0 0 174 174
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.03 0.27 0.48 12 -0.48 78 90
EPAS1 0 0.13 0.31 35 -0.26 41 76
SP1 0.04 0.011 0.11 8 -10000 0 8
ABCG2 -0.047 0.26 0.43 40 -0.44 93 133
EFNA1 -0.042 0.24 0.44 30 -0.45 74 104
FXN -0.041 0.24 0.44 35 -0.42 75 110
POU5F1 -0.041 0.24 0.44 32 -0.42 81 113
neuron apoptosis 0.03 0.26 0.47 78 -0.47 13 91
EP300 0.033 0.011 -10000 0 0 50 50
EGLN3 0.018 0.04 0.11 15 -0.04 62 77
EGLN2 0.022 0.042 0.11 19 -0.039 61 80
EGLN1 0.022 0.042 0.11 19 -0.04 62 81
VHL/Elongin B/Elongin C 0.045 0.024 -10000 0 -0.12 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.016 0.043 0.11 7 -0.05 42 49
SLC2A1 -0.053 0.24 0.45 26 -0.45 74 100
TWIST1 -0.062 0.21 0.42 15 -0.43 87 102
ELK1 0.038 0.036 0.12 29 -0.095 25 54
HIF2A/ARNT/Cbp/p300 -0.001 0.19 0.38 31 -0.31 58 89
VEGFA -0.041 0.24 0.44 32 -0.42 81 113
CREBBP 0.036 0.005 -10000 0 0 9 9
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.034 0.01 -9999 0 0 39 39
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.036 0.004 -9999 0 0 7 7
TCEB1 0.035 0.007 -9999 0 0 22 22
HIF1A/p53 -0.063 0.14 -9999 0 -0.27 141 141
HIF1A -0.059 0.12 -9999 0 -0.28 122 122
COPS5 0.036 0.006 -9999 0 0 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2 0.046 0.06 -9999 0 -0.13 22 22
FIH (dimer) 0.025 0.017 -9999 0 0 156 156
CDKN2A 0.004 0.012 -9999 0 0 448 448
ARNT/IPAS 0.05 0.015 -9999 0 -10000 0 0
HIF1AN 0.025 0.017 -9999 0 0 156 156
GNB2L1 0.037 0.002 -9999 0 0 2 2
HIF1A/ARNT -0.062 0.14 -9999 0 -0.28 141 141
CUL2 0.025 0.017 -9999 0 0 158 158
OS9 0.031 0.013 -9999 0 0 73 73
RACK1/Elongin B/Elongin C 0.068 0.032 -9999 0 -0.14 10 10
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.075 0.13 -9999 0 -0.27 143 143
PHD1-3/OS9 0.062 0.065 -9999 0 -0.14 30 30
HIF1A/RACK1/Elongin B/Elongin C -0.043 0.15 -9999 0 -0.27 140 140
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.063 0.14 -9999 0 -0.28 144 144
EGLN3 0.03 0.014 -9999 0 0 93 93
EGLN2 0.035 0.009 -9999 0 0 29 29
EGLN1 0.034 0.009 -9999 0 0 34 34
TP53 0.031 0.013 -9999 0 0 73 73
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.005 0.1 -9999 0 -0.61 12 12
ARNT 0.036 0.004 -9999 0 0 6 6
ARD1A 0.036 0.003 -9999 0 0 4 4
RBX1 0.033 0.011 -9999 0 0 47 47
HIF1A/p19ARF -0.065 0.12 -9999 0 -0.26 120 120
EGFR-dependent Endothelin signaling events

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
HRAS 0.034 0.009 -10000 0 0 36 36
EGFR 0.009 0.016 -10000 0 0 379 379
EGF/EGFR 0.001 0.054 -10000 0 -0.11 65 65
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.058 -10000 0 -0.12 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.016 -10000 0 0 123 123
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.035 0.008 -10000 0 0 25 25
EGF/EGFR dimer/SHC 0 0.056 -10000 0 -0.13 61 61
mol:GDP 0.004 0.056 -10000 0 -0.12 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.033 0.011 -10000 0 0 52 52
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
HRAS/GTP -0.004 0.052 -10000 0 -0.12 69 69
SHC1 0.033 0.011 -10000 0 0 52 52
HRAS/GDP 0 0.059 -10000 0 -0.12 69 69
FRAP1 0.092 0.12 0.18 302 -0.19 4 306
EGF/EGFR dimer -0.005 0.058 -10000 0 -0.14 64 64
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 18 18
ETA receptor/Endothelin-1 0.023 0.06 -10000 0 -0.14 51 51
Effects of Botulinum toxin

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
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 18 18
STXBP1 0.029 0.015 -10000 0 0 107 107
ACh/CHRNA1 0.028 0.055 0.097 53 -0.075 91 144
RAB3GAP2/RIMS1/UNC13B 0.053 0.05 -10000 0 -0.13 23 23
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.035 0.007 -10000 0 0 21 21
mol:ACh 0.019 0.066 0.097 152 -0.09 87 239
RAB3GAP2 0.035 0.009 -10000 0 0 29 29
STX1A/SNAP25/VAMP2 0.026 0.1 0.18 18 -0.15 79 97
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.054 0.097 53 -0.075 91 144
UNC13B 0.032 0.013 -10000 0 0 68 68
CHRNA1 0.035 0.007 -10000 0 0 18 18
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.014 0.043 0.1 22 -0.086 40 62
SNAP25 0.002 0.003 -10000 0 0 274 274
VAMP2 0.004 0.001 -10000 0 0 49 49
SYT1 0.018 0.018 -10000 0 0 264 264
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.017 0.016 0.089 1 -10000 0 1
STX1A/SNAP25 fragment 1/VAMP2 0.026 0.1 0.18 18 -0.15 79 97
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.033 0.046 0.12 72 -0.039 84 156
AES 0.032 0.042 0.11 66 -0.036 80 146
FBXW11 0.035 0.007 -10000 0 0 22 22
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -10000 0 0
SMAD4 0.032 0.012 -10000 0 0 59 59
DKK2 0.035 0.009 -10000 0 0 31 31
TLE1 0.032 0.042 0.11 70 -0.036 85 155
MACF1 0.034 0.011 -10000 0 0 49 49
CTNNB1 0.048 0.11 0.25 28 -0.35 14 42
WIF1 0.028 0.015 -10000 0 0 112 112
beta catenin/RanBP3 0.074 0.16 0.41 66 -0.35 8 74
KREMEN2 0.036 0.005 -10000 0 0 9 9
DKK1 0.017 0.018 -10000 0 0 277 277
beta catenin/beta TrCP1 0.062 0.11 0.26 27 -0.33 16 43
FZD1 0.024 0.017 -10000 0 0 175 175
AXIN2 -0.024 0.094 0.1 9 -0.23 69 78
AXIN1 0.038 0.001 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
Axin1/APC/GSK3/beta catenin 0.017 0.16 -10000 0 -0.6 29 29
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.13 0.24 13 -0.42 20 33
Axin1/APC/GSK3 0.005 0.087 0.24 4 -0.38 16 20
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.14 0.27 10 -0.4 27 37
HNF1A 0.007 0.03 0.071 78 -0.03 11 89
CTBP1 0.031 0.042 0.11 63 -0.037 84 147
MYC -0.1 0.41 0.73 14 -1.3 51 65
RANBP3 0.035 0.008 -10000 0 0 22 22
DKK2/LRP6/Kremen 2 0.064 0.027 -10000 0 -0.13 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.03 0.039 0.11 60 -0.036 68 128
TCF3 0.033 0.043 0.11 71 -0.036 82 153
WNT1/LRP6/FZD1/Axin1 0.06 0.046 -10000 0 -10000 0 0
Ran/GTP 0.026 0.016 -10000 0 -0.13 5 5
CtBP/CBP/TCF/TLE1/AES 0.037 0.19 0.46 68 -0.32 26 94
LEF1 0.034 0.044 0.11 74 -0.037 86 160
DVL1 0.01 0.096 -10000 0 -0.42 17 17
CSNK2A1 0.033 0.011 -10000 0 0 51 51
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.009 0.16 0.25 11 -0.48 33 44
DKK1/LRP6/Kremen 2 0.03 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 40 40
CSNK1A1 0.035 0.047 0.12 73 -0.039 86 159
NLK 0.027 0.023 -10000 0 -0.032 57 57
CCND1 -0.083 0.36 0.89 2 -1.3 39 41
WNT1 0.036 0.007 -10000 0 0 18 18
GSK3A 0.035 0.009 -10000 0 0 28 28
GSK3B 0.034 0.01 -10000 0 0 39 39
FRAT1 0.025 0.017 -10000 0 0 163 163
PPP2R5D 0.025 0.042 -10000 0 -0.24 6 6
APC 0.041 0.1 0.18 163 -10000 0 163
WNT1/LRP6/FZD1 0.001 0.047 -10000 0 -0.23 12 12
CREBBP 0.034 0.043 0.11 73 -0.036 86 159
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 -0.027 0.19 -9999 0 -0.45 74 74
Syndecan-3/Neurocan -0.066 0.18 -9999 0 -0.48 79 79
POMC 0.036 0.006 -9999 0 0 13 13
EGFR 0.009 0.016 -9999 0 0 379 379
Syndecan-3/EGFR -0.058 0.16 -9999 0 -0.42 78 78
AGRP 0.036 0.005 -9999 0 0 8 8
NCSTN 0.035 0.009 -9999 0 0 29 29
PSENEN 0.035 0.009 -9999 0 0 31 31
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.036 0.006 -9999 0 0 14 14
APH1A 0.036 0.006 -9999 0 0 12 12
NCAN 0 0 -9999 0 -10000 0 0
long-term memory -0.034 0.2 -9999 0 -0.5 79 79
Syndecan-3/IL8 -0.057 0.18 -9999 0 -0.48 79 79
PSEN1 0.033 0.011 -9999 0 0 47 47
Src/Cortactin 0.049 0.018 -9999 0 -0.14 1 1
FYN 0.03 0.014 -9999 0 0 88 88
limb bud formation -0.067 0.18 -9999 0 -0.5 79 79
MC4R 0.035 0.007 -9999 0 0 21 21
SRC 0.034 0.009 -9999 0 0 34 34
PTN 0.022 0.018 -9999 0 0 207 207
FGFR/FGF/Syndecan-3 -0.067 0.19 -9999 0 -0.5 79 79
neuron projection morphogenesis -0.072 0.16 -9999 0 -0.44 74 74
Syndecan-3/AgRP -0.044 0.19 -9999 0 -0.49 79 79
Syndecan-3/AgRP/MC4R -0.025 0.2 -9999 0 -0.48 78 78
Fyn/Cortactin 0.029 0.062 -9999 0 -0.15 53 53
SDC3 -0.068 0.19 -9999 0 -0.51 79 79
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.056 0.18 -9999 0 -0.47 79 79
IL8 0.019 0.018 -9999 0 0 244 244
Syndecan-3/Fyn/Cortactin -0.034 0.21 -9999 0 -0.51 79 79
Syndecan-3/CASK -0.066 0.18 -9999 0 -0.48 79 79
alpha-MSH/MC4R 0.051 0.014 -9999 0 -10000 0 0
Gamma Secretase 0.08 0.072 -9999 0 -0.16 28 28
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 20 20
FZD3 0.029 0.015 -9999 0 0 109 109
WNT5A 0.03 0.015 -9999 0 0 99 99
WNT11 0.036 0.006 -9999 0 0 15 15
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.014 0.035 -10000 0 -0.11 38 38
ARNO/beta Arrestin1-2 0.042 0.025 -10000 0 -0.095 7 7
EGFR 0.009 0.016 -10000 0 0 379 379
EPHA2 0.033 0.011 -10000 0 0 55 55
USP6 0.035 0.007 -10000 0 0 18 18
IQSEC1 0.036 0.007 -10000 0 0 19 19
EGFR/EGFR/EGF/EGF -0.005 0.058 -10000 0 -0.14 64 64
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
mol:GTP 0.002 0.011 0.049 1 -0.063 2 3
ARRB1 0.036 0.005 -10000 0 0 11 11
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.033 0.011 -10000 0 0 51 51
EGF 0.035 0.008 -10000 0 0 25 25
somatostatin receptor activity 0 0 0.001 152 0 6 158
ARAP2 0 0 0 130 0 3 133
mol:GDP 0.068 0.068 0.16 125 -0.16 4 129
mol:PI-3-4-5-P3 0 0 0 128 0 5 133
ITGA2B 0.037 0.003 -10000 0 0 3 3
ARF6 0.035 0.009 -10000 0 0 29 29
Ephrin A1/EPHA2/NCK1/GIT1 0.075 0.055 -10000 0 -0.13 25 25
ADAP1 0 0 0 70 0 1 71
KIF13B 0.032 0.012 -10000 0 0 63 63
HGF/MET 0.032 0.027 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 7 7
ARF6/GTP 0.084 0.088 0.19 129 -0.2 5 134
EGFR/EGFR/EGF/EGF/ARFGEP100 0.001 0.056 -10000 0 -0.13 62 62
ADRB2 0.034 0.01 -10000 0 0 40 40
receptor agonist activity 0 0 0 135 0 4 139
actin filament binding 0 0 0 140 0 6 146
SRC 0.034 0.009 -10000 0 0 34 34
ITGB3 0.037 0.003 -10000 0 0 4 4
GNAQ 0.035 0.009 -10000 0 0 30 30
EFA6/PI-4-5-P2 0.001 0.001 0.001 169 -0.001 4 173
ARF6/GDP 0.035 0.062 0.16 14 -0.19 16 30
ARF6/GDP/GULP/ACAP1 0.055 0.074 0.21 17 -0.17 2 19
alphaIIb/beta3 Integrin/paxillin/GIT1 0.093 0.01 -10000 0 -10000 0 0
ACAP1 0 0 0 63 -10000 0 63
ACAP2 0 0 0 106 0 3 109
LHCGR/beta Arrestin2 0.03 0.024 -10000 0 -0.14 7 7
EFNA1 0.033 0.011 -10000 0 0 52 52
HGF 0.024 0.018 -10000 0 0 177 177
CYTH3 0 0 0.001 142 0 5 147
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 0 138 0 5 143
endosomal lumen acidification 0 0 0 138 0 5 143
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.025 0.017 -10000 0 0 168 168
GNAQ/ARNO 0.027 0.008 0.041 6 0 30 36
mol:Phosphatidic acid 0 0 0 106 0 3 109
PIP3-E 0.03 0.014 -10000 0 0 90 90
MET 0.023 0.018 -10000 0 0 190 190
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GIT1 0.037 0.003 -10000 0 0 3 3
mol:PI-4-5-P2 0 0 0.001 149 -0.001 5 154
GNA11 0.033 0.011 -10000 0 0 51 51
LHCGR 0.037 0.002 -10000 0 0 2 2
AGTR1 0.035 0.008 -10000 0 0 22 22
desensitization of G-protein coupled receptor protein signaling pathway 0.03 0.024 -10000 0 -0.14 7 7
IPCEF1/ARNO 0.007 0.044 -10000 0 -0.093 51 51
alphaIIb/beta3 Integrin 0.054 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.024 0.14 -10000 0 -0.28 54 54
MAP3K8 0.022 0.018 -10000 0 0 201 201
FOS 0.019 0.1 0.21 1 -0.32 19 20
PRKCA 0.029 0.026 -10000 0 -0.03 78 78
PTPN7 0.028 0.029 0.067 53 -0.03 90 143
HRAS 0.034 0.01 -10000 0 0 36 36
PRKCB 0 0.008 0.017 61 -0.012 79 140
NRAS 0.032 0.012 -10000 0 0 63 63
RAS family/GTP 0.043 0.067 -10000 0 -0.14 54 54
MAPK3 0.035 0.05 -10000 0 -0.3 2 2
MAP2K1 0.008 0.057 -10000 0 -0.22 13 13
ELK1 0.026 0.029 -10000 0 -0.04 81 81
BRAF 0.007 0.021 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.003 61 -0.004 80 141
MAPK1 0.008 0.12 -10000 0 -0.42 34 34
RAF1 -0.001 0.068 -10000 0 -0.34 17 17
KRAS 0.034 0.009 -10000 0 0 34 34
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.006 0.058 -10000 0 -0.15 61 61
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.096 0.21 13 -0.21 39 52
AP1 -0.01 0.076 0.089 17 -0.15 93 110
mol:PIP3 -0.024 0.05 -10000 0 -0.13 77 77
AKT1 0 0.094 0.2 21 -0.23 34 55
PTK2B -0.002 0.058 0.12 6 -0.15 58 64
RHOA 0.02 0.077 0.16 30 -0.32 12 42
PIK3CB 0.035 0.007 -10000 0 0 17 17
mol:Ca2+ -0.009 0.038 0.17 4 -0.14 19 23
MAGI3 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
apoptosis 0.002 0.063 0.1 36 -0.16 54 90
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
positive regulation of microtubule depolymerization -0.021 0.074 0.17 10 -0.2 47 57
NF kappa B1 p50/RelA -0.02 0.067 0.077 78 -0.17 54 132
endothelial cell migration -0.018 0.099 -10000 0 -0.3 54 54
ADCY4 -0.005 0.09 0.15 13 -0.25 38 51
ADCY5 -0.005 0.09 0.15 13 -0.25 38 51
ADCY6 0.001 0.091 0.15 18 -0.24 37 55
ADCY7 -0.002 0.096 0.16 17 -0.24 43 60
ADCY1 -0.009 0.081 0.15 10 -0.25 33 43
ADCY2 -0.001 0.093 0.16 15 -0.24 40 55
ADCY3 -0.005 0.09 0.15 13 -0.25 38 51
ADCY8 -0.002 0.091 0.15 20 -0.24 39 59
ADCY9 0 0.092 0.16 18 -0.24 40 58
GSK3B -0.009 0.065 0.18 7 -0.16 56 63
arachidonic acid secretion -0.018 0.11 0.15 15 -0.25 65 80
GNG2 0 0.001 0.002 1 -0.003 12 13
TRIP6 -0.017 0.085 -10000 0 -0.25 57 57
GNAO1 0.003 0.058 0.12 24 -0.16 48 72
HRAS 0.034 0.009 -10000 0 0 36 36
NFKBIA -0.017 0.084 0.18 15 -0.22 37 52
GAB1 0.033 0.011 -10000 0 0 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.21 -10000 0 -0.8 31 31
JUN 0.034 0.01 -10000 0 0 41 41
LPA/LPA2/NHERF2 0.019 0.029 -10000 0 -0.062 54 54
TIAM1 -0.013 0.25 -10000 0 -0.98 31 31
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 -0.008 0.037 0.17 3 -0.14 19 22
PLCB3 0.006 0.036 0.2 5 -0.063 52 57
FOS 0.025 0.017 -10000 0 0 162 162
positive regulation of mitosis -0.018 0.11 0.15 15 -0.25 65 80
LPA/LPA1-2-3 -0.008 0.041 -10000 0 -0.13 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -0.002 1 1
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.009 0.068 -10000 0 -0.28 10 10
GNAZ 0.002 0.064 0.12 28 -0.17 49 77
EGFR/PI3K-beta/Gab1 -0.02 0.054 -10000 0 -0.13 77 77
positive regulation of dendritic cell cytokine production -0.008 0.041 -10000 0 -0.12 54 54
LPA/LPA2/MAGI-3 -0.004 0.017 -10000 0 -0.052 54 54
ARHGEF1 0.037 0.12 0.19 150 -0.17 34 184
GNAI2 0.004 0.07 0.12 40 -0.18 54 94
GNAI3 0.006 0.064 0.12 39 -0.16 54 93
GNAI1 0.003 0.046 0.13 18 -0.16 28 46
LPA/LPA3 -0.006 0.021 -10000 0 -0.067 54 54
LPA/LPA2 -0.006 0.021 -10000 0 -0.066 54 54
LPA/LPA1 -0.012 0.055 -10000 0 -0.17 54 54
HB-EGF/EGFR -0.012 0.059 -10000 0 -0.14 77 77
HBEGF 0.011 0.046 0.094 114 -10000 0 114
mol:DAG -0.008 0.037 0.17 3 -0.14 19 22
cAMP biosynthetic process 0.001 0.11 0.18 37 -0.26 46 83
NFKB1 0.035 0.007 -10000 0 0 18 18
SRC 0.034 0.009 -10000 0 0 34 34
GNB1 0.035 0.007 -10000 0 0 20 20
LYN -0.023 0.096 0.17 19 -0.22 64 83
GNAQ 0.008 0.026 0.057 38 -0.058 56 94
LPAR2 0 0.001 0.002 1 -0.003 4 5
LPAR3 0 0.001 -10000 0 -0.002 8 8
LPAR1 -0.01 0.033 -10000 0 -0.11 54 54
IL8 -0.13 0.2 0.3 13 -0.4 158 171
PTK2 0.013 0.057 0.12 38 -0.14 50 88
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
CASP3 0.002 0.063 0.1 36 -0.16 54 90
EGFR 0.009 0.016 -10000 0 0 379 379
PLCG1 0.005 0.038 0.077 6 -0.13 24 30
PLD2 0.015 0.054 0.12 38 -0.12 53 91
G12/G13 0.019 0.063 -10000 0 -0.15 46 46
PI3K-beta -0.014 0.068 -10000 0 -0.22 32 32
cell migration -0.001 0.073 -10000 0 -0.25 28 28
SLC9A3R2 0.036 0.005 -10000 0 0 8 8
PXN 0.008 0.069 -10000 0 -0.29 10 10
HRAS/GTP -0.019 0.11 0.16 9 -0.26 62 71
RAC1 0.025 0.017 -10000 0 0 163 163
MMP9 0.017 0.018 -10000 0 0 280 280
PRKCE 0.036 0.003 -10000 0 0 3 3
PRKCD -0.004 0.054 0.19 14 -0.2 3 17
Gi(beta/gamma) -0.01 0.12 0.17 12 -0.27 58 70
mol:LPA -0.01 0.033 -10000 0 -0.11 54 54
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.08 -10000 0 -0.24 35 35
MAPKKK cascade -0.018 0.11 0.15 15 -0.25 65 80
contractile ring contraction involved in cytokinesis 0.02 0.079 0.17 27 -0.32 13 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.026 0.057 37 -0.058 56 93
GNA15 0.008 0.025 0.056 34 -0.058 52 86
GNA12 0.023 0.018 -10000 0 0 189 189
GNA13 0.035 0.007 -10000 0 0 20 20
MAPT -0.021 0.076 0.17 10 -0.19 58 68
GNA11 0.011 0.023 0.057 38 -0.058 35 73
Rac1/GTP -0.008 0.22 -10000 0 -0.85 31 31
MMP2 -0.018 0.1 -10000 0 -0.31 54 54
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.027 -10000 0 -0.051 59 59
CDKN2C -0.009 0.021 -10000 0 -0.037 109 109
CDKN2A 0.005 0.014 -10000 0 -10000 0 0
CCND2 -0.002 0.019 0.11 6 -10000 0 6
RB1 -0.046 0.092 0.16 2 -0.19 142 144
CDK4 -0.001 0.021 0.13 6 -10000 0 6
CDK6 -0.001 0.02 0.13 6 -10000 0 6
G1/S progression 0.056 0.098 0.19 163 -0.16 2 165
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.032 0.16 -10000 0 -0.46 43 43
Syndecan-4/Syndesmos -0.14 0.28 -10000 0 -0.73 63 63
positive regulation of JNK cascade -0.13 0.26 -10000 0 -0.61 77 77
Syndecan-4/ADAM12 -0.13 0.28 -10000 0 -0.74 62 62
CCL5 0.033 0.011 -10000 0 0 54 54
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
DNM2 0.035 0.008 -10000 0 0 27 27
ITGA5 0.033 0.012 -10000 0 0 58 58
SDCBP 0.035 0.007 -10000 0 0 21 21
PLG 0.029 0.024 -10000 0 -0.044 37 37
ADAM12 0.024 0.018 -10000 0 0 177 177
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.024 0.022 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.28 -10000 0 -0.73 63 63
Syndecan-4/CXCL12/CXCR4 -0.14 0.28 -10000 0 -0.66 77 77
Syndecan-4/Laminin alpha3 -0.12 0.29 -10000 0 -0.73 63 63
MDK 0.03 0.014 -10000 0 0 92 92
Syndecan-4/FZD7 -0.14 0.3 -10000 0 -0.64 92 92
Syndecan-4/Midkine -0.13 0.3 -10000 0 -0.67 80 80
FZD7 0.026 0.017 -10000 0 0 143 143
Syndecan-4/FGFR1/FGF -0.096 0.28 -10000 0 -0.69 60 60
THBS1 0.03 0.014 -10000 0 0 92 92
integrin-mediated signaling pathway -0.13 0.28 -10000 0 -0.63 83 83
positive regulation of MAPKKK cascade -0.13 0.26 -10000 0 -0.61 77 77
Syndecan-4/TACI -0.12 0.29 -10000 0 -0.74 63 63
CXCR4 0.029 0.015 -10000 0 0 103 103
cell adhesion -0.01 0.055 0.21 3 -0.25 18 21
Syndecan-4/Dynamin -0.12 0.29 -10000 0 -0.72 63 63
Syndecan-4/TSP1 -0.13 0.28 -10000 0 -0.75 61 61
Syndecan-4/GIPC -0.12 0.29 -10000 0 -0.72 63 63
Syndecan-4/RANTES -0.13 0.29 -10000 0 -0.73 63 63
ITGB1 0.026 0.017 -10000 0 0 144 144
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.033 0.011 -10000 0 0 48 48
RAC1 0.025 0.017 -10000 0 0 163 163
PRKCA 0.004 0.12 1 6 -10000 0 6
Syndecan-4/alpha-Actinin -0.13 0.3 -10000 0 -0.65 85 85
TFPI 0.029 0.015 -10000 0 0 103 103
F2 0.01 0.042 -10000 0 -0.044 183 183
alpha5/beta1 Integrin 0.028 0.043 -10000 0 -0.14 21 21
positive regulation of cell adhesion -0.13 0.27 -10000 0 -0.7 63 63
ACTN1 0.028 0.016 -10000 0 0 119 119
TNC 0.028 0.016 -10000 0 0 121 121
Syndecan-4/CXCL12 -0.14 0.28 -10000 0 -0.74 62 62
FGF6 0.035 0.008 -10000 0 0 28 28
RHOA 0.035 0.007 -10000 0 0 21 21
CXCL12 0.022 0.018 -10000 0 0 206 206
TNFRSF13B 0.036 0.005 -10000 0 0 9 9
FGF2 0.035 0.008 -10000 0 0 25 25
FGFR1 0.036 0.005 -10000 0 0 9 9
Syndecan-4/PI-4-5-P2 -0.14 0.28 -10000 0 -0.73 63 63
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.028 0.025 -10000 0 -0.045 41 41
cell migration -0.011 0.016 -10000 0 -10000 0 0
PRKCD 0.028 0.024 -10000 0 -0.044 37 37
vasculogenesis -0.13 0.27 -10000 0 -0.7 62 62
SDC4 -0.14 0.3 -10000 0 -0.8 62 62
Syndecan-4/Tenascin C -0.13 0.3 -10000 0 -0.67 82 82
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.12 0.29 -10000 0 -0.74 64 64
MMP9 0.011 0.024 -10000 0 -0.042 39 39
Rac1/GTP -0.01 0.057 0.21 3 -0.26 18 21
cytoskeleton organization -0.13 0.26 -10000 0 -0.69 64 64
GIPC1 0.035 0.008 -10000 0 0 24 24
Syndecan-4/TFPI -0.13 0.29 -10000 0 -0.7 71 71
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.005 0.11 0.24 51 -10000 0 51
GNAI2 0.034 0.01 -10000 0 0 44 44
S1P/S1P5/G12 0.01 0.031 -10000 0 -0.11 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
RhoA/GTP 0.005 0.11 -10000 0 -0.24 51 51
negative regulation of cAMP metabolic process -0.008 0.099 -10000 0 -0.2 83 83
GNAZ 0.031 0.013 -10000 0 0 80 80
GNAI3 0.036 0.006 -10000 0 0 14 14
GNA12 0.023 0.018 -10000 0 0 189 189
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.009 0.1 -10000 0 -0.2 83 83
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
RHOA 0.035 0.007 -10000 0 0 21 21
GNAI1 0.018 0.018 -10000 0 0 262 262
Nongenotropic Androgen signaling

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
PTK2 -0.011 0.003 0 34 -10000 0 34
GNB1/GNG2 0.039 0.031 -10000 0 -0.11 20 20
regulation of S phase of mitotic cell cycle -0.004 0.08 -10000 0 -0.19 69 69
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.01 -10000 0 0 36 36
SHBG/T-DHT 0.024 0.004 -10000 0 -10000 0 0
PELP1 0.035 0.007 -10000 0 0 17 17
AKT1 -0.01 0.004 0 54 -10000 0 54
MAP2K1 -0.029 0.083 0.18 29 -0.18 69 98
T-DHT/AR 0.025 0.009 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.003 61 -0.006 79 140
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
GNAI1 0.018 0.018 -10000 0 0 262 262
mol:GDP -0.019 0.036 -10000 0 -0.15 15 15
cell proliferation -0.053 0.19 0.27 17 -0.41 86 103
PIK3CA 0.031 0.014 -10000 0 0 82 82
FOS -0.084 0.28 0.32 7 -0.69 84 91
mol:Ca2+ -0.004 0.02 0.031 1 -0.054 60 61
MAPK3 -0.037 0.14 0.26 17 -0.3 75 92
MAPK1 -0.036 0.16 0.24 5 -0.37 60 65
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0 0.002 0.003 59 -0.004 77 136
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 77 136
HRAS/GTP 0.041 0.066 -10000 0 -0.096 72 72
actin cytoskeleton reorganization 0.02 0.054 -10000 0 -0.12 43 43
SRC 0.034 0.009 -10000 0 0 34 34
voltage-gated calcium channel activity 0 0.002 0.003 59 -0.004 77 136
PI3K 0.019 0.064 -10000 0 -0.13 72 72
apoptosis 0.043 0.19 0.42 85 -0.26 13 98
T-DHT/AR/PELP1 0.043 0.025 -10000 0 -0.11 8 8
HRAS/GDP 0.01 0.062 -10000 0 -0.18 17 17
CREB1 -0.064 0.19 0.26 13 -0.45 86 99
RAC1-CDC42/GTP 0.028 0.06 -10000 0 -0.13 43 43
AR 0.035 0.008 -10000 0 0 22 22
GNB1 0.035 0.007 -10000 0 0 20 20
RAF1 -0.02 0.078 0.19 29 -0.22 14 43
RAC1-CDC42/GDP 0.022 0.054 -10000 0 -0.17 12 12
T-DHT/AR/PELP1/Src 0.058 0.034 -10000 0 -0.1 9 9
MAP2K2 -0.032 0.076 0.17 20 -0.17 66 86
T-DHT/AR/PELP1/Src/PI3K -0.004 0.081 -10000 0 -0.19 69 69
GNAZ 0.031 0.013 -10000 0 0 80 80
SHBG 0.036 0.006 -10000 0 0 15 15
Gi family/GNB1/GNG2/GDP -0.038 0.17 -10000 0 -0.48 48 48
mol:T-DHT 0 0.001 0.002 1 -0.004 25 26
RAC1 0.025 0.017 -10000 0 0 163 163
GNRH1 -0.011 0.002 0 12 -10000 0 12
Gi family/GTP -0.006 0.083 -10000 0 -0.19 62 62
CDC42 0.035 0.008 -10000 0 0 26 26
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
CDC42/GTP 0.005 0.11 -10000 0 -0.27 39 39
PLCG1 -0.012 0.095 0.12 5 -0.2 84 89
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
G12/G13 0.025 0.048 -10000 0 -0.14 28 28
cell migration 0.005 0.1 -10000 0 -0.27 39 39
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.013 0.098 0.12 4 -0.2 89 93
MAPK1 -0.006 0.092 0.12 5 -0.19 79 84
S1P/S1P5/Gi -0.009 0.1 -10000 0 -0.2 83 83
GNAI1 0.018 0.018 -10000 0 0 262 262
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.031 -10000 0 -0.11 28 28
RHOA 0.041 0.1 0.19 156 -0.18 2 158
S1P/S1P4/Gi -0.009 0.1 -10000 0 -0.2 83 83
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.031 0.013 -10000 0 0 80 80
S1P/S1P4/G12/G13 0.023 0.038 -10000 0 -0.1 28 28
GNA12 0.023 0.018 -10000 0 0 189 189
GNA13 0.035 0.007 -10000 0 0 20 20
CDC42 0.035 0.008 -10000 0 0 26 26
Syndecan-1-mediated signaling events

Figure 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 54 54
SDCBP 0.035 0.007 -10000 0 0 21 21
FGFR/FGF2/Syndecan-1 0.015 0.1 0.21 24 -0.25 11 35
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 0.018 0.11 0.22 18 -0.25 13 31
Syndecan-1/Syntenin 0.026 0.11 0.24 24 -0.24 15 39
MAPK3 0.005 0.1 0.2 20 -0.24 20 40
HGF/MET 0.032 0.027 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.012 -10000 0 0 66 66
BSG 0.032 0.012 -10000 0 0 62 62
keratinocyte migration 0.018 0.1 0.22 18 -0.24 13 31
Syndecan-1/RANTES 0.021 0.11 0.25 17 -0.25 12 29
Syndecan-1/CD147 0.026 0.12 0.24 14 -0.25 16 30
Syndecan-1/Syntenin/PIP2 0.024 0.11 0.22 24 -0.24 15 39
LAMA5 0.032 0.012 -10000 0 0 66 66
positive regulation of cell-cell adhesion 0.023 0.11 0.22 24 -0.23 15 39
MMP7 0.027 0.016 -10000 0 0 138 138
HGF 0.024 0.018 -10000 0 0 177 177
Syndecan-1/CASK -0.001 0.087 0.15 5 -0.24 12 17
Syndecan-1/HGF/MET 0.024 0.09 0.26 7 -0.25 6 13
regulation of cell adhesion -0.003 0.11 0.24 29 -0.25 16 45
HPSE 0.032 0.012 -10000 0 0 59 59
positive regulation of cell migration 0.015 0.1 0.21 24 -0.25 11 35
SDC1 0.012 0.097 0.17 36 -0.25 11 47
Syndecan-1/Collagen 0.015 0.1 0.21 24 -0.25 11 35
PPIB 0.034 0.009 -10000 0 0 36 36
MET 0.023 0.018 -10000 0 0 190 190
PRKACA 0.035 0.008 -10000 0 0 24 24
MMP9 0.017 0.018 -10000 0 0 280 280
MAPK1 0.004 0.1 0.2 18 -0.25 16 34
homophilic cell adhesion 0.017 0.1 0.22 28 -0.25 11 39
MMP1 0.032 0.013 -10000 0 0 72 72
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.012 -10000 0 0 62 62
LAT2 -0.016 0.094 0.14 2 -0.28 48 50
AP1 -0.062 0.18 -10000 0 -0.39 74 74
mol:PIP3 0.021 0.14 0.26 37 -0.28 46 83
IKBKB 0.011 0.094 0.19 36 -0.19 39 75
AKT1 -0.055 0.1 0.24 12 -0.27 46 58
IKBKG 0.01 0.093 0.19 33 -0.19 38 71
MS4A2 0.039 0.007 0.065 4 0 4 8
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.013 -10000 0 0 82 82
MAP3K1 -0.023 0.12 0.23 9 -0.31 52 61
mol:Ca2+ 0.022 0.12 0.23 42 -0.22 46 88
LYN 0.03 0.015 -10000 0 -0.003 80 80
CBLB -0.022 0.11 0.15 3 -0.28 67 70
SHC1 0.033 0.011 -10000 0 0 52 52
RasGAP/p62DOK 0.048 0.053 -10000 0 -0.12 37 37
positive regulation of cell migration -0.011 0.003 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.032 0.072 0.26 15 -0.17 12 27
PTPN13 -0.036 0.19 -10000 0 -0.6 39 39
PTPN11 0.031 0.022 -10000 0 -0.035 47 47
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.036 0.11 0.24 8 -0.32 39 47
SYK 0.03 0.015 -10000 0 -0.033 7 7
GRB2 0.036 0.007 -10000 0 0 18 18
LAT/PLCgamma1/GRB2/SLP76/GADs 0.011 0.12 0.21 6 -0.27 55 61
LAT -0.021 0.11 0.16 2 -0.28 65 67
PAK2 -0.023 0.13 0.21 10 -0.32 55 65
NFATC2 -0.013 0.013 -10000 0 -0.043 72 72
HRAS -0.021 0.14 0.19 14 -0.32 65 79
GAB2 0.033 0.011 -10000 0 0 48 48
PLA2G1B -0.007 0.19 -10000 0 -0.91 20 20
Fc epsilon R1 0.042 0.068 -10000 0 -0.11 73 73
Antigen/IgE/Fc epsilon R1 0.044 0.061 -10000 0 -0.096 72 72
mol:GDP -0.013 0.14 0.21 10 -0.35 54 64
JUN 0.034 0.01 -10000 0 0 41 41
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
FOS 0.025 0.017 -10000 0 0 162 162
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.12 -10000 0 -0.28 73 73
CHUK 0.011 0.091 0.19 36 -0.18 40 76
KLRG1 -0.018 0.099 0.13 8 -0.22 80 88
VAV1 -0.021 0.11 0.16 4 -0.27 64 68
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.023 0.11 0.16 2 -0.28 68 70
negative regulation of mast cell degranulation -0.021 0.092 0.12 2 -0.22 71 73
BTK -0.012 0.14 -10000 0 -0.37 46 46
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.18 145 145
GAB2/PI3K/SHP2 -0.069 0.075 -10000 0 -0.2 88 88
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.005 0.078 -10000 0 -0.2 62 62
RAF1 -0.007 0.2 -10000 0 -0.97 20 20
Fc epsilon R1/FcgammaRIIB/SHIP 0.023 0.097 -10000 0 -0.13 130 130
FCER1G 0.029 0.016 -10000 0 0 113 113
FCER1A 0.033 0.013 -10000 0 -0.032 9 9
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.083 -10000 0 -0.11 102 102
MAPK3 -0.005 0.19 -10000 0 -0.9 20 20
MAPK1 -0.014 0.2 -10000 0 -0.95 20 20
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.13 0.28 -10000 0 -0.55 148 148
DUSP1 0.031 0.013 -10000 0 0 76 76
NF-kappa-B/RelA 0.018 0.066 0.14 34 -0.13 40 74
actin cytoskeleton reorganization -0.027 0.2 -10000 0 -0.6 37 37
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.011 0.15 0.23 8 -0.31 71 79
FER -0.021 0.12 0.16 3 -0.27 71 74
RELA 0.036 0.004 -10000 0 0 7 7
ITK 0.003 0.037 -10000 0 -0.3 2 2
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.002 0.14 0.24 16 -0.31 61 77
cytokine secretion 0.01 0.046 0.087 29 -0.088 51 80
SPHK1 -0.019 0.12 0.15 4 -0.28 66 70
PTK2 -0.03 0.2 -10000 0 -0.64 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.028 0.13 0.24 15 -0.28 50 65
EDG1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG 0.002 0.15 0.25 31 -0.3 59 90
MAP2K2 -0.006 0.19 -10000 0 -0.92 20 20
MAP2K1 -0.017 0.18 -10000 0 -0.92 20 20
MAP2K7 0.035 0.007 -10000 0 0 22 22
KLRG1/SHP2 0.002 0.098 0.2 10 -0.23 55 65
MAP2K4 0.024 0.14 -10000 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.025 0.1 -10000 0 -0.14 130 130
mol:Choline -0.032 0.071 0.25 15 -0.17 12 27
SHC/Grb2/SOS1 0.012 0.13 0.2 1 -0.27 68 69
FYN 0.03 0.014 -10000 0 0 88 88
DOK1 0.037 0.002 -10000 0 0 2 2
PXN -0.031 0.19 -10000 0 -0.58 38 38
HCLS1 -0.025 0.13 0.16 7 -0.32 67 74
PRKCB 0.013 0.12 0.22 36 -0.23 52 88
FCGR2B 0.02 0.018 -10000 0 0 226 226
IGHE -0.001 0.004 0.02 3 -10000 0 3
KLRG1/SHIP -0.022 0.094 0.12 2 -0.22 71 73
LCP2 0.032 0.013 -10000 0 0 75 75
PLA2G4A -0.016 0.12 0.16 10 -0.31 61 71
RASA1 0.035 0.009 -10000 0 0 30 30
mol:Phosphatidic acid -0.032 0.071 0.25 15 -0.17 12 27
IKK complex 0.008 0.079 0.18 28 -0.16 22 50
WIPF1 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.068 0.06 -10000 0 -0.12 33 33
MAP4K1 0.035 0.008 -10000 0 0 27 27
MAP3K8 0.022 0.018 -10000 0 0 200 200
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.035 0.008 -10000 0 0 28 28
MAP3K1 -0.001 0.055 0.13 1 -0.16 44 45
JUN -0.14 0.24 -10000 0 -0.52 143 143
MAP3K7 -0.001 0.053 -10000 0 -0.17 38 38
GRAP2 0.034 0.01 -10000 0 0 37 37
CRK 0.035 0.008 -10000 0 0 23 23
MAP2K4 -0.016 0.071 0.15 1 -0.24 25 26
LAT 0.036 0.005 -10000 0 0 9 9
LCP2 0.031 0.013 -10000 0 0 75 75
MAPK8 -0.14 0.25 -10000 0 -0.54 143 143
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.009 0.06 -10000 0 -0.16 46 46
LAT/GRAP2/SLP76/HPK1/HIP-55 0.063 0.056 -10000 0 -0.11 33 33
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.028 0.087 -10000 0 -0.14 90 90
alphaM/beta2 Integrin/GPIbA 0.048 0.071 -10000 0 -0.12 62 62
alphaM/beta2 Integrin/proMMP-9 -0.01 0.091 -10000 0 -0.14 139 139
PLAUR 0.03 0.014 -10000 0 0 90 90
HMGB1 0.039 0.014 0.083 1 -10000 0 1
alphaM/beta2 Integrin/Talin 0.038 0.073 -10000 0 -0.13 57 57
AGER 0.041 0.01 0.08 2 -10000 0 2
RAP1A 0.036 0.005 -10000 0 0 10 10
SELPLG 0.036 0.004 -10000 0 0 7 7
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.075 0.086 -10000 0 -0.12 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.017 0.018 -10000 0 0 280 280
CYR61 0.025 0.017 -10000 0 0 166 166
TLN1 0.029 0.015 -10000 0 0 101 101
Rap1/GTP 0.028 0.072 -10000 0 -0.22 18 18
RHOA 0.035 0.007 -10000 0 0 21 21
P-selectin oligomer 0.036 0.006 -10000 0 0 15 15
MYH2 0.024 0.072 0.19 3 -0.27 8 11
MST1R 0.035 0.008 -10000 0 0 23 23
leukocyte activation during inflammatory response 0.055 0.066 -10000 0 -0.11 57 57
APOB 0.036 0.006 -10000 0 0 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.029 0.015 -10000 0 0 109 109
JAM3 0.033 0.011 -10000 0 0 52 52
GP1BA 0.036 0.005 -10000 0 0 10 10
alphaM/beta2 Integrin/CTGF 0.02 0.088 -10000 0 -0.13 104 104
alphaM/beta2 Integrin 0.023 0.075 0.17 1 -0.24 17 18
JAM3 homodimer 0.033 0.011 -10000 0 0 52 52
ICAM2 0.034 0.009 -10000 0 0 32 32
ICAM1 0.031 0.014 -10000 0 0 83 83
phagocytosis triggered by activation of immune response cell surface activating receptor 0.024 0.076 0.17 1 -0.23 18 19
cell adhesion 0.047 0.07 -10000 0 -0.12 62 62
NFKB1 -0.003 0.08 0.22 16 -10000 0 16
THY1 0.031 0.014 -10000 0 0 82 82
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Lipoprotein(a) 0.045 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.037 0.1 -10000 0 -0.15 102 102
IL6 -0.016 0.039 -10000 0 -10000 0 0
ITGB2 0.033 0.019 0.078 1 -10000 0 1
elevation of cytosolic calcium ion concentration 0.026 0.09 -10000 0 -0.15 72 72
alphaM/beta2 Integrin/JAM2/JAM3 0.048 0.1 -10000 0 -0.15 89 89
JAM2 0.033 0.012 -10000 0 0 57 57
alphaM/beta2 Integrin/ICAM1 0.076 0.078 -10000 0 -0.12 47 47
alphaM/beta2 Integrin/uPA/Plg 0.036 0.085 -10000 0 -0.13 66 66
RhoA/GTP 0.029 0.073 0.19 3 -0.28 8 11
positive regulation of phagocytosis 0.016 0.1 0.19 2 -0.25 45 47
Ron/MSP 0.051 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.027 0.092 -10000 0 -0.15 72 72
alphaM/beta2 Integrin/uPAR 0.036 0.079 -10000 0 -0.14 68 68
PLAU 0.019 0.018 -10000 0 0 239 239
PLAT 0.027 0.016 -10000 0 0 129 129
actin filament polymerization 0.027 0.073 0.21 6 -0.26 8 14
MST1 0.035 0.008 -10000 0 0 27 27
alphaM/beta2 Integrin/lipoprotein(a) 0.062 0.07 -10000 0 -0.11 57 57
TNF 0.005 0.089 0.21 19 -10000 0 19
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.017 0.075 -10000 0 -0.14 68 68
fibrinolysis 0.035 0.083 -10000 0 -0.13 66 66
HCK 0.027 0.016 -10000 0 0 141 141
dendritic cell antigen processing and presentation 0.024 0.076 0.17 1 -0.23 18 19
VTN 0.036 0.004 -10000 0 0 5 5
alphaM/beta2 Integrin/CYR61 0.01 0.095 -10000 0 -0.14 125 125
LPA 0.034 0.009 -10000 0 0 33 33
LRP1 0.032 0.013 -10000 0 0 70 70
cell migration -0.001 0.11 0.16 12 -0.15 146 158
FN1 0.035 0.009 -10000 0 0 30 30
alphaM/beta2 Integrin/Thy1 0.029 0.087 -10000 0 -0.14 92 92
MPO 0.036 0.004 -10000 0 0 6 6
KNG1 0.035 0.008 -10000 0 0 28 28
RAP1/GDP 0.024 0.007 -10000 0 -0.11 1 1
ROCK1 0.024 0.073 0.19 3 -0.27 10 13
ELA2 0.035 0.008 -10000 0 0 28 28
PLG 0.034 0.009 -10000 0 0 35 35
CTGF 0.027 0.016 -10000 0 0 139 139
alphaM/beta2 Integrin/Hck 0.029 0.092 -10000 0 -0.18 69 69
ITGAM 0.042 0.01 0.08 2 -10000 0 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.074 -10000 0 -0.12 56 56
HP 0.027 0.016 -10000 0 0 137 137
leukocyte adhesion 0.021 0.12 -10000 0 -0.26 36 36
SELP 0.036 0.006 -10000 0 0 15 15
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.033 0.014 -10000 0 -0.005 57 57
ELF1 0.042 0.016 -10000 0 -10000 0 0
CCNA2 0.028 0.016 -10000 0 0 118 118
PIK3CA 0.03 0.015 -10000 0 -0.002 89 89
JAK3 0.034 0.012 -10000 0 -0.008 34 34
PIK3R1 0.032 0.014 -10000 0 -0.002 68 68
JAK1 0.034 0.012 -10000 0 -0.004 46 46
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.02 0.18 0.24 2 -0.53 39 41
SHC1 0.032 0.014 -10000 0 -0.004 60 60
SP1 -0.01 0.12 -10000 0 -0.27 87 87
IL2RA 0.011 0.012 -10000 0 -10000 0 0
IL2RB 0.032 0.014 -10000 0 -0.004 61 61
SOS1 0 0.002 -10000 0 -10000 0 0
IL2RG 0.035 0.011 -10000 0 -0.006 30 30
G1/S transition of mitotic cell cycle -0.068 0.27 0.27 12 -0.58 95 107
PTPN11 0.035 0.01 -10000 0 -0.012 18 18
CCND2 -0.072 0.19 -10000 0 -0.5 87 87
LCK 0.035 0.01 -10000 0 -0.008 25 25
GRB2 0.035 0.01 -10000 0 -0.008 25 25
IL2 0.036 0.009 -10000 0 -0.013 16 16
CDK6 0.024 0.018 -10000 0 0 177 177
CCND3 -0.026 0.2 0.36 3 -0.75 27 30
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.013 0.062 0.14 2 -0.13 70 72
EPHB2 0.034 0.01 -10000 0 0 40 40
Syndecan-2/TACI 0.017 0.056 0.14 2 -0.12 66 68
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.021 0.074 -10000 0 -0.12 84 84
HRAS 0.034 0.009 -10000 0 0 36 36
Syndecan-2/CASK -0.009 0.042 -10000 0 -0.11 69 69
ITGA5 0.033 0.012 -10000 0 0 58 58
BAX -0.008 0.073 -10000 0 -0.9 3 3
EPB41 0.036 0.005 -10000 0 0 10 10
positive regulation of cell-cell adhesion 0.012 0.055 -10000 0 -0.12 73 73
LAMA3 0.033 0.011 -10000 0 0 48 48
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.018 -10000 0 0 245 245
Syndecan-2/MMP2 0.008 0.063 0.14 1 -0.14 66 67
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.018 0.055 -10000 0 -0.14 42 42
dendrite morphogenesis 0.016 0.054 0.14 2 -0.12 61 63
Syndecan-2/GM-CSF 0.017 0.056 0.14 2 -0.12 65 67
determination of left/right symmetry 0.007 0.023 0.086 5 -0.24 4 9
Syndecan-2/PKC delta 0.016 0.055 0.14 1 -0.12 62 63
GNB2L1 0.037 0.002 -10000 0 0 2 2
MAPK3 -0.023 0.051 0.12 34 -0.19 4 38
MAPK1 -0.022 0.053 0.12 31 -0.2 9 40
Syndecan-2/RACK1 0.029 0.065 0.14 3 -0.11 78 81
NF1 0.036 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.023 0.086 5 -0.24 4 9
ITGA2 0.029 0.015 -10000 0 0 112 112
MAPK8 -0.004 0.038 0.13 3 -0.39 3 6
Syndecan-2/alpha2/beta1 Integrin 0.007 0.064 0.14 1 -0.11 92 93
Syndecan-2/Kininogen 0.017 0.055 0.14 2 -0.12 63 65
ITGB1 0.026 0.017 -10000 0 0 144 144
SRC -0.026 0.052 0.17 11 -0.19 8 19
Syndecan-2/CASK/Protein 4.1 0.015 0.05 -10000 0 -0.11 68 68
extracellular matrix organization 0.014 0.053 0.14 1 -0.12 57 58
actin cytoskeleton reorganization 0.013 0.062 0.14 2 -0.13 70 72
Syndecan-2/Caveolin-2/Ras 0.006 0.068 0.15 1 -0.13 78 79
Syndecan-2/Laminin alpha3 0.016 0.053 0.14 1 -0.12 61 62
Syndecan-2/RasGAP 0.036 0.08 -10000 0 -0.12 91 91
alpha5/beta1 Integrin 0.028 0.043 -10000 0 -0.14 21 21
PRKCD 0.034 0.01 -10000 0 0 40 40
Syndecan-2 dimer 0.016 0.054 0.14 2 -0.12 61 63
GO:0007205 0.001 0.01 -10000 0 -0.11 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.013 0.067 0.19 2 -0.13 75 77
RHOA 0.035 0.007 -10000 0 0 21 21
SDCBP 0.035 0.007 -10000 0 0 21 21
TNFRSF13B 0.036 0.005 -10000 0 0 9 9
RASA1 0.035 0.009 -10000 0 0 30 30
alpha2/beta1 Integrin 0.018 0.055 -10000 0 -0.14 42 42
Syndecan-2/Synbindin 0.016 0.06 0.14 2 -0.13 67 69
TGFB1 0.032 0.012 -10000 0 0 66 66
CASP3 -0.018 0.055 0.12 32 -0.18 10 42
FN1 0.035 0.009 -10000 0 0 30 30
Syndecan-2/IL8 -0.004 0.07 -10000 0 -0.18 62 62
SDC2 0.007 0.023 0.086 5 -0.24 4 9
KNG1 0.035 0.008 -10000 0 0 28 28
Syndecan-2/Neurofibromin 0.017 0.057 0.14 2 -0.12 68 70
TRAPPC4 0.036 0.006 -10000 0 0 16 16
CSF2 0.036 0.005 -10000 0 0 8 8
Syndecan-2/TGFB1 0.014 0.053 0.14 1 -0.12 57 58
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.055 -10000 0 -0.12 73 73
Syndecan-2/Ezrin 0.014 0.054 -10000 0 -0.11 70 70
PRKACA -0.021 0.052 0.12 35 -0.19 4 39
angiogenesis -0.004 0.07 -10000 0 -0.18 62 62
MMP2 0.029 0.015 -10000 0 0 109 109
IL8 0.019 0.018 -10000 0 0 244 244
calcineurin-NFAT signaling pathway 0.017 0.056 0.14 2 -0.12 66 68
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.046 0.081 0.32 3 -10000 0 3
CRKL 0.042 0.089 0.16 173 -10000 0 173
mol:DAG 0.017 0.061 0.2 3 -0.19 26 29
HRAS 0.041 0.098 0.23 56 -0.19 2 58
MAPK8 0.01 0.074 0.16 78 -10000 0 78
RAP1A 0.048 0.093 0.17 157 -10000 0 157
GAB1 0.039 0.086 0.16 160 -10000 0 160
MAPK14 0.032 0.1 0.17 149 -10000 0 149
EPO 0.027 0.02 -10000 0 -0.033 2 2
PLCG1 0.017 0.061 0.2 3 -0.19 26 29
EPOR/TRPC2/IP3 Receptors 0.042 0.013 -10000 0 -0.033 2 2
RAPGEF1 0.035 0.007 -10000 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.051 0.038 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.062 0.071 0.21 29 -10000 0 29
EPO/EPOR (dimer) 0.039 0.03 -10000 0 -10000 0 0
IRS2 0.037 0.088 0.16 152 -0.16 4 156
STAT1 0.02 0.066 0.22 6 -0.19 27 33
STAT5B 0.02 0.066 0.21 6 -0.19 28 34
cell proliferation 0.007 0.074 0.16 80 -10000 0 80
GAB1/SHIP/PIK3R1/SHP2/SHC 0.039 0.063 0.16 3 -0.18 6 9
TEC 0.047 0.093 0.16 184 -10000 0 184
SOCS3 0.036 0.005 -10000 0 0 8 8
STAT1 (dimer) 0.021 0.066 0.22 7 -0.19 27 34
JAK2 0.037 0.018 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
EPO/EPOR (dimer)/JAK2 0.048 0.053 0.22 11 -10000 0 11
EPO/EPOR 0.039 0.03 -10000 0 -10000 0 0
LYN 0.033 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.059 0.07 0.21 34 -10000 0 34
elevation of cytosolic calcium ion concentration 0.042 0.013 -10000 0 -0.033 2 2
SHC1 0.033 0.011 -10000 0 0 52 52
EPO/EPOR (dimer)/LYN 0.041 0.059 -10000 0 -0.13 29 29
mol:IP3 0.017 0.061 0.2 3 -0.19 26 29
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.021 0.094 0.16 135 -0.17 12 147
SH2B3 -0.001 0.006 0.026 8 -10000 0 8
NFKB1 0.032 0.099 0.17 146 -10000 0 146
EPO/EPOR (dimer)/JAK2/SOCS3 0.015 0.015 -10000 0 -10000 0 0
PTPN6 0.046 0.092 0.17 161 -10000 0 161
TEC/VAV2/GRB2 0.082 0.07 0.23 34 -10000 0 34
EPOR 0.042 0.013 -10000 0 -0.033 2 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.061 0.071 0.21 29 -10000 0 29
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.032 0.012 -10000 0 0 63 63
CRKL/CBL/C3G 0.08 0.066 0.22 28 -10000 0 28
VAV2 0.045 0.092 0.16 173 -10000 0 173
CBL 0.046 0.092 0.16 150 -10000 0 150
SHC/Grb2/SOS1 0.023 0.035 -10000 0 -0.11 8 8
STAT5A 0.02 0.065 0.21 5 -0.19 27 32
GRB2 0.035 0.007 -10000 0 0 18 18
STAT5 (dimer) 0.036 0.072 0.27 5 -0.21 7 12
LYN/PLCgamma2 0.025 0.074 -10000 0 -0.18 55 55
PTPN11 0.036 0.005 -10000 0 0 11 11
BTK 0.045 0.093 0.16 182 -10000 0 182
BCL2 0.047 0.082 0.32 1 -10000 0 1
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 0.61 0.76 36 -1 129 165
IL23A 0.091 0.37 0.79 20 -0.98 20 40
NF kappa B1 p50/RelA/I kappa B alpha 0.082 0.34 0.62 31 -0.82 25 56
positive regulation of T cell mediated cytotoxicity 0.092 0.4 0.78 37 -0.91 25 62
ITGA3 0.09 0.36 0.75 23 -0.86 24 47
IL17F 0.036 0.27 0.52 33 -0.58 27 60
IL12B 0.061 0.081 0.2 69 -0.075 2 71
STAT1 (dimer) 0.072 0.36 0.65 36 -0.89 25 61
CD4 0.073 0.42 0.74 37 -1 33 70
IL23 0.098 0.36 0.74 16 -0.94 21 37
IL23R 0.068 0.14 0.29 90 -0.15 10 100
IL1B 0.085 0.4 0.76 30 -1.1 26 56
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.099 0.36 0.7 33 -0.84 21 54
TYK2 0.042 0.06 0.15 49 -10000 0 49
STAT4 0.035 0.009 -10000 0 0 29 29
STAT3 0.034 0.01 -10000 0 0 37 37
IL18RAP 0.035 0.008 -10000 0 -0.01 13 13
IL12RB1 0.045 0.06 0.15 52 -10000 0 52
PIK3CA 0.031 0.014 -10000 0 0 82 82
IL12Rbeta1/TYK2 0.055 0.076 0.19 37 -0.14 11 48
IL23R/JAK2 0.1 0.17 0.4 72 -0.19 16 88
positive regulation of chronic inflammatory response 0.092 0.4 0.78 37 -0.91 25 62
natural killer cell activation -0.005 0.011 -10000 0 -0.032 39 39
JAK2 0.056 0.081 0.2 68 -10000 0 68
PIK3R1 0.032 0.012 -10000 0 0 63 63
NFKB1 0.039 0.009 0.068 2 -10000 0 2
RELA 0.04 0.008 0.068 2 0 7 9
positive regulation of dendritic cell antigen processing and presentation 0.099 0.35 0.73 18 -0.89 21 39
ALOX12B 0.087 0.36 0.7 32 -0.83 24 56
CXCL1 0.097 0.37 0.77 32 -0.83 24 56
T cell proliferation 0.092 0.4 0.78 37 -0.91 25 62
NFKBIA 0.036 0.014 0.068 2 0 57 59
IL17A 0.06 0.24 0.46 52 -0.46 28 80
PI3K 0.048 0.35 0.65 21 -0.86 25 46
IFNG 0.019 0.034 0.099 29 -0.08 6 35
STAT3 (dimer) 0.049 0.34 0.62 28 -0.82 27 55
IL18R1 0.035 0.008 -10000 0 -0.015 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.096 0.27 0.56 51 -0.51 18 69
IL18/IL18R 0.062 0.036 -10000 0 -0.12 7 7
macrophage activation -0.002 0.016 0.039 1 -0.043 14 15
TNF 0.093 0.36 0.73 29 -0.88 22 51
STAT3/STAT4 0.071 0.36 0.62 30 -0.86 26 56
STAT4 (dimer) 0.072 0.36 0.64 31 -0.89 25 56
IL18 0.031 0.013 -10000 0 0 75 75
IL19 0.1 0.36 0.71 30 -0.84 21 51
STAT5A (dimer) 0.086 0.37 0.65 36 -0.88 25 61
STAT1 0.034 0.01 -10000 0 0 40 40
SOCS3 0.036 0.005 -10000 0 0 8 8
CXCL9 0.1 0.36 0.75 32 -0.83 24 56
MPO 0.089 0.36 0.76 19 -0.88 18 37
positive regulation of humoral immune response 0.092 0.4 0.78 37 -0.91 25 62
IL23/IL23R/JAK2/TYK2 0.09 0.4 0.78 37 -0.95 24 61
IL6 0.15 0.37 0.76 44 -0.86 19 63
STAT5A 0.036 0.004 -10000 0 0 5 5
IL2 0.02 0.032 0.076 1 -0.035 123 124
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.032 39 39
CD3E 0.088 0.36 0.69 37 -0.82 25 62
keratinocyte proliferation 0.092 0.4 0.78 37 -0.91 25 62
NOS2 0.089 0.36 0.69 38 -0.82 25 63
Glypican 2 network

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.002 0.079 0.19 3 -0.19 39 42
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.12 0.25 1 -0.31 47 48
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.082 -10000 0 -0.15 80 80
AP1 -0.014 0.15 0.28 6 -0.28 83 89
ILK -0.032 0.073 0.2 2 -0.24 33 35
bone resorption -0.04 0.085 0.18 7 -0.23 40 47
PTK2B 0.036 0.006 -10000 0 0 16 16
PYK2/p130Cas 0.045 0.091 -10000 0 -0.16 62 62
ITGAV 0.031 0.026 -10000 0 -0.056 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.02 0.07 -10000 0 -0.14 74 74
alphaV/beta3 Integrin/Osteopontin 0.05 0.094 -10000 0 -0.16 77 77
MAP3K1 -0.03 0.064 0.22 1 -0.21 27 28
JUN 0.034 0.01 -10000 0 0 41 41
MAPK3 -0.032 0.086 0.18 7 -0.24 42 49
MAPK1 -0.03 0.088 0.17 12 -0.26 39 51
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.028 0.061 0.23 1 -0.21 27 28
ITGB3 0.032 0.026 -10000 0 -0.055 40 40
NFKBIA -0.039 0.11 0.19 5 -0.32 46 51
FOS 0.025 0.017 -10000 0 0 162 162
CD44 0.029 0.015 -10000 0 0 110 110
CHUK 0.025 0.017 -10000 0 0 165 165
PLAU -0.074 0.26 -10000 0 -0.96 34 34
NF kappa B1 p50/RelA -0.001 0.13 0.24 3 -0.33 41 44
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
alphaV beta3 Integrin 0.04 0.058 -10000 0 -0.13 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.032 0.066 0.19 2 -0.23 29 31
VAV3 -0.026 0.075 0.16 6 -0.23 35 41
MAP3K14 -0.028 0.076 0.17 5 -0.21 34 39
ROCK2 0.035 0.007 -10000 0 0 20 20
SPP1 0.03 0.026 -10000 0 -0.058 30 30
RAC1 0.025 0.017 -10000 0 0 163 163
Rac1/GTP -0.021 0.072 0.15 4 -0.22 28 32
MMP2 -0.062 0.12 -10000 0 -0.33 62 62
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.031 0.014 -10000 0 0 83 83
PLK4 0.035 0.007 -10000 0 0 19 19
regulation of centriole replication -0.011 0.032 0.093 43 -9999 0 43
Signaling events mediated by PTP1B

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
PDGFRB 0.035 0.008 -10000 0 0 26 26
Jak2/Leptin Receptor -0.002 0.13 -10000 0 -0.3 57 57
PTP1B/AKT1 0.003 0.11 0.19 1 -0.25 52 53
FYN 0.03 0.014 -10000 0 0 88 88
p210 bcr-abl/PTP1B -0.008 0.11 0.18 5 -0.26 45 50
EGFR 0.009 0.017 -10000 0 0 382 382
EGF/EGFR -0.032 0.089 -10000 0 -0.28 39 39
CSF1 0.036 0.004 -10000 0 0 7 7
AKT1 0.033 0.012 -10000 0 0 54 54
INSR 0.035 0.008 -10000 0 -0.001 24 24
PTP1B/N-cadherin -0.003 0.12 0.19 2 -0.26 56 58
Insulin Receptor/Insulin 0.022 0.11 -10000 0 -0.25 35 35
HCK 0.027 0.016 -10000 0 0 141 141
CRK 0.035 0.008 -10000 0 0 23 23
TYK2 -0.008 0.12 0.28 21 -0.27 50 71
EGF 0.027 0.024 -10000 0 -0.023 92 92
YES1 0.034 0.01 -10000 0 0 39 39
CAV1 0.01 0.14 0.22 39 -0.28 57 96
TXN 0.035 0.01 -10000 0 0 37 37
PTP1B/IRS1/GRB2 0.009 0.12 0.2 2 -0.26 51 53
cell migration 0.008 0.11 0.26 45 -0.18 5 50
STAT3 0.034 0.01 -10000 0 0 37 37
PRLR 0.038 0.004 -10000 0 -10000 0 0
ITGA2B 0.036 0.003 -10000 0 0 3 3
CSF1R 0.027 0.016 -10000 0 0 132 132
Prolactin Receptor/Prolactin 0.057 0.012 -10000 0 -10000 0 0
FGR 0.033 0.011 -10000 0 0 56 56
PTP1B/p130 Cas -0.01 0.1 0.15 5 -0.25 46 51
Crk/p130 Cas 0 0.11 0.18 2 -0.25 49 51
DOK1 -0.006 0.1 0.18 9 -0.28 35 44
JAK2 -0.013 0.13 -10000 0 -0.32 57 57
Jak2/Leptin Receptor/Leptin -0.013 0.12 -10000 0 -0.3 36 36
PIK3R1 0.032 0.012 -10000 0 0 63 63
PTPN1 -0.008 0.11 0.18 5 -0.27 45 50
LYN 0.031 0.013 -10000 0 0 74 74
CDH2 0.033 0.011 -10000 0 0 55 55
SRC 0.017 0.093 -10000 0 -0.48 13 13
ITGB3 0.036 0.003 -10000 0 0 4 4
CAT1/PTP1B -0.005 0.17 0.26 26 -0.36 63 89
CAPN1 0.036 0.004 -10000 0 0 5 5
CSK 0.035 0.007 -10000 0 0 18 18
PI3K 0.013 0.13 -10000 0 -0.28 47 47
mol:H2O2 0.004 0.005 0.024 5 -10000 0 5
STAT3 (dimer) -0.011 0.11 -10000 0 -0.28 34 34
negative regulation of transcription -0.012 0.13 -10000 0 -0.31 57 57
FCGR2A 0.028 0.015 -10000 0 0 117 117
FER 0.037 0.007 -10000 0 0 13 13
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
BLK 0.036 0.007 -10000 0 0 17 17
Insulin Receptor/Insulin/Shc 0.06 0.036 -10000 0 -0.13 8 8
RHOA 0.035 0.007 -10000 0 0 21 21
LEPR 0.035 0.007 -10000 0 0 19 19
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.035 0.007 -10000 0 0 18 18
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.002 0.15 0.21 11 -0.35 57 68
PRL 0.038 0.007 -10000 0 -10000 0 0
SOCS3 0.022 0.051 -10000 0 -1.1 1 1
SPRY2 0.029 0.018 -10000 0 0 140 140
Insulin Receptor/Insulin/IRS1 0.056 0.046 -10000 0 -0.13 22 22
CSF1/CSF1R -0.002 0.13 0.2 2 -0.27 56 58
Ras protein signal transduction -0.009 0.074 0.58 6 -10000 0 6
IRS1 0.033 0.011 -10000 0 0 51 51
INS 0.036 0.007 -10000 0 -0.002 17 17
LEP 0.024 0.017 -10000 0 0 170 170
STAT5B -0.003 0.1 0.18 3 -0.28 31 34
STAT5A -0.002 0.1 0.18 3 -0.28 31 34
GRB2 0.035 0.007 -10000 0 0 18 18
PDGFB-D/PDGFRB 0.003 0.12 0.19 2 -0.26 46 48
CSN2 0.012 0.041 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
LAT -0.026 0.18 -10000 0 -0.46 65 65
YBX1 0.039 0.042 -10000 0 -0.29 8 8
LCK 0.035 0.007 -10000 0 0 18 18
SHC1 0.033 0.011 -10000 0 0 52 52
NOX4 0.034 0.016 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0 0.048 -10000 0 -10000 0 0
PLK1 -0.06 0.2 -10000 0 -0.61 26 26
CDKN1B -0.12 0.21 0.41 4 -0.36 148 152
FOXO3 -0.066 0.22 0.33 5 -0.48 85 90
KAT2B -0.001 0.021 0.047 17 -0.041 80 97
FOXO1/SIRT1 0.013 0.051 -10000 0 -0.24 8 8
CAT -0.076 0.26 -10000 0 -0.91 25 25
CTNNB1 0.036 0.006 -10000 0 0 15 15
AKT1 0.021 0.043 -10000 0 -0.063 55 55
FOXO1 0.003 0.053 0.22 1 -0.26 7 8
MAPK10 0.045 0.094 0.19 131 -0.15 19 150
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
FOXO4 -0.032 0.19 0.26 14 -0.45 60 74
response to oxidative stress 0 0.023 0.054 12 -0.049 36 48
FOXO3A/SIRT1 -0.062 0.22 0.3 5 -0.46 89 94
XPO1 0.036 0.004 -10000 0 0 5 5
EP300 0.034 0.011 -10000 0 -10000 0 0
BCL2L11 0.024 0.031 -10000 0 -10000 0 0
FOXO1/SKP2 0.019 0.056 -10000 0 -0.23 8 8
mol:GDP 0 0.023 0.054 12 -0.049 36 48
RAN 0.034 0.011 -10000 0 -0.015 20 20
GADD45A -0.16 0.33 0.43 2 -0.82 78 80
YWHAQ 0.036 0.005 -10000 0 0 8 8
FOXO1/14-3-3 family 0.007 0.15 -10000 0 -0.52 21 21
MST1 0.022 0.043 0.11 1 -0.06 87 88
CSNK1D 0.035 0.007 -10000 0 0 20 20
CSNK1E 0.032 0.013 -10000 0 0 68 68
FOXO4/14-3-3 family -0.004 0.15 -10000 0 -0.49 25 25
YWHAB 0.034 0.01 -10000 0 0 41 41
MAPK8 0.024 0.076 0.18 77 -0.14 12 89
MAPK9 0.053 0.097 0.19 154 -0.14 14 168
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 0.43 4 -0.79 94 98
RBL2 -0.072 0.28 -10000 0 -0.99 31 31
RAL/GDP 0.018 0.049 -10000 0 -0.14 19 19
CHUK 0.012 0.038 -10000 0 -0.059 74 74
Ran/GTP 0.018 0.025 -10000 0 -0.12 6 6
CSNK1G2 0.035 0.008 -10000 0 0 27 27
RAL/GTP 0.017 0.05 0.15 2 -0.12 19 21
CSNK1G1 0.036 0.005 -10000 0 0 11 11
FASLG 0.022 0.042 -10000 0 -0.59 1 1
SKP2 0.036 0.006 -10000 0 0 16 16
USP7 0.034 0.011 -10000 0 -0.012 23 23
IKBKB 0.023 0.044 0.11 1 -0.06 91 92
CCNB1 -0.17 0.42 0.5 1 -1.1 85 86
FOXO1-3a-4/beta catenin -0.041 0.21 0.38 9 -0.4 79 88
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.055 0.2 1 -0.23 8 9
CSNK1A1 0.036 0.006 -10000 0 0 12 12
SGK1 -0.001 0.021 0.047 17 -0.041 80 97
CSNK1G3 0.036 0.005 -10000 0 0 11 11
Ran/GTP/Exportin 1 0.039 0.036 -10000 0 -0.16 6 6
ZFAND5 -0.019 0.16 0.25 14 -0.36 59 73
SFN 0.031 0.013 -10000 0 0 80 80
CDK2 0.036 0.012 -10000 0 -0.031 3 3
FOXO3A/14-3-3 -0.013 0.16 -10000 0 -0.48 30 30
CREBBP 0.038 0.008 -10000 0 -0.031 3 3
FBXO32 -0.06 0.2 0.3 6 -0.44 85 91
BCL6 -0.094 0.32 -10000 0 -0.98 47 47
RALB 0.033 0.014 -10000 0 -0.016 32 32
RALA 0.023 0.018 -10000 0 -0.001 186 186
YWHAH 0.031 0.013 -10000 0 0 73 73
BCR signaling pathway

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
JUN -0.009 0.12 0.26 3 -0.31 38 41
IKBKB 0.018 0.08 0.27 4 -0.26 10 14
AKT1 0.005 0.086 0.22 29 -0.18 18 47
IKBKG 0.01 0.072 0.25 1 -0.24 12 13
CALM1 -0.029 0.13 0.21 4 -0.36 46 50
PIK3CA 0.031 0.014 -10000 0 0 82 82
MAP3K1 0.021 0.13 0.29 7 -0.35 35 42
MAP3K7 0.034 0.01 -10000 0 0 43 43
mol:Ca2+ -0.026 0.14 0.22 6 -0.37 46 52
DOK1 0.037 0.002 -10000 0 0 2 2
AP-1 -0.018 0.096 0.19 10 -0.21 50 60
LYN 0.031 0.013 -10000 0 0 74 74
BLNK 0.019 0.018 -10000 0 0 248 248
SHC1 0.033 0.011 -10000 0 0 52 52
BCR complex 0.05 0.015 -10000 0 -10000 0 0
CD22 -0.016 0.093 -10000 0 -0.3 35 35
CAMK2G -0.019 0.12 0.2 4 -0.34 45 49
CSNK2A1 0.033 0.011 -10000 0 0 51 51
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.035 0.057 -10000 0 -0.2 24 24
GO:0007205 -0.028 0.14 0.22 5 -0.38 47 52
SYK 0.031 0.013 -10000 0 0 74 74
ELK1 -0.033 0.13 0.21 5 -0.37 45 50
NFATC1 -0.023 0.093 0.26 3 -0.27 34 37
B-cell antigen/BCR complex 0.05 0.015 -10000 0 -10000 0 0
PAG1/CSK 0.024 0.023 -10000 0 -0.13 10 10
NFKBIB 0.021 0.042 0.16 1 -0.13 17 18
HRAS -0.029 0.12 0.2 10 -0.32 48 58
NFKBIA 0.021 0.038 0.16 1 -0.12 13 14
NF-kappa-B/RelA/I kappa B beta 0.026 0.037 0.16 1 -0.11 14 15
RasGAP/Csk 0.044 0.098 -10000 0 -0.12 117 117
mol:GDP -0.026 0.13 0.22 5 -0.36 46 51
PTEN 0.025 0.017 -10000 0 0 168 168
CD79B 0.036 0.005 -10000 0 0 11 11
NF-kappa-B/RelA/I kappa B alpha 0.026 0.036 0.16 1 -0.11 9 10
GRB2 0.035 0.007 -10000 0 0 18 18
PI3K/BCAP/CD19 -0.038 0.16 0.38 1 -0.43 48 49
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 -0.027 0.14 0.22 6 -0.38 45 51
CSK 0.035 0.007 -10000 0 0 18 18
FOS -0.031 0.13 0.2 7 -0.35 49 56
CHUK -0.06 0.14 0.25 1 -0.25 143 144
IBTK 0.035 0.008 -10000 0 0 28 28
CARD11/BCL10/MALT1/TAK1 -0.004 0.13 0.23 2 -0.34 41 43
PTPN6 -0.021 0.094 0.19 7 -0.3 34 41
RELA 0.036 0.004 -10000 0 0 7 7
BCL2A1 0.018 0.034 0.098 12 -0.095 17 29
VAV2 -0.016 0.11 -10000 0 -0.32 37 37
ubiquitin-dependent protein catabolic process 0.022 0.041 0.16 1 -0.13 17 18
BTK 0.018 0.012 -10000 0 -10000 0 0
CD19 -0.017 0.096 -10000 0 -0.29 39 39
MAP4K1 0.035 0.008 -10000 0 0 27 27
CD72 0.033 0.011 -10000 0 0 54 54
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.017 0.12 0.27 7 -0.31 35 42
SH3BP5 0.033 0.011 -10000 0 0 52 52
PIK3AP1 -0.025 0.14 0.22 7 -0.36 57 64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.036 0.18 -10000 0 -0.46 64 64
RAF1 -0.033 0.11 0.2 7 -0.31 49 56
RasGAP/p62DOK/SHIP 0.036 0.085 -10000 0 -0.11 114 114
CD79A 0.034 0.009 -10000 0 0 34 34
re-entry into mitotic cell cycle -0.018 0.095 0.19 10 -0.21 50 60
RASA1 0.035 0.009 -10000 0 0 30 30
MAPK3 -0.039 0.099 0.19 4 -0.3 39 43
MAPK1 -0.038 0.1 0.19 6 -0.31 40 46
CD72/SHP1 -0.003 0.11 0.26 8 -0.29 37 45
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 0.017 0.12 0.27 7 -0.31 33 40
actin cytoskeleton organization 0.029 0.11 0.27 12 -0.3 22 34
NF-kappa-B/RelA 0.044 0.087 0.28 1 -0.25 19 20
Calcineurin -0.01 0.13 0.23 1 -0.33 45 46
PI3K -0.034 0.087 -10000 0 -0.27 36 36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.02 0.14 0.23 6 -0.38 53 59
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.014 0.15 -10000 0 -0.61 10 10
DAPP1 -0.004 0.16 -10000 0 -0.72 9 9
cytokine secretion -0.021 0.089 0.26 3 -0.26 34 37
mol:DAG -0.027 0.14 0.22 6 -0.38 45 51
PLCG2 0.032 0.012 -10000 0 0 63 63
MAP2K1 -0.037 0.11 0.2 4 -0.31 46 50
B-cell antigen/BCR complex/FcgammaRIIB 0.015 0.075 -10000 0 -0.12 97 97
mol:PI-3-4-5-P3 -0.018 0.072 0.19 13 -0.22 19 32
ETS1 -0.03 0.11 0.2 3 -0.32 46 49
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.032 0.094 -10000 0 -0.16 61 61
B-cell antigen/BCR complex/LYN -0.012 0.1 -10000 0 -0.3 40 40
MALT1 0.034 0.009 -10000 0 0 34 34
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.027 0.12 0.27 11 -0.31 22 33
B-cell antigen/BCR complex/LYN/SYK 0.023 0.11 -10000 0 -0.28 34 34
CARD11 -0.027 0.13 0.21 5 -0.36 47 52
FCGR2B 0.02 0.018 -10000 0 0 226 226
PPP3CA 0.034 0.01 -10000 0 0 37 37
BCL10 0.035 0.007 -10000 0 0 19 19
IKK complex 0.004 0.044 0.13 5 -0.12 9 14
PTPRC 0.029 0.015 -10000 0 0 110 110
PDPK1 -0.016 0.056 0.16 14 -0.17 14 28
PPP3CB 0.025 0.017 -10000 0 0 158 158
PPP3CC 0.036 0.006 -10000 0 0 12 12
POU2F2 0.016 0.03 0.1 3 -0.085 18 21
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.02 0.11 0.2 3 -0.36 31 34
adherens junction organization 0.002 0.077 0.16 3 -0.31 19 22
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.027 0.11 0.17 119 -0.28 22 141
FMN1 0.01 0.066 0.16 3 -0.27 16 19
mol:IP3 -0.007 0.079 0.14 5 -0.26 29 34
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.015 0.068 0.16 3 -0.28 15 18
CTNNB1 0.035 0.006 -10000 0 0 15 15
AKT1 -0.002 0.09 0.14 6 -0.33 24 30
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.031 0.069 -10000 0 -0.49 4 4
CTNND1 0.035 0.009 -10000 0 0 31 31
mol:PI-4-5-P2 0.005 0.068 0.16 4 -0.27 18 22
VASP 0.004 0.065 0.15 3 -0.28 16 19
ZYX 0.008 0.054 0.15 4 -0.31 8 12
JUB 0.01 0.066 0.16 3 -0.27 16 19
EGFR(dimer) 0.001 0.062 -10000 0 -0.3 14 14
E-cadherin/beta catenin-gamma catenin 0.064 0.029 -10000 0 -0.12 3 3
mol:PI-3-4-5-P3 0.024 0.096 0.2 3 -0.3 22 25
PIK3CA 0.03 0.016 -10000 0 -0.003 89 89
PI3K 0.025 0.098 0.21 3 -0.31 22 25
FYN -0.039 0.13 0.25 1 -0.32 72 73
mol:Ca2+ -0.007 0.077 0.14 5 -0.26 29 34
JUP 0.033 0.011 0.056 1 0 51 52
PIK3R1 0.032 0.015 -10000 0 -0.003 70 70
mol:DAG -0.007 0.079 0.14 5 -0.26 29 34
CDH1 0.034 0.01 -10000 0 0 37 37
RhoA/GDP 0.056 0.12 0.18 205 -0.29 22 227
establishment of polarity of embryonic epithelium 0.003 0.065 0.15 3 -0.27 17 20
SRC 0.034 0.009 -10000 0 0 34 34
RAC1 0.025 0.017 -10000 0 0 163 163
RHOA 0.035 0.007 -10000 0 0 21 21
EGFR 0.009 0.016 -10000 0 0 379 379
CASR -0.023 0.076 0.14 20 -0.28 23 43
RhoA/GTP 0.01 0.086 0.16 1 -0.27 25 26
AKT2 -0.002 0.082 0.14 5 -0.29 23 28
actin cable formation 0.001 0.063 0.15 3 -0.27 17 20
apoptosis 0.007 0.099 0.34 27 -0.17 13 40
CTNNA1 0.036 0.008 -10000 0 -0.002 19 19
mol:GDP -0.021 0.072 0.19 4 -0.3 21 25
PIP5K1A 0.005 0.068 0.18 2 -0.28 17 19
PLCG1 -0.008 0.081 0.14 5 -0.27 29 34
Rac1/GTP -0.003 0.066 -10000 0 -0.28 14 14
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.03 0.17 -10000 0 -0.47 63 63
HDAC1 0.027 0.034 0.08 55 -0.039 84 139
AES 0.034 0.013 0.069 11 -0.004 43 54
FBXW11 0.035 0.007 -10000 0 0 22 22
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -10000 0 0
TLE1 0.034 0.013 0.07 9 -0.008 32 41
AP1 -0.012 0.078 -10000 0 -0.21 59 59
NCSTN 0.035 0.009 -10000 0 0 29 29
ADAM10 0.033 0.012 -10000 0 0 56 56
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.01 0.13 -10000 0 -0.48 15 15
NICD/RBPSUH -0.033 0.17 -10000 0 -0.47 63 63
WIF1 0.029 0.015 -10000 0 0 112 112
NOTCH1 -0.029 0.18 -10000 0 -0.5 62 62
PSENEN 0.034 0.009 -10000 0 0 31 31
KREMEN2 0.036 0.005 -10000 0 0 9 9
DKK1 0.017 0.018 -10000 0 0 277 277
beta catenin/beta TrCP1 0.064 0.093 0.24 22 -0.31 8 30
APH1B 0.036 0.006 -10000 0 0 14 14
APH1A 0.036 0.006 -10000 0 0 12 12
AXIN1 0.014 0.065 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.012 0.072 0.17 49 -0.2 11 60
PSEN1 0.033 0.011 -10000 0 0 47 47
FOS 0.025 0.017 -10000 0 0 162 162
JUN 0.034 0.01 -10000 0 0 41 41
MAP3K7 0.032 0.018 0.063 8 -0.011 63 71
CTNNB1 0.051 0.09 0.22 38 -0.3 6 44
MAPK3 0.036 0.003 -10000 0 0 4 4
DKK2/LRP6/Kremen 2 0.064 0.027 -10000 0 -0.13 1 1
HNF1A 0 0.006 0.033 10 -10000 0 10
CTBP1 0.034 0.013 0.07 9 -0.007 35 44
MYC -0.082 0.37 -10000 0 -1.2 52 52
NKD1 0 0.003 -10000 0 -10000 0 0
FZD1 0.024 0.017 -10000 0 0 175 175
NOTCH1 precursor/Deltex homolog 1 -0.033 0.17 -10000 0 -0.47 63 63
apoptosis -0.013 0.078 -10000 0 -0.21 60 60
Delta 1/NOTCHprecursor -0.033 0.17 -10000 0 -0.47 63 63
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.025 0.037 -10000 0 -10000 0 0
Gamma Secretase 0.08 0.072 -10000 0 -0.16 28 28
APC -0.02 0.17 -10000 0 -0.65 28 28
DVL1 0.019 0.087 -10000 0 -0.41 15 15
CSNK2A1 0.033 0.011 -10000 0 0 51 51
MAP3K7IP1 0.032 0.018 0.063 8 -0.012 56 64
DKK1/LRP6/Kremen 2 0.03 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 40 40
CSNK1A1 0.036 0.006 -10000 0 0 12 12
NLK 0.01 0.053 0.14 1 -0.21 22 23
CCND1 -0.047 0.34 -10000 0 -1.2 42 42
WNT1 0.035 0.007 -10000 0 0 18 18
Axin1/APC/beta catenin 0.016 0.13 0.29 1 -0.43 28 29
DKK2 0.035 0.009 -10000 0 0 31 31
NOTCH1 precursor/DVL1 -0.004 0.19 -10000 0 -0.5 52 52
GSK3B 0.034 0.01 -10000 0 0 39 39
FRAT1 0.025 0.017 -10000 0 0 163 163
NOTCH/Deltex homolog 1 -0.03 0.17 -10000 0 -0.47 63 63
PPP2R5D 0.026 0.037 -10000 0 -0.25 4 4
MAPK1 0.034 0.01 -10000 0 0 44 44
WNT1/LRP6/FZD1 0.057 0.046 -10000 0 -10000 0 0
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.032 0.021 0.07 5 -0.019 63 68
Ephrin B reverse signaling

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
EFNB2 0.028 0.015 -10000 0 0 115 115
EPHB2 0.034 0.01 -10000 0 0 40 40
EFNB1 -0.017 0.02 0.092 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.049 0.054 -10000 0 -0.15 8 8
Ephrin B2/EPHB1-2 0.032 0.057 -10000 0 -0.11 52 52
neuron projection morphogenesis 0.034 0.041 -10000 0 -0.13 11 11
Ephrin B1/EPHB1-2/Tiam1 0.058 0.049 -10000 0 -0.1 28 28
DNM1 0.035 0.008 -10000 0 0 26 26
cell-cell signaling 0 0.003 0.023 1 -10000 0 1
MAP2K4 -0.054 0.16 -10000 0 -0.52 52 52
YES1 -0.054 0.24 -10000 0 -0.75 52 52
Ephrin B1/EPHB1-2/NCK2 0.062 0.044 -10000 0 -0.1 20 20
PI3K -0.019 0.19 -10000 0 -0.56 51 51
mol:GDP 0.056 0.048 -10000 0 -0.1 28 28
ITGA2B 0.037 0.003 -10000 0 0 3 3
endothelial cell proliferation 0.016 0.047 -10000 0 -0.12 45 45
FYN -0.065 0.24 -10000 0 -0.77 52 52
MAP3K7 -0.051 0.16 -10000 0 -0.54 51 51
FGR -0.051 0.23 -10000 0 -0.72 51 51
TIAM1 0.033 0.011 -10000 0 0 46 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
RGS3 0.035 0.007 -10000 0 0 22 22
cell adhesion -0.031 0.17 -10000 0 -0.53 51 51
LYN -0.061 0.23 -10000 0 -0.74 52 52
Ephrin B1/EPHB1-2/Src Family Kinases -0.057 0.21 -10000 0 -0.68 52 52
Ephrin B1/EPHB1-2 -0.047 0.18 -10000 0 -0.57 51 51
SRC -0.05 0.23 -10000 0 -0.72 52 52
ITGB3 0.036 0.003 -10000 0 0 4 4
EPHB1 0.03 0.015 -10000 0 0 94 94
EPHB4 0.025 0.017 -10000 0 0 164 164
RAC1 0.025 0.017 -10000 0 0 163 163
Ephrin B2/EPHB4 0.016 0.047 -10000 0 -0.12 45 45
alphaIIb/beta3 Integrin 0.054 0.005 -10000 0 -10000 0 0
BLK -0.052 0.23 -10000 0 -0.72 52 52
HCK -0.065 0.23 -10000 0 -0.74 52 52
regulation of stress fiber formation -0.06 0.043 0.1 20 -10000 0 20
MAPK8 -0.056 0.15 -10000 0 -0.5 52 52
Ephrin B1/EPHB1-2/RGS3 0.068 0.034 -10000 0 -0.11 6 6
endothelial cell migration 0.006 0.17 0.22 39 -0.45 44 83
NCK2 0.036 0.007 -10000 0 0 17 17
PTPN13 0.034 0.014 -10000 0 0 60 60
regulation of focal adhesion formation -0.06 0.043 0.1 20 -10000 0 20
chemotaxis -0.065 0.033 0.11 6 -10000 0 6
PIK3CA 0.031 0.014 -10000 0 0 82 82
Rac1/GTP 0.042 0.048 -10000 0 -0.14 9 9
angiogenesis -0.048 0.18 -10000 0 -0.57 52 52
LCK -0.05 0.22 -10000 0 -0.72 51 51
IL2 signaling events mediated by PI3K

Figure 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
BCL2L1 0.01 0.098 0.33 2 -0.41 4 6
UGCG -0.026 0.19 -10000 0 -0.74 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT -0.007 0.13 0.26 10 -0.34 39 49
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.024 0.18 -10000 0 -0.73 30 30
mol:DAG -0.007 0.031 0.17 15 -10000 0 15
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.18 0.29 8 -0.42 63 71
FRAP1 -0.035 0.2 0.31 9 -0.47 63 72
FOXO3 -0.035 0.2 0.29 11 -0.46 67 78
AKT1 -0.04 0.21 0.32 7 -0.49 68 75
GAB2 0.03 0.019 -10000 0 -0.012 81 81
SMPD1 0.002 0.096 -10000 0 -0.52 14 14
SGMS1 -0.003 0.034 0.066 19 -0.072 67 86
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.028 0.046 0.077 7 -0.13 72 79
CALM1 0.033 0.012 -10000 0 0 57 57
cell proliferation -0.032 0.19 0.28 11 -0.38 74 85
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.078 -10000 0 -0.16 72 72
RPS6KB1 0.029 0.028 -10000 0 -10000 0 0
mol:sphingomyelin -0.007 0.031 0.17 15 -10000 0 15
natural killer cell activation 0 0.004 0.007 28 -0.01 47 75
JAK3 0.034 0.017 -10000 0 -0.028 25 25
PIK3R1 0.031 0.02 -10000 0 -0.029 26 26
JAK1 0.032 0.019 -10000 0 -0.028 30 30
NFKB1 0.035 0.007 -10000 0 0 18 18
MYC -0.069 0.3 0.42 10 -0.81 61 71
MYB 0.033 0.042 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.16 0.27 7 -0.4 49 56
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.16 0.28 8 -0.39 49 57
Rac1/GDP 0.005 0.05 0.12 6 -0.13 44 50
T cell proliferation -0.024 0.15 0.26 8 -0.36 49 57
SHC1 0.029 0.019 -10000 0 -0.011 85 85
RAC1 0.025 0.017 -10000 0 0 163 163
positive regulation of cyclin-dependent protein kinase activity 0.005 0.012 0.058 24 -10000 0 24
PRKCZ -0.025 0.16 0.26 8 -0.38 49 57
NF kappa B1 p50/RelA -0.013 0.19 0.31 8 -0.42 63 71
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.094 0.21 3 -0.29 26 29
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
IL2RA 0.021 0.021 -10000 0 -0.004 205 205
IL2RB 0.032 0.019 -10000 0 -0.028 25 25
TERT 0.036 0.006 -10000 0 0 15 15
E2F1 0.035 0.032 -10000 0 -10000 0 0
SOS1 0 0.003 0.007 36 -0.009 47 83
RPS6 0.031 0.014 -10000 0 0 86 86
mol:cAMP -0.003 0.007 -10000 0 -0.032 25 25
PTPN11 0.032 0.018 -10000 0 -0.023 48 48
IL2RG 0.034 0.017 -10000 0 -0.03 26 26
actin cytoskeleton organization -0.024 0.15 0.26 8 -0.36 49 57
GRB2 0.033 0.017 -10000 0 -0.018 46 46
IL2 0.035 0.017 -10000 0 -0.03 26 26
PIK3CA 0.029 0.02 -10000 0 -0.029 27 27
Rac1/GTP 0.028 0.064 0.16 5 -0.12 44 49
LCK 0.034 0.017 -10000 0 -0.03 26 26
BCL2 -0.022 0.16 0.32 2 -0.44 34 36
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.014 -10000 0 -10000 0 0
cell-cell adhesion 0.031 0.041 0.15 36 -10000 0 36
Ephrin B/EPHB2/RasGAP 0.06 0.091 -10000 0 -0.14 75 75
ITSN1 0.035 0.007 -10000 0 0 21 21
PIK3CA 0.031 0.014 -10000 0 0 82 82
SHC1 0.033 0.011 -10000 0 0 52 52
Ephrin B1/EPHB3 0.045 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.039 0.025 -10000 0 -0.12 6 6
HRAS/GDP 0.003 0.084 0.17 1 -0.22 41 42
Ephrin B/EPHB1/GRB7 0.068 0.076 -10000 0 -0.12 47 47
Endophilin/SYNJ1 -0.028 0.055 0.19 12 -0.19 2 14
KRAS 0.034 0.009 -10000 0 0 34 34
Ephrin B/EPHB1/Src 0.063 0.077 -10000 0 -0.12 52 52
endothelial cell migration 0.02 0.073 -10000 0 -0.14 65 65
GRB2 0.035 0.007 -10000 0 0 18 18
GRB7 0.036 0.006 -10000 0 0 15 15
PAK1 -0.03 0.059 0.19 16 -10000 0 16
HRAS 0.034 0.009 -10000 0 0 36 36
RRAS -0.027 0.055 0.21 8 -0.19 10 18
DNM1 0.035 0.008 -10000 0 0 26 26
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.02 0.065 0.18 18 -0.19 11 29
lamellipodium assembly -0.031 0.041 -10000 0 -0.15 36 36
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.075 -10000 0 -0.28 16 16
PIK3R1 0.032 0.012 -10000 0 0 63 63
EPHB2 0.034 0.01 -10000 0 0 40 40
EPHB3 0.033 0.011 -10000 0 0 52 52
EPHB1 0.03 0.014 -10000 0 0 94 94
EPHB4 0.025 0.017 -10000 0 0 164 164
mol:GDP 0.017 0.12 0.2 101 -0.24 35 136
Ephrin B/EPHB2 0.052 0.069 -10000 0 -0.11 65 65
Ephrin B/EPHB3 0.051 0.069 -10000 0 -0.11 64 64
JNK cascade -0.007 0.067 0.23 19 -0.2 4 23
Ephrin B/EPHB1 0.052 0.066 -10000 0 -0.11 54 54
RAP1/GDP 0.026 0.12 0.2 105 -0.23 36 141
EFNB2 0.028 0.015 -10000 0 0 115 115
EFNB3 0.035 0.009 -10000 0 0 29 29
EFNB1 0.037 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.031 0.059 -10000 0 -0.11 52 52
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 10 10
CDC42/GTP 0.044 0.084 -10000 0 -0.19 34 34
Rap1/GTP -0.045 0.053 0.053 9 -0.21 22 31
axon guidance 0.045 0.014 -10000 0 -10000 0 0
MAPK3 -0.007 0.072 0.16 3 -0.28 16 19
MAPK1 -0.007 0.075 0.17 2 -0.28 20 22
Rac1/GDP -0.01 0.094 0.24 21 -0.24 34 55
actin cytoskeleton reorganization -0.041 0.061 -10000 0 -0.2 44 44
CDC42/GDP 0.033 0.13 0.22 108 -0.24 35 143
PI3K 0.024 0.077 -10000 0 -0.14 65 65
EFNA5 0.036 0.004 -10000 0 0 5 5
Ephrin B2/EPHB4 0.016 0.048 -10000 0 -0.12 45 45
Ephrin B/EPHB2/Intersectin/N-WASP 0.001 0.063 -10000 0 -0.17 45 45
CDC42 0.035 0.008 -10000 0 0 26 26
RAS family/GTP -0.053 0.062 0.05 32 -0.24 24 56
PTK2 -0.014 0.084 0.53 10 -10000 0 10
MAP4K4 -0.007 0.067 0.23 19 -0.2 4 23
SRC 0.034 0.009 -10000 0 0 34 34
KALRN 0.035 0.007 -10000 0 0 22 22
Intersectin/N-WASP 0.033 0.034 -10000 0 -0.14 8 8
neuron projection morphogenesis 0.058 0.17 0.33 121 -0.23 14 135
MAP2K1 0.001 0.073 -10000 0 -0.27 18 18
WASL 0.025 0.017 -10000 0 0 167 167
Ephrin B1/EPHB1-2/NCK1 0.082 0.039 -10000 0 -0.12 10 10
cell migration -0.012 0.087 0.22 1 -0.29 20 21
NRAS 0.032 0.012 -10000 0 0 63 63
SYNJ1 -0.028 0.056 0.2 12 -0.19 2 14
PXN 0.036 0.004 -10000 0 0 7 7
TF -0.023 0.051 0.2 5 -0.19 21 26
HRAS/GTP 0.034 0.08 -10000 0 -0.15 61 61
Ephrin B1/EPHB1-2 0.053 0.035 -10000 0 -0.11 6 6
cell adhesion mediated by integrin 0.019 0.046 0.15 6 -0.24 5 11
RAC1 0.025 0.017 -10000 0 0 163 163
mol:GTP 0.042 0.078 -10000 0 -0.14 62 62
RAC1-CDC42/GTP -0.031 0.047 -10000 0 -0.2 13 13
RASA1 0.035 0.009 -10000 0 0 30 30
RAC1-CDC42/GDP 0.01 0.096 0.25 18 -0.24 33 51
ruffle organization 0.067 0.17 0.31 138 -0.22 16 154
NCK1 0.035 0.008 -10000 0 0 27 27
receptor internalization -0.033 0.052 0.18 12 -0.19 2 14
Ephrin B/EPHB2/KALRN 0.066 0.08 -10000 0 -0.12 62 62
ROCK1 -0.009 0.045 0.12 47 -10000 0 47
RAS family/GDP -0.043 0.064 -10000 0 -0.21 44 44
Rac1/GTP -0.029 0.046 -10000 0 -0.2 13 13
Ephrin B/EPHB1/Src/Paxillin 0.009 0.064 -10000 0 -0.21 7 7
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.042 0.011 -10000 0 -0.042 1 1
NFATC2 0.015 0.16 0.28 6 -0.33 51 57
NFATC3 0.018 0.13 0.27 25 -0.24 73 98
CD40LG -0.018 0.34 0.49 44 -0.69 72 116
ITCH 0.033 0.047 0.19 8 -10000 0 8
CBLB 0.036 0.049 0.2 11 -10000 0 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.054 0.26 0.38 13 -0.6 61 74
JUNB 0.031 0.014 -10000 0 0 84 84
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.029 -10000 0 -0.14 7 7
T cell anergy 0.016 0.068 0.22 19 -0.24 1 20
TLE4 0.01 0.11 -10000 0 -0.31 22 22
Jun/NFAT1-c-4/p21SNFT -0.018 0.33 0.45 2 -0.73 72 74
AP-1/NFAT1-c-4 -0.035 0.35 -10000 0 -0.78 68 68
IKZF1 0.006 0.1 0.17 13 -0.22 49 62
T-helper 2 cell differentiation -0.088 0.23 -10000 0 -0.64 41 41
AP-1/NFAT1 0.017 0.15 0.28 18 -0.29 49 67
CALM1 0.046 0.024 0.14 2 -10000 0 2
EGR2 -0.077 0.42 0.5 14 -0.97 76 90
EGR3 -0.055 0.42 0.49 20 -0.98 72 92
NFAT1/FOXP3 0.039 0.12 0.25 4 -0.25 39 43
EGR1 0.029 0.015 0.071 1 0 107 108
JUN 0.032 0.042 0.11 34 -0.055 8 42
EGR4 0.037 0.004 0.071 1 0 5 6
mol:Ca2+ 0.005 0.003 -10000 0 -10000 0 0
GBP3 0.006 0.1 0.17 13 -0.22 49 62
FOSL1 0.033 0.011 -10000 0 0 53 53
NFAT1-c-4/MAF/IRF4 0.009 0.33 -10000 0 -0.72 75 75
DGKA 0.011 0.1 0.21 1 -0.27 30 31
CREM 0.026 0.016 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.006 0.33 -10000 0 -0.73 74 74
CTLA4 0.009 0.093 0.18 1 -0.23 30 31
NFAT1-c-4 (dimer)/EGR1 -0.029 0.34 -10000 0 -0.76 76 76
NFAT1-c-4 (dimer)/EGR4 0.001 0.34 -10000 0 -0.74 74 74
FOS 0.023 0.038 0.11 19 -0.051 7 26
IFNG -0.01 0.13 -10000 0 -0.4 21 21
T cell activation -0.014 0.22 -10000 0 -0.56 31 31
MAF 0.035 0.009 -10000 0 0 34 34
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.28 0.6 73 -0.46 21 94
TNF -0.041 0.31 0.4 12 -0.7 76 88
FASLG -0.1 0.46 -10000 0 -1.1 75 75
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 0.007 0.12 0.43 2 -0.32 32 34
NFAT1-c-4/ICER1 -0.033 0.32 -10000 0 -0.73 74 74
GATA3 0.027 0.018 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.004 0.14 -10000 0 -0.4 21 21
IL2RA -0.064 0.25 0.34 2 -0.57 72 74
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.008 0.11 -10000 0 -0.33 28 28
E2F1 0.036 0.051 0.11 2 -0.25 12 14
PPARG 0.035 0.008 -10000 0 -10000 0 0
SLC3A2 0.006 0.12 0.24 2 -0.36 31 33
IRF4 0.037 0.002 -10000 0 0 1 1
PTGS2 -0.074 0.28 0.44 3 -0.69 68 71
CSF2 -0.019 0.34 0.49 44 -0.69 72 116
JunB/Fra1/NFAT1-c-4 -0.014 0.31 -10000 0 -0.71 72 72
IL4 -0.091 0.24 -10000 0 -0.67 40 40
IL5 -0.019 0.34 0.49 44 -0.69 72 116
IL2 -0.015 0.22 -10000 0 -0.57 30 30
IL3 0.009 0.082 -10000 0 -0.6 5 5
RNF128 0.014 0.023 0.17 1 -10000 0 1
NFATC1 -0.006 0.28 0.46 21 -0.6 73 94
CDK4 -0.01 0.27 0.52 37 -1 14 51
PTPRK -0.003 0.14 -10000 0 -0.42 39 39
IL8 -0.1 0.3 0.46 7 -0.74 68 75
POU2F1 0.039 0.008 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.019 0.038 -10000 0 -0.055 95 95
HSPA8 0.036 0.009 -10000 0 0 25 25
SMAD3/SMAD4/ER alpha 0.043 0.088 0.23 10 -0.14 39 49
AKT1 0.03 0.02 -10000 0 -0.029 34 34
GSC 0.001 0.028 0.1 12 -0.065 3 15
NKX2-5 0.034 0.017 0.071 9 -0.061 12 21
muscle cell differentiation -0.017 0.13 0.31 52 -10000 0 52
SMAD2-3/SMAD4/SP1 0.051 0.14 0.34 5 -0.24 50 55
SMAD4 0.021 0.057 0.14 4 -0.13 36 40
CBFB 0.036 0.006 -10000 0 0 14 14
SAP18 0.034 0.01 -10000 0 0 43 43
Cbp/p300/MSG1 0.01 0.088 -10000 0 -0.14 97 97
SMAD3/SMAD4/VDR 0.044 0.12 -10000 0 -0.2 36 36
MYC 0.029 0.014 -10000 0 -10000 0 0
CDKN2B -0.21 0.19 -10000 0 -0.53 30 30
AP1 -0.004 0.1 0.21 2 -0.24 53 55
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.012 0.13 -10000 0 -0.37 38 38
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.002 0.083 -10000 0 -0.28 31 31
SP3 0.035 0.016 0.081 11 -0.055 10 21
CREB1 0.036 0.004 -10000 0 0 7 7
FOXH1 0.035 0.016 0.072 10 -0.061 12 22
SMAD3/SMAD4/GR 0.04 0.093 0.24 2 -0.16 46 48
GATA3 0.027 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.004 0.094 -10000 0 -0.3 28 28
MEF2C/TIF2 -0.02 0.074 0.28 8 -0.22 18 26
endothelial cell migration 0.2 0.5 1.2 106 -10000 0 106
MAX 0.027 0.043 0.084 90 -0.054 89 179
RBBP7 0.037 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 57 57
RUNX2 0.037 0.002 -10000 0 0 1 1
RUNX3 0.034 0.009 -10000 0 0 34 34
RUNX1 0.036 0.005 -10000 0 0 10 10
CTBP1 0.035 0.008 -10000 0 0 27 27
NR3C1 0.027 0.043 0.085 88 -0.054 90 178
VDR 0.035 0.007 -10000 0 0 21 21
CDKN1A -0.11 0.36 0.4 1 -1.1 59 60
KAT2B -0.003 0.008 -10000 0 -0.023 17 17
SMAD2/SMAD2/SMAD4/FOXH1 0.048 0.078 0.2 2 -0.16 39 41
DCP1A 0.035 0.008 -10000 0 0 24 24
SKI 0.037 0.001 -10000 0 -10000 0 0
SERPINE1 -0.2 0.5 -10000 0 -1.2 106 106
SMAD3/SMAD4/ATF2 0.04 0.088 0.21 1 -0.15 55 56
SMAD3/SMAD4/ATF3 0.019 0.1 -10000 0 -0.17 87 87
SAP30 0.036 0.007 -10000 0 0 18 18
Cbp/p300/PIAS3 0.041 0.074 -10000 0 -0.095 91 91
JUN -0.015 0.1 0.19 9 -0.25 49 58
SMAD3/SMAD4/IRF7 0.043 0.092 -10000 0 -0.16 49 49
TFE3 0.016 0.06 0.11 8 -0.096 103 111
COL1A2 -0.041 0.21 -10000 0 -0.63 52 52
mesenchymal cell differentiation -0.04 0.088 0.15 54 -0.21 1 55
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.035 0.008 -10000 0 0 26 26
FOS 0.02 0.03 0.12 2 -0.046 46 48
SMAD3/SMAD4/Max 0.04 0.089 0.24 2 -0.16 30 32
Cbp/p300/SNIP1 0.043 0.056 -10000 0 -0.13 8 8
ZBTB17 0.035 0.006 -10000 0 -10000 0 0
LAMC1 -0.035 0.1 0.16 5 -0.31 41 46
TGIF2/HDAC complex/SMAD3/SMAD4 0.037 0.086 0.21 1 -0.15 50 51
IRF7 0.034 0.01 -10000 0 -10000 0 0
ESR1 0.037 0.04 0.12 67 -0.026 61 128
HNF4A 0.034 0.01 -10000 0 0 37 37
MEF2C -0.028 0.069 0.28 8 -0.23 20 28
SMAD2-3/SMAD4 0.041 0.097 0.23 2 -0.19 38 40
Cbp/p300/Src-1 0.031 0.076 -10000 0 -0.13 51 51
IGHV3OR16-13 0.005 0.057 -10000 0 -0.49 6 6
TGIF2/HDAC complex 0.034 0.01 -10000 0 0 44 44
CREBBP 0.022 0.034 -10000 0 -0.045 102 102
SKIL 0.036 0.006 -10000 0 0 13 13
HDAC1 0.036 0.008 -10000 0 0 21 21
HDAC2 0.033 0.012 -10000 0 0 59 59
SNIP1 0.036 0.007 -10000 0 0 15 15
GCN5L2 0.021 0.034 -10000 0 -0.04 116 116
SMAD3/SMAD4/TFE3 0.03 0.13 0.27 5 -0.23 57 62
MSG1/HSC70 0.008 0.081 -10000 0 -0.15 102 102
SMAD2 0.035 0.017 0.091 2 -0.049 11 13
SMAD3 0.018 0.06 0.14 3 -0.12 43 46
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.075 -10000 0 -0.18 48 48
SMAD2/SMAD2/SMAD4 -0.013 0.072 0.18 8 -0.2 43 51
NCOR1 0.035 0.008 -10000 0 0 27 27
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA1 0.033 0.011 -10000 0 0 49 49
MYOD/E2A 0.051 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.06 0.15 0.34 5 -0.24 47 52
IFNB1 -0.006 0.059 0.17 6 -0.18 10 16
SMAD3/SMAD4/MEF2C 0.026 0.095 0.26 4 -0.23 24 28
CITED1 0.026 0.017 -10000 0 0 153 153
SMAD2-3/SMAD4/ARC105 0.041 0.088 0.22 3 -0.17 34 37
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.1 -10000 0 -0.34 29 29
RUNX1-3/PEBPB2 0.067 0.023 -10000 0 -10000 0 0
SMAD7 -0.041 0.18 0.28 3 -0.44 59 62
MYC/MIZ-1 0.027 0.059 -10000 0 -0.15 49 49
SMAD3/SMAD4 -0.081 0.24 0.22 3 -0.47 115 118
IL10 -0.008 0.063 0.19 8 -0.2 4 12
PIASy/HDAC complex 0.028 0.031 0.071 9 -0.031 89 98
PIAS3 0.023 0.029 -10000 0 -0.031 109 109
CDK2 0.021 0.032 -10000 0 -0.043 91 91
IL5 -0.01 0.065 0.19 9 -0.2 4 13
CDK4 0.021 0.031 -10000 0 -0.046 73 73
PIAS4 0.028 0.031 0.071 9 -0.031 89 98
ATF3 0.028 0.016 -10000 0 0 128 128
SMAD3/SMAD4/SP1 0.031 0.14 0.26 13 -0.23 67 80
FOXG1 0.001 0.007 0.023 23 -10000 0 23
FOXO3 -0.008 0.008 -10000 0 -10000 0 0
FOXO1 -0.008 0.007 -10000 0 -10000 0 0
FOXO4 -0.008 0.007 -10000 0 -10000 0 0
heart looping -0.028 0.069 0.28 8 -0.23 20 28
CEBPB 0.032 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.024 0.075 0.18 2 -0.14 56 58
MYOD1 0.036 0.004 -10000 0 0 7 7
SMAD3/SMAD4/HNF4 0.037 0.087 0.21 1 -0.15 54 55
SMAD3/SMAD4/GATA3 0.032 0.087 -10000 0 -0.17 27 27
SnoN/SIN3/HDAC complex/NCoR1 0.036 0.006 -10000 0 0 13 13
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.069 0.095 -10000 0 -0.15 23 23
SMAD3/SMAD4/SP1-3 0.048 0.14 0.34 3 -0.24 50 53
MED15 0 0 -10000 0 -10000 0 0
SP1 0.015 0.075 0.12 18 -0.12 105 123
SIN3B 0.035 0.009 -10000 0 0 33 33
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.07 0.086 0.24 2 -0.16 39 41
ITGB5 -0.032 0.1 0.21 6 -0.26 37 43
TGIF/SIN3/HDAC complex/CtBP -0.01 0.099 -10000 0 -0.32 31 31
SMAD3/SMAD4/AR 0.04 0.088 0.21 1 -0.15 51 52
AR 0.035 0.007 -10000 0 0 22 22
negative regulation of cell growth -0.016 0.12 -10000 0 -0.3 57 57
SMAD3/SMAD4/MYOD 0.04 0.088 0.21 1 -0.15 52 53
E2F5 0.036 0.005 -10000 0 0 8 8
E2F4 0.036 0.005 -10000 0 0 10 10
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.061 0.099 0.24 1 -0.16 45 46
SMAD2-3/SMAD4/FOXO1-3a-4 -0.006 0.099 -10000 0 -0.31 32 32
TFDP1 0.033 0.011 -10000 0 0 53 53
SMAD3/SMAD4/AP1 0.022 0.12 0.25 3 -0.24 53 56
SMAD3/SMAD4/RUNX2 0.04 0.089 0.21 1 -0.15 54 55
TGIF2 0.034 0.01 -10000 0 0 44 44
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.005 -10000 0 0 11 11
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.1 -10000 0 -0.26 27 27
mol:DAG -0.012 0.089 0.18 5 -0.25 26 31
PLCG1 -0.013 0.091 0.18 5 -0.26 26 31
YES1 -0.017 0.086 0.14 2 -0.18 86 88
FZD3 0.029 0.015 -10000 0 0 109 109
FZD6 0.027 0.016 -10000 0 0 130 130
G protein 0.002 0.11 0.21 24 -0.28 26 50
MAP3K7 -0.035 0.075 0.14 7 -0.23 32 39
mol:Ca2+ -0.012 0.087 0.17 5 -0.24 26 31
mol:IP3 -0.012 0.089 0.18 5 -0.25 26 31
NLK -0.037 0.25 -10000 0 -0.77 52 52
GNB1 0.035 0.007 -10000 0 0 20 20
CAMK2A -0.03 0.078 0.16 6 -0.24 26 32
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
Noncanonical Wnts/FZD -0.006 0.089 -10000 0 -0.17 89 89
CSNK1A1 0.036 0.006 -10000 0 0 12 12
GNAS -0.016 0.081 0.14 2 -0.17 84 86
GO:0007205 -0.019 0.084 0.17 5 -0.26 26 31
WNT6 0.037 0.002 -10000 0 0 1 1
WNT4 0.035 0.007 -10000 0 0 20 20
NFAT1/CK1 alpha -0.005 0.099 0.22 5 -0.27 27 32
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.03 0.015 -10000 0 0 99 99
WNT11 0.036 0.006 -10000 0 0 15 15
CDC42 -0.026 0.084 0.17 5 -0.27 23 28
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.017 0.2 -10000 0 -0.82 26 26
regulation of axonogenesis 0.004 0.066 0.21 39 -10000 0 39
myoblast fusion -0.014 0.094 0.35 28 -0.17 2 30
mol:GTP 0.014 0.067 -10000 0 -0.18 52 52
regulation of calcium-dependent cell-cell adhesion -0.025 0.075 0.15 64 -0.15 1 65
ARF1/GTP 0.034 0.063 -10000 0 -0.14 53 53
mol:GM1 0.002 0.048 -10000 0 -0.13 51 51
mol:Choline -0.016 0.042 0.086 3 -0.13 44 47
lamellipodium assembly -0.009 0.1 -10000 0 -0.36 35 35
MAPK3 0.011 0.084 0.14 37 -0.29 27 64
ARF6/GTP/NME1/Tiam1 0.026 0.075 0.15 1 -0.15 64 65
ARF1 0.035 0.008 -10000 0 0 24 24
ARF6/GDP 0.014 0.095 -10000 0 -0.35 28 28
ARF1/GDP 0.012 0.1 -10000 0 -0.28 48 48
ARF6 0.039 0.042 -10000 0 -0.13 26 26
RAB11A 0.036 0.006 -10000 0 0 16 16
TIAM1 0.029 0.023 -10000 0 -0.044 34 34
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.011 0.083 -10000 0 -0.3 26 26
actin filament bundle formation -0.017 0.11 0.28 52 -10000 0 52
KALRN 0.006 0.071 0.13 3 -0.26 29 32
RAB11FIP3/RAB11A 0.048 0.035 -10000 0 -0.16 12 12
RhoA/GDP 0.018 0.11 -10000 0 -0.28 52 52
NME1 -0.001 0.008 -10000 0 -0.03 26 26
Rac1/GDP 0.013 0.091 -10000 0 -0.29 32 32
substrate adhesion-dependent cell spreading 0.014 0.067 -10000 0 -0.18 52 52
cortical actin cytoskeleton organization -0.009 0.1 -10000 0 -0.37 35 35
RAC1 0.025 0.017 -10000 0 0 163 163
liver development 0.014 0.067 -10000 0 -0.18 52 52
ARF6/GTP 0.014 0.067 -10000 0 -0.18 52 52
RhoA/GTP 0.033 0.065 -10000 0 -0.14 55 55
mol:GDP -0.007 0.1 0.18 2 -0.3 50 52
ARF6/GTP/RAB11FIP3/RAB11A 0.05 0.07 -10000 0 -0.13 61 61
RHOA 0.035 0.007 -10000 0 0 21 21
PLD1 0.011 0.053 -10000 0 -0.14 48 48
RAB11FIP3 0.036 0.006 -10000 0 0 15 15
tube morphogenesis -0.009 0.1 -10000 0 -0.36 35 35
ruffle organization -0.004 0.066 -10000 0 -0.21 39 39
regulation of epithelial cell migration 0.014 0.067 -10000 0 -0.18 52 52
PLD2 0.012 0.053 -10000 0 -0.14 50 50
PIP5K1A -0.004 0.067 -10000 0 -0.21 39 39
mol:Phosphatidic acid -0.016 0.042 0.086 3 -0.13 44 47
Rac1/GTP -0.009 0.1 -10000 0 -0.37 35 35
Reelin signaling pathway

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
CDK5R1/CDK5 0.029 0.041 -10000 0 -0.14 17 17
VLDLR 0.027 0.016 -10000 0 0 137 137
CRKL 0.035 0.008 -10000 0 0 28 28
LRPAP1 0.036 0.007 -10000 0 0 17 17
FYN 0.03 0.014 -10000 0 0 88 88
ITGA3 0.033 0.011 -10000 0 0 56 56
RELN/VLDLR/Fyn 0.017 0.062 -10000 0 -0.13 53 53
MAPK8IP1/MKK7/MAP3K11/JNK1 0.067 0.062 -10000 0 -0.12 4 4
AKT1 -0.014 0.067 -10000 0 -0.19 49 49
MAP2K7 0.035 0.007 -10000 0 0 22 22
RAPGEF1 0.035 0.007 -10000 0 0 18 18
DAB1 0.036 0.005 -10000 0 0 8 8
RELN/LRP8/DAB1 0.042 0.036 -10000 0 -0.11 2 2
LRPAP1/LRP8 0.045 0.036 -10000 0 -0.15 14 14
RELN/LRP8/DAB1/Fyn 0.042 0.06 -10000 0 -0.12 33 33
DAB1/alpha3/beta1 Integrin 0.028 0.059 -10000 0 -0.12 20 20
long-term memory 0.042 0.064 -10000 0 -0.12 30 30
DAB1/LIS1 0.048 0.072 -10000 0 -0.13 30 30
DAB1/CRLK/C3G 0.038 0.059 -10000 0 -0.12 23 23
PIK3CA 0.031 0.014 -10000 0 0 82 82
DAB1/NCK2 0.049 0.072 -10000 0 -0.13 28 28
ARHGEF2 0.035 0.007 -10000 0 0 21 21
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.036 0.007 -10000 0 0 17 17
CDK5R1 0.035 0.008 -10000 0 0 25 25
RELN 0.023 0.018 -10000 0 0 186 186
PIK3R1 0.032 0.012 -10000 0 0 63 63
RELN/LRP8/Fyn 0.03 0.056 -10000 0 -0.13 34 34
GRIN2A/RELN/LRP8/DAB1/Fyn 0.052 0.071 -10000 0 -0.12 33 33
MAPK8 0.026 0.017 -10000 0 0 143 143
RELN/VLDLR/DAB1 0.03 0.045 -10000 0 -0.11 20 20
ITGB1 0.026 0.017 -10000 0 0 144 144
MAP1B 0.023 0.083 0.16 108 -0.21 4 112
RELN/LRP8 0.04 0.043 -10000 0 -0.13 10 10
GRIN2B/RELN/LRP8/DAB1/Fyn 0.052 0.07 -10000 0 -0.12 31 31
PI3K 0.018 0.076 -10000 0 -0.16 72 72
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.027 -10000 0 -0.14 1 1
RAP1A 0.031 0.11 0.25 37 -10000 0 37
PAFAH1B1 0.035 0.008 -10000 0 0 25 25
MAPK8IP1 0.035 0.008 -10000 0 0 24 24
CRLK/C3G 0.05 0.015 -10000 0 -10000 0 0
GRIN2B 0.035 0.008 -10000 0 0 23 23
NCK2 0.036 0.007 -10000 0 0 17 17
neuron differentiation 0.008 0.065 -10000 0 -0.22 16 16
neuron adhesion 0.031 0.11 0.25 41 -10000 0 41
LRP8 0.034 0.009 -10000 0 0 34 34
GSK3B -0.008 0.077 -10000 0 -0.21 36 36
RELN/VLDLR/DAB1/Fyn 0.03 0.066 -10000 0 -0.12 53 53
MAP3K11 0.036 0.005 -10000 0 0 8 8
RELN/VLDLR/DAB1/P13K -0.007 0.073 -10000 0 -0.19 54 54
CDK5 0.023 0.018 -10000 0 0 185 185
MAPT -0.014 0.069 0.32 6 -10000 0 6
neuron migration 0 0.12 0.2 77 -0.28 32 109
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.008 0.065 -10000 0 -0.22 16 16
RELN/VLDLR 0.044 0.06 -10000 0 -0.12 25 25
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.044 0.043 -10000 0 -0.14 24 24
AKT1 -0.013 0.17 0.29 16 -0.42 44 60
PTK2B -0.001 0.11 0.25 24 -0.4 11 35
VEGFR2 homodimer/Frs2 0.026 0.083 0.19 2 -0.33 15 17
CAV1 0.016 0.018 -10000 0 0 288 288
CALM1 0.033 0.012 -10000 0 0 57 57
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.022 0.086 0.18 1 -0.3 18 19
endothelial cell proliferation 0.018 0.15 0.31 30 -0.39 26 56
mol:Ca2+ 0.007 0.13 0.24 54 -0.32 20 74
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.02 0.088 0.2 2 -0.27 22 24
RP11-342D11.1 -0.004 0.1 0.18 48 -0.34 18 66
CDH5 0.03 0.014 -10000 0 0 92 92
VEGFA homodimer 0.036 0.034 -10000 0 -0.1 13 13
SHC1 0.033 0.011 -10000 0 0 52 52
SHC2 0.032 0.012 -10000 0 0 61 61
HRAS/GDP 0.004 0.091 -10000 0 -0.24 46 46
SH2D2A 0.036 0.006 -10000 0 0 15 15
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.022 0.11 0.28 2 -0.37 17 19
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.087 0.18 1 -0.32 17 18
VEGFR1 homodimer 0.034 0.009 -10000 0 0 34 34
SHC/GRB2/SOS1 0.037 0.1 -10000 0 -0.23 46 46
GRB10 -0.012 0.11 0.21 33 -0.33 32 65
PTPN11 0.036 0.005 -10000 0 0 11 11
GRB2 0.035 0.007 -10000 0 0 18 18
PAK1 0.036 0.006 -10000 0 0 16 16
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.038 0.12 0.24 1 -0.28 37 38
HRAS 0.034 0.009 -10000 0 0 36 36
VEGF/Rho/ROCK1/Integrin Complex 0.012 0.11 0.18 5 -0.32 30 35
HIF1A 0.034 0.01 -10000 0 0 44 44
FRS2 0.035 0.009 -10000 0 0 30 30
oxygen and reactive oxygen species metabolic process 0.018 0.085 0.2 2 -0.27 22 24
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.036 0.005 -10000 0 0 10 10
Nck/Pak 0.048 0.025 -10000 0 -0.14 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.01 0.1 -10000 0 -0.3 29 29
mol:GDP 0.018 0.094 -10000 0 -0.23 46 46
mol:NADP 0.035 0.12 0.32 22 -0.33 17 39
eNOS/Hsp90 0.032 0.12 0.3 22 -0.32 17 39
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.007 0.13 0.25 54 -0.32 20 74
HIF1A/ARNT 0.046 0.032 -10000 0 -0.14 11 11
SHB 0.033 0.011 -10000 0 0 51 51
VEGFA -0.003 0.013 -10000 0 -0.041 52 52
VEGFC 0.033 0.011 -10000 0 0 50 50
FAK1/Vinculin 0.013 0.12 0.27 12 -0.45 19 31
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.037 0.1 0.21 1 -0.29 25 26
PTPN6 0.033 0.011 -10000 0 0 53 53
EPAS1 0.033 0.062 -10000 0 -0.31 11 11
mol:L-citrulline 0.035 0.12 0.32 22 -0.33 17 39
ITGAV 0.035 0.009 -10000 0 0 31 31
PIK3CA 0.031 0.014 -10000 0 0 82 82
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.039 0.095 0.21 1 -0.29 20 21
VEGFR2 homodimer/VEGFA homodimer 0.012 0.099 -10000 0 -0.26 46 46
VEGFR2/3 heterodimer 0.026 0.085 0.19 2 -0.33 16 18
VEGFB 0.036 0.004 -10000 0 0 7 7
MAPK11 0.009 0.13 0.28 36 -0.35 20 56
VEGFR2 homodimer -0.005 0.082 0.2 1 -0.4 14 15
FLT1 0.034 0.009 -10000 0 0 34 34
NEDD4 0.029 0.034 0.093 7 -0.057 54 61
MAPK3 0.018 0.13 0.29 43 -0.3 20 63
MAPK1 0.015 0.13 0.29 45 -0.3 20 65
VEGFA145/NRP2 0.023 0.022 -10000 0 -0.038 38 38
VEGFR1/2 heterodimer 0.024 0.084 0.19 1 -0.33 16 17
KDR -0.005 0.082 0.2 1 -0.4 14 15
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.1 0.2 11 -0.23 46 57
SRC 0.034 0.009 -10000 0 0 34 34
platelet activating factor biosynthetic process 0.018 0.13 0.29 43 -0.31 20 63
PI3K 0.004 0.14 0.28 17 -0.38 32 49
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.021 0.087 0.18 1 -0.31 18 19
FES 0.008 0.13 0.24 69 -0.34 18 87
GAB1 0.013 0.12 0.26 10 -0.38 24 34
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.085 -10000 0 -0.3 18 18
CTNNB1 0.036 0.006 -10000 0 0 15 15
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.036 0.004 -10000 0 0 6 6
eNOS/Caveolin-1 0.01 0.096 0.3 5 -0.39 11 16
VEGFR2 homodimer/VEGFA homodimer/Yes 0.019 0.09 -10000 0 -0.31 20 20
PI3K/GAB1 0.002 0.16 0.28 20 -0.4 45 65
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.06 0.098 0.24 2 -0.28 17 19
PRKACA 0.035 0.008 -10000 0 0 24 24
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.081 -10000 0 -0.31 14 14
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.007 0.13 0.23 67 -0.34 18 85
actin cytoskeleton reorganization 0.023 0.086 0.18 1 -0.32 17 18
PTK2 0.013 0.13 0.26 20 -0.48 18 38
EDG1 0 0.14 0.23 65 -0.36 28 93
mol:DAG 0.007 0.13 0.25 54 -0.32 20 74
CaM/Ca2+ 0.019 0.12 0.26 23 -0.31 25 48
MAP2K3 0 0.12 0.27 35 -0.34 17 52
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.045 0.14 0.23 102 -0.3 43 145
PLCG1 0.006 0.13 0.25 54 -0.33 20 74
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.035 0.089 0.21 1 -0.29 18 19
IQGAP1 0.033 0.011 -10000 0 0 47 47
YES1 0.034 0.01 -10000 0 0 39 39
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.022 0.09 0.18 1 -0.31 20 21
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.019 0.087 0.18 1 -0.3 19 20
cell migration 0.006 0.13 0.26 23 -0.4 29 52
mol:PI-3-4-5-P3 0.005 0.14 0.27 18 -0.36 32 50
FYN 0.03 0.014 -10000 0 0 88 88
VEGFB/NRP1 0.006 0.12 0.22 56 -0.33 18 74
mol:NO 0.035 0.12 0.32 22 -0.33 17 39
PXN 0.036 0.004 -10000 0 0 7 7
HRAS/GTP -0.045 0.07 -10000 0 -0.24 43 43
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.006 0.098 -10000 0 -0.3 43 43
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.036 0.003 -10000 0 0 4 4
NOS3 0.034 0.13 0.33 20 -0.37 17 37
VEGFR2 homodimer/VEGFA homodimer/Sck 0.016 0.094 -10000 0 -0.3 26 26
RAC1 0.025 0.017 -10000 0 0 163 163
PRKCA 0.001 0.12 0.27 34 -0.31 20 54
PRKCB 0.004 0.12 0.26 35 -0.31 20 55
VCL 0.026 0.017 -10000 0 0 154 154
VEGFA165/NRP1 -0.025 0.083 0.13 38 -0.23 46 84
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.087 0.18 1 -0.31 18 19
VEGFA165/NRP2 0.023 0.022 -10000 0 -0.038 38 38
MAPKKK cascade -0.03 0.093 0.17 11 -0.32 32 43
NRP2 0.036 0.005 -10000 0 0 8 8
VEGFC homodimer 0.033 0.011 -10000 0 0 50 50
NCK1 0.035 0.008 -10000 0 0 27 27
ROCK1 0.036 0.006 -10000 0 0 15 15
FAK1/Paxillin 0.03 0.13 0.27 16 -0.46 18 34
MAP3K13 0.007 0.13 0.28 38 -0.35 17 55
PDPK1 -0.013 0.13 0.25 30 -0.33 31 61
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 0.012 0.11 0.22 1 -0.18 77 78
NFATC4 -0.022 0.067 0.17 17 -0.2 5 22
ERBB2IP 0.035 0.01 -10000 0 -0.001 37 37
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.03 0.078 0.18 7 -0.18 20 27
JUN -0.005 0.086 0.22 5 -0.36 7 12
HRAS 0.034 0.009 -10000 0 0 36 36
DOCK7 -0.037 0.068 0.16 9 -0.16 71 80
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.026 0.081 0.21 14 -0.13 86 100
AKT1 -0.01 0.008 0.014 29 -10000 0 29
BAD -0.015 0.014 0.085 7 -10000 0 7
MAPK10 0.004 0.07 0.16 35 -0.15 12 47
mol:GTP 0 0.002 0.003 1 -0.005 26 27
ErbB2/ErbB3/neuregulin 1 beta -0.031 0.083 0.2 7 -0.2 18 25
RAF1 -0.021 0.1 0.25 10 -0.24 34 44
ErbB2/ErbB3/neuregulin 2 0.001 0.073 0.21 15 -0.13 91 106
STAT3 -0.024 0.24 -10000 0 -0.9 35 35
cell migration -0.01 0.067 0.18 16 -0.17 17 33
mol:PI-3-4-5-P3 -0.001 0.002 0.004 16 -0.004 20 36
cell proliferation -0.042 0.24 0.44 3 -0.58 60 63
FOS -0.032 0.2 0.38 6 -0.42 93 99
NRAS 0.032 0.012 -10000 0 0 63 63
mol:Ca2+ -0.03 0.078 0.18 7 -0.18 20 27
MAPK3 -0.02 0.18 0.4 3 -0.48 40 43
MAPK1 -0.044 0.22 0.4 3 -0.57 52 55
JAK2 -0.028 0.076 0.17 17 -0.18 19 36
NF2 0.01 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.005 0.08 0.15 12 -0.17 89 101
NRG1 0.036 0.005 -10000 0 0 9 9
GRB2/SOS1 0.024 0.021 -10000 0 -0.14 8 8
MAPK8 -0.018 0.088 0.18 3 -0.23 48 51
MAPK9 0.01 0.073 0.16 46 -0.14 4 50
ERBB2 -0.016 0.069 0.26 30 -10000 0 30
ERBB3 0.018 0.018 -10000 0 0 257 257
SHC1 0.033 0.011 -10000 0 0 52 52
RAC1 0.025 0.017 -10000 0 0 163 163
apoptosis 0.012 0.03 0.2 10 -0.069 4 14
STAT3 (dimer) -0.022 0.24 -10000 0 -0.88 35 35
RNF41 -0.021 0.02 0.076 10 -0.12 6 16
FRAP1 -0.016 0.012 0.084 5 -10000 0 5
RAC1-CDC42/GTP -0.023 0.044 -10000 0 -0.13 47 47
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.008 -10000 0 -10000 0 0
CHRNA1 -0.007 0.15 0.36 5 -0.36 44 49
myelination -0.036 0.071 0.22 9 -0.21 5 14
PPP3CB -0.022 0.067 0.17 16 -0.18 16 32
KRAS 0.034 0.009 -10000 0 0 34 34
RAC1-CDC42/GDP 0.021 0.075 0.22 1 -0.16 48 49
NRG2 0.036 0.004 -10000 0 0 7 7
mol:GDP -0.005 0.08 0.15 12 -0.17 89 101
SOS1 0 0.001 -10000 0 -0.004 9 9
MAP2K2 -0.029 0.1 0.22 11 -0.25 41 52
SRC 0.034 0.009 -10000 0 0 34 34
mol:cAMP -0.001 0.001 0.003 4 -0.004 1 5
PTPN11 -0.033 0.082 0.17 20 -0.18 20 40
MAP2K1 -0.038 0.2 0.39 2 -0.56 37 39
heart morphogenesis -0.03 0.078 0.18 7 -0.18 20 27
RAS family/GDP 0.02 0.11 0.24 1 -0.18 79 80
GRB2 0.035 0.007 -10000 0 0 18 18
PRKACA 0.018 0.009 -10000 0 -10000 0 0
CHRNE 0.001 0.025 0.076 2 -0.13 7 9
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.008 -10000 0 -0.014 29 29
nervous system development -0.03 0.078 0.18 7 -0.18 20 27
CDC42 0.035 0.008 -10000 0 0 26 26
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.011 -10000 0 0 46 46
VLDLR 0.027 0.016 -10000 0 0 137 137
LRPAP1 0.036 0.007 -10000 0 0 17 17
NUDC 0.035 0.008 -10000 0 0 28 28
RELN/LRP8 0.04 0.043 -10000 0 -0.13 10 10
CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
KATNA1 0.034 0.01 -10000 0 0 45 45
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.036 0.1 0.19 138 -0.2 5 143
IQGAP1/CaM 0.031 0.059 -10000 0 -0.15 45 45
DAB1 0.036 0.005 -10000 0 0 8 8
IQGAP1 0.033 0.011 -10000 0 0 47 47
PLA2G7 0.033 0.011 -10000 0 0 51 51
CALM1 0.033 0.012 -10000 0 0 57 57
DYNLT1 0.034 0.01 -10000 0 0 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 25 25
LIS1/Poliovirus Protein 3A -0.023 0.029 -10000 0 -0.14 24 24
CDK5R2 0.036 0.006 -10000 0 0 16 16
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.031 0.048 -10000 0 -0.13 20 20
YWHAE 0.035 0.008 -10000 0 0 27 27
NDEL1/14-3-3 E 0.06 0.17 0.32 135 -0.26 17 152
MAP1B -0.014 0.067 -10000 0 -0.2 51 51
RAC1 -0.003 0.051 -10000 0 -0.27 11 11
p35/CDK5 -0.026 0.055 0.2 7 -0.21 11 18
RELN 0.023 0.018 -10000 0 0 186 186
PAFAH/LIS1 0.021 0.04 -10000 0 -0.15 22 22
LIS1/CLIP170 -0.023 0.029 -10000 0 -0.14 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.037 0.074 0.14 9 -0.27 26 35
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.013 0.088 0.17 1 -0.23 53 54
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.053 0.16 0.3 131 -0.26 14 145
LIS1/IQGAP1 0.013 0.059 -10000 0 -0.15 50 50
RHOA -0.006 0.066 -10000 0 -0.27 19 19
PAFAH1B1 -0.02 0.008 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.013 -10000 0 0 78 78
PAFAH1B2 0.036 0.005 -10000 0 0 8 8
MAP1B/LIS1/Dynein heavy chain 0.005 0.079 -10000 0 -0.2 55 55
NDEL1/Katanin 60/Dynein heavy chain 0.079 0.15 0.33 111 -0.25 23 134
LRP8 0.034 0.009 -10000 0 0 34 34
NDEL1/Katanin 60 0.053 0.16 0.31 127 -0.25 18 145
P39/CDK5 -0.025 0.055 0.2 7 -0.21 11 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.053 -10000 0 -0.19 26 26
CDK5 -0.013 0.043 0.19 8 -0.2 5 13
PPP2R5D 0.036 0.004 -10000 0 0 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.018 0.024 -10000 0 -0.12 24 24
CSNK2A1 0.033 0.011 -10000 0 0 51 51
RELN/VLDLR/DAB1/LIS1 0.033 0.061 -10000 0 -0.14 32 32
RELN/VLDLR 0.044 0.06 -10000 0 -0.12 25 25
CDC42 -0.003 0.048 -10000 0 -0.2 17 17
Paxillin-dependent events mediated by a4b1

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
CRKL 0.035 0.008 -10000 0 0 28 28
Rac1/GDP 0.025 0.02 -10000 0 -0.025 11 11
DOCK1 0.024 0.018 -10000 0 0 183 183
ITGA4 0.036 0.006 -10000 0 0 13 13
RAC1 0.025 0.017 -10000 0 0 163 163
alpha4/beta7 Integrin 0.052 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.051 0.035 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.052 0.018 -10000 0 -10000 0 0
lamellipodium assembly -0.047 0.14 -10000 0 -0.35 80 80
PIK3CA 0.031 0.014 -10000 0 0 82 82
PI3K 0.018 0.076 -10000 0 -0.16 72 72
ARF6 0.035 0.009 -10000 0 0 29 29
TLN1 0.029 0.015 -10000 0 0 101 101
PXN -0.021 0.01 0.093 3 -10000 0 3
PIK3R1 0.032 0.012 -10000 0 0 63 63
ARF6/GTP 0.048 0.049 -10000 0 -0.12 1 1
cell adhesion 0.044 0.052 -10000 0 -0.12 12 12
CRKL/CBL 0.051 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.039 0.027 -10000 0 -10000 0 0
ITGB1 0.026 0.017 -10000 0 0 144 144
ITGB7 0.036 0.006 -10000 0 0 14 14
ARF6/GDP 0.035 0.015 -10000 0 -0.025 13 13
alpha4/beta1 Integrin/Paxillin/VCAM1 0.011 0.081 -10000 0 -0.12 117 117
p130Cas/Crk/Dock1 0.027 0.036 -10000 0 -0.11 18 18
VCAM1 0.023 0.018 -10000 0 0 195 195
alpha4/beta1 Integrin/Paxillin/Talin 0.046 0.053 -10000 0 -0.12 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.048 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.05 0.047 -10000 0 -10000 0 0
CBL 0.036 0.005 -10000 0 0 8 8
PRKACA 0.035 0.008 -10000 0 0 24 24
GIT1 0.037 0.003 -10000 0 0 3 3
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.046 0.053 -10000 0 -0.12 12 12
Rac1/GTP -0.053 0.16 -10000 0 -0.39 80 80
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.035 0.009 -10000 0 0 31 31
SPHK1 0.033 0.011 -10000 0 0 51 51
GNAI2 0.034 0.01 -10000 0 0 44 44
mol:S1P 0.018 0.016 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
mol:Sphinganine-1-P -0.011 0.032 0.093 43 -10000 0 43
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.028 0.046 -10000 0 -0.18 3 3
GNAI3 0.036 0.006 -10000 0 0 14 14
G12/G13 0.025 0.048 -10000 0 -0.14 28 28
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.034 0.01 -10000 0 0 45 45
S1P1/S1P 0.035 0.033 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.018 0.018 -10000 0 0 262 262
S1P/S1P5/G12 0.017 0.037 -10000 0 -0.18 3 3
S1P/S1P3/Gq 0.027 0.04 0.15 6 -0.26 6 12
S1P/S1P4/Gi -0.004 0.11 -10000 0 -0.29 43 43
GNAQ 0.035 0.009 -10000 0 0 30 30
GNAZ 0.031 0.013 -10000 0 0 80 80
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GNA12 0.023 0.018 -10000 0 0 189 189
GNA13 0.035 0.007 -10000 0 0 20 20
GNA11 0.033 0.011 -10000 0 0 51 51
ABCC1 0.035 0.007 -10000 0 0 19 19
BMP receptor signaling

Figure 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
BMP7/BMPR2/BMPR1A-1B/FS 0.063 0.065 -9999 0 -0.12 12 12
SMAD6-7/SMURF1 0.045 0.038 -9999 0 -0.13 3 3
NOG 0 0 -9999 0 -10000 0 0
SMAD9 -0.025 0.15 -9999 0 -0.44 54 54
SMAD4 0.032 0.012 -9999 0 0 59 59
SMAD5 -0.027 0.095 -9999 0 -0.3 42 42
BMP7/USAG1 0.033 0.027 -9999 0 -10000 0 0
SMAD5/SKI -0.021 0.11 -9999 0 -0.3 45 45
SMAD1 -0.033 0.15 -9999 0 -0.38 58 58
BMP2 0.028 0.016 -9999 0 0 125 125
SMAD1/SMAD1/SMAD4 -0.011 0.13 -9999 0 -0.35 46 46
BMPR1A 0.025 0.017 -9999 0 0 169 169
BMPR1B 0.036 0.006 -9999 0 0 12 12
BMPR1A-1B/BAMBI 0.021 0.06 -9999 0 -0.13 48 48
AHSG 0.035 0.009 -9999 0 0 29 29
CER1 0.032 0.013 -9999 0 0 71 71
BMP2-4/CER1 0.037 0.055 -9999 0 -0.12 34 34
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.077 -9999 0 -0.25 26 26
BMP2-4 (homodimer) 0.028 0.051 -9999 0 -0.14 34 34
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.054 0.058 -9999 0 -0.12 12 12
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.025 0.017 -9999 0 0 164 164
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.068 -9999 0 -0.16 58 58
BMP2-4/USAG1 0.033 0.045 -9999 0 -0.12 14 14
SMAD6/SMURF1/SMAD5 -0.012 0.09 -9999 0 -0.28 35 35
SOSTDC1 0.023 0.018 -9999 0 0 184 184
BMP7/BMPR2/BMPR1A-1B 0.054 0.058 -9999 0 -0.12 14 14
SKI 0.037 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.035 0.008 -9999 0 0 25 25
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.034 0.009 -9999 0 0 35 35
MAP3K7 0.034 0.01 -9999 0 0 43 43
BMP2-4/CHRD 0.041 0.055 -9999 0 -0.12 33 33
SMAD5/SMAD5/SMAD4 -0.023 0.11 -9999 0 -0.31 45 45
MAPK1 0.034 0.01 -9999 0 0 44 44
TAK1/TAB family 0.019 0.084 -9999 0 -0.21 15 15
BMP7 (homodimer) 0.034 0.01 -9999 0 0 41 41
NUP214 0.035 0.007 -9999 0 0 18 18
BMP6/FETUA 0.049 0.016 -9999 0 -10000 0 0
SMAD1/SKI -0.016 0.15 -9999 0 -0.36 60 60
SMAD6 0.036 0.005 -9999 0 0 9 9
CTDSP2 0.033 0.012 -9999 0 0 58 58
BMP2-4/FETUA 0.04 0.055 -9999 0 -0.12 34 34
MAP3K7IP1 0.034 0.009 -9999 0 0 36 36
GREM1 0.032 0.012 -9999 0 0 60 60
BMPR2 (homodimer) 0.036 0.005 -9999 0 0 10 10
GADD34/PP1CA 0.051 0.055 -9999 0 -0.13 33 33
BMPR1A-1B (homodimer) 0.034 0.032 -9999 0 -0.14 6 6
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.019 0.16 -9999 0 -0.38 60 60
SMAD6-7/SMURF1/SMAD1 0.003 0.14 -9999 0 -0.36 47 47
SMAD6/SMURF1 0.025 0.017 -9999 0 0 164 164
BAMBI 0.018 0.018 -9999 0 0 259 259
SMURF2 0.035 0.007 -9999 0 0 19 19
BMP2-4/CHRDL1 0.026 0.044 -9999 0 -0.12 34 34
BMP2-4/GREM1 0.037 0.055 -9999 0 -0.12 33 33
SMAD7 0.034 0.01 -9999 0 0 45 45
SMAD8A/SMAD8A/SMAD4 -0.014 0.15 -9999 0 -0.41 61 61
SMAD1/SMAD6 -0.017 0.14 -9999 0 -0.36 51 51
TAK1/SMAD6 0.033 0.034 -9999 0 -0.14 8 8
BMP7 0.034 0.01 -9999 0 0 41 41
BMP6 0.035 0.008 -9999 0 0 25 25
MAP3K7IP2 0.033 0.011 -9999 0 0 47 47
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.003 0.056 -9999 0 -0.22 16 16
PPM1A 0.035 0.009 -9999 0 0 31 31
SMAD1/SMURF2 -0.017 0.16 -9999 0 -0.38 58 58
SMAD7/SMURF1 0.033 0.03 -9999 0 -0.14 3 3
CTDSPL 0.036 0.006 -9999 0 0 13 13
PPP1CA 0.035 0.007 -9999 0 0 19 19
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.036 0.006 -9999 0 0 15 15
PPP1R15A 0.033 0.011 -9999 0 0 53 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.013 0.069 -9999 0 -0.21 28 28
CHRD 0.035 0.008 -9999 0 0 23 23
BMPR2 0.036 0.005 -9999 0 0 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.019 0.07 -9999 0 -0.17 55 55
BMP4 0.033 0.011 -9999 0 0 51 51
FST 0.033 0.011 -9999 0 0 48 48
BMP2-4/NOG 0.026 0.044 -9999 0 -0.12 34 34
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.051 0.062 -9999 0 -0.12 9 9
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.036 0.006 -10000 0 0 15 15
MKNK1 0.034 0.009 -10000 0 0 35 35
mol:PIP3 -0.019 0.058 0.093 5 -0.24 21 26
FRAP1 0.035 0.1 0.28 2 -0.5 11 13
AKT1 0.015 0.11 0.16 118 -0.26 30 148
INSR 0.035 0.008 -10000 0 0 23 23
Insulin Receptor/Insulin 0.046 0.013 -10000 0 -10000 0 0
mol:GTP 0.04 0.11 0.2 75 -0.25 33 108
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.046 -10000 0 -0.19 15 15
TSC2 0.035 0.008 -10000 0 0 28 28
RHEB/GDP 0.006 0.076 0.13 2 -0.21 36 38
TSC1 0.034 0.01 -10000 0 0 40 40
Insulin Receptor/IRS1 0.023 0.06 -10000 0 -0.25 22 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.071 -10000 0 -0.23 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.043 0.086 0.25 10 -0.32 4 14
MAP3K5 -0.027 0.085 0.16 1 -0.23 73 74
PIK3R1 0.033 0.012 -10000 0 0 63 63
apoptosis -0.026 0.085 0.16 1 -0.23 73 74
mol:LY294002 0 0 0.001 9 -0.001 18 27
EIF4B 0.037 0.082 0.23 13 -0.3 5 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.073 0.23 7 -0.27 4 11
eIF4E/eIF4G1/eIF4A1 0.011 0.074 -10000 0 -0.33 12 12
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.083 -10000 0 -0.23 33 33
mTOR/RHEB/GTP/Raptor/GBL 0.013 0.065 0.19 18 -0.2 12 30
FKBP1A 0.032 0.012 -10000 0 0 63 63
RHEB/GTP 0.022 0.089 0.2 17 -0.21 34 51
mol:Amino Acids 0 0 0.001 9 -0.001 18 27
FKBP12/Rapamycin 0.021 0.024 -10000 0 -0.14 10 10
PDPK1 -0.02 0.063 0.16 17 -0.23 20 37
EIF4E 0.034 0.01 -10000 0 0 38 38
ASK1/PP5C -0.031 0.24 -10000 0 -0.56 79 79
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.015 0.11 -10000 0 -0.34 32 32
TSC1/TSC2 0.044 0.12 0.21 75 -0.27 33 108
tumor necrosis factor receptor activity 0 0 0.001 18 -0.001 9 27
RPS6 0.031 0.014 -10000 0 0 86 86
PPP5C 0.034 0.01 -10000 0 0 39 39
EIF4G1 0.033 0.011 -10000 0 0 50 50
IRS1 0.001 0.059 -10000 0 -0.26 23 23
INS 0.036 0.006 -10000 0 0 16 16
PTEN 0.025 0.017 -10000 0 0 168 168
PDK2 -0.019 0.064 0.16 17 -0.23 21 38
EIF4EBP1 -0.024 0.26 -10000 0 -1.1 26 26
PIK3CA 0.031 0.014 -10000 0 0 82 82
PPP2R5D 0.029 0.094 0.27 3 -0.45 11 14
peptide biosynthetic process -0.021 0.017 0.18 3 -10000 0 3
RHEB 0.025 0.017 -10000 0 0 167 167
EIF4A1 0.035 0.007 -10000 0 0 18 18
mol:Rapamycin 0 0.001 0.004 17 -0.003 14 31
EEF2 -0.021 0.017 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.008 0.25 -10000 0 -1.1 26 26
IL6-mediated 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
BCL2L1 0.067 0.27 0.56 21 -0.68 26 47
CRP 0.058 0.26 0.57 13 -0.69 24 37
cell cycle arrest 0.05 0.29 0.53 19 -0.75 32 51
TIMP1 0.004 0.37 0.56 16 -0.79 72 88
IL6ST 0.028 0.033 0.09 2 -0.045 52 54
Rac1/GDP 0.041 0.11 0.3 16 -0.31 11 27
AP1 0.012 0.2 -10000 0 -0.56 38 38
GAB2 0.034 0.012 -10000 0 -0.041 1 1
TNFSF11 0.056 0.26 0.57 9 -0.74 20 29
HSP90B1 0.001 0.22 0.3 3 -0.84 30 33
GAB1 0.033 0.012 -10000 0 -0.042 1 1
MAPK14 0.028 0.067 0.21 2 -0.31 3 5
AKT1 -0.012 0.17 -10000 0 -0.6 27 27
FOXO1 -0.013 0.16 -10000 0 -0.53 31 31
MAP2K6 0.028 0.072 0.19 2 -0.26 8 10
mol:GTP 0 0.004 -10000 0 -0.022 1 1
MAP2K4 0.035 0.14 0.35 23 -0.35 17 40
MITF 0.031 0.085 0.23 12 -0.29 9 21
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.01 -10000 0 0 45 45
A2M -0.076 0.34 -10000 0 -1.2 44 44
CEBPB 0.031 0.014 -10000 0 0 82 82
GRB2/SOS1/GAB family/SHP2 0.021 0.13 0.32 1 -0.48 24 25
STAT3 0.04 0.3 0.54 18 -0.8 32 50
STAT1 0.022 0.065 -10000 0 -0.71 3 3
CEBPD 0.023 0.34 0.55 11 -0.86 47 58
PIK3CA 0.031 0.014 -10000 0 0 83 83
PI3K 0.019 0.076 -10000 0 -0.16 73 73
JUN 0.034 0.01 -10000 0 0 41 41
PIAS3/MITF 0.078 0.11 0.27 24 -0.27 13 37
MAPK11 0.025 0.065 0.21 1 -0.31 3 4
STAT3 (dimer)/FOXO1 -0.021 0.26 0.46 8 -0.62 54 62
GRB2/SOS1/GAB family 0.043 0.13 0.24 2 -0.31 31 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.004 0.1 0.19 10 -0.28 39 49
GRB2 0.036 0.008 -10000 0 -0.002 19 19
JAK2 0.031 0.014 -10000 0 0 83 83
LBP 0.067 0.26 0.54 18 -0.62 28 46
PIK3R1 0.033 0.013 -10000 0 -0.042 1 1
JAK1 0.03 0.026 -10000 0 -0.043 47 47
MYC 0.011 0.37 0.56 16 -0.86 62 78
FGG 0.056 0.26 0.57 9 -0.74 20 29
macrophage differentiation 0.05 0.29 0.53 19 -0.75 32 51
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.074 -10000 0 -0.19 6 6
JUNB 0.051 0.3 0.51 28 -0.79 33 61
FOS 0.025 0.017 -10000 0 0 162 162
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.029 0.085 0.23 14 -0.29 10 24
STAT1/PIAS1 0.072 0.13 0.31 13 -0.35 7 20
GRB2/SOS1/GAB family/SHP2/PI3K 0 0.17 -10000 0 -0.52 32 32
STAT3 (dimer) 0.042 0.3 0.54 18 -0.79 32 50
PRKCD 0.11 0.22 0.4 107 -0.43 23 130
IL6R 0.03 0.027 -10000 0 -0.041 57 57
SOCS3 0.06 0.087 0.42 3 -10000 0 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.044 0.089 0.18 1 -0.17 46 47
Rac1/GTP 0.038 0.12 0.3 14 -0.32 13 27
HCK 0.027 0.017 -10000 0 0 141 141
MAPKKK cascade 0.013 0.19 0.34 2 -0.6 34 36
bone resorption 0.058 0.25 0.56 9 -0.69 21 30
IRF1 0.05 0.3 0.54 20 -0.85 27 47
mol:GDP 0.031 0.09 0.24 16 -0.28 10 26
SOS1 0.001 0.004 0.026 10 -0.022 1 11
VAV1 0.03 0.09 0.24 17 -0.28 10 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.02 0.078 -10000 0 -0.33 13 13
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 0.075 -10000 0 -0.15 44 44
gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.065 -10000 0 -0.12 35 35
IL6 0.015 0.027 -10000 0 -0.041 25 25
PIAS3 0.036 0.006 -10000 0 0 15 15
PTPRE 0.009 0.03 -10000 0 -0.056 36 36
PIAS1 0.035 0.008 -10000 0 0 25 25
RAC1 0.025 0.018 -10000 0 0 163 163
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.057 0.17 4 -0.22 6 10
LMO4 0.029 0.033 0.09 2 -0.046 50 52
STAT3 (dimer)/PIAS3 0.012 0.27 0.48 5 -0.72 34 39
MCL1 -0.014 0.16 -10000 0 -0.7 17 17
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.022 0.054 0.16 16 -0.22 9 25
DAPP1 -0.022 0.13 0.18 1 -0.3 63 64
Src family/SYK family/BLNK-LAT/BTK-ITK -0.044 0.19 0.26 2 -0.49 57 59
mol:DAG -0.007 0.091 0.19 21 -0.2 48 69
HRAS 0.035 0.02 0.077 2 -0.032 25 27
RAP1A 0.038 0.014 0.063 4 -0.019 20 24
ARF5/GDP 0.001 0.095 -10000 0 -0.32 30 30
PLCG2 0.032 0.012 -10000 0 0 63 63
PLCG1 0.034 0.01 -10000 0 0 37 37
ARF5 0.024 0.017 -10000 0 0 171 171
mol:GTP -0.024 0.052 0.15 17 -0.2 10 27
ARF1/GTP -0.018 0.047 0.12 16 -0.2 12 28
RHOA 0.035 0.007 -10000 0 0 21 21
YES1 0.034 0.01 -10000 0 0 39 39
RAP1A/GTP -0.023 0.053 0.16 17 -0.2 10 27
ADAP1 -0.024 0.046 0.13 14 -0.19 10 24
ARAP3 -0.024 0.051 0.15 17 -0.2 10 27
INPPL1 0.036 0.006 -10000 0 0 13 13
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.033 0.011 -10000 0 0 48 48
ARHGEF7 0.033 0.012 -10000 0 0 57 57
ARF1 0.035 0.008 -10000 0 0 24 24
NRAS 0.035 0.018 0.068 1 -0.033 12 13
FYN 0.03 0.014 -10000 0 0 88 88
ARF6 0.035 0.009 -10000 0 0 29 29
FGR 0.033 0.011 -10000 0 0 56 56
mol:Ca2+ 0.007 0.061 0.15 35 -0.12 17 52
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.033 0.011 -10000 0 0 46 46
ZAP70 0.037 0.002 -10000 0 0 2 2
mol:IP3 -0.008 0.065 0.17 23 -0.17 18 41
LYN 0.031 0.013 -10000 0 0 74 74
ARF1/GDP 0.01 0.11 -10000 0 -0.34 34 34
RhoA/GDP 0.028 0.09 0.18 14 -0.22 30 44
PDK1/Src/Hsp90 0.046 0.014 -10000 0 -10000 0 0
BLNK 0.019 0.018 -10000 0 0 248 248
actin cytoskeleton reorganization 0.011 0.11 0.19 27 -0.29 26 53
SRC 0.034 0.009 -10000 0 0 34 34
PLEKHA2 -0.012 0.024 0.086 29 -10000 0 29
RAC1 0.025 0.017 -10000 0 0 163 163
PTEN 0.025 0.022 -10000 0 -0.033 17 17
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.055 0.16 17 -0.2 10 27
RhoA/GTP -0.026 0.058 0.17 18 -0.21 11 29
Src family/SYK family/BLNK-LAT -0.05 0.16 -10000 0 -0.35 84 84
BLK 0.036 0.007 -10000 0 0 17 17
PDPK1 0.036 0.005 -10000 0 0 8 8
CYTH1 -0.024 0.046 0.13 14 -0.19 10 24
HCK 0.027 0.016 -10000 0 0 141 141
CYTH3 -0.024 0.046 0.13 14 -0.19 10 24
CYTH2 -0.024 0.046 0.13 14 -0.19 10 24
KRAS 0.034 0.021 0.077 2 -0.032 30 32
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.003 0.031 0.21 2 -0.15 3 5
SGK1 0 0.03 0.21 1 -0.16 3 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.005 0.11 0.21 1 -0.34 35 36
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.031 0.013 -10000 0 0 74 74
ARF6/GDP -0.025 0.067 0.17 15 -0.22 27 42
mol:PI-3-4-5-P3 -0.025 0.049 0.14 14 -0.2 10 24
ARAP3/RAP1A/GTP -0.023 0.053 0.16 17 -0.2 10 27
VAV1 0.034 0.009 -10000 0 0 33 33
mol:PI-3-4-P2 -0.011 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.068 0.097 0.21 123 -0.14 41 164
PLEKHA1 -0.007 0.022 0.086 23 -10000 0 23
Rac1/GDP 0.002 0.098 -10000 0 -0.31 31 31
LAT 0.036 0.005 -10000 0 0 9 9
Rac1/GTP -0.004 0.15 0.16 1 -0.46 36 37
ITK -0.027 0.049 0.13 15 -0.2 10 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.021 0.11 0.23 10 -0.28 53 63
LCK 0.035 0.007 -10000 0 0 18 18
BTK -0.026 0.052 0.14 18 -0.2 10 28
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.041 0.089 0.24 21 -0.21 7 28
TBX21 0.069 0.2 0.58 6 -0.59 3 9
B2M 0.035 0.008 -10000 0 0 24 24
TYK2 0.036 0.039 0.12 16 -0.05 29 45
IL12RB1 0.037 0.04 0.12 15 -0.051 31 46
GADD45B 0.06 0.29 0.52 18 -0.99 24 42
IL12RB2 0.04 0.041 0.12 20 -0.052 23 43
GADD45G 0.093 0.19 0.54 9 -0.55 3 12
natural killer cell activation 0.012 0.024 0.056 75 -0.036 9 84
RELB 0.034 0.009 -10000 0 0 32 32
RELA 0.036 0.004 -10000 0 0 7 7
IL18 0.034 0.022 0.089 2 -0.043 17 19
IL2RA 0.024 0.018 -10000 0 0 177 177
IFNG 0.035 0.009 -10000 0 0 30 30
STAT3 (dimer) 0.073 0.22 0.47 20 -0.57 19 39
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 45 45
FASLG 0.073 0.2 0.58 6 -0.6 2 8
NF kappa B2 p52/RelB 0.051 0.18 0.45 8 -0.51 10 18
CD4 0.024 0.027 -10000 0 -0.017 130 130
SOCS1 0.036 0.005 -10000 0 0 9 9
EntrezGene:6955 -0.001 0.01 -10000 0 -0.025 57 57
CD3D 0.025 0.028 -10000 0 -0.025 110 110
CD3E 0.028 0.027 -10000 0 -0.035 78 78
CD3G 0.027 0.029 -10000 0 -0.034 86 86
IL12Rbeta2/JAK2 0.055 0.059 0.18 18 -10000 0 18
CCL3 0.072 0.2 0.5 16 -0.51 11 27
CCL4 0.041 0.33 0.6 12 -1 31 43
HLA-A 0.036 0.006 -10000 0 0 12 12
IL18/IL18R 0.095 0.063 0.22 26 -0.11 16 42
NOS2 0.074 0.19 0.44 31 -0.44 14 45
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.088 0.24 18 -0.21 7 25
IL1R1 0.071 0.2 0.59 8 -0.57 4 12
IL4 0.004 0.048 -10000 0 -0.077 74 74
JAK2 0.033 0.038 0.12 11 -0.051 22 33
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 45 45
TCR/CD3/MHC I/CD8 0.006 0.046 0.11 1 -0.18 16 17
RAB7A 0.092 0.2 0.45 29 -0.53 20 49
lysosomal transport 0.093 0.2 0.44 29 -0.51 20 49
FOS -0.11 0.49 0.44 29 -1 101 130
STAT4 (dimer) 0.086 0.2 0.46 27 -0.5 15 42
STAT5A (dimer) 0.078 0.19 0.44 8 -0.51 11 19
GZMA 0.069 0.2 0.57 10 -0.59 3 13
GZMB 0.068 0.2 0.58 11 -0.54 7 18
HLX 0 0 -10000 0 -10000 0 0
LCK 0.062 0.2 0.52 15 -0.53 11 26
TCR/CD3/MHC II/CD4 -0.022 0.12 0.17 22 -0.2 126 148
IL2/IL2R 0.059 0.05 -10000 0 -10000 0 0
MAPK14 0.094 0.23 0.51 19 -0.64 19 38
CCR5 0.077 0.18 0.4 34 -0.4 16 50
IL1B 0.029 0.037 0.12 7 -0.051 26 33
STAT6 0.053 0.099 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 0 157 157
IL12B 0.04 0.041 0.12 20 -0.051 26 46
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.041 0.088 0.21 7 -0.24 22 29
IL2RB 0.033 0.011 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.087 0.2 0.46 28 -0.47 15 43
IL2RG 0.035 0.008 -10000 0 0 24 24
IL12 0.062 0.06 0.2 13 -10000 0 13
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 9 9
SPHK2 0.035 0.009 -10000 0 0 31 31
FRAP1 0.036 0.006 -10000 0 0 16 16
IL12A 0.038 0.04 0.12 19 -0.051 32 51
IL12/IL12R/TYK2/JAK2 0.065 0.21 0.54 18 -0.56 11 29
MAP2K3 0.088 0.23 0.54 12 -0.65 19 31
RIPK2 0.036 0.006 -10000 0 0 14 14
MAP2K6 0.092 0.22 0.5 19 -0.59 19 38
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.021 0.027 -10000 0 -0.012 183 183
IL18RAP 0.039 0.02 0.084 3 -0.041 22 25
IL12Rbeta1/TYK2 0.049 0.063 0.18 7 -0.16 14 21
EOMES -0.019 0.038 0.076 2 -0.1 47 49
STAT1 (dimer) 0.086 0.19 0.45 21 -0.47 8 29
T cell proliferation 0.075 0.18 0.4 34 -0.41 19 53
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.039 0.02 0.084 3 -0.041 22 25
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.17 -10000 0 -0.47 23 23
ATF2 0.086 0.22 0.47 19 -0.6 19 38
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.001 0.04 -10000 0 -10000 0 0
CRKL 0.035 0.008 -10000 0 0 28 28
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
DOCK1 0.024 0.018 -10000 0 0 183 183
ITGA4 0.036 0.006 -10000 0 0 13 13
alpha4/beta7 Integrin/MAdCAM1 0.082 0.038 -10000 0 -0.12 6 6
EPO 0.025 0.017 -10000 0 0 164 164
alpha4/beta7 Integrin 0.052 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.038 0.025 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.036 0.026 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.1 -10000 0 -0.38 22 22
PIK3CA 0.031 0.014 -10000 0 0 82 82
PI3K 0.018 0.076 -10000 0 -0.16 72 72
ARF6 0.035 0.009 -10000 0 0 29 29
JAK2 0.009 0.031 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 7 7
PIK3R1 0.032 0.012 -10000 0 0 63 63
MADCAM1 0.035 0.009 -10000 0 0 29 29
cell adhesion 0.079 0.037 -10000 0 -0.12 6 6
CRKL/CBL 0.051 0.014 -10000 0 -10000 0 0
ITGB1 0.026 0.017 -10000 0 0 144 144
SRC -0.034 0.059 0.19 4 -10000 0 4
ITGB7 0.036 0.006 -10000 0 0 14 14
RAC1 0.025 0.017 -10000 0 0 163 163
alpha4/beta1 Integrin/VCAM1 0.002 0.078 -10000 0 -0.12 126 126
p130Cas/Crk/Dock1 -0.031 0.065 0.2 4 -0.2 7 11
VCAM1 0.023 0.018 -10000 0 0 195 195
RHOA 0.035 0.007 -10000 0 0 21 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.05 -10000 0 -10000 0 0
BCAR1 -0.033 0.052 0.18 4 -10000 0 4
EPOR 0.035 0.008 -10000 0 0 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.036 0.005 -10000 0 0 8 8
GIT1 0.037 0.003 -10000 0 0 3 3
Rac1/GTP -0.016 0.11 -10000 0 -0.39 22 22
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 47 47
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.12 -10000 0 -0.29 60 60
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 0.093 95 -10000 0 95
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.052 -10000 0 -0.13 30 30
IL1R2 0.03 0.014 -10000 0 0 90 90
IL1R1 0.036 0.006 -10000 0 0 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.1 -10000 0 -0.29 40 40
TOLLIP 0.035 0.009 -10000 0 0 31 31
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.005 -10000 0 0 8 8
TAK1/TAB1/TAB2 0.055 0.05 -10000 0 -0.15 21 21
IKK complex/ELKS -0.046 0.097 -10000 0 -0.26 17 17
JUN -0.039 0.042 0.15 2 -0.21 10 12
MAP3K7 0.034 0.01 -10000 0 0 43 43
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.031 0.11 -10000 0 -0.15 112 112
IL1 alpha/IL1R1/IL1RAP/MYD88 0.065 0.069 -10000 0 -0.13 49 49
PIK3R1 0.032 0.012 -10000 0 0 63 63
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.074 0.075 -10000 0 -0.13 48 48
IL1 beta fragment/IL1R1/IL1RAP 0.025 0.083 0.16 8 -0.14 83 91
NFKB1 0.035 0.007 -10000 0 0 18 18
MAPK8 -0.034 0.036 0.17 2 -0.2 8 10
IRAK1 -0.018 0.011 -10000 0 -0.12 5 5
IL1RN/IL1R1 0.053 0.01 -10000 0 -10000 0 0
IRAK4 0.035 0.007 -10000 0 0 19 19
PRKCI 0.035 0.008 -10000 0 0 27 27
TRAF6 0.036 0.005 -10000 0 0 10 10
PI3K 0.018 0.076 -10000 0 -0.16 72 72
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.12 -10000 0 -0.28 59 59
CHUK 0.025 0.017 -10000 0 0 165 165
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.025 0.083 0.16 8 -0.14 83 91
IL1 beta/IL1R2 0.017 0.072 -10000 0 -0.14 71 71
IRAK/TRAF6/TAK1/TAB1/TAB2 0.058 0.07 -10000 0 -0.14 36 36
NF kappa B1 p50/RelA 0.015 0.1 -10000 0 -0.15 107 107
IRAK3 0.035 0.008 -10000 0 0 27 27
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.038 0.083 -10000 0 -0.13 81 81
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.076 -10000 0 -0.28 15 15
IL1 alpha/IL1R1/IL1RAP 0.049 0.054 -10000 0 -0.13 33 33
RELA 0.036 0.004 -10000 0 0 7 7
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
SQSTM1 0.034 0.009 -10000 0 0 35 35
MYD88 0.034 0.009 -10000 0 0 36 36
IRAK/TRAF6/MEKK3 0.05 0.038 -10000 0 -0.12 22 22
IL1RAP 0.03 0.014 -10000 0 0 95 95
UBE2N 0.036 0.006 -10000 0 0 12 12
IRAK/TRAF6 -0.039 0.063 0.063 70 -0.2 24 94
CASP1 0.029 0.015 -10000 0 0 110 110
IL1RN/IL1R2 0.045 0.021 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.038 0.097 -10000 0 -0.15 91 91
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.1 -10000 0 -0.31 36 36
PIK3CA 0.031 0.014 -10000 0 0 82 82
IL1RN 0.036 0.004 -10000 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.064 0.061 -10000 0 -0.14 24 24
MAP2K6 -0.039 0.034 0.17 3 -0.21 8 11
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.011 0.052 -10000 0 -0.12 47 47
TRAF2/ASK1 0.032 0.044 -10000 0 -0.12 36 36
ATM 0.034 0.01 -10000 0 0 37 37
MAP2K3 0.011 0.1 0.23 2 -0.3 29 31
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.093 0.23 2 -0.28 25 27
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.032 0.012 -10000 0 0 65 65
TXN 0.007 0.002 -10000 0 0 37 37
CALM1 0.033 0.012 -10000 0 0 57 57
GADD45A 0.031 0.013 -10000 0 0 77 77
GADD45B 0.031 0.014 -10000 0 0 84 84
MAP3K1 0.035 0.007 -10000 0 0 20 20
MAP3K6 0.035 0.007 -10000 0 0 22 22
MAP3K7 0.034 0.01 -10000 0 0 43 43
MAP3K4 0.032 0.012 -10000 0 0 65 65
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.054 -10000 0 -0.14 39 39
TAK1/TAB family 0.009 0.056 -10000 0 -0.33 11 11
RAC1/OSM/MEKK3 0.031 0.026 -10000 0 -0.1 5 5
TRAF2 0.036 0.006 -10000 0 0 16 16
RAC1/OSM/MEKK3/MKK3 0.011 0.078 -10000 0 -0.26 23 23
TRAF6 0.009 0.033 -10000 0 -0.2 12 12
RAC1 0.025 0.017 -10000 0 0 163 163
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.017 0.018 -10000 0 0 275 275
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.008 0.056 -10000 0 -0.14 53 53
MAPK11 0.033 0.011 -10000 0 0 54 54
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.009 0.069 -10000 0 -0.14 67 67
OSM/MEKK3 0.027 0.003 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 0 37 37
TAOK2 0.012 0.024 -10000 0 -0.2 6 6
TAOK3 0.006 0.041 -10000 0 -0.2 19 19
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
MAPK14 0.036 0.004 -10000 0 0 5 5
MAP3K7IP2 0.033 0.011 -10000 0 0 47 47
MAP3K5 0.03 0.014 -10000 0 0 90 90
MAP3K10 0.035 0.008 -10000 0 0 28 28
MAP3K3 0.036 0.005 -10000 0 0 8 8
TRX/ASK1 0.023 0.035 -10000 0 -0.17 13 13
GADD45/MTK1/MTK1 0.044 0.077 -10000 0 -0.13 66 66
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.056 -10000 0 -0.13 35 35
fibroblast growth factor receptor signaling pathway 0.051 0.056 -10000 0 -0.13 35 35
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.031 0.013 -10000 0 0 74 74
GPC1/SLIT2 0.032 0.046 -10000 0 -0.14 24 24
SMAD2 -0.023 0.049 0.18 11 -0.2 3 14
GPC1/PrPc/Cu2+ 0.024 0.058 -10000 0 -0.14 50 50
GPC1/Laminin alpha1 0.015 0.04 -10000 0 -0.13 34 34
TDGF1 0.035 0.007 -10000 0 0 18 18
CRIPTO/GPC1 0.038 0.047 -10000 0 -0.14 28 28
APP/GPC1 0.034 0.058 -10000 0 -0.16 37 37
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.023 0.033 0.09 22 -0.13 23 45
FLT1 0.034 0.009 -10000 0 0 34 34
GPC1/TGFB/TGFBR1/TGFBR2 0.052 0.053 -10000 0 -0.12 33 33
SERPINC1 0.036 0.006 -10000 0 0 12 12
FYN -0.018 0.029 0.09 24 -0.13 8 32
FGR -0.022 0.033 0.09 22 -0.13 21 43
positive regulation of MAPKKK cascade -0.031 0.13 0.19 22 -0.3 60 82
SLIT2 0.029 0.015 -10000 0 0 102 102
GPC1/NRG 0.037 0.051 -10000 0 -0.14 34 34
NRG1 0.036 0.005 -10000 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.032 0.043 -10000 0 -0.12 34 34
LYN -0.022 0.034 0.09 22 -0.13 23 45
mol:Spermine -0.01 0.004 -10000 0 -10000 0 0
cell growth 0.051 0.056 -10000 0 -0.13 35 35
BMP signaling pathway -0.032 0.012 0 64 -10000 0 64
SRC -0.024 0.035 0.09 23 -0.13 27 50
TGFBR1 0.036 0.006 -10000 0 0 16 16
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.018 0.018 -10000 0 0 264 264
GPC1 0.032 0.012 -10000 0 0 64 64
TGFBR1 (dimer) 0.036 0.006 -10000 0 0 16 16
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.025 0.035 0.09 24 -0.13 26 50
HCK -0.018 0.031 0.09 19 -0.13 16 35
FGF2 0.035 0.008 -10000 0 0 25 25
FGFR1 0.036 0.005 -10000 0 0 9 9
VEGFR1 homodimer 0.034 0.009 -10000 0 0 34 34
TGFBR2 0.035 0.009 -10000 0 0 29 29
cell death 0.034 0.058 -10000 0 -0.16 37 37
ATIII/GPC1 0.038 0.049 -10000 0 -0.14 31 31
PLA2G2A/GPC1 -0.005 0.075 -10000 0 -0.15 92 92
LCK -0.024 0.034 0.09 24 -0.13 24 48
neuron differentiation 0.037 0.051 -10000 0 -0.14 34 34
PrPc/Cu2+ 0.015 0.038 -10000 0 -0.13 30 30
APP 0.035 0.007 -10000 0 0 20 20
TGFBR2 (dimer) 0.035 0.009 -10000 0 0 29 29
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.009 0.024 2 -0.032 18 20
BUB1B -0.022 0.085 0.12 21 -0.23 60 81
PLK1 0.004 0.023 0.081 19 -0.068 5 24
PLK1S1 0.003 0.014 0.048 22 -0.038 3 25
KIF2A 0.005 0.021 0.071 19 -0.061 5 24
regulation of mitotic centrosome separation 0.005 0.023 0.081 19 -0.068 5 24
GOLGA2 0.035 0.008 -10000 0 0 27 27
Hec1/SPC24 -0.004 0.01 -10000 0 -0.054 7 7
WEE1 -0.031 0.13 -10000 0 -0.45 37 37
cytokinesis -0.022 0.11 0.15 13 -0.3 61 74
PP2A-alpha B56 0.054 0.078 -10000 0 -0.51 6 6
AURKA 0.003 0.016 0.055 22 -0.04 3 25
PICH/PLK1 -0.034 0.075 0.071 10 -0.18 89 99
CENPE 0.004 0.049 0.15 30 -0.11 6 36
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization 0.005 0.021 0.071 19 -0.06 5 24
PPP2CA 0.035 0.007 -10000 0 0 20 20
FZR1 0.035 0.008 -10000 0 0 25 25
TPX2 -0.026 0.089 0.12 1 -0.22 85 86
PAK1 0.036 0.007 -10000 0 0 16 16
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 22 22
CLSPN 0.01 0.027 -10000 0 -0.2 6 6
GORASP1 0.034 0.009 -10000 0 0 33 33
metaphase 0.001 0.003 0.016 9 -0.011 2 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.003 0.014 0.048 22 -0.038 3 25
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 0.081 19 -0.068 5 24
ODF2 0.035 0.009 -10000 0 0 29 29
BUB1 0.021 0.063 -10000 0 -0.56 5 5
TPT1 -0.003 0.052 -10000 0 -0.18 38 38
CDC25C 0.013 0.026 -10000 0 -0.22 5 5
CDC25B 0.012 0.031 -10000 0 -0.029 167 167
SGOL1 0.001 0.009 0.032 18 -0.024 2 20
RHOA 0.035 0.007 -10000 0 0 21 21
CCNB1/CDK1 -0.022 0.13 -10000 0 -0.23 103 103
CDC14B -0.011 0.004 0.01 8 -10000 0 8
CDC20 0.028 0.016 -10000 0 0 127 127
PLK1/PBIP1 -0.015 0.037 0.07 8 -0.091 78 86
mitosis -0.001 0.003 0.012 10 -10000 0 10
FBXO5 -0.016 0.063 0.12 17 -0.17 51 68
CDC2 0.015 0.023 -10000 0 -0.031 41 41
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.06 -10000 0 -0.26 24 24
ERCC6L -0.045 0.1 -10000 0 -0.22 98 98
NLP/gamma Tubulin 0.002 0.028 0.075 11 -0.1 21 32
microtubule cytoskeleton organization -0.003 0.052 -10000 0 -0.18 38 38
G2/M transition DNA damage checkpoint -0.001 0.002 0.01 6 -10000 0 6
PPP1R12A 0.035 0.008 -10000 0 0 22 22
interphase -0.001 0.002 0.01 6 -10000 0 6
PLK1/PRC1-2 0.007 0.077 0.13 1 -0.14 91 92
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.053 -10000 0 -0.12 29 29
RAB1A 0.035 0.007 -10000 0 0 19 19
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.018 0.064 21 -0.048 2 23
mitotic prometaphase 0 0.005 0.02 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process -0.05 0.1 0.18 2 -0.21 124 126
microtubule-based process 0.02 0.025 0.098 6 -0.063 5 11
Golgi organization 0.005 0.023 0.081 19 -0.068 5 24
Cohesin/SA2 0.021 0.033 0.096 6 -0.096 21 27
PPP1CB/MYPT1 0.047 0.036 -10000 0 -0.16 14 14
KIF20A 0.029 0.015 -10000 0 0 110 110
APC/C/CDC20 0.02 0.025 0.11 5 -0.061 3 8
PPP2R1A 0.032 0.012 -10000 0 0 59 59
chromosome segregation -0.014 0.036 0.069 8 -0.089 78 86
PRC1 0.028 0.016 -10000 0 0 122 122
ECT2 0.002 0.061 0.17 33 -0.13 5 38
C13orf34 0.004 0.02 0.067 20 -0.055 3 23
NUDC 0.002 0.06 -10000 0 -0.26 24 24
regulation of attachment of spindle microtubules to kinetochore -0.021 0.085 0.12 21 -0.22 60 81
spindle assembly 0.002 0.026 0.083 16 -0.078 14 30
spindle stabilization 0.003 0.014 0.048 22 -0.038 3 25
APC/C/HCDH1 0.024 0.026 0.09 1 -0.12 15 16
MKLP2/PLK1 0.02 0.025 0.098 6 -0.064 5 11
CCNB1 0.015 0.027 -10000 0 -0.028 108 108
PPP1CB 0.036 0.006 -10000 0 0 14 14
BTRC 0.026 0.017 -10000 0 0 155 155
ROCK2 0.017 0.03 -10000 0 -0.2 4 4
TUBG1 0.002 0.05 -10000 0 -0.22 22 22
G2/M transition of mitotic cell cycle -0.047 0.11 0.14 17 -0.23 94 111
MLF1IP -0.009 0.006 0.01 2 -10000 0 2
INCENP 0.036 0.004 -10000 0 0 6 6
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.056 0.22 7 -0.21 21 28
RFC1 -0.02 0.048 0.18 2 -0.21 25 27
PRKDC -0.017 0.055 0.19 7 -0.21 24 31
RIPK1 0.028 0.021 -10000 0 -0.023 73 73
CASP7 -0.17 0.29 -10000 0 -0.58 164 164
FASLG/FAS/FADD/FAF1 -0.016 0.087 0.16 28 -0.18 44 72
MAP2K4 -0.046 0.14 0.22 2 -0.33 39 41
mol:ceramide 0.002 0.094 0.19 5 -0.25 20 25
GSN -0.008 0.058 0.19 11 -0.21 19 30
FASLG/FAS/FADD/FAF1/Caspase 8 -0.014 0.097 0.19 8 -0.26 24 32
FAS 0.021 0.02 -10000 0 -10000 0 0
BID -0.032 0.034 -10000 0 -0.13 23 23
MAP3K1 -0.1 0.19 -10000 0 -0.37 164 164
MAP3K7 0.035 0.011 -10000 0 0 43 43
RB1 -0.017 0.045 0.23 1 -0.21 23 24
CFLAR 0.029 0.021 -10000 0 -0.028 60 60
HGF/MET 0.035 0.049 -10000 0 -0.13 21 21
ARHGDIB -0.015 0.056 0.22 7 -0.22 21 28
FADD 0.038 0.007 -10000 0 -10000 0 0
actin filament polymerization 0.008 0.058 0.21 19 -0.19 11 30
NFKB1 0.029 0.11 -10000 0 -0.65 10 10
MAPK8 -0.036 0.14 0.24 1 -0.37 21 22
DFFA -0.017 0.048 0.22 3 -0.21 24 27
DNA fragmentation during apoptosis -0.016 0.046 0.22 2 -0.2 24 26
FAS/FADD/MET 0.025 0.053 -10000 0 -0.12 28 28
CFLAR/RIP1 0.048 0.02 -10000 0 -0.065 9 9
FAIM3 0.034 0.009 -10000 0 0 35 35
FAF1 0.038 0.011 -10000 0 -10000 0 0
PARP1 -0.019 0.048 0.22 1 -0.21 26 27
DFFB -0.016 0.045 0.22 2 -0.2 23 25
CHUK 0.016 0.099 -10000 0 -0.61 10 10
FASLG 0.039 0.008 -10000 0 -10000 0 0
FAS/FADD 0.021 0.054 -10000 0 -0.15 36 36
HGF 0.024 0.018 -10000 0 0 177 177
LMNA -0.02 0.049 0.2 5 -0.19 24 29
CASP6 -0.017 0.046 0.17 3 -0.2 24 27
CASP10 0.039 0.004 -10000 0 -10000 0 0
CASP3 -0.011 0.05 -10000 0 -0.22 25 25
PTPN13 0.032 0.012 -10000 0 0 60 60
CASP8 -0.029 0.014 0.085 4 -10000 0 4
IL6 0.02 0.13 -10000 0 -0.66 5 5
MET 0.023 0.018 -10000 0 0 190 190
ICAD/CAD -0.021 0.049 0.25 4 -0.2 23 27
FASLG/FAS/FADD/FAF1/Caspase 10 0.002 0.095 0.19 5 -0.25 20 25
activation of caspase activity by cytochrome c -0.031 0.033 -10000 0 -0.13 23 23
PAK2 -0.015 0.049 0.15 2 -0.2 25 27
BCL2 0.035 0.007 -10000 0 0 20 20
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.008 0.059 -10000 0 -0.22 25 25
epithelial cell differentiation 0.064 0.052 -10000 0 -0.14 25 25
CYFIP2 0.031 0.013 -10000 0 0 76 76
ENAH -0.042 0.072 0.24 12 -0.24 11 23
EGFR 0.009 0.016 -10000 0 0 379 379
EPHA2 0.033 0.011 -10000 0 0 55 55
MYO6 -0.029 0.05 0.18 9 -0.22 13 22
CTNNB1 0.036 0.006 -10000 0 0 15 15
ABI1/Sra1/Nap1 0.029 0.065 -10000 0 -0.12 60 60
AQP5 -0.021 0.053 0.19 3 -0.29 10 13
CTNND1 0.035 0.009 -10000 0 0 31 31
mol:PI-4-5-P2 -0.031 0.045 0.17 7 -0.21 13 20
regulation of calcium-dependent cell-cell adhesion -0.028 0.044 0.18 8 -0.19 8 16
EGF 0.035 0.008 -10000 0 0 25 25
NCKAP1 0.037 0.002 -10000 0 0 2 2
AQP3 -0.034 0.075 -10000 0 -0.3 31 31
cortical microtubule organization 0.064 0.052 -10000 0 -0.14 25 25
GO:0000145 -0.03 0.041 0.16 7 -0.2 13 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.071 0.054 -10000 0 -0.14 25 25
MLLT4 0.034 0.009 -10000 0 0 34 34
ARF6/GDP -0.053 0.04 -10000 0 -0.22 13 13
ARF6 0.035 0.009 -10000 0 0 29 29
Ephrin A1/EPHA2/NCK1/GIT1 0.075 0.055 -10000 0 -0.13 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.031 0.087 0.16 1 -0.3 36 37
PVRL2 0.034 0.009 -10000 0 0 35 35
ZYX -0.022 0.045 0.18 6 -0.22 15 21
ARF6/GTP 0.079 0.061 -10000 0 -0.13 24 24
CDH1 0.034 0.01 -10000 0 0 37 37
EGFR/EGFR/EGF/EGF -0.001 0.06 -10000 0 -0.13 67 67
RhoA/GDP 0.064 0.057 -10000 0 -0.14 29 29
actin cytoskeleton organization -0.024 0.047 0.16 7 -0.23 12 19
IGF-1R heterotetramer 0.033 0.011 -10000 0 0 53 53
GIT1 0.037 0.003 -10000 0 0 3 3
IGF1R 0.033 0.011 -10000 0 0 53 53
IGF1 0.035 0.007 -10000 0 0 21 21
DIAPH1 -0.13 0.28 -10000 0 -0.51 156 156
Wnt receptor signaling pathway -0.064 0.052 0.14 25 -10000 0 25
RHOA 0.035 0.007 -10000 0 0 21 21
RhoA/GTP -0.054 0.042 -10000 0 -0.21 17 17
CTNNA1 0.035 0.007 -10000 0 0 18 18
VCL -0.024 0.048 0.17 7 -0.23 12 19
EFNA1 0.033 0.011 -10000 0 0 52 52
LPP -0.03 0.048 0.18 4 -0.24 13 17
Ephrin A1/EPHA2 0.046 0.063 -10000 0 -0.14 41 41
SEC6/SEC8 -0.044 0.029 -10000 0 -0.14 26 26
MGAT3 -0.028 0.045 0.18 8 -0.2 8 16
HGF/MET 0.037 0.048 -10000 0 -0.14 15 15
HGF 0.024 0.018 -10000 0 0 177 177
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.008 0.06 -10000 0 -0.22 25 25
actin cable formation -0.04 0.1 0.31 10 -0.3 33 43
KIAA1543 -0.025 0.037 0.16 7 -0.18 8 15
KIFC3 -0.031 0.042 0.19 5 -0.2 8 13
NCK1 0.035 0.008 -10000 0 0 27 27
EXOC3 0.036 0.003 -10000 0 0 4 4
ACTN1 -0.027 0.051 0.19 7 -0.22 16 23
NCK1/GIT1 0.05 0.024 -10000 0 -0.14 6 6
mol:GDP 0.064 0.052 -10000 0 -0.14 25 25
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.028 0.031 0.053 22 -0.13 25 47
PIP5K1C -0.031 0.046 0.18 7 -0.21 13 20
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.017 -10000 0 0 158 158
ROCK1 -0.035 0.086 0.3 15 -0.28 6 21
adherens junction assembly -0.024 0.072 0.22 6 -0.33 14 20
IGF-1R heterotetramer/IGF1 0.05 0.062 -10000 0 -0.15 37 37
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
MET 0.023 0.018 -10000 0 0 190 190
PLEKHA7 -0.028 0.031 0.053 22 -0.13 25 47
mol:GTP 0.072 0.053 -10000 0 -0.13 25 25
establishment of epithelial cell apical/basal polarity -0.039 0.039 0.12 12 -0.19 10 22
cortical actin cytoskeleton stabilization 0.008 0.059 -10000 0 -0.22 25 25
regulation of cell-cell adhesion -0.024 0.047 0.16 7 -0.23 12 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.008 0.06 -10000 0 -0.22 25 25
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.017 0.021 0.093 16 -10000 0 16
BAD/BCL-XL/YWHAZ 0.047 0.034 -10000 0 -0.13 11 11
CDKN1B -0.024 0.12 0.2 5 -0.33 57 62
CDKN1A -0.027 0.12 -10000 0 -0.33 60 60
FRAP1 0.036 0.006 -10000 0 0 16 16
PRKDC 0.034 0.01 -10000 0 0 45 45
FOXO3 -0.018 0.11 -10000 0 -0.31 61 61
AKT1 -0.018 0.12 -10000 0 -0.33 58 58
BAD 0.036 0.006 -10000 0 0 13 13
AKT3 0.015 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.018 0.11 -10000 0 -0.31 61 61
AKT1/ASK1 -0.009 0.13 0.25 1 -0.32 60 61
BAD/YWHAZ 0.064 0.037 -10000 0 -0.13 12 12
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.035 0.008 -10000 0 0 28 28
JNK cascade 0.009 0.12 0.31 61 -0.24 1 62
TSC1 -0.025 0.12 0.2 1 -0.33 59 60
YWHAZ 0.035 0.007 -10000 0 0 21 21
AKT1/RAF1 0 0.13 0.26 1 -0.33 62 63
EP300 0.033 0.011 -10000 0 0 50 50
mol:GDP -0.018 0.12 -10000 0 -0.32 60 60
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.026 0.12 -10000 0 -0.33 62 62
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.001 0.022 0.12 14 -10000 0 14
MAP3K5 0.03 0.014 -10000 0 0 90 90
MAPKAP1 0.034 0.009 -10000 0 0 32 32
negative regulation of cell cycle 0.003 0.11 0.36 24 -10000 0 24
YWHAH 0.031 0.013 -10000 0 0 73 73
AKT1S1 -0.018 0.11 -10000 0 -0.31 61 61
CASP9 -0.02 0.12 0.2 3 -0.32 59 62
YWHAB 0.034 0.01 -10000 0 0 41 41
p27Kip1/KPNA1 -0.006 0.13 0.29 4 -0.32 60 64
GBL 0.036 0.006 -10000 0 0 15 15
PDK1/Src/Hsp90 0.046 0.014 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
SRC 0.034 0.009 -10000 0 0 34 34
AKT2/p21CIP1 -0.024 0.11 0.23 1 -0.28 61 62
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.07 -10000 0 -0.46 7 7
CHUK -0.022 0.1 -10000 0 -0.33 47 47
BAD/BCL-XL 0.003 0.12 -10000 0 -0.32 56 56
mTORC2 0.06 0.032 -10000 0 -0.12 9 9
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.005 0.13 -10000 0 -0.42 28 28
PDPK1 0.036 0.005 -10000 0 0 8 8
MDM2 -0.016 0.12 0.2 10 -0.32 58 68
MAPKKK cascade 0 0.13 0.33 62 -0.26 1 63
MDM2/Cbp/p300 0.015 0.13 0.27 1 -0.31 59 60
TSC1/TSC2 -0.029 0.13 0.26 8 -0.34 62 70
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.12 0.26 1 -0.3 59 60
glucose import -0.008 0.022 0.2 3 -10000 0 3
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.013 0.084 -10000 0 -0.34 10 10
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.022 0.2 3 -10000 0 3
GSK3A -0.019 0.12 0.25 8 -0.32 57 65
FOXO1 -0.018 0.11 -10000 0 -0.31 61 61
GSK3B -0.024 0.12 0.2 4 -0.34 60 64
SFN 0.031 0.013 -10000 0 0 80 80
G1/S transition of mitotic cell cycle -0.028 0.13 0.25 9 -0.33 62 71
p27Kip1/14-3-3 family 0.011 0.11 -10000 0 -0.55 12 12
PRKACA 0.035 0.008 -10000 0 0 24 24
KPNA1 0.035 0.008 -10000 0 0 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.025 0.017 -10000 0 0 167 167
CREBBP 0.036 0.005 -10000 0 0 9 9
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.052 -10000 0 -0.19 28 28
PDGFRB 0.036 0.009 -10000 0 -0.001 27 27
SPHK1 0.016 0.04 -10000 0 -0.76 1 1
mol:S1P 0.018 0.042 -10000 0 -0.68 1 1
S1P1/S1P/Gi -0.001 0.14 0.25 15 -0.47 27 42
GNAO1 0.033 0.015 0.064 1 0 87 88
PDGFB-D/PDGFRB/PLCgamma1 0.03 0.15 0.25 33 -0.4 28 61
PLCG1 -0.004 0.13 0.23 22 -0.43 27 49
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.036 0.009 -10000 0 -0.001 27 27
GNAI2 0.036 0.012 -10000 0 0 44 44
GNAI3 0.038 0.007 -10000 0 0 14 14
GNAI1 0.019 0.02 -10000 0 0 262 262
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.009 0.076 0.12 11 -0.28 28 39
S1P1/S1P 0.025 0.08 0.22 3 -0.3 15 18
negative regulation of cAMP metabolic process 0 0.14 0.24 15 -0.46 27 42
MAPK3 0.001 0.14 0.28 18 -0.46 25 43
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
KDR 0.027 0.035 0.094 1 -0.13 18 19
PLCB2 0.038 0.092 0.23 20 -0.28 15 35
RAC1 0.025 0.017 -10000 0 0 163 163
RhoA/GTP 0.017 0.068 -10000 0 -0.25 18 18
receptor internalization 0.024 0.076 0.21 3 -0.28 15 18
PTGS2 0.033 0.15 0.36 7 -0.47 15 22
Rac1/GTP 0.009 0.059 -10000 0 -0.28 12 12
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFA -0.001 0.022 -10000 0 -0.1 23 23
negative regulation of T cell proliferation 0 0.14 0.24 15 -0.46 27 42
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.033 0.015 -10000 0 0 80 80
MAPK1 0.004 0.14 0.29 15 -0.48 22 37
S1P1/S1P/PDGFB-D/PDGFRB 0.055 0.11 0.25 15 -0.3 20 35
ABCC1 0.037 0.008 -10000 0 0 19 19
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.033 0.11 0.3 18 -0.3 22 40
PDGFB-D/PDGFRB/SLAP 0.017 0.075 -10000 0 -0.16 72 72
PDGFB-D/PDGFRB/APS/CBL 0.045 0.024 -10000 0 -0.12 8 8
AKT1 -0.024 0.092 0.26 14 -0.24 16 30
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.025 0.11 0.28 16 -0.32 21 37
PIK3CA 0.031 0.014 -10000 0 0 82 82
FGR 0.005 0.1 0.24 3 -0.46 15 18
mol:Ca2+ 0.017 0.1 0.25 18 -0.35 20 38
MYC 0.01 0.26 0.37 40 -0.66 54 94
SHC1 0.033 0.011 -10000 0 0 52 52
HRAS/GDP 0.015 0.07 0.18 36 -0.16 21 57
LRP1/PDGFRB/PDGFB 0.048 0.057 -10000 0 -0.14 32 32
GRB10 0.021 0.018 -10000 0 0 222 222
PTPN11 0.036 0.005 -10000 0 0 11 11
GO:0007205 0.016 0.1 0.25 18 -0.36 20 38
PTEN 0.025 0.017 -10000 0 0 168 168
GRB2 0.035 0.007 -10000 0 0 18 18
GRB7 0.036 0.006 -10000 0 0 15 15
PDGFB-D/PDGFRB/SHP2 0.047 0.035 -10000 0 -0.15 14 14
PDGFB-D/PDGFRB/GRB10 0.02 0.052 -10000 0 -0.15 32 32
cell cycle arrest 0.017 0.075 -10000 0 -0.16 72 72
HRAS 0.034 0.009 -10000 0 0 36 36
HIF1A -0.029 0.084 0.23 14 -0.25 16 30
GAB1 0.012 0.13 0.29 13 -0.37 29 42
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.011 0.12 0.32 17 -0.33 28 45
PDGFB-D/PDGFRB 0.054 0.054 -10000 0 -0.1 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.044 0.042 -10000 0 -0.15 21 21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.12 0.27 5 -0.29 34 39
positive regulation of MAPKKK cascade 0.047 0.035 -10000 0 -0.15 14 14
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.017 0.11 0.25 18 -0.36 20 38
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -0.01 26 26
PDGFB-D/PDGFRB/GRB7 0.05 0.024 -10000 0 -0.14 5 5
SHB 0.033 0.011 -10000 0 0 51 51
BLK 0.014 0.078 0.24 2 -0.43 7 9
PTPN2 0.033 0.018 0.07 1 -0.02 49 50
PDGFB-D/PDGFRB/SNX15 0.05 0.027 -10000 0 -0.14 8 8
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0 0.16 0.3 17 -0.39 48 65
CBL 0.036 0.005 -10000 0 0 8 8
PDGFB-D/PDGFRB/DEP1 0.049 0.028 -10000 0 -0.14 8 8
LCK 0.018 0.063 0.24 2 -0.36 3 5
PDGFRB 0.031 0.022 0.07 2 -0.019 73 75
ACP1 0.035 0.007 -10000 0 0 18 18
HCK -0.042 0.18 -10000 0 -0.5 59 59
ABL1 0.007 0.12 0.25 20 -0.33 30 50
PDGFB-D/PDGFRB/CBL 0.011 0.13 0.32 8 -0.41 27 35
PTPN1 0.03 0.019 -10000 0 -0.013 75 75
SNX15 0.036 0.003 -10000 0 0 4 4
STAT3 0.034 0.01 -10000 0 0 37 37
STAT1 0.034 0.01 -10000 0 0 40 40
cell proliferation 0.017 0.24 0.35 43 -0.59 55 98
SLA 0.027 0.016 -10000 0 0 133 133
actin cytoskeleton reorganization -0.016 0.071 0.19 38 -0.2 7 45
SRC 0.014 0.047 0.22 1 -10000 0 1
PI3K -0.047 0.045 -10000 0 -0.16 46 46
PDGFB-D/PDGFRB/GRB7/SHC 0.061 0.038 -10000 0 -0.13 11 11
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.025 0.11 0.29 16 -0.33 21 37
LYN -0.035 0.16 0.22 1 -0.47 54 55
LRP1 0.032 0.013 -10000 0 0 70 70
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.036 0.004 -10000 0 0 5 5
STAT5A 0.036 0.004 -10000 0 0 5 5
NCK1-2/p130 Cas 0.064 0.067 -10000 0 -0.14 26 26
SPHK1 0.034 0.012 0.061 3 0 51 54
EDG1 0.034 0.011 0.061 3 0 45 48
mol:DAG 0.017 0.11 0.25 18 -0.36 20 38
PLCG1 0.016 0.11 0.27 13 -0.37 20 33
NHERF/PDGFRB 0.063 0.037 -10000 0 -0.13 12 12
YES1 -0.005 0.13 0.23 2 -0.54 22 24
cell migration 0.062 0.037 -10000 0 -0.13 12 12
SHC/Grb2/SOS1 0.066 0.062 -10000 0 -0.14 21 21
SLC9A3R2 0.036 0.005 -10000 0 0 8 8
SLC9A3R1 0.034 0.009 -10000 0 0 36 36
NHERF1-2/PDGFRB/PTEN 0.055 0.056 -10000 0 -0.11 13 13
FYN -0.052 0.19 -10000 0 -0.45 78 78
DOK1 -0.013 0.06 0.17 38 -0.13 4 42
HRAS/GTP 0.021 0.028 -10000 0 -0.13 16 16
PDGFB 0.034 0.01 -10000 0 0 38 38
RAC1 0.032 0.19 0.34 46 -0.43 50 96
PRKCD -0.009 0.063 0.18 39 -0.14 3 42
FER -0.011 0.063 0.18 38 -0.14 4 42
MAPKKK cascade -0.009 0.068 0.16 49 -0.18 5 54
RASA1 -0.01 0.064 0.18 38 -0.17 6 44
NCK1 0.035 0.008 -10000 0 0 27 27
NCK2 0.036 0.007 -10000 0 0 17 17
p62DOK/Csk -0.01 0.066 0.17 39 -0.2 3 42
PDGFB-D/PDGFRB/SHB 0.045 0.028 -10000 0 -0.14 6 6
chemotaxis 0.008 0.12 0.25 20 -0.32 30 50
STAT1-3-5/STAT1-3-5 0.06 0.073 -10000 0 -0.14 40 40
Bovine Papilomavirus E5/PDGFRB 0.02 0.026 -10000 0 -0.14 8 8
PTPRJ 0.036 0.005 -10000 0 0 11 11
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 0.031 0.034 -10000 0 -0.14 8 8
CRKL 0.048 0.11 0.28 7 -0.4 16 23
mol:PIP3 0 0.054 -10000 0 -0.85 1 1
AKT1 -0.012 0.054 -10000 0 -0.75 1 1
PTK2B 0.036 0.006 -10000 0 0 16 16
RAPGEF1 0.045 0.1 0.29 10 -0.38 16 26
RANBP10 0.036 0.005 -10000 0 0 8 8
PIK3CA 0.031 0.014 -10000 0 0 82 82
HGF/MET/SHIP2 0.043 0.038 -10000 0 -0.13 2 2
MAP3K5 0.044 0.11 0.28 6 -0.37 17 23
HGF/MET/CIN85/CBL/ENDOPHILINS 0.041 0.035 -10000 0 -10000 0 0
AP1 0.033 0.081 0.15 100 -0.15 46 146
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 52 52
apoptosis -0.12 0.36 -10000 0 -0.78 113 113
STAT3 (dimer) 0.012 0.058 -10000 0 -0.27 10 10
GAB1/CRKL/SHP2/PI3K 0.064 0.12 0.31 2 -0.39 18 20
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.064 0.11 0.28 4 -0.39 16 20
PTPN11 0.036 0.005 -10000 0 0 11 11
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.034 0.01 -10000 0 0 37 37
PTEN 0.025 0.017 -10000 0 0 168 168
ELK1 0.11 0.18 0.35 179 -10000 0 179
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.032 0.16 1 -0.14 12 13
PAK1 -0.017 0.053 -10000 0 -0.72 1 1
HGF/MET/RANBP10 0.043 0.037 -10000 0 -10000 0 0
HRAS 0.012 0.081 -10000 0 -0.47 10 10
DOCK1 0.036 0.1 0.26 9 -0.39 16 25
GAB1 0.047 0.1 -10000 0 -0.41 16 16
CRK 0.048 0.11 0.28 4 -0.4 16 20
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.066 -10000 0 -0.42 9 9
JUN 0.034 0.01 -10000 0 0 41 41
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.018 -10000 0 -0.12 1 1
PIK3R1 0.032 0.012 -10000 0 0 63 63
cell morphogenesis 0.031 0.11 0.26 31 -0.31 14 45
GRB2/SHC 0.075 0.065 0.17 106 -0.12 2 108
FOS 0.025 0.017 -10000 0 0 162 162
GLMN 0.003 0.012 0.069 2 -0.17 2 4
cell motility 0.11 0.18 0.35 179 -10000 0 179
HGF/MET/MUC20 0.029 0.024 -10000 0 -10000 0 0
cell migration 0.073 0.063 0.17 106 -0.12 2 108
GRB2 0.035 0.007 -10000 0 0 18 18
CBL 0.036 0.005 -10000 0 0 8 8
MET/RANBP10 0.034 0.027 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.046 -10000 0 -0.18 18 18
MET/MUC20 0.017 0.013 -10000 0 -10000 0 0
RAP1B 0.045 0.099 0.27 11 -0.36 16 27
RAP1A 0.039 0.1 0.28 10 -0.36 15 25
HGF/MET/RANBP9 0.041 0.041 -10000 0 -0.12 7 7
RAF1 0.039 0.1 0.28 2 -0.44 13 15
STAT3 0.009 0.054 -10000 0 -0.29 9 9
cell proliferation 0.038 0.079 0.24 13 -0.27 8 21
RPS6KB1 0.014 0.018 -10000 0 -10000 0 0
MAPK3 0.08 0.16 0.33 127 -10000 0 127
MAPK1 0.11 0.21 0.4 146 -10000 0 146
RANBP9 0.036 0.006 -10000 0 0 16 16
MAPK8 -0.047 0.16 0.27 1 -0.34 65 66
SRC 0.008 0.044 -10000 0 -0.18 17 17
PI3K 0.058 0.074 0.17 90 -0.16 8 98
MET/Glomulin 0.015 0.028 -10000 0 -0.087 21 21
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.029 0.1 0.26 2 -0.42 14 16
MET 0.023 0.018 -10000 0 0 190 190
MAP4K1 0.053 0.11 0.3 4 -0.37 16 20
PTK2 0.034 0.009 -10000 0 0 34 34
MAP2K2 0.037 0.1 0.3 13 -0.4 13 26
BAD -0.019 0.053 -10000 0 -0.72 1 1
MAP2K4 0.037 0.1 0.27 9 -0.34 17 26
SHP2/GRB2/SOS1/GAB1 0.021 0.077 -10000 0 -0.34 17 17
INPPL1 0.036 0.006 -10000 0 0 13 13
PXN 0.036 0.004 -10000 0 0 7 7
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.001 0.018 0.082 3 -0.12 1 4
PLCgamma1/PKC 0.024 0.014 -10000 0 -0.13 3 3
HGF 0.024 0.018 -10000 0 0 177 177
RASA1 0.035 0.009 -10000 0 0 30 30
NCK1 0.035 0.008 -10000 0 0 27 27
PTPRJ 0.036 0.005 -10000 0 0 11 11
NCK/PLCgamma1 0.079 0.059 0.17 111 -10000 0 111
PDPK1 -0.004 0.054 -10000 0 -0.79 1 1
HGF/MET/SHIP 0.029 0.024 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.074 -10000 0 -0.13 40 40
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.035 0.008 -10000 0 0 28 28
STAT1 (dimer)/Cbp/p300 0.021 0.084 0.27 5 -0.22 19 24
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.063 -10000 0 -0.14 41 41
antigen processing and presentation of peptide antigen via MHC class I -0.026 0.08 0.13 5 -0.19 59 64
CaM/Ca2+ 0.046 0.08 -10000 0 -0.14 42 42
RAP1A 0.036 0.005 -10000 0 0 10 10
STAT1 (dimer)/SHP2 -0.023 0.06 0.16 17 -0.19 9 26
AKT1 -0.033 0.085 0.19 14 -0.23 32 46
MAP2K1 -0.028 0.056 0.14 21 -0.21 8 29
MAP3K11 -0.023 0.059 0.16 22 -0.18 7 29
IFNGR1 0.031 0.019 -10000 0 -0.037 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.03 0.13 -10000 0 -0.35 45 45
Rap1/GTP -0.04 0.036 0.05 1 -0.15 10 11
CRKL/C3G 0.05 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.064 0.077 -10000 0 -0.13 35 35
CEBPB -0.006 0.12 0.35 3 -0.43 22 25
STAT3 0.034 0.01 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.06 0.096 -10000 0 -0.74 4 4
STAT1 -0.026 0.06 0.17 18 -0.19 9 27
CALM1 0.033 0.012 -10000 0 0 57 57
IFN-gamma (dimer) 0.03 0.022 -10000 0 -0.037 39 39
PIK3CA 0.031 0.014 -10000 0 0 82 82
STAT1 (dimer)/PIAS1 -0.027 0.07 0.18 18 -0.21 17 35
CEBPB/PTGES2/Cbp/p300 0.01 0.09 -10000 0 -0.28 27 27
mol:Ca2+ 0.046 0.072 -10000 0 -0.12 40 40
MAPK3 0.007 0.074 0.34 2 -0.52 2 4
STAT1 (dimer) -0.027 0.11 0.19 7 -0.26 53 60
MAPK1 -0.04 0.2 0.34 2 -0.75 34 36
JAK2 0.027 0.022 -10000 0 -0.038 34 34
PIK3R1 0.032 0.012 -10000 0 0 63 63
JAK1 0.033 0.017 -10000 0 -0.036 18 18
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.001 0.096 0.3 4 -0.4 12 16
SMAD7 -0.009 0.061 0.16 23 -0.14 21 44
CBL/CRKL/C3G 0.019 0.071 0.25 5 -0.18 6 11
PI3K 0.026 0.095 -10000 0 -0.16 71 71
IFNG 0.03 0.022 -10000 0 -0.037 39 39
apoptosis 0.014 0.086 0.31 3 -0.44 7 10
CAMK2G 0.024 0.018 -10000 0 0 180 180
STAT3 (dimer) 0.034 0.01 -10000 0 0 37 37
CAMK2A 0.036 0.005 -10000 0 0 8 8
CAMK2B 0.017 0.018 -10000 0 0 275 275
FRAP1 -0.039 0.077 0.17 14 -0.23 32 46
PRKCD -0.033 0.081 0.21 12 -0.22 25 37
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.026 0.08 0.13 5 -0.19 59 64
PTPN2 0.036 0.007 -10000 0 0 17 17
EP300 0.034 0.011 -10000 0 0 50 50
IRF1 -0.036 0.059 0.21 3 -0.28 13 16
STAT1 (dimer)/PIASy -0.026 0.065 0.19 14 -0.19 8 22
SOCS1 0.017 0.095 -10000 0 -1 4 4
mol:GDP -0.023 0.066 0.17 22 -0.19 4 26
CASP1 -0.02 0.074 0.17 17 -0.16 65 82
PTGES2 0.035 0.007 -10000 0 0 20 20
IRF9 -0.002 0.044 0.12 16 -0.12 21 37
mol:PI-3-4-5-P3 0.013 0.084 -10000 0 -0.15 73 73
RAP1/GDP -0.032 0.052 0.11 17 -0.17 7 24
CBL -0.024 0.058 0.16 21 -0.18 6 27
MAP3K1 -0.023 0.056 0.15 18 -0.18 6 24
PIAS1 0.035 0.008 -10000 0 0 25 25
PIAS4 0.035 0.008 -10000 0 0 24 24
antigen processing and presentation of peptide antigen via MHC class II -0.026 0.08 0.13 5 -0.19 59 64
PTPN11 -0.018 0.059 0.16 25 -0.18 6 31
CREBBP 0.037 0.005 -10000 0 0 9 9
RAPGEF1 0.035 0.007 -10000 0 0 18 18
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.047 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 0 20 20
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.004 -10000 0 0 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.035 0.007 -10000 0 0 21 21
RAC1-CDC42/GTP/PAK family 0.002 0.049 -10000 0 -0.14 43 43
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.034 0.01 -10000 0 0 39 39
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.005 -10000 0 0 8 8
FYN 0.03 0.014 -10000 0 0 88 88
MAP3K12 0.036 0.006 -10000 0 0 12 12
FGR 0.033 0.011 -10000 0 0 56 56
p38 alpha/TAB1 0.02 0.11 0.18 6 -0.26 38 44
PRKG1 0.026 0.017 -10000 0 0 147 147
DUSP8 0.034 0.01 -10000 0 0 40 40
PGK/cGMP/p38 alpha 0.004 0.096 0.17 1 -0.25 38 39
apoptosis 0.019 0.1 0.18 6 -0.25 38 44
RAL/GTP 0.027 0.037 -10000 0 -0.12 19 19
LYN 0.031 0.013 -10000 0 0 74 74
DUSP1 0.031 0.013 -10000 0 0 76 76
PAK1 0.036 0.006 -10000 0 0 16 16
SRC 0.034 0.009 -10000 0 0 34 34
RAC1/OSM/MEKK3/MKK3 0.046 0.037 -10000 0 -0.11 5 5
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.025 0.017 -10000 0 0 163 163
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.031 0.028 -10000 0 -0.12 5 5
MAPK11 0.001 0.13 0.21 6 -0.32 39 45
BLK 0.036 0.007 -10000 0 0 17 17
HCK 0.027 0.016 -10000 0 0 141 141
MAP2K3 0.036 0.005 -10000 0 0 10 10
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.033 0.011 -10000 0 0 49 49
TRAF6/MEKK3 0.045 0.011 -10000 0 -0.1 1 1
MAP3K7IP1 0.034 0.009 -10000 0 0 36 36
MAPK14 0.012 0.11 0.18 9 -0.27 38 47
positive regulation of innate immune response 0.005 0.14 0.23 6 -0.34 43 49
LCK 0.035 0.007 -10000 0 0 18 18
p38alpha-beta/MKP7 0.002 0.13 0.22 6 -0.33 43 49
p38alpha-beta/MKP5 0.017 0.14 0.24 6 -0.34 36 42
PGK/cGMP 0.019 0.012 -10000 0 -10000 0 0
PAK2 0.035 0.007 -10000 0 0 21 21
p38alpha-beta/MKP1 0.008 0.14 0.24 6 -0.34 43 49
CDC42 0.035 0.008 -10000 0 0 26 26
RALB 0.036 0.006 -10000 0 0 16 16
RALA 0.024 0.018 -10000 0 0 182 182
PAK3 0.027 0.016 -10000 0 0 139 139
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 0.036 0.007 -10000 0 0 17 17
PTK2 0.034 0.009 -10000 0 0 34 34
CRKL -0.018 0.044 0.097 27 -0.15 24 51
GRB2/SOS1/SHC 0.04 0.032 -10000 0 -0.12 14 14
HRAS 0.034 0.009 -10000 0 0 36 36
IRS1/Crk 0.019 0.048 -10000 0 -0.14 36 36
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.055 -10000 0 -0.15 28 28
AKT1 -0.034 0.075 0.15 28 -0.21 37 65
BAD -0.039 0.073 0.14 27 -0.22 30 57
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.045 0.099 28 -0.16 24 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.026 0.049 0.22 1 -0.15 29 30
RAF1 -0.035 0.15 -10000 0 -0.55 29 29
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.047 0.054 -10000 0 -0.14 30 30
YWHAZ 0.035 0.007 -10000 0 0 21 21
IGF-1R heterotetramer/IGF1/IRS1 0.034 0.049 -10000 0 -0.16 24 24
PIK3CA 0.031 0.014 -10000 0 0 82 82
RPS6KB1 -0.032 0.072 0.16 31 -0.2 23 54
GNB2L1 0.037 0.002 -10000 0 0 2 2
positive regulation of MAPKKK cascade -0.033 0.12 0.23 3 -0.43 29 32
PXN 0.036 0.004 -10000 0 0 7 7
PIK3R1 0.032 0.012 -10000 0 0 63 63
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
HRAS/GTP 0.016 0.054 -10000 0 -0.14 43 43
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.067 0.056 -10000 0 -0.12 34 34
IGF-1R heterotetramer 0.036 0.014 -10000 0 -0.034 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.049 0.06 -10000 0 -0.14 35 35
Crk/p130 Cas/Paxillin 0.038 0.055 0.22 1 -0.14 36 37
IGF1R 0.036 0.014 -10000 0 -0.034 1 1
IGF1 0.034 0.025 -10000 0 -0.059 29 29
IRS2/Crk -0.03 0.058 0.1 19 -0.19 31 50
PI3K 0.04 0.088 -10000 0 -0.14 77 77
apoptosis 0.038 0.077 0.22 30 -0.16 22 52
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
PRKCD 0.005 0.064 0.18 9 -0.21 24 33
RAF1/14-3-3 E -0.012 0.14 -10000 0 -0.48 29 29
BAD/14-3-3 -0.04 0.08 0.17 22 -0.23 30 52
PRKCZ -0.027 0.07 0.16 32 -0.2 23 55
Crk/p130 Cas/Paxillin/FAK1 -0.046 0.074 0.13 27 -0.22 31 58
PTPN1 0.034 0.01 -10000 0 0 43 43
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.007 0.06 -10000 0 -0.22 25 25
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.038 0.071 -10000 0 -0.14 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.028 0.051 0.13 3 -0.14 35 38
GRB10 0.021 0.018 -10000 0 0 222 222
PTPN11 -0.018 0.045 0.099 28 -0.15 24 52
IRS1 0.01 0.041 0.12 3 -0.16 24 27
IRS2 -0.02 0.049 0.1 20 -0.2 24 44
IGF-1R heterotetramer/IGF1 0.04 0.051 -10000 0 -0.17 24 24
GRB2 0.035 0.007 -10000 0 0 18 18
PDPK1 -0.026 0.077 0.17 32 -0.21 23 55
YWHAE 0.035 0.008 -10000 0 0 27 27
PRKD1 -0.002 0.064 0.15 1 -0.24 28 29
SHC1 0.033 0.011 -10000 0 0 52 52
Neurotrophic factor-mediated Trk 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
CRKL 0.035 0.008 -10000 0 0 28 28
RAS family/GTP/Tiam1 -0.006 0.086 -10000 0 -0.2 63 63
NT3 (dimer)/TRKC 0.047 0.026 -10000 0 -0.14 6 6
NT3 (dimer)/TRKB 0.026 0.07 -10000 0 -0.13 74 74
SHC/Grb2/SOS1/GAB1/PI3K -0.007 0.095 -10000 0 -0.21 74 74
RAPGEF1 0.035 0.007 -10000 0 0 18 18
BDNF 0.032 0.012 -10000 0 0 66 66
PIK3CA 0.031 0.014 -10000 0 0 82 82
DYNLT1 0.034 0.01 -10000 0 0 44 44
NTRK1 0.036 0.007 -10000 0 0 17 17
NTRK2 0.027 0.016 -10000 0 0 138 138
NTRK3 0.034 0.009 -10000 0 0 34 34
NT-4/5 (dimer)/TRKB 0.013 0.059 -10000 0 -0.12 78 78
neuron apoptosis -0.008 0.12 0.32 39 -0.23 1 40
SHC 2-3/Grb2 0.007 0.13 0.24 1 -0.35 39 40
SHC1 0.033 0.011 -10000 0 0 52 52
SHC2 -0.01 0.12 -10000 0 -0.44 28 28
SHC3 -0.008 0.12 -10000 0 -0.41 29 29
STAT3 (dimer) 0.021 0.088 -10000 0 -0.29 37 37
NT3 (dimer)/TRKA 0.059 0.031 -10000 0 -10000 0 0
RIN/GDP 0.001 0.075 0.18 7 -0.22 25 32
GIPC1 0.035 0.008 -10000 0 0 24 24
KRAS 0.034 0.009 -10000 0 0 34 34
DNAJA3 -0.005 0.04 0.14 3 -0.18 2 5
RIN/GTP 0.011 0.036 -10000 0 -0.13 26 26
CCND1 -0.012 0.11 -10000 0 -0.5 26 26
MAGED1 0.035 0.008 -10000 0 0 26 26
PTPN11 0.036 0.005 -10000 0 0 11 11
RICS 0.033 0.011 -10000 0 0 47 47
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.04 0.032 -10000 0 -0.12 14 14
GRB2 0.035 0.007 -10000 0 0 18 18
NGF (dimer)/TRKA/MATK 0.045 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 0 259 259
RhoG/GTP/ELMO1/DOCK1 0.008 0.045 -10000 0 -0.12 45 45
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.009 -10000 0 0 36 36
DOCK1 0.024 0.018 -10000 0 0 183 183
GAB2 0.033 0.011 -10000 0 0 48 48
RIT2 0.025 0.017 -10000 0 0 168 168
RIT1 0.032 0.012 -10000 0 0 62 62
FRS2 0.035 0.009 -10000 0 0 30 30
DNM1 0.035 0.008 -10000 0 0 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.01 0.047 0.16 2 -0.17 10 12
mol:GDP -0.002 0.1 0.21 8 -0.32 24 32
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.002 0.044 -10000 0 -0.13 44 44
RIT1/GDP 0.007 0.082 0.19 7 -0.24 22 29
TIAM1 0.033 0.011 -10000 0 0 46 46
PIK3R1 0.032 0.012 -10000 0 0 63 63
BDNF (dimer)/TRKB 0.027 0.071 -10000 0 -0.13 72 72
KIDINS220/CRKL/C3G 0.05 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.052 -10000 0 -0.16 31 31
FRS2 family/SHP2 0.067 0.028 -10000 0 -0.13 6 6
SHC/GRB2/SOS1/GAB1 0.049 0.046 -10000 0 -0.12 25 25
RIT1/GTP 0.014 0.041 -10000 0 -0.13 36 36
NT3 (dimer) 0.035 0.008 -10000 0 0 25 25
RAP1/GDP -0.002 0.061 -10000 0 -0.18 25 25
KIDINS220/CRKL 0.035 0.008 -10000 0 0 28 28
BDNF (dimer) 0.032 0.012 -10000 0 0 66 66
ubiquitin-dependent protein catabolic process 0.043 0.017 -10000 0 -0.12 1 1
Schwann cell development -0.011 0.016 -10000 0 -0.055 37 37
EHD4 0.034 0.01 -10000 0 0 38 38
FRS2 family/GRB2/SOS1 0.062 0.029 -10000 0 -0.11 8 8
FRS2 family/SHP2/CRK family/C3G/GAB2 0.008 0.071 -10000 0 -0.25 20 20
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 10 10
CDC42/GTP 0.018 0.083 -10000 0 -0.15 81 81
ABL1 0.032 0.013 -10000 0 0 69 69
SH2B family/GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
Rap1/GTP 0.003 0.069 -10000 0 -0.23 14 14
STAT3 0.021 0.088 -10000 0 -0.29 37 37
axon guidance 0.005 0.072 -10000 0 -0.14 81 81
MAPK3 -0.008 0.053 0.18 35 -10000 0 35
MAPK1 -0.009 0.049 0.18 29 -10000 0 29
CDC42/GDP 0.01 0.08 0.18 10 -0.22 23 33
NTF3 0.035 0.008 -10000 0 0 25 25
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.025 -10000 0 -0.12 9 9
PI3K 0.018 0.076 -10000 0 -0.16 72 72
FRS3 0.037 0.002 -10000 0 0 2 2
FAIM 0.035 0.009 -10000 0 0 29 29
GAB1 0.033 0.011 -10000 0 0 55 55
RASGRF1 -0.004 0.042 0.18 4 -0.14 1 5
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.018 0.021 0.09 11 -0.13 2 13
RGS19 0.033 0.011 -10000 0 0 52 52
CDC42 0.035 0.008 -10000 0 0 26 26
RAS family/GTP 0.009 0.1 0.23 1 -0.37 24 25
Rac1/GDP 0.01 0.069 0.18 8 -0.23 17 25
NGF (dimer)/TRKA/GRIT 0.039 0.035 -10000 0 -0.12 21 21
neuron projection morphogenesis -0.035 0.24 -10000 0 -0.87 36 36
NGF (dimer)/TRKA/NEDD4-2 0.044 0.017 -10000 0 -0.12 1 1
MAP2K1 -0.011 0.06 0.18 19 -0.19 6 25
NGFR 0.032 0.013 -10000 0 0 71 71
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.042 -10000 0 -0.24 7 7
RAS family/GTP/PI3K -0.023 0.11 -10000 0 -0.21 99 99
FRS2 family/SHP2/GRB2/SOS1 0.076 0.04 -10000 0 -0.14 10 10
NRAS 0.032 0.012 -10000 0 0 63 63
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
PRKCI 0.035 0.008 -10000 0 0 27 27
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.017 -10000 0 0 163 163
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.087 -10000 0 -0.47 13 13
RASA1 0.035 0.009 -10000 0 0 30 30
TRKA/c-Abl 0.032 0.059 -10000 0 -0.14 48 48
SQSTM1 0.034 0.009 -10000 0 0 35 35
BDNF (dimer)/TRKB/GIPC 0.048 0.076 -10000 0 -0.12 67 67
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.035 -10000 0 -0.1 16 16
MATK 0.035 0.008 -10000 0 0 27 27
NEDD4L 0.034 0.01 -10000 0 0 45 45
RAS family/GDP -0.02 0.057 -10000 0 -0.16 47 47
NGF (dimer)/TRKA 0.01 0.04 0.15 4 -0.13 4 8
Rac1/GTP -0.014 0.055 -10000 0 -0.2 23 23
FRS2 family/SHP2/CRK family 0.087 0.057 -10000 0 -0.13 18 18
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.032 0.012 -10000 0 0 59 59
GNB1/GNG2 0.029 0.034 -10000 0 -0.12 14 14
forebrain development 0.034 0.061 0.25 4 -0.36 3 7
GNAO1 0.031 0.014 -10000 0 0 87 87
SMO/beta Arrestin2 0.034 0.031 -10000 0 -0.14 4 4
SMO 0.025 0.018 -10000 0 0 171 171
ARRB2 0.035 0.008 -10000 0 0 25 25
GLI3/SPOP 0.002 0.11 0.22 1 -0.3 38 39
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.01 -10000 0 0 39 39
GNAI2 0.034 0.01 -10000 0 0 44 44
SIN3/HDAC complex 0.055 0.042 -10000 0 -0.13 17 17
GNAI1 0.018 0.018 -10000 0 0 262 262
XPO1 0.037 0.005 -10000 0 0 5 5
GLI1/Su(fu) 0.012 0.045 -10000 0 -0.26 6 6
SAP30 0.035 0.007 -10000 0 0 18 18
mol:GDP 0.025 0.018 -10000 0 0 171 171
MIM/GLI2A 0.041 0.014 0.12 11 -10000 0 11
IFT88 0.034 0.009 -10000 0 0 32 32
GNAI3 0.036 0.006 -10000 0 0 14 14
GLI2 0.001 0.088 -10000 0 -0.35 20 20
GLI3 -0.013 0.099 0.21 1 -0.3 34 35
CSNK1D 0.035 0.007 -10000 0 0 20 20
CSNK1E 0.032 0.013 -10000 0 0 68 68
SAP18 0.034 0.01 -10000 0 0 43 43
embryonic digit morphogenesis 0.034 0.009 -10000 0 0 32 32
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.012 0.088 -10000 0 -0.26 38 38
SIN3B 0.034 0.009 -10000 0 0 33 33
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.012 0.072 -10000 0 -0.26 26 26
GLI2/Su(fu) -0.003 0.072 -10000 0 -0.31 18 18
FOXA2 0.049 0.037 -10000 0 -0.49 1 1
neural tube patterning 0.034 0.061 0.25 4 -0.36 3 7
SPOP 0.035 0.008 -10000 0 0 23 23
Su(fu)/PIAS1 0.046 0.038 0.098 147 -0.088 8 155
GNB1 0.035 0.007 -10000 0 0 20 20
CSNK1G2 0.035 0.008 -10000 0 0 27 27
CSNK1G3 0.036 0.005 -10000 0 0 11 11
MTSS1 0.041 0.014 0.12 11 -10000 0 11
embryonic limb morphogenesis 0.034 0.061 0.25 4 -0.36 3 7
SUFU 0.002 0.01 -10000 0 -0.11 4 4
LGALS3 0.028 0.015 -10000 0 0 117 117
catabolic process 0.012 0.14 0.29 2 -0.43 32 34
GLI3A/CBP 0.045 0.009 -10000 0 -10000 0 0
KIF3A 0.033 0.011 -10000 0 0 53 53
GLI1 0.034 0.062 0.25 4 -0.36 3 7
RAB23 0.035 0.009 -10000 0 0 31 31
CSNK1A1 0.036 0.006 -10000 0 0 12 12
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.036 0.005 -10000 0 0 8 8
Su(fu)/Galectin3 0.037 0.04 0.098 119 -0.12 7 126
GNAZ 0.031 0.013 -10000 0 0 80 80
RBBP4 0.033 0.012 -10000 0 0 57 57
CSNK1G1 0.036 0.005 -10000 0 0 11 11
PIAS1 0.035 0.008 -10000 0 0 25 25
PRKACA 0.035 0.008 -10000 0 0 24 24
GLI2/SPOP 0.017 0.097 -10000 0 -0.32 25 25
STK36 0.001 0.003 0.022 4 -10000 0 4
Gi family/GNB1/GNG2/GDP -0.017 0.1 -10000 0 -0.34 31 31
PTCH1 0.033 0.058 0.24 4 -0.33 3 7
MIM/GLI1 0.057 0.068 0.35 2 -0.33 3 5
CREBBP 0.045 0.009 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.001 0.093 0.17 1 -0.31 27 28
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.028 0.074 0.21 12 -0.27 10 22
FYN -0.01 0.11 0.24 11 -0.3 34 45
LAT/GRAP2/SLP76 0.021 0.075 0.22 5 -0.29 12 17
IKBKB 0.036 0.003 -10000 0 0 4 4
AKT1 0.005 0.084 0.21 15 -0.24 23 38
B2M 0.037 0.009 -10000 0 0 24 24
IKBKG -0.003 0.034 0.097 11 -0.1 8 19
MAP3K8 0.022 0.018 -10000 0 0 200 200
mol:Ca2+ -0.01 0.009 -10000 0 -0.04 3 3
integrin-mediated signaling pathway 0.024 0.007 -10000 0 -0.11 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.008 0.1 0.25 15 -0.3 21 36
TRPV6 0.39 0.59 1.2 163 -10000 0 163
CD28 0.037 0.001 -10000 0 -10000 0 0
SHC1 0.019 0.079 0.2 26 -0.32 10 36
receptor internalization 0.019 0.064 0.17 9 -0.3 9 18
PRF1 -0.14 0.31 -10000 0 -0.6 149 149
KRAS 0.034 0.009 -10000 0 0 34 34
GRB2 0.035 0.007 -10000 0 0 18 18
COT/AKT1 0.006 0.064 0.2 4 -0.21 18 22
LAT 0.012 0.075 0.21 13 -0.3 12 25
EntrezGene:6955 0.001 0.004 0.014 41 -10000 0 41
CD3D 0.035 0.011 -10000 0 0 45 45
CD3E 0.038 0.007 -10000 0 0 10 10
CD3G 0.037 0.008 -10000 0 0 18 18
RASGRP2 0.006 0.018 -10000 0 -0.15 4 4
RASGRP1 -0.021 0.13 0.22 25 -0.25 92 117
HLA-A 0.038 0.007 -10000 0 0 12 12
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.024 0.007 -10000 0 -0.11 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.054 0.13 35 -0.1 19 54
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.037 -10000 0 -0.12 28 28
PRKCA 0.001 0.06 0.17 22 -0.18 6 28
GRAP2 0.034 0.01 -10000 0 0 37 37
mol:IP3 0.003 0.055 -10000 0 -0.23 10 10
EntrezGene:6957 0.001 0.004 0.015 41 -10000 0 41
TCR/CD3/MHC I/CD8 0.019 0.05 0.15 12 -0.23 6 18
ORAI1 -0.34 0.5 -10000 0 -1.1 163 163
CSK 0.013 0.075 0.21 14 -0.3 12 26
B7 family/CD28 0.063 0.098 0.26 25 -0.28 11 36
CHUK 0.025 0.017 -10000 0 0 165 165
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.016 0.077 0.2 10 -0.33 12 22
PTPN6 0.008 0.08 0.23 13 -0.3 14 27
VAV1 0.018 0.077 0.21 25 -0.31 9 34
Monovalent TCR/CD3 0.022 0.017 0.11 7 -10000 0 7
CBL 0.036 0.005 -10000 0 0 8 8
LCK 0.006 0.093 0.24 14 -0.3 19 33
PAG1 0.015 0.074 0.21 11 -0.3 12 23
RAP1A 0.036 0.005 -10000 0 0 10 10
TCR/CD3/MHC I/CD8/LCK 0.015 0.078 0.21 10 -0.32 13 23
CD80 0.036 0.007 -10000 0 0 16 16
CD86 0.033 0.012 -10000 0 0 65 65
PDK1/CARD11/BCL10/MALT1 0.002 0.046 -10000 0 -0.14 27 27
HRAS 0.034 0.009 -10000 0 0 36 36
GO:0035030 0.012 0.075 0.2 23 -0.25 11 34
CD8A 0.001 0.004 0.015 41 -10000 0 41
CD8B 0.001 0.004 0.015 43 -10000 0 43
PTPRC 0.029 0.015 -10000 0 0 110 110
PDK1/PKC theta 0.007 0.092 0.24 22 -0.28 15 37
CSK/PAG1 0.011 0.072 0.21 13 -0.29 12 25
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.05 0.035 -10000 0 -0.15 13 13
GRAP2/SLP76 0.03 0.085 0.24 4 -0.3 15 19
STIM1 -0.071 0.11 1 1 -10000 0 1
RAS family/GTP 0.005 0.072 0.17 17 -0.18 29 46
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.019 0.066 0.18 9 -0.32 9 18
mol:DAG -0.019 0.038 -10000 0 -0.21 10 10
RAP1A/GDP 0.009 0.028 0.073 24 -0.052 16 40
PLCG1 0.034 0.01 -10000 0 0 37 37
CD247 0.001 0.004 0.014 41 -10000 0 41
cytotoxic T cell degranulation -0.13 0.3 -10000 0 -0.58 151 151
RAP1A/GTP 0.004 0.007 -10000 0 -0.054 4 4
mol:PI-3-4-5-P3 0.009 0.091 0.24 16 -0.26 21 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.069 0.18 1 -0.27 10 11
NRAS 0.032 0.012 -10000 0 0 63 63
ZAP70 0.037 0.002 -10000 0 0 2 2
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
LAT/GRAP2/SLP76/VAV1 0.01 0.068 0.2 3 -0.29 8 11
MALT1 0.034 0.009 -10000 0 0 34 34
TRAF6 0.036 0.005 -10000 0 0 10 10
CD8 heterodimer 0.003 0.008 0.028 43 -10000 0 43
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.028 -10000 0 -0.15 10 10
PRKCE 0.001 0.06 0.17 23 -0.18 6 29
PRKCQ 0.009 0.096 0.25 21 -0.29 17 38
LCP2 0.031 0.013 -10000 0 0 75 75
BCL10 0.035 0.007 -10000 0 0 19 19
regulation of survival gene product expression 0.005 0.077 0.2 15 -0.22 18 33
IKK complex 0 0.039 0.13 13 -0.11 1 14
RAS family/GDP -0.004 0.015 -10000 0 -0.041 38 38
MAP3K14 0.01 0.064 0.18 23 -0.17 18 41
PDPK1 0.005 0.08 0.21 18 -0.23 19 37
TCR/CD3/MHC I/CD8/Fyn 0.01 0.069 0.18 1 -0.29 13 14
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.026 0.017 -9999 0 0 144 144
ITGB7 0.036 0.006 -9999 0 0 14 14
ITGA4 0.036 0.006 -9999 0 0 13 13
alpha4/beta7 Integrin 0.052 0.012 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.038 0.025 -9999 0 -9999 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.003 0.1 -10000 0 -0.39 30 30
Crk/p130 Cas/Paxillin -0.058 0.094 -10000 0 -0.19 142 142
JUN -0.016 0.047 -10000 0 -0.26 10 10
HRAS 0.034 0.009 -10000 0 0 36 36
RET51/GFRalpha1/GDNF/GRB10 0.036 0.06 -10000 0 -0.12 28 28
RAP1A 0.036 0.005 -10000 0 0 10 10
FRS2 0.035 0.009 -10000 0 0 30 30
RAP1A/GDP 0.026 0.008 -10000 0 -0.13 1 1
RET51/GFRalpha1/GDNF/DOK1 0.062 0.046 -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 21 21
RAP1A/GTP 0.055 0.048 -10000 0 -0.11 1 1
GRB7 0.036 0.006 -10000 0 0 15 15
RET51/GFRalpha1/GDNF 0.061 0.047 -10000 0 -10000 0 0
MAPKKK cascade -0.007 0.075 -10000 0 -0.18 15 15
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.038 0.046 -10000 0 -0.11 23 23
lamellipodium assembly -0.027 0.083 0.13 1 -0.19 67 68
RET51/GFRalpha1/GDNF/SHC 0.058 0.051 -10000 0 -0.12 8 8
PIK3CA 0.031 0.014 -10000 0 0 82 82
RET9/GFRalpha1/GDNF/SHC 0.04 0.039 -10000 0 -0.11 8 8
RET9/GFRalpha1/GDNF/Shank3 0.032 0.022 -10000 0 -10000 0 0
MAPK3 -0.026 0.035 0.2 7 -10000 0 7
DOK1 0.037 0.002 -10000 0 0 2 2
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 7 7
neurite development -0.021 0.039 0.25 3 -0.21 8 11
DOK5 0.029 0.015 -10000 0 0 108 108
GFRA1 0.025 0.017 -10000 0 0 164 164
MAPK8 0 0.044 -10000 0 -0.17 20 20
HRAS/GTP 0.02 0.094 -10000 0 -0.12 119 119
tube development 0.025 0.028 0.2 3 -0.1 8 11
MAPK1 -0.025 0.035 0.22 5 -10000 0 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.013 0.064 -10000 0 -0.22 15 15
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
SRC 0.034 0.009 -10000 0 0 34 34
PDLIM7 0.036 0.005 -10000 0 0 9 9
RET51/GFRalpha1/GDNF/Dok6 0.057 0.043 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 52 52
RET51/GFRalpha1/GDNF/Dok4 0.062 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.037 0.073 -10000 0 -0.12 67 67
PRKCA 0.036 0.004 -10000 0 0 6 6
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
CREB1 -0.034 0.098 -10000 0 -0.19 126 126
PIK3R1 0.032 0.012 -10000 0 0 63 63
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.012 0.066 -10000 0 -0.17 30 30
RET51/GFRalpha1/GDNF/Grb7 0.062 0.046 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.027 0.016 -10000 0 0 137 137
DOK4 0.036 0.006 -10000 0 0 13 13
JNK cascade -0.017 0.048 -10000 0 -0.24 12 12
RET9/GFRalpha1/GDNF/FRS2 0.046 0.034 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.035 0.009 -10000 0 0 30 30
NCK1 0.035 0.008 -10000 0 0 27 27
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.014 0.06 -10000 0 -0.18 18 18
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.027 0.094 -10000 0 -0.19 115 115
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.035 0.099 -10000 0 -0.19 133 133
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.009 0.048 -10000 0 -0.18 17 17
PI3K -0.058 0.13 0.19 1 -0.25 125 126
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.039 0.039 -10000 0 -0.1 8 8
GRB10 0.021 0.018 -10000 0 0 222 222
activation of MAPKK activity 0.011 0.051 -10000 0 -0.26 14 14
RET51/GFRalpha1/GDNF/FRS2 0.059 0.047 -10000 0 -10000 0 0
GAB1 0.033 0.011 -10000 0 0 55 55
IRS1 0.033 0.011 -10000 0 0 51 51
IRS2 0.03 0.014 -10000 0 0 94 94
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.01 0.055 -10000 0 -0.17 26 26
RET51/GFRalpha1/GDNF/PKC alpha 0.062 0.047 -10000 0 -10000 0 0
GRB2 0.035 0.007 -10000 0 0 18 18
PRKACA 0.035 0.008 -10000 0 0 24 24
GDNF 0.036 0.004 -10000 0 0 6 6
RAC1 0.025 0.017 -10000 0 0 163 163
RET51/GFRalpha1/GDNF/IRS1 0.055 0.057 -10000 0 -0.11 22 22
Rac1/GTP -0.029 0.099 -10000 0 -0.23 63 63
RET9/GFRalpha1/GDNF 0.033 0.023 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.037 0.026 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.036 0.028 -9999 0 -0.14 2 2
FBXW11 0.035 0.007 -9999 0 0 22 22
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 22 22
CHUK 0.025 0.017 -9999 0 0 165 165
NF kappa B2 p100/RelB 0.065 0.063 -9999 0 -0.11 13 13
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 0 157 157
NF kappa B2 p52/RelB 0.033 0.023 -9999 0 -10000 0 0
regulation of B cell activation 0.033 0.023 -9999 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.052 0.038 -10000 0 -0.1 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.039 0.17 -10000 0 -0.54 38 38
AKT1 -0.05 0.23 -10000 0 -0.63 56 56
PIK3CA 0.031 0.014 -10000 0 0 82 82
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.045 0.23 -10000 0 -0.65 55 55
mol:Ca2+ 0.006 0.052 0.17 18 -0.25 3 21
IGF1R 0.033 0.011 -10000 0 0 53 53
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 0.05 0.22 0.6 58 -10000 0 58
RhoA/GTP -0.042 0.04 -10000 0 -0.14 50 50
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.012 0.15 -10000 0 -0.4 42 42
regulation of stress fiber formation 0.038 0.061 0.18 22 -0.18 8 30
E2/ERA-ERB (dimer) 0.045 0.015 -10000 0 -10000 0 0
KRAS 0.034 0.009 -10000 0 0 34 34
G13/GTP 0.043 0.014 -10000 0 -10000 0 0
pseudopodium formation -0.038 0.061 0.18 8 -0.18 22 30
E2/ER alpha (dimer)/PELP1 0.044 0.023 -10000 0 -0.12 7 7
GRB2 0.035 0.007 -10000 0 0 18 18
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 87 87
HRAS 0.034 0.009 -10000 0 0 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.16 -10000 0 -0.44 44 44
E2/ER beta (dimer) 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.003 0.058 0.13 3 -0.19 26 29
mol:NADP -0.012 0.16 -10000 0 -0.44 44 44
PIK3R1 0.032 0.012 -10000 0 0 63 63
mol:IP3 0.007 0.05 0.17 18 -0.34 1 19
IGF-1R heterotetramer 0.033 0.011 -10000 0 0 53 53
PLCB1 0.01 0.04 -10000 0 -0.34 1 1
PLCB2 0.009 0.04 -10000 0 -0.34 1 1
IGF1 0.035 0.007 -10000 0 0 21 21
mol:L-citrulline -0.012 0.16 -10000 0 -0.44 44 44
RHOA 0.035 0.007 -10000 0 0 21 21
Gai/GDP -0.067 0.24 -10000 0 -0.64 70 70
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.035 0.009 -10000 0 0 31 31
GNAQ 0.035 0.009 -10000 0 0 30 30
ESR1 0.035 0.009 -10000 0 0 30 30
Gq family/GDP/Gbeta gamma -0.002 0.15 -10000 0 -0.51 32 32
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.14 -10000 0 -0.69 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.004 0.16 0.25 8 -0.43 38 46
GNAZ 0.031 0.013 -10000 0 0 80 80
E2/ER alpha (dimer) 0.026 0.006 -10000 0 -10000 0 0
STRN 0.036 0.003 -10000 0 0 4 4
GNAL 0.036 0.006 -10000 0 0 13 13
PELP1 0.036 0.007 -10000 0 0 17 17
MAPK11 -0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 0 44 44
GNAI3 0.036 0.006 -10000 0 0 14 14
GNAI1 0.018 0.018 -10000 0 0 262 262
HBEGF -0.01 0.18 0.34 25 -0.49 38 63
cAMP biosynthetic process 0.037 0.016 -10000 0 -10000 0 0
SRC -0.04 0.16 0.21 8 -0.5 40 48
PI3K 0.018 0.076 -10000 0 -0.16 72 72
GNB1 0.035 0.007 -10000 0 0 20 20
G13/GDP/Gbeta gamma 0.021 0.069 -10000 0 -0.17 34 34
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.12 -10000 0 -0.35 39 39
Gs family/GTP 0.047 0.02 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.065 -10000 0 -0.13 54 54
vasodilation -0.01 0.16 0.22 1 -0.42 44 45
mol:DAG 0.007 0.05 0.17 18 -0.34 1 19
Gs family/GDP/Gbeta gamma 0.003 0.062 -10000 0 -0.18 30 30
MSN -0.042 0.061 0.18 6 -0.2 22 28
Gq family/GTP 0.023 0.042 -10000 0 -0.35 1 1
mol:PI-3-4-5-P3 -0.043 0.22 -10000 0 -0.61 57 57
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 0.42 44 -0.22 1 45
GRB2/SOS1 0.024 0.02 -10000 0 -0.13 8 8
RhoA/GDP 0.017 0.068 -10000 0 -0.19 29 29
NOS3 -0.014 0.17 -10000 0 -0.46 44 44
GNA11 0.033 0.011 -10000 0 0 51 51
MAPKKK cascade 0.003 0.15 -10000 0 -0.47 35 35
E2/ER alpha (dimer)/PELP1/Src 0.001 0.17 0.27 9 -0.44 39 48
ruffle organization -0.038 0.061 0.18 8 -0.18 22 30
ROCK2 -0.033 0.064 0.2 7 -0.2 13 20
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GNA13 0.035 0.007 -10000 0 0 20 20
MMP9 -0.023 0.17 0.36 9 -0.48 41 50
MMP2 -0.024 0.17 0.25 11 -0.49 41 52
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.051 0.39 0.77 2 -1 27 29
STAT6 (cleaved dimer) -0.068 0.35 -10000 0 -0.89 37 37
IGHG1 -0.013 0.26 0.44 20 -0.8 22 42
IGHG3 -0.067 0.36 0.64 1 -0.87 39 40
AKT1 -0.024 0.27 0.52 5 -0.72 31 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.016 0.19 0.47 5 -0.55 7 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.008 0.26 0.5 5 -0.72 22 27
THY1 -0.13 0.5 0.8 2 -1.2 64 66
MYB 0.033 0.011 -10000 0 0 55 55
HMGA1 0.036 0.005 -10000 0 0 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3 0 0.26 0.54 9 -0.58 16 25
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.007 0.25 0.5 4 -0.77 17 21
SP1 0.029 0.076 0.12 95 -0.14 68 163
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.045 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.054 0.37 -10000 0 -0.93 31 31
SOCS1 -0.041 0.3 0.51 4 -0.66 33 37
SOCS3 -0.004 0.22 0.5 1 -0.64 3 4
FCER2 -0.028 0.32 0.66 1 -0.77 15 16
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.064 0.38 0.73 1 -0.95 33 34
GRB2 0.035 0.007 -10000 0 0 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.003 0.22 0.45 10 -0.58 18 28
T cell proliferation -0.071 0.38 0.67 1 -0.96 35 36
IL4R/JAK1 -0.072 0.38 0.67 1 -0.97 33 34
EGR2 -0.12 0.5 0.73 1 -1.2 58 59
JAK2 0.019 0.066 0.16 18 -10000 0 18
JAK3 0.034 0.016 -10000 0 -0.042 4 4
PIK3R1 0.032 0.012 -10000 0 0 63 63
JAK1 0.027 0.039 0.11 8 -10000 0 8
COL1A2 -0.11 0.48 0.54 2 -1.2 76 78
CCL26 -0.063 0.38 0.69 2 -0.9 39 41
IL4R -0.059 0.41 0.81 3 -1.1 27 30
PTPN6 0.015 0.037 -10000 0 -0.057 11 11
IL13RA2 -0.32 0.66 0.77 3 -1.1 179 182
IL13RA1 0.024 0.067 0.16 18 -10000 0 18
IRF4 0.047 0.11 -10000 0 -10000 0 0
ARG1 0.005 0.21 0.52 3 -0.77 10 13
CBL -0.008 0.24 0.49 6 -0.56 17 23
GTF3A 0.048 0.035 0.12 70 -0.15 3 73
PIK3CA 0.031 0.014 -10000 0 0 82 82
IL13RA1/JAK2 0.026 0.1 0.24 10 -0.16 23 33
IRF4/BCL6 0.042 0.11 -10000 0 -10000 0 0
CD40LG 0.041 0.004 0.14 1 -10000 0 1
MAPK14 -0.006 0.24 0.49 5 -0.56 15 20
mitosis -0.019 0.26 0.51 5 -0.67 31 36
STAT6 -0.069 0.43 0.79 6 -1 39 45
SPI1 0.038 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.25 0.48 6 -0.66 30 36
STAT6 (dimer) -0.068 0.43 0.79 6 -1 39 45
STAT6 (dimer)/PARP14 -0.083 0.38 -10000 0 -0.95 39 39
mast cell activation -0.002 0.016 -10000 0 -0.041 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.007 0.21 0.49 4 -0.56 6 10
FRAP1 -0.023 0.27 0.52 5 -0.71 31 36
LTA -0.066 0.38 0.73 1 -0.99 27 28
FES 0.036 0.006 -10000 0 0 14 14
T-helper 1 cell differentiation 0.063 0.43 0.99 39 -0.79 6 45
CCL11 -0.068 0.36 -10000 0 -0.97 26 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.011 0.22 0.51 5 -0.59 4 9
IL2RG 0.034 0.016 -10000 0 -0.044 1 1
IL10 -0.051 0.39 0.72 3 -1 25 28
IRS1 0.033 0.011 -10000 0 0 51 51
IRS2 0.03 0.014 -10000 0 0 94 94
IL4 0.027 0.17 0.58 1 -0.84 5 6
IL5 -0.066 0.38 0.73 1 -1 27 28
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.059 0.39 0.67 12 -0.89 40 52
COL1A1 0.017 0.26 0.56 19 -0.81 15 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.076 0.38 -10000 0 -1.1 26 26
IL2R gamma/JAK3 0.054 0.019 -10000 0 -10000 0 0
TFF3 -0.06 0.38 0.73 1 -0.97 29 30
ALOX15 -0.066 0.38 0.73 1 -0.99 28 29
MYBL1 0.03 0.014 -10000 0 0 96 96
T-helper 2 cell differentiation -0.046 0.34 0.64 4 -0.77 37 41
SHC1 0.033 0.011 -10000 0 0 52 52
CEBPB 0.034 0.016 0.11 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.016 0.26 0.52 5 -0.74 22 27
mol:PI-3-4-5-P3 -0.023 0.27 0.52 5 -0.71 31 36
PI3K -0.028 0.28 0.52 5 -0.76 31 36
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.005 0.047 -10000 0 -0.087 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.004 0.22 0.44 11 -0.56 23 34
ITGB3 -0.066 0.38 0.73 1 -1 24 25
PIGR -0.054 0.38 0.72 2 -1 25 27
IGHE -0.003 0.079 0.18 39 -0.18 13 52
MAPKKK cascade 0.005 0.21 0.44 11 -0.55 23 34
BCL6 0.031 0.013 -10000 0 0 71 71
OPRM1 -0.065 0.38 0.73 1 -0.99 27 28
RETNLB -0.063 0.38 0.69 2 -0.9 39 41
SELP -0.062 0.38 0.8 2 -1 26 28
AICDA -0.064 0.36 -10000 0 -0.96 25 25
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.008 0.071 -10000 0 -0.3 21 21
KLHL20 0.049 0.094 0.2 71 -0.19 18 89
CYFIP2 0.031 0.013 -10000 0 0 76 76
Rac1/GDP 0.009 0.062 0.2 1 -0.26 12 13
ENAH 0.007 0.074 -10000 0 -0.32 20 20
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 39 0 9 48
RAP1A 0.036 0.005 -10000 0 0 10 10
CTNNB1 0.036 0.006 -10000 0 0 15 15
CDC42/GTP -0.023 0.056 0.12 24 -0.21 21 45
ABI1/Sra1/Nap1 -0.015 0.034 -10000 0 -0.13 29 29
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.083 0.039 -10000 0 -0.13 8 8
RAPGEF1 0 0.078 0.22 1 -0.29 16 17
CTNND1 0.035 0.009 -10000 0 0 31 31
regulation of calcium-dependent cell-cell adhesion 0.021 0.075 -10000 0 -0.3 22 22
CRK 0.007 0.08 -10000 0 -0.29 20 20
E-cadherin/gamma catenin/alpha catenin 0.062 0.035 -10000 0 -0.13 8 8
alphaE/beta7 Integrin 0.049 0.026 -10000 0 -0.14 7 7
IQGAP1 0.033 0.011 -10000 0 0 47 47
NCKAP1 0.037 0.002 -10000 0 0 2 2
Rap1/GTP/I-afadin 0.043 0.015 -10000 0 -0.1 1 1
DLG1 0.008 0.075 -10000 0 -0.3 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.034 0.044 -10000 0 -0.18 29 29
MLLT4 0.034 0.009 -10000 0 0 34 34
ARF6/GTP/NME1/Tiam1 0.036 0.033 -10000 0 -0.1 23 23
PI3K -0.041 0.058 0.06 1 -0.23 29 30
ARF6 0.035 0.009 -10000 0 0 29 29
mol:Ca2+ 0 0 0.001 68 0 29 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+ 0.071 0.054 -10000 0 -0.14 25 25
AKT1 -0.02 0.056 0.13 9 -0.18 24 33
PIK3R1 0.032 0.012 -10000 0 0 63 63
CDH1 0.034 0.01 -10000 0 0 37 37
RhoA/GDP 0.017 0.074 0.2 5 -0.25 15 20
actin cytoskeleton organization 0.041 0.076 0.17 72 -0.14 17 89
CDC42/GDP 0.016 0.072 0.2 4 -0.25 14 18
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.05 -10000 0 -0.2 23 23
ITGB7 0.036 0.006 -10000 0 0 14 14
RAC1 0.025 0.017 -10000 0 0 163 163
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.077 0.058 -10000 0 -0.15 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin 0.056 0.031 -10000 0 -0.11 10 10
mol:GDP 0 0.076 0.2 4 -0.29 13 17
CDC42/GTP/IQGAP1 0.035 0.042 -10000 0 -0.12 33 33
JUP 0.033 0.011 -10000 0 0 51 51
p120 catenin/RhoA/GDP 0.031 0.082 0.22 5 -0.25 18 23
RAC1/GTP/IQGAP1 0.024 0.043 -10000 0 -0.12 30 30
PIP5K1C/AP1M1 0.02 0.03 -10000 0 -0.13 18 18
RHOA 0.035 0.007 -10000 0 0 21 21
CDC42 0.035 0.008 -10000 0 0 26 26
CTNNA1 0.036 0.007 -10000 0 0 18 18
positive regulation of S phase of mitotic cell cycle 0.015 0.048 0.12 18 -0.12 32 50
NME1 0 0 -10000 0 0 32 32
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.009 0.073 -10000 0 -0.3 20 20
regulation of cell-cell adhesion -0.027 0.04 -10000 0 -0.17 25 25
WASF2 -0.008 0.018 -10000 0 -0.073 29 29
Rap1/GTP -0.019 0.067 0.15 32 -0.22 22 54
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.091 0.051 -10000 0 -0.13 12 12
CCND1 0.017 0.057 0.14 18 -0.15 32 50
VAV2 0.024 0.11 -10000 0 -0.52 10 10
RAP1/GDP -0.006 0.069 0.16 29 -0.25 15 44
adherens junction assembly 0.009 0.071 -10000 0 -0.3 20 20
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.017 -10000 0 0 158 158
PIP5K1C 0.033 0.011 -10000 0 0 47 47
regulation of heterotypic cell-cell adhesion 0.069 0.047 0.2 3 -0.14 13 16
E-cadherin/beta catenin 0.007 0.02 -10000 0 -0.099 5 5
mol:GTP 0 0 0.001 63 0 32 95
SRC 0.007 0.07 -10000 0 -0.29 21 21
PIK3CA 0.031 0.014 -10000 0 0 82 82
Rac1/GTP -0.008 0.07 0.17 2 -0.29 18 20
E-cadherin/beta catenin/alpha catenin 0.064 0.036 -10000 0 -0.14 10 10
ITGAE 0.035 0.007 -10000 0 0 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.077 -10000 0 -0.3 22 22
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.016 0.11 0.26 10 -0.38 21 31
CRKL 0.02 0.1 0.23 10 -0.39 22 32
HRAS 0.032 0.1 0.25 7 -0.32 22 29
mol:PIP3 0.058 0.12 0.3 27 -0.34 21 48
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.036 0.004 -10000 0 0 7 7
GAB1 0.025 0.11 0.24 11 -0.4 22 33
FOXO3 0.055 0.16 0.31 34 -0.35 41 75
AKT1 0.056 0.17 0.33 32 -0.37 41 73
BAD 0.048 0.16 0.31 32 -0.36 42 74
megakaryocyte differentiation 0.025 0.1 0.24 11 -0.39 20 31
GSK3B 0.048 0.17 0.32 34 -0.37 43 77
RAF1 0.022 0.091 0.24 14 -0.27 23 37
SHC1 0.033 0.011 -10000 0 0 52 52
STAT3 0.018 0.1 0.23 5 -0.4 22 27
STAT1 0.015 0.2 -10000 0 -0.87 21 21
HRAS/SPRED1 0.024 0.089 0.22 8 -0.27 23 31
cell proliferation 0.009 0.094 0.23 4 -0.38 22 26
PIK3CA 0.031 0.014 -10000 0 0 82 82
TEC 0.036 0.004 -10000 0 0 6 6
RPS6KB1 0.056 0.12 0.27 20 -0.37 21 41
HRAS/SPRED2 0.043 0.099 0.25 10 -0.27 22 32
LYN/TEC/p62DOK 0.066 0.12 -10000 0 -0.4 22 22
MAPK3 0.02 0.087 0.26 20 -0.21 22 42
STAP1 0.025 0.1 0.23 5 -0.39 22 27
GRAP2 0.034 0.01 -10000 0 0 37 37
JAK2 0.015 0.17 -10000 0 -0.74 21 21
STAT1 (dimer) 0.02 0.2 -10000 0 -0.85 21 21
mol:Gleevec -0.002 0.006 -10000 0 -0.023 1 1
GRB2/SOCS1/VAV1 0.073 0.12 0.28 1 -0.38 22 23
actin filament polymerization 0.027 0.1 0.23 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 0.033 0.012 -10000 0 0 63 63
CBL/CRKL/GRB2 0.053 0.11 0.29 3 -0.38 21 24
PI3K 0.064 0.14 0.3 18 -0.38 21 39
PTEN 0.025 0.017 -10000 0 0 168 168
SCF/KIT/EPO/EPOR 0.023 0.22 -10000 0 -1 21 21
MAPK8 0.008 0.095 0.24 3 -0.39 22 25
STAT3 (dimer) 0.02 0.1 0.24 7 -0.39 22 29
positive regulation of transcription 0.02 0.078 0.23 22 -0.18 18 40
mol:GDP 0.042 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 0.26 5 -0.38 21 26
FER 0.023 0.1 0.24 6 -0.39 22 28
SH2B3 0.025 0.1 0.23 5 -0.39 22 27
PDPK1 0.051 0.12 0.29 27 -0.32 21 48
SNAI2 0.026 0.11 0.23 11 -0.4 21 32
positive regulation of cell proliferation 0.028 0.17 -10000 0 -0.66 21 21
KITLG 0.039 0.021 -10000 0 -0.051 20 20
cell motility 0.028 0.17 -10000 0 -0.66 21 21
PTPN6 0.023 0.025 -10000 0 -0.033 68 68
EPOR 0.048 0.085 -10000 0 -10000 0 0
STAT5A (dimer) 0.032 0.14 0.3 2 -0.54 21 23
SOCS1 0.036 0.005 -10000 0 0 9 9
cell migration -0.022 0.1 0.38 22 -0.24 6 28
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.026 0.022 -10000 0 -0.036 14 14
VAV1 0.034 0.009 -10000 0 0 33 33
GRB10 0.011 0.088 0.3 4 -0.36 18 22
PTPN11 0.027 0.022 -10000 0 -0.027 67 67
SCF/KIT 0.029 0.11 0.25 5 -0.41 22 27
GO:0007205 -0.002 0.007 0.021 20 -0.021 3 23
MAP2K1 0.012 0.082 0.22 13 -0.22 26 39
CBL 0.036 0.005 -10000 0 0 8 8
KIT 0.005 0.24 -10000 0 -1.1 21 21
MAP2K2 0.017 0.091 0.3 19 -0.22 23 42
SHC/Grb2/SOS1 0.053 0.11 -10000 0 -0.36 21 21
STAT5A 0.033 0.14 0.3 2 -0.56 21 23
GRB2 0.035 0.007 -10000 0 0 18 18
response to radiation 0.027 0.11 0.23 12 -0.4 21 33
SHC/GRAP2 0.043 0.031 -10000 0 -0.14 8 8
PTPRO 0.024 0.1 0.24 11 -0.4 20 31
SH2B2 0.025 0.1 0.23 5 -0.39 22 27
DOK1 0.037 0.002 -10000 0 0 2 2
MATK 0.019 0.1 0.23 4 -0.39 22 26
CREBBP 0.052 0.045 0.14 4 -0.12 21 25
BCL2 0.039 0.14 -10000 0 -1 4 4
Retinoic acid receptors-mediated signaling

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
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC3 0.036 0.004 -10000 0 0 7 7
VDR 0.035 0.007 -10000 0 0 21 21
Cbp/p300/PCAF 0.042 0.024 -10000 0 -0.12 7 7
EP300 0.033 0.011 -10000 0 0 50 50
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.049 -10000 0 -0.22 7 7
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.004 -10000 0 0 5 5
AKT1 0.007 0.08 0.16 55 -0.23 11 66
RAR alpha/9cRA/Cyclin H -0.027 0.13 -10000 0 -0.3 38 38
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.056 -10000 0 -0.2 21 21
CDC2 0.018 0.02 -10000 0 -0.001 249 249
response to UV -0.001 0.007 -10000 0 -0.026 33 33
RAR alpha/Jnk1 0.022 0.028 0.16 1 -10000 0 1
NCOR2 0.037 0.002 -10000 0 0 2 2
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.028 0.15 -10000 0 -0.54 33 33
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA3 0.034 0.01 -10000 0 0 41 41
NCOA1 0.033 0.011 -10000 0 0 49 49
VDR/VDR/DNA 0.035 0.007 -10000 0 0 21 21
RARG 0.032 0.017 -10000 0 -0.023 44 44
RAR gamma1/9cRA 0.046 0.013 -10000 0 -10000 0 0
MAPK3 0.032 0.018 -10000 0 -0.031 37 37
MAPK1 0.034 0.01 -10000 0 0 44 44
MAPK8 0.024 0.022 -10000 0 -0.006 164 164
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.022 0.12 -10000 0 -0.36 33 33
RARA 0.006 0.037 -10000 0 -0.2 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.041 -10000 0 -0.17 10 10
PRKCA 0.031 0.027 0.076 4 -0.072 32 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.031 0.16 -10000 0 -0.62 33 33
RXRG 0.019 0.028 -10000 0 -10000 0 0
RXRA -0.012 0.082 0.15 3 -0.3 24 27
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 0 142 142
CRBP1/9-cic-RA -0.004 0.061 -10000 0 -0.13 90 90
RARB 0.032 0.021 -10000 0 -0.046 33 33
PRKCG 0.031 0.027 0.075 3 -0.071 33 36
MNAT1 0.034 0.01 -10000 0 0 38 38
RAR alpha/RXRs -0.015 0.13 -10000 0 -0.41 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.006 0.09 -10000 0 -0.3 24 24
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.057 -10000 0 -0.19 13 13
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.03 0.16 -10000 0 -0.62 33 33
positive regulation of DNA binding -0.032 0.12 -10000 0 -0.28 39 39
NRIP1 -0.054 0.27 -10000 0 -1.1 33 33
RXRs/RARs -0.008 0.12 -10000 0 -0.41 33 33
RXRs/RXRs/DNA/9cRA -0.035 0.11 -10000 0 -0.36 33 33
PRKACA 0.035 0.008 -10000 0 0 24 24
CDK7 0.035 0.008 -10000 0 0 24 24
TFIIH 0.059 0.051 -10000 0 -0.17 19 19
RAR alpha/9cRA 0.021 0.089 -10000 0 -0.18 23 23
CCNH 0.036 0.006 -10000 0 0 16 16
CREBBP 0.036 0.005 -10000 0 0 9 9
RAR gamma2/9cRA 0.056 0.051 -10000 0 -0.15 19 19
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 -0.009 0.087 -10000 0 -0.28 28 28
ACTA1 -0.037 0.09 0.16 1 -0.29 33 34
NUMA1 -0.002 0.084 -10000 0 -0.34 14 14
SPTAN1 -0.045 0.091 0.2 5 -0.29 36 41
LIMK1 0.01 0.11 0.19 75 -0.35 13 88
BIRC3 0.031 0.014 -10000 0 0 82 82
BIRC2 0.036 0.006 -10000 0 0 12 12
BAX 0.034 0.01 -10000 0 0 43 43
CASP10 -0.008 0.032 0.083 47 -10000 0 47
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.09 -10000 0 -0.3 25 25
DIABLO 0.036 0.004 -10000 0 0 6 6
apoptotic nuclear changes -0.044 0.091 0.2 5 -0.29 36 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.036 0.005 -10000 0 0 11 11
GSN -0.038 0.096 0.2 5 -0.3 33 38
MADD 0.036 0.006 -10000 0 0 15 15
TFAP2A 0.045 0.054 -10000 0 -0.44 5 5
BID -0.001 0.041 0.11 5 -0.19 18 23
MAP3K1 -0.002 0.051 -10000 0 -0.39 5 5
TRADD 0.036 0.005 -10000 0 0 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.05 0.018 -10000 0 -0.14 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.042 0.098 0.2 12 -0.3 36 48
CASP9 0.034 0.009 -10000 0 0 34 34
DNA repair 0.034 0.071 0.22 33 -10000 0 33
neuron apoptosis 0.017 0.11 -10000 0 -0.61 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.025 0.088 -10000 0 -0.32 25 25
APAF1 0.036 0.003 -10000 0 0 3 3
CASP6 0.026 0.11 -10000 0 -0.84 6 6
TRAF2 0.036 0.006 -10000 0 0 16 16
ICAD/CAD -0.047 0.084 0.21 1 -0.3 29 30
CASP7 -0.08 0.11 -10000 0 -0.23 144 144
KRT18 0.026 0.054 -10000 0 -0.45 5 5
apoptosis -0.034 0.092 -10000 0 -0.34 20 20
DFFA -0.043 0.086 0.17 1 -0.3 31 32
DFFB -0.041 0.085 -10000 0 -0.31 29 29
PARP1 -0.034 0.071 -10000 0 -0.22 33 33
actin filament polymerization -0.017 0.1 0.32 13 -0.18 75 88
TNF 0.036 0.003 -10000 0 0 4 4
CYCS 0.015 0.039 0.18 3 -0.24 3 6
SATB1 0.018 0.11 -10000 0 -0.73 6 6
SLK -0.025 0.084 -10000 0 -0.29 31 31
p15 BID/BAX 0.001 0.061 0.15 2 -0.16 44 46
CASP2 0.06 0.1 0.22 128 -0.26 7 135
JNK cascade 0.002 0.051 0.38 5 -10000 0 5
CASP3 -0.04 0.09 -10000 0 -0.3 33 33
LMNB2 0.062 0.092 0.23 10 -0.37 4 14
RIPK1 0.035 0.007 -10000 0 0 20 20
CASP4 0.03 0.014 -10000 0 0 94 94
Mammalian IAPs/DIABLO 0.061 0.032 -10000 0 -0.16 6 6
negative regulation of DNA binding 0.045 0.054 -10000 0 -0.43 5 5
stress fiber formation -0.036 0.084 -10000 0 -0.29 31 31
GZMB -0.005 0.033 0.093 47 -10000 0 47
CASP1 -0.01 0.066 -10000 0 -0.2 54 54
LMNB1 0.043 0.13 0.24 11 -0.4 14 25
APP 0.017 0.11 -10000 0 -0.62 15 15
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.011 0.002 0 13 -10000 0 13
VIM -0.034 0.095 -10000 0 -0.35 21 21
LMNA 0.066 0.09 0.23 17 -0.39 3 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.018 0.058 0.16 1 -0.23 13 14
LRDD 0.035 0.007 -10000 0 0 21 21
SREBF1 -0.042 0.087 0.18 1 -0.31 30 31
APAF-1/Caspase 9 0.014 0.1 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.002 0.083 -10000 0 -0.34 14 14
CFL2 0.016 0.11 0.18 75 -0.33 13 88
GAS2 -0.033 0.091 0.2 2 -0.3 30 32
positive regulation of apoptosis 0.062 0.1 0.23 22 -0.38 7 29
PRF1 0.023 0.018 -10000 0 0 193 193
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 0.022 0.13 -10000 0 -0.63 18 18
epithelial cell differentiation -0.006 0.14 -10000 0 -0.65 18 18
ITCH 0.029 0.031 0.11 1 -0.11 20 21
WWP1 -0.021 0.22 -10000 0 -1.1 18 18
FYN 0.03 0.014 -10000 0 0 88 88
EGFR 0.009 0.016 -10000 0 0 379 379
PRL 0.036 0.006 -10000 0 0 15 15
neuron projection morphogenesis -0.026 0.11 0.25 6 -0.52 18 24
PTPRZ1 0.022 0.018 -10000 0 0 199 199
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.056 0.12 -10000 0 -0.54 18 18
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.11 -10000 0 -0.57 18 18
ADAM17 0.03 0.031 -10000 0 -0.1 22 22
ErbB4/ErbB4 0 0.14 -10000 0 -0.69 18 18
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.009 0.12 -10000 0 -0.62 18 18
NCOR1 0.035 0.008 -10000 0 0 27 27
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.12 -10000 0 -0.58 18 18
GRIN2B -0.026 0.11 0.23 2 -0.55 18 20
ErbB4/ErbB2/betacellulin 0.026 0.12 -10000 0 -0.55 18 18
STAT1 0.034 0.01 -10000 0 0 40 40
HBEGF 0.035 0.007 -10000 0 0 21 21
PRLR 0.036 0.004 -10000 0 0 6 6
E4ICDs/ETO2 0.022 0.13 -10000 0 -0.63 18 18
axon guidance -0.029 0.16 -10000 0 -0.79 18 18
NEDD4 0.029 0.031 0.11 1 -0.11 20 21
Prolactin receptor/Prolactin receptor/Prolactin 0.052 0.011 -10000 0 -10000 0 0
CBFA2T3 0.035 0.008 -10000 0 0 27 27
ErbB4/ErbB2/HBEGF 0.025 0.11 -10000 0 -0.55 18 18
MAPK3 -0.018 0.11 0.29 3 -0.52 18 21
STAT1 (dimer) 0.02 0.13 -10000 0 -0.63 18 18
MAPK1 -0.021 0.11 0.29 3 -0.53 18 21
JAK2 0.031 0.014 -10000 0 0 83 83
ErbB4/ErbB2/neuregulin 1 beta 0.005 0.11 -10000 0 -0.55 18 18
NRG1 -0.022 0.02 0.092 4 -0.084 18 22
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.036 0.004 -10000 0 0 7 7
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.029 0.16 -10000 0 -0.79 18 18
neural crest cell migration 0.005 0.11 -10000 0 -0.54 18 18
ERBB2 -0.022 0.022 0.1 7 -0.084 18 25
WWOX/E4ICDs 0.023 0.13 -10000 0 -0.63 18 18
SHC1 0.033 0.011 -10000 0 0 52 52
ErbB4/EGFR/neuregulin 4 -0.014 0.096 -10000 0 -0.46 18 18
apoptosis -0.006 0.12 0.58 18 -10000 0 18
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.024 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB2/epiregulin 0.025 0.12 -10000 0 -0.55 18 18
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.13 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.064 0.13 -10000 0 -0.57 18 18
MDM2 -0.002 0.13 0.27 7 -0.6 18 25
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.019 0.1 -10000 0 -0.51 18 18
STAT5A -0.035 0.15 -10000 0 -0.76 18 18
ErbB4/EGFR/neuregulin 1 beta -0.003 0.087 -10000 0 -0.42 18 18
DLG4 0.036 0.006 -10000 0 0 12 12
GRB2/SHC 0.043 0.037 -10000 0 -0.15 14 14
E4ICDs/TAB2/NCoR1 0.031 0.13 -10000 0 -0.62 18 18
STAT5A (dimer) 0.002 0.16 -10000 0 -0.72 18 18
MAP3K7IP2 0.033 0.011 -10000 0 0 47 47
STAT5B (dimer) -0.016 0.16 -10000 0 -0.76 18 18
LRIG1 0.031 0.014 -10000 0 0 85 85
EREG 0.035 0.008 -10000 0 0 23 23
BTC 0.036 0.005 -10000 0 0 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.03 0.16 -10000 0 -0.8 18 18
ERBB4 0 0.14 -10000 0 -0.69 18 18
STAT5B 0.036 0.004 -10000 0 0 5 5
YAP1 -0.07 0.2 -10000 0 -0.49 92 92
GRB2 0.035 0.007 -10000 0 0 18 18
ErbB4/ErbB2/neuregulin 4 0.002 0.11 -10000 0 -0.55 18 18
glial cell differentiation -0.03 0.13 0.62 18 -10000 0 18
WWOX 0.036 0.006 -10000 0 0 15 15
cell proliferation -0.011 0.11 -10000 0 -0.57 18 18
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.023 0.058 0.16 1 -0.2 26 27
BIRC5 0.029 0.015 -10000 0 0 111 111
NFKBIA -0.008 0.042 0.21 3 -0.18 16 19
CPEB1 0.033 0.011 -10000 0 0 55 55
AKT1 -0.006 0.033 0.17 2 -0.18 7 9
NDEL1 0.035 0.007 -10000 0 0 20 20
Aurora A/BRCA1 0.023 0.043 0.14 1 -0.15 23 24
NDEL1/TACC3 0.036 0.058 0.16 1 -0.14 37 38
GADD45A 0.031 0.013 -10000 0 0 77 77
GSK3B 0.035 0.015 0.089 25 0 39 64
PAK1/Aurora A 0.029 0.05 0.16 1 -0.16 24 25
MDM2 0.034 0.01 -10000 0 0 45 45
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.012 0.026 0.093 25 -10000 0 25
TP53 0.002 0.073 -10000 0 -0.24 35 35
DLG7 -0.004 0.042 0.1 41 -0.18 13 54
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.033 0.012 -10000 0 0 57 57
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.038 0.061 0.17 1 -0.16 37 38
G2/M transition of mitotic cell cycle 0.023 0.043 -10000 0 -0.15 23 23
AURKA 0.006 0.05 0.13 24 -0.21 19 43
AURKB 0.008 0.034 -10000 0 -0.14 26 26
CDC25B -0.001 0.075 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 0.016 0.052 0.14 1 -0.13 46 47
Aurora A/TACC1/TRAP/chTOG 0.051 0.082 -10000 0 -0.16 51 51
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 0.057 0.15 1 -0.14 37 38
spindle assembly 0.049 0.081 -10000 0 -0.16 51 51
TDRD7 0.034 0.01 -10000 0 0 39 39
Aurora A/RasGAP/Survivin 0.039 0.074 -10000 0 -0.19 25 25
CENPA 0.002 0.063 -10000 0 -0.26 24 24
Aurora A/PP2A 0.029 0.05 0.16 1 -0.16 25 26
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.007 0.052 0.13 1 -0.2 20 21
negative regulation of DNA binding 0.002 0.073 -10000 0 -0.24 36 36
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.041 0.046 -10000 0 -0.14 27 27
RASA1 0.035 0.009 -10000 0 0 30 30
Ajuba/Aurora A 0.001 0.036 0.089 1 -0.14 23 24
mitotic prometaphase -0.004 0.01 0.068 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.05 0.13 24 -0.21 19 43
TACC1 0.035 0.008 -10000 0 0 23 23
TACC3 0.033 0.012 -10000 0 0 57 57
Aurora A/Antizyme1 0.023 0.044 0.14 1 -0.15 24 25
Aurora A/RasGAP 0.027 0.06 0.16 1 -0.22 23 24
OAZ1 0.035 0.009 -10000 0 0 30 30
RAN 0.036 0.005 -10000 0 0 10 10
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.036 0.015 0.088 27 0 24 51
GIT1 0.037 0.003 -10000 0 0 3 3
GIT1/beta-PIX/PAK1 0.058 0.047 -10000 0 -0.13 26 26
Importin alpha/Importin beta/TPX2 -0.012 0.026 0.093 25 -10000 0 25
PPP2R5D 0.036 0.004 -10000 0 0 5 5
Aurora A/TPX2 -0.028 0.056 0.096 4 -0.23 21 25
PAK1 0.036 0.006 -10000 0 0 16 16
CKAP5 0.034 0.01 -10000 0 0 37 37
Signaling events mediated by HDAC Class III

Figure 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
EP300 0.033 0.011 -10000 0 0 50 50
HDAC4 0.035 0.009 -10000 0 0 30 30
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.003 0.04 -10000 0 -0.13 45 45
CDKN1A -0.038 0.12 -10000 0 -0.46 37 37
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.034 0.01 -10000 0 0 43 43
FOXO3 0.001 0.033 0.25 7 -10000 0 7
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.023 -10000 0 -0.18 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.034 0.01 -10000 0 0 40 40
TAT 0.036 0.006 -10000 0 0 12 12
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.001 -10000 0 -10000 0 0
PPARGC1A 0.031 0.013 -10000 0 0 79 79
FHL2 0.028 0.016 -10000 0 0 126 126
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.038 0.046 0.16 30 -0.15 5 35
HIST2H4A 0.003 0.04 0.13 45 -10000 0 45
SIRT1/FOXO3a 0.027 0.041 0.15 40 -10000 0 40
SIRT1 0.033 0.047 0.18 40 -10000 0 40
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.056 0.17 26 -0.13 16 42
SIRT1/Histone H1b 0.028 0.045 0.18 2 -0.16 5 7
apoptosis -0.048 0.052 0.12 10 -0.17 28 38
SIRT1/PGC1A 0.03 0.044 0.15 28 -0.12 13 41
p53/SIRT1 0.042 0.091 0.33 36 -0.15 20 56
SIRT1/FOXO4 0.025 0.043 0.15 30 -0.14 11 41
FOXO1/FHL2/SIRT1 0.022 0.042 0.14 22 -0.1 21 43
HIST1H1E 0.013 0.023 -10000 0 -0.18 6 6
SIRT1/p300 0.036 0.05 0.16 32 -0.14 11 43
muscle cell differentiation 0.004 0.037 0.12 4 -0.12 33 37
TP53 0.04 0.046 0.18 42 -10000 0 42
KU70/SIRT1/BAX 0.048 0.053 0.17 28 -0.12 10 38
CREBBP 0.036 0.005 -10000 0 0 9 9
MEF2D 0.036 0.006 -10000 0 0 12 12
HIV-1 Tat/SIRT1 0.039 0.045 0.16 31 -0.15 4 35
ACSS2 0.003 0.04 0.13 45 -10000 0 45
SIRT1/PCAF/MYOD -0.004 0.037 0.12 33 -0.12 4 37
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.027 0.086 36 -10000 0 36
SNTA1 0.032 0.013 -10000 0 0 71 71
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.017 0.037 0.083 52 -0.13 12 64
MAPK12 -0.01 0.031 0.2 4 -0.17 9 13
CCND1 -0.019 0.1 -10000 0 -0.37 40 40
p38 gamma/SNTA1 -0.01 0.038 0.2 4 -0.16 10 14
MAP2K3 0.036 0.005 -10000 0 0 10 10
PKN1 0.033 0.011 -10000 0 0 48 48
G2/M transition checkpoint -0.01 0.03 0.2 4 -0.17 9 13
MAP2K6 -0.005 0.036 0.22 6 -0.18 10 16
MAPT -0.025 0.077 0.16 5 -0.2 74 79
MAPK13 -0.014 0.03 0.093 36 -10000 0 36
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.032 -10000 0 -0.2 11 11
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.036 0.005 -10000 0 0 11 11
Caspase 8 (4 units) -0.011 0.097 -10000 0 -0.24 24 24
NEF 0.002 0 -10000 0 -10000 0 0
NFKBIA 0.038 0.019 0.078 64 -10000 0 64
BIRC3 -0.025 0.029 0.18 2 -0.2 2 4
CYCS -0.004 0.078 0.18 46 -0.24 9 55
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 -0.4 6 6
protein ubiquitination 0.012 0.065 0.21 3 -0.25 7 10
CRADD 0.036 0.005 -10000 0 0 11 11
DAXX 0.036 0.004 -10000 0 0 6 6
FAS 0.019 0.018 -10000 0 0 241 241
BID -0.003 0.057 -10000 0 -0.28 9 9
NF-kappa-B/RelA/I kappa B alpha 0.076 0.055 -10000 0 -0.14 17 17
TRADD 0.036 0.005 -10000 0 0 10 10
MAP3K5 0.03 0.014 -10000 0 0 90 90
CFLAR 0.036 0.005 -10000 0 0 8 8
FADD 0.036 0.006 -10000 0 0 12 12
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.076 0.055 -10000 0 -0.14 17 17
MAPK8 -0.006 0.094 -10000 0 -0.37 7 7
APAF1 0.037 0.003 -10000 0 0 3 3
TRAF1 0.035 0.008 -10000 0 0 24 24
TRAF2 0.036 0.006 -10000 0 0 16 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.061 -10000 0 -0.28 9 9
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.029 0.077 -10000 0 -0.28 11 11
CHUK 0.012 0.067 0.21 3 -0.27 7 10
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.039 0.084 -10000 0 -0.12 61 61
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 -0.13 41 41
CASP6 0.005 0.11 -10000 0 -0.56 7 7
CASP7 -0.034 0.14 0.28 10 -0.33 26 36
RELA 0.043 0.015 0.079 74 -10000 0 74
CASP2 0.025 0.017 -10000 0 0 165 165
CASP3 -0.001 0.11 0.27 9 -0.35 12 21
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
TNFR1A/BAG4 0.035 0.055 -10000 0 -0.14 42 42
CASP8 0.036 0.006 -10000 0 0 13 13
CASP9 0.034 0.009 -10000 0 0 34 34
MAP3K14 0.024 0.077 0.19 2 -0.29 8 10
APAF-1/Caspase 9 -0.011 0.084 0.17 9 -0.27 6 15
BCL2 -0.016 0.091 0.27 1 -0.34 6 7
Insulin Pathway

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
CBL/APS/CAP 0.031 0.049 -10000 0 -0.11 21 21
TC10/GTP 0.026 0.048 -10000 0 -0.12 21 21
Insulin Receptor/Insulin/IRS1/Shp2 0.076 0.059 -10000 0 -0.13 27 27
HRAS 0.034 0.009 -10000 0 0 36 36
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.032 0.013 -10000 0 0 70 70
FOXO3 -0.009 0.016 0.019 8 -0.041 67 75
AKT1 -0.025 0.088 0.22 17 -0.21 25 42
INSR 0.033 0.022 -10000 0 -0.039 34 34
Insulin Receptor/Insulin 0.055 0.063 0.22 3 -0.14 34 37
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.018 -10000 0 0 222 222
SORBS1 0.025 0.017 -10000 0 0 158 158
CRK 0.035 0.008 -10000 0 0 23 23
PTPN1 -0.023 0.048 0.15 16 -0.26 8 24
CAV1 -0.011 0.037 0.17 6 -0.19 8 14
CBL/APS/CAP/Crk-II/C3G 0.049 0.054 -10000 0 -0.11 14 14
Insulin Receptor/Insulin/IRS1/NCK2 0.074 0.064 -10000 0 -0.14 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.079 -10000 0 -0.13 76 76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.025 0.074 -10000 0 -0.32 12 12
RPS6KB1 -0.031 0.081 0.2 19 -0.21 25 44
PARD6A 0.035 0.007 -10000 0 0 19 19
CBL 0.036 0.005 -10000 0 0 8 8
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.021 0.019 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.033 0.086 0.17 22 -0.22 27 49
HRAS/GTP -0.034 0.035 -10000 0 -0.13 41 41
Insulin Receptor 0.033 0.022 -10000 0 -0.039 34 34
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.084 0.069 -10000 0 -0.13 32 32
PRKCI 0.025 0.088 -10000 0 -0.41 17 17
Insulin Receptor/Insulin/GRB14/PDK1 0.015 0.068 -10000 0 -0.14 71 71
SHC1 0.033 0.011 -10000 0 0 52 52
negative regulation of MAPKKK cascade 0.029 0.056 -10000 0 -10000 0 0
PI3K 0.047 0.087 -10000 0 -0.14 76 76
NCK2 0.036 0.007 -10000 0 0 17 17
RHOQ 0.036 0.006 -10000 0 0 16 16
mol:H2O2 -0.004 0.006 0.031 1 -0.034 8 9
HRAS/GDP 0.021 0.028 -10000 0 -0.13 16 16
AKT2 -0.026 0.079 0.21 16 -0.2 14 30
PRKCZ 0.003 0.077 -10000 0 -0.39 17 17
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.014 0.05 0.16 20 -0.15 4 24
F2RL2 0.036 0.004 -10000 0 0 6 6
TRIP10 0.034 0.009 -10000 0 0 35 35
Insulin Receptor/Insulin/Shc 0.058 0.038 -10000 0 -0.13 8 8
TC10/GTP/CIP4/Exocyst 0.042 0.03 -10000 0 -0.12 14 14
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.048 -10000 0 -0.13 14 14
RAPGEF1 0.035 0.007 -10000 0 0 18 18
RASA1 0.035 0.009 -10000 0 0 30 30
NCK1 0.035 0.008 -10000 0 0 27 27
CBL/APS/CAP/Crk-II 0.044 0.041 -10000 0 -0.11 14 14
TC10/GDP 0.023 0.025 -10000 0 -0.13 12 12
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.066 -10000 0 -0.14 30 30
INPP5D -0.018 0.03 0.064 24 -0.11 21 45
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.006 0.005 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 11 11
IRS1 0.033 0.011 -10000 0 0 51 51
p62DOK/RasGAP 0.03 0.057 -10000 0 -10000 0 0
INS 0.035 0.024 0.082 30 -0.039 33 63
mol:PI-3-4-P2 -0.018 0.029 0.064 24 -0.11 21 45
GRB2 0.035 0.007 -10000 0 0 18 18
EIF4EBP1 -0.034 0.079 0.2 14 -0.22 24 38
PTPRA 0.032 0.017 -10000 0 -0.052 7 7
PIK3CA 0.031 0.014 -10000 0 0 82 82
TC10/GTP/CIP4 0.042 0.03 -10000 0 -0.12 14 14
PDPK1 0.036 0.005 -10000 0 0 8 8
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.015 0.054 0.14 1 -0.16 32 33
Insulin Receptor/Insulin/IRS1 0.056 0.047 -10000 0 -0.12 21 21
Insulin Receptor/Insulin/IRS3 0.048 0.033 -10000 0 -0.07 7 7
Par3/Par6 0.074 0.041 -10000 0 -0.11 16 16
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.032 0.012 -10000 0 0 59 59
SMAD2 -0.018 0.066 0.16 3 -0.22 31 34
SMAD3 0.004 0.06 -10000 0 -0.34 8 8
SMAD3/SMAD4 -0.009 0.17 -10000 0 -0.5 44 44
SMAD4/Ubc9/PIASy 0.054 0.054 -10000 0 -0.13 35 35
SMAD2/SMAD2/SMAD4 0.025 0.1 -10000 0 -0.25 29 29
PPM1A 0.035 0.009 -10000 0 0 31 31
CALM1 0.033 0.012 -10000 0 0 57 57
SMAD2/SMAD4 -0.001 0.069 -10000 0 -0.21 31 31
MAP3K1 0.035 0.007 -10000 0 0 20 20
TRAP-1/SMAD4 0.036 0.054 -10000 0 -0.14 40 40
MAPK3 0.036 0.003 -10000 0 0 4 4
MAPK1 0.034 0.01 -10000 0 0 44 44
NUP214 0.035 0.007 -10000 0 0 18 18
CTDSP1 0.036 0.006 -10000 0 0 15 15
CTDSP2 0.033 0.012 -10000 0 0 58 58
CTDSPL 0.036 0.006 -10000 0 0 13 13
KPNB1 0.035 0.008 -10000 0 0 23 23
TGFBRAP1 0.036 0.005 -10000 0 0 10 10
UBE2I 0.036 0.004 -10000 0 0 6 6
NUP153 0.035 0.009 -10000 0 0 30 30
KPNA2 0.034 0.01 -10000 0 0 40 40
PIAS4 0.035 0.008 -10000 0 0 24 24
p75(NTR)-mediated signaling

Figure 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
Sortilin/TRAF6 0.05 0.024 -10000 0 -0.14 6 6
Necdin/E2F1 -0.017 0.085 -10000 0 -0.14 148 148
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.073 0.048 -10000 0 -0.12 23 23
NGF (dimer)/p75(NTR)/BEX1 0.01 0.064 -10000 0 -0.12 95 95
NT-4/5 (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
IKBKB 0.036 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 66 66
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.009 -10000 0 -10000 0 0
FURIN 0.036 0.005 -10000 0 0 9 9
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.034 -10000 0 -0.13 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.022 0.069 -10000 0 -0.16 50 50
proBDNF (dimer) 0.032 0.012 -10000 0 0 66 66
NTRK1 0.036 0.007 -10000 0 0 17 17
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.005 0.11 0.28 1 -0.37 28 29
IRAK1 0.035 0.007 -10000 0 0 19 19
SHC1 -0.003 0.036 0.092 61 -10000 0 61
ARHGDIA 0.035 0.007 -10000 0 0 18 18
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
Gamma Secretase 0.08 0.072 -10000 0 -0.16 28 28
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.039 0.059 -10000 0 -0.11 54 54
MAGEH1 0.032 0.013 -10000 0 0 70 70
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.004 0.076 -10000 0 -0.11 147 147
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.16 6 6
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.035 0.008 -10000 0 0 26 26
APP 0.035 0.007 -10000 0 0 20 20
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.009 -10000 0 0 36 36
RhoA/GDP/RHOGDI 0.05 0.03 0.18 1 -0.1 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.003 0.054 0.22 7 -10000 0 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.017 0.056 -10000 0 -0.18 32 32
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.019 -10000 0 -0.12 1 1
NCSTN 0.035 0.009 -10000 0 0 29 29
mol:GTP 0.031 0.041 -10000 0 -0.12 29 29
PSENEN 0.035 0.009 -10000 0 0 31 31
mol:ceramide -0.007 0.044 0.19 7 -10000 0 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.054 -10000 0 -0.27 10 10
p75(NTR)/beta APP 0.043 0.032 -10000 0 -0.14 9 9
BEX1 0.028 0.015 -10000 0 0 115 115
mol:GDP -0.008 0.003 -10000 0 -10000 0 0
NGF (dimer) 0.046 0.034 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.04 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 63 63
RAC1/GTP 0.024 0.024 -10000 0 -0.097 5 5
MYD88 0.034 0.009 -10000 0 0 36 36
CHUK 0.025 0.017 -10000 0 0 165 165
NGF (dimer)/p75(NTR)/PKA 0.032 0.041 -10000 0 -0.12 29 29
RHOB 0.031 0.013 -10000 0 0 74 74
RHOA 0.035 0.007 -10000 0 0 21 21
MAGE-G1/E2F1 0.025 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.035 0.008 -10000 0 0 25 25
TP53 -0.015 0.063 0.22 7 -0.21 6 13
PRDM4 -0.007 0.045 0.19 7 -10000 0 7
BDNF (dimer) 0.08 0.035 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
SORT1 0.036 0.006 -10000 0 0 14 14
activation of caspase activity 0.066 0.046 -10000 0 -0.12 23 23
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.031 -10000 0 -0.11 5 5
RHOC 0.035 0.007 -10000 0 0 19 19
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.013 0.1 0.2 31 -0.31 16 47
DIABLO 0.036 0.004 -10000 0 0 6 6
SMPD2 -0.007 0.044 0.19 7 -10000 0 7
APH1B 0.036 0.006 -10000 0 0 14 14
APH1A 0.036 0.006 -10000 0 0 12 12
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.023 -10000 0 -0.12 4 4
PSEN1 0.033 0.011 -10000 0 0 47 47
APAF-1/Pro-Caspase 9 0.05 0.018 -10000 0 -0.14 2 2
NT3 (dimer)/p75(NTR) 0.044 0.021 -10000 0 -10000 0 0
MAPK8 0 0.076 0.2 17 -0.27 8 25
MAPK9 0.025 0.086 0.2 36 -0.26 8 44
APAF1 0.037 0.003 -10000 0 0 3 3
NTF3 0.035 0.008 -10000 0 0 25 25
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.018 0.018 -10000 0 0 259 259
RAC1/GDP 0.017 0.02 -10000 0 -0.13 5 5
RhoA-B-C/GDP 0.049 0.074 -10000 0 -0.15 54 54
p75 CTF/Sortilin/TRAF6/NRIF 0.076 0.056 -10000 0 -0.12 32 32
RhoA-B-C/GTP 0.031 0.041 -10000 0 -0.12 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.088 0.059 -10000 0 -0.12 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.086 0.029 -10000 0 -0.12 2 2
PRKACB 0.033 0.011 -10000 0 0 48 48
proBDNF (dimer)/p75 ECD 0.046 0.019 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.031 0.014 -10000 0 0 82 82
BIRC2 0.036 0.006 -10000 0 0 12 12
neuron projection morphogenesis -0.016 0.071 0.14 26 -0.16 29 55
BAD 0.008 0.089 0.2 20 -0.28 14 34
RIPK2 0.036 0.006 -10000 0 0 14 14
NGFR 0.032 0.013 -10000 0 0 71 71
CYCS -0.012 0.041 0.2 4 -0.19 3 7
ADAM17 0.036 0.006 -10000 0 0 13 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.057 0.03 -10000 0 -0.11 3 3
BCL2L11 0.008 0.089 0.2 20 -0.28 13 33
BDNF (dimer)/p75(NTR) 0.041 0.023 -10000 0 -10000 0 0
PI3K 0.028 0.068 -10000 0 -0.12 70 70
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.021 -10000 0 -0.1 4 4
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
PRKCI 0.035 0.008 -10000 0 0 27 27
NGF (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.05 0.048 -10000 0 -0.12 27 27
TRAF6 0.036 0.005 -10000 0 0 10 10
RAC1 0.025 0.017 -10000 0 0 163 163
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.009 -10000 0 0 35 35
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.032 0.035 0.14 16 -0.15 2 18
SQSTM1 0.034 0.009 -10000 0 0 35 35
NGFRAP1 0.036 0.006 -10000 0 0 13 13
CASP3 0.008 0.088 0.19 21 -0.27 15 36
E2F1 0.034 0.009 -10000 0 0 36 36
CASP9 0.034 0.009 -10000 0 0 34 34
IKK complex 0.038 0.068 -10000 0 -0.24 10 10
NGF (dimer)/TRKA 0.026 0.005 -10000 0 -10000 0 0
MMP7 0.027 0.016 -10000 0 0 138 138
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.071 0.051 -10000 0 -0.11 31 31
MMP3 0.035 0.007 -10000 0 0 21 21
APAF-1/Caspase 9 -0.023 0.04 -10000 0 -0.21 6 6
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.024 -10000 0 -0.13 10 10
alphaV beta3 Integrin 0.06 0.049 -10000 0 -0.13 27 27
PTK2 0.011 0.09 0.24 10 -0.29 20 30
IGF1R 0.033 0.011 -10000 0 0 53 53
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.036 0.006 -10000 0 0 16 16
SRC 0.034 0.009 -10000 0 0 34 34
CDKN1B 0 0.093 -10000 0 -0.32 38 38
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.011 0.072 -10000 0 -0.3 24 24
ROCK1 0.036 0.006 -10000 0 0 15 15
AKT1 -0.003 0.069 0.2 1 -0.31 21 22
PTK2B -0.003 0.073 0.18 50 -0.19 4 54
alphaV/beta3 Integrin/JAM-A 0.071 0.047 0.18 7 -0.12 20 27
CBL 0.036 0.005 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.062 0.044 -10000 0 -0.13 24 24
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.069 0.068 -10000 0 -0.14 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.057 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Syndecan-1 0.055 0.043 -10000 0 -0.13 16 16
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.05 0.084 -10000 0 -0.15 67 67
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.014 -10000 0 0 82 82
alphaV/beta3 Integrin/Osteopontin 0.047 0.071 -10000 0 -0.14 59 59
RPS6KB1 -0.046 0.064 0.24 3 -0.21 19 22
TLN1 0.029 0.015 -10000 0 0 101 101
MAPK3 0.001 0.086 -10000 0 -0.35 23 23
GPR124 0.035 0.008 -10000 0 0 24 24
MAPK1 -0.002 0.088 -10000 0 -0.36 23 23
PXN 0.036 0.004 -10000 0 0 7 7
PIK3R1 0.032 0.012 -10000 0 0 63 63
alphaV/beta3 Integrin/Tumstatin 0.064 0.044 -10000 0 -0.13 24 24
cell adhesion 0.049 0.053 -10000 0 -0.16 26 26
ANGPTL3 0.036 0.005 -10000 0 0 9 9
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.029 -10000 0 -0.12 9 9
IGF-1R heterotetramer 0.033 0.011 -10000 0 0 53 53
Rac1/GDP 0.017 0.02 -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 0.007 -10000 0 0 21 21
RAC1 0.025 0.017 -10000 0 0 163 163
regulation of cell-matrix adhesion 0.059 0.045 -10000 0 -0.13 24 24
apoptosis 0.034 0.009 -10000 0 0 31 31
CD47 0.035 0.008 -10000 0 0 24 24
alphaV/beta3 Integrin/CD47 0.06 0.048 -10000 0 -0.13 26 26
VCL 0.026 0.017 -10000 0 0 154 154
alphaV/beta3 Integrin/Del1 0.063 0.044 -10000 0 -0.13 24 24
CSF1 0.036 0.004 -10000 0 0 7 7
PIK3C2A 0.01 0.018 -10000 0 -0.097 2 2
PI4 Kinase/Pyk2 0.026 0.042 -10000 0 -0.12 29 29
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.051 -10000 0 -0.13 28 28
FAK1/Vinculin 0.014 0.077 0.24 7 -0.27 15 22
alphaV beta3/Integrin/ppsTEM5 0.06 0.045 -10000 0 -0.13 24 24
RHOA 0.035 0.007 -10000 0 0 21 21
VTN 0.036 0.004 -10000 0 0 5 5
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.035 0.008 -10000 0 0 25 25
F11R -0.012 0.033 0.093 44 -10000 0 44
alphaV/beta3 Integrin/Lactadherin 0.061 0.046 -10000 0 -0.13 24 24
alphaV/beta3 Integrin/TGFBR2 0.059 0.047 -10000 0 -0.13 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.06 0.04 -10000 0 -0.11 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.047 0.05 -10000 0 -0.12 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.035 0.009 -10000 0 0 30 30
alphaV/beta3 Integrin/Pyk2 0.064 0.062 0.19 45 -0.12 28 73
SDC1 0.031 0.014 -10000 0 0 82 82
VAV3 -0.026 0.03 0.18 2 -0.19 5 7
PTPN11 0.036 0.005 -10000 0 0 11 11
IRS1 0.033 0.011 -10000 0 0 51 51
FAK1/Paxillin 0.028 0.084 0.23 10 -0.25 20 30
cell migration -0.003 0.071 0.22 7 -0.28 10 17
ITGAV 0.035 0.009 -10000 0 0 31 31
PI3K 0.055 0.087 -10000 0 -0.14 67 67
SPP1 0.033 0.011 -10000 0 0 54 54
KDR 0.029 0.015 -10000 0 0 103 103
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.009 -10000 0 0 31 31
COL4A3 0.037 0 -10000 0 -10000 0 0
angiogenesis -0.001 0.095 -10000 0 -0.37 26 26
Rac1/GTP -0.026 0.035 0.18 1 -0.18 6 7
EDIL3 0.036 0.003 -10000 0 0 4 4
cell proliferation 0.058 0.047 -10000 0 -0.12 27 27
Regulation of Telomerase

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
Telomerase catalytic core complex 0.026 0.16 -10000 0 -0.52 14 14
RAD9A 0.036 0.005 -10000 0 0 9 9
AP1 0.009 0.083 -10000 0 -0.18 72 72
IFNAR2 0.033 0.021 -10000 0 -0.035 37 37
AKT1 0.013 0.056 -10000 0 -0.26 19 19
ER alpha/Oestrogen 0.024 0.014 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.006 0.085 -10000 0 -0.27 33 33
EGF 0.033 0.016 -10000 0 -0.015 46 46
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.053 -10000 0 -0.17 22 22
TERT/c-Abl 0.033 0.16 -10000 0 -0.51 19 19
SAP18 0.034 0.01 -10000 0 0 43 43
MRN complex 0.069 0.024 -10000 0 -0.13 4 4
WT1 0.033 0.021 -10000 0 -0.035 37 37
WRN 0.035 0.009 -10000 0 0 29 29
SP1 0.034 0.023 -10000 0 -0.043 37 37
SP3 0.034 0.016 -10000 0 -0.031 26 26
TERF2IP 0.034 0.01 -10000 0 0 39 39
Telomerase/Nucleolin 0.039 0.16 -10000 0 -0.49 19 19
Mad/Max 0.047 0.028 -10000 0 -10000 0 0
TERT 0.023 0.16 -10000 0 -0.56 11 11
CCND1 -0.016 0.29 -10000 0 -0.95 40 40
MAX 0.032 0.018 -10000 0 -0.03 30 30
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 57 57
TERF2 0.028 0.011 0.084 6 -10000 0 6
PTGES3 0.036 0.006 -10000 0 0 15 15
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.048 0.1 -10000 0 -0.41 14 14
CDKN1B -0.028 0.084 0.1 35 -0.34 27 62
RAD1 0.035 0.007 -10000 0 0 18 18
XRCC5 0.036 0.005 -10000 0 0 9 9
XRCC6 0.034 0.01 -10000 0 0 40 40
SAP30 0.036 0.007 -10000 0 0 18 18
TRF2/PARP2 0.032 0.058 -10000 0 -0.14 47 47
UBE3A 0.035 0.012 -10000 0 -0.023 19 19
JUN 0.032 0.016 -10000 0 -0.03 18 18
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.025 0.021 -10000 0 -0.11 5 5
FOS 0.024 0.02 -10000 0 -0.03 16 16
IFN-gamma/IRF1 0.033 0.07 -10000 0 -0.19 39 39
PARP2 0.035 0.008 -10000 0 0 23 23
BLM 0.029 0.015 -10000 0 0 106 106
Telomerase 0.016 0.055 -10000 0 -0.32 9 9
IRF1 0.025 0.04 0.093 1 -0.1 35 36
ESR1 0.035 0.009 -10000 0 0 30 30
KU/TER 0.047 0.029 -10000 0 -0.14 9 9
ATM/TRF2 0.044 0.028 -10000 0 -0.1 9 9
ubiquitin-dependent protein catabolic process 0.003 0.083 -10000 0 -0.28 25 25
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.002 0.085 -10000 0 -0.29 25 25
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC2 0.03 0.024 -10000 0 -0.042 34 34
ATM 0.022 0.038 0.13 38 -0.18 5 43
SMAD3 -0.014 0.028 0.091 28 -10000 0 28
ABL1 0.032 0.013 -10000 0 0 69 69
MXD1 0.034 0.016 -10000 0 -0.03 30 30
MRE11A 0.036 0.005 -10000 0 0 8 8
HUS1 0.025 0.017 -10000 0 0 165 165
RPS6KB1 0.036 0.005 -10000 0 0 9 9
TERT/NF kappa B1/14-3-3 0.041 0.17 -10000 0 -0.53 17 17
NR2F2 0.022 0.023 -10000 0 -0.03 52 52
MAPK3 -0.017 0.017 0.094 2 -10000 0 2
MAPK1 -0.014 0.022 0.097 10 -10000 0 10
TGFB1/TGF beta receptor Type II 0.032 0.012 -10000 0 0 66 66
NFKB1 0.035 0.007 -10000 0 0 18 18
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.022 0.038 0.13 38 -0.18 5 43
NBN 0.036 0.006 -10000 0 0 13 13
EGFR 0.009 0.016 -10000 0 0 380 380
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.057 -10000 0 -0.14 64 64
MYC 0.028 0.019 -10000 0 -0.029 20 20
IL2 0.034 0.023 -10000 0 -0.043 37 37
KU 0.047 0.029 -10000 0 -0.14 9 9
RAD50 0.036 0.006 -10000 0 0 12 12
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.032 0.012 -10000 0 0 66 66
TRF2/BLM 0.01 0.08 -10000 0 -0.15 94 94
FRAP1 0.036 0.006 -10000 0 0 16 16
KU/TERT 0.049 0.16 -10000 0 -0.51 15 15
SP1/HDAC2 0.042 0.047 -10000 0 -0.14 14 14
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.022 0.14 -10000 0 -0.46 19 19
Smad3/Myc 0.01 0.053 -10000 0 -0.13 51 51
911 complex 0.047 0.039 -10000 0 -0.13 4 4
IFNG 0.027 0.04 0.093 1 -0.11 35 36
Telomerase/PinX1 0.022 0.14 -10000 0 -0.46 19 19
Telomerase/AKT1/mTOR/p70S6K 0.022 0.094 0.22 1 -0.43 11 12
SIN3B 0.035 0.009 -10000 0 0 33 33
YWHAE 0.035 0.008 -10000 0 0 27 27
Telomerase/EST1B 0.022 0.14 -10000 0 -0.46 19 19
response to DNA damage stimulus 0.009 0.018 -10000 0 -0.084 11 11
MRN complex/TRF2/Rap1 0.076 0.073 -10000 0 -0.14 41 41
TRF2/WRN 0.034 0.046 -10000 0 -0.12 40 40
Telomerase/hnRNP C1/C2 0.022 0.14 -10000 0 -0.46 19 19
E2F1 0.032 0.021 -10000 0 -0.035 35 35
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.036 0.007 -10000 0 0 17 17
DKC1 0.035 0.007 -10000 0 0 18 18
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.033 0.012 -10000 0 0 57 57
mol:Halofuginone -0.002 0.03 -10000 0 -0.17 15 15
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.026 0.15 -10000 0 -0.42 57 57
PRL-3/alpha Tubulin 0.018 0.033 -10000 0 -0.13 21 21
mol:Ca2+ -0.017 0.044 0.26 11 -10000 0 11
AGT 0.029 0.015 -10000 0 0 109 109
CCNA2 -0.025 0.12 -10000 0 -0.6 14 14
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.06 -10000 0 -0.33 15 15
CDK2/Cyclin E1 -0.003 0.15 -10000 0 -0.37 59 59
MAPK3 -0.013 0.03 0.093 37 -10000 0 37
PRL-2 /Rab GGTase beta 0.047 0.035 -10000 0 -0.16 12 12
MAPK1 -0.01 0.032 0.093 42 -10000 0 42
PTP4A1 -0.023 0.1 -10000 0 -0.62 14 14
PTP4A3 0.031 0.013 -10000 0 0 75 75
PTP4A2 0.036 0.006 -10000 0 0 16 16
ITGB1 -0.009 0.026 0.093 27 -10000 0 27
SRC 0.034 0.009 -10000 0 0 34 34
RAC1 -0.004 0.091 -10000 0 -0.39 22 22
Rab GGTase beta/Rab GGTase alpha 0.045 0.032 -10000 0 -0.14 11 11
PRL-1/ATF-5 -0.029 0.11 0.3 2 -0.57 15 17
RABGGTA 0.034 0.01 -10000 0 0 41 41
BCAR1 -0.009 0.055 0.25 21 -10000 0 21
RHOC -0.008 0.12 -10000 0 -0.39 37 37
RHOA -0.009 0.13 -10000 0 -0.44 35 35
cell motility -0.003 0.13 0.26 1 -0.4 33 34
PRL-1/alpha Tubulin -0.036 0.1 -10000 0 -0.56 15 15
PRL-3/alpha1 Integrin 0.018 0.033 -10000 0 -0.13 21 21
ROCK1 -0.002 0.13 0.26 1 -0.4 33 34
RABGGTB 0.035 0.008 -10000 0 0 25 25
CDK2 0.034 0.01 -10000 0 0 40 40
mitosis -0.023 0.1 -10000 0 -0.61 14 14
ATF5 0.034 0.009 -10000 0 0 34 34
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.001 0.013 -10000 0 -0.092 9 9
STMN1 -0.015 0.028 0.092 30 -10000 0 30
Aurora B/RasGAP/Survivin 0.034 0.076 -10000 0 -0.14 73 73
Chromosomal passenger complex/Cul3 protein complex -0.033 0.078 -10000 0 -0.2 66 66
BIRC5 0.029 0.015 -10000 0 0 111 111
DES 0.025 0.093 -10000 0 -0.64 9 9
Aurora C/Aurora B/INCENP 0.063 0.021 -10000 0 -10000 0 0
Aurora B/TACC1 0.042 0.026 -10000 0 -0.12 9 9
Aurora B/PP2A 0.05 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.001 0.05 -10000 0 -0.19 28 28
mitotic metaphase/anaphase transition -0.001 0.003 0.009 22 -0.009 1 23
NDC80 -0.01 0.006 0.012 16 -10000 0 16
Cul3 protein complex 0.027 0.033 -10000 0 -0.14 8 8
KIF2C -0.019 0.12 -10000 0 -0.44 35 35
PEBP1 -0.001 0.003 0.009 17 -0.009 11 28
KIF20A 0.029 0.015 -10000 0 0 110 110
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.04 0.045 -10000 0 -0.15 25 25
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.001 0.08 -10000 0 -0.48 9 9
PSMA3 0.034 0.01 -10000 0 0 37 37
G2/M transition of mitotic cell cycle -0.001 0.002 0.008 13 -0.006 1 14
H3F3B 0.009 0.032 -10000 0 -0.2 11 11
AURKB 0.032 0.015 -10000 0 -0.009 55 55
AURKC 0.036 0.006 -10000 0 0 15 15
CDCA8 0.032 0.013 -10000 0 -0.003 59 59
cytokinesis -0.026 0.15 0.19 6 -0.41 53 59
Aurora B/Septin1 -0.014 0.14 0.19 4 -0.38 54 58
AURKA -0.001 0.002 0.008 13 -0.006 1 14
INCENP 0.034 0.014 0.058 1 -0.024 26 27
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.036 0.006 0.058 1 0 11 12
hSgo1/Aurora B/Survivin 0.021 0.051 -10000 0 -0.11 58 58
EVI5 0.036 0.007 -10000 0 0 16 16
RhoA/GTP 0.01 0.13 -10000 0 -0.32 54 54
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.005 0.079 0.13 1 -0.28 33 34
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.045 0.03 -10000 0 -0.15 8 8
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.048 0.026 -10000 0 -0.15 6 6
RHOA 0.035 0.007 -10000 0 0 21 21
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 0.005 0.068 -10000 0 -0.31 17 17
RASA1 0.035 0.009 -10000 0 0 30 30
KLHL9 0.021 0.018 -10000 0 0 213 213
mitotic prometaphase -0.001 0.003 0.009 17 -0.009 11 28
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.03 -10000 0 -0.15 8 8
PPP1CC 0.036 0.005 -10000 0 0 9 9
Centraspindlin 0.001 0.13 -10000 0 -0.34 53 53
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
NSUN2 0.002 0.042 -10000 0 -0.29 9 9
MYLK -0.015 0.07 -10000 0 -0.2 63 63
KIF23 0.029 0.018 -10000 0 -0.006 101 101
VIM -0.013 0.02 0.089 12 -10000 0 12
RACGAP1 0.03 0.016 -10000 0 -0.003 88 88
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.003 0.065 -10000 0 -0.28 23 23
Chromosomal passenger complex -0.016 0.1 0.14 5 -0.25 61 66
Chromosomal passenger complex/EVI5 0.061 0.086 -10000 0 -0.15 57 57
TACC1 0.035 0.008 -10000 0 0 23 23
PPP2R5D 0.036 0.004 -10000 0 0 5 5
CUL3 0.037 0.002 -10000 0 0 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.041 0.01 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.009 0.061 -10000 0 -0.12 88 88
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.036 0.004 -10000 0 0 7 7
RGS9-1/Gbeta5/R9AP 0.046 0.015 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.047 0.012 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.036 0.005 -10000 0 0 8 8
Cone Metarhodopsin II/X-Arrestin 0.027 0 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.056 0.18 2 -0.11 71 73
Cone PDE6 0.053 0.048 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.016 0.065 -10000 0 -0.11 87 87
GNAT2/GDP 0.059 0.021 -10000 0 -0.1 1 1
GNB5 0.035 0.007 -10000 0 0 22 22
mol:GMP (4 units) -0.011 0.033 0.18 13 -10000 0 13
Cone Transducin 0.045 0.011 -10000 0 -10000 0 0
SLC24A2 0.029 0.015 -10000 0 0 101 101
GNB3/GNGT2 0.026 0.005 -10000 0 -10000 0 0
GNB3 0.035 0.007 -10000 0 0 20 20
GNAT2/GTP 0.027 0.003 -10000 0 -10000 0 0
CNGA3 0.022 0.018 -10000 0 0 199 199
ARR3 0.037 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.01 0.062 -10000 0 -0.12 88 88
mol:Pi 0.045 0.015 -10000 0 -0.12 1 1
Cone CNG Channel 0.025 0.076 -10000 0 -0.11 84 84
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.029 0.015 -10000 0 0 101 101
RGS9 0.035 0.007 -10000 0 0 18 18
PDE6C 0.025 0.017 -10000 0 0 157 157
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
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 0.033 0.011 -10000 0 0 48 48
NFATC1 0.004 0.1 -10000 0 -0.39 24 24
NFATC2 -0.036 0.084 -10000 0 -0.16 121 121
NFATC3 0.01 0.02 -10000 0 -0.1 14 14
YWHAE 0.035 0.008 -10000 0 0 27 27
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.076 0.16 4 -0.23 24 28
Exportin 1/Ran/NUP214 0.068 0.03 -10000 0 -0.16 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.019 0.091 -10000 0 -0.22 21 21
BCL2/BAX 0.047 0.024 -10000 0 -0.14 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.027 -10000 0 -0.13 14 14
CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
BAX 0.034 0.01 -10000 0 0 43 43
MAPK14 0.036 0.004 -10000 0 0 5 5
BAD 0.036 0.006 -10000 0 0 13 13
CABIN1/MEF2D 0.006 0.082 -10000 0 -0.22 23 23
Calcineurin A alpha-beta B1/BCL2 0.035 0.007 -10000 0 0 20 20
FKBP8 0.035 0.009 -10000 0 0 31 31
activation-induced cell death of T cells -0.006 0.081 0.22 23 -10000 0 23
KPNB1 0.035 0.008 -10000 0 0 23 23
KPNA2 0.034 0.01 -10000 0 0 40 40
XPO1 0.036 0.004 -10000 0 0 5 5
SFN 0.031 0.013 -10000 0 0 80 80
MAP3K8 0.022 0.018 -10000 0 0 200 200
NFAT4/CK1 alpha 0.024 0.044 0.17 1 -0.16 17 18
MEF2D/NFAT1/Cbp/p300 0.009 0.11 0.23 1 -0.21 35 36
CABIN1 -0.008 0.076 0.16 4 -0.23 24 28
CALM1 0.033 0.012 -10000 0 0 57 57
RAN 0.036 0.005 -10000 0 0 10 10
MAP3K1 0.035 0.007 -10000 0 0 20 20
CAMK4 0.036 0.005 -10000 0 0 8 8
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.036 0.003 -10000 0 0 4 4
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 0.034 0.01 -10000 0 0 41 41
MAPK8 0.026 0.017 -10000 0 0 143 143
MAPK9 0.036 0.006 -10000 0 0 13 13
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.032 0.012 -10000 0 0 63 63
NFAT1-c-4/YWHAQ 0 0.11 -10000 0 -0.38 20 20
PRKCH 0.034 0.01 -10000 0 0 42 42
CABIN1/Cbp/p300 0.047 0.028 -10000 0 -0.14 7 7
CASP3 0.034 0.009 -10000 0 0 32 32
PIM1 0.036 0.005 -10000 0 0 8 8
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.02 -10000 0 -0.11 10 10
apoptosis 0.019 0.035 -10000 0 -0.17 11 11
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.097 -10000 0 -0.31 27 27
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.037 0.003 -10000 0 0 3 3
JNK2/NFAT4 0.026 0.035 -10000 0 -0.12 19 19
BAD/BCL-XL 0.046 0.027 -10000 0 -0.14 6 6
PRKCD 0.034 0.01 -10000 0 0 40 40
NUP214 0.035 0.007 -10000 0 0 18 18
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.036 0.004 -10000 0 0 6 6
PRKCG 0.037 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.017 -10000 0 0 165 165
FKBP38/BCL2 0.049 0.016 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 0 50 50
PRKCB1 0.031 0.014 -10000 0 0 82 82
CSNK2A1 0.033 0.011 -10000 0 0 51 51
NFATc/JNK1 0.01 0.1 -10000 0 -0.38 22 22
CaM/Ca2+/FKBP38 0.039 0.031 -10000 0 -0.12 14 14
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 10 10
CSNK1A1 -0.016 0.022 0.088 12 -0.12 10 22
CaM/Ca2+/CAMK IV 0.041 0.03 -10000 0 -0.12 13 13
NFATc/ERK1 0.022 0.1 -10000 0 -0.38 22 22
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.018 0.093 -10000 0 -0.22 22 22
NR4A1 -0.025 0.08 0.16 9 -0.2 25 34
GSK3B 0.034 0.01 -10000 0 0 39 39
positive T cell selection 0.01 0.02 -10000 0 -0.1 14 14
NFAT1/CK1 alpha -0.021 0.07 -10000 0 -0.18 45 45
RCH1/ KPNB1 0.035 0.059 -10000 0 -0.15 44 44
YWHAQ 0.036 0.005 -10000 0 0 8 8
PRKACA 0.035 0.008 -10000 0 0 24 24
AKAP5 0.034 0.009 -10000 0 0 32 32
MEF2D 0.036 0.006 -10000 0 0 12 12
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.035 0.007 -10000 0 0 21 21
NFATc/p38 alpha 0.021 0.1 -10000 0 -0.38 22 22
CREBBP 0.036 0.005 -10000 0 0 9 9
BCL2 0.035 0.007 -10000 0 0 20 20
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.035 0.008 -10000 0 0 26 26
mol:S1P 0.001 0.002 0.019 3 -10000 0 3
S1P1/S1P/Gi -0.02 0.11 -10000 0 -0.37 32 32
GNAO1 0.031 0.014 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.024 0.038 -10000 0 -0.1 28 28
AKT1 -0.014 0.16 -10000 0 -0.48 47 47
AKT3 0.01 0.077 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.008 -10000 0 0 26 26
GNAI2 0.034 0.011 -10000 0 -10000 0 0
GNAI3 0.037 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 0.019 3 -10000 0 3
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.034 0.01 -10000 0 0 45 45
mol:Ca2+ -0.002 0.1 0.2 1 -0.29 36 37
MAPK3 -0.009 0.099 0.18 1 -0.28 37 38
MAPK1 -0.003 0.093 0.18 1 -0.28 30 31
JAK2 -0.01 0.11 0.21 5 -0.32 40 45
CXCR4 -0.007 0.099 0.18 1 -0.28 39 40
FLT1 0.036 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Rac1/GDP 0.017 0.02 -10000 0 -0.13 5 5
SRC -0.009 0.097 -10000 0 -0.29 35 35
S1P/S1P3/Gi -0.002 0.1 0.2 1 -0.29 36 37
RAC1 0.025 0.017 -10000 0 0 163 163
RhoA/GTP 0.01 0.11 0.18 1 -0.27 40 41
VEGFA 0.002 0.002 0.032 3 -10000 0 3
S1P/S1P2/Gi -0.006 0.1 0.16 1 -0.26 47 48
VEGFR1 homodimer/VEGFA homodimer 0.029 0.01 0.11 3 -10000 0 3
RHOA 0.035 0.007 -10000 0 0 21 21
S1P/S1P3/Gq 0.015 0.04 -10000 0 -0.15 26 26
GNAQ 0.035 0.009 -10000 0 0 30 30
GNAZ 0.032 0.014 -10000 0 -10000 0 0
G12/G13 0.025 0.048 -10000 0 -0.14 28 28
GNA14 0.035 0.009 -10000 0 0 29 29
GNA15 0.033 0.011 -10000 0 0 51 51
GNA12 0.023 0.018 -10000 0 0 189 189
GNA13 0.035 0.007 -10000 0 0 20 20
GNA11 0.033 0.011 -10000 0 0 51 51
Rac1/GTP 0 0.092 -10000 0 -0.31 23 23
TRAIL signaling pathway

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
TNFSF10 0.029 0.015 -10000 0 0 109 109
positive regulation of NF-kappaB transcription factor activity 0.035 0.046 -10000 0 -0.14 25 25
MAP2K4 0.015 0.06 0.21 2 -0.29 8 10
IKBKB 0.036 0.003 -10000 0 0 4 4
TNFRSF10B 0.035 0.008 -10000 0 0 25 25
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.014 0.028 -10000 0 -0.11 20 20
IKBKG 0.037 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.036 0.006 -10000 0 0 12 12
TRAIL/TRAILR2 0.034 0.045 -10000 0 -0.14 24 24
TRAIL/TRAILR3 0.035 0.046 -10000 0 -0.14 25 25
TRAIL/TRAILR1 0.014 0.036 -10000 0 -0.13 26 26
TRAIL/TRAILR4 0.035 0.046 -10000 0 -0.14 25 25
TRAIL/TRAILR1/DAP3/GTP 0.029 0.04 -10000 0 -0.11 33 33
IKK complex -0.034 0.12 -10000 0 -0.22 135 135
RIPK1 0.035 0.007 -10000 0 0 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.023 0.025 -10000 0 -0.13 12 12
MAPK3 -0.005 0.039 0.093 68 -10000 0 68
MAP3K1 0.022 0.055 -10000 0 -0.28 7 7
TRAILR4 (trimer) 0.036 0.006 -10000 0 0 12 12
TRADD 0.036 0.005 -10000 0 0 10 10
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.018 0.049 -10000 0 -0.17 23 23
CFLAR 0.036 0.005 -10000 0 0 8 8
MAPK1 -0.004 0.039 0.093 68 -10000 0 68
TRAIL/TRAILR1/FADD/TRADD/RIP 0.07 0.048 -10000 0 -0.11 25 25
mol:ceramide 0.014 0.028 -10000 0 -0.11 20 20
FADD 0.036 0.006 -10000 0 0 12 12
MAPK8 0.007 0.047 0.19 1 -0.28 6 7
TRAF2 0.036 0.006 -10000 0 0 16 16
TRAILR3 (trimer) 0.036 0.006 -10000 0 0 14 14
CHUK 0.025 0.017 -10000 0 0 165 165
TRAIL/TRAILR1/FADD 0.033 0.039 -10000 0 -0.12 25 25
DAP3 0.035 0.008 -10000 0 0 23 23
CASP10 -0.004 0.052 0.14 16 -0.17 22 38
JNK cascade 0.035 0.046 -10000 0 -0.14 25 25
TRAIL (trimer) 0.029 0.015 -10000 0 0 109 109
TNFRSF10C 0.036 0.006 -10000 0 0 14 14
TRAIL/TRAILR1/DAP3/GTP/FADD 0.042 0.047 -10000 0 -0.11 32 32
TRAIL/TRAILR2/FADD 0.05 0.048 -10000 0 -0.12 23 23
cell death 0.014 0.028 -10000 0 -0.11 20 20
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.024 0.05 -10000 0 -0.25 4 4
TRAILR2 (trimer) 0.035 0.008 -10000 0 0 25 25
CASP8 0.016 0.023 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.087 0.057 -10000 0 -0.12 22 22
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 0.039 -10000 0 -0.14 18 18
ATM 0.034 0.01 -10000 0 0 37 37
UBE2D3 0.036 0.006 -10000 0 0 12 12
PRKDC 0.034 0.01 -10000 0 0 45 45
ATR 0.035 0.008 -10000 0 0 25 25
UBE2L3 0.034 0.009 -10000 0 0 32 32
FANCD2 0.008 0.036 -10000 0 -0.2 14 14
protein ubiquitination 0.077 0.056 -10000 0 -0.13 22 22
XRCC5 0.036 0.005 -10000 0 0 9 9
XRCC6 0.034 0.01 -10000 0 0 40 40
M/R/N Complex 0.069 0.024 -10000 0 -0.13 4 4
MRE11A 0.036 0.005 -10000 0 0 8 8
DNA-PK 0.056 0.05 -10000 0 -0.14 23 23
FA complex/FANCD2/Ubiquitin 0.003 0.084 -10000 0 -0.3 22 22
FANCF 0.035 0.008 -10000 0 0 26 26
BRCA1 0.036 0.006 -10000 0 0 12 12
CCNE1 0.033 0.012 -10000 0 0 57 57
CDK2/Cyclin E1 0.045 0.023 -10000 0 -0.14 2 2
FANCG 0.031 0.014 -10000 0 0 85 85
BRCA1/BACH1/BARD1 0.046 0.038 -10000 0 -0.14 19 19
FANCE 0.036 0.003 -10000 0 0 4 4
FANCC 0.036 0.006 -10000 0 0 15 15
NBN 0.036 0.006 -10000 0 0 13 13
FANCA 0.036 0.007 -10000 0 0 17 17
DNA repair -0.013 0.085 0.21 10 -0.33 11 21
BRCA1/BARD1/ubiquitin 0.046 0.038 -10000 0 -0.14 19 19
BARD1/DNA-PK 0.069 0.066 -10000 0 -0.14 35 35
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.039 0.14 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.064 -10000 0 -0.22 27 27
BRCA1/BACH1/BARD1/TopBP1 0.051 0.062 -10000 0 -0.14 46 46
BRCA1/BARD1/P53 0.066 0.069 -10000 0 -0.13 47 47
BARD1/CSTF1/BRCA1 0.061 0.042 -10000 0 -0.13 18 18
BRCA1/BACH1 0.036 0.006 -10000 0 0 12 12
BARD1 0.035 0.007 -10000 0 0 21 21
PCNA 0.032 0.012 -10000 0 0 62 62
BRCA1/BARD1/UbcH5C 0.063 0.043 -10000 0 -0.14 20 20
BRCA1/BARD1/UbcH7 0.059 0.048 -10000 0 -0.13 24 24
BRCA1/BARD1/RAD51/PCNA 0.069 0.062 -10000 0 -0.13 33 33
BARD1/DNA-PK/P53 0.067 0.084 -10000 0 -0.14 58 58
BRCA1/BARD1/Ubiquitin 0.046 0.038 -10000 0 -0.14 19 19
BRCA1/BARD1/CTIP 0.04 0.059 -10000 0 -0.14 44 44
FA complex 0.013 0.058 -10000 0 -0.2 23 23
BARD1/EWS 0.043 0.039 -10000 0 -0.14 19 19
RBBP8 -0.013 0.029 0.093 34 -10000 0 34
TP53 0.031 0.013 -10000 0 0 73 73
TOPBP1 0.033 0.011 -10000 0 0 51 51
G1/S transition of mitotic cell cycle -0.064 0.068 0.13 47 -10000 0 47
BRCA1/BARD1 0.085 0.06 -10000 0 -0.13 22 22
CSTF1 0.034 0.009 -10000 0 0 33 33
BARD1/EWS-Fli1 0.021 0.031 -10000 0 -0.13 19 19
CDK2 0.034 0.01 -10000 0 0 40 40
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.007 -10000 0 0 21 21
RAD50 0.036 0.006 -10000 0 0 12 12
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.046 0.038 -10000 0 -0.14 19 19
EWSR1 0.034 0.009 -10000 0 0 34 34
Glucocorticoid receptor regulatory network

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
PCK2 -0.024 0.1 -10000 0 -0.48 17 17
SMARCC2 0.034 0.01 -10000 0 0 44 44
SMARCC1 0.034 0.009 -10000 0 0 33 33
TBX21 0.032 0.055 0.34 1 -10000 0 1
SUMO2 0.033 0.019 0.071 1 -0.03 35 36
STAT1 (dimer) 0.036 0.039 0.11 22 -0.17 14 36
FKBP4 0.034 0.009 -10000 0 0 34 34
FKBP5 0.028 0.016 -10000 0 0 118 118
GR alpha/HSP90/FKBP51/HSP90 -0.025 0.065 -10000 0 -0.18 12 12
PRL 0.039 0.058 0.54 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.042 0.12 -10000 0 -0.32 2 2
RELA 0.015 0.11 0.18 32 -0.16 127 159
FGG -0.049 0.1 -10000 0 -0.32 2 2
GR beta/TIF2 -0.024 0.076 -10000 0 -0.2 5 5
IFNG 0.036 0.083 0.36 1 -10000 0 1
apoptosis -0.022 0.2 0.44 27 -0.49 37 64
CREB1 0.043 0.01 -10000 0 -10000 0 0
histone acetylation 0.022 0.055 0.22 1 -0.21 2 3
BGLAP 0.04 0.062 0.3 1 -10000 0 1
GR/PKAc 0.021 0.092 -10000 0 -0.19 18 18
NF kappa B1 p50/RelA 0.03 0.18 0.3 30 -0.26 119 149
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 0.028 0.03 0.16 8 -0.091 18 26
CSF2 0.006 0.032 -10000 0 -10000 0 0
GSK3B 0.032 0.02 0.071 1 -0.03 32 33
NR1I3 -0.014 0.18 0.45 18 -0.48 21 39
CSN2 -0.046 0.09 0.26 1 -0.29 2 3
BRG1/BAF155/BAF170/BAF60A 0.064 0.074 -10000 0 -0.17 38 38
NFATC1 0.041 0.008 -10000 0 -10000 0 0
POU2F1 0.04 0.012 -10000 0 -10000 0 0
CDKN1A -0.12 0.41 -10000 0 -1.2 59 59
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 0.029 26 -10000 0 26
SFN 0.031 0.013 -10000 0 0 80 80
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.011 0.069 -10000 0 -0.16 4 4
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.07 0.28 0.43 18 -0.66 72 90
JUN 0.024 0.053 0.36 3 -10000 0 3
IL4 0.036 0.053 -10000 0 -10000 0 0
CDK5R1 0.035 0.009 -10000 0 0 25 25
PRKACA 0.035 0.008 -10000 0 0 24 24
cortisol/GR alpha (monomer)/AP-1 -0.049 0.053 -10000 0 -0.23 12 12
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.005 0.074 -10000 0 -0.16 18 18
cortisol/GR alpha (monomer) -0.057 0.12 -10000 0 -0.37 2 2
NCOA2 0.036 0.006 -10000 0 0 12 12
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.039 0.032 0.17 7 -10000 0 7
AP-1/NFAT1-c-4 0.047 0.077 0.45 2 -10000 0 2
AFP 0.024 0.067 -10000 0 -10000 0 0
SUV420H1 0.033 0.011 -10000 0 0 50 50
IRF1 -0.029 0.13 -10000 0 -0.66 15 15
TP53 -0.013 0.17 -10000 0 -0.49 56 56
PPP5C 0.034 0.01 -10000 0 0 39 39
KRT17 0.041 0.082 0.4 2 -10000 0 2
KRT14 0.031 0.068 -10000 0 -10000 0 0
TBP 0.042 0.018 -10000 0 -10000 0 0
CREBBP 0.029 0.018 -10000 0 -0.094 10 10
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.011 -10000 0 -10000 0 0
AP-1 0.048 0.077 0.45 2 -10000 0 2
MAPK14 0.034 0.019 -10000 0 -0.03 33 33
MAPK10 0.029 0.021 0.073 1 -0.03 27 28
MAPK11 0.03 0.021 0.071 1 -0.03 32 33
KRT5 0.04 0.08 0.46 1 -10000 0 1
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.033 0.018 0.077 1 -0.067 9 10
STAT1 0.036 0.039 0.11 22 -0.17 14 36
CGA 0.036 0.055 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.034 0.071 -10000 0 -0.37 7 7
MAPK3 0.034 0.02 0.075 2 -0.03 38 40
MAPK1 0.031 0.02 -10000 0 -0.03 32 32
ICAM1 0.03 0.14 0.34 16 -10000 0 16
NFKB1 0.016 0.11 0.18 30 -0.16 119 149
MAPK8 0.034 0.059 0.34 1 -10000 0 1
MAPK9 0.033 0.019 -10000 0 -0.03 32 32
cortisol/GR alpha (dimer) -0.024 0.2 0.44 26 -0.51 38 64
BAX -0.033 0.18 -10000 0 -0.85 10 10
POMC 0.032 0.075 0.48 1 -10000 0 1
EP300 0.026 0.019 -10000 0 -0.094 10 10
cortisol/GR alpha (dimer)/p53 -0.071 0.13 -10000 0 -0.41 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.069 0.24 31 -10000 0 31
SGK1 -0.017 0.06 -10000 0 -0.24 14 14
IL13 0.028 0.064 -10000 0 -10000 0 0
IL6 0.031 0.13 0.34 19 -10000 0 19
PRKACG 0.036 0.005 -10000 0 0 10 10
IL5 0.021 0.072 0.41 1 -10000 0 1
IL2 0.041 0.077 -10000 0 -10000 0 0
CDK5 0.024 0.018 -10000 0 0 185 185
PRKACB 0.033 0.011 -10000 0 0 48 48
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.11 0.4 0.34 18 -0.79 126 144
CDK5R1/CDK5 0.029 0.042 -10000 0 -0.14 17 17
NF kappa B1 p50/RelA/PKAc 0.056 0.17 0.3 28 -0.21 111 139
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.038 0.11 -10000 0 -0.34 2 2
SMARCA4 0.032 0.012 -10000 0 0 62 62
chromatin remodeling -0.038 0.11 -10000 0 -0.37 28 28
NF kappa B1 p50/RelA/Cbp 0.046 0.16 0.3 21 -0.22 110 131
JUN (dimer) 0.024 0.053 0.36 3 -10000 0 3
YWHAH 0.031 0.013 -10000 0 0 73 73
VIPR1 0.035 0.065 0.38 5 -10000 0 5
NR3C1 -0.04 0.086 -10000 0 -0.35 1 1
NR4A1 0.039 0.009 -10000 0 -10000 0 0
TIF2/SUV420H1 0.036 0.055 -10000 0 -0.14 42 42
MAPKKK cascade -0.022 0.2 0.44 27 -0.49 37 64
cortisol/GR alpha (dimer)/Src-1 -0.049 0.12 -10000 0 -0.37 3 3
PBX1 0.04 0.01 -10000 0 -10000 0 0
POU1F1 0.041 0.011 -10000 0 -10000 0 0
SELE 0.027 0.13 0.34 2 -10000 0 2
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.038 0.11 -10000 0 -0.38 28 28
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.038 0.11 -10000 0 -0.34 2 2
mol:cortisol -0.035 0.061 -10000 0 -0.2 1 1
MMP1 0.038 0.073 0.36 1 -0.49 3 4
Coregulation of Androgen receptor activity

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
NRIP1 0.035 0.01 -10000 0 -10000 0 0
SVIL 0.024 0.018 -10000 0 -10000 0 0
ZNF318 0.035 0.005 -10000 0 -0.045 1 1
JMJD2C 0.036 0.014 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.053 0.041 -10000 0 -10000 0 0
CARM1 0.035 0.008 -10000 0 0 28 28
PRDX1 0.035 0.007 -10000 0 0 20 20
PELP1 0.035 0.007 -10000 0 0 17 17
CTNNB1 0.036 0.006 -10000 0 -10000 0 0
AKT1 0.032 0.012 -10000 0 -0.001 55 55
PTK2B 0.036 0.007 -10000 0 0 16 16
MED1 0 0 -10000 0 -10000 0 0
MAK 0.033 0.009 -10000 0 -0.045 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.022 0.018 -10000 0 -10000 0 0
GSN 0.032 0.013 -10000 0 -10000 0 0
NCOA2 0.036 0.006 -10000 0 0 12 12
NCOA6 0.033 0.012 -10000 0 -10000 0 0
DNA-PK 0.055 0.05 -10000 0 -0.15 22 22
NCOA4 0.026 0.017 -10000 0 0 147 147
PIAS3 0.036 0.006 -10000 0 -10000 0 0
cell proliferation 0.023 0.045 -10000 0 -0.45 4 4
XRCC5 0.036 0.005 -10000 0 0 9 9
UBE3A 0.038 0.003 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.032 0.033 0.12 1 -0.071 33 34
FHL2 0.018 0.2 -10000 0 -0.69 33 33
RANBP9 0.036 0.007 -10000 0 -10000 0 0
JMJD1A 0.044 0.012 -10000 0 -10000 0 0
CDK6 0.024 0.017 -10000 0 0 177 177
TGFB1I1 0.033 0.012 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.034 0.057 -10000 0 -0.1 54 54
XRCC6 0.034 0.01 -10000 0 0 40 40
T-DHT/AR 0.049 0.06 0.22 1 -0.13 33 34
CTDSP1 0.036 0.006 -10000 0 0 15 15
CTDSP2 0.031 0.012 -10000 0 -0.038 1 1
BRCA1 0.037 0.006 -10000 0 -10000 0 0
TCF4 0.032 0.012 -10000 0 -0.034 1 1
CDKN2A 0.004 0.012 -10000 0 0 448 448
SRF 0.04 0.056 0.11 90 -0.15 33 123
NKX3-1 0.026 0.07 -10000 0 -0.28 21 21
KLK3 0.016 0.047 -10000 0 -10000 0 0
TMF1 0.036 0.007 -10000 0 0 18 18
HNRNPA1 -0.001 0 -10000 0 -10000 0 0
AOF2 0.034 0.011 -10000 0 -10000 0 0
APPL1 -0.011 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.05 0.041 -10000 0 -0.08 33 33
AR 0.036 0.031 -10000 0 -0.069 33 33
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 -0.001 0 -10000 0 -10000 0 0
PAWR 0.036 0.006 -10000 0 0 13 13
PRKDC 0.033 0.01 -10000 0 0 45 45
PA2G4 0.034 0.008 -10000 0 -0.032 1 1
UBE2I 0.036 0.004 -10000 0 0 6 6
T-DHT/AR/Cyclin D3/CDK11 p58 0.045 0.044 0.14 1 -0.079 42 43
RPS6KA3 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.038 0.046 -10000 0 -0.087 20 20
LATS2 -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.046 0.043 0.14 1 -0.08 39 40
Cyclin D3/CDK11 p58 0.021 0.028 -10000 0 -0.14 16 16
VAV3 0.029 0.015 -10000 0 -10000 0 0
KLK2 0.025 0.057 -10000 0 -0.32 11 11
CASP8 0.036 0.006 -10000 0 0 13 13
T-DHT/AR/TIF2/CARM1 0.07 0.046 -10000 0 -0.11 1 1
TMPRSS2 0.026 0.071 -10000 0 -0.3 15 15
CCND1 0.029 0.015 -10000 0 0 111 111
PIAS1 0.036 0.008 -10000 0 -10000 0 0
mol:T-DHT 0.004 0.017 0.052 1 -0.049 33 34
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.036 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.037 0.041 -10000 0 -0.081 8 8
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.017 0.052 1 -0.049 33 34
CCND3 0.035 0.008 -10000 0 0 25 25
TGIF1 -0.001 0 -10000 0 -10000 0 0
FKBP4 0.035 0.009 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.018 0.091 -10000 0 -0.24 38 38
CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
AKT1 0.033 0.011 -10000 0 0 54 54
AKT2 0.035 0.008 -10000 0 0 28 28
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.002 0.089 0.17 2 -0.25 38 40
YWHAZ 0.035 0.007 -10000 0 0 21 21
CALM1 0.033 0.012 -10000 0 0 57 57
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.016 0.021 0.093 16 -10000 0 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.013 -10000 0 0 73 73
YWHAB 0.034 0.01 -10000 0 0 41 41
SNARE/Synip 0.021 0.018 -10000 0 -0.11 8 8
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.034 0.009 -10000 0 0 34 34
PRKCI 0.035 0.008 -10000 0 0 27 27
AS160/CaM/Ca2+ 0.02 0.027 -10000 0 -0.13 14 14
RHOQ 0.036 0.006 -10000 0 0 16 16
GYS1 0.001 0.039 0.24 2 -0.21 6 8
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.034 0.009 -10000 0 0 35 35
TC10/GTP/CIP4/Exocyst 0.042 0.03 -10000 0 -0.12 14 14
AS160/14-3-3 -0.005 0.098 -10000 0 -0.41 18 18
VAMP2 0.033 0.011 -10000 0 0 49 49
SLC2A4 -0.004 0.096 0.17 2 -0.27 40 42
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.004 0.077 -10000 0 -0.3 27 27
SFN 0.031 0.013 -10000 0 0 80 80
LNPEP 0.036 0.005 -10000 0 0 8 8
YWHAE 0.035 0.008 -10000 0 0 27 27
Nectin adhesion pathway

Figure 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
PDGFRB 0.035 0.008 -10000 0 0 26 26
alphaV beta3 Integrin 0.044 0.043 -10000 0 -0.14 24 24
PTK2 0.012 0.11 -10000 0 -0.33 29 29
positive regulation of JNK cascade 0.021 0.09 -10000 0 -0.28 18 18
CDC42/GDP 0.036 0.12 -10000 0 -0.34 34 34
Rac1/GDP 0.029 0.1 -10000 0 -0.36 11 11
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 10 10
CTNNB1 0.036 0.006 -10000 0 0 15 15
CDC42/GTP 0.029 0.11 -10000 0 -0.35 18 18
nectin-3/I-afadin 0.044 0.027 -10000 0 -0.14 5 5
RAPGEF1 0.005 0.12 -10000 0 -0.35 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.005 0.12 -10000 0 -0.39 34 34
PDGFB-D/PDGFRB 0.035 0.008 -10000 0 0 26 26
TLN1 -0.006 0.058 0.16 21 -0.23 13 34
Rap1/GTP -0.001 0.083 -10000 0 -0.27 35 35
IQGAP1 0.033 0.011 -10000 0 0 47 47
Rap1/GTP/I-afadin 0.043 0.015 -10000 0 -0.1 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.027 -10000 0 -0.14 5 5
PVR 0.035 0.009 -10000 0 0 31 31
Necl-5(dimer) 0.034 0.009 -10000 0 0 31 31
mol:GDP 0.021 0.13 -10000 0 -0.41 29 29
MLLT4 0.034 0.009 -10000 0 0 34 34
PIK3CA 0.031 0.014 -10000 0 0 82 82
PI3K 0.057 0.09 -10000 0 -0.14 72 72
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.05 0.015 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.02 0.077 -10000 0 -0.28 12 12
PVRL1 0.036 0.005 -10000 0 0 8 8
PVRL3 0.032 0.012 -10000 0 0 60 60
PVRL2 0.034 0.009 -10000 0 0 35 35
PIK3R1 0.032 0.012 -10000 0 0 63 63
CDH1 0.034 0.01 -10000 0 0 37 37
CLDN1 0.034 0.009 -10000 0 0 36 36
JAM-A/CLDN1 0.074 0.045 -10000 0 -0.12 8 8
SRC 0.012 0.13 -10000 0 -0.41 34 34
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 0.026 0.14 -10000 0 -0.48 15 15
RAC1 0.025 0.017 -10000 0 0 163 163
CTNNA1 0.035 0.007 -10000 0 0 18 18
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.035 -10000 0 -0.12 5 5
nectin-1/I-afadin 0.05 0.015 -10000 0 -10000 0 0
nectin-2/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.024 0.043 -10000 0 -0.12 30 30
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.059 0.034 -10000 0 -0.12 5 5
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.042 -10000 0 -0.12 33 33
F11R 0.033 0.011 -10000 0 0 52 52
positive regulation of filopodium formation 0.021 0.09 -10000 0 -0.28 18 18
alphaV/beta3 Integrin/Talin 0.031 0.087 0.22 26 -0.22 23 49
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.047 0.023 -10000 0 -0.14 3 3
PIP5K1C -0.01 0.041 0.09 4 -0.21 15 19
VAV2 0.025 0.14 -10000 0 -0.45 20 20
RAP1/GDP 0.026 0.11 -10000 0 -0.31 35 35
ITGAV 0.035 0.009 -10000 0 0 31 31
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.056 0.038 -10000 0 -0.14 7 7
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.027 -10000 0 -0.14 5 5
Rac1/GTP 0.026 0.093 -10000 0 -0.34 12 12
PTPRM 0.008 0.045 -10000 0 -0.23 16 16
E-cadherin/beta catenin/alpha catenin 0.083 0.059 -10000 0 -0.13 13 13
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 0 26 26
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.054 0.094 -10000 0 -0.2 46 46
Ran/GTP/Exportin 1/HDAC1 -0.029 0.022 -10000 0 -0.11 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.11 -10000 0 -0.27 47 47
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 35 35
Histones 0.035 0.076 -10000 0 -0.24 22 22
YY1/LSF 0.015 0.064 -10000 0 -0.22 19 19
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
I kappa B alpha/HDAC3 0 0.078 -10000 0 -0.2 52 52
I kappa B alpha/HDAC1 0.008 0.097 -10000 0 -0.22 62 62
SAP18 0.034 0.01 -10000 0 0 43 43
RELA -0.003 0.081 0.19 1 -0.28 18 19
HDAC1/Smad7 0.043 0.041 -10000 0 -0.13 6 6
RANGAP1 0.033 0.011 -10000 0 0 46 46
HDAC3/TR2 0.027 0.071 -10000 0 -0.26 20 20
NuRD/MBD3 Complex -0.01 0.11 -10000 0 -0.33 38 38
NF kappa B1 p50/RelA 0.012 0.088 -10000 0 -0.29 18 18
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.035 0.008 -10000 0 0 23 23
GATA1 0.037 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.11 -10000 0 -0.34 35 35
RBBP7 0.036 0.005 -10000 0 0 8 8
NPC 0.017 0.021 -10000 0 -0.09 18 18
RBBP4 0.033 0.012 -10000 0 0 57 57
MAX 0.034 0.009 -10000 0 0 32 32
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 22 22
NFKBIA -0.001 0.082 -10000 0 -0.32 27 27
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.09 -10000 0 -0.29 29 29
SIN3 complex 0.055 0.042 -10000 0 -0.13 17 17
SMURF1 0.025 0.017 -10000 0 0 164 164
CHD3 0.036 0.006 -10000 0 0 13 13
SAP30 0.035 0.007 -10000 0 0 18 18
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.035 0.008 -10000 0 0 27 27
YY1/HDAC3 -0.002 0.078 -10000 0 -0.24 31 31
YY1/HDAC2 0.014 0.061 -10000 0 -0.21 19 19
YY1/HDAC1 0.016 0.063 -10000 0 -0.22 19 19
NuRD/MBD2 Complex (MeCP1) -0.004 0.095 -10000 0 -0.28 35 35
PPARG 0.002 0.078 -10000 0 -0.21 52 52
HDAC8/hEST1B 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.036 0.004 -10000 0 0 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 22 22
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
HDAC3/SMRT (N-CoR2) 0.027 0.071 -10000 0 -0.26 20 20
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.043 0.04 -10000 0 -0.13 6 6
CREBBP 0.036 0.005 -10000 0 0 9 9
NuRD/MBD3/MBD3L2 Complex -0.005 0.11 -10000 0 -0.33 34 34
HDAC1 0.035 0.007 -10000 0 0 21 21
HDAC3 0.006 0.064 -10000 0 -0.3 16 16
HDAC2 0.032 0.012 -10000 0 0 59 59
YY1 0.01 0.028 -10000 0 -0.21 7 7
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.034 0.01 -10000 0 0 45 45
NCOR2 0.037 0.002 -10000 0 0 2 2
MXD1 0.037 0.003 -10000 0 0 3 3
STAT3 0.006 0.06 -10000 0 -0.22 33 33
NFKB1 0.035 0.007 -10000 0 0 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 25 25
YY1/LSF/HDAC1 0.029 0.072 -10000 0 -0.22 19 19
YY1/SAP30/HDAC1 0.031 0.07 -10000 0 -0.21 19 19
EP300 0.033 0.011 -10000 0 0 50 50
STAT3 (dimer non-phopshorylated) 0.006 0.06 -10000 0 -0.22 33 33
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.082 -10000 0 -0.32 27 27
histone deacetylation -0.004 0.095 -10000 0 -0.28 35 35
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.094 -10000 0 -0.31 29 29
nuclear export -0.023 0.005 -10000 0 -10000 0 0
PRKACA 0.035 0.008 -10000 0 0 24 24
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.033 0.011 -10000 0 0 55 55
GATA2/HDAC3 0.026 0.07 -10000 0 -0.26 19 19
GATA1/HDAC1 0.051 0.023 -10000 0 -0.14 6 6
GATA1/HDAC3 0.027 0.071 -10000 0 -0.26 20 20
CHD4 0.034 0.01 -10000 0 0 37 37
TNF-alpha/TNFR1A 0.035 0.056 -10000 0 -0.14 43 43
SIN3/HDAC complex/Mad/Max -0.004 0.085 -10000 0 -0.3 25 25
NuRD Complex -0.003 0.11 -10000 0 -0.34 34 34
positive regulation of chromatin silencing 0.033 0.074 -10000 0 -0.24 22 22
SIN3B 0.034 0.009 -10000 0 0 33 33
MTA2 0.036 0.004 -10000 0 0 5 5
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.036 0.004 -10000 0 0 5 5
SUMO1/HDAC1 0.036 0.056 -10000 0 -0.22 6 6
HDAC complex 0.066 0.073 -10000 0 -0.15 42 42
GATA1/Fog1 0.027 0 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.054 0.05 -10000 0 -0.14 22 22
TNF 0.036 0.003 -10000 0 0 4 4
negative regulation of cell growth -0.004 0.085 -10000 0 -0.29 26 26
NuRD/MBD2/PRMT5 Complex -0.004 0.095 -10000 0 -0.28 35 35
Ran/GTP/Exportin 1 0.036 0.06 -10000 0 -0.16 21 21
NF kappa B/RelA/I kappa B alpha -0.005 0.093 -10000 0 -0.25 52 52
SIN3/HDAC complex/NCoR1 -0.003 0.093 -10000 0 -0.33 24 24
TFCP2 0.035 0.008 -10000 0 0 25 25
NR2C1 0.036 0.003 -10000 0 0 4 4
MBD3 0.034 0.01 -10000 0 0 40 40
MBD2 0.036 0.007 -10000 0 0 17 17
Regulation of Androgen receptor activity

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
HDAC1 -0.011 0.002 0.001 22 -10000 0 22
SMARCC1 -0.005 0.12 -10000 0 -1.2 4 4
REL 0.036 0.004 -10000 0 -0.011 3 3
HDAC7 -0.03 0.057 0.17 5 -0.21 19 24
JUN 0.034 0.01 -10000 0 0 41 41
EP300 0.033 0.011 -10000 0 0 50 50
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.017 0.019 0.09 4 -10000 0 4
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR 0.018 0.079 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 0.015 -10000 0 -0.033 16 16
SMARCA2 0.032 0.013 -10000 0 0 68 68
PDE9A -0.013 0.2 -10000 0 -0.8 28 28
NCOA2 0.036 0.006 -10000 0 0 12 12
CEBPA 0.028 0.016 -10000 0 0 121 121
EHMT2 0.037 0.002 -10000 0 0 1 1
cell proliferation -0.019 0.093 0.26 7 -0.29 19 26
NR0B1 0.03 0.014 -10000 0 0 88 88
EGR1 0.029 0.015 -10000 0 0 107 107
RXRs/9cRA 0.067 0.018 -10000 0 -0.11 1 1
AR/RACK1/Src -0.013 0.063 0.21 4 -0.22 2 6
AR/GR 0.002 0.061 0.16 1 -0.2 25 26
GNB2L1 0.037 0.002 -10000 0 0 2 2
PKN1 0.033 0.011 -10000 0 0 48 48
RCHY1 0.036 0.006 -10000 0 0 16 16
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.011 0.02 0.089 7 -10000 0 7
T-DHT/AR/TIF2/CARM1 0.014 0.057 0.21 5 -0.2 4 9
SRC -0.02 0.037 0.18 10 -10000 0 10
NR3C1 0.035 0.007 -10000 0 0 22 22
KLK3 -0.003 0.074 0.37 2 -0.33 2 4
APPBP2 0.034 0.015 -10000 0 -0.034 16 16
TRIM24 0.024 0.018 -10000 0 0 182 182
T-DHT/AR/TIP60 -0.024 0.028 0.082 2 -0.15 10 12
TMPRSS2 0.017 0.081 -10000 0 -0.56 7 7
RXRG 0.036 0.006 -10000 0 0 14 14
mol:9cRA 0 0 0.002 1 -10000 0 1
RXRA 0.035 0.007 -10000 0 0 21 21
RXRB 0.037 0.002 -10000 0 0 1 1
CARM1 0.035 0.008 -10000 0 0 28 28
NR2C2 0.036 0.005 -10000 0 0 8 8
KLK2 -0.002 0.046 0.21 1 -0.25 1 2
AR -0.004 0.044 0.15 5 -0.2 17 22
SENP1 0 0 0.003 1 -10000 0 1
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.011 -10000 0 -0.001 46 46
SRY 0.036 0.004 -10000 0 -0.009 4 4
GATA2 0.035 0.008 -10000 0 0 23 23
MYST2 0.034 0.01 -10000 0 0 37 37
HOXB13 0.037 0.003 -10000 0 0 4 4
T-DHT/AR/RACK1/Src -0.015 0.064 0.19 12 -0.23 2 14
positive regulation of transcription 0.035 0.008 -10000 0 0 23 23
DNAJA1 0.032 0.017 -10000 0 -0.034 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.037 -10000 0 -0.26 8 8
NCOA1 0.037 0.034 0.14 3 -0.27 4 7
SPDEF 0.037 0.003 -10000 0 0 4 4
T-DHT/AR/TIF2 -0.032 0.085 0.19 2 -0.24 42 44
T-DHT/AR/Hsp90 -0.024 0.028 0.082 2 -0.15 10 12
GSK3B 0.034 0.01 -10000 0 0 39 39
NR2C1 0.036 0.003 -10000 0 0 4 4
mol:T-DHT -0.018 0.035 0.17 9 -0.12 4 13
SIRT1 0.024 0.017 -10000 0 0 174 174
ZMIZ2 -0.001 0.001 -10000 0 -0.02 1 1
POU2F1 0.037 0.035 0.12 13 -0.11 22 35
T-DHT/AR/DAX-1 -0.021 0.038 0.2 2 -0.18 4 6
CREBBP 0.036 0.005 -10000 0 0 9 9
SMARCE1 0.037 0.004 -10000 0 0 7 7
RXR and RAR heterodimerization with other nuclear receptor

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 -0.009 0.14 0.34 1 -1 8 9
VDR 0.035 0.007 -10000 0 0 21 21
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.012 0.099 0.25 2 -0.27 41 43
RXRs/LXRs/DNA/Oxysterols 0.005 0.14 0.31 2 -0.4 46 48
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0 0.016 0.043 4 -0.047 46 50
RARs/THRs/DNA/Src-1 0.016 0.054 -10000 0 -0.21 6 6
RXRs/NUR77 0.079 0.065 -10000 0 -0.12 32 32
RXRs/PPAR 0.019 0.048 -10000 0 -0.18 6 6
NCOR2 0.037 0.002 -10000 0 0 2 2
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.081 0.024 -10000 0 -10000 0 0
RARA 0.037 0.003 -10000 0 0 3 3
NCOA1 0.033 0.011 -10000 0 0 49 49
VDR/VDR/DNA 0.035 0.007 -10000 0 0 21 21
RARs/RARs/DNA/9cRA 0.056 0.032 -10000 0 -10000 0 0
RARG 0.036 0.005 -10000 0 0 11 11
RPS6KB1 -0.004 0.087 0.51 8 -0.4 8 16
RARs/THRs/DNA/SMRT 0.03 0.025 -10000 0 -0.18 4 4
THRA 0.036 0.006 -10000 0 0 12 12
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.058 0.074 0.29 3 -0.16 39 42
NR1H4 0.036 0.004 -10000 0 0 6 6
RXRs/LXRs/DNA 0.085 0.1 0.31 2 -0.22 38 40
NR1H2 0.029 0.031 0.091 2 -0.062 46 48
NR1H3 0.03 0.033 0.093 2 -0.069 44 46
RXRs/VDR/DNA/Vit D3 0.071 0.061 0.21 1 -0.11 35 36
NR4A1 0.036 0.006 -10000 0 0 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.04 0.13 1 -0.14 6 7
RXRG 0.03 0.03 0.089 2 -0.06 46 48
RXR alpha/CCPG 0.023 0.021 -10000 0 -0.065 6 6
RXRA 0.03 0.03 0.089 2 -0.061 44 46
RXRB 0.031 0.033 0.09 2 -0.066 49 51
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 -0.4 38 38
mol:Oxysterols 0 0.015 0.039 5 -0.042 49 54
cholesterol transport 0.005 0.14 0.31 2 -0.4 46 48
PPARA 0.034 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 0.03 -10000 0 -0.15 2 2
SREBF1 -0.01 0.17 0.35 2 -0.51 39 41
RXRs/RXRs/DNA/9cRA 0.058 0.074 0.28 3 -0.16 39 42
ABCA1 -0.044 0.26 0.35 2 -0.82 48 50
RARs/THRs 0.1 0.027 -10000 0 -0.12 1 1
RXRs/FXR 0.079 0.065 0.22 1 -0.12 36 37
BCL2 0.035 0.007 -10000 0 0 20 20
IL27-mediated 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
TGFB1 0.032 0.012 -10000 0 0 66 66
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.002 0.067 0.44 3 -10000 0 3
IL27/IL27R/JAK1 0.041 0.062 -10000 0 -10000 0 0
TBX21 -0.015 0.092 0.35 18 -10000 0 18
IL12B 0.037 0.004 -10000 0 0 6 6
IL12A -0.011 0.002 0.014 2 -10000 0 2
IL6ST 0.034 0.011 -10000 0 -0.033 1 1
IL27RA/JAK1 0.026 0.046 -10000 0 -10000 0 0
IL27 -0.001 0.004 -10000 0 -10000 0 0
TYK2 0.034 0.011 -10000 0 -0.033 1 1
T-helper cell lineage commitment 0.063 0.083 0.18 150 -0.18 2 152
T-helper 2 cell differentiation 0.002 0.067 0.44 3 -10000 0 3
T cell proliferation during immune response 0.002 0.067 0.44 3 -10000 0 3
MAPKKK cascade -0.002 0.067 -10000 0 -0.44 3 3
STAT3 0.034 0.01 -10000 0 0 37 37
STAT2 0.036 0.006 -10000 0 0 13 13
STAT1 0.034 0.01 -10000 0 0 40 40
IL12RB1 0.035 0.008 -10000 0 0 26 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.016 0.09 0.35 17 -10000 0 17
IL27/IL27R/JAK2/TYK2 -0.002 0.067 -10000 0 -0.45 3 3
positive regulation of T cell mediated cytotoxicity -0.002 0.067 -10000 0 -0.44 3 3
STAT1 (dimer) 0.048 0.081 -10000 0 -0.34 5 5
JAK2 0.03 0.014 -10000 0 -0.032 1 1
JAK1 0.034 0.01 -10000 0 0 40 40
STAT2 (dimer) 0.014 0.099 -10000 0 -0.35 9 9
T cell proliferation 0.003 0.062 -10000 0 -0.32 4 4
IL12/IL12R/TYK2/JAK2 0.011 0.18 -10000 0 -0.77 24 24
IL17A 0.061 0.082 0.18 143 -0.18 2 145
mast cell activation 0.002 0.067 0.44 3 -10000 0 3
IFNG 0.003 0.029 -10000 0 -0.088 23 23
T cell differentiation -0.001 0.003 -10000 0 -0.017 9 9
STAT3 (dimer) 0.011 0.11 -10000 0 -0.38 12 12
STAT5A (dimer) 0.015 0.1 -10000 0 -0.35 10 10
STAT4 (dimer) 0.014 0.098 -10000 0 -0.38 6 6
STAT4 0.035 0.009 -10000 0 0 29 29
T cell activation -0.005 0.005 -10000 0 -0.086 1 1
IL27R/JAK2/TYK2 0.038 0.063 -10000 0 -10000 0 0
GATA3 0.007 0.092 0.67 9 -10000 0 9
IL18 -0.01 0.004 0 74 -10000 0 74
positive regulation of mast cell cytokine production 0.011 0.11 -10000 0 -0.38 12 12
IL27/EBI3 0.025 0.011 -10000 0 -10000 0 0
IL27RA 0.002 0.027 -10000 0 -10000 0 0
IL6 0.02 0.018 -10000 0 0 236 236
STAT5A 0.036 0.004 -10000 0 0 5 5
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.028 0.35 1 -10000 0 1
IL1B -0.009 0.005 0 101 -10000 0 101
EBI3 0.034 0.011 -10000 0 -0.033 1 1
TNF -0.011 0.001 0 4 -10000 0 4
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.007 0.034 0.093 48 -10000 0 48
MAP4K4 0.003 0.053 -10000 0 -0.21 11 11
BAG4 0.036 0.005 -10000 0 0 11 11
PKC zeta/ceramide 0.004 0.048 -10000 0 -0.23 12 12
NFKBIA 0.033 0.012 -10000 0 0 57 57
BIRC3 0.031 0.014 -10000 0 0 82 82
BAX 0.002 0.075 -10000 0 -0.32 23 23
RIPK1 0.035 0.007 -10000 0 0 20 20
AKT1 -0.012 0.04 0.38 3 -10000 0 3
BAD -0.003 0.048 -10000 0 -0.24 11 11
SMPD1 -0.003 0.054 0.13 3 -0.19 22 25
RB1 -0.003 0.048 0.21 1 -0.23 12 13
FADD/Caspase 8 0.015 0.051 -10000 0 -0.24 6 6
MAP2K4 -0.006 0.053 0.2 4 -0.23 12 16
NSMAF 0.035 0.009 -10000 0 0 29 29
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.052 0.2 7 -0.24 11 18
EGF 0.035 0.008 -10000 0 0 25 25
mol:ceramide 0.005 0.052 -10000 0 -0.24 12 12
MADD 0.036 0.006 -10000 0 0 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.007 0.035 0.093 51 -10000 0 51
ASAH1 0.036 0.007 -10000 0 0 17 17
negative regulation of cell cycle -0.002 0.048 0.2 1 -0.23 12 13
cell proliferation 0.02 0.054 0.22 1 -0.24 4 5
BID 0.004 0.15 -10000 0 -0.58 26 26
MAP3K1 0 0.051 0.14 2 -0.24 12 14
EIF2A -0.009 0.05 0.2 5 -0.22 12 17
TRADD 0.036 0.005 -10000 0 0 10 10
CRADD 0.036 0.005 -10000 0 0 11 11
MAPK3 -0.006 0.049 0.19 7 -0.25 4 11
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.063 0.19 7 -0.22 20 27
Cathepsin D/ceramide 0.021 0.056 -10000 0 -0.24 12 12
FADD 0.009 0.047 -10000 0 -0.22 5 5
KSR1 -0.003 0.048 -10000 0 -0.24 12 12
MAPK8 -0.04 0.095 0.18 1 -0.19 104 105
PRKRA -0.005 0.052 0.23 2 -0.23 13 15
PDGFA 0.027 0.016 -10000 0 0 134 134
TRAF2 0.036 0.006 -10000 0 0 16 16
IGF1 0.035 0.007 -10000 0 0 21 21
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.005 0.051 -10000 0 -0.24 12 12
CTSD 0.033 0.011 -10000 0 0 56 56
regulation of nitric oxide biosynthetic process 0.05 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.022 0.058 0.24 1 -0.26 4 5
PRKCD 0.034 0.01 -10000 0 0 40 40
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.007 0.035 0.093 51 -10000 0 51
RelA/NF kappa B1 0.05 0.025 -10000 0 -0.14 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.036 0.006 -10000 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.054 -10000 0 -0.24 7 7
TNFR1A/BAG4/TNF-alpha 0.053 0.056 -10000 0 -0.13 41 41
mol:Sphingosine-1-phosphate -0.007 0.034 0.093 48 -10000 0 48
MAP2K1 -0.016 0.051 0.18 7 -0.23 11 18
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.036 0.004 -10000 0 0 7 7
CYCS 0.025 0.062 0.14 22 -0.18 11 33
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
NFKB1 0.035 0.007 -10000 0 0 18 18
TNFR1A/BAG4 0.035 0.055 -10000 0 -0.14 42 42
EIF2AK2 -0.01 0.053 0.21 5 -0.22 13 18
TNF-alpha/TNFR1A/FAN 0.047 0.067 -10000 0 -0.14 55 55
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.049 -10000 0 -0.27 4 4
MAP2K2 -0.008 0.052 0.19 17 -0.32 2 19
SMPD3 0.007 0.054 0.16 1 -0.27 8 9
TNF 0.036 0.003 -10000 0 0 4 4
PKC zeta/PAR4 0.026 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.006 0.044 0.13 8 -0.15 14 22
NF kappa B1/RelA/I kappa B alpha 0.07 0.048 -10000 0 -0.12 20 20
AIFM1 -0.003 0.049 0.14 2 -0.19 18 20
BCL2 0.035 0.007 -10000 0 0 20 20
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.063 0.03 -9999 0 -0.13 3 3
E-cadherin/beta catenin 0.048 0.022 -9999 0 -0.14 3 3
CTNNB1 0.036 0.006 -9999 0 0 15 15
JUP 0.033 0.011 -9999 0 0 51 51
CDH1 0.034 0.01 -9999 0 0 37 37
Atypical NF-kappaB pathway

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
BCL3/RelA 0.05 0.018 -10000 0 -0.14 2 2
FBXW11 0.035 0.007 -10000 0 0 22 22
NF kappa B1 p50/c-Rel 0.033 0.018 -10000 0 -0.13 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.07 0.18 2 -0.26 14 16
NFKBIA 0.005 0.059 -10000 0 -0.18 28 28
MAPK14 0.036 0.004 -10000 0 0 5 5
NF kappa B1 p105/p50 0.029 0.031 -10000 0 -0.13 16 16
ARRB2 0.012 0.025 -10000 0 -0.2 7 7
REL 0.037 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.019 -10000 0 -0.13 5 5
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.021 -10000 0 -0.13 7 7
PIK3CA 0.031 0.014 -10000 0 0 82 82
NF kappa B1 p50 dimer -0.02 0.029 0.18 7 -0.14 5 12
PIK3R1 0.032 0.012 -10000 0 0 63 63
NFKB1 -0.021 0.011 0.093 4 -10000 0 4
RELA 0.036 0.004 -10000 0 0 7 7
positive regulation of anti-apoptosis 0.015 0.041 0.14 2 -0.14 22 24
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.027 0.073 0.18 2 -0.26 15 17
SRC 0.034 0.009 -10000 0 0 34 34
PI3K 0.018 0.076 -10000 0 -0.16 72 72
NF kappa B1 p50/RelA 0.015 0.041 0.14 2 -0.14 22 24
IKBKB 0.036 0.003 -10000 0 0 4 4
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 22 22
SYK 0.031 0.013 -10000 0 0 74 74
I kappa B alpha/PIK3R1 0.018 0.073 0.22 1 -0.24 24 25
cell death 0.026 0.071 0.18 2 -0.25 15 17
NF kappa B1 p105/c-Rel 0.033 0.018 -10000 0 -0.13 5 5
LCK 0.035 0.007 -10000 0 0 18 18
BCL3 0.035 0.009 -10000 0 0 31 31
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.003 0.038 0.097 26 -0.11 10 36
NFATC2 -0.001 0.027 0.083 16 -0.098 12 28
NFATC3 -0.003 0.038 0.097 26 -0.11 12 38
CD40LG 0.01 0.11 0.35 17 -0.24 3 20
PTGS2 -0.021 0.068 0.38 1 -0.24 3 4
JUNB 0.031 0.014 -10000 0 0 84 84
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.028 -10000 0 -0.12 13 13
CaM/Ca2+ 0.026 0.028 -10000 0 -0.12 13 13
CALM1 0.035 0.014 -10000 0 -10000 0 0
JUN 0.037 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.021 0.02 -10000 0 -0.11 10 10
FOSL1 0.033 0.011 -10000 0 0 53 53
CREM 0.026 0.016 -10000 0 0 147 147
Jun/NFAT1-c-4/p21SNFT 0.056 0.071 0.26 13 -0.18 4 17
FOS 0.027 0.019 -10000 0 -10000 0 0
IFNG 0.009 0.11 0.36 15 -0.25 1 16
AP-1/NFAT1-c-4 0.09 0.12 0.37 7 -0.27 3 10
FASLG 0.009 0.11 0.34 16 -0.25 1 17
NFAT1-c-4/ICER1 0.039 0.051 0.21 11 -10000 0 11
IL2RA 0.001 0.086 0.37 3 -10000 0 3
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 10 10
CSF2 0.009 0.11 0.34 16 -0.24 3 19
JunB/Fra1/NFAT1-c-4 0.055 0.06 0.22 6 -0.19 1 7
IL4 0.009 0.11 0.34 16 -0.25 1 17
IL2 0.013 0.086 -10000 0 -0.84 5 5
IL3 0.033 0.075 -10000 0 -0.58 7 7
FKBP1A 0.032 0.012 -10000 0 0 63 63
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.039 0.008 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.06 0.039 -10000 0 -0.12 20 20
HDAC3 0.036 0.004 -10000 0 0 7 7
Ran/GTP/Exportin 1/HDAC4 -0.03 0.023 -10000 0 -0.11 35 35
GATA1/HDAC4 0.047 0.035 -10000 0 -0.14 15 15
GATA1/HDAC5 0.053 0.012 -10000 0 -0.14 1 1
GATA2/HDAC5 0.05 0.016 -10000 0 -0.14 1 1
HDAC5/BCL6/BCoR 0.052 0.051 -10000 0 -0.13 28 28
HDAC9 0.022 0.018 -10000 0 0 207 207
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.029 -10000 0 -0.12 15 15
HDAC4/ANKRA2 0.044 0.041 -10000 0 -0.15 20 20
HDAC5/YWHAB 0.047 0.029 -10000 0 -0.16 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.034 -10000 0 -0.15 21 21
GATA2 0.035 0.008 -10000 0 0 23 23
HDAC4/RFXANK 0.038 0.05 -10000 0 -0.15 30 30
BCOR 0.034 0.009 -10000 0 0 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.036 0.006 -10000 0 0 14 14
GNB1/GNG2 0.021 0.031 -10000 0 -0.13 20 20
Histones 0.023 0.066 -10000 0 -0.17 38 38
ADRBK1 0.036 0.005 -10000 0 0 10 10
HDAC4 0.035 0.009 -10000 0 0 30 30
XPO1 0.036 0.004 -10000 0 0 5 5
HDAC5/ANKRA2 0.05 0.025 -10000 0 -0.14 7 7
HDAC4/Ubc9 0.046 0.035 -10000 0 -0.14 15 15
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.047 0.031 -10000 0 -0.14 11 11
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.037 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.044 0.039 -10000 0 -0.14 18 18
CAMK4 0.036 0.005 -10000 0 0 8 8
Tubulin/HDAC6 0.036 0.044 -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 0.034 0.01 -10000 0 0 41 41
GATA1 0.037 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.035 0.008 -10000 0 0 27 27
NR3C1 0.035 0.007 -10000 0 0 22 22
SUMO1/HDAC4 0.033 0.059 -10000 0 -0.24 6 6
SRF 0.037 0.002 -10000 0 0 1 1
HDAC4/YWHAB 0.041 0.043 -10000 0 -0.16 20 20
Tubulin 0.015 0.042 -10000 0 -0.13 38 38
HDAC4/14-3-3 E 0.042 0.045 -10000 0 -0.15 24 24
GNB1 0.035 0.007 -10000 0 0 20 20
RANGAP1 0.033 0.011 -10000 0 0 46 46
BCL6/BCoR 0.036 0.047 -10000 0 -0.14 28 28
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.038 -10000 0 -0.13 16 16
HDAC4/SRF 0.066 0.036 -10000 0 -0.13 14 14
HDAC4/ER alpha 0.044 0.036 -10000 0 -0.14 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.023 0.066 -10000 0 -0.17 38 38
cell motility 0.036 0.044 -10000 0 -0.12 38 38
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.036 0.004 -10000 0 0 6 6
HDAC7/HDAC3 0.027 0.008 -10000 0 -0.13 1 1
BCL6 0.032 0.013 -10000 0 0 71 71
HDAC4/CaMK II delta B 0.035 0.009 -10000 0 0 30 30
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 0.035 0.009 -10000 0 0 30 30
HDAC6/HDAC11 0.054 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.06 -10000 0 -0.16 21 21
NPC 0.017 0.021 -10000 0 -0.09 18 18
MEF2C 0.035 0.008 -10000 0 0 28 28
RAN 0.036 0.005 -10000 0 0 10 10
HDAC4/MEF2C 0.093 0.055 -10000 0 -0.12 26 26
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.037 0.002 -10000 0 0 2 2
TUBB2A 0.034 0.01 -10000 0 0 45 45
HDAC11 0.036 0.005 -10000 0 0 8 8
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 25 25
ANKRA2 0.036 0.006 -10000 0 0 13 13
RFXANK 0.034 0.01 -10000 0 0 44 44
nuclear import -0.028 0.059 0.21 26 -10000 0 26
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.036 0.007 -10000 0 0 17 17
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0 -10000 0 -10000 0 0
monocyte activation -0.068 0.16 -10000 0 -0.34 135 135
MAP2K2 0.019 0.039 -10000 0 -0.59 2 2
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.002 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -10000 0 0
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B 0 0.04 0.081 71 -0.076 57 128
Channel 0.023 0.004 -10000 0 -10000 0 0
NLRP1 -0.001 0 -10000 0 -10000 0 0
CALM1 0.033 0.012 -10000 0 0 57 57
negative regulation of phagocytosis -0.02 0.12 -10000 0 -0.41 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0 -10000 0 -10000 0 0
MAPK3 -0.009 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.003 -10000 0 -10000 0 0
PGR -0.009 0.002 -10000 0 -10000 0 0
PA/Cellular Receptors 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.002 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
macrophage activation -0.012 0.011 0.068 8 -10000 0 8
TNF 0.036 0.003 -10000 0 0 4 4
VCAM1 -0.068 0.16 -10000 0 -0.34 134 134
platelet activation -0.02 0.12 -10000 0 -0.41 44 44
MAPKKK cascade 0.003 0.02 0.065 3 -0.069 29 32
IL18 -0.005 0.036 0.086 40 -0.076 60 100
negative regulation of macrophage activation -0.002 0 -10000 0 -10000 0 0
LEF -0.002 0 -10000 0 -10000 0 0
CASP1 0.003 0.004 0.025 13 -10000 0 13
mol:cAMP -0.02 0.12 -10000 0 -0.41 44 44
necrosis -0.002 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.047 0.065 -10000 0 -10000 0 0
MKNK1 0.034 0.009 -10000 0 0 35 35
MAPK14 0.047 0.037 0.16 3 -0.083 22 25
ATF2/c-Jun -0.001 0.094 -10000 0 -0.32 32 32
MAPK11 0.043 0.039 0.16 3 -0.083 22 25
MITF 0.031 0.049 0.17 8 -0.2 7 15
MAPKAPK5 0.034 0.039 0.22 1 -10000 0 1
KRT8 0.035 0.04 0.18 8 -10000 0 8
MAPKAPK3 0.035 0.007 -10000 0 0 19 19
MAPKAPK2 0.034 0.01 -10000 0 0 43 43
p38alpha-beta/CK2 0.062 0.057 0.23 3 -10000 0 3
CEBPB 0.024 0.069 0.18 16 -0.21 26 42
SLC9A1 0.032 0.041 -10000 0 -0.26 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.031 0.055 0.26 4 -0.26 2 6
p38alpha-beta/MNK1 0.064 0.069 -10000 0 -0.15 18 18
JUN -0.005 0.092 -10000 0 -0.33 31 31
PPARGC1A 0.032 0.057 0.23 2 -0.21 13 15
USF1 0.028 0.038 0.18 3 -10000 0 3
RAB5/GDP/GDI1 0.012 0.078 -10000 0 -0.22 26 26
NOS2 0.028 0.037 0.18 3 -10000 0 3
DDIT3 0.029 0.062 0.17 10 -0.2 20 30
RAB5A 0.034 0.009 -10000 0 0 32 32
HSPB1 0.084 0.13 0.28 140 -10000 0 140
p38alpha-beta/HBP1 0.053 0.058 0.24 1 -10000 0 1
CREB1 0.023 0.071 0.23 1 -0.23 2 3
RAB5/GDP 0.019 0.034 -10000 0 -0.13 24 24
EIF4E -0.015 0.057 0.2 8 -0.2 6 14
RPS6KA4 0.034 0.039 0.22 1 -10000 0 1
PLA2G4A -0.015 0.053 0.2 4 -0.2 10 14
GDI1 0.024 0.059 0.19 2 -0.23 17 19
TP53 0.01 0.051 0.17 10 -10000 0 10
RPS6KA5 0.034 0.042 0.22 1 -0.19 1 2
ESR1 0.032 0.038 0.22 1 -10000 0 1
HBP1 0.025 0.017 -10000 0 0 164 164
MEF2C 0.031 0.049 0.22 1 -0.22 7 8
MEF2A 0.031 0.047 0.22 1 -0.21 6 7
EIF4EBP1 0.019 0.076 0.23 1 -0.34 3 4
KRT19 0.035 0.04 0.21 2 -10000 0 2
ELK4 0.031 0.037 0.17 1 -10000 0 1
ATF6 0.033 0.038 -10000 0 -10000 0 0
ATF1 0.018 0.073 0.23 1 -0.3 2 3
p38alpha-beta/MAPKAPK2 0.07 0.056 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.072 0.058 0.23 2 -0.14 2 4
Arf6 trafficking events

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
SLC2A4 0.036 0.006 -10000 0 0 12 12
CLTC 0.011 0.088 -10000 0 -0.31 29 29
calcium ion-dependent exocytosis 0.017 0.064 0.13 1 -0.21 19 20
Dynamin 2/GTP 0.026 0.011 -10000 0 -0.1 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.003 0.079 -10000 0 -0.28 29 29
CPE -0.015 0.009 -10000 0 -0.12 1 1
CTNNB1 0.036 0.006 -10000 0 0 15 15
membrane fusion 0.02 0.063 -10000 0 -0.16 31 31
CTNND1 -0.019 0.011 0.087 1 -0.18 1 2
DNM2 0.035 0.008 -10000 0 0 27 27
mol:PI-4-5-P2 0.011 0.065 0.15 7 -0.22 19 26
TSHR -0.016 0.009 0.092 1 -0.12 1 2
INS 0.01 0.086 -10000 0 -0.44 16 16
BIN1 0.031 0.013 -10000 0 0 76 76
mol:Choline 0.02 0.063 -10000 0 -0.16 31 31
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.005 -10000 0 -0.11 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.009 -10000 0 0 29 29
mol:Ca2+ 0.026 0.011 -10000 0 -0.1 1 1
JUP 0.012 0.069 -10000 0 -0.26 23 23
ASAP2/amphiphysin II 0.028 0.046 -10000 0 -0.11 48 48
ARF6/GTP 0.025 0.009 -10000 0 -0.13 1 1
CDH1 0.009 0.072 -10000 0 -0.26 26 26
clathrin-independent pinocytosis 0.025 0.009 -10000 0 -0.13 1 1
MAPK8IP3 0.036 0.004 -10000 0 0 7 7
positive regulation of endocytosis 0.025 0.009 -10000 0 -0.13 1 1
EXOC2 0.036 0.006 -10000 0 0 15 15
substrate adhesion-dependent cell spreading 0.004 0.053 -10000 0 -0.31 5 5
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.034 0.01 -10000 0 0 37 37
regulation of calcium-dependent cell-cell adhesion -0.038 0.077 0.27 23 -10000 0 23
positive regulation of phagocytosis -0.015 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.046 0.015 -10000 0 -0.12 1 1
ACAP1 0.021 0.061 -10000 0 -0.21 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.004 0.055 -10000 0 -0.27 14 14
clathrin heavy chain/ACAP1 0.016 0.083 0.2 8 -0.23 30 38
JIP4/KLC1 0.036 0.036 -10000 0 -0.11 26 26
EXOC1 0.033 0.011 -10000 0 0 50 50
exocyst 0.003 0.052 -10000 0 -0.31 5 5
RALA/GTP 0.013 0.029 -10000 0 -0.13 16 16
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.039 -10000 0 -0.12 26 26
receptor recycling 0.025 0.009 -10000 0 -0.13 1 1
CTNNA1 -0.02 0.011 0.087 1 -0.18 1 2
NME1 -0.009 0.005 -10000 0 -0.11 1 1
clathrin coat assembly 0.011 0.088 -10000 0 -0.3 29 29
IL2RA 0.007 0.066 -10000 0 -0.33 14 14
VAMP3 -0.015 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.031 0.082 -10000 0 -0.22 30 30
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0 0.038 -10000 0 -0.19 14 14
PLD2 0 0.038 -10000 0 -0.19 14 14
EXOC5 0.03 0.014 -10000 0 0 87 87
PIP5K1C 0.009 0.061 -10000 0 -0.22 16 16
SDC1 0.013 0.073 -10000 0 -0.26 26 26
ARF6/GDP 0.026 0.006 -10000 0 0 29 29
EXOC7 0.036 0.005 -10000 0 0 11 11
E-cadherin/beta catenin 0.04 0.08 -10000 0 -0.28 23 23
mol:Phosphatidic acid 0.02 0.063 -10000 0 -0.16 31 31
endocytosis -0.026 0.045 0.11 48 -10000 0 48
SCAMP2 0.035 0.008 -10000 0 0 28 28
ADRB2 0.01 0.087 0.23 1 -0.3 28 29
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 0.09 1 -0.1 1 2
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.004 0.084 -10000 0 -0.3 29 29
RALA 0.024 0.018 -10000 0 0 182 182
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.084 0.22 1 -0.26 28 29
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.028 -10000 0 -0.13 11 11
VEGFR1 homodimer/NRP1 -0.014 0.016 -10000 0 -10000 0 0
mol:DAG -0.018 0.032 0.19 1 -10000 0 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.017 -10000 0 -10000 0 0
CaM/Ca2+ -0.023 0.041 0.16 3 -0.2 3 6
HIF1A 0.04 0.013 -10000 0 -10000 0 0
GAB1 0.033 0.011 -10000 0 0 55 55
AKT1 -0.032 0.088 0.2 7 -0.3 27 34
PLCG1 -0.018 0.032 0.19 1 -10000 0 1
NOS3 0.007 0.067 -10000 0 -0.3 8 8
CBL 0.036 0.005 -10000 0 0 8 8
mol:NO 0.014 0.076 0.23 1 -0.3 7 8
FLT1 0.016 0.008 -10000 0 -10000 0 0
PGF 0.031 0.013 -10000 0 0 74 74
VEGFR1 homodimer/NRP2/VEGFR121 0.03 0.025 -10000 0 -0.11 11 11
CALM1 0.033 0.012 -10000 0 0 57 57
PIK3CA 0.031 0.014 -10000 0 0 82 82
eNOS/Hsp90 -0.001 0.069 -10000 0 -0.29 7 7
endothelial cell proliferation -0.002 0.052 0.2 4 -0.25 3 7
mol:Ca2+ -0.018 0.032 0.15 3 -10000 0 3
MAPK3 -0.027 0.033 0.15 3 -10000 0 3
MAPK1 -0.027 0.033 0.15 1 -0.19 1 2
PIK3R1 0.032 0.012 -10000 0 0 63 63
PLGF homodimer 0.031 0.013 -10000 0 0 74 74
PRKACA 0.035 0.008 -10000 0 0 24 24
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.018 -10000 0 0 288 288
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.014 0.016 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.025 0.048 0.22 1 -0.19 1 2
PI3K 0.036 0.078 -10000 0 -0.2 15 15
PRKCA -0.023 0.031 0.17 1 -10000 0 1
PRKCB -0.017 0.029 0.17 1 -10000 0 1
VEGFR1 homodimer/PLGF homodimer 0.03 0.029 -10000 0 -0.13 11 11
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.036 0.004 -10000 0 0 7 7
mol:IP3 -0.018 0.032 0.19 1 -10000 0 1
RASA1 -0.026 0.027 0.15 3 -0.2 5 8
NRP2 0.036 0.005 -10000 0 0 8 8
VEGFR1 homodimer 0.016 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.036 0.004 -10000 0 0 7 7
NCK1 0.035 0.008 -10000 0 0 27 27
eNOS/Caveolin-1 0.001 0.072 -10000 0 -0.28 16 16
PTPN11 0.036 0.005 -10000 0 0 11 11
mol:PI-3-4-5-P3 0.035 0.077 -10000 0 -0.2 15 15
mol:L-citrulline 0.014 0.076 0.23 1 -0.3 7 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.04 0.044 -10000 0 -0.14 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.029 -10000 0 -0.2 1 1
CD2AP 0.034 0.01 -10000 0 0 40 40
PI3K/GAB1 0.042 0.088 -10000 0 -0.2 22 22
PDPK1 -0.029 0.067 0.24 4 -0.2 13 17
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.029 -10000 0 -0.2 1 1
mol:NADP 0.014 0.076 0.23 1 -0.3 7 8
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.043 -10000 0 -0.13 10 10
VEGFR1 homodimer/NRP2 0.032 0.028 -10000 0 -0.13 11 11
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.033 0.021 0.078 8 -0.059 18 26
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.08 -10000 0 -0.26 14 14
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.011 -10000 0 -0.13 2 2
NFKBIA -0.033 0.047 0.2 1 -0.28 14 15
BIRC2 0.036 0.006 -10000 0 0 12 12
IKBKB 0.036 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 0.073 -10000 0 -0.26 9 9
NEMO/A20/RIP2 0.036 0.006 -10000 0 0 14 14
XPO1 0.036 0.004 -10000 0 0 5 5
NEMO/ATM 0.039 0.055 -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 0.023 -10000 0 -0.15 6 6
IKK complex/ELKS 0.028 0.052 -10000 0 -0.25 7 7
BCL10/MALT1/TRAF6 0.063 0.035 -10000 0 -0.13 10 10
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.033 0.02 0.078 9 -0.056 18 27
RELA 0.034 0.021 0.078 9 -0.073 15 24
MALT1 0.034 0.009 -10000 0 0 34 34
cIAP1/UbcH5C 0.05 0.028 -10000 0 -0.18 6 6
ATM 0.034 0.01 -10000 0 0 37 37
TNF/TNFR1A 0.035 0.056 -10000 0 -0.14 43 43
TRAF6 0.036 0.005 -10000 0 0 10 10
PRKCA 0.036 0.004 -10000 0 0 6 6
CHUK 0.025 0.017 -10000 0 0 165 165
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 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.03 0.055 0.2 9 -0.28 14 23
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.021 0.078 8 -0.059 18 26
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
IKK complex 0.04 0.061 -10000 0 -0.26 7 7
CYLD 0.036 0.006 -10000 0 0 14 14
IKK complex/PKC alpha 0.05 0.067 -10000 0 -0.26 7 7
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.03 0.15 -10000 0 -0.99 10 10
CLOCK 0.033 0.019 -10000 0 -0.067 10 10
TIMELESS/CRY2 0.024 0.16 -10000 0 -1 10 10
DEC1/BMAL1 0.033 0.057 -10000 0 -0.13 49 49
ATR 0.035 0.008 -10000 0 0 25 25
NR1D1 0.014 0.066 -10000 0 -0.38 2 2
ARNTL 0.032 0.02 -10000 0 -0.069 8 8
TIMELESS 0.001 0.16 -10000 0 -1.1 10 10
NPAS2 0.037 0.017 -10000 0 -0.067 10 10
CRY2 0.035 0.007 -10000 0 0 21 21
mol:CO -0.01 0.027 0.13 10 -0.1 2 12
CHEK1 0.033 0.011 -10000 0 0 50 50
mol:HEME 0.01 0.027 0.1 2 -0.13 10 12
PER1 0.033 0.011 -10000 0 0 53 53
BMAL/CLOCK/NPAS2 0.056 0.076 0.23 1 -0.14 51 52
BMAL1/CLOCK 0.011 0.12 -10000 0 -0.52 17 17
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 0.1 2 -0.13 10 12
PER1/TIMELESS 0.022 0.16 -10000 0 -1 10 10
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.036 0.006 -10000 0 0 16 16
ceramide signaling 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
MAP4K4 0.004 0.083 -10000 0 -0.28 22 22
BAG4 0.036 0.005 -10000 0 0 11 11
BAD -0.004 0.033 0.1 2 -0.14 11 13
NFKBIA 0.033 0.012 -10000 0 0 57 57
BIRC3 0.031 0.014 -10000 0 0 82 82
BAX 0.001 0.044 0.19 13 -0.14 9 22
EnzymeConsortium:3.1.4.12 0.004 0.021 0.061 2 -0.076 12 14
IKBKB -0.005 0.082 0.2 3 -0.29 18 21
MAP2K2 -0.008 0.052 0.18 23 -0.16 6 29
MAP2K1 -0.015 0.039 0.17 5 -0.17 6 11
SMPD1 0.003 0.029 0.11 1 -0.12 15 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.012 0.078 -10000 0 -0.32 10 10
MAP2K4 -0.007 0.036 0.16 4 -0.15 5 9
protein ubiquitination -0.007 0.082 -10000 0 -0.3 18 18
EnzymeConsortium:2.7.1.37 -0.014 0.046 0.17 8 -0.18 6 14
response to UV 0 0 0.002 4 -0.002 1 5
RAF1 -0.01 0.038 0.18 5 -0.15 9 14
CRADD 0.036 0.005 -10000 0 0 11 11
mol:ceramide 0.003 0.032 0.11 1 -0.12 13 14
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.033 -10000 0 -0.12 18 18
MADD 0.035 0.006 -10000 0 0 15 15
MAP3K1 -0.002 0.033 0.15 2 -0.14 8 10
TRADD 0.036 0.005 -10000 0 0 10 10
RELA/p50 0.036 0.004 -10000 0 0 7 7
MAPK3 -0.006 0.046 0.18 9 -0.17 5 14
MAPK1 -0.013 0.056 0.18 8 -0.2 13 21
p50/RELA/I-kappa-B-alpha 0.043 0.039 -10000 0 -0.14 18 18
FADD 0.009 0.076 -10000 0 -0.31 9 9
KSR1 -0.004 0.031 0.11 1 -0.14 8 9
MAPK8 -0.009 0.031 0.16 3 -0.15 3 6
TRAF2 0.036 0.006 -10000 0 0 16 16
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.009 0.077 -10000 0 -0.3 16 16
TNF R/SODD 0.035 0.055 -10000 0 -0.14 42 42
TNF 0.036 0.003 -10000 0 0 4 4
CYCS 0.016 0.052 0.15 19 -0.14 9 28
IKBKG -0.006 0.08 -10000 0 -0.29 18 18
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.015 0.085 -10000 0 -0.3 17 17
RELA 0.036 0.004 -10000 0 0 7 7
RIPK1 0.035 0.007 -10000 0 0 20 20
AIFM1 -0.005 0.039 0.13 11 -0.14 12 23
TNF/TNF R/SODD 0.053 0.056 -10000 0 -0.13 41 41
TNFRSF1A 0.032 0.012 -10000 0 0 65 65
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.038 0.071 -10000 0 -0.57 6 6
NSMAF 0.007 0.084 0.21 5 -0.3 17 22
response to hydrogen peroxide 0 0 0.002 4 -0.002 1 5
BCL2 0.035 0.007 -10000 0 0 20 20
Arf1 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
coatomer protein complex 0.008 0.034 0.14 27 -0.18 3 30
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.01 0.047 0.12 2 -0.18 9 11
AP2 0.021 0.028 -10000 0 -0.13 15 15
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.029 0.036 -10000 0 -0.12 14 14
CLTB 0.036 0.005 -10000 0 0 9 9
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0.03 -10000 0 -0.19 9 9
CD4 0.031 0.013 -10000 0 0 74 74
CLTA 0.034 0.01 -10000 0 0 41 41
mol:GTP -0.003 0.002 -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 0.018 -10000 0 -0.1 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.031 -10000 0 -0.18 9 9
mol:Choline 0.008 0.019 0.11 11 -10000 0 11
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.035 0.008 -10000 0 0 24 24
DDEF1 0.006 0.018 0.1 9 -10000 0 9
ARF1/GDP 0.006 0.012 -10000 0 -0.08 5 5
AP2M1 0.034 0.01 -10000 0 0 40 40
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.017 0.067 1 -0.12 8 9
Rac/GTP 0.017 0.02 -10000 0 -0.14 5 5
ARF1/GTP/GGA3/ARF-GAP1 0.041 0.025 -10000 0 -0.11 8 8
ARFIP2 0.032 0.015 -10000 0 -0.038 13 13
COPA 0.036 0.006 -10000 0 0 14 14
RAC1 0.025 0.017 -10000 0 0 163 163
ARF1/GTP/coatomer protein complex 0.005 0.043 -10000 0 -0.18 10 10
ARF1/GTP/ARHGAP10 0.021 0.016 -10000 0 -0.12 6 6
GGA3 0.036 0.005 -10000 0 0 8 8
ARF1/GTP/Membrin 0.027 0.028 -10000 0 -0.24 4 4
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.006 0.034 -10000 0 -0.18 10 10
ARF1/GDP/Membrin 0.03 0.031 -10000 0 -0.27 4 4
Arfaptin 2/Rac/GDP 0.028 0.035 -10000 0 -0.12 14 14
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 0.02 -10000 0 -0.13 5 5
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.004 0.058 -10000 0 -0.19 29 29
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 0.037 -10000 0 -0.1 10 10
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.019 0.11 11 -10000 0 11
KDEL Receptor/Ligand/ARF-GAP1 -0.011 0.003 0 41 -10000 0 41
GOSR2 0.015 0.028 -10000 0 -0.32 3 3
USO1 0.002 0.006 0.03 17 -0.031 4 21
GBF1 -0.075 0.15 -10000 0 -0.31 141 141
ARF1/GTP/Arfaptin 2 0.042 0.034 -10000 0 -0.12 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.046 -10000 0 -0.13 35 35
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.054 0.018 -10000 0 -10000 0 0
KIRREL 0.038 0.01 0.075 1 -0.041 1 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.054 0.018 -10000 0 -10000 0 0
PLCG1 0.034 0.01 -10000 0 0 37 37
ARRB2 0.035 0.008 -10000 0 0 25 25
WASL 0.025 0.017 -10000 0 0 167 167
Nephrin/NEPH1/podocin/CD2AP 0.084 0.05 0.2 1 -0.12 17 18
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.037 -10000 0 -0.22 6 6
FYN -0.008 0.046 0.18 24 -10000 0 24
mol:Ca2+ 0.082 0.039 0.19 1 -0.13 3 4
mol:DAG 0.084 0.04 0.2 1 -0.13 3 4
NPHS2 0.039 0.008 0.075 1 -0.041 1 2
mol:IP3 0.084 0.04 0.2 1 -0.13 3 4
regulation of endocytosis 0.052 0.051 -10000 0 -0.14 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.069 0.027 0.15 8 -10000 0 8
establishment of cell polarity 0.054 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.095 0.059 -10000 0 -0.14 17 17
Nephrin/NEPH1/beta Arrestin2 0.055 0.052 -10000 0 -0.14 4 4
NPHS1 0.039 0.01 0.077 7 -10000 0 7
Nephrin/NEPH1/podocin 0.052 0.045 0.21 1 -0.067 51 52
TJP1 0.034 0.009 -10000 0 0 33 33
NCK1 0.035 0.008 -10000 0 0 27 27
NCK2 0.036 0.007 -10000 0 0 17 17
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.085 0.041 0.2 1 -0.13 3 4
CD2AP 0.034 0.01 -10000 0 0 40 40
Nephrin/NEPH1/podocin/GRB2 0.087 0.043 0.2 1 -0.13 7 8
GRB2 0.035 0.007 -10000 0 0 18 18
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.051 0.18 26 -10000 0 26
cytoskeleton organization -0.01 0.036 0.17 9 -0.2 3 12
Nephrin/NEPH1 0.046 0.016 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.065 0.038 -10000 0 -0.14 9 9
Signaling events mediated by the Hedgehog family

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
TGFB2 0.035 0.032 -10000 0 -10000 0 0
IHH 0.052 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 0.014 0.028 -10000 0 -0.11 16 16
LRPAP1 0.036 0.007 -10000 0 0 17 17
dorsoventral neural tube patterning -0.014 0.027 0.11 16 -10000 0 16
SMO/beta Arrestin2 0.09 0.063 0.26 12 -10000 0 12
SMO 0.025 0.031 0.19 1 -10000 0 1
AKT1 -0.008 0.13 -10000 0 -0.44 30 30
ARRB2 0.035 0.008 -10000 0 0 25 25
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.036 0.005 -10000 0 0 10 10
heart looping 0.026 0.034 0.22 3 -10000 0 3
STIL 0.05 0.092 0.19 145 -10000 0 145
DHH N/PTCH2 0.027 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.017 0.021 0.12 21 -10000 0 21
PIK3CA 0.031 0.014 -10000 0 0 82 82
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.038 0.048 -10000 0 -10000 0 0
determination of left/right symmetry 0.026 0.034 0.22 3 -10000 0 3
PIK3R1 0.032 0.012 -10000 0 0 63 63
skeletal system development 0.038 0.048 -10000 0 -10000 0 0
IHH N/Hhip 0.034 0.008 -10000 0 -10000 0 0
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.026 0.034 0.22 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.035 0.007 -10000 0 0 18 18
PI3K 0.018 0.076 -10000 0 -0.16 72 72
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.031 0.014 -10000 0 0 86 86
somite specification 0.026 0.034 0.22 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.018 0.025 0.17 1 -10000 0 1
SHH Np/Cholesterol/PTCH2 0.021 0.016 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.02 0.016 -10000 0 -10000 0 0
SHH -0.015 0.012 0.093 1 -10000 0 1
catabolic process 0.02 0.026 0.14 22 -10000 0 22
SMO/Vitamin D3 0.022 0.037 0.19 14 -10000 0 14
SHH Np/Cholesterol/Hhip -0.01 0.008 -10000 0 -10000 0 0
LRP2 0.036 0.006 -10000 0 0 12 12
receptor-mediated endocytosis 0.023 0.039 0.18 16 -10000 0 16
SHH Np/Cholesterol/BOC -0.01 0.008 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.021 0.016 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.01 0.008 -10000 0 -10000 0 0
mol:Vitamin D3 0.075 0.087 0.2 163 -10000 0 163
IHH N/PTCH2 0.061 0.011 -10000 0 -10000 0 0
CDON 0.036 0.004 -10000 0 0 7 7
IHH N/PTCH1 0.046 0.028 0.17 21 -10000 0 21
Megalin/LRPAP1 0.049 0.029 -10000 0 -0.14 10 10
PTCH2 0.036 0.005 -10000 0 0 8 8
SHH Np/Cholesterol 0.012 0.009 -10000 0 -10000 0 0
PTCH1 0.02 0.026 0.14 22 -10000 0 22
HHIP 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.037 0.028 -9999 0 -0.097 20 20
MAPK9 0.008 0.001 -9999 0 0 13 13
adrenocorticotropin secretion -0.011 0.002 0 17 -10000 0 17
GNB1/GNG2 0.02 0.026 -9999 0 -0.11 20 20
GNB1 0.035 0.007 -9999 0 0 20 20
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.008 0.001 -9999 0 0 5 5
Gs family/GTP 0.023 0.004 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.003 0 -9999 0 -10000 0 0
GNAL 0.036 0.006 -9999 0 0 13 13
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.036 0.007 -9999 0 0 17 17
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.003 -9999 0 0 143 143
MAPK11 0.007 0.002 -9999 0 0 54 54
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.035 0.007 -10000 0 0 21 21
Ran/GTP/Exportin 1/HDAC4 -0.033 0.031 -10000 0 -0.16 20 20
MDM2/SUMO1 0.034 0.054 -10000 0 -0.21 6 6
HDAC4 0.035 0.009 -10000 0 0 30 30
Ran/GTP/Exportin 1/HDAC1 -0.031 0.03 -10000 0 -0.16 18 18
SUMO1 0.036 0.003 -10000 0 0 4 4
NPC/RanGAP1/SUMO1 0.005 0.035 -10000 0 -0.15 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.009 0.041 -10000 0 -0.16 21 21
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 0 10 10
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.008 -10000 0 0 25 25
SUMO1/HDAC4 0.033 0.059 -10000 0 -0.24 6 6
SUMO1/HDAC1 0.036 0.056 -10000 0 -0.22 6 6
RANGAP1 0.033 0.011 -10000 0 0 46 46
MDM2/SUMO1/SUMO1 0.077 0.048 -10000 0 -0.12 17 17
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.007 0.034 -10000 0 -0.15 21 21
Ran/GTP 0.019 0.05 -10000 0 -0.15 21 21
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.01 -10000 0 0 45 45
UBE2I 0.036 0.004 -10000 0 0 6 6
Ran/GTP/Exportin 1 0.013 0.052 0.2 1 -0.27 5 6
NPC 0.017 0.021 -10000 0 -0.09 18 18
PIAS2 0.035 0.007 -10000 0 0 19 19
PIAS1 0.035 0.008 -10000 0 0 25 25
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL 0.041 0.2 0.61 1 -0.7 17 18
PCK1 0.045 0.12 0.43 2 -0.67 2 4
HNF4A 0.052 0.17 0.69 4 -0.71 6 10
KCNJ11 0.067 0.18 0.48 4 -0.59 16 20
AKT1 0.058 0.13 0.44 1 -0.38 16 17
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.08 0.19 0.57 3 -0.61 13 16
NKX2-1 0.03 0.11 0.28 3 -0.34 13 16
ACADM 0.05 0.18 0.53 2 -0.75 9 11
TAT 0.051 0.13 0.53 2 -0.64 5 7
CEBPB 0.033 0.015 0.12 1 -10000 0 1
CEBPA 0.031 0.018 0.094 1 -10000 0 1
TTR 0.032 0.19 0.67 3 -0.65 11 14
PKLR 0.056 0.17 0.49 4 -0.69 7 11
APOA1 0.078 0.22 0.65 5 -0.84 7 12
CPT1C 0.055 0.17 0.47 4 -0.57 13 17
ALAS1 0.031 0.24 0.43 1 -1.2 15 16
TFRC 0.021 0.3 0.53 5 -0.96 35 40
FOXF1 0.031 0.013 -10000 0 -10000 0 0
NF1 0.034 0.036 0.11 1 -0.17 15 16
HNF1A (dimer) 0.006 0.005 0.12 1 -10000 0 1
CPT1A 0.052 0.17 0.61 1 -0.69 7 8
HMGCS1 0.057 0.17 0.52 4 -0.65 8 12
NR3C1 0.047 0.02 -10000 0 -10000 0 0
CPT1B 0.053 0.17 0.49 3 -0.69 7 10
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.036 0.006 -10000 0 -10000 0 0
GCK 0.093 0.19 0.52 16 -0.59 8 24
CREB1 0.044 0.013 0.15 1 -10000 0 1
IGFBP1 0.053 0.13 -10000 0 -0.65 4 4
PDX1 0.053 0.11 0.33 4 -0.34 8 12
UCP2 0.023 0.25 0.49 5 -0.69 42 47
ALDOB 0.066 0.19 0.5 3 -0.67 10 13
AFP 0.015 0.033 0.28 2 -10000 0 2
BDH1 0.044 0.2 0.51 2 -0.68 18 20
HADH 0.067 0.18 0.48 4 -0.59 16 20
F2 0.076 0.21 0.78 2 -0.84 7 9
HNF1A 0.006 0.005 0.12 1 -10000 0 1
G6PC 0.009 0.082 0.43 1 -10000 0 1
SLC2A2 0.063 0.13 0.45 1 -0.46 2 3
INS 0.025 0.043 0.19 14 -0.097 34 48
FOXA1 0.014 0.013 0.15 2 -10000 0 2
FOXA3 0.019 0.057 0.2 5 -0.19 23 28
FOXA2 0.1 0.23 0.63 3 -0.67 16 19
ABCC8 0.067 0.19 0.52 2 -0.69 9 11
ALB 0.016 0.033 0.31 1 -10000 0 1
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.036 0.004 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.063 0.022 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.005 0.064 -9999 0 -0.39 13 13
AURKB 0.034 0.01 -9999 0 0 41 41
AURKC 0.036 0.006 -9999 0 0 15 15
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.036 0.005 0 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 3 -9999 0 3
ADCY5 -0.009 0.001 0 3 -9999 0 3
ADCY6 -0.017 0.006 0.086 1 -9999 0 1
ADCY7 -0.014 0.018 0.086 15 -9999 0 15
ADCY1 -0.012 0.009 -10000 0 -9999 0 0
ADCY2 -0.017 0.007 0.086 2 -9999 0 2
ADCY3 -0.009 0.001 0 3 -9999 0 3
ADCY8 -0.006 0.032 0.086 54 -9999 0 54
PRKCE -0.011 0.001 0 3 -9999 0 3
ADCY9 -0.017 0.009 0.086 4 -9999 0 4
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.017 0.043 0.17 11 -9999 0 11
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.036 0.005 -10000 0 0 10 10
GNAT1/GTP 0.026 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.047 0.01 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.048 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.036 0.006 -10000 0 0 13 13
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.069 0.024 -10000 0 -10000 0 0
mol:Na + 0.044 0.015 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.046 0.015 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.055 0.018 -10000 0 -10000 0 0
CNGB1 0.036 0.006 -10000 0 0 14 14
RDH5 0.035 0.007 -10000 0 0 19 19
SAG 0.036 0.005 -10000 0 0 10 10
mol:Ca2+ -0.034 0.026 0.16 8 -10000 0 8
Na + (4 Units) 0.041 0.018 -10000 0 -10000 0 0
RGS9 0.035 0.007 -10000 0 0 18 18
GNB1/GNGT1 0.031 0.038 -10000 0 -0.14 13 13
GNAT1/GDP 0.058 0.022 -10000 0 -0.1 1 1
GUCY2D 0.036 0.006 -10000 0 0 12 12
GNGT1 0.024 0.017 -10000 0 0 170 170
GUCY2F 0.037 0 -10000 0 -10000 0 0
GNB5 0.035 0.007 -10000 0 0 22 22
mol:GMP (4 units) 0.029 0.007 -10000 0 -10000 0 0
mol:11-cis-retinal 0.035 0.007 -10000 0 0 19 19
mol:cGMP 0.029 0.006 -10000 0 -10000 0 0
GNB1 0.035 0.007 -10000 0 0 20 20
Rhodopsin 0.051 0.013 -10000 0 -10000 0 0
SLC24A1 0.036 0.005 -10000 0 0 10 10
CNGA1 0.036 0.005 -10000 0 0 9 9
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.046 0.007 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.008 0.032 -10000 0 -0.15 14 14
GCAP Family/Ca ++ 0.023 0.001 -10000 0 -10000 0 0
PDE6A/B 0.053 0.008 -10000 0 -10000 0 0
mol:Pi 0.045 0.015 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.041 0.042 -10000 0 -0.11 13 13
PDE6B 0.036 0.004 -10000 0 0 5 5
PDE6A 0.036 0.004 -10000 0 0 7 7
PDE6G 0.037 0.003 -10000 0 0 3 3
RHO 0.036 0.006 -10000 0 0 13 13
PDE6 0.085 0.026 -10000 0 -0.11 1 1
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.047 0.002 -10000 0 -10000 0 0
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.037 0.002 -10000 0 0 1 1
Ephrin A reverse signaling

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

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

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

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1971139/2.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/2008379/1.GetReducedSegments.Finished/GBM.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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