Glioblastoma Multiforme: Paradigm Report
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 95 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 123
FOXM1 transcription factor network 102
Syndecan-4-mediated signaling events 94
Angiopoietin receptor Tie2-mediated signaling 85
Endothelins 84
TCGA08_p53 71
Thromboxane A2 receptor signaling 69
PDGFR-alpha signaling pathway 68
TCGA08_rtk_signaling 68
EGFR-dependent Endothelin signaling events 67
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 123 9359 76 -0.083 0.1 1000 -1000 -0.009 -1000
FOXM1 transcription factor network 102 5225 51 -0.32 0.055 1000 -1000 -0.039 -1000
Syndecan-4-mediated signaling events 94 6354 67 -0.14 0.036 1000 -1000 -0.029 -1000
Angiopoietin receptor Tie2-mediated signaling 85 7494 88 -0.28 0.051 1000 -1000 -0.043 -1000
Endothelins 84 8115 96 -0.14 0.035 1000 -1000 -0.023 -1000
TCGA08_p53 71 500 7 -0.002 0.032 1000 -1000 -0.01 -1000
Thromboxane A2 receptor signaling 69 7341 105 -0.061 0.043 1000 -1000 -0.024 -1000
PDGFR-alpha signaling pathway 68 3025 44 -0.093 0.036 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 68 1780 26 -0.026 0.087 1000 -1000 -0.007 -1000
EGFR-dependent Endothelin signaling events 67 1413 21 -0.004 0.093 1000 -1000 -0.006 -1000
HIF-2-alpha transcription factor network 64 2773 43 -0.066 0.046 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 64 1681 26 -0.008 0.051 1000 -1000 -0.01 -1000
PLK2 and PLK4 events 63 189 3 -0.018 0.035 1000 -1000 -0.018 -1000
Syndecan-3-mediated signaling events 61 2141 35 -0.073 0.076 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 61 3141 51 -0.1 0.068 1000 -1000 -0.021 -1000
Ras signaling in the CD4+ TCR pathway 60 1023 17 -0.001 0.041 1000 -1000 -0.013 -1000
Syndecan-1-mediated signaling events 59 2033 34 -0.009 0.035 1000 -1000 -0.013 -1000
TCGA08_retinoblastoma 59 476 8 -0.046 0.054 1000 -1000 -0.002 -1000
Arf6 signaling events 58 3626 62 -0.004 0.092 1000 -1000 -0.008 -1000
Ceramide signaling pathway 58 4445 76 -0.084 0.07 1000 -1000 -0.019 -1000
S1P5 pathway 58 999 17 -0.014 0.035 1000 -1000 -0.017 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 58 1915 33 -0.049 0.066 1000 -1000 -0.012 -1000
LPA receptor mediated events 57 5865 102 -0.12 0.036 1000 -1000 -0.049 -1000
S1P4 pathway 57 1446 25 -0.016 0.035 1000 -1000 -0.012 -1000
Nongenotropic Androgen signaling 55 2860 52 -0.086 0.059 1000 -1000 -0.021 -1000
Wnt signaling 52 365 7 -0.006 0.036 1000 -1000 -0.007 -1000
Glypican 2 network 51 206 4 0 0.006 1000 -1000 0 -1000
IL2 signaling events mediated by STAT5 51 1123 22 -0.071 0.042 1000 -1000 -0.011 -1000
amb2 Integrin signaling 49 4044 82 -0.017 0.077 1000 -1000 -0.018 -1000
JNK signaling in the CD4+ TCR pathway 47 801 17 -0.14 0.061 1000 -1000 -0.011 -1000
EPO signaling pathway 47 2585 55 -0.001 0.083 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 47 4650 97 -0.12 0.047 1000 -1000 -0.04 -1000
Syndecan-2-mediated signaling events 46 3212 69 -0.026 0.037 1000 -1000 -0.031 -1000
IL23-mediated signaling events 46 2817 60 -0.052 0.15 1000 -1000 -0.034 -1000
E-cadherin signaling in keratinocytes 46 2020 43 -0.035 0.061 1000 -1000 -0.014 -1000
Osteopontin-mediated events 45 1726 38 -0.065 0.049 1000 -1000 -0.017 -1000
FoxO family signaling 45 2922 64 -0.16 0.042 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 43 2670 61 -0.08 0.076 1000 -1000 -0.032 -1000
Ephrin B reverse signaling 43 2109 48 -0.065 0.065 1000 -1000 -0.049 -1000
ErbB2/ErbB3 signaling events 41 2723 65 -0.039 0.036 1000 -1000 -0.037 -1000
Signaling events mediated by PTP1B 41 3149 76 -0.032 0.058 1000 -1000 -0.016 -1000
BCR signaling pathway 41 4120 99 -0.048 0.049 1000 -1000 -0.023 -1000
Reelin signaling pathway 40 2242 56 -0.014 0.065 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 40 1451 36 -0.058 0.055 1000 -1000 -0.043 -1000
IL2 signaling events mediated by PI3K 40 2358 58 -0.068 0.037 1000 -1000 -0.017 -1000
EPHB forward signaling 40 3466 85 -0.051 0.08 1000 -1000 -0.041 -1000
S1P3 pathway 40 1721 42 -0.021 0.036 1000 -1000 -0.009 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 39 2143 54 -0.031 0.068 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 39 1866 47 -0.14 0.047 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 38 4867 125 -0.044 0.058 1000 -1000 -0.037 -1000
IL6-mediated signaling events 38 2869 75 -0.066 0.096 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 38 2595 68 -0.1 0.045 1000 -1000 -0.047 -1000
Class I PI3K signaling events 38 2836 73 -0.05 0.056 1000 -1000 -0.017 -1000
IL12-mediated signaling events 37 3302 87 -0.098 0.099 1000 -1000 -0.028 -1000
Sphingosine 1-phosphate (S1P) pathway 37 1060 28 -0.019 0.035 1000 -1000 -0.018 -1000
BMP receptor signaling 37 3002 81 -0.026 0.056 1000 -1000 -0.012 -1000
Glypican 1 network 37 1821 48 -0.037 0.051 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 37 1378 37 -0.034 0.078 1000 -1000 -0.014 -1000
Regulation of nuclear SMAD2/3 signaling 36 5013 136 -0.2 0.2 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 36 2709 74 -0.11 0.079 1000 -1000 -0.051 -1000
p38 MAPK signaling pathway 36 1608 44 0 0.041 1000 -1000 -0.006 -1000
Hedgehog signaling events mediated by Gli proteins 35 2288 65 -0.025 0.058 1000 -1000 -0.012 -1000
Arf6 downstream pathway 35 1506 43 -0.027 0.051 1000 -1000 -0.029 -1000
mTOR signaling pathway 35 1872 53 -0.03 0.045 1000 -1000 -0.029 -1000
IL1-mediated signaling events 35 2223 62 -0.039 0.073 1000 -1000 -0.037 -1000
IGF1 pathway 35 2015 57 -0.043 0.065 1000 -1000 -0.028 -1000
Plasma membrane estrogen receptor signaling 35 3031 86 -0.069 0.057 1000 -1000 -0.018 -1000
PLK1 signaling events 34 2923 85 -0.043 0.056 1000 -1000 -0.022 -1000
IFN-gamma pathway 34 2326 68 -0.038 0.065 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 34 2377 68 -0.033 0.061 1000 -1000 -0.018 -1000
Signaling events mediated by PRL 34 1164 34 -0.035 0.047 1000 -1000 -0.03 -1000
Noncanonical Wnt signaling pathway 33 860 26 -0.038 0.036 1000 -1000 -0.036 -1000
Regulation of p38-alpha and p38-beta 33 1791 54 -0.008 0.049 1000 -1000 -0.009 -1000
Neurotrophic factor-mediated Trk receptor signaling 33 4035 120 -0.037 0.087 1000 -1000 -0.022 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 32 2759 85 -0.11 0.12 1000 -1000 -0.029 -1000
ErbB4 signaling events 31 2153 69 -0.081 0.059 1000 -1000 -0.021 -1000
PDGFR-beta signaling pathway 31 3100 97 -0.053 0.067 1000 -1000 -0.043 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 31 2457 78 -0.023 0.073 1000 -1000 -0.032 -1000
Caspase cascade in apoptosis 30 2220 74 -0.072 0.056 1000 -1000 -0.022 -1000
LPA4-mediated signaling events 29 348 12 -0.017 0.015 1000 -1000 -0.015 -1000
Signaling events regulated by Ret tyrosine kinase 29 2391 82 -0.052 0.061 1000 -1000 -0.026 -1000
Signaling mediated by p38-gamma and p38-delta 29 449 15 -0.024 0.036 1000 -1000 -0.018 -1000
TCR signaling in naïve CD8+ T cells 29 2778 93 -0.27 0.32 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 29 1341 45 -0.03 0.074 1000 -1000 -0.021 -1000
E-cadherin signaling in the nascent adherens junction 29 2271 76 -0.039 0.089 1000 -1000 -0.033 -1000
Regulation of Telomerase 29 3031 102 -0.025 0.076 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 29 381 13 0 0.067 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 28 652 23 -0.017 0.053 1000 -1000 -0.006 -1000
a4b1 and a4b7 Integrin signaling 28 140 5 0.027 0.052 1000 -1000 0.033 -1000
p75(NTR)-mediated signaling 28 3596 125 -0.025 0.084 1000 -1000 -0.038 -1000
IL4-mediated signaling events 28 2595 91 -0.31 0.059 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class III 28 1159 40 -0.05 0.05 1000 -1000 -0.047 -1000
Insulin Pathway 28 2077 74 -0.034 0.08 1000 -1000 -0.033 -1000
Aurora A signaling 27 1678 60 -0.026 0.057 1000 -1000 -0.018 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 27 2305 83 -0.034 0.066 1000 -1000 -0.015 -1000
Integrins in angiogenesis 26 2259 84 -0.043 0.069 1000 -1000 -0.025 -1000
Aurora B signaling 26 1774 67 -0.033 0.062 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 25 1455 58 -0.059 0.059 1000 -1000 -0.032 -1000
BARD1 signaling events 24 1380 57 -0.062 0.081 1000 -1000 -0.056 -1000
Visual signal transduction: Cones 24 930 38 -0.013 0.058 1000 -1000 -0.012 -1000
Nectin adhesion pathway 23 1498 63 -0.01 0.08 1000 -1000 -0.028 -1000
Glucocorticoid receptor regulatory network 23 2722 114 -0.13 0.059 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class I 23 2399 104 -0.028 0.066 1000 -1000 -0.024 -1000
TRAIL signaling pathway 22 1070 48 -0.023 0.085 1000 -1000 -0.018 -1000
S1P1 pathway 22 802 36 -0.011 0.049 1000 -1000 -0.018 -1000
Calcium signaling in the CD4+ TCR pathway 22 706 31 -0.022 0.081 1000 -1000 -0.024 -1000
E-cadherin signaling events 22 112 5 0.033 0.061 1000 -1000 0.033 -1000
Coregulation of Androgen receptor activity 21 1600 76 -0.018 0.065 1000 -1000 -0.01 -1000
Insulin-mediated glucose transport 21 674 32 -0.018 0.041 1000 -1000 -0.018 -1000
Regulation of Androgen receptor activity 21 1499 70 -0.03 0.066 1000 -1000 -0.025 -1000
IL27-mediated signaling events 19 1000 51 -0.011 0.05 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 18 1404 75 -0.029 0.092 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 18 718 39 -0.073 0.036 1000 -1000 -0.012 -1000
RXR and RAR heterodimerization with other nuclear receptor 18 968 52 -0.044 0.1 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 18 572 31 -0.021 0.036 1000 -1000 -0.019 -1000
VEGFR1 specific signals 18 1034 56 -0.027 0.041 1000 -1000 -0.023 -1000
Circadian rhythm pathway 17 390 22 -0.009 0.053 1000 -1000 -0.024 -1000
ceramide signaling pathway 17 871 49 -0.012 0.052 1000 -1000 -0.02 -1000
Arf6 trafficking events 17 1246 71 -0.038 0.046 1000 -1000 -0.032 -1000
Canonical NF-kappaB pathway 16 644 39 -0.031 0.064 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 15 423 27 -0.032 0.074 1000 -1000 -0.026 -1000
Rapid glucocorticoid signaling 15 319 20 -0.011 0.035 1000 -1000 -0.01 -1000
Arf1 pathway 15 843 54 -0.06 0.044 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 14 495 34 -0.053 0.093 1000 -1000 -0.039 -1000
Signaling events mediated by the Hedgehog family 14 735 52 -0.017 0.078 1000 -1000 -0.021 -1000
Aurora C signaling 14 102 7 0 0.059 1000 -1000 -0.004 -1000
Signaling mediated by p38-alpha and p38-beta 14 639 44 -0.013 0.076 1000 -1000 -0.013 -1000
FOXA2 and FOXA3 transcription factor networks 12 552 46 0 0.099 1000 -1000 -0.02 -1000
Visual signal transduction: Rods 8 426 52 -0.032 0.084 1000 -1000 -0.004 -1000
Class IB PI3K non-lipid kinase events 8 24 3 -0.036 0.036 1000 -1000 -0.033 -1000
Ephrin A reverse signaling 1 13 7 -0.019 0.048 1000 -1000 -0.011 -1000
Total 4932 277358 7203 -6.7 8.3 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 0.037 0.47 0.61 88 -0.75 82 170
HDAC7 -0.001 0.005 -10000 0 -0.051 3 3
HIF1A/ARNT/Cbp/p300/Src-1 -0.03 0.38 0.57 34 -0.69 74 108
SMAD4 0.033 0.013 0.079 11 -10000 0 11
ID2 0.059 0.48 0.63 102 -0.75 82 184
AP1 0.013 0.082 -10000 0 -0.17 73 73
ABCG2 0.022 0.47 0.63 87 -0.76 84 171
HIF1A 0.045 0.13 0.24 75 -0.16 60 135
TFF3 0.051 0.47 0.62 107 -0.75 80 187
GATA2 0.039 0.013 0.073 27 -0.009 16 43
AKT1 0.054 0.14 0.25 87 -0.19 42 129
response to hypoxia 0.009 0.087 0.16 73 -0.12 50 123
MCL1 0.063 0.48 0.63 102 -0.75 81 183
NDRG1 0.004 0.46 0.63 64 -0.75 87 151
SERPINE1 -0.056 0.4 0.58 39 -0.77 79 118
FECH 0.049 0.47 0.63 96 -0.75 81 177
FURIN 0.063 0.48 0.63 105 -0.75 81 186
NCOA2 0.037 0.005 -10000 0 -10000 0 0
EP300 0.074 0.19 0.37 92 -0.3 33 125
HMOX1 -0.014 0.46 0.62 68 -0.77 85 153
BHLHE40 -0.055 0.4 0.55 70 -0.73 84 154
BHLHE41 -0.055 0.4 0.55 70 -0.73 84 154
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.071 0.18 0.35 44 -0.22 44 88
ENG 0.037 0.16 0.31 54 -0.25 19 73
JUN 0.035 0.013 0.063 1 -0.002 41 42
RORA 0.032 0.47 0.62 88 -0.75 83 171
ABCB1 -0.054 0.21 -10000 0 -0.86 25 25
TFRC 0.041 0.48 0.63 92 -0.75 84 176
CXCR4 0.023 0.47 0.62 85 -0.76 86 171
TF -0.071 0.41 0.64 43 -0.75 86 129
CITED2 0.02 0.46 0.62 79 -0.76 82 161
HIF1A/ARNT -0.083 0.44 0.64 15 -0.88 73 88
LDHA -0.066 0.28 -10000 0 -0.99 37 37
ETS1 0.066 0.48 0.63 105 -0.76 79 184
PGK1 0.058 0.49 0.63 104 -0.77 81 185
NOS2 -0.055 0.4 0.55 70 -0.73 84 154
ITGB2 0.013 0.46 0.62 81 -0.76 85 166
ALDOA 0.067 0.48 0.63 106 -0.75 82 188
Cbp/p300/CITED2 -0.027 0.45 0.6 60 -0.81 79 139
FOS 0.026 0.018 -10000 0 0 148 148
HK2 0.067 0.48 0.63 107 -0.75 82 189
SP1 0.033 0.057 0.1 39 -0.14 37 76
GCK 0.1 0.25 0.58 47 -0.51 7 54
HK1 0.017 0.46 0.63 81 -0.75 81 162
NPM1 0.063 0.48 0.64 97 -0.75 80 177
EGLN1 0.06 0.48 0.64 91 -0.76 80 171
CREB1 0.031 0.035 -10000 0 -0.1 29 29
PGM1 0.061 0.48 0.64 103 -0.75 82 185
SMAD3 0.037 0.008 0.079 12 -10000 0 12
EDN1 0.056 0.22 0.46 31 -0.52 22 53
IGFBP1 0.003 0.43 0.63 64 -0.76 73 137
VEGFA -0.017 0.34 0.49 69 -0.58 79 148
HIF1A/JAB1 0.045 0.1 0.2 55 -0.16 26 81
CP -0.027 0.45 0.61 66 -0.76 87 153
CXCL12 -0.031 0.42 0.61 49 -0.75 79 128
COPS5 0.036 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.04 0.05 0.14 6 -0.14 30 36
BNIP3 -0.006 0.45 0.66 65 -0.76 79 144
EGLN3 0.013 0.45 0.62 77 -0.75 81 158
CA9 -0.01 0.43 0.61 61 -0.75 79 140
TERT 0.06 0.48 0.63 103 -0.75 81 184
ENO1 0.057 0.48 0.65 95 -0.76 80 175
PFKL 0.065 0.48 0.63 105 -0.75 81 186
NCOA1 0.033 0.01 -10000 0 0 43 43
ADM -0.014 0.46 0.62 69 -0.76 88 157
ARNT 0.049 0.12 0.24 77 -0.14 58 135
HNF4A 0.038 0.009 -10000 0 -10000 0 0
ADFP -0.024 0.44 0.62 59 -0.77 84 143
SLC2A1 0.017 0.37 0.55 68 -0.61 78 146
LEP 0.025 0.44 0.64 77 -0.75 73 150
HIF1A/ARNT/Cbp/p300 -0.046 0.38 0.57 29 -0.69 76 105
EPO 0.032 0.32 0.56 54 -0.6 39 93
CREBBP 0.081 0.18 0.36 95 -0.26 30 125
HIF1A/ARNT/Cbp/p300/HDAC7 -0.05 0.37 0.54 28 -0.68 76 104
PFKFB3 0.015 0.46 0.64 80 -0.75 83 163
NT5E -0.017 0.45 0.63 68 -0.75 86 154
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 -0.091 0.65 0.99 29 -1.2 97 126
PLK1 0.052 0.16 0.59 13 -0.73 9 22
BIRC5 -0.072 0.44 0.64 12 -1.2 57 69
HSPA1B -0.092 0.65 0.97 29 -1.2 99 128
MAP2K1 0.045 0.1 0.25 50 -10000 0 50
BRCA2 -0.086 0.66 1 29 -1.2 96 125
FOXM1 -0.24 0.97 1.2 27 -1.9 99 126
XRCC1 -0.082 0.66 1 30 -1.2 99 129
FOXM1B/p19 -0.32 0.57 -10000 0 -1.4 97 97
Cyclin D1/CDK4 -0.11 0.58 0.87 25 -1.1 99 124
CDC2 -0.11 0.72 1.1 29 -1.3 101 130
TGFA -0.069 0.58 0.86 35 -1 98 133
SKP2 -0.089 0.66 1 30 -1.2 95 125
CCNE1 0.023 0.036 0.097 21 -0.034 106 127
CKS1B -0.097 0.68 1 29 -1.2 100 129
RB1 -0.077 0.37 0.55 10 -1 48 58
FOXM1C/SP1 -0.18 0.74 0.89 20 -1.5 101 121
AURKB 0.055 0.15 0.68 9 -1 3 12
CENPF -0.11 0.7 1.1 29 -1.2 110 139
CDK4 0.025 0.051 0.15 28 -10000 0 28
MYC -0.11 0.56 0.81 29 -1 104 133
CHEK2 0.034 0.087 0.22 42 -10000 0 42
ONECUT1 -0.09 0.63 0.9 35 -1.1 101 136
CDKN2A 0.004 0.015 -10000 0 -0.097 3 3
LAMA4 -0.094 0.65 0.97 30 -1.2 98 128
FOXM1B/HNF6 -0.17 0.77 0.96 27 -1.5 101 128
FOS -0.14 0.7 1 29 -1.2 126 155
SP1 0.033 0.019 0.069 1 -0.027 37 38
CDC25B -0.096 0.67 0.96 31 -1.2 102 133
response to radiation 0.023 0.066 0.15 68 -10000 0 68
CENPB -0.085 0.66 0.97 33 -1.2 94 127
CENPA -0.094 0.66 1 29 -1.2 99 128
NEK2 -0.084 0.66 1.1 29 -1.2 96 125
HIST1H2BA -0.092 0.65 0.97 29 -1.2 99 128
CCNA2 0.022 0.031 0.09 5 -0.034 74 79
EP300 0.033 0.011 -10000 0 0 49 49
CCNB1/CDK1 -0.19 0.83 1.1 25 -1.6 103 128
CCNB2 -0.11 0.69 1 30 -1.3 101 131
CCNB1 -0.12 0.74 1.1 28 -1.3 103 131
ETV5 -0.12 0.69 0.98 31 -1.2 119 150
ESR1 -0.088 0.65 0.97 30 -1.2 99 129
CCND1 -0.11 0.61 0.89 33 -1.1 100 133
GSK3A 0.037 0.082 0.21 44 -10000 0 44
Cyclin A-E1/CDK1-2 0.045 0.1 0.24 23 -0.16 40 63
CDK2 0.024 0.036 0.097 16 -0.034 114 130
G2/M transition of mitotic cell cycle 0.027 0.081 0.17 74 -10000 0 74
FOXM1B/Cbp/p300 -0.16 0.68 0.79 16 -1.4 99 115
GAS1 -0.092 0.67 0.99 33 -1.2 103 136
MMP2 -0.12 0.69 0.98 32 -1.2 107 139
RB1/FOXM1C -0.15 0.6 0.86 22 -1.2 97 119
CREBBP 0.036 0.004 -10000 0 0 5 5
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.031 0.16 -10000 0 -0.47 39 39
Syndecan-4/Syndesmos -0.14 0.27 -10000 0 -0.43 171 171
positive regulation of JNK cascade -0.13 0.25 -10000 0 -0.42 159 159
Syndecan-4/ADAM12 -0.13 0.28 -10000 0 -0.44 169 169
CCL5 0.033 0.011 -10000 0 0 50 50
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
DNM2 0.034 0.009 -10000 0 0 34 34
ITGA5 0.032 0.012 -10000 0 0 56 56
SDCBP 0.035 0.007 -10000 0 0 21 21
PLG 0.03 0.02 -10000 0 -0.043 23 23
ADAM12 0.024 0.017 -10000 0 0 169 169
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 0.27 -10000 0 -0.43 171 171
Syndecan-4/CXCL12/CXCR4 -0.14 0.27 -10000 0 -0.45 159 159
Syndecan-4/Laminin alpha3 -0.12 0.28 -10000 0 -0.44 162 162
MDK 0.029 0.014 -10000 0 0 94 94
Syndecan-4/FZD7 -0.14 0.29 -10000 0 -0.47 162 162
Syndecan-4/Midkine -0.13 0.29 -10000 0 -0.45 169 169
FZD7 0.026 0.016 -10000 0 0 135 135
Syndecan-4/FGFR1/FGF -0.099 0.27 -10000 0 -0.42 158 158
THBS1 0.03 0.014 -10000 0 0 90 90
integrin-mediated signaling pathway -0.13 0.27 -10000 0 -0.44 165 165
positive regulation of MAPKKK cascade -0.13 0.25 -10000 0 -0.42 159 159
Syndecan-4/TACI -0.12 0.29 -10000 0 -0.44 170 170
CXCR4 0.029 0.015 -10000 0 0 97 97
cell adhesion -0.011 0.057 0.21 3 -0.24 20 23
Syndecan-4/Dynamin -0.12 0.28 -10000 0 -0.44 164 164
Syndecan-4/TSP1 -0.13 0.28 -10000 0 -0.44 164 164
Syndecan-4/GIPC -0.12 0.28 -10000 0 -0.44 164 164
Syndecan-4/RANTES -0.13 0.28 -10000 0 -0.44 166 166
ITGB1 0.027 0.016 -10000 0 0 118 118
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.033 0.011 -10000 0 0 45 45
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA 0 0.1 0.96 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.13 0.29 -10000 0 -0.46 163 163
TFPI 0.029 0.015 -10000 0 0 97 97
F2 0.01 0.04 -10000 0 -0.044 164 164
alpha5/beta1 Integrin 0.03 0.043 -10000 0 -0.14 20 20
positive regulation of cell adhesion -0.13 0.27 -10000 0 -0.43 162 162
ACTN1 0.028 0.015 -10000 0 0 106 106
TNC 0.028 0.016 -10000 0 0 117 117
Syndecan-4/CXCL12 -0.14 0.27 -10000 0 -0.44 161 161
FGF6 0.034 0.009 -10000 0 0 34 34
RHOA 0.035 0.007 -10000 0 0 21 21
CXCL12 0.022 0.018 -10000 0 0 195 195
TNFRSF13B 0.036 0.005 -10000 0 0 8 8
FGF2 0.034 0.008 -10000 0 0 25 25
FGFR1 0.035 0.005 -10000 0 0 11 11
Syndecan-4/PI-4-5-P2 -0.14 0.27 -10000 0 -0.43 171 171
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.031 0.019 -10000 0 -0.043 22 22
cell migration -0.01 0.015 -10000 0 -10000 0 0
PRKCD 0.031 0.02 -10000 0 -0.043 21 21
vasculogenesis -0.12 0.26 -10000 0 -0.42 164 164
SDC4 -0.14 0.3 -10000 0 -0.46 171 171
Syndecan-4/Tenascin C -0.13 0.29 -10000 0 -0.46 165 165
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 -0.44 168 168
MMP9 0.012 0.024 -10000 0 -0.042 39 39
Rac1/GTP -0.012 0.058 0.21 3 -0.24 20 23
cytoskeleton organization -0.13 0.26 -10000 0 -0.41 171 171
GIPC1 0.034 0.009 -10000 0 0 30 30
Syndecan-4/TFPI -0.13 0.28 -10000 0 -0.45 165 165
Angiopoietin receptor Tie2-mediated signaling

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 -0.22 0.41 -10000 0 -0.79 151 151
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.38 128 128
NCK1/Dok-R -0.13 0.35 -10000 0 -0.86 89 89
PIK3CA 0.03 0.014 -10000 0 0 85 85
mol:beta2-estradiol 0.029 0.096 0.23 89 -0.076 3 92
RELA 0.036 0.005 -10000 0 0 10 10
SHC1 0.032 0.011 -10000 0 0 48 48
Rac/GDP 0.018 0.02 -10000 0 -0.13 6 6
F2 0.051 0.11 0.27 82 -0.089 62 144
TNIP2 0.035 0.006 -10000 0 0 13 13
NF kappa B/RelA -0.11 0.35 -10000 0 -0.83 89 89
FN1 0.034 0.009 -10000 0 0 29 29
PLD2 -0.14 0.36 -10000 0 -0.89 89 89
PTPN11 0.036 0.005 -10000 0 0 9 9
GRB14 0.031 0.013 -10000 0 0 67 67
ELK1 -0.14 0.33 -10000 0 -0.82 89 89
GRB7 0.035 0.006 -10000 0 0 13 13
PAK1 0.035 0.007 -10000 0 0 17 17
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.86 89 89
CDKN1A -0.19 0.36 -10000 0 -0.66 161 161
ITGA5 0.032 0.012 -10000 0 0 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.13 0.35 -10000 0 -0.86 89 89
CRK 0.035 0.008 -10000 0 0 23 23
mol:NO -0.13 0.32 0.39 5 -0.57 148 153
PLG -0.15 0.36 -10000 0 -0.89 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.74 121 121
GRB2 0.035 0.006 -10000 0 0 16 16
PIK3R1 0.031 0.012 -10000 0 0 61 61
ANGPT2 -0.22 0.45 -10000 0 -0.87 136 136
BMX -0.14 0.36 -10000 0 -0.89 89 89
ANGPT1 -0.16 0.42 -10000 0 -1 89 89
tube development -0.21 0.36 0.38 1 -0.69 159 160
ANGPT4 0.023 0.028 -10000 0 -0.029 104 104
response to hypoxia -0.012 0.026 0.034 1 -0.063 89 90
Tie2/Ang1/GRB14 -0.14 0.37 -10000 0 -0.9 89 89
alpha5/beta1 Integrin 0.03 0.043 -10000 0 -0.14 20 20
FGF2 0.035 0.016 -10000 0 -0.011 41 41
STAT5A (dimer) -0.23 0.45 -10000 0 -0.81 167 167
mol:L-citrulline -0.13 0.32 0.39 5 -0.57 148 153
AGTR1 0.021 0.034 -10000 0 -0.038 108 108
MAPK14 -0.15 0.37 -10000 0 -0.9 90 90
Tie2/SHP2 -0.071 0.23 -10000 0 -0.82 29 29
TEK -0.082 0.24 -10000 0 -0.95 26 26
RPS6KB1 -0.2 0.37 -10000 0 -0.77 130 130
Angiotensin II/AT1 0.014 0.036 -10000 0 -0.057 80 80
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -0.9 89 89
MAPK3 -0.15 0.34 -10000 0 -0.84 89 89
MAPK1 -0.14 0.33 -10000 0 -0.84 89 89
Tie2/Ang1/GRB7 -0.14 0.37 -10000 0 -0.91 89 89
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.15 0.35 -10000 0 -0.89 89 89
PI3K -0.24 0.44 -10000 0 -0.91 128 128
FES -0.15 0.38 -10000 0 -0.9 90 90
Crk/Dok-R -0.13 0.36 -10000 0 -0.86 89 89
Tie2/Ang1/ABIN2 -0.14 0.37 -10000 0 -0.91 89 89
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.2 0.37 -10000 0 -0.7 152 152
STAT5A 0.036 0.004 -10000 0 0 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.37 -10000 0 -0.77 129 129
Tie2/Ang2 -0.28 0.51 -10000 0 -0.97 156 156
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 89 89
FOXO1 -0.22 0.39 -10000 0 -0.74 160 160
ELF1 0.028 0.036 0.1 2 -0.045 76 78
ELF2 -0.14 0.35 -10000 0 -0.87 89 89
mol:Choline -0.14 0.35 -10000 0 -0.86 89 89
cell migration -0.065 0.097 -10000 0 -0.21 130 130
FYN -0.24 0.41 -10000 0 -0.8 157 157
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.16 0.32 0.38 3 -0.59 161 164
ETS1 0 0.12 0.12 2 -0.25 86 88
PXN -0.17 0.31 -10000 0 -0.64 130 130
ITGB1 0.027 0.016 -10000 0 0 118 118
NOS3 -0.16 0.36 0.41 4 -0.65 146 150
RAC1 0.027 0.016 -10000 0 0 123 123
TNF -0.001 0.12 0.12 1 -0.25 84 85
MAPKKK cascade -0.14 0.35 -10000 0 -0.86 89 89
RASA1 0.034 0.009 -10000 0 0 30 30
Tie2/Ang1/Shc -0.14 0.37 -10000 0 -0.9 89 89
NCK1 0.034 0.008 -10000 0 0 26 26
vasculogenesis -0.11 0.29 0.39 5 -0.51 148 153
mol:Phosphatidic acid -0.14 0.35 -10000 0 -0.86 89 89
mol:Angiotensin II -0.004 0.013 -10000 0 -0.032 72 72
mol:NADP -0.13 0.32 0.39 5 -0.57 148 153
Rac1/GTP -0.17 0.34 -10000 0 -0.7 126 126
MMP2 -0.15 0.36 -10000 0 -0.9 89 89
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.019 0.14 0.2 84 -0.25 88 172
PTK2B 0.035 0.006 -10000 0 0 15 15
mol:Ca2+ -0.097 0.25 0.37 3 -0.52 85 88
EDN1 0.004 0.09 0.14 12 -0.16 97 109
EDN3 0.034 0.009 -10000 0 0 30 30
EDN2 0.035 0.006 -10000 0 0 14 14
HRAS/GDP -0.007 0.18 0.3 21 -0.37 54 75
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.12 0.2 11 -0.24 56 67
ADCY4 -0.035 0.095 0.12 45 -0.2 96 141
ADCY5 -0.035 0.095 0.12 45 -0.2 96 141
ADCY6 -0.005 0.13 0.19 95 -0.22 66 161
ADCY7 -0.011 0.13 0.19 83 -0.23 66 149
ADCY1 0 0.12 0.19 80 -0.24 46 126
ADCY2 -0.005 0.13 0.19 95 -0.23 67 162
ADCY3 -0.035 0.095 0.12 45 -0.2 96 141
ADCY8 -0.008 0.13 0.19 88 -0.22 61 149
ADCY9 -0.007 0.13 0.19 93 -0.23 68 161
arachidonic acid secretion -0.069 0.26 0.33 28 -0.5 97 125
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.11 0.18 10 -0.26 43 53
GNAO1 0.03 0.014 -10000 0 0 81 81
HRAS 0.034 0.009 -10000 0 0 32 32
ETA receptor/Endothelin-1/G12/GTP 0.003 0.12 -10000 0 -0.22 88 88
ETA receptor/Endothelin-1/Gs/GTP 0.005 0.12 -10000 0 -0.2 103 103
mol:GTP 0 0.006 0.024 3 -0.023 5 8
COL3A1 -0.074 0.15 0.17 11 -0.36 97 108
EDNRB 0.023 0.044 0.095 61 -0.083 44 105
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.017 0.14 0.2 82 -0.25 83 165
CYSLTR1 -0.038 0.12 0.16 46 -0.23 99 145
SLC9A1 -0.014 0.087 0.13 30 -0.18 74 104
mol:GDP -0.016 0.17 0.29 23 -0.38 52 75
SLC9A3 -0.12 0.29 -10000 0 -0.65 78 78
RAF1 -0.028 0.21 0.31 28 -0.41 78 106
JUN -0.14 0.33 0.47 1 -0.72 82 83
JAK2 -0.018 0.13 0.2 71 -0.25 81 152
mol:IP3 -0.005 0.12 0.21 16 -0.28 42 58
ETA receptor/Endothelin-1 -0.027 0.14 -10000 0 -0.27 107 107
PLCB1 0.033 0.012 -10000 0 -0.005 38 38
PLCB2 0.028 0.022 -10000 0 -0.022 75 75
ETA receptor/Endothelin-3 0.006 0.089 0.14 1 -0.14 106 107
FOS -0.086 0.35 0.38 26 -0.83 78 104
Gai/GDP -0.07 0.27 -10000 0 -0.73 65 65
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca ++ -0.018 0.17 0.25 58 -0.33 74 132
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.002 0.12 0.23 24 -0.3 38 62
GNAQ 0.027 0.026 -10000 0 -0.033 67 67
GNAZ 0.03 0.013 -10000 0 0 79 79
GNAL 0.035 0.006 -10000 0 0 13 13
Gs family/GDP -0.006 0.16 0.29 20 -0.35 52 72
ETA receptor/Endothelin-1/Gq/GTP -0.008 0.12 0.2 10 -0.26 60 70
MAPK14 -0.01 0.098 0.18 5 -0.26 37 42
TRPC6 -0.1 0.26 0.38 3 -0.54 83 86
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
GNAI1 0.018 0.018 -10000 0 0 246 246
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.1 0.18 14 -0.26 40 54
ETB receptor/Endothelin-2 0.018 0.071 -10000 0 -0.12 83 83
ETB receptor/Endothelin-3 0.016 0.07 -10000 0 -0.11 89 89
ETB receptor/Endothelin-1 -0.001 0.1 0.17 26 -0.16 108 134
MAPK3 -0.068 0.32 0.36 28 -0.73 78 106
MAPK1 -0.082 0.34 0.37 26 -0.77 81 107
Rac1/GDP -0.005 0.16 0.3 18 -0.37 44 62
cAMP biosynthetic process 0.017 0.12 0.2 67 -0.22 46 113
MAPK8 -0.13 0.31 0.34 3 -0.57 134 137
SRC 0.035 0.006 -10000 0 0 13 13
ETB receptor/Endothelin-1/Gi/GTP -0.035 0.14 0.14 10 -0.34 62 72
p130Cas/CRK/Src/PYK2 -0.016 0.18 0.34 19 -0.46 42 61
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.009 0.16 0.3 17 -0.37 49 66
COL1A2 -0.053 0.17 0.22 1 -0.48 56 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.007 0.089 -10000 0 -0.14 108 108
mol:DAG -0.006 0.12 0.21 16 -0.28 42 58
MAP2K2 -0.042 0.26 0.35 40 -0.56 78 118
MAP2K1 -0.056 0.26 0.34 23 -0.57 80 103
EDNRA -0.007 0.1 0.13 24 -0.19 93 117
positive regulation of muscle contraction 0.012 0.14 0.21 115 -0.24 64 179
Gq family/GDP 0.003 0.16 0.3 4 -0.34 53 57
HRAS/GTP -0.009 0.16 0.27 28 -0.35 53 81
PRKCH -0.007 0.12 0.23 17 -0.3 36 53
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.011 0.12 0.21 18 -0.29 44 62
PRKCB -0.005 0.12 0.21 22 -0.27 45 67
PRKCE -0.011 0.12 0.21 17 -0.29 42 59
PRKCD -0.008 0.12 0.24 22 -0.3 40 62
PRKCG -0.01 0.12 0.22 17 -0.3 39 56
regulation of vascular smooth muscle contraction -0.11 0.42 0.43 17 -1 78 95
PRKCQ -0.003 0.11 0.24 18 -0.31 28 46
PLA2G4A -0.079 0.28 0.34 27 -0.55 97 124
GNA14 0.027 0.026 -10000 0 -0.033 67 67
GNA15 0.029 0.019 -10000 0 -0.034 23 23
GNA12 0.026 0.016 -10000 0 0 136 136
GNA11 0.031 0.017 -10000 0 -0.035 14 14
Rac1/GTP 0.007 0.12 -10000 0 -0.22 75 75
MMP1 0.02 0.073 0.17 66 -10000 0 66
TCGA08_p53

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
CDKN2A -0.002 0.004 0 417 -10000 0 417
TP53 0.004 0.036 -9999 0 -0.25 7 7
Senescence 0.003 0.038 -9999 0 -0.24 9 9
Apoptosis 0.003 0.038 -9999 0 -0.24 9 9
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 -0.002 0.005 -9999 0 -10000 0 0
MDM4 0.032 0.012 -9999 0 0 58 58
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.035 0.008 -10000 0 0 24 24
GNB1/GNG2 -0.045 0.076 -10000 0 -0.17 120 120
AKT1 -0.003 0.16 0.3 27 -0.3 35 62
EGF 0.034 0.008 -10000 0 0 24 24
mol:TXA2 0 0.001 0.003 1 -10000 0 1
FGR -0.007 0.08 0.26 30 -0.17 2 32
mol:Ca2+ 0.002 0.19 0.34 28 -0.27 115 143
LYN -0.007 0.083 0.26 32 -0.16 8 40
RhoA/GTP -0.004 0.08 0.15 24 -0.13 101 125
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.011 0.21 0.35 32 -0.32 115 147
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.034 0.008 -10000 0 0 27 27
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.075 -10000 0 -0.24 30 30
G beta5/gamma2 -0.052 0.1 -10000 0 -0.22 118 118
PRKCH -0.012 0.2 0.35 27 -0.32 117 144
DNM1 0.035 0.008 -10000 0 0 23 23
TXA2/TP beta/beta Arrestin3 0.017 0.019 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.005 54 -0.002 6 60
PTGDR 0.035 0.007 -10000 0 0 20 20
G12 family/GTP -0.042 0.15 -10000 0 -0.29 105 105
ADRBK1 0.035 0.006 -10000 0 0 14 14
ADRBK2 0.034 0.01 -10000 0 0 36 36
RhoA/GTP/ROCK1 0.043 0.027 -10000 0 -0.12 10 10
mol:GDP -0.01 0.14 0.43 16 -0.28 20 36
mol:NADP 0.027 0.016 -10000 0 0 118 118
RAB11A 0.035 0.006 -10000 0 0 16 16
PRKG1 0.027 0.016 -10000 0 0 124 124
mol:IP3 -0.009 0.22 0.37 26 -0.34 116 142
cell morphogenesis 0.043 0.027 -10000 0 -0.12 10 10
PLCB2 -0.032 0.27 0.43 17 -0.45 118 135
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.005 0.084 0.26 34 -10000 0 34
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.012 0.071 0.23 26 -0.17 10 36
RHOA 0.035 0.007 -10000 0 0 21 21
PTGIR 0.034 0.009 -10000 0 0 34 34
PRKCB1 -0.014 0.22 0.36 25 -0.34 116 141
GNAQ 0.034 0.009 -10000 0 0 31 31
mol:L-citrulline 0.027 0.016 -10000 0 0 118 118
TXA2/TXA2-R family -0.042 0.28 0.44 17 -0.47 121 138
LCK -0.005 0.084 0.25 35 -10000 0 35
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.035 0.043 0.19 11 -0.13 1 12
TXA2-R family/G12 family/GDP/G beta/gamma -0.026 0.16 -10000 0 -0.47 52 52
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.032 0.045 0.19 11 -0.13 1 12
MAPK14 0 0.15 0.28 37 -0.22 108 145
TGM2/GTP -0.012 0.24 0.4 21 -0.38 111 132
MAPK11 -0.002 0.15 0.29 36 -0.22 110 146
ARHGEF1 0.005 0.12 0.22 42 -0.17 101 143
GNAI2 0.033 0.01 -10000 0 0 42 42
JNK cascade -0.016 0.22 0.37 28 -0.35 121 149
RAB11/GDP 0.033 0.011 -10000 0 -0.011 24 24
ICAM1 0 0.18 0.31 38 -0.27 116 154
cAMP biosynthetic process -0.01 0.2 0.34 28 -0.32 108 136
Gq family/GTP/EBP50 0.012 0.053 0.25 6 -0.16 30 36
actin cytoskeleton reorganization 0.043 0.027 -10000 0 -0.12 10 10
SRC -0.011 0.073 0.23 28 -10000 0 28
GNB5 0.035 0.007 -10000 0 0 18 18
GNB1 0.033 0.01 -10000 0 0 37 37
EGF/EGFR -0.005 0.11 0.26 31 -0.22 44 75
VCAM1 -0.018 0.21 0.32 35 -0.33 125 160
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.075 -10000 0 -0.24 30 30
platelet activation -0.004 0.19 0.35 34 -0.28 113 147
PGI2/IP 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.014 0.023 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.006 0.065 0.18 1 -0.21 29 30
TXA2/TP beta/beta Arrestin2 0.004 0.054 -10000 0 -0.29 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.02 -10000 0 -10000 0 0
mol:DAG -0.018 0.24 0.38 25 -0.38 117 142
EGFR 0.01 0.016 -10000 0 0 355 355
TXA2/TP alpha -0.024 0.26 0.43 17 -0.42 112 129
Gq family/GTP 0.009 0.045 0.2 11 -0.12 27 38
YES1 -0.007 0.084 0.26 33 -0.16 7 40
GNAI2/GTP 0.008 0.047 -10000 0 -0.14 4 4
PGD2/DP 0.026 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.009 -10000 0 0 34 34
FYN -0.009 0.08 0.25 28 -0.16 20 48
mol:NO 0.027 0.016 -10000 0 0 118 118
GNA15 0.032 0.012 -10000 0 0 59 59
PGK/cGMP 0.029 0.024 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.011 -10000 0 -0.009 29 29
TP alpha/TGM2/GDP/G beta/gamma 0.032 0.045 0.18 9 -0.13 4 13
NOS3 0.027 0.016 -10000 0 0 118 118
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.012 0.21 0.35 26 -0.32 118 144
PRKCB -0.012 0.21 0.35 27 -0.32 121 148
PRKCE -0.013 0.21 0.35 27 -0.33 115 142
PRKCD -0.016 0.22 0.35 31 -0.35 121 152
PRKCG -0.016 0.22 0.36 28 -0.35 119 147
muscle contraction -0.035 0.26 0.41 21 -0.44 117 138
PRKCZ -0.011 0.2 0.35 28 -0.31 121 149
ARR3 0.036 0 -10000 0 -10000 0 0
TXA2/TP beta 0.038 0.041 0.18 9 -0.13 2 11
PRKCQ -0.02 0.2 0.35 25 -0.32 114 139
MAPKKK cascade -0.027 0.24 0.39 22 -0.4 119 141
SELE -0.006 0.18 0.33 28 -0.27 122 150
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.056 0.18 9 -0.16 16 25
ROCK1 0.035 0.006 -10000 0 0 14 14
GNA14 0.034 0.008 -10000 0 0 28 28
chemotaxis -0.061 0.32 0.46 15 -0.56 125 140
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
GNA11 0.032 0.012 -10000 0 0 60 60
Rac1/GTP 0.019 0.021 -10000 0 -0.13 6 6
PDGFR-alpha signaling pathway

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
PDGFRA 0.017 0.031 0.082 3 -0.056 49 52
PDGF/PDGFRA/CRKL 0.008 0.067 -10000 0 -0.14 64 64
positive regulation of JUN kinase activity 0.025 0.061 -10000 0 -0.11 62 62
CRKL 0.034 0.008 -10000 0 0 25 25
PDGF/PDGFRA/Caveolin-3 0.009 0.068 -10000 0 -0.14 65 65
AP1 -0.085 0.24 0.3 1 -0.6 73 74
mol:IP3 -0.018 0.041 0.052 45 -0.098 56 101
PLCG1 -0.018 0.041 0.052 45 -0.098 56 101
PDGF/PDGFRA/alphaV Integrin 0.004 0.075 -10000 0 -0.15 73 73
RAPGEF1 0.035 0.007 -10000 0 0 18 18
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca2+ -0.018 0.04 0.052 45 -0.098 56 101
CAV3 0.036 0.005 -10000 0 0 9 9
CAV1 0.016 0.018 -10000 0 0 269 269
SHC/Grb2/SOS1 0.026 0.062 -10000 0 -0.11 62 62
PDGF/PDGFRA/Shf -0.005 0.054 -10000 0 -0.091 111 111
FOS -0.093 0.23 0.28 3 -0.61 68 71
JUN -0.026 0.057 0.22 9 -0.2 16 25
oligodendrocyte development 0.004 0.075 -10000 0 -0.15 73 73
GRB2 0.035 0.006 -10000 0 0 16 16
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:DAG -0.018 0.041 0.052 45 -0.098 56 101
PDGF/PDGFRA 0.017 0.031 0.082 3 -0.056 49 52
actin cytoskeleton reorganization 0.006 0.066 -10000 0 -0.14 63 63
SRF -0.015 0.02 0.033 65 -10000 0 65
SHC1 0.033 0.011 -10000 0 0 48 48
PI3K 0.006 0.09 -10000 0 -0.15 103 103
PDGF/PDGFRA/Crk/C3G 0.027 0.072 -10000 0 -0.13 72 72
JAK1 -0.011 0.019 0.025 55 -10000 0 55
ELK1/SRF -0.019 0.084 0.14 69 -0.16 57 126
SHB 0.033 0.011 -10000 0 0 48 48
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.034 0.078 2 -0.031 104 106
GO:0007205 -0.028 0.069 0.1 20 -0.2 53 73
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.025 0.061 -10000 0 -0.11 62 62
PDGF/PDGFRA/SHB 0.006 0.066 -10000 0 -0.14 63 63
PDGF/PDGFRA/Caveolin-1 -0.012 0.075 -10000 0 -0.17 78 78
ITGAV 0.034 0.009 -10000 0 0 30 30
ELK1 -0.033 0.067 0.12 6 -0.15 94 100
PIK3CA 0.03 0.014 -10000 0 0 85 85
PDGF/PDGFRA/Crk 0.006 0.073 -10000 0 -0.15 73 73
JAK-STAT cascade -0.011 0.019 0.025 55 -10000 0 55
cell proliferation -0.005 0.054 -10000 0 -0.091 111 111
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.025 0.017 -10000 0 0 157 157
HRAS 0.034 0.009 -10000 0 0 32 32
EGFR 0.01 0.016 -10000 0 0 355 355
AKT 0.084 0.11 0.23 108 -0.18 10 118
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.032 0.011 -10000 0 0 53 53
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.035 0.007 -10000 0 0 21 21
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.023 0.018 -10000 0 0 183 183
PIK3CA 0.03 0.014 -10000 0 0 85 85
PIK3CB 0.035 0.006 -10000 0 0 16 16
NRAS 0.032 0.012 -10000 0 0 58 58
PIK3CG 0.026 0.016 -10000 0 0 139 139
PIK3R3 0.035 0.006 -10000 0 0 14 14
PIK3R2 0.034 0.009 -10000 0 0 31 31
NF1 0.036 0.003 -10000 0 0 4 4
RAS -0.002 0.052 -10000 0 -0.24 10 10
ERBB2 0.036 0.004 -10000 0 0 5 5
proliferation/survival/translation -0.026 0.055 0.23 5 -0.19 18 23
PI3K 0.033 0.08 0.19 62 -0.16 11 73
PIK3R1 0.032 0.012 -10000 0 0 61 61
KRAS 0.033 0.01 -10000 0 0 37 37
FOXO 0.087 0.084 0.19 149 -10000 0 149
AKT2 0.034 0.008 -10000 0 0 26 26
PTEN 0.027 0.016 -10000 0 0 130 130
EGFR-dependent Endothelin signaling events

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
HRAS 0.034 0.009 -10000 0 0 32 32
EGFR 0.01 0.016 -10000 0 0 355 355
EGF/EGFR 0.002 0.051 -10000 0 -0.11 58 58
EGF/EGFR dimer/SHC/GRB2/SOS1 0.007 0.058 -10000 0 -0.11 59 59
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.016 -10000 0 0 117 117
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.034 0.008 -10000 0 0 24 24
EGF/EGFR dimer/SHC 0.001 0.056 -10000 0 -0.13 58 58
mol:GDP 0.005 0.055 -10000 0 -0.11 59 59
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.033 0.011 -10000 0 0 50 50
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
HRAS/GTP -0.004 0.051 -10000 0 -0.11 67 67
SHC1 0.033 0.011 -10000 0 0 48 48
HRAS/GDP 0 0.058 -10000 0 -0.12 67 67
FRAP1 0.093 0.12 0.19 285 -0.18 4 289
EGF/EGFR dimer -0.004 0.056 -10000 0 -0.14 60 60
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.035 0.006 -10000 0 0 16 16
ETA receptor/Endothelin-1 0.023 0.058 -10000 0 -0.14 47 47
HIF-2-alpha transcription factor network

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
MMP14 -0.006 0.14 -10000 0 -0.65 20 20
oxygen homeostasis 0.005 0.021 0.047 64 -0.025 26 90
TCEB2 0.036 0.004 -10000 0 0 5 5
TCEB1 0.035 0.007 -10000 0 0 20 20
VHL/Elongin B/Elongin C/HIF2A 0.016 0.14 0.29 28 -0.24 41 69
EPO -0.032 0.2 0.41 17 -0.44 48 65
FIH (dimer) 0.018 0.039 0.11 19 -0.04 57 76
APEX1 0.017 0.041 0.1 8 -0.05 39 47
SERPINE1 -0.066 0.2 0.37 5 -0.45 73 78
FLT1 -0.007 0.14 -10000 0 -0.62 21 21
ADORA2A -0.023 0.23 0.44 35 -0.43 61 96
germ cell development -0.027 0.22 0.43 29 -0.41 67 96
SLC11A2 -0.02 0.24 0.46 33 -0.44 65 98
BHLHE40 -0.03 0.23 0.43 28 -0.42 67 95
HIF1AN 0.018 0.039 0.11 19 -0.04 57 76
HIF2A/ARNT/SIRT1 -0.007 0.16 0.33 21 -0.3 50 71
ETS1 0.046 0.032 0.12 42 -0.11 11 53
CITED2 -0.053 0.26 -10000 0 -0.87 40 40
KDR 0.002 0.16 -10000 0 -0.85 14 14
PGK1 -0.026 0.25 0.44 39 -0.45 72 111
SIRT1 0.026 0.017 -10000 0 0 143 143
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.015 0.26 0.49 9 -0.48 66 75
EPAS1 0.007 0.13 0.31 37 -0.25 36 73
SP1 0.04 0.011 0.11 8 -10000 0 8
ABCG2 -0.033 0.25 0.46 31 -0.46 73 104
EFNA1 -0.028 0.24 0.44 29 -0.44 69 98
FXN -0.025 0.23 0.44 34 -0.42 67 101
POU5F1 -0.03 0.23 0.43 28 -0.42 67 95
neuron apoptosis 0.014 0.26 0.47 66 -0.48 9 75
EP300 0.033 0.011 -10000 0 0 49 49
EGLN3 0.02 0.039 0.11 16 -0.04 61 77
EGLN2 0.024 0.041 0.11 21 -0.04 54 75
EGLN1 0.025 0.041 0.11 21 -0.039 58 79
VHL/Elongin B/Elongin C 0.044 0.024 -10000 0 -0.12 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.018 0.041 0.1 8 -0.049 46 54
SLC2A1 -0.045 0.22 0.43 22 -0.44 69 91
TWIST1 -0.062 0.2 0.41 10 -0.42 83 93
ELK1 0.037 0.036 0.11 30 -0.097 24 54
HIF2A/ARNT/Cbp/p300 0.013 0.18 0.38 30 -0.31 49 79
VEGFA -0.03 0.23 0.43 28 -0.42 67 95
CREBBP 0.036 0.004 -10000 0 0 5 5
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 -0.008 0.005 0 155 -10000 0 155
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.039 0.039 -10000 0 -0.14 17 17
STXBP1 0.029 0.015 -10000 0 0 99 99
ACh/CHRNA1 0.025 0.054 0.096 37 -0.075 91 128
RAB3GAP2/RIMS1/UNC13B 0.051 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 0.034 0.009 -10000 0 0 33 33
mol:ACh 0.013 0.063 0.094 126 -0.09 87 213
RAB3GAP2 0.034 0.008 -10000 0 0 25 25
STX1A/SNAP25/VAMP2 0.018 0.098 0.17 15 -0.16 74 89
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.024 0.054 0.096 37 -0.075 91 128
UNC13B 0.032 0.012 -10000 0 0 62 62
CHRNA1 0.035 0.006 -10000 0 0 14 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.012 0.042 0.1 13 -0.086 41 54
SNAP25 0.002 0.003 -10000 0 0 255 255
VAMP2 0.004 0.001 -10000 0 0 47 47
SYT1 0.018 0.018 -10000 0 0 249 249
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.018 0.016 0.086 1 -10000 0 1
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.098 0.17 15 -0.16 74 89
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.03 0.014 -9999 0 0 81 81
PLK4 0.035 0.007 -9999 0 0 17 17
regulation of centriole replication -0.018 0.009 0 91 -9999 0 91
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 0.035 0.006 -9999 0 0 15 15
Syndecan-3/Src/Cortactin -0.024 0.19 -9999 0 -0.45 71 71
Syndecan-3/Neurocan -0.065 0.18 -9999 0 -0.48 73 73
POMC 0.036 0.005 -9999 0 0 10 10
EGFR 0.01 0.016 -9999 0 0 355 355
Syndecan-3/EGFR -0.056 0.16 -9999 0 -0.42 72 72
AGRP 0.036 0.004 -9999 0 0 7 7
NCSTN 0.034 0.008 -9999 0 0 28 28
PSENEN 0.034 0.009 -9999 0 0 33 33
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.035 0.006 -9999 0 0 14 14
APH1A 0.035 0.006 -9999 0 0 16 16
NCAN 0 0 -9999 0 -10000 0 0
long-term memory -0.032 0.2 -9999 0 -0.5 73 73
Syndecan-3/IL8 -0.055 0.18 -9999 0 -0.47 73 73
PSEN1 0.033 0.01 -9999 0 0 41 41
Src/Cortactin 0.051 0.015 -9999 0 -0.14 1 1
FYN 0.03 0.014 -9999 0 0 83 83
limb bud formation -0.065 0.18 -9999 0 -0.5 73 73
MC4R 0.035 0.007 -9999 0 0 17 17
SRC 0.035 0.006 -9999 0 0 13 13
PTN 0.023 0.017 -9999 0 0 178 178
FGFR/FGF/Syndecan-3 -0.066 0.18 -9999 0 -0.5 73 73
neuron projection morphogenesis -0.073 0.16 -9999 0 -0.44 71 71
Syndecan-3/AgRP -0.042 0.19 -9999 0 -0.49 73 73
Syndecan-3/AgRP/MC4R -0.024 0.19 -9999 0 -0.48 73 73
Fyn/Cortactin 0.028 0.061 -9999 0 -0.14 51 51
SDC3 -0.067 0.19 -9999 0 -0.51 73 73
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.054 0.18 -9999 0 -0.47 73 73
IL8 0.019 0.018 -9999 0 0 233 233
Syndecan-3/Fyn/Cortactin -0.033 0.21 -9999 0 -0.51 73 73
Syndecan-3/CASK -0.065 0.18 -9999 0 -0.48 73 73
alpha-MSH/MC4R 0.051 0.012 -9999 0 -10000 0 0
Gamma Secretase 0.076 0.072 -9999 0 -0.15 29 29
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.033 0.046 0.12 67 -0.038 83 150
AES 0.03 0.042 0.11 60 -0.035 79 139
FBXW11 0.035 0.007 -10000 0 0 20 20
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -0.14 1 1
SMAD4 0.032 0.011 -10000 0 0 53 53
DKK2 0.034 0.009 -10000 0 0 29 29
TLE1 0.031 0.041 0.11 63 -0.035 83 146
MACF1 0.033 0.011 -10000 0 0 48 48
CTNNB1 0.045 0.11 0.26 26 -0.34 14 40
WIF1 0.028 0.015 -10000 0 0 106 106
beta catenin/RanBP3 0.068 0.16 0.41 61 -0.34 9 70
KREMEN2 0.036 0.004 -10000 0 0 5 5
DKK1 0.018 0.018 -10000 0 0 240 240
beta catenin/beta TrCP1 0.059 0.11 0.28 24 -0.33 15 39
FZD1 0.025 0.017 -10000 0 0 155 155
AXIN2 -0.024 0.093 0.12 2 -0.24 64 66
AXIN1 0.037 0.004 -10000 0 0 6 6
RAN 0.036 0.006 -10000 0 0 13 13
Axin1/APC/GSK3/beta catenin 0.011 0.16 -10000 0 -0.59 29 29
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.13 0.26 9 -0.42 18 27
Axin1/APC/GSK3 0.005 0.091 0.22 5 -0.36 18 23
Axin1/APC/GSK3/beta catenin/Macf1 0.029 0.13 0.27 12 -0.37 29 41
HNF1A 0.007 0.03 0.07 73 -0.035 4 77
CTBP1 0.031 0.042 0.11 59 -0.036 82 141
MYC -0.1 0.4 0.73 13 -1.2 48 61
RANBP3 0.035 0.008 -10000 0 0 27 27
DKK2/LRP6/Kremen 2 0.064 0.026 -10000 0 -0.12 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.03 0.039 0.11 58 -0.036 67 125
TCF3 0.031 0.042 0.11 60 -0.035 81 141
WNT1/LRP6/FZD1/Axin1 0.061 0.045 -10000 0 -10000 0 0
Ran/GTP 0.025 0.016 -10000 0 -0.13 5 5
CtBP/CBP/TCF/TLE1/AES 0.035 0.19 0.46 63 -0.34 17 80
LEF1 0.033 0.044 0.11 68 -0.036 84 152
DVL1 0.008 0.096 -10000 0 -0.42 16 16
CSNK2A1 0.034 0.009 -10000 0 0 31 31
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.011 0.16 0.25 8 -0.49 30 38
DKK1/LRP6/Kremen 2 0.034 0.037 -10000 0 -10000 0 0
LRP6 0.034 0.01 -10000 0 0 37 37
CSNK1A1 0.034 0.047 0.12 65 -0.037 84 149
NLK 0.026 0.023 -10000 0 -0.032 52 52
CCND1 -0.081 0.35 0.74 3 -1.2 37 40
WNT1 0.035 0.007 -10000 0 0 16 16
GSK3A 0.034 0.009 -10000 0 0 28 28
GSK3B 0.034 0.01 -10000 0 0 35 35
FRAT1 0.026 0.016 -10000 0 0 130 130
PPP2R5D 0.023 0.044 0.15 1 -0.22 8 9
APC 0.037 0.1 0.19 143 -10000 0 143
WNT1/LRP6/FZD1 0.005 0.043 -10000 0 -0.24 8 8
CREBBP 0.033 0.043 0.11 67 -0.035 86 153
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.018 0.14 -10000 0 -0.36 25 25
MAP3K8 0.022 0.018 -10000 0 0 182 182
FOS 0.016 0.11 -10000 0 -0.33 18 18
PRKCA 0.028 0.026 -10000 0 -0.029 75 75
PTPN7 0.028 0.029 0.066 52 -0.029 88 140
HRAS 0.034 0.009 -10000 0 0 32 32
PRKCB 0 0.008 0.017 59 -0.013 74 133
NRAS 0.032 0.012 -10000 0 0 58 58
RAS family/GTP 0.041 0.066 -10000 0 -0.13 50 50
MAPK3 0.033 0.057 -10000 0 -0.34 4 4
MAP2K1 0.007 0.058 0.16 1 -0.22 13 14
ELK1 0.026 0.028 -10000 0 -0.039 76 76
BRAF 0.007 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.003 59 -0.004 75 134
MAPK1 0.006 0.13 -10000 0 -0.44 29 29
RAF1 -0.001 0.068 -10000 0 -0.34 16 16
KRAS 0.034 0.01 -10000 0 0 37 37
Syndecan-1-mediated signaling events

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
TGFB1 0.032 0.012 -10000 0 0 62 62
CCL5 0.033 0.011 -10000 0 0 50 50
SDCBP 0.035 0.007 -10000 0 0 21 21
FGFR/FGF2/Syndecan-1 0.014 0.097 0.18 42 -0.24 10 52
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 0.022 0.1 0.2 28 -0.23 13 41
Syndecan-1/Syntenin 0.028 0.11 0.21 37 -0.23 14 51
MAPK3 0.005 0.099 0.18 23 -0.22 19 42
HGF/MET 0.031 0.027 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.012 -10000 0 0 62 62
BSG 0.031 0.013 -10000 0 0 74 74
keratinocyte migration 0.021 0.1 0.2 28 -0.23 13 41
Syndecan-1/RANTES 0.021 0.1 0.21 28 -0.22 12 40
Syndecan-1/CD147 0.024 0.11 0.22 14 -0.22 19 33
Syndecan-1/Syntenin/PIP2 0.025 0.1 0.2 37 -0.23 14 51
LAMA5 0.033 0.011 -10000 0 0 46 46
positive regulation of cell-cell adhesion 0.024 0.1 0.19 37 -0.22 14 51
MMP7 0.026 0.016 -10000 0 0 131 131
HGF 0.024 0.017 -10000 0 0 158 158
Syndecan-1/CASK -0.009 0.077 0.15 3 -0.21 13 16
Syndecan-1/HGF/MET 0.025 0.088 0.24 9 -0.23 6 15
regulation of cell adhesion 0.003 0.11 0.23 39 -0.22 21 60
HPSE 0.032 0.012 -10000 0 0 56 56
positive regulation of cell migration 0.014 0.097 0.18 42 -0.24 10 52
SDC1 0.007 0.089 0.16 26 -0.15 77 103
Syndecan-1/Collagen 0.014 0.097 0.18 42 -0.24 10 52
PPIB 0.034 0.009 -10000 0 0 33 33
MET 0.023 0.018 -10000 0 0 183 183
PRKACA 0.034 0.009 -10000 0 0 29 29
MMP9 0.017 0.018 -10000 0 0 254 254
MAPK1 0.003 0.097 0.18 22 -0.22 20 42
homophilic cell adhesion 0.018 0.1 0.18 51 -0.23 10 61
MMP1 0.031 0.013 -10000 0 0 71 71
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.026 -10000 0 -0.052 53 53
CDKN2C -0.007 0.022 -10000 0 -0.033 117 117
CDKN2A 0.006 0.016 0.085 1 -10000 0 1
CCND2 -0.001 0.02 0.11 7 -10000 0 7
RB1 -0.046 0.089 0.17 1 -0.19 131 132
CDK4 -0.001 0.021 0.13 7 -10000 0 7
CDK6 -0.001 0.021 0.13 7 -10000 0 7
G1/S progression 0.054 0.095 0.19 147 -0.13 5 152
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.035 -10000 0 -0.11 38 38
ARNO/beta Arrestin1-2 0.041 0.026 -10000 0 -0.094 7 7
EGFR 0.01 0.016 -10000 0 0 355 355
EPHA2 0.032 0.011 -10000 0 0 53 53
USP6 0.035 0.007 -10000 0 0 19 19
IQSEC1 0.035 0.007 -10000 0 0 16 16
EGFR/EGFR/EGF/EGF -0.004 0.056 -10000 0 -0.14 60 60
ARRB2 0.012 0.026 -10000 0 -0.2 7 7
mol:GTP 0.002 0.014 0.16 1 -0.064 2 3
ARRB1 0.035 0.005 -10000 0 0 11 11
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.034 0.01 -10000 0 0 39 39
EGF 0.035 0.008 -10000 0 0 24 24
somatostatin receptor activity 0 0 0.001 127 0 4 131
ARAP2 0 0 0 113 0 2 115
mol:GDP 0.068 0.065 0.16 103 -10000 0 103
mol:PI-3-4-5-P3 0 0 0 115 0 4 119
ITGA2B 0.036 0.003 -10000 0 0 3 3
ARF6 0.035 0.007 -10000 0 0 21 21
Ephrin A1/EPHA2/NCK1/GIT1 0.074 0.052 -10000 0 -0.13 21 21
ADAP1 0 0 0 56 -10000 0 56
KIF13B 0.032 0.012 -10000 0 0 62 62
HGF/MET 0.031 0.027 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 5 5
ARF6/GTP 0.083 0.084 0.19 112 -0.2 4 116
EGFR/EGFR/EGF/EGF/ARFGEP100 0.002 0.055 -10000 0 -0.12 58 58
ADRB2 0.033 0.01 -10000 0 0 40 40
receptor agonist activity 0 0 0 118 0 4 122
actin filament binding 0 0 0 125 0 4 129
SRC 0.035 0.006 -10000 0 0 13 13
ITGB3 0.036 0.004 -10000 0 0 5 5
GNAQ 0.034 0.009 -10000 0 0 31 31
EFA6/PI-4-5-P2 0.001 0.001 0.001 149 -0.001 3 152
ARF6/GDP 0.038 0.061 0.16 15 -0.2 11 26
ARF6/GDP/GULP/ACAP1 0.056 0.072 0.2 17 -0.16 2 19
alphaIIb/beta3 Integrin/paxillin/GIT1 0.092 0.01 -10000 0 -10000 0 0
ACAP1 0 0 0 45 -10000 0 45
ACAP2 0 0 0 68 0 3 71
LHCGR/beta Arrestin2 0.029 0.025 -10000 0 -0.14 7 7
EFNA1 0.033 0.011 -10000 0 0 47 47
HGF 0.024 0.017 -10000 0 0 158 158
CYTH3 0 0 0.001 122 -0.001 3 125
CYTH2 0 0.001 0.003 5 -0.004 4 9
NCK1 0.034 0.008 -10000 0 0 26 26
fibronectin binding 0 0 0 130 0 3 133
endosomal lumen acidification 0 0 0 123 0 2 125
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.024 0.017 -10000 0 0 161 161
GNAQ/ARNO 0.026 0.008 0.04 6 0 31 37
mol:Phosphatidic acid 0 0 0 68 0 3 71
PIP3-E 0.03 0.014 -10000 0 0 87 87
MET 0.023 0.018 -10000 0 0 183 183
GNA14 0.034 0.009 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GIT1 0.036 0.003 -10000 0 0 4 4
mol:PI-4-5-P2 0 0 0.001 132 -0.001 3 135
GNA11 0.032 0.012 -10000 0 0 60 60
LHCGR 0.036 0.002 -10000 0 0 2 2
AGTR1 0.035 0.007 -10000 0 0 20 20
desensitization of G-protein coupled receptor protein signaling pathway 0.029 0.025 -10000 0 -0.14 7 7
IPCEF1/ARNO 0.005 0.041 -10000 0 -0.092 47 47
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.013 0.011 0 211 -10000 0 211
MAP4K4 0.003 0.054 -10000 0 -0.21 11 11
BAG4 0.035 0.005 -10000 0 0 11 11
PKC zeta/ceramide -0.045 0.13 -10000 0 -0.23 111 111
NFKBIA 0.033 0.011 -10000 0 0 47 47
BIRC3 0.03 0.013 -10000 0 0 77 77
BAX -0.022 0.1 -10000 0 -0.35 32 32
RIPK1 0.035 0.007 -10000 0 0 18 18
AKT1 -0.001 0.088 0.67 6 -10000 0 6
BAD -0.05 0.13 0.22 2 -0.24 109 111
SMPD1 -0.003 0.05 0.15 1 -0.18 20 21
RB1 -0.047 0.14 0.21 10 -0.24 110 120
FADD/Caspase 8 0.015 0.051 -10000 0 -0.23 6 6
MAP2K4 -0.051 0.13 0.19 5 -0.24 107 112
NSMAF 0.034 0.008 -10000 0 0 28 28
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.053 0.13 0.19 9 -0.24 108 117
EGF 0.034 0.008 -10000 0 0 24 24
mol:ceramide -0.046 0.14 -10000 0 -0.25 111 111
MADD 0.035 0.006 -10000 0 0 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.013 0.011 0 207 -10000 0 207
ASAH1 0.035 0.007 -10000 0 0 17 17
negative regulation of cell cycle -0.046 0.13 0.21 10 -0.24 110 120
cell proliferation -0.022 0.12 0.2 5 -0.22 95 100
BID -0.037 0.2 -10000 0 -0.62 46 46
MAP3K1 -0.048 0.13 0.17 2 -0.24 107 109
EIF2A -0.053 0.12 0.19 2 -0.23 108 110
TRADD 0.036 0.004 -10000 0 0 7 7
CRADD 0.035 0.006 -10000 0 0 12 12
MAPK3 -0.045 0.12 0.2 8 -0.22 97 105
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.054 0.13 0.19 9 -0.24 106 115
Cathepsin D/ceramide -0.033 0.14 -10000 0 -0.24 111 111
FADD 0.008 0.048 -10000 0 -0.21 5 5
KSR1 -0.051 0.13 -10000 0 -0.24 111 111
MAPK8 -0.084 0.16 0.16 2 -0.25 174 176
PRKRA -0.053 0.13 -10000 0 -0.24 111 111
PDGFA 0.021 0.018 -10000 0 0 201 201
TRAF2 0.035 0.006 -10000 0 0 14 14
IGF1 0.035 0.007 -10000 0 0 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.046 0.14 -10000 0 -0.25 111 111
CTSD 0.032 0.012 -10000 0 0 55 55
regulation of nitric oxide biosynthetic process 0.049 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.023 0.13 0.21 5 -0.23 95 100
PRKCD 0.034 0.01 -10000 0 0 36 36
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.013 0.011 0 207 -10000 0 207
RelA/NF kappa B1 0.049 0.025 -10000 0 -0.14 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.035 0.006 -10000 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.054 -10000 0 -0.23 6 6
TNFR1A/BAG4/TNF-alpha 0.053 0.055 -10000 0 -0.12 39 39
mol:Sphingosine-1-phosphate -0.013 0.011 0 211 -10000 0 211
MAP2K1 -0.057 0.12 0.18 9 -0.23 108 117
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 10 10
CYCS -0.013 0.085 0.13 1 -0.27 28 29
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
NFKB1 0.035 0.007 -10000 0 0 17 17
TNFR1A/BAG4 0.034 0.054 -10000 0 -0.14 40 40
EIF2AK2 -0.056 0.13 0.2 2 -0.24 108 110
TNF-alpha/TNFR1A/FAN 0.047 0.066 -10000 0 -0.13 52 52
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.033 0.053 -10000 0 -0.3 5 5
MAP2K2 -0.046 0.12 0.18 21 -0.23 99 120
SMPD3 0.006 0.056 0.16 1 -0.31 6 7
TNF 0.036 0.004 -10000 0 0 6 6
PKC zeta/PAR4 0.026 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.023 0.075 0.13 7 -0.14 102 109
NF kappa B1/RelA/I kappa B alpha 0.07 0.045 -10000 0 -0.12 18 18
AIFM1 -0.034 0.095 0.13 1 -0.23 50 51
BCL2 0.035 0.007 -10000 0 0 17 17
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 -0.003 0.11 0.19 88 -10000 0 88
GNAI2 0.033 0.01 -10000 0 0 42 42
S1P/S1P5/G12 0.011 0.032 -10000 0 -0.11 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
RhoA/GTP 0.003 0.11 -10000 0 -0.2 88 88
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.21 84 84
GNAZ 0.03 0.013 -10000 0 0 79 79
GNAI3 0.035 0.006 -10000 0 0 12 12
GNA12 0.026 0.016 -10000 0 0 136 136
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.21 84 84
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 0 246 246
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.033 0.01 -9999 0 0 41 41
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.036 0.004 -9999 0 0 5 5
TCEB1 0.035 0.007 -9999 0 0 20 20
HIF1A/p53 -0.036 0.12 -9999 0 -0.27 88 88
HIF1A -0.031 0.11 -9999 0 -0.27 75 75
COPS5 0.035 0.006 -9999 0 0 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2 0.05 0.058 -9999 0 -0.13 20 20
FIH (dimer) 0.027 0.016 -9999 0 0 124 124
CDKN2A 0.005 0.013 -9999 0 0 417 417
ARNT/IPAS 0.048 0.016 -9999 0 -10000 0 0
HIF1AN 0.027 0.016 -9999 0 0 124 124
GNB2L1 0.035 0.005 -9999 0 0 11 11
HIF1A/ARNT -0.034 0.13 -9999 0 -0.28 88 88
CUL2 0.026 0.016 -9999 0 0 131 131
OS9 0.03 0.014 -9999 0 0 89 89
RACK1/Elongin B/Elongin C 0.066 0.032 -9999 0 -0.13 9 9
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.049 0.12 -9999 0 -0.27 90 90
PHD1-3/OS9 0.056 0.062 -9999 0 -0.14 25 25
HIF1A/RACK1/Elongin B/Elongin C -0.015 0.14 -9999 0 -0.27 89 89
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.035 0.13 -9999 0 -0.28 92 92
EGLN3 0.03 0.014 -9999 0 0 83 83
EGLN2 0.034 0.008 -9999 0 0 27 27
EGLN1 0.034 0.009 -9999 0 0 31 31
TP53 0.031 0.013 -9999 0 0 75 75
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.007 0.1 -9999 0 -0.61 12 12
ARNT 0.036 0.005 -9999 0 0 10 10
ARD1A 0.036 0.003 -9999 0 0 4 4
RBX1 0.033 0.01 -9999 0 0 41 41
HIF1A/p19ARF -0.045 0.1 -9999 0 -0.26 82 82
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.004 0.058 -10000 0 -0.14 60 60
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.096 0.2 12 -0.21 36 48
AP1 -0.012 0.074 0.09 1 -0.14 92 93
mol:PIP3 -0.021 0.048 -10000 0 -0.13 65 65
AKT1 -0.006 0.093 0.22 14 -0.24 29 43
PTK2B -0.002 0.059 0.12 4 -0.15 57 61
RHOA 0.011 0.077 0.17 18 -0.34 12 30
PIK3CB 0.035 0.007 -10000 0 0 16 16
mol:Ca2+ -0.009 0.04 0.17 5 -0.14 19 24
MAGI3 0 0 -10000 0 -0.002 1 1
RELA 0.036 0.005 -10000 0 0 10 10
apoptosis 0.001 0.064 0.1 35 -0.16 53 88
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
positive regulation of microtubule depolymerization -0.02 0.074 0.17 9 -0.21 35 44
NF kappa B1 p50/RelA -0.021 0.066 0.085 28 -0.17 49 77
endothelial cell migration -0.018 0.099 -10000 0 -0.3 53 53
ADCY4 -0.016 0.083 0.15 12 -0.23 39 51
ADCY5 -0.016 0.083 0.15 12 -0.23 39 51
ADCY6 -0.003 0.089 0.17 11 -0.24 35 46
ADCY7 -0.006 0.094 0.16 11 -0.24 40 51
ADCY1 -0.009 0.082 0.16 6 -0.25 32 38
ADCY2 -0.005 0.092 0.17 11 -0.24 39 50
ADCY3 -0.016 0.083 0.15 12 -0.23 39 51
ADCY8 -0.005 0.089 0.16 12 -0.24 37 49
ADCY9 -0.004 0.091 0.16 12 -0.24 38 50
GSK3B -0.009 0.064 0.18 5 -0.16 53 58
arachidonic acid secretion -0.021 0.11 0.15 10 -0.24 67 77
GNG2 0 0.001 0.002 2 -0.003 17 19
TRIP6 -0.014 0.082 -10000 0 -0.25 51 51
GNAO1 0.003 0.059 0.13 25 -0.16 47 72
HRAS 0.034 0.009 -10000 0 0 32 32
NFKBIA -0.013 0.083 0.17 14 -0.21 39 53
GAB1 0.031 0.013 -10000 0 0 75 75
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.005 0.21 -10000 0 -0.81 30 30
JUN 0.033 0.01 -10000 0 0 39 39
LPA/LPA2/NHERF2 0.018 0.029 -10000 0 -0.061 53 53
TIAM1 -0.016 0.25 -10000 0 -0.98 30 30
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 -0.008 0.039 0.18 4 -0.14 19 23
PLCB3 0.006 0.034 0.2 3 -10000 0 3
FOS 0.025 0.017 -10000 0 0 147 147
positive regulation of mitosis -0.021 0.11 0.15 10 -0.24 67 77
LPA/LPA1-2-3 -0.008 0.041 -10000 0 -0.12 53 53
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.009 0.067 -10000 0 -0.28 9 9
GNAZ 0.002 0.063 0.12 26 -0.17 47 73
EGFR/PI3K-beta/Gab1 -0.017 0.052 -10000 0 -0.13 66 66
positive regulation of dendritic cell cytokine production -0.009 0.041 -10000 0 -0.12 53 53
LPA/LPA2/MAGI-3 -0.004 0.017 -10000 0 -0.052 53 53
ARHGEF1 0.018 0.1 0.18 106 -0.16 39 145
GNAI2 0.003 0.07 0.13 38 -0.17 53 91
GNAI3 0.006 0.064 0.13 39 -0.16 53 92
GNAI1 0.002 0.047 0.13 18 -0.16 28 46
LPA/LPA3 -0.006 0.021 -10000 0 -0.066 53 53
LPA/LPA2 -0.006 0.021 -10000 0 -0.066 53 53
LPA/LPA1 -0.013 0.055 -10000 0 -0.17 53 53
HB-EGF/EGFR -0.01 0.056 0.099 10 -0.13 66 76
HBEGF -0.01 0.011 0 264 -10000 0 264
mol:DAG -0.008 0.039 0.18 4 -0.14 19 23
cAMP biosynthetic process -0.004 0.11 0.18 27 -0.25 45 72
NFKB1 0.035 0.007 -10000 0 0 17 17
SRC 0.035 0.006 -10000 0 0 13 13
GNB1 0.033 0.01 -10000 0 0 37 37
LYN -0.02 0.095 0.17 16 -0.22 57 73
GNAQ 0.008 0.027 0.057 37 -0.058 55 92
LPAR2 0 0.001 0.002 1 -0.003 3 4
LPAR3 0 0.001 -10000 0 -0.002 4 4
LPAR1 -0.01 0.033 -10000 0 -0.1 53 53
IL8 -0.12 0.2 0.32 8 -0.39 151 159
PTK2 0.013 0.059 0.12 39 -0.14 51 90
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
CASP3 0.001 0.064 0.1 35 -0.16 53 88
EGFR 0.01 0.016 -10000 0 0 355 355
PLCG1 0.004 0.039 0.069 11 -0.084 55 66
PLD2 0.015 0.054 0.12 37 -0.12 50 87
G12/G13 0.015 0.064 -10000 0 -0.15 52 52
PI3K-beta -0.014 0.071 -10000 0 -0.23 28 28
cell migration 0.001 0.075 -10000 0 -0.25 29 29
SLC9A3R2 0.036 0.004 -10000 0 0 5 5
PXN 0.009 0.068 -10000 0 -0.29 9 9
HRAS/GTP -0.023 0.11 0.15 8 -0.25 65 73
RAC1 0.027 0.016 -10000 0 0 123 123
MMP9 0.017 0.018 -10000 0 0 254 254
PRKCE 0.036 0.004 -10000 0 0 7 7
PRKCD -0.004 0.055 0.18 13 -0.2 3 16
Gi(beta/gamma) -0.014 0.12 0.16 10 -0.26 62 72
mol:LPA -0.01 0.033 -10000 0 -0.1 53 53
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.082 -10000 0 -0.3 21 21
MAPKKK cascade -0.021 0.11 0.15 10 -0.24 67 77
contractile ring contraction involved in cytokinesis 0.014 0.078 0.17 20 -0.34 12 32
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.027 0.057 36 -0.058 55 91
GNA15 0.007 0.026 0.057 32 -0.058 53 85
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
MAPT -0.02 0.075 0.17 9 -0.22 35 44
GNA11 0.01 0.023 0.057 36 -0.057 36 72
Rac1/GTP -0.006 0.22 -10000 0 -0.86 30 30
MMP2 -0.018 0.1 -10000 0 -0.3 53 53
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
CDC42/GTP 0.002 0.11 -10000 0 -0.19 89 89
PLCG1 -0.016 0.1 0.11 1 -0.2 86 87
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
G12/G13 0.028 0.049 -10000 0 -0.14 30 30
cell migration 0.002 0.11 -10000 0 -0.19 89 89
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.016 0.1 0.11 1 -0.2 91 92
MAPK1 -0.008 0.094 0.11 1 -0.19 79 80
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.21 84 84
GNAI1 0.018 0.018 -10000 0 0 246 246
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.011 0.032 -10000 0 -0.11 31 31
RHOA 0.02 0.09 0.18 111 -0.18 3 114
S1P/S1P4/Gi -0.014 0.1 -10000 0 -0.21 84 84
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.03 0.013 -10000 0 0 79 79
S1P/S1P4/G12/G13 0.026 0.038 -10000 0 -0.1 30 30
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
CDC42 0.035 0.008 -10000 0 0 22 22
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.003 0 29 -10000 0 29
GNB1/GNG2 0.037 0.032 -10000 0 -0.1 20 20
regulation of S phase of mitotic cell cycle -0.006 0.081 -10000 0 -0.18 72 72
GNAO1 0.03 0.014 -10000 0 0 81 81
HRAS 0.034 0.01 -10000 0 -0.001 33 33
SHBG/T-DHT 0.024 0.005 -10000 0 -10000 0 0
PELP1 0.035 0.008 -10000 0 -0.002 20 20
AKT1 -0.01 0.004 0 53 -10000 0 53
MAP2K1 -0.036 0.076 0.18 14 -0.17 70 84
T-DHT/AR 0.025 0.007 -10000 0 -0.026 1 1
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.003 49 -0.006 73 122
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
GNAI1 0.018 0.018 -10000 0 0 246 246
mol:GDP -0.021 0.035 -10000 0 -0.15 14 14
cell proliferation -0.057 0.18 0.27 15 -0.42 82 97
PIK3CA 0.03 0.014 -10000 0 0 85 85
FOS -0.086 0.28 0.3 7 -0.69 79 86
mol:Ca2+ -0.005 0.021 0.027 5 -0.054 62 67
MAPK3 -0.041 0.13 0.26 15 -0.3 79 94
MAPK1 -0.04 0.16 0.24 3 -0.48 39 42
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0 0.002 0.003 57 -0.004 72 129
cAMP biosynthetic process -0.001 0.014 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 0.003 57 -0.004 72 129
HRAS/GTP 0.042 0.066 -10000 0 -0.094 72 72
actin cytoskeleton reorganization 0.019 0.055 -10000 0 -0.12 47 47
SRC 0.035 0.006 -10000 0 0 13 13
voltage-gated calcium channel activity 0 0.002 0.003 57 -0.004 72 129
PI3K 0.017 0.063 -10000 0 -0.13 73 73
apoptosis 0.047 0.19 0.43 79 -0.25 11 90
T-DHT/AR/PELP1 0.043 0.024 -10000 0 -0.11 8 8
HRAS/GDP 0.007 0.062 -10000 0 -0.18 16 16
CREB1 -0.067 0.2 0.25 11 -0.47 79 90
RAC1-CDC42/GTP 0.029 0.061 -10000 0 -0.12 47 47
AR 0.034 0.008 -10000 0 -0.001 22 22
GNB1 0.033 0.01 -10000 0 0 37 37
RAF1 -0.027 0.068 0.2 12 -0.22 13 25
RAC1-CDC42/GDP 0.025 0.057 -10000 0 -0.17 13 13
T-DHT/AR/PELP1/Src 0.059 0.032 -10000 0 -0.12 7 7
MAP2K2 -0.039 0.068 0.17 5 -0.17 67 72
T-DHT/AR/PELP1/Src/PI3K -0.006 0.082 -10000 0 -0.18 72 72
GNAZ 0.03 0.013 -10000 0 0 79 79
SHBG 0.035 0.007 -10000 0 0 18 18
Gi family/GNB1/GNG2/GDP -0.047 0.18 -10000 0 -0.43 63 63
mol:T-DHT 0 0.001 0.002 1 -0.004 20 21
RAC1 0.027 0.016 -10000 0 0 123 123
GNRH1 -0.011 0.002 0.001 12 -10000 0 12
Gi family/GTP -0.01 0.087 -10000 0 -0.19 70 70
CDC42 0.035 0.008 -10000 0 0 22 22
Wnt signaling

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
Noncanonical Wnts/FZD -0.006 0.088 -9999 0 -0.28 16 16
FZD6 0.027 0.016 -9999 0 0 121 121
WNT6 0.036 0.002 -9999 0 0 2 2
WNT4 0.035 0.007 -9999 0 0 18 18
FZD3 0.028 0.015 -9999 0 0 104 104
WNT5A 0.03 0.014 -9999 0 0 89 89
WNT11 0.035 0.006 -9999 0 0 15 15
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.029 0.014 -9999 0 0 94 94
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.006 0.05 -9999 0 -0.13 56 56
neuron projection morphogenesis 0.006 0.05 -9999 0 -0.13 56 56
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 0.032 0.013 -10000 0 -0.004 52 52
ELF1 0.042 0.015 -10000 0 -10000 0 0
CCNA2 0.028 0.015 -10000 0 0 109 109
PIK3CA 0.029 0.016 -10000 0 -0.002 92 92
JAK3 0.033 0.012 -10000 0 -0.007 38 38
PIK3R1 0.031 0.014 -10000 0 -0.002 66 66
JAK1 0.033 0.012 -10000 0 -0.003 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.019 0.18 0.23 2 -0.51 40 42
SHC1 0.032 0.014 -10000 0 -0.004 56 56
SP1 -0.013 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 -0.003 60 60
SOS1 0 0.002 -10000 0 -10000 0 0
IL2RG 0.034 0.011 -10000 0 -0.006 30 30
G1/S transition of mitotic cell cycle -0.071 0.27 0.28 13 -0.58 91 104
PTPN11 0.035 0.009 -10000 0 -0.013 16 16
CCND2 -0.071 0.19 -10000 0 -0.49 82 82
LCK 0.035 0.01 -10000 0 -0.008 23 23
GRB2 0.035 0.01 -10000 0 -0.009 23 23
IL2 0.035 0.009 -10000 0 -0.014 15 15
CDK6 0.025 0.017 -10000 0 0 156 156
CCND3 -0.026 0.2 0.35 2 -0.72 28 30
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.029 0.085 -10000 0 -0.14 82 82
alphaM/beta2 Integrin/GPIbA 0.05 0.068 -10000 0 -0.12 53 53
alphaM/beta2 Integrin/proMMP-9 -0.007 0.09 -10000 0 -0.13 137 137
PLAUR 0.03 0.014 -10000 0 0 89 89
HMGB1 0.039 0.013 0.081 2 -10000 0 2
alphaM/beta2 Integrin/Talin 0.039 0.071 -10000 0 -0.13 51 51
AGER 0.041 0.011 0.081 2 -10000 0 2
RAP1A 0.036 0.005 -10000 0 0 8 8
SELPLG 0.036 0.004 -10000 0 0 6 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.077 0.082 -10000 0 -0.12 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.017 0.018 -10000 0 0 254 254
CYR61 0.025 0.017 -10000 0 0 157 157
TLN1 0.029 0.014 -10000 0 0 94 94
Rap1/GTP 0.028 0.069 -10000 0 -0.22 14 14
RHOA 0.035 0.007 -10000 0 0 21 21
P-selectin oligomer 0.035 0.006 -10000 0 0 14 14
MYH2 0.028 0.07 0.19 5 -0.28 6 11
MST1R 0.035 0.007 -10000 0 0 19 19
leukocyte activation during inflammatory response 0.051 0.061 -10000 0 -0.1 43 43
APOB 0.035 0.006 -10000 0 0 12 12
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 0 103 103
JAM3 0.033 0.011 -10000 0 0 50 50
GP1BA 0.035 0.006 -10000 0 0 12 12
alphaM/beta2 Integrin/CTGF 0.022 0.085 -10000 0 -0.13 96 96
alphaM/beta2 Integrin 0.025 0.071 -10000 0 -0.24 14 14
JAM3 homodimer 0.032 0.011 -10000 0 0 50 50
ICAM2 0.034 0.009 -10000 0 0 29 29
ICAM1 0.03 0.014 -10000 0 0 89 89
phagocytosis triggered by activation of immune response cell surface activating receptor 0.024 0.071 -10000 0 -0.23 15 15
cell adhesion 0.049 0.067 -10000 0 -0.12 53 53
NFKB1 -0.002 0.078 0.21 21 -0.2 2 23
THY1 0.031 0.013 -10000 0 0 76 76
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Lipoprotein(a) 0.042 0.017 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.036 0.1 -10000 0 -0.15 94 94
IL6 -0.017 0.036 -10000 0 -10000 0 0
ITGB2 0.033 0.019 0.079 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.029 0.084 -10000 0 -0.14 63 63
alphaM/beta2 Integrin/JAM2/JAM3 0.048 0.099 -10000 0 -0.15 81 81
JAM2 0.032 0.011 -10000 0 0 53 53
alphaM/beta2 Integrin/ICAM1 0.077 0.072 -10000 0 -0.12 36 36
alphaM/beta2 Integrin/uPA/Plg 0.038 0.081 -10000 0 -0.12 59 59
RhoA/GTP 0.033 0.073 0.19 5 -0.25 10 15
positive regulation of phagocytosis 0.016 0.1 -10000 0 -0.24 44 44
Ron/MSP 0.05 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.086 -10000 0 -0.14 63 63
alphaM/beta2 Integrin/uPAR 0.038 0.074 -10000 0 -0.13 57 57
PLAU 0.02 0.018 -10000 0 0 213 213
PLAT 0.027 0.016 -10000 0 0 124 124
actin filament polymerization 0.029 0.071 0.2 7 -0.27 6 13
MST1 0.034 0.008 -10000 0 0 24 24
alphaM/beta2 Integrin/lipoprotein(a) 0.06 0.064 -10000 0 -0.11 43 43
TNF 0.006 0.089 0.21 41 -10000 0 41
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.072 -10000 0 -0.13 61 61
fibrinolysis 0.036 0.079 -10000 0 -0.12 59 59
HCK 0.027 0.016 -10000 0 0 123 123
dendritic cell antigen processing and presentation 0.024 0.071 -10000 0 -0.23 15 15
VTN 0.036 0.004 -10000 0 0 5 5
alphaM/beta2 Integrin/CYR61 0.012 0.093 -10000 0 -0.14 115 115
LPA 0.032 0.012 -10000 0 0 56 56
LRP1 0.031 0.013 -10000 0 0 68 68
cell migration -0.001 0.1 0.15 6 -0.14 140 146
FN1 0.034 0.009 -10000 0 0 29 29
alphaM/beta2 Integrin/Thy1 0.031 0.084 -10000 0 -0.14 81 81
MPO 0.036 0.003 -10000 0 0 4 4
KNG1 0.035 0.006 -10000 0 0 15 15
RAP1/GDP 0.024 0.007 -10000 0 -0.11 1 1
ROCK1 0.027 0.072 0.19 5 -0.27 8 13
ELA2 0.033 0.01 -10000 0 0 38 38
PLG 0.034 0.009 -10000 0 0 34 34
CTGF 0.027 0.016 -10000 0 0 128 128
alphaM/beta2 Integrin/Hck 0.03 0.091 -10000 0 -0.17 67 67
ITGAM 0.041 0.01 0.08 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.07 -10000 0 -0.12 48 48
HP 0.026 0.016 -10000 0 0 132 132
leukocyte adhesion 0.022 0.11 -10000 0 -0.27 31 31
SELP 0.035 0.006 -10000 0 0 14 14
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.066 0.058 -10000 0 -0.12 30 30
MAP4K1 0.034 0.008 -10000 0 0 26 26
MAP3K8 0.023 0.018 -10000 0 0 182 182
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.034 0.008 -10000 0 0 25 25
MAP3K1 0.002 0.051 -10000 0 -0.15 29 29
JUN -0.14 0.24 0.22 1 -0.51 133 134
MAP3K7 0.002 0.051 -10000 0 -0.16 28 28
GRAP2 0.034 0.009 -10000 0 0 33 33
CRK 0.035 0.008 -10000 0 0 23 23
MAP2K4 -0.013 0.068 -10000 0 -0.24 18 18
LAT 0.036 0.005 -10000 0 0 9 9
LCP2 0.031 0.013 -10000 0 0 71 71
MAPK8 -0.13 0.25 -10000 0 -0.53 133 133
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.012 0.056 -10000 0 -0.16 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.061 0.054 -10000 0 -0.11 30 30
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.046 0.081 0.34 2 -0.32 1 3
CRKL 0.048 0.097 0.17 148 -10000 0 148
mol:DAG 0.017 0.063 0.21 4 -0.18 26 30
HRAS 0.052 0.11 0.24 65 -0.19 2 67
MAPK8 0.015 0.074 0.16 83 -10000 0 83
RAP1A 0.049 0.098 0.17 154 -10000 0 154
GAB1 0.041 0.092 0.17 144 -10000 0 144
MAPK14 0.025 0.089 0.16 128 -10000 0 128
EPO 0.029 0.02 -10000 0 -0.032 2 2
PLCG1 0.017 0.064 0.22 4 -0.19 26 30
EPOR/TRPC2/IP3 Receptors 0.04 0.015 0.092 2 -0.032 2 4
RAPGEF1 0.035 0.007 -10000 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.053 0.038 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.06 0.074 0.23 29 -10000 0 29
EPO/EPOR (dimer) 0.04 0.03 -10000 0 -10000 0 0
IRS2 0.038 0.091 0.17 129 -0.16 3 132
STAT1 0.022 0.068 0.24 6 -0.23 7 13
STAT5B 0.021 0.065 0.23 5 -0.2 9 14
cell proliferation 0.012 0.075 0.16 85 -10000 0 85
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.062 0.15 4 -0.18 6 10
TEC 0.05 0.098 0.17 156 -10000 0 156
SOCS3 0.036 0.004 -10000 0 0 5 5
STAT1 (dimer) 0.022 0.067 0.24 6 -0.22 7 13
JAK2 0.036 0.018 0.075 1 -10000 0 1
PIK3R1 0.032 0.012 -10000 0 0 61 61
EPO/EPOR (dimer)/JAK2 0.045 0.052 0.22 8 -10000 0 8
EPO/EPOR 0.04 0.03 -10000 0 -10000 0 0
LYN 0.032 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.063 0.072 0.22 36 -10000 0 36
elevation of cytosolic calcium ion concentration 0.04 0.015 0.092 2 -0.032 2 4
SHC1 0.033 0.011 -10000 0 0 48 48
EPO/EPOR (dimer)/LYN 0.041 0.059 -10000 0 -0.13 28 28
mol:IP3 0.017 0.063 0.21 4 -0.18 26 30
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.089 0.23 31 -0.17 13 44
SH2B3 -0.001 0.006 0.025 19 -10000 0 19
NFKB1 0.025 0.089 0.16 127 -0.2 1 128
EPO/EPOR (dimer)/JAK2/SOCS3 0.015 0.013 -10000 0 -10000 0 0
PTPN6 0.047 0.095 0.18 152 -10000 0 152
TEC/VAV2/GRB2 0.083 0.074 0.24 37 -10000 0 37
EPOR 0.04 0.015 0.092 2 -0.032 2 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.059 0.074 0.23 29 -10000 0 29
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.032 0.012 -10000 0 0 61 61
CRKL/CBL/C3G 0.082 0.073 0.24 37 -10000 0 37
VAV2 0.049 0.097 0.17 156 -10000 0 156
CBL 0.05 0.098 0.17 171 -10000 0 171
SHC/Grb2/SOS1 0.02 0.034 -10000 0 -0.11 1 1
STAT5A 0.021 0.064 0.24 4 -0.18 23 27
GRB2 0.035 0.006 -10000 0 0 16 16
STAT5 (dimer) 0.035 0.072 0.26 8 -0.22 1 9
LYN/PLCgamma2 0.026 0.069 -10000 0 -0.17 49 49
PTPN11 0.036 0.005 -10000 0 0 9 9
BTK 0.047 0.098 0.17 151 -10000 0 151
BCL2 0.047 0.083 0.31 1 -10000 0 1
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.032 0.012 -10000 0 0 57 57
LAT2 -0.014 0.088 0.12 2 -0.26 43 45
AP1 -0.055 0.18 -10000 0 -0.39 65 65
mol:PIP3 0.021 0.13 0.25 38 -0.3 30 68
IKBKB 0.012 0.092 0.19 36 -0.19 32 68
AKT1 -0.049 0.11 0.23 16 -0.26 50 66
IKBKG 0.011 0.09 0.19 31 -0.19 32 63
MS4A2 0.039 0.007 0.064 5 0 3 8
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
MAP3K1 -0.015 0.12 0.22 13 -0.31 41 54
mol:Ca2+ 0.022 0.11 0.22 42 -0.24 29 71
LYN 0.03 0.015 -10000 0 -0.033 6 6
CBLB -0.02 0.11 0.18 1 -0.27 60 61
SHC1 0.033 0.011 -10000 0 0 48 48
RasGAP/p62DOK 0.047 0.052 -10000 0 -0.12 36 36
positive regulation of cell migration -0.01 0.003 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.07 0.3 10 -0.17 13 23
PTPN13 -0.03 0.18 -10000 0 -0.62 29 29
PTPN11 0.031 0.022 -10000 0 -0.034 44 44
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.03 0.11 0.24 6 -0.31 33 39
SYK 0.03 0.015 -10000 0 -0.033 6 6
GRB2 0.035 0.007 -10000 0 0 16 16
LAT/PLCgamma1/GRB2/SLP76/GADs 0.011 0.11 0.21 7 -0.28 45 52
LAT -0.018 0.11 0.13 5 -0.27 58 63
PAK2 -0.014 0.12 0.22 14 -0.33 42 56
NFATC2 -0.012 0.013 -10000 0 -0.042 64 64
HRAS -0.014 0.13 0.2 13 -0.34 47 60
GAB2 0.033 0.01 -10000 0 0 44 44
PLA2G1B -0.005 0.19 -10000 0 -0.91 19 19
Fc epsilon R1 0.041 0.066 -10000 0 -0.11 66 66
Antigen/IgE/Fc epsilon R1 0.042 0.059 -10000 0 -0.093 65 65
mol:GDP -0.007 0.13 0.2 11 -0.36 43 54
JUN 0.033 0.01 -10000 0 0 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
FOS 0.025 0.017 -10000 0 0 147 147
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.11 -10000 0 -0.28 62 62
CHUK 0.013 0.089 0.18 36 -0.18 35 71
KLRG1 -0.017 0.094 0.12 2 -0.26 45 47
VAV1 -0.018 0.1 0.14 8 -0.28 53 61
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.02 0.11 0.18 1 -0.27 61 62
negative regulation of mast cell degranulation -0.02 0.087 -10000 0 -0.25 44 44
BTK -0.009 0.13 -10000 0 -0.36 41 41
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.025 0.1 -10000 0 -0.2 97 97
GAB2/PI3K/SHP2 -0.067 0.073 -10000 0 -0.2 84 84
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.004 0.071 -10000 0 -0.18 56 56
RAF1 -0.008 0.2 -10000 0 -0.97 19 19
Fc epsilon R1/FcgammaRIIB/SHIP 0.023 0.093 -10000 0 -0.13 121 121
FCER1G 0.029 0.015 -10000 0 0 106 106
FCER1A 0.033 0.012 -10000 0 -0.032 6 6
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.081 -10000 0 -0.11 92 92
MAPK3 -0.004 0.19 -10000 0 -0.9 19 19
MAPK1 -0.014 0.2 -10000 0 -0.95 19 19
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.12 0.28 -10000 0 -0.55 140 140
DUSP1 0.031 0.013 -10000 0 0 75 75
NF-kappa-B/RelA 0.018 0.064 0.14 27 -0.13 32 59
actin cytoskeleton reorganization -0.02 0.18 -10000 0 -0.6 30 30
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.01 0.14 0.23 4 -0.32 59 63
FER -0.019 0.11 0.14 6 -0.27 62 68
RELA 0.036 0.005 -10000 0 0 10 10
ITK 0.003 0.036 -10000 0 -0.21 4 4
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.002 0.13 0.24 18 -0.34 41 59
cytokine secretion 0.01 0.044 0.085 26 -0.093 34 60
SPHK1 -0.016 0.11 0.15 4 -0.27 60 64
PTK2 -0.023 0.19 -10000 0 -0.63 30 30
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.024 0.12 0.26 9 -0.28 44 53
EDG1 -0.01 0.003 -10000 0 -10000 0 0
mol:DAG 0.005 0.14 0.24 34 -0.32 41 75
MAP2K2 -0.004 0.2 -10000 0 -0.92 19 19
MAP2K1 -0.018 0.18 -10000 0 -0.92 19 19
MAP2K7 0.034 0.009 -10000 0 0 30 30
KLRG1/SHP2 0.004 0.094 0.2 10 -0.24 42 52
MAP2K4 0.021 0.15 -10000 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.025 0.1 -10000 0 -0.14 121 121
mol:Choline -0.031 0.069 0.3 10 -0.17 13 23
SHC/Grb2/SOS1 0.015 0.12 0.19 1 -0.27 60 61
FYN 0.03 0.014 -10000 0 0 83 83
DOK1 0.036 0.002 -10000 0 0 2 2
PXN -0.024 0.18 -10000 0 -0.59 29 29
HCLS1 -0.022 0.12 0.16 7 -0.3 61 68
PRKCB 0.014 0.11 0.21 38 -0.24 35 73
FCGR2B 0.02 0.018 -10000 0 0 214 214
IGHE -0.001 0.004 0.02 2 -10000 0 2
KLRG1/SHIP -0.021 0.089 -10000 0 -0.26 44 44
LCP2 0.031 0.013 -10000 0 0 71 71
PLA2G4A -0.012 0.11 0.14 11 -0.29 54 65
RASA1 0.034 0.009 -10000 0 0 30 30
mol:Phosphatidic acid -0.031 0.069 0.3 10 -0.17 13 23
IKK complex 0.008 0.077 0.18 27 -0.16 20 47
WIPF1 0 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling 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
Syndecan-2/Fibronectin 0.014 0.06 -10000 0 -0.13 62 62
EPHB2 0.034 0.009 -10000 0 0 35 35
Syndecan-2/TACI 0.018 0.054 -10000 0 -0.12 59 59
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.071 -10000 0 -0.12 76 76
HRAS 0.034 0.009 -10000 0 0 32 32
Syndecan-2/CASK -0.008 0.041 -10000 0 -0.11 62 62
ITGA5 0.032 0.012 -10000 0 0 56 56
BAX -0.009 0.068 -10000 0 -0.83 3 3
EPB41 0.036 0.005 -10000 0 0 10 10
positive regulation of cell-cell adhesion 0.014 0.054 -10000 0 -0.11 66 66
LAMA3 0.033 0.011 -10000 0 0 45 45
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 0 232 232
Syndecan-2/MMP2 0.009 0.061 -10000 0 -0.14 59 59
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.02 0.053 -10000 0 -0.14 39 39
dendrite morphogenesis 0.016 0.053 -10000 0 -0.12 57 57
Syndecan-2/GM-CSF 0.018 0.054 -10000 0 -0.12 58 58
determination of left/right symmetry 0.007 0.024 -10000 0 -0.24 4 4
Syndecan-2/PKC delta 0.017 0.053 -10000 0 -0.12 56 56
GNB2L1 0.035 0.005 -10000 0 0 11 11
MAPK3 -0.022 0.05 0.11 33 -0.19 4 37
MAPK1 -0.019 0.048 0.11 30 -0.21 4 34
Syndecan-2/RACK1 0.03 0.062 -10000 0 -0.11 68 68
NF1 0.036 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.024 -10000 0 -0.24 4 4
ITGA2 0.028 0.015 -10000 0 0 108 108
MAPK8 -0.004 0.038 -10000 0 -0.37 3 3
Syndecan-2/alpha2/beta1 Integrin 0.009 0.062 -10000 0 -0.11 85 85
Syndecan-2/Kininogen 0.018 0.054 -10000 0 -0.12 58 58
ITGB1 0.027 0.016 -10000 0 0 118 118
SRC -0.026 0.051 0.16 9 -0.19 9 18
Syndecan-2/CASK/Protein 4.1 0.016 0.049 -10000 0 -0.11 62 62
extracellular matrix organization 0.015 0.051 -10000 0 -0.12 54 54
actin cytoskeleton reorganization 0.014 0.06 -10000 0 -0.13 62 62
Syndecan-2/Caveolin-2/Ras 0.008 0.066 -10000 0 -0.13 70 70
Syndecan-2/Laminin alpha3 0.016 0.052 -10000 0 -0.12 56 56
Syndecan-2/RasGAP 0.037 0.078 -10000 0 -0.12 80 80
alpha5/beta1 Integrin 0.03 0.043 -10000 0 -0.14 20 20
PRKCD 0.034 0.01 -10000 0 0 36 36
Syndecan-2 dimer 0.017 0.053 -10000 0 -0.12 57 57
GO:0007205 0.001 0.011 -10000 0 -0.11 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.014 0.067 0.19 1 -0.2 18 19
RHOA 0.035 0.007 -10000 0 0 21 21
SDCBP 0.035 0.007 -10000 0 0 21 21
TNFRSF13B 0.036 0.005 -10000 0 0 8 8
RASA1 0.034 0.009 -10000 0 0 30 30
alpha2/beta1 Integrin 0.02 0.053 -10000 0 -0.14 39 39
Syndecan-2/Synbindin 0.017 0.058 -10000 0 -0.13 60 60
TGFB1 0.032 0.012 -10000 0 0 62 62
CASP3 -0.015 0.052 0.11 32 -0.19 4 36
FN1 0.034 0.009 -10000 0 0 29 29
Syndecan-2/IL8 -0.002 0.068 -10000 0 -0.18 55 55
SDC2 0.007 0.024 -10000 0 -0.24 4 4
KNG1 0.035 0.006 -10000 0 0 15 15
Syndecan-2/Neurofibromin 0.017 0.055 -10000 0 -0.12 62 62
TRAPPC4 0.035 0.006 -10000 0 0 14 14
CSF2 0.036 0.005 -10000 0 0 8 8
Syndecan-2/TGFB1 0.015 0.051 -10000 0 -0.12 54 54
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.054 -10000 0 -0.11 66 66
Syndecan-2/Ezrin 0.015 0.052 -10000 0 -0.11 63 63
PRKACA -0.02 0.048 0.11 33 -0.17 3 36
angiogenesis -0.002 0.068 -10000 0 -0.18 55 55
MMP2 0.029 0.015 -10000 0 0 103 103
IL8 0.019 0.018 -10000 0 0 233 233
calcineurin-NFAT signaling pathway 0.018 0.054 -10000 0 -0.12 59 59
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.052 0.6 0.76 30 -1 119 149
IL23A 0.098 0.37 0.76 21 -0.96 20 41
NF kappa B1 p50/RelA/I kappa B alpha 0.089 0.34 0.64 17 -0.83 22 39
positive regulation of T cell mediated cytotoxicity 0.1 0.39 0.76 36 -0.93 22 58
ITGA3 0.099 0.35 0.71 27 -0.85 23 50
IL17F 0.04 0.27 0.5 35 -0.58 25 60
IL12B 0.061 0.079 0.19 73 -10000 0 73
STAT1 (dimer) 0.078 0.36 0.65 28 -0.89 23 51
CD4 0.081 0.41 0.75 27 -1 30 57
IL23 0.098 0.35 0.72 19 -0.92 21 40
IL23R 0.07 0.14 0.28 92 -0.15 9 101
IL1B 0.092 0.4 0.74 30 -1.1 22 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.097 0.35 0.69 29 -0.85 19 48
TYK2 0.042 0.059 0.15 49 -10000 0 49
STAT4 0.034 0.009 -10000 0 0 30 30
STAT3 0.033 0.01 -10000 0 0 37 37
IL18RAP 0.035 0.008 -10000 0 -0.031 3 3
IL12RB1 0.045 0.059 0.15 52 -10000 0 52
PIK3CA 0.03 0.014 -10000 0 0 85 85
IL12Rbeta1/TYK2 0.052 0.076 0.18 38 -0.14 12 50
IL23R/JAK2 0.1 0.16 0.38 75 -0.19 10 85
positive regulation of chronic inflammatory response 0.1 0.39 0.76 36 -0.93 22 58
natural killer cell activation -0.005 0.011 -10000 0 -0.029 43 43
JAK2 0.055 0.078 0.19 69 -10000 0 69
PIK3R1 0.032 0.012 -10000 0 0 61 61
NFKB1 0.038 0.009 0.064 3 0 17 20
RELA 0.039 0.008 0.064 3 0 10 13
positive regulation of dendritic cell antigen processing and presentation 0.1 0.34 0.71 19 -0.88 21 40
ALOX12B 0.095 0.35 0.74 18 -0.88 18 36
CXCL1 0.1 0.36 0.75 31 -0.88 18 49
T cell proliferation 0.1 0.39 0.76 36 -0.93 22 58
NFKBIA 0.036 0.013 0.065 2 0 47 49
IL17A 0.068 0.24 0.45 55 -0.46 26 81
PI3K 0.047 0.34 0.64 19 -0.87 23 42
IFNG 0.019 0.033 0.097 26 -0.085 3 29
STAT3 (dimer) 0.048 0.34 0.62 21 -0.82 25 46
IL18R1 0.035 0.008 -10000 0 -0.031 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.1 0.26 0.56 47 -0.51 17 64
IL18/IL18R 0.06 0.035 -10000 0 -0.12 6 6
macrophage activation -0.002 0.015 0.035 2 -0.042 17 19
TNF 0.1 0.36 0.75 21 -0.93 17 38
STAT3/STAT4 0.077 0.35 0.61 24 -0.85 24 48
STAT4 (dimer) 0.079 0.35 0.64 25 -0.89 23 48
IL18 0.031 0.013 -10000 0 -10000 0 0
IL19 0.098 0.35 0.74 17 -0.87 17 34
STAT5A (dimer) 0.092 0.36 0.65 28 -0.88 23 51
STAT1 0.033 0.01 -10000 0 0 40 40
SOCS3 0.036 0.004 -10000 0 0 5 5
CXCL9 0.11 0.36 0.75 26 -0.88 18 44
MPO 0.095 0.35 0.74 17 -0.88 17 34
positive regulation of humoral immune response 0.1 0.39 0.76 36 -0.93 22 58
IL23/IL23R/JAK2/TYK2 0.092 0.39 0.76 33 -0.96 22 55
IL6 0.15 0.36 0.74 42 -0.88 17 59
STAT5A 0.036 0.004 -10000 0 0 6 6
IL2 0.021 0.03 -10000 0 -0.035 103 103
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.029 43 43
CD3E 0.095 0.35 0.72 20 -0.88 17 37
keratinocyte proliferation 0.1 0.39 0.76 36 -0.93 22 58
NOS2 0.096 0.35 0.67 36 -0.82 23 59
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.015 0.11 0.15 21 -0.25 55 76
adherens junction organization 0.003 0.072 0.15 5 -0.3 18 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.11 0.17 142 -0.28 21 163
FMN1 0.01 0.062 0.15 4 -0.25 16 20
mol:IP3 -0.007 0.077 0.14 3 -0.26 28 31
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.015 0.066 0.16 4 -0.26 16 20
CTNNB1 0.034 0.008 -10000 0 0 21 21
AKT1 -0.005 0.085 -10000 0 -0.29 29 29
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.026 0.065 -10000 0 -0.39 5 5
CTNND1 0.034 0.009 -10000 0 0 30 30
mol:PI-4-5-P2 0.005 0.067 0.15 6 -0.26 19 25
VASP 0.004 0.061 0.15 5 -0.25 16 21
ZYX 0.01 0.052 0.15 4 -0.26 9 13
JUB 0.01 0.062 0.15 4 -0.25 16 20
EGFR(dimer) 0.003 0.061 0.18 1 -0.26 16 17
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -10000 0 -0.11 2 2
mol:PI-3-4-5-P3 0.02 0.09 -10000 0 -0.26 28 28
PIK3CA 0.03 0.015 -10000 0 -0.002 89 89
PI3K 0.021 0.092 -10000 0 -0.26 28 28
FYN -0.035 0.13 0.14 22 -0.31 70 92
mol:Ca2+ -0.006 0.075 0.14 3 -0.25 28 31
JUP 0.033 0.011 -10000 0 0 50 50
PIK3R1 0.031 0.015 -10000 0 -0.003 68 68
mol:DAG -0.007 0.077 0.14 3 -0.26 28 31
CDH1 0.033 0.01 -10000 0 0 37 37
RhoA/GDP 0.059 0.12 0.18 200 -0.28 20 220
establishment of polarity of embryonic epithelium 0.004 0.061 0.15 5 -0.25 17 22
SRC 0.035 0.006 -10000 0 0 13 13
RAC1 0.027 0.016 -10000 0 0 123 123
RHOA 0.035 0.007 -10000 0 0 21 21
EGFR 0.01 0.016 -10000 0 0 355 355
CASR -0.019 0.077 0.14 26 -0.27 24 50
RhoA/GTP 0.012 0.085 0.15 1 -0.24 29 30
AKT2 -0.004 0.076 0.14 1 -0.25 28 29
actin cable formation 0 0.06 0.14 5 -0.25 17 22
apoptosis 0.007 0.098 0.33 27 -0.16 21 48
CTNNA1 0.035 0.008 -10000 0 -0.002 19 19
mol:GDP -0.016 0.068 0.16 7 -0.26 21 28
PIP5K1A 0.005 0.067 0.15 6 -0.26 18 24
PLCG1 -0.007 0.078 0.14 3 -0.26 28 31
Rac1/GTP -0.002 0.067 -10000 0 -0.27 15 15
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.003 0.077 0.2 2 -0.19 36 38
NF kappa B1 p50/RelA/I kappa B alpha -0.013 0.12 0.24 1 -0.32 40 41
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.08 -10000 0 -0.15 71 71
AP1 -0.015 0.14 0.28 3 -0.28 79 82
ILK -0.03 0.073 0.17 3 -0.24 31 34
bone resorption -0.039 0.081 0.18 7 -0.23 32 39
PTK2B 0.035 0.006 -10000 0 0 15 15
PYK2/p130Cas 0.045 0.089 -10000 0 -0.16 53 53
ITGAV 0.031 0.026 -10000 0 -0.056 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.021 0.068 -10000 0 -0.14 68 68
alphaV/beta3 Integrin/Osteopontin 0.049 0.092 -10000 0 -0.16 68 68
MAP3K1 -0.029 0.064 0.2 2 -0.2 25 27
JUN 0.034 0.01 -10000 0 0 39 39
MAPK3 -0.03 0.084 0.18 7 -0.24 39 46
MAPK1 -0.028 0.086 0.17 12 -0.25 38 50
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.026 0.06 0.2 2 -0.2 27 29
ITGB3 0.032 0.026 -10000 0 -0.056 37 37
NFKBIA -0.034 0.11 0.18 7 -0.31 43 50
FOS 0.026 0.017 -10000 0 0 147 147
CD44 0.029 0.015 -10000 0 0 102 102
CHUK 0.026 0.016 -10000 0 0 133 133
PLAU -0.065 0.25 0.31 1 -0.95 30 31
NF kappa B1 p50/RelA 0.005 0.13 0.24 3 -0.32 38 41
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 10 10
alphaV beta3 Integrin 0.04 0.058 -10000 0 -0.12 49 49
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.03 0.064 0.19 2 -0.23 26 28
VAV3 -0.031 0.066 0.19 1 -0.23 31 32
MAP3K14 -0.027 0.074 0.17 5 -0.2 36 41
ROCK2 0.035 0.007 -10000 0 0 21 21
SPP1 0.03 0.025 -10000 0 -0.057 28 28
RAC1 0.027 0.016 -10000 0 0 123 123
Rac1/GTP -0.022 0.073 0.14 4 -0.22 31 35
MMP2 -0.061 0.12 0.18 1 -0.32 62 63
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0 0.05 -10000 0 -10000 0 0
PLK1 -0.06 0.2 -10000 0 -0.56 32 32
CDKN1B -0.1 0.21 0.47 3 -0.37 124 127
FOXO3 -0.064 0.22 0.32 5 -0.48 79 84
KAT2B -0.001 0.021 0.048 14 -0.041 83 97
FOXO1/SIRT1 0.013 0.055 -10000 0 -0.25 10 10
CAT -0.075 0.26 -10000 0 -0.77 34 34
CTNNB1 0.035 0.007 -10000 0 0 21 21
AKT1 0.021 0.042 -10000 0 -0.061 65 65
FOXO1 0.002 0.054 0.22 1 -0.26 9 10
MAPK10 0.036 0.086 0.19 99 -0.14 19 118
mol:GTP -0.001 0.004 -10000 0 -0.021 1 1
FOXO4 -0.042 0.19 0.27 9 -0.39 80 89
response to oxidative stress 0 0.023 0.051 13 -0.044 63 76
FOXO3A/SIRT1 -0.06 0.22 0.3 1 -0.47 82 83
XPO1 0.036 0.004 -10000 0 0 5 5
EP300 0.033 0.011 -10000 0 -10000 0 0
BCL2L11 0.023 0.031 -10000 0 -10000 0 0
FOXO1/SKP2 0.018 0.057 0.2 1 -0.25 9 10
mol:GDP 0 0.023 0.051 13 -0.044 63 76
RAN 0.034 0.011 -10000 0 -0.013 23 23
GADD45A -0.15 0.33 0.4 2 -0.78 83 85
YWHAQ 0.036 0.005 -10000 0 0 8 8
FOXO1/14-3-3 family 0.006 0.15 -10000 0 -0.47 24 24
MST1 0.021 0.042 0.11 1 -0.059 85 86
CSNK1D 0.035 0.007 -10000 0 0 19 19
CSNK1E 0.031 0.012 -10000 0 0 64 64
FOXO4/14-3-3 family -0.006 0.15 -10000 0 -0.48 26 26
YWHAB 0.035 0.007 -10000 0 0 21 21
MAPK8 0.021 0.074 0.18 64 -0.14 14 78
MAPK9 0.042 0.092 0.18 117 -0.14 19 136
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
YWHAZ 0.035 0.007 -10000 0 0 17 17
SIRT1 0.021 0.022 -10000 0 -0.034 31 31
SOD2 -0.13 0.34 0.4 4 -0.74 96 100
RBL2 -0.079 0.29 -10000 0 -0.93 37 37
RAL/GDP 0.02 0.051 -10000 0 -0.13 22 22
CHUK 0.013 0.039 -10000 0 -0.059 75 75
Ran/GTP 0.018 0.025 -10000 0 -0.079 11 11
CSNK1G2 0.033 0.01 -10000 0 0 37 37
RAL/GTP 0.019 0.052 0.14 2 -0.11 26 28
CSNK1G1 0.036 0.005 -10000 0 0 8 8
FASLG 0.02 0.042 -10000 0 -0.59 1 1
SKP2 0.035 0.006 -10000 0 0 16 16
USP7 0.034 0.01 -10000 0 -0.012 20 20
IKBKB 0.022 0.043 0.11 1 -0.059 89 90
CCNB1 -0.16 0.41 0.49 1 -1.1 78 79
FOXO1-3a-4/beta catenin -0.044 0.21 0.36 11 -0.4 82 93
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.056 0.2 1 -0.24 9 10
CSNK1A1 0.035 0.006 -10000 0 0 12 12
SGK1 -0.001 0.021 0.048 14 -0.041 83 97
CSNK1G3 0.035 0.005 -10000 0 0 11 11
Ran/GTP/Exportin 1 0.038 0.036 -10000 0 -0.12 9 9
ZFAND5 -0.028 0.16 0.24 10 -0.31 79 89
SFN 0.031 0.013 -10000 0 0 74 74
CDK2 0.035 0.012 -10000 0 -0.03 2 2
FOXO3A/14-3-3 -0.013 0.16 -10000 0 -0.44 32 32
CREBBP 0.038 0.007 -10000 0 -0.03 2 2
FBXO32 -0.058 0.2 0.29 5 -0.44 79 84
BCL6 -0.099 0.33 -10000 0 -0.98 47 47
RALB 0.033 0.013 -10000 0 -0.016 30 30
RALA 0.025 0.017 -10000 0 -0.001 147 147
YWHAH 0.031 0.013 -10000 0 0 74 74
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.035 0.17 -10000 0 -0.46 64 64
HDAC1 0.026 0.034 0.08 55 -0.038 83 138
AES 0.033 0.013 0.068 9 -0.002 50 59
FBXW11 0.035 0.007 -10000 0 0 20 20
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.027 -10000 0 -0.14 1 1
TLE1 0.034 0.011 0.067 10 -0.005 27 37
AP1 -0.012 0.077 -10000 0 -0.21 58 58
NCSTN 0.034 0.008 -10000 0 0 28 28
ADAM10 0.032 0.012 -10000 0 0 57 57
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.008 0.13 -10000 0 -0.45 14 14
NICD/RBPSUH -0.041 0.17 -10000 0 -0.46 64 64
WIF1 0.028 0.015 -10000 0 0 106 106
NOTCH1 -0.037 0.18 -10000 0 -0.49 63 63
PSENEN 0.034 0.009 -10000 0 0 33 33
KREMEN2 0.036 0.004 -10000 0 0 5 5
DKK1 0.018 0.018 -10000 0 0 240 240
beta catenin/beta TrCP1 0.057 0.093 0.22 26 -0.27 11 37
APH1B 0.035 0.006 -10000 0 0 14 14
APH1A 0.035 0.006 -10000 0 0 16 16
AXIN1 0.01 0.069 0.25 1 -0.37 1 2
CtBP/CBP/TCF1/TLE1/AES 0.013 0.073 0.17 49 -0.18 17 66
PSEN1 0.033 0.01 -10000 0 0 41 41
FOS 0.025 0.017 -10000 0 0 147 147
JUN 0.033 0.01 -10000 0 0 39 39
MAP3K7 0.032 0.017 0.061 12 -0.01 55 67
CTNNB1 0.044 0.088 0.21 31 -0.27 8 39
MAPK3 0.036 0.003 -10000 0 0 4 4
DKK2/LRP6/Kremen 2 0.064 0.026 -10000 0 -0.12 1 1
HNF1A 0 0.006 0.032 10 -10000 0 10
CTBP1 0.034 0.012 0.069 8 -0.005 28 36
MYC -0.08 0.36 -10000 0 -1.2 49 49
NKD1 0 0.002 -10000 0 -10000 0 0
FZD1 0.025 0.017 -10000 0 0 155 155
NOTCH1 precursor/Deltex homolog 1 -0.041 0.17 -10000 0 -0.46 64 64
apoptosis -0.013 0.077 -10000 0 -0.2 59 59
Delta 1/NOTCHprecursor -0.041 0.17 -10000 0 -0.46 64 64
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.019 0.066 -10000 0 -0.68 3 3
Gamma Secretase 0.076 0.073 -10000 0 -0.15 29 29
APC -0.022 0.16 -10000 0 -0.62 27 27
DVL1 0.016 0.091 -10000 0 -0.33 23 23
CSNK2A1 0.034 0.01 -10000 0 -0.001 32 32
MAP3K7IP1 0.032 0.017 0.062 10 -0.01 48 58
DKK1/LRP6/Kremen 2 0.033 0.037 -10000 0 -10000 0 0
LRP6 0.033 0.01 -10000 0 0 37 37
CSNK1A1 0.035 0.007 -10000 0 -0.002 13 13
NLK 0.01 0.053 -10000 0 -0.21 22 22
CCND1 -0.054 0.34 -10000 0 -1.1 42 42
WNT1 0.035 0.006 -10000 0 0 16 16
Axin1/APC/beta catenin 0.011 0.14 0.29 4 -0.42 27 31
DKK2 0.034 0.009 -10000 0 0 29 29
NOTCH1 precursor/DVL1 -0.018 0.19 -10000 0 -0.46 62 62
GSK3B 0.034 0.01 -10000 0 0 35 35
FRAT1 0.027 0.016 -10000 0 0 130 130
NOTCH/Deltex homolog 1 -0.035 0.17 -10000 0 -0.46 64 64
PPP2R5D 0.025 0.037 -10000 0 -0.25 4 4
MAPK1 0.033 0.011 -10000 0 0 48 48
WNT1/LRP6/FZD1 0.058 0.044 -10000 0 -10000 0 0
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.032 0.021 0.07 7 -0.018 61 68
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.028 0.015 -10000 0 0 110 110
EPHB2 0.034 0.01 -10000 0 0 35 35
EFNB1 -0.018 0.015 0.023 53 -10000 0 53
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.054 -10000 0 -0.12 16 16
Ephrin B2/EPHB1-2 0.031 0.056 -10000 0 -0.1 51 51
neuron projection morphogenesis 0.035 0.042 -10000 0 -0.12 16 16
Ephrin B1/EPHB1-2/Tiam1 0.056 0.049 -10000 0 -0.1 28 28
DNM1 0.035 0.008 -10000 0 0 23 23
cell-cell signaling 0 0.003 0.023 1 -10000 0 1
MAP2K4 -0.053 0.16 0.2 1 -0.52 48 49
YES1 -0.054 0.23 -10000 0 -0.74 49 49
Ephrin B1/EPHB1-2/NCK2 0.06 0.043 -10000 0 -0.1 19 19
PI3K -0.021 0.19 -10000 0 -0.57 48 48
mol:GDP 0.054 0.048 -10000 0 -0.1 28 28
ITGA2B 0.036 0.003 -10000 0 0 3 3
endothelial cell proliferation 0.016 0.048 -10000 0 -0.11 46 46
FYN -0.065 0.24 -10000 0 -0.76 49 49
MAP3K7 -0.05 0.16 -10000 0 -0.54 47 47
FGR -0.05 0.22 -10000 0 -0.72 48 48
TIAM1 0.033 0.01 -10000 0 0 43 43
PIK3R1 0.032 0.012 -10000 0 0 61 61
RGS3 0.035 0.007 -10000 0 0 20 20
cell adhesion -0.033 0.17 -10000 0 -0.54 48 48
LYN -0.059 0.23 -10000 0 -0.73 48 48
Ephrin B1/EPHB1-2/Src Family Kinases -0.055 0.21 -10000 0 -0.68 49 49
Ephrin B1/EPHB1-2 -0.046 0.17 -10000 0 -0.57 47 47
SRC -0.049 0.22 -10000 0 -0.72 49 49
ITGB3 0.036 0.004 -10000 0 0 5 5
EPHB1 0.03 0.014 -10000 0 0 87 87
EPHB4 0.026 0.016 -10000 0 0 141 141
RAC1 0.027 0.016 -10000 0 0 123 123
Ephrin B2/EPHB4 0.016 0.048 -10000 0 -0.11 46 46
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
BLK -0.051 0.22 -10000 0 -0.72 49 49
HCK -0.063 0.23 -10000 0 -0.73 49 49
regulation of stress fiber formation -0.058 0.042 0.1 19 -10000 0 19
MAPK8 -0.056 0.15 -10000 0 -0.5 48 48
Ephrin B1/EPHB1-2/RGS3 0.065 0.033 -10000 0 -0.11 6 6
endothelial cell migration 0.002 0.17 0.2 112 -0.45 44 156
NCK2 0.035 0.007 -10000 0 0 19 19
PTPN13 0.034 0.013 -10000 0 0 56 56
regulation of focal adhesion formation -0.058 0.042 0.1 19 -10000 0 19
chemotaxis -0.063 0.032 0.11 6 -10000 0 6
PIK3CA 0.03 0.014 -10000 0 0 85 85
Rac1/GTP 0.045 0.048 -10000 0 -0.12 16 16
angiogenesis -0.045 0.17 -10000 0 -0.57 47 47
LCK -0.048 0.22 -10000 0 -0.72 48 48
ErbB2/ErbB3 signaling events

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
USP8 -0.015 0.011 0.018 18 -10000 0 18
RAS family/GTP 0.014 0.1 0.21 1 -0.18 67 68
NFATC4 -0.018 0.069 0.18 20 -0.2 4 24
ERBB2IP 0.034 0.011 -10000 0 -0.002 38 38
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.03 0.07 0.17 4 -0.18 14 18
JUN -0.006 0.085 0.2 7 -0.36 7 14
HRAS 0.034 0.01 -10000 0 -0.001 33 33
DOCK7 -0.034 0.064 0.15 7 -0.16 62 69
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.077 0.21 13 -0.12 77 90
AKT1 -0.009 0.009 0.014 41 -10000 0 41
BAD -0.015 0.007 0.001 68 -10000 0 68
MAPK10 0.004 0.074 0.17 43 -0.15 14 57
mol:GTP 0 0.001 0.003 2 -0.005 25 27
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.077 0.19 6 -0.19 14 20
RAF1 -0.015 0.1 0.23 12 -0.23 32 44
ErbB2/ErbB3/neuregulin 2 0.003 0.07 0.2 14 -0.13 83 97
STAT3 -0.026 0.24 -10000 0 -0.89 35 35
cell migration -0.009 0.071 0.17 25 -0.16 25 50
mol:PI-3-4-5-P3 -0.001 0.002 0.004 16 -0.004 74 90
cell proliferation -0.036 0.24 0.39 2 -0.59 51 53
FOS -0.027 0.2 0.33 10 -0.42 85 95
NRAS 0.032 0.012 -10000 0 -0.001 59 59
mol:Ca2+ -0.03 0.07 0.17 4 -0.18 14 18
MAPK3 -0.014 0.18 0.34 3 -0.48 38 41
MAPK1 -0.039 0.22 0.34 3 -0.57 50 53
JAK2 -0.023 0.072 0.16 13 -0.18 12 25
NF2 0.01 0.009 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.076 0.14 10 -0.16 79 89
NRG1 0.035 0.005 -10000 0 0 9 9
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
MAPK8 -0.022 0.091 0.18 4 -0.22 53 57
MAPK9 0.01 0.079 0.17 53 -0.14 5 58
ERBB2 -0.015 0.069 0.26 29 -10000 0 29
ERBB3 0.017 0.018 -10000 0 0 254 254
SHC1 0.033 0.011 -10000 0 0 48 48
RAC1 0.027 0.016 -10000 0 0 123 123
apoptosis 0.012 0.031 0.2 11 -0.07 1 12
STAT3 (dimer) -0.025 0.24 -10000 0 -0.87 35 35
RNF41 -0.019 0.016 0.08 6 -0.12 1 7
FRAP1 -0.015 0.007 0.001 70 -10000 0 70
RAC1-CDC42/GTP -0.023 0.046 -10000 0 -0.13 50 50
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.008 0.015 2 -10000 0 2
CHRNA1 -0.003 0.15 0.32 4 -0.38 36 40
myelination -0.025 0.082 0.22 22 -0.21 4 26
PPP3CB -0.02 0.067 0.17 13 -0.18 14 27
KRAS 0.034 0.01 -10000 0 0 37 37
RAC1-CDC42/GDP 0.022 0.078 0.22 1 -0.16 54 55
NRG2 0.036 0.005 -10000 0 0 9 9
mol:GDP -0.004 0.076 0.14 10 -0.16 79 89
SOS1 0 0.001 -10000 0 -0.004 9 9
MAP2K2 -0.022 0.1 0.21 15 -0.24 35 50
SRC 0.035 0.006 -10000 0 0 13 13
mol:cAMP -0.001 0.001 0.003 12 -0.004 1 13
PTPN11 -0.028 0.079 0.17 14 -0.18 14 28
MAP2K1 -0.033 0.2 -10000 0 -0.59 30 30
heart morphogenesis -0.03 0.07 0.17 4 -0.18 14 18
RAS family/GDP 0.021 0.11 0.23 1 -0.17 75 76
GRB2 0.035 0.007 -10000 0 0 16 16
PRKACA 0.017 0.01 -10000 0 -10000 0 0
CHRNE 0.001 0.025 0.064 4 -0.13 7 11
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.009 -10000 0 -0.014 41 41
nervous system development -0.03 0.07 0.17 4 -0.18 14 18
CDC42 0.035 0.008 -10000 0 0 22 22
Signaling events mediated by PTP1B

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
PDGFRB 0.034 0.008 -10000 0 0 25 25
Jak2/Leptin Receptor 0.002 0.13 -10000 0 -0.33 40 40
PTP1B/AKT1 0 0.11 -10000 0 -0.27 39 39
FYN 0.03 0.014 -10000 0 0 83 83
p210 bcr-abl/PTP1B -0.01 0.11 0.17 1 -0.27 39 40
EGFR 0.009 0.017 -10000 0 0 358 358
EGF/EGFR -0.032 0.089 -10000 0 -0.28 36 36
CSF1 0.036 0.004 -10000 0 0 5 5
AKT1 0.033 0.012 -10000 0 0 53 53
INSR 0.034 0.009 -10000 0 -0.001 29 29
PTP1B/N-cadherin -0.006 0.12 -10000 0 -0.27 50 50
Insulin Receptor/Insulin 0.018 0.11 -10000 0 -0.27 28 28
HCK 0.027 0.016 -10000 0 0 123 123
CRK 0.035 0.008 -10000 0 0 23 23
TYK2 -0.007 0.12 0.27 25 -0.29 40 65
EGF 0.027 0.024 -10000 0 -0.022 88 88
YES1 0.033 0.01 -10000 0 0 37 37
CAV1 0.005 0.14 0.22 27 -0.29 49 76
TXN 0.034 0.01 -10000 0 0 38 38
PTP1B/IRS1/GRB2 0.008 0.12 -10000 0 -0.29 34 34
cell migration 0.01 0.11 0.27 39 -0.17 1 40
STAT3 0.034 0.01 -10000 0 0 37 37
PRLR 0.038 0.005 -10000 0 -10000 0 0
ITGA2B 0.036 0.003 -10000 0 0 3 3
CSF1R 0.027 0.016 -10000 0 0 121 121
Prolactin Receptor/Prolactin 0.056 0.012 -10000 0 -10000 0 0
FGR 0.032 0.011 -10000 0 0 52 52
PTP1B/p130 Cas -0.012 0.1 0.15 1 -0.26 41 42
Crk/p130 Cas -0.002 0.11 -10000 0 -0.26 43 43
DOK1 -0.008 0.1 0.19 4 -0.3 29 33
JAK2 -0.01 0.12 -10000 0 -0.34 41 41
Jak2/Leptin Receptor/Leptin -0.008 0.12 -10000 0 -0.32 30 30
PIK3R1 0.032 0.012 -10000 0 0 61 61
PTPN1 -0.011 0.11 0.17 1 -0.28 39 40
LYN 0.031 0.013 -10000 0 0 72 72
CDH2 0.032 0.011 -10000 0 0 53 53
SRC 0.015 0.099 -10000 0 -0.48 15 15
ITGB3 0.036 0.004 -10000 0 0 5 5
CAT1/PTP1B -0.014 0.16 0.25 14 -0.37 59 73
CAPN1 0.035 0.005 -10000 0 0 8 8
CSK 0.035 0.007 -10000 0 0 17 17
PI3K 0.009 0.12 -10000 0 -0.29 37 37
mol:H2O2 0.003 0.005 0.023 3 -10000 0 3
STAT3 (dimer) -0.007 0.11 -10000 0 -0.29 29 29
negative regulation of transcription -0.009 0.12 -10000 0 -0.34 41 41
FCGR2A 0.028 0.015 -10000 0 0 105 105
FER 0.036 0.007 -10000 0 0 14 14
alphaIIb/beta3 Integrin 0.053 0.006 -10000 0 -10000 0 0
BLK 0.035 0.007 -10000 0 0 17 17
Insulin Receptor/Insulin/Shc 0.058 0.035 -10000 0 -0.13 7 7
RHOA 0.034 0.008 -10000 0 0 21 21
LEPR 0.035 0.007 -10000 0 0 18 18
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.035 0.006 -10000 0 0 16 16
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.009 0.15 0.21 4 -0.36 56 60
PRL 0.037 0.006 -10000 0 -10000 0 0
SOCS3 0.024 0.015 -10000 0 -10000 0 0
SPRY2 0.029 0.018 -10000 0 0 129 129
Insulin Receptor/Insulin/IRS1 0.054 0.047 -10000 0 -0.13 23 23
CSF1/CSF1R -0.003 0.13 -10000 0 -0.28 45 45
Ras protein signal transduction -0.005 0.085 0.59 8 -10000 0 8
IRS1 0.032 0.011 -10000 0 0 51 51
INS 0.035 0.007 -10000 0 -0.002 16 16
LEP 0.026 0.016 -10000 0 0 131 131
STAT5B -0.003 0.1 -10000 0 -0.3 25 25
STAT5A -0.003 0.1 -10000 0 -0.29 26 26
GRB2 0.035 0.006 -10000 0 0 16 16
PDGFB-D/PDGFRB 0 0.11 -10000 0 -0.27 42 42
CSN2 0.013 0.041 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
LAT -0.025 0.17 -10000 0 -0.48 56 56
YBX1 0.038 0.04 -10000 0 -0.29 7 7
LCK 0.035 0.007 -10000 0 0 17 17
SHC1 0.033 0.011 -10000 0 0 48 48
NOX4 0.034 0.015 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0 0.11 0.26 3 -0.28 36 39
IKBKB 0.016 0.079 0.26 4 -0.26 11 15
AKT1 0.004 0.089 0.22 36 -0.18 17 53
IKBKG 0.011 0.073 0.23 2 -0.25 10 12
CALM1 -0.024 0.12 0.23 4 -0.36 40 44
PIK3CA 0.03 0.014 -10000 0 0 85 85
MAP3K1 0.024 0.12 0.28 8 -0.35 23 31
MAP3K7 0.033 0.01 -10000 0 0 38 38
mol:Ca2+ -0.021 0.13 0.24 5 -0.37 40 45
DOK1 0.036 0.002 -10000 0 0 2 2
AP-1 -0.01 0.091 0.19 12 -0.21 41 53
LYN 0.031 0.013 -10000 0 0 72 72
BLNK 0.02 0.018 -10000 0 0 219 219
SHC1 0.033 0.011 -10000 0 0 48 48
BCR complex 0.049 0.015 -10000 0 -10000 0 0
CD22 -0.011 0.088 -10000 0 -0.29 29 29
CAMK2G -0.016 0.12 0.22 5 -0.35 39 44
CSNK2A1 0.034 0.009 -10000 0 0 31 31
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.008 0.063 -10000 0 -0.2 20 20
GO:0007205 -0.022 0.14 0.24 5 -0.38 40 45
SYK 0.031 0.013 -10000 0 0 72 72
ELK1 -0.027 0.13 0.22 5 -0.37 40 45
NFATC1 -0.017 0.091 0.23 5 -0.26 32 37
B-cell antigen/BCR complex 0.049 0.015 -10000 0 -10000 0 0
PAG1/CSK 0.023 0.023 -10000 0 -0.13 10 10
NFKBIB 0.021 0.043 0.13 1 -0.13 18 19
HRAS -0.023 0.12 0.19 9 -0.32 41 50
NFKBIA 0.022 0.039 0.13 1 -0.12 14 15
NF-kappa-B/RelA/I kappa B beta 0.026 0.038 0.13 1 -0.1 18 19
RasGAP/Csk 0.044 0.093 -10000 0 -0.12 104 104
mol:GDP -0.02 0.13 0.23 5 -0.37 40 45
PTEN 0.027 0.016 -10000 0 0 130 130
CD79B 0.036 0.005 -10000 0 0 9 9
NF-kappa-B/RelA/I kappa B alpha 0.026 0.037 0.12 2 -0.1 12 14
GRB2 0.035 0.006 -10000 0 0 16 16
PI3K/BCAP/CD19 -0.032 0.16 0.37 1 -0.42 42 43
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 -0.022 0.13 0.25 4 -0.38 40 44
CSK 0.035 0.007 -10000 0 0 17 17
FOS -0.025 0.13 0.2 9 -0.36 40 49
CHUK -0.048 0.13 0.23 2 -0.25 111 113
IBTK 0.034 0.008 -10000 0 0 24 24
CARD11/BCL10/MALT1/TAK1 0.001 0.13 0.28 2 -0.34 38 40
PTPN6 -0.02 0.085 0.15 4 -0.3 28 32
RELA 0.036 0.005 -10000 0 0 10 10
BCL2A1 0.018 0.033 0.09 11 -0.091 18 29
VAV2 -0.012 0.097 -10000 0 -0.31 30 30
ubiquitin-dependent protein catabolic process 0.023 0.042 0.13 1 -0.13 18 19
BTK 0.018 0.012 -10000 0 -10000 0 0
CD19 -0.01 0.089 -10000 0 -0.28 30 30
MAP4K1 0.034 0.008 -10000 0 0 26 26
CD72 0.033 0.011 -10000 0 0 48 48
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.11 0.26 8 -0.31 23 31
SH3BP5 0.033 0.011 -10000 0 0 47 47
PIK3AP1 -0.021 0.14 0.25 4 -0.35 53 57
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.03 0.18 -10000 0 -0.5 47 47
RAF1 -0.026 0.11 0.21 8 -0.32 41 49
RasGAP/p62DOK/SHIP 0.036 0.081 -10000 0 -0.11 100 100
CD79A 0.034 0.009 -10000 0 0 35 35
re-entry into mitotic cell cycle -0.01 0.091 0.19 12 -0.22 40 52
RASA1 0.034 0.009 -10000 0 0 30 30
MAPK3 -0.033 0.097 0.19 5 -0.29 38 43
MAPK1 -0.03 0.1 0.21 7 -0.3 36 43
CD72/SHP1 0.007 0.1 0.25 14 -0.28 29 43
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 0.02 0.11 0.26 8 -0.31 23 31
actin cytoskeleton organization 0.026 0.11 0.24 24 -0.29 17 41
NF-kappa-B/RelA 0.045 0.086 0.24 1 -0.24 21 22
Calcineurin -0.005 0.13 0.23 2 -0.33 39 41
PI3K -0.029 0.081 -10000 0 -0.26 30 30
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.017 0.13 0.22 5 -0.37 47 52
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.02 0.14 -10000 0 -0.51 13 13
DAPP1 0.001 0.14 -10000 0 -0.65 8 8
cytokine secretion -0.015 0.087 0.23 5 -0.24 32 37
mol:DAG -0.022 0.13 0.25 4 -0.38 40 44
PLCG2 0.032 0.012 -10000 0 0 61 61
MAP2K1 -0.03 0.11 0.2 6 -0.3 41 47
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.072 -10000 0 -0.12 86 86
mol:PI-3-4-5-P3 -0.015 0.075 0.19 22 -0.21 15 37
ETS1 -0.024 0.11 0.21 5 -0.33 37 42
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.036 0.089 -10000 0 -0.15 55 55
B-cell antigen/BCR complex/LYN -0.007 0.092 -10000 0 -0.3 30 30
MALT1 0.034 0.009 -10000 0 0 29 29
TRAF6 0.036 0.005 -10000 0 0 8 8
RAC1 0.023 0.11 0.25 14 -0.31 17 31
B-cell antigen/BCR complex/LYN/SYK 0.026 0.099 0.26 1 -0.27 26 27
CARD11 -0.021 0.13 0.23 5 -0.36 40 45
FCGR2B 0.02 0.018 -10000 0 0 214 214
PPP3CA 0.034 0.009 -10000 0 0 35 35
BCL10 0.035 0.006 -10000 0 0 15 15
IKK complex 0.006 0.043 0.14 4 -0.12 8 12
PTPRC 0.029 0.015 -10000 0 0 103 103
PDPK1 -0.013 0.06 0.16 23 -0.16 10 33
PPP3CB 0.026 0.016 -10000 0 0 132 132
PPP3CC 0.035 0.006 -10000 0 0 14 14
POU2F2 0.016 0.031 0.1 7 -0.082 19 26
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.032 0.042 -10000 0 -0.14 18 18
VLDLR 0.027 0.016 -10000 0 0 128 128
CRKL 0.034 0.008 -10000 0 0 25 25
LRPAP1 0.035 0.006 -10000 0 0 16 16
FYN 0.03 0.014 -10000 0 0 83 83
ITGA3 0.032 0.012 -10000 0 0 55 55
RELN/VLDLR/Fyn 0.017 0.063 -10000 0 -0.13 54 54
MAPK8IP1/MKK7/MAP3K11/JNK1 0.065 0.061 -10000 0 -0.11 5 5
AKT1 -0.014 0.069 -10000 0 -0.19 51 51
MAP2K7 0.034 0.009 -10000 0 0 30 30
RAPGEF1 0.035 0.007 -10000 0 0 18 18
DAB1 0.035 0.005 -10000 0 0 11 11
RELN/LRP8/DAB1 0.042 0.036 -10000 0 -0.11 3 3
LRPAP1/LRP8 0.044 0.036 -10000 0 -0.15 13 13
RELN/LRP8/DAB1/Fyn 0.043 0.058 -10000 0 -0.12 30 30
DAB1/alpha3/beta1 Integrin 0.028 0.059 -10000 0 -0.12 28 28
long-term memory 0.043 0.062 -10000 0 -0.12 28 28
DAB1/LIS1 0.046 0.073 -10000 0 -0.13 36 36
DAB1/CRLK/C3G 0.036 0.06 -10000 0 -0.12 30 30
PIK3CA 0.03 0.014 -10000 0 0 85 85
DAB1/NCK2 0.048 0.073 -10000 0 -0.13 33 33
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 0.035 0.006 -10000 0 0 13 13
CDK5R1 0.035 0.007 -10000 0 0 21 21
RELN 0.024 0.017 -10000 0 0 163 163
PIK3R1 0.032 0.012 -10000 0 0 61 61
RELN/LRP8/Fyn 0.031 0.056 -10000 0 -0.13 31 31
GRIN2A/RELN/LRP8/DAB1/Fyn 0.054 0.069 -10000 0 -0.12 30 30
MAPK8 0.026 0.016 -10000 0 0 133 133
RELN/VLDLR/DAB1 0.03 0.046 -10000 0 -0.11 23 23
ITGB1 0.027 0.016 -10000 0 0 118 118
MAP1B 0.017 0.079 0.16 87 -0.21 4 91
RELN/LRP8 0.041 0.044 -10000 0 -0.13 11 11
GRIN2B/RELN/LRP8/DAB1/Fyn 0.054 0.069 -10000 0 -0.12 28 28
PI3K 0.016 0.075 -10000 0 -0.16 73 73
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.035 0.027 -10000 0 -0.14 1 1
RAP1A 0.029 0.11 0.24 40 -0.19 1 41
PAFAH1B1 0.034 0.008 -10000 0 0 26 26
MAPK8IP1 0.034 0.008 -10000 0 0 24 24
CRLK/C3G 0.049 0.015 -10000 0 -10000 0 0
GRIN2B 0.035 0.007 -10000 0 0 18 18
NCK2 0.035 0.007 -10000 0 0 19 19
neuron differentiation 0.005 0.07 -10000 0 -0.24 16 16
neuron adhesion 0.03 0.11 0.25 41 -10000 0 41
LRP8 0.034 0.009 -10000 0 0 35 35
GSK3B -0.01 0.074 -10000 0 -0.2 44 44
RELN/VLDLR/DAB1/Fyn 0.03 0.065 -10000 0 -0.11 53 53
MAP3K11 0.035 0.005 -10000 0 0 11 11
RELN/VLDLR/DAB1/P13K -0.009 0.074 -10000 0 -0.18 57 57
CDK5 0.026 0.016 -10000 0 0 137 137
MAPT -0.009 0.078 0.82 2 -10000 0 2
neuron migration -0.01 0.11 0.21 41 -0.27 32 73
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.005 0.07 -10000 0 -0.25 16 16
RELN/VLDLR 0.043 0.062 -10000 0 -0.12 31 31
Paxillin-dependent events mediated by a4b1

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
CRKL 0.034 0.008 -10000 0 0 25 25
Rac1/GDP 0.027 0.02 -10000 0 -0.024 14 14
DOCK1 0.023 0.017 -10000 0 0 178 178
ITGA4 0.035 0.006 -10000 0 0 12 12
RAC1 0.027 0.016 -10000 0 0 123 123
alpha4/beta7 Integrin 0.052 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.053 0.033 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.051 0.018 -10000 0 -10000 0 0
lamellipodium assembly -0.051 0.15 -10000 0 -0.35 79 79
PIK3CA 0.03 0.014 -10000 0 0 85 85
PI3K 0.016 0.075 -10000 0 -0.16 73 73
ARF6 0.035 0.007 -10000 0 0 21 21
TLN1 0.029 0.014 -10000 0 0 94 94
PXN -0.021 0.006 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
ARF6/GTP 0.052 0.047 -10000 0 -0.11 1 1
cell adhesion 0.046 0.049 0.17 9 -0.12 12 21
CRKL/CBL 0.05 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.026 -10000 0 -10000 0 0
ITGB1 0.027 0.016 -10000 0 0 118 118
ITGB7 0.036 0.005 -10000 0 0 10 10
ARF6/GDP 0.034 0.016 -10000 0 -0.024 17 17
alpha4/beta1 Integrin/Paxillin/VCAM1 0.014 0.077 0.18 5 -0.11 104 109
p130Cas/Crk/Dock1 0.026 0.036 -10000 0 -0.12 17 17
VCAM1 0.022 0.018 -10000 0 0 186 186
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.051 0.18 9 -0.12 12 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.046 0.18 12 -10000 0 12
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.053 0.045 -10000 0 -0.17 12 12
CBL 0.036 0.004 -10000 0 0 6 6
PRKACA 0.034 0.009 -10000 0 0 29 29
GIT1 0.036 0.003 -10000 0 0 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.051 0.18 9 -0.12 12 21
Rac1/GTP -0.058 0.16 -10000 0 -0.39 79 79
IL2 signaling events mediated by PI3K

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
BCL2L1 0.004 0.093 -10000 0 -0.38 2 2
UGCG -0.027 0.19 -10000 0 -0.74 29 29
AKT1/mTOR/p70S6K/Hsp90/TERT -0.006 0.13 0.26 8 -0.33 38 46
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.025 0.18 -10000 0 -0.73 29 29
mol:DAG -0.007 0.031 0.17 14 -10000 0 14
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.18 0.31 5 -0.41 60 65
FRAP1 -0.035 0.2 0.32 7 -0.46 61 68
FOXO3 -0.034 0.2 0.3 7 -0.46 63 70
AKT1 -0.041 0.21 0.31 4 -0.5 62 66
GAB2 0.029 0.019 -10000 0 -0.012 76 76
SMPD1 0.003 0.095 -10000 0 -0.52 13 13
SGMS1 -0.004 0.034 0.072 11 -0.07 67 78
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 -0.029 0.045 0.098 2 -0.13 73 75
CALM1 0.033 0.011 -10000 0 0 49 49
cell proliferation -0.032 0.19 0.28 9 -0.4 66 75
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.078 -10000 0 -0.15 73 73
RPS6KB1 0.028 0.043 -10000 0 -0.71 1 1
mol:sphingomyelin -0.007 0.031 0.17 14 -10000 0 14
natural killer cell activation 0 0.004 0.007 23 -0.01 44 67
JAK3 0.033 0.017 -10000 0 -0.028 22 22
PIK3R1 0.031 0.019 -10000 0 -0.029 24 24
JAK1 0.032 0.019 -10000 0 -0.028 28 28
NFKB1 0.035 0.007 -10000 0 0 17 17
MYC -0.068 0.29 0.44 7 -0.83 55 62
MYB 0.033 0.041 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.16 0.25 6 -0.38 49 55
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.045 -10000 0 -0.65 1 1
mol:PI-3-4-5-P3 -0.024 0.16 0.25 6 -0.37 49 55
Rac1/GDP 0.005 0.051 0.11 4 -0.13 48 52
T cell proliferation -0.023 0.14 0.25 4 -0.35 48 52
SHC1 0.029 0.019 -10000 0 -0.011 80 80
RAC1 0.027 0.016 -10000 0 0 123 123
positive regulation of cyclin-dependent protein kinase activity 0.005 0.011 0.056 23 -10000 0 23
PRKCZ -0.025 0.15 0.26 4 -0.36 49 53
NF kappa B1 p50/RelA -0.013 0.19 0.33 4 -0.42 60 64
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.094 -10000 0 -0.29 22 22
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.036 0.005 -10000 0 0 10 10
IL2RA 0.021 0.021 -10000 0 -0.004 190 190
IL2RB 0.031 0.018 -10000 0 -0.028 23 23
TERT 0.035 0.006 -10000 0 0 15 15
E2F1 0.033 0.028 -10000 0 -10000 0 0
SOS1 0 0.003 0.008 27 -0.009 43 70
RPS6 0.031 0.013 -10000 0 0 72 72
mol:cAMP -0.003 0.006 -10000 0 -0.031 24 24
PTPN11 0.032 0.017 -10000 0 -0.023 41 41
IL2RG 0.033 0.017 -10000 0 -0.029 23 23
actin cytoskeleton organization -0.023 0.14 0.25 4 -0.35 48 52
GRB2 0.032 0.016 -10000 0 -0.017 41 41
IL2 0.035 0.016 -10000 0 -0.029 23 23
PIK3CA 0.029 0.02 -10000 0 -0.029 26 26
Rac1/GTP 0.028 0.065 0.16 6 -0.12 48 54
LCK 0.034 0.017 -10000 0 -0.029 24 24
BCL2 -0.021 0.16 -10000 0 -0.45 27 27
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.013 -10000 0 -10000 0 0
cell-cell adhesion 0.032 0.041 0.14 37 -10000 0 37
Ephrin B/EPHB2/RasGAP 0.059 0.089 -10000 0 -0.13 72 72
ITSN1 0.035 0.006 -10000 0 0 16 16
PIK3CA 0.03 0.014 -10000 0 0 85 85
SHC1 0.033 0.011 -10000 0 0 48 48
Ephrin B1/EPHB3 0.045 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.039 0.025 -10000 0 -0.12 6 6
HRAS/GDP 0.005 0.082 -10000 0 -0.2 44 44
Ephrin B/EPHB1/GRB7 0.067 0.074 -10000 0 -0.12 45 45
Endophilin/SYNJ1 -0.026 0.055 0.19 12 -0.18 2 14
KRAS 0.033 0.01 -10000 0 0 37 37
Ephrin B/EPHB1/Src 0.064 0.076 -10000 0 -0.12 52 52
endothelial cell migration 0.021 0.072 -10000 0 -0.14 63 63
GRB2 0.035 0.006 -10000 0 0 16 16
GRB7 0.035 0.006 -10000 0 0 13 13
PAK1 -0.027 0.06 0.19 16 -10000 0 16
HRAS 0.034 0.009 -10000 0 0 32 32
RRAS -0.025 0.056 0.2 10 -0.18 11 21
DNM1 0.035 0.008 -10000 0 0 23 23
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.02 0.063 0.18 14 -0.18 10 24
lamellipodium assembly -0.032 0.041 -10000 0 -0.14 37 37
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.071 -10000 0 -0.28 13 13
PIK3R1 0.032 0.012 -10000 0 0 61 61
EPHB2 0.034 0.009 -10000 0 0 35 35
EPHB3 0.033 0.01 -10000 0 0 44 44
EPHB1 0.03 0.014 -10000 0 0 87 87
EPHB4 0.026 0.016 -10000 0 0 141 141
mol:GDP 0.014 0.11 0.19 86 -0.22 37 123
Ephrin B/EPHB2 0.051 0.067 -10000 0 -0.11 62 62
Ephrin B/EPHB3 0.051 0.066 -10000 0 -0.11 58 58
JNK cascade -0.006 0.068 0.23 18 -0.19 4 22
Ephrin B/EPHB1 0.051 0.065 -10000 0 -0.11 52 52
RAP1/GDP 0.023 0.12 0.21 83 -0.22 34 117
EFNB2 0.028 0.015 -10000 0 0 110 110
EFNB3 0.034 0.008 -10000 0 0 25 25
EFNB1 0.036 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.031 0.058 -10000 0 -0.11 51 51
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 8 8
CDC42/GTP 0.044 0.082 -10000 0 -0.19 32 32
Rap1/GTP -0.044 0.052 0.052 8 -0.21 20 28
axon guidance 0.045 0.013 -10000 0 -10000 0 0
MAPK3 -0.01 0.068 0.16 2 -0.27 14 16
MAPK1 -0.009 0.073 0.17 3 -0.27 18 21
Rac1/GDP -0.002 0.1 0.26 23 -0.24 31 54
actin cytoskeleton reorganization -0.038 0.06 -10000 0 -0.2 37 37
CDC42/GDP 0.03 0.13 0.22 92 -0.23 34 126
PI3K 0.024 0.076 -10000 0 -0.14 63 63
EFNA5 0.036 0.003 -10000 0 0 4 4
Ephrin B2/EPHB4 0.016 0.048 -10000 0 -0.12 46 46
Ephrin B/EPHB2/Intersectin/N-WASP 0.002 0.062 -10000 0 -0.17 43 43
CDC42 0.035 0.008 -10000 0 0 22 22
RAS family/GTP -0.051 0.06 -10000 0 -0.24 23 23
PTK2 -0.012 0.077 0.53 8 -0.2 14 22
MAP4K4 -0.006 0.068 0.24 18 -0.19 4 22
SRC 0.035 0.006 -10000 0 0 13 13
KALRN 0.034 0.008 -10000 0 0 24 24
Intersectin/N-WASP 0.033 0.033 -10000 0 -0.14 7 7
neuron projection morphogenesis 0.05 0.16 0.32 100 -0.22 14 114
MAP2K1 -0.002 0.069 -10000 0 -0.26 16 16
WASL 0.025 0.017 -10000 0 0 155 155
Ephrin B1/EPHB1-2/NCK1 0.08 0.038 -10000 0 -0.12 10 10
cell migration -0.014 0.087 0.21 3 -0.27 21 24
NRAS 0.032 0.012 -10000 0 0 58 58
SYNJ1 -0.026 0.056 0.19 12 -0.18 2 14
PXN 0.036 0.004 -10000 0 0 5 5
TF -0.022 0.05 0.19 5 -0.18 19 24
HRAS/GTP 0.033 0.079 -10000 0 -0.14 63 63
Ephrin B1/EPHB1-2 0.053 0.034 -10000 0 -0.11 6 6
cell adhesion mediated by integrin 0.018 0.046 0.15 5 -0.24 5 10
RAC1 0.027 0.016 -10000 0 0 123 123
mol:GTP 0.041 0.077 -10000 0 -0.13 61 61
RAC1-CDC42/GTP -0.034 0.048 -10000 0 -0.2 16 16
RASA1 0.034 0.009 -10000 0 0 30 30
RAC1-CDC42/GDP 0.017 0.1 0.26 22 -0.23 32 54
ruffle organization 0.053 0.16 0.31 106 -0.22 16 122
NCK1 0.034 0.008 -10000 0 0 26 26
receptor internalization -0.031 0.052 0.18 11 -0.18 2 13
Ephrin B/EPHB2/KALRN 0.064 0.078 -10000 0 -0.12 59 59
ROCK1 -0.01 0.043 0.18 15 -10000 0 15
RAS family/GDP -0.042 0.063 -10000 0 -0.2 42 42
Rac1/GTP -0.031 0.046 -10000 0 -0.15 37 37
Ephrin B/EPHB1/Src/Paxillin 0.008 0.066 -10000 0 -0.15 56 56
S1P3 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
PDGFRB 0.034 0.008 -10000 0 0 25 25
mol:S1P 0.001 0.002 0.019 4 -10000 0 4
S1P1/S1P/Gi -0.021 0.11 -10000 0 -0.23 82 82
GNAO1 0.031 0.014 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.027 0.039 -10000 0 -0.1 30 30
AKT1 -0.017 0.16 -10000 0 -0.49 46 46
AKT3 0.01 0.075 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.008 -10000 0 0 25 25
GNAI2 0.034 0.011 -10000 0 0 42 42
GNAI3 0.036 0.006 -10000 0 0 12 12
GNAI1 0.018 0.019 -10000 0 0 246 246
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 0.02 4 -10000 0 4
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.033 0.01 -10000 0 0 38 38
mol:Ca2+ -0.008 0.1 0.2 1 -0.26 47 48
MAPK3 -0.011 0.1 0.18 1 -0.25 49 50
MAPK1 -0.004 0.095 0.18 1 -0.26 38 39
JAK2 -0.016 0.11 0.17 1 -0.3 44 45
CXCR4 -0.009 0.1 0.14 4 -0.2 78 82
FLT1 0.035 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
SRC -0.011 0.1 0.18 1 -0.25 48 49
S1P/S1P3/Gi -0.008 0.1 0.2 1 -0.27 47 48
RAC1 0.027 0.016 -10000 0 0 123 123
RhoA/GTP 0.008 0.11 0.19 1 -0.25 48 49
VEGFA 0.002 0.002 0.028 4 -10000 0 4
S1P/S1P2/Gi -0.012 0.1 0.16 1 -0.21 83 84
VEGFR1 homodimer/VEGFA homodimer 0.029 0.01 0.093 4 -10000 0 4
RHOA 0.035 0.007 -10000 0 0 21 21
S1P/S1P3/Gq 0.014 0.04 -10000 0 -0.15 25 25
GNAQ 0.034 0.009 -10000 0 0 31 31
GNAZ 0.031 0.014 -10000 0 0 79 79
G12/G13 0.028 0.049 -10000 0 -0.14 30 30
GNA14 0.034 0.008 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
GNA11 0.032 0.012 -10000 0 0 60 60
Rac1/GTP -0.001 0.099 -10000 0 -0.25 41 41
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.011 -10000 0 0 45 45
VLDLR 0.027 0.016 -10000 0 0 128 128
LRPAP1 0.035 0.006 -10000 0 0 16 16
NUDC 0.034 0.008 -10000 0 0 25 25
RELN/LRP8 0.041 0.044 -10000 0 -0.13 11 11
CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
KATNA1 0.033 0.01 -10000 0 0 39 39
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.031 0.098 0.19 117 -0.21 7 124
IQGAP1/CaM 0.032 0.058 -10000 0 -0.15 42 42
DAB1 0.035 0.005 -10000 0 0 11 11
IQGAP1 0.033 0.01 -10000 0 0 43 43
PLA2G7 0.032 0.011 -10000 0 0 51 51
CALM1 0.033 0.011 -10000 0 0 49 49
DYNLT1 0.033 0.01 -10000 0 0 41 41
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.044 0.036 -10000 0 -0.15 13 13
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.035 0.007 -10000 0 0 21 21
LIS1/Poliovirus Protein 3A -0.023 0.029 -10000 0 -0.14 24 24
CDK5R2 0.035 0.006 -10000 0 0 16 16
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.031 0.05 -10000 0 -0.12 23 23
YWHAE 0.034 0.009 -10000 0 0 29 29
NDEL1/14-3-3 E 0.048 0.16 0.29 116 -0.27 18 134
MAP1B -0.015 0.069 -10000 0 -0.2 52 52
RAC1 -0.004 0.055 -10000 0 -0.34 8 8
p35/CDK5 -0.018 0.072 0.2 26 -0.21 12 38
RELN 0.024 0.017 -10000 0 0 163 163
PAFAH/LIS1 0.021 0.039 -10000 0 -0.15 21 21
LIS1/CLIP170 -0.023 0.029 -10000 0 -0.14 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.031 0.085 0.14 23 -0.27 26 49
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.015 0.086 -10000 0 -0.22 49 49
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.041 0.15 0.27 117 -0.27 16 133
LIS1/IQGAP1 0.014 0.059 -10000 0 -0.15 49 49
RHOA -0.007 0.068 -10000 0 -0.27 20 20
PAFAH1B1 -0.02 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.013 -10000 0 0 72 72
PAFAH1B2 0.036 0.004 -10000 0 0 5 5
MAP1B/LIS1/Dynein heavy chain 0.005 0.079 -10000 0 -0.2 54 54
NDEL1/Katanin 60/Dynein heavy chain 0.068 0.14 0.32 76 -0.26 22 98
LRP8 0.034 0.009 -10000 0 0 35 35
NDEL1/Katanin 60 0.041 0.15 0.29 108 -0.26 19 127
P39/CDK5 -0.016 0.073 0.19 28 -0.21 12 40
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.053 -10000 0 -0.19 26 26
CDK5 -0.006 0.061 0.19 27 -0.22 7 34
PPP2R5D 0.036 0.004 -10000 0 0 6 6
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.019 0.024 -10000 0 -0.12 24 24
CSNK2A1 0.034 0.009 -10000 0 0 31 31
RELN/VLDLR/DAB1/LIS1 0.031 0.062 0.18 3 -0.13 38 41
RELN/VLDLR 0.043 0.062 -10000 0 -0.12 31 31
CDC42 -0.003 0.047 -10000 0 -0.2 16 16
FAS signaling pathway (CD95)

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
SPTAN1 -0.02 0.057 0.22 5 -0.22 23 28
RFC1 -0.021 0.051 0.18 2 -0.22 25 27
PRKDC -0.017 0.058 0.19 7 -0.22 23 30
RIPK1 0.032 0.012 -10000 0 -0.013 30 30
CASP7 -0.14 0.28 -10000 0 -0.58 139 139
FASLG/FAS/FADD/FAF1 -0.006 0.085 0.16 32 -0.18 40 72
MAP2K4 -0.036 0.14 0.21 1 -0.34 34 35
mol:ceramide 0.008 0.092 0.18 5 -0.24 20 25
GSN -0.008 0.06 0.19 9 -0.22 20 29
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.096 0.18 12 -0.25 26 38
FAS 0.022 0.02 -10000 0 0 207 207
BID -0.029 0.032 0.075 26 -0.13 18 44
MAP3K1 -0.087 0.19 -10000 0 -0.37 137 137
MAP3K7 0.034 0.01 -10000 0 0 38 38
RB1 -0.014 0.056 0.22 9 -0.21 24 33
CFLAR 0.033 0.01 -10000 0 -0.016 18 18
HGF/MET 0.033 0.049 -10000 0 -0.12 21 21
ARHGDIB -0.017 0.06 0.22 7 -0.22 22 29
FADD 0.038 0.008 -10000 0 0 13 13
actin filament polymerization 0.008 0.06 0.22 20 -0.19 9 29
NFKB1 0.029 0.11 -10000 0 -0.65 10 10
MAPK8 -0.026 0.14 -10000 0 -0.36 21 21
DFFA -0.019 0.051 0.22 3 -0.21 25 28
DNA fragmentation during apoptosis -0.018 0.047 0.22 1 -0.21 24 25
FAS/FADD/MET 0.025 0.049 -10000 0 -0.12 22 22
CFLAR/RIP1 0.047 0.019 -10000 0 -0.13 2 2
FAIM3 0.035 0.006 -10000 0 0 13 13
FAF1 0.038 0.011 -10000 0 -10000 0 0
PARP1 -0.019 0.052 0.22 3 -0.22 26 29
DFFB -0.018 0.047 0.22 1 -0.21 24 25
CHUK 0.017 0.1 -10000 0 -0.61 10 10
FASLG 0.039 0.008 -10000 0 -10000 0 0
FAS/FADD 0.024 0.053 -10000 0 -0.14 32 32
HGF 0.024 0.017 -10000 0 0 158 158
LMNA -0.02 0.052 0.17 9 -0.2 24 33
CASP6 -0.018 0.049 0.17 3 -0.21 24 27
CASP10 0.039 0.004 -10000 0 -10000 0 0
CASP3 -0.01 0.048 -10000 0 -0.24 19 19
PTPN13 0.032 0.012 -10000 0 0 56 56
CASP8 -0.03 0.007 -10000 0 -10000 0 0
IL6 0.025 0.13 -10000 0 -0.65 5 5
MET 0.023 0.018 -10000 0 0 183 183
ICAD/CAD -0.023 0.05 0.27 3 -0.2 24 27
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.093 0.18 5 -0.24 20 25
activation of caspase activity by cytochrome c -0.03 0.033 0.075 26 -0.13 20 46
PAK2 -0.012 0.057 0.21 8 -0.21 23 31
BCL2 0.035 0.007 -10000 0 0 17 17
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.043 0.042 -10000 0 -0.14 23 23
AKT1 -0.019 0.17 0.26 15 -0.41 46 61
PTK2B -0.005 0.11 0.21 43 -0.37 12 55
VEGFR2 homodimer/Frs2 0.025 0.082 -10000 0 -0.34 15 15
CAV1 0.016 0.018 -10000 0 0 269 269
CALM1 0.033 0.011 -10000 0 0 49 49
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.016 0.082 0.19 1 -0.31 17 18
endothelial cell proliferation 0.007 0.14 0.27 26 -0.37 29 55
mol:Ca2+ 0.002 0.12 0.24 48 -0.33 19 67
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.022 0.09 -10000 0 -0.28 22 22
RP11-342D11.1 -0.013 0.095 0.15 43 -0.32 18 61
CDH5 0.03 0.014 -10000 0 0 83 83
VEGFA homodimer 0.036 0.034 -10000 0 -0.084 17 17
SHC1 0.033 0.011 -10000 0 0 48 48
SHC2 0.031 0.013 -10000 0 0 69 69
HRAS/GDP 0.006 0.091 -10000 0 -0.24 45 45
SH2D2A 0.035 0.005 -10000 0 0 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.015 0.11 -10000 0 -0.35 21 21
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.016 0.083 0.19 1 -0.31 18 19
VEGFR1 homodimer 0.034 0.009 -10000 0 0 31 31
SHC/GRB2/SOS1 0.035 0.1 -10000 0 -0.23 45 45
GRB10 -0.016 0.11 0.2 29 -0.33 35 64
PTPN11 0.036 0.005 -10000 0 0 9 9
GRB2 0.035 0.006 -10000 0 0 16 16
PAK1 0.035 0.007 -10000 0 0 17 17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.12 -10000 0 -0.28 34 34
HRAS 0.034 0.009 -10000 0 0 32 32
VEGF/Rho/ROCK1/Integrin Complex 0.008 0.1 -10000 0 -0.32 29 29
HIF1A 0.033 0.01 -10000 0 0 37 37
FRS2 0.035 0.008 -10000 0 0 22 22
oxygen and reactive oxygen species metabolic process 0.02 0.089 -10000 0 -0.28 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.036 0.005 -10000 0 0 8 8
Nck/Pak 0.048 0.025 -10000 0 -0.14 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.003 0.096 0.19 1 -0.29 29 30
mol:GDP 0.013 0.091 -10000 0 -0.23 45 45
mol:NADP 0.025 0.12 0.29 17 -0.33 17 34
eNOS/Hsp90 0.023 0.11 0.27 17 -0.31 17 34
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.002 0.12 0.24 48 -0.33 19 67
HIF1A/ARNT 0.045 0.032 -10000 0 -0.14 11 11
SHB 0.033 0.011 -10000 0 0 48 48
VEGFA -0.003 0.013 -10000 0 -0.041 49 49
VEGFC 0.033 0.011 -10000 0 0 45 45
FAK1/Vinculin 0.011 0.12 0.25 8 -0.45 18 26
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 0.033 0.099 0.2 1 -0.29 23 24
PTPN6 0.033 0.011 -10000 0 0 50 50
EPAS1 0.03 0.061 -10000 0 -0.26 14 14
mol:L-citrulline 0.025 0.12 0.29 17 -0.33 17 34
ITGAV 0.034 0.009 -10000 0 0 30 30
PIK3CA 0.03 0.014 -10000 0 0 85 85
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.036 0.092 0.2 1 -0.31 18 19
VEGFR2 homodimer/VEGFA homodimer 0.012 0.098 -10000 0 -0.25 46 46
VEGFR2/3 heterodimer 0.026 0.083 -10000 0 -0.33 16 16
VEGFB 0.036 0.005 -10000 0 0 9 9
MAPK11 0.004 0.13 0.28 27 -0.34 20 47
VEGFR2 homodimer -0.003 0.083 0.2 1 -0.39 14 15
FLT1 0.034 0.009 -10000 0 0 31 31
NEDD4 0.028 0.033 0.087 5 -0.056 52 57
MAPK3 0.008 0.12 0.27 32 -0.3 19 51
MAPK1 0.008 0.12 0.27 37 -0.3 20 57
VEGFA145/NRP2 0.023 0.022 -10000 0 -0.047 6 6
VEGFR1/2 heterodimer 0.024 0.083 -10000 0 -0.33 16 16
KDR -0.003 0.083 0.2 1 -0.39 14 15
VEGFA165/NRP1/VEGFR2 homodimer 0.022 0.096 -10000 0 -0.23 46 46
SRC 0.035 0.006 -10000 0 0 13 13
platelet activating factor biosynthetic process 0.008 0.12 0.27 34 -0.31 19 53
PI3K -0.009 0.14 0.28 7 -0.38 33 40
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.014 0.083 0.19 1 -0.31 17 18
FES 0.002 0.12 0.24 48 -0.34 17 65
GAB1 0.01 0.12 0.24 11 -0.36 23 34
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.083 -10000 0 -0.32 17 17
CTNNB1 0.035 0.007 -10000 0 0 21 21
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.036 0.005 -10000 0 0 10 10
eNOS/Caveolin-1 0.009 0.094 0.3 4 -0.36 12 16
VEGFR2 homodimer/VEGFA homodimer/Yes 0.011 0.087 0.19 1 -0.32 19 20
PI3K/GAB1 -0.006 0.16 0.27 15 -0.41 41 56
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.058 0.095 -10000 0 -0.29 16 16
PRKACA 0.034 0.009 -10000 0 0 29 29
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.08 -10000 0 -0.3 14 14
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.001 0.12 0.21 70 -0.34 17 87
actin cytoskeleton reorganization 0.016 0.082 0.19 1 -0.3 18 19
PTK2 0.007 0.13 0.25 13 -0.49 17 30
EDG1 -0.005 0.13 0.24 46 -0.35 26 72
mol:DAG 0.002 0.12 0.24 48 -0.33 19 67
CaM/Ca2+ 0.019 0.12 0.25 22 -0.24 46 68
MAP2K3 -0.004 0.12 0.23 44 -0.34 16 60
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.033 0.13 0.22 73 -0.3 43 116
PLCG1 0.002 0.12 0.24 48 -0.34 19 67
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.033 0.089 -10000 0 -0.3 17 17
IQGAP1 0.033 0.01 -10000 0 0 43 43
YES1 0.033 0.01 -10000 0 0 37 37
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.015 0.085 0.19 1 -0.3 20 21
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.012 0.084 0.19 1 -0.3 19 20
cell migration 0.004 0.13 0.25 16 -0.43 24 40
mol:PI-3-4-5-P3 -0.006 0.13 0.27 9 -0.36 33 42
FYN 0.03 0.014 -10000 0 0 83 83
VEGFB/NRP1 0.001 0.12 0.2 72 -0.32 17 89
mol:NO 0.025 0.12 0.29 17 -0.33 17 34
PXN 0.036 0.004 -10000 0 0 5 5
HRAS/GTP -0.044 0.07 -10000 0 -0.24 41 41
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.1 -10000 0 -0.3 43 43
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.036 0.004 -10000 0 0 5 5
NOS3 0.024 0.12 0.3 15 -0.36 17 32
VEGFR2 homodimer/VEGFA homodimer/Sck 0.007 0.093 -10000 0 -0.29 27 27
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.004 0.12 0.22 48 -0.32 19 67
PRKCB 0 0.12 0.22 48 -0.31 19 67
VCL 0.027 0.016 -10000 0 0 127 127
VEGFA165/NRP1 -0.028 0.079 0.11 29 -0.23 46 75
VEGFR1/2 heterodimer/VEGFA homodimer 0.014 0.082 0.19 1 -0.31 18 19
VEGFA165/NRP2 0.023 0.022 -10000 0 -0.047 6 6
MAPKKK cascade -0.033 0.094 0.18 7 -0.32 34 41
NRP2 0.036 0.005 -10000 0 0 9 9
VEGFC homodimer 0.033 0.011 -10000 0 0 45 45
NCK1 0.034 0.008 -10000 0 0 26 26
ROCK1 0.035 0.006 -10000 0 0 14 14
FAK1/Paxillin 0.024 0.13 0.25 12 -0.46 17 29
MAP3K13 0.002 0.12 0.24 46 -0.35 16 62
PDPK1 -0.023 0.12 0.24 20 -0.34 31 51
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.26 0.59 11 -0.73 19 30
CRP 0.054 0.26 0.6 8 -0.69 22 30
cell cycle arrest 0.047 0.29 0.54 13 -0.75 29 42
TIMP1 -0.001 0.37 0.57 12 -0.79 70 82
IL6ST 0.028 0.032 0.089 1 -0.043 49 50
Rac1/GDP 0.05 0.11 0.3 18 -0.3 10 28
AP1 0.017 0.19 0.3 1 -0.52 38 39
GAB2 0.034 0.012 0.063 1 -0.001 45 46
TNFSF11 0.053 0.26 0.58 7 -0.73 19 26
HSP90B1 0.002 0.22 0.3 2 -0.84 27 29
GAB1 0.031 0.014 -10000 0 -0.001 76 76
MAPK14 0.03 0.065 -10000 0 -0.32 2 2
AKT1 -0.013 0.17 -10000 0 -0.53 32 32
FOXO1 -0.009 0.16 0.24 2 -0.5 33 35
MAP2K6 0.032 0.072 -10000 0 -0.24 8 8
mol:GTP 0 0.004 -10000 0 -0.023 2 2
MAP2K4 0.041 0.14 0.33 25 -0.34 17 42
MITF 0.034 0.083 0.22 12 -0.28 8 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.032 0.011 -10000 0 0 54 54
A2M -0.066 0.32 -10000 0 -1.2 38 38
CEBPB 0.032 0.012 -10000 0 0 62 62
GRB2/SOS1/GAB family/SHP2 0.023 0.12 0.22 1 -0.45 22 23
STAT3 0.029 0.29 0.54 12 -0.8 29 41
STAT1 0.022 0.068 -10000 0 -0.74 3 3
CEBPD 0.02 0.33 0.57 7 -0.86 44 51
PIK3CA 0.03 0.015 -10000 0 0 86 86
PI3K 0.017 0.076 -10000 0 -0.15 74 74
JUN 0.033 0.01 -10000 0 0 39 39
PIAS3/MITF 0.075 0.11 0.28 15 -0.27 10 25
MAPK11 0.026 0.063 -10000 0 -0.32 2 2
STAT3 (dimer)/FOXO1 -0.014 0.26 0.45 8 -0.61 52 60
GRB2/SOS1/GAB family 0.04 0.11 0.22 1 -0.27 29 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.005 0.1 0.18 8 -0.25 43 51
GRB2 0.036 0.008 -10000 0 -0.002 17 17
JAK2 0.03 0.014 -10000 0 0 86 86
LBP 0.06 0.25 0.5 18 -0.58 32 50
PIK3R1 0.032 0.013 -10000 0 -0.001 62 62
JAK1 0.029 0.026 -10000 0 -0.041 47 47
MYC 0.009 0.36 0.62 8 -0.88 55 63
FGG 0.053 0.26 0.57 7 -0.75 18 25
macrophage differentiation 0.047 0.29 0.54 13 -0.75 29 42
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.055 0.073 -10000 0 -0.18 5 5
JUNB 0.052 0.29 0.53 20 -0.84 24 44
FOS 0.025 0.017 -10000 0 0 147 147
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.036 0.086 0.23 12 -0.27 9 21
STAT1/PIAS1 0.073 0.12 0.29 13 -0.32 7 20
GRB2/SOS1/GAB family/SHP2/PI3K -0.001 0.17 -10000 0 -0.5 32 32
STAT3 (dimer) 0.032 0.29 0.54 12 -0.79 29 41
PRKCD 0.096 0.22 0.42 72 -0.42 24 96
IL6R 0.03 0.026 -10000 0 -0.04 56 56
SOCS3 0.057 0.083 0.46 2 -10000 0 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.043 0.087 0.18 1 -0.17 42 43
Rac1/GTP 0.042 0.12 0.31 8 -0.31 12 20
HCK 0.027 0.016 -10000 0 0 123 123
MAPKKK cascade 0.017 0.18 0.34 1 -0.56 34 35
bone resorption 0.055 0.25 0.57 7 -0.69 19 26
IRF1 0.046 0.29 0.57 11 -0.85 25 36
mol:GDP 0.033 0.088 0.23 13 -0.26 9 22
SOS1 0.001 0.005 0.025 11 -0.022 1 12
VAV1 0.031 0.087 0.24 11 -0.27 9 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.025 0.076 -10000 0 -0.33 12 12
PTPN11 0.023 0.078 -10000 0 -0.76 4 4
IL6/IL6RA 0.025 0.038 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.045 0.075 -10000 0 -0.15 42 42
gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.062 -10000 0 -0.12 31 31
IL6 0.017 0.028 -10000 0 -0.041 23 23
PIAS3 0.035 0.007 -10000 0 0 17 17
PTPRE 0.009 0.029 -10000 0 -0.057 29 29
PIAS1 0.035 0.008 -10000 0 0 23 23
RAC1 0.027 0.016 -10000 0 0 123 123
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.028 0.059 0.17 4 -0.22 5 9
LMO4 0.029 0.033 0.089 1 -0.044 50 51
STAT3 (dimer)/PIAS3 0.02 0.27 0.48 3 -0.72 31 34
MCL1 -0.005 0.17 0.4 1 -0.65 19 20
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.041 0.01 -10000 0 -10000 0 0
NFATC2 0.014 0.16 0.27 4 -0.39 31 35
NFATC3 0.02 0.13 0.27 20 -0.24 66 86
CD40LG -0.011 0.34 0.49 45 -0.71 61 106
ITCH 0.035 0.047 0.19 8 -10000 0 8
CBLB 0.037 0.048 0.19 11 -10000 0 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.052 0.26 0.39 12 -0.64 48 60
JUNB 0.03 0.014 -10000 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.028 -10000 0 -0.14 6 6
T cell anergy 0.016 0.067 0.25 10 -0.24 1 11
TLE4 0.011 0.11 -10000 0 -0.32 19 19
Jun/NFAT1-c-4/p21SNFT -0.018 0.32 0.44 2 -0.73 66 68
AP-1/NFAT1-c-4 -0.042 0.34 -10000 0 -0.81 58 58
IKZF1 0.007 0.1 0.17 1 -0.26 30 31
T-helper 2 cell differentiation -0.08 0.23 -10000 0 -0.62 39 39
AP-1/NFAT1 0.015 0.15 0.28 18 -0.29 42 60
CALM1 0.045 0.023 0.13 2 -10000 0 2
EGR2 -0.069 0.41 0.51 10 -1 67 77
EGR3 -0.054 0.42 0.5 12 -1 64 76
NFAT1/FOXP3 0.038 0.12 0.26 2 -0.31 21 23
EGR1 0.029 0.015 0.07 1 0 103 104
JUN 0.033 0.042 0.11 34 -0.053 8 42
EGR4 0.036 0.004 0.07 1 -10000 0 1
mol:Ca2+ 0.005 0.003 -10000 0 -10000 0 0
GBP3 0.007 0.1 0.17 1 -0.26 30 31
FOSL1 0.032 0.012 -10000 0 0 56 56
NFAT1-c-4/MAF/IRF4 0.011 0.33 -10000 0 -0.72 67 67
DGKA 0.012 0.1 -10000 0 -0.31 19 19
CREM 0.027 0.015 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.004 0.32 -10000 0 -0.73 67 67
CTLA4 0.01 0.093 -10000 0 -0.27 19 19
NFAT1-c-4 (dimer)/EGR1 -0.027 0.34 -10000 0 -0.77 68 68
NFAT1-c-4 (dimer)/EGR4 0.004 0.33 -10000 0 -0.74 67 67
FOS 0.024 0.038 0.11 20 -0.05 7 27
IFNG -0.01 0.13 -10000 0 -0.48 5 5
T cell activation -0.01 0.22 0.44 1 -0.56 28 29
MAF 0.034 0.009 -10000 0 0 35 35
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.28 0.61 66 -0.45 19 85
TNF -0.036 0.31 0.41 7 -0.71 68 75
FASLG -0.095 0.46 -10000 0 -1.1 70 70
TBX21 0.04 0.007 0.11 3 -10000 0 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.027 0.018 -10000 0 -10000 0 0
PTPN1 0.008 0.12 -10000 0 -0.36 23 23
NFAT1-c-4/ICER1 -0.026 0.32 -10000 0 -0.74 67 67
GATA3 0.027 0.017 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.004 0.14 -10000 0 -0.47 6 6
IL2RA -0.066 0.24 0.32 4 -0.62 54 58
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.009 0.11 -10000 0 -0.36 22 22
E2F1 0.036 0.053 -10000 0 -0.24 14 14
PPARG 0.034 0.008 -10000 0 -10000 0 0
SLC3A2 0.008 0.12 0.23 2 -0.38 25 27
IRF4 0.036 0.005 -10000 0 0 8 8
PTGS2 -0.072 0.28 0.43 3 -0.71 59 62
CSF2 -0.011 0.34 0.49 45 -0.71 61 106
JunB/Fra1/NFAT1-c-4 -0.019 0.3 -10000 0 -0.71 65 65
IL4 -0.083 0.23 -10000 0 -0.64 39 39
IL5 -0.012 0.34 0.49 45 -0.71 61 106
IL2 -0.011 0.22 -10000 0 -0.57 26 26
IL3 0.008 0.082 -10000 0 -0.68 4 4
RNF128 0.014 0.022 0.17 1 -10000 0 1
NFATC1 -0.006 0.28 0.45 19 -0.61 66 85
CDK4 -0.015 0.28 0.6 29 -1 14 43
PTPRK -0.004 0.14 -10000 0 -0.43 37 37
IL8 -0.1 0.29 0.45 7 -0.75 60 67
POU2F1 0.039 0.008 -10000 0 -10000 0 0
Class I PI3K signaling events

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.022 0.055 0.16 20 -0.22 10 30
DAPP1 -0.024 0.12 -10000 0 -0.29 62 62
Src family/SYK family/BLNK-LAT/BTK-ITK -0.045 0.19 0.24 2 -0.49 55 57
mol:DAG -0.012 0.091 0.2 20 -0.2 45 65
HRAS 0.034 0.019 0.085 1 -0.014 56 57
RAP1A 0.037 0.014 0.063 2 -0.022 19 21
ARF5/GDP -0.002 0.1 -10000 0 -0.32 32 32
PLCG2 0.032 0.012 -10000 0 0 61 61
PLCG1 0.035 0.007 -10000 0 0 20 20
ARF5 0.026 0.016 -10000 0 0 138 138
mol:GTP -0.024 0.053 0.14 21 -0.19 11 32
ARF1/GTP -0.018 0.053 0.14 23 -0.2 14 37
RHOA 0.035 0.007 -10000 0 0 21 21
YES1 0.033 0.01 -10000 0 0 37 37
RAP1A/GTP -0.023 0.056 0.16 21 -0.19 11 32
ADAP1 -0.024 0.049 0.14 18 -0.19 11 29
ARAP3 -0.024 0.052 0.14 21 -0.19 11 32
INPPL1 0.035 0.006 -10000 0 0 12 12
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.033 0.011 -10000 0 0 47 47
ARHGEF7 0.032 0.012 -10000 0 0 56 56
ARF1 0.035 0.007 -10000 0 0 21 21
NRAS 0.033 0.017 -10000 0 -0.032 11 11
FYN 0.03 0.014 -10000 0 0 83 83
ARF6 0.035 0.007 -10000 0 0 21 21
FGR 0.032 0.011 -10000 0 0 52 52
mol:Ca2+ 0.004 0.061 0.14 42 -0.12 17 59
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.033 0.01 -10000 0 0 43 43
ZAP70 0.036 0.003 -10000 0 0 3 3
mol:IP3 -0.007 0.07 0.17 33 -0.17 19 52
LYN 0.031 0.013 -10000 0 0 72 72
ARF1/GDP 0.005 0.11 -10000 0 -0.33 37 37
RhoA/GDP 0.021 0.091 0.18 17 -0.21 31 48
PDK1/Src/Hsp90 0.047 0.009 -10000 0 -10000 0 0
BLNK 0.02 0.018 -10000 0 0 219 219
actin cytoskeleton reorganization 0.001 0.1 0.2 24 -0.3 24 48
SRC 0.035 0.006 -10000 0 0 13 13
PLEKHA2 -0.016 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.016 -10000 0 0 123 123
PTEN 0.026 0.022 -10000 0 -0.032 21 21
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.057 0.15 23 -0.2 11 34
RhoA/GTP -0.027 0.059 0.16 22 -0.2 12 34
Src family/SYK family/BLNK-LAT -0.05 0.16 -10000 0 -0.35 75 75
BLK 0.035 0.007 -10000 0 0 17 17
PDPK1 0.036 0.003 -10000 0 0 4 4
CYTH1 -0.024 0.049 0.14 18 -0.19 11 29
HCK 0.027 0.016 -10000 0 0 123 123
CYTH3 -0.024 0.049 0.14 18 -0.19 11 29
CYTH2 -0.024 0.049 0.14 18 -0.19 11 29
KRAS 0.033 0.02 0.085 1 -0.032 27 28
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.002 0.031 0.18 2 -0.15 2 4
SGK1 0.001 0.032 0.18 2 -0.15 2 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.11 0.17 3 -0.32 39 42
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.031 0.013 -10000 0 0 72 72
ARF6/GDP -0.027 0.07 0.17 20 -0.22 27 47
mol:PI-3-4-5-P3 -0.025 0.052 0.14 18 -0.19 11 29
ARAP3/RAP1A/GTP -0.023 0.056 0.16 21 -0.19 11 32
VAV1 0.033 0.01 -10000 0 0 38 38
mol:PI-3-4-P2 -0.011 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.056 0.089 0.21 85 -0.14 40 125
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.1 -10000 0 -0.31 34 34
LAT 0.036 0.005 -10000 0 0 9 9
Rac1/GTP -0.012 0.15 0.16 1 -0.39 46 47
ITK -0.027 0.052 0.14 21 -0.19 11 32
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.024 0.12 0.22 15 -0.27 51 66
LCK 0.035 0.007 -10000 0 0 17 17
BTK -0.027 0.052 0.14 21 -0.19 11 32
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.088 0.23 24 -0.21 8 32
TBX21 0.072 0.2 0.56 6 -0.55 5 11
B2M 0.035 0.007 -10000 0 0 19 19
TYK2 0.035 0.039 0.12 13 -0.054 11 24
IL12RB1 0.036 0.04 0.12 15 -0.051 31 46
GADD45B 0.064 0.28 0.56 10 -0.99 21 31
IL12RB2 0.039 0.04 0.12 21 -0.054 14 35
GADD45G 0.093 0.19 0.5 14 -0.53 4 18
natural killer cell activation 0.012 0.024 0.055 70 -0.036 10 80
RELB 0.034 0.009 -10000 0 0 33 33
RELA 0.036 0.005 -10000 0 0 10 10
IL18 0.034 0.021 0.086 2 -0.041 15 17
IL2RA 0.024 0.017 -10000 0 0 163 163
IFNG 0.034 0.009 -10000 0 0 32 32
STAT3 (dimer) 0.076 0.22 0.45 25 -0.51 26 51
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 45 45
FASLG 0.077 0.2 0.56 6 -0.58 3 9
NF kappa B2 p52/RelB 0.057 0.19 0.44 9 -0.49 12 21
CD4 0.024 0.027 -10000 0 -0.017 127 127
SOCS1 0.036 0.004 -10000 0 0 7 7
EntrezGene:6955 -0.001 0.01 -10000 0 -0.025 61 61
CD3D 0.025 0.029 -10000 0 -0.026 105 105
CD3E 0.027 0.027 -10000 0 -0.036 74 74
CD3G 0.026 0.029 -10000 0 -0.035 81 81
IL12Rbeta2/JAK2 0.053 0.058 0.18 15 -10000 0 15
CCL3 0.074 0.2 0.45 27 -0.48 15 42
CCL4 0.044 0.33 0.57 15 -1 30 45
HLA-A 0.035 0.007 -10000 0 0 19 19
IL18/IL18R 0.088 0.064 0.21 27 -0.12 7 34
NOS2 0.076 0.19 0.43 31 -0.43 16 47
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.087 0.23 21 -0.22 9 30
IL1R1 0.074 0.2 0.58 7 -0.6 2 9
IL4 0.003 0.048 -10000 0 -0.074 73 73
JAK2 0.033 0.037 0.11 14 -0.055 7 21
EntrezGene:6957 -0.001 0.009 -10000 0 -0.023 45 45
TCR/CD3/MHC I/CD8 0.007 0.041 0.11 1 -0.16 14 15
RAB7A 0.096 0.2 0.44 28 -0.53 18 46
lysosomal transport 0.097 0.2 0.44 29 -0.51 18 47
FOS -0.098 0.47 0.46 18 -1 86 104
STAT4 (dimer) 0.092 0.2 0.45 30 -0.49 15 45
STAT5A (dimer) 0.079 0.19 0.42 13 -0.47 15 28
GZMA 0.072 0.2 0.55 11 -0.58 3 14
GZMB 0.071 0.2 0.56 11 -0.55 5 16
HLX 0 0 -10000 0 -10000 0 0
LCK 0.058 0.2 0.48 21 -0.5 15 36
TCR/CD3/MHC II/CD4 -0.021 0.12 0.16 22 -0.2 117 139
IL2/IL2R 0.057 0.049 -10000 0 -10000 0 0
MAPK14 0.099 0.22 0.5 21 -0.62 18 39
CCR5 0.079 0.18 0.4 34 -0.39 16 50
IL1B 0.029 0.037 0.11 7 -0.05 27 34
STAT6 0.046 0.1 0.29 11 -0.44 3 14
STAT4 0.034 0.009 -10000 0 0 30 30
STAT3 0.033 0.01 -10000 0 0 37 37
STAT1 0.033 0.01 -10000 0 0 40 40
NFKB1 0.035 0.007 -10000 0 0 17 17
NFKB2 0.027 0.016 -10000 0 0 127 127
IL12B 0.04 0.04 0.12 17 -0.051 26 43
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 -0.042 0.087 0.21 8 -0.23 24 32
IL2RB 0.032 0.011 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.2 0.45 31 -0.46 15 46
IL2RG 0.034 0.008 -10000 0 0 24 24
IL12 0.062 0.06 0.18 18 -10000 0 18
STAT5A 0.036 0.004 -10000 0 0 6 6
CD247 -0.001 0.009 -10000 0 -0.023 45 45
IL2 0.036 0.005 -10000 0 0 8 8
SPHK2 0.034 0.01 -10000 0 0 36 36
FRAP1 0.035 0.006 -10000 0 0 14 14
IL12A 0.038 0.04 0.12 14 -0.053 16 30
IL12/IL12R/TYK2/JAK2 0.064 0.21 0.5 24 -0.52 15 39
MAP2K3 0.093 0.22 0.5 19 -0.62 18 37
RIPK2 0.035 0.005 -10000 0 0 11 11
MAP2K6 0.097 0.22 0.49 21 -0.58 18 39
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.02 0.027 -10000 0 -0.011 183 183
IL18RAP 0.039 0.019 0.086 2 -0.04 19 21
IL12Rbeta1/TYK2 0.047 0.063 0.18 6 -0.15 15 21
EOMES -0.02 0.038 0.074 2 -0.1 45 47
STAT1 (dimer) 0.085 0.19 0.44 24 -0.46 9 33
T cell proliferation 0.08 0.18 0.4 34 -0.4 18 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.039 0.019 0.086 2 -0.04 19 21
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.043 0.16 -10000 0 -0.47 21 21
ATF2 0.091 0.21 0.5 14 -0.59 18 32
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.034 0.01 -10000 0 0 36 36
SPHK1 0.033 0.011 -10000 0 0 47 47
GNAI2 0.033 0.01 -10000 0 0 42 42
mol:S1P 0.018 0.015 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
mol:Sphinganine-1-P -0.019 0.008 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.032 0.046 -10000 0 -0.16 3 3
GNAI3 0.035 0.006 -10000 0 0 12 12
G12/G13 0.028 0.049 -10000 0 -0.14 30 30
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.033 0.01 -10000 0 0 38 38
S1P1/S1P 0.035 0.034 -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 0 246 246
S1P/S1P5/G12 0.019 0.039 -10000 0 -0.16 3 3
S1P/S1P3/Gq 0.024 0.04 -10000 0 -0.23 6 6
S1P/S1P4/Gi -0.006 0.11 0.14 9 -0.22 77 86
GNAQ 0.034 0.009 -10000 0 0 31 31
GNAZ 0.03 0.013 -10000 0 0 79 79
GNA14 0.034 0.008 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GNA12 0.026 0.016 -10000 0 0 136 136
GNA13 0.035 0.007 -10000 0 0 18 18
GNA11 0.032 0.012 -10000 0 0 60 60
ABCC1 0.035 0.007 -10000 0 0 19 19
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.065 0.064 -10000 0 -0.12 13 13
SMAD6-7/SMURF1 0.048 0.037 -10000 0 -0.12 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.012 0.13 -10000 0 -0.44 39 39
SMAD4 0.032 0.011 -10000 0 0 53 53
SMAD5 -0.022 0.094 -10000 0 -0.32 31 31
BMP7/USAG1 0.035 0.026 -10000 0 -10000 0 0
SMAD5/SKI -0.015 0.1 -10000 0 -0.3 38 38
SMAD1 -0.026 0.15 -10000 0 -0.42 40 40
BMP2 0.028 0.015 -10000 0 0 109 109
SMAD1/SMAD1/SMAD4 -0.008 0.13 -10000 0 -0.39 34 34
BMPR1A 0.026 0.017 -10000 0 0 142 142
BMPR1B 0.035 0.005 -10000 0 0 11 11
BMPR1A-1B/BAMBI 0.02 0.062 -10000 0 -0.12 52 52
AHSG 0.035 0.007 -10000 0 0 18 18
CER1 0.032 0.012 -10000 0 0 61 61
BMP2-4/CER1 0.038 0.054 -10000 0 -0.12 33 33
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.078 -10000 0 -0.22 38 38
BMP2-4 (homodimer) 0.028 0.051 -10000 0 -0.14 33 33
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.056 0.056 -10000 0 -0.12 13 13
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.026 0.016 -10000 0 0 136 136
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.017 0.067 -10000 0 -0.17 53 53
BMP2-4/USAG1 0.034 0.046 -10000 0 -0.12 16 16
SMAD6/SMURF1/SMAD5 -0.012 0.093 -10000 0 -0.3 32 32
SOSTDC1 0.025 0.017 -10000 0 0 155 155
BMP7/BMPR2/BMPR1A-1B 0.056 0.057 -10000 0 -0.12 15 15
SKI 0.035 0.007 -10000 0 0 18 18
BMP6 (homodimer) 0.034 0.008 -10000 0 0 25 25
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.034 0.009 -10000 0 0 35 35
MAP3K7 0.033 0.01 -10000 0 0 38 38
BMP2-4/CHRD 0.042 0.054 -10000 0 -0.12 32 32
SMAD5/SMAD5/SMAD4 -0.019 0.11 -10000 0 -0.31 40 40
MAPK1 0.033 0.011 -10000 0 0 48 48
TAK1/TAB family 0.018 0.087 -10000 0 -0.2 23 23
BMP7 (homodimer) 0.035 0.007 -10000 0 0 19 19
NUP214 0.035 0.008 -10000 0 0 23 23
BMP6/FETUA 0.049 0.015 -10000 0 -10000 0 0
SMAD1/SKI -0.008 0.15 0.23 1 -0.41 40 41
SMAD6 0.036 0.004 -10000 0 0 6 6
CTDSP2 0.03 0.013 -10000 0 0 77 77
BMP2-4/FETUA 0.042 0.054 -10000 0 -0.12 33 33
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
GREM1 0.032 0.012 -10000 0 0 63 63
BMPR2 (homodimer) 0.035 0.006 -10000 0 0 16 16
GADD34/PP1CA 0.049 0.054 -10000 0 -0.13 31 31
BMPR1A-1B (homodimer) 0.035 0.032 -10000 0 -0.14 7 7
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.01 0.16 0.23 1 -0.41 43 44
SMAD6-7/SMURF1/SMAD1 0.008 0.14 -10000 0 -0.41 33 33
SMAD6/SMURF1 0.026 0.016 -10000 0 0 136 136
BAMBI 0.018 0.018 -10000 0 0 238 238
SMURF2 0.035 0.007 -10000 0 0 18 18
BMP2-4/CHRDL1 0.027 0.043 -10000 0 -0.11 33 33
BMP2-4/GREM1 0.037 0.054 -10000 0 -0.12 31 31
SMAD7 0.034 0.01 -10000 0 0 36 36
SMAD8A/SMAD8A/SMAD4 -0.005 0.14 -10000 0 -0.41 48 48
SMAD1/SMAD6 -0.011 0.14 0.23 1 -0.43 33 34
TAK1/SMAD6 0.033 0.035 -10000 0 -0.14 10 10
BMP7 0.035 0.007 -10000 0 0 19 19
BMP6 0.034 0.008 -10000 0 0 25 25
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.005 0.058 -10000 0 -0.22 17 17
PPM1A 0.034 0.008 -10000 0 0 25 25
SMAD1/SMURF2 -0.009 0.16 0.23 1 -0.41 42 43
SMAD7/SMURF1 0.035 0.028 -10000 0 -0.14 2 2
CTDSPL 0.034 0.009 -10000 0 0 29 29
PPP1CA 0.035 0.008 -10000 0 0 22 22
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.035 0.006 -10000 0 0 14 14
PPP1R15A 0.032 0.012 -10000 0 0 59 59
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.012 0.07 -10000 0 -0.17 52 52
CHRD 0.035 0.007 -10000 0 0 17 17
BMPR2 0.035 0.006 -10000 0 0 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.017 0.069 -10000 0 -0.18 50 50
BMP4 0.033 0.011 -10000 0 0 46 46
FST 0.033 0.01 -10000 0 0 43 43
BMP2-4/NOG 0.027 0.043 -10000 0 -0.11 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.052 0.063 -10000 0 -0.11 12 12
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.051 0.056 -10000 0 -0.13 35 35
fibroblast growth factor receptor signaling pathway 0.05 0.056 -10000 0 -0.13 35 35
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.032 0.011 -10000 0 0 54 54
GPC1/SLIT2 0.031 0.046 -10000 0 -0.14 24 24
SMAD2 -0.023 0.049 0.18 10 -0.2 3 13
GPC1/PrPc/Cu2+ 0.024 0.059 -10000 0 -0.14 53 53
GPC1/Laminin alpha1 0.014 0.041 -10000 0 -0.13 35 35
TDGF1 0.035 0.006 -10000 0 0 16 16
CRIPTO/GPC1 0.037 0.048 -10000 0 -0.14 30 30
APP/GPC1 0.033 0.059 -10000 0 -0.16 38 38
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.023 0.034 0.089 22 -0.12 24 46
FLT1 0.034 0.009 -10000 0 0 31 31
GPC1/TGFB/TGFBR1/TGFBR2 0.051 0.053 -10000 0 -0.12 34 34
SERPINC1 0.036 0.005 -10000 0 0 10 10
FYN -0.017 0.029 0.089 24 -0.12 8 32
FGR -0.022 0.034 0.089 23 -0.12 22 45
positive regulation of MAPKKK cascade -0.037 0.12 0.18 10 -0.31 54 64
SLIT2 0.029 0.014 -10000 0 0 96 96
GPC1/NRG 0.036 0.051 -10000 0 -0.14 35 35
NRG1 0.036 0.005 -10000 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.031 0.044 -10000 0 -0.12 35 35
LYN -0.022 0.034 0.089 22 -0.12 25 47
mol:Spermine -0.01 0.004 -10000 0 -10000 0 0
cell growth 0.05 0.056 -10000 0 -0.13 35 35
BMP signaling pathway -0.032 0.012 0 62 -10000 0 62
SRC -0.025 0.036 0.089 24 -0.12 30 54
TGFBR1 0.035 0.006 -10000 0 0 15 15
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.017 0.018 -10000 0 0 256 256
GPC1 0.032 0.012 -10000 0 0 62 62
TGFBR1 (dimer) 0.035 0.006 -10000 0 0 15 15
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.024 0.036 0.089 25 -0.12 28 53
HCK -0.018 0.032 0.089 20 -0.12 17 37
FGF2 0.034 0.008 -10000 0 0 25 25
FGFR1 0.035 0.005 -10000 0 0 11 11
VEGFR1 homodimer 0.034 0.009 -10000 0 0 31 31
TGFBR2 0.034 0.008 -10000 0 0 27 27
cell death 0.033 0.059 -10000 0 -0.16 38 38
ATIII/GPC1 0.036 0.05 -10000 0 -0.14 33 33
PLA2G2A/GPC1 -0.006 0.074 -10000 0 -0.15 91 91
LCK -0.024 0.034 0.089 23 -0.12 25 48
neuron differentiation 0.036 0.051 -10000 0 -0.14 35 35
PrPc/Cu2+ 0.016 0.038 -10000 0 -0.13 30 30
APP 0.035 0.007 -10000 0 0 19 19
TGFBR2 (dimer) 0.034 0.008 -10000 0 0 27 27
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 0.004 0.038 -10000 0 -10000 0 0
CRKL 0.034 0.008 -10000 0 0 25 25
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
DOCK1 0.023 0.017 -10000 0 0 178 178
ITGA4 0.035 0.006 -10000 0 0 12 12
alpha4/beta7 Integrin/MAdCAM1 0.078 0.039 -10000 0 -0.12 7 7
EPO 0.026 0.016 -10000 0 0 138 138
alpha4/beta7 Integrin 0.052 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin 0.04 0.024 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.037 0.025 -10000 0 -10000 0 0
lamellipodium assembly -0.011 0.098 -10000 0 -0.3 29 29
PIK3CA 0.03 0.014 -10000 0 0 85 85
PI3K 0.016 0.075 -10000 0 -0.16 73 73
ARF6 0.035 0.007 -10000 0 0 21 21
JAK2 0.009 0.029 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
MADCAM1 0.033 0.01 -10000 0 0 40 40
cell adhesion 0.076 0.038 -10000 0 -0.12 7 7
CRKL/CBL 0.05 0.013 -10000 0 -10000 0 0
ITGB1 0.027 0.016 -10000 0 0 118 118
SRC -0.034 0.059 0.17 4 -10000 0 4
ITGB7 0.036 0.005 -10000 0 0 10 10
RAC1 0.027 0.016 -10000 0 0 123 123
alpha4/beta1 Integrin/VCAM1 0.004 0.077 -10000 0 -0.12 117 117
p130Cas/Crk/Dock1 -0.031 0.063 0.18 4 -0.19 8 12
VCAM1 0.022 0.018 -10000 0 0 186 186
RHOA 0.035 0.007 -10000 0 0 21 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.065 0.048 -10000 0 -10000 0 0
BCAR1 -0.032 0.052 0.16 4 -10000 0 4
EPOR 0.034 0.009 -10000 0 0 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.036 0.004 -10000 0 0 6 6
GIT1 0.036 0.003 -10000 0 0 4 4
Rac1/GTP -0.012 0.1 -10000 0 -0.31 29 29
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.037 -10000 0 -0.055 87 87
HSPA8 0.035 0.009 -10000 0 0 22 22
SMAD3/SMAD4/ER alpha 0.042 0.085 0.23 8 -0.16 15 23
AKT1 0.03 0.019 -10000 0 -0.029 29 29
GSC 0.004 0.031 0.11 17 -0.063 2 19
NKX2-5 0.033 0.017 0.071 8 -0.059 12 20
muscle cell differentiation -0.019 0.13 0.33 37 -10000 0 37
SMAD2-3/SMAD4/SP1 0.051 0.14 0.32 5 -0.24 48 53
SMAD4 0.021 0.056 0.14 1 -0.13 30 31
CBFB 0.035 0.006 -10000 0 0 12 12
SAP18 0.034 0.01 -10000 0 0 39 39
Cbp/p300/MSG1 0.007 0.086 -10000 0 -0.11 144 144
SMAD3/SMAD4/VDR 0.044 0.12 -10000 0 -0.2 34 34
MYC 0.028 0.014 -10000 0 -10000 0 0
CDKN2B -0.2 0.19 -10000 0 -0.56 20 20
AP1 -0.002 0.1 0.24 1 -0.25 41 42
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.007 0.13 -10000 0 -0.37 35 35
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.081 -10000 0 -0.28 28 28
SP3 0.035 0.015 0.083 8 -0.051 8 16
CREB1 0.036 0.004 -10000 0 0 6 6
FOXH1 0.035 0.014 0.072 10 -0.053 9 19
SMAD3/SMAD4/GR 0.039 0.091 0.26 1 -0.19 18 19
GATA3 0.028 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.093 -10000 0 -0.3 27 27
MEF2C/TIF2 -0.013 0.08 0.24 15 -0.23 15 30
endothelial cell migration 0.2 0.49 1.2 98 -10000 0 98
MAX 0.027 0.042 0.084 83 -0.053 85 168
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.012 -10000 0 0 53 53
RUNX2 0.036 0.002 -10000 0 0 2 2
RUNX3 0.034 0.009 -10000 0 0 30 30
RUNX1 0.035 0.006 -10000 0 0 12 12
CTBP1 0.035 0.008 -10000 0 0 23 23
NR3C1 0.026 0.042 0.085 79 -0.053 86 165
VDR 0.035 0.007 -10000 0 0 17 17
CDKN1A -0.11 0.36 0.4 1 -1.1 57 58
KAT2B -0.003 0.008 -10000 0 -0.023 14 14
SMAD2/SMAD2/SMAD4/FOXH1 0.047 0.076 0.2 2 -0.16 32 34
DCP1A 0.035 0.007 -10000 0 0 20 20
SKI 0.035 0.007 -10000 0 0 18 18
SERPINE1 -0.2 0.49 -10000 0 -1.2 98 98
SMAD3/SMAD4/ATF2 0.04 0.086 0.22 1 -0.17 26 27
SMAD3/SMAD4/ATF3 0.017 0.1 -10000 0 -0.19 48 48
SAP30 0.035 0.006 -10000 0 0 15 15
Cbp/p300/PIAS3 0.04 0.073 -10000 0 -0.096 86 86
JUN -0.013 0.099 0.21 9 -0.26 38 47
SMAD3/SMAD4/IRF7 0.042 0.09 -10000 0 -0.17 26 26
TFE3 0.017 0.058 0.11 9 -0.093 95 104
COL1A2 -0.056 0.2 -10000 0 -0.63 50 50
mesenchymal cell differentiation -0.04 0.086 0.17 25 -0.21 1 26
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.033 0.01 -10000 0 0 37 37
FOS 0.021 0.029 0.12 2 -0.048 28 30
SMAD3/SMAD4/Max 0.041 0.086 0.24 2 -0.17 13 15
Cbp/p300/SNIP1 0.043 0.057 -10000 0 -0.081 32 32
ZBTB17 0.035 0.006 -10000 0 -10000 0 0
LAMC1 -0.033 0.1 0.17 6 -0.31 38 44
TGIF2/HDAC complex/SMAD3/SMAD4 0.039 0.085 0.22 1 -0.17 26 27
IRF7 0.034 0.01 -10000 0 -10000 0 0
ESR1 0.041 0.032 0.12 61 -0.03 1 62
HNF4A 0.035 0.006 -10000 0 0 15 15
MEF2C -0.02 0.075 0.23 17 -0.23 16 33
SMAD2-3/SMAD4 0.041 0.094 0.24 1 -0.2 26 27
Cbp/p300/Src-1 0.032 0.075 -10000 0 -0.13 51 51
IGHV3OR16-13 0.005 0.053 -10000 0 -0.49 5 5
TGIF2/HDAC complex 0.034 0.009 -10000 0 0 30 30
CREBBP 0.022 0.034 -10000 0 -0.045 96 96
SKIL 0.035 0.006 -10000 0 0 12 12
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.033 0.011 -10000 0 0 51 51
SNIP1 0.036 0.007 -10000 0 0 12 12
GCN5L2 0.022 0.034 -10000 0 -0.045 95 95
SMAD3/SMAD4/TFE3 0.031 0.12 0.27 3 -0.24 47 50
MSG1/HSC70 0.009 0.079 -10000 0 -0.14 95 95
SMAD2 0.034 0.017 0.09 2 -0.052 11 13
SMAD3 0.019 0.059 0.14 1 -0.12 39 40
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.072 -10000 0 -0.2 27 27
SMAD2/SMAD2/SMAD4 -0.011 0.068 0.16 7 -0.2 36 43
NCOR1 0.035 0.008 -10000 0 0 25 25
NCOA2 0.036 0.005 -10000 0 0 9 9
NCOA1 0.033 0.01 -10000 0 0 43 43
MYOD/E2A 0.049 0.015 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.059 0.14 0.34 4 -0.24 43 47
IFNB1 -0.004 0.06 0.19 3 -0.19 3 6
SMAD3/SMAD4/MEF2C 0.03 0.093 0.25 3 -0.24 17 20
CITED1 0.025 0.017 -10000 0 0 146 146
SMAD2-3/SMAD4/ARC105 0.041 0.085 0.22 2 -0.18 23 25
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.1 -10000 0 -0.36 23 23
RUNX1-3/PEBPB2 0.066 0.023 -10000 0 -10000 0 0
SMAD7 -0.037 0.17 0.28 1 -0.44 53 54
MYC/MIZ-1 0.027 0.058 -10000 0 -0.14 47 47
SMAD3/SMAD4 -0.079 0.23 -10000 0 -0.48 105 105
IL10 -0.01 0.063 0.2 3 -0.21 1 4
PIASy/HDAC complex 0.027 0.03 0.071 15 -0.03 84 99
PIAS3 0.024 0.028 -10000 0 -0.03 100 100
CDK2 0.021 0.031 -10000 0 -0.042 84 84
IL5 -0.009 0.064 0.19 4 -0.21 1 5
CDK4 0.021 0.03 -10000 0 -0.045 63 63
PIAS4 0.027 0.03 0.071 15 -0.03 84 99
ATF3 0.027 0.016 -10000 0 0 121 121
SMAD3/SMAD4/SP1 0.029 0.14 0.32 2 -0.25 52 54
FOXG1 0.001 0.007 0.023 22 -10000 0 22
FOXO3 -0.007 0.009 -10000 0 -10000 0 0
FOXO1 -0.007 0.008 -10000 0 -10000 0 0
FOXO4 -0.007 0.008 -10000 0 -10000 0 0
heart looping -0.02 0.075 0.23 17 -0.23 16 33
CEBPB 0.032 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.023 0.073 0.19 1 -0.14 41 42
MYOD1 0.036 0.004 -10000 0 0 6 6
SMAD3/SMAD4/HNF4 0.04 0.086 0.22 1 -0.17 27 28
SMAD3/SMAD4/GATA3 0.033 0.085 -10000 0 -0.18 14 14
SnoN/SIN3/HDAC complex/NCoR1 0.035 0.006 -10000 0 0 12 12
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.067 0.093 -10000 0 -0.16 15 15
SMAD3/SMAD4/SP1-3 0.046 0.14 0.32 1 -0.24 50 51
MED15 0 0 -10000 0 -10000 0 0
SP1 0.016 0.073 0.12 19 -0.12 100 119
SIN3B 0.034 0.01 -10000 0 0 35 35
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.067 0.083 0.24 1 -0.17 29 30
ITGB5 -0.029 0.1 0.24 7 -0.28 32 39
TGIF/SIN3/HDAC complex/CtBP -0.005 0.097 -10000 0 -0.32 28 28
SMAD3/SMAD4/AR 0.039 0.085 0.22 1 -0.17 27 28
AR 0.035 0.007 -10000 0 0 21 21
negative regulation of cell growth -0.017 0.12 -10000 0 -0.3 57 57
SMAD3/SMAD4/MYOD 0.041 0.086 0.22 1 -0.17 25 26
E2F5 0.036 0.004 -10000 0 0 6 6
E2F4 0.036 0.004 -10000 0 0 7 7
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.058 0.097 0.24 1 -0.18 31 32
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.097 -10000 0 -0.32 26 26
TFDP1 0.033 0.011 -10000 0 0 49 49
SMAD3/SMAD4/AP1 0.021 0.12 0.25 2 -0.26 39 41
SMAD3/SMAD4/RUNX2 0.041 0.086 0.22 1 -0.17 25 26
TGIF2 0.034 0.009 -10000 0 0 30 30
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.005 -10000 0 0 10 10
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.009 0.056 -10000 0 -0.22 20 20
epithelial cell differentiation 0.062 0.049 -10000 0 -0.14 20 20
CYFIP2 0.031 0.013 -10000 0 0 73 73
ENAH -0.034 0.078 0.24 16 -0.23 10 26
EGFR 0.01 0.016 -10000 0 0 355 355
EPHA2 0.032 0.011 -10000 0 0 53 53
MYO6 -0.025 0.053 0.17 14 -0.22 11 25
CTNNB1 0.035 0.007 -10000 0 0 21 21
ABI1/Sra1/Nap1 0.031 0.066 -10000 0 -0.13 57 57
AQP5 -0.015 0.052 0.16 14 -0.28 7 21
CTNND1 0.034 0.009 -10000 0 0 30 30
mol:PI-4-5-P2 -0.025 0.049 0.17 13 -0.21 10 23
regulation of calcium-dependent cell-cell adhesion -0.023 0.05 0.17 15 -0.19 7 22
EGF 0.034 0.008 -10000 0 0 24 24
NCKAP1 0.036 0.002 -10000 0 0 1 1
AQP3 -0.029 0.076 0.15 14 -0.3 28 42
cortical microtubule organization 0.062 0.049 -10000 0 -0.14 20 20
GO:0000145 -0.024 0.045 0.16 13 -0.2 10 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.069 0.051 -10000 0 -0.14 20 20
MLLT4 0.034 0.009 -10000 0 0 35 35
ARF6/GDP -0.049 0.039 -10000 0 -0.22 10 10
ARF6 0.035 0.007 -10000 0 0 21 21
Ephrin A1/EPHA2/NCK1/GIT1 0.074 0.051 -10000 0 -0.13 21 21
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.025 0.082 0.17 8 -0.28 31 39
PVRL2 0.034 0.01 -10000 0 0 36 36
ZYX -0.019 0.047 0.17 11 -0.21 12 23
ARF6/GTP 0.079 0.057 -10000 0 -0.13 20 20
CDH1 0.033 0.01 -10000 0 0 37 37
EGFR/EGFR/EGF/EGF 0.002 0.056 -10000 0 -0.12 58 58
RhoA/GDP 0.062 0.054 -10000 0 -0.14 24 24
actin cytoskeleton organization -0.021 0.049 0.15 12 -0.23 11 23
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 56 56
GIT1 0.036 0.003 -10000 0 0 4 4
IGF1R 0.032 0.012 -10000 0 0 56 56
IGF1 0.035 0.007 -10000 0 0 20 20
DIAPH1 -0.11 0.27 -10000 0 -0.5 133 133
Wnt receptor signaling pathway -0.062 0.049 0.14 20 -10000 0 20
RHOA 0.035 0.007 -10000 0 0 21 21
RhoA/GTP -0.05 0.041 -10000 0 -0.24 11 11
CTNNA1 0.035 0.007 -10000 0 0 18 18
VCL -0.022 0.05 0.16 12 -0.23 11 23
EFNA1 0.033 0.011 -10000 0 0 47 47
LPP -0.027 0.05 0.16 9 -0.24 12 21
Ephrin A1/EPHA2 0.045 0.059 -10000 0 -0.14 34 34
SEC6/SEC8 -0.04 0.028 -10000 0 -0.14 21 21
MGAT3 -0.023 0.05 0.17 15 -0.2 7 22
HGF/MET 0.035 0.045 -10000 0 -0.14 11 11
HGF 0.024 0.017 -10000 0 0 158 158
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.056 -10000 0 -0.22 20 20
actin cable formation -0.033 0.1 0.3 12 -0.29 30 42
KIAA1543 -0.021 0.04 0.15 13 -0.18 7 20
KIFC3 -0.026 0.048 0.17 12 -0.2 7 19
NCK1 0.034 0.008 -10000 0 0 26 26
EXOC3 0.035 0.006 -10000 0 0 16 16
ACTN1 -0.024 0.053 0.17 11 -0.22 14 25
NCK1/GIT1 0.049 0.024 -10000 0 -0.14 6 6
mol:GDP 0.062 0.049 -10000 0 -0.14 20 20
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.026 0.03 0.055 22 -0.13 20 42
PIP5K1C -0.025 0.05 0.17 13 -0.21 10 23
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.016 -10000 0 0 127 127
ROCK1 -0.026 0.091 0.27 21 -0.27 6 27
adherens junction assembly -0.018 0.07 0.21 5 -0.26 19 24
IGF-1R heterotetramer/IGF1 0.048 0.059 -10000 0 -0.14 33 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
MET 0.023 0.018 -10000 0 0 183 183
PLEKHA7 -0.026 0.03 0.055 22 -0.13 20 42
mol:GTP 0.071 0.05 -10000 0 -0.13 21 21
establishment of epithelial cell apical/basal polarity -0.032 0.044 0.13 20 -0.18 8 28
cortical actin cytoskeleton stabilization 0.009 0.056 -10000 0 -0.22 20 20
regulation of cell-cell adhesion -0.021 0.049 0.15 12 -0.23 11 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.056 -10000 0 -0.22 20 20
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.012 0.05 -10000 0 -0.11 60 60
TRAF2/ASK1 0.032 0.043 -10000 0 -0.12 34 34
ATM 0.034 0.01 -10000 0 0 36 36
MAP2K3 0.009 0.099 -10000 0 -0.3 27 27
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.091 0.22 1 -0.27 28 29
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.031 0.012 -10000 0 0 64 64
TXN 0.007 0.002 -10000 0 0 38 38
CALM1 0.033 0.011 -10000 0 0 49 49
GADD45A 0.031 0.013 -10000 0 0 74 74
GADD45B 0.03 0.014 -10000 0 0 90 90
MAP3K1 0.035 0.007 -10000 0 0 18 18
MAP3K6 0.035 0.007 -10000 0 0 20 20
MAP3K7 0.033 0.01 -10000 0 0 38 38
MAP3K4 0.032 0.012 -10000 0 0 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.033 0.052 -10000 0 -0.14 35 35
TAK1/TAB family 0.006 0.061 -10000 0 -0.26 18 18
RAC1/OSM/MEKK3 0.033 0.025 -10000 0 -0.1 6 6
TRAF2 0.035 0.006 -10000 0 0 14 14
RAC1/OSM/MEKK3/MKK3 0.011 0.08 -10000 0 -0.25 23 23
TRAF6 0.009 0.032 -10000 0 -0.2 11 11
RAC1 0.027 0.016 -10000 0 0 123 123
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.019 0.018 -10000 0 0 236 236
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.009 0.057 -10000 0 -0.13 58 58
MAPK11 0.033 0.011 -10000 0 0 48 48
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.012 0.07 -10000 0 -0.13 69 69
OSM/MEKK3 0.027 0.003 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 0 36 36
TAOK2 0.012 0.024 -10000 0 -0.2 6 6
TAOK3 0.006 0.042 -10000 0 -0.2 19 19
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
MAPK14 0.036 0.004 -10000 0 0 6 6
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
MAP3K5 0.03 0.014 -10000 0 0 82 82
MAP3K10 0.034 0.008 -10000 0 0 25 25
MAP3K3 0.036 0.004 -10000 0 0 5 5
TRX/ASK1 0.022 0.035 -10000 0 -0.16 13 13
GADD45/MTK1/MTK1 0.041 0.074 -10000 0 -0.13 62 62
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.032 0.011 -10000 0 0 51 51
GNB1/GNG2 0.029 0.035 -10000 0 -0.12 16 16
forebrain development 0.036 0.071 0.26 10 -0.38 3 13
GNAO1 0.03 0.014 -10000 0 0 81 81
SMO/beta Arrestin2 0.036 0.03 -10000 0 -0.14 4 4
SMO 0.026 0.016 -10000 0 0 135 135
ARRB2 0.034 0.008 -10000 0 0 27 27
GLI3/SPOP 0.003 0.11 -10000 0 -0.29 41 41
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.009 -10000 0 0 35 35
GNAI2 0.033 0.01 -10000 0 0 42 42
SIN3/HDAC complex 0.054 0.042 -10000 0 -0.12 18 18
GNAI1 0.018 0.018 -10000 0 0 246 246
XPO1 0.037 0.005 0.062 1 0 5 6
GLI1/Su(fu) 0.012 0.05 0.24 1 -0.27 6 7
SAP30 0.035 0.006 -10000 0 0 15 15
mol:GDP 0.026 0.016 -10000 0 0 135 135
MIM/GLI2A 0.041 0.013 0.12 11 -10000 0 11
IFT88 0.034 0.009 -10000 0 0 29 29
GNAI3 0.036 0.006 -10000 0 0 12 12
GLI2 0.005 0.088 0.23 1 -0.35 18 19
GLI3 -0.011 0.1 -10000 0 -0.3 35 35
CSNK1D 0.035 0.007 -10000 0 0 19 19
CSNK1E 0.031 0.012 -10000 0 0 64 64
SAP18 0.033 0.01 -10000 0 0 39 39
embryonic digit morphogenesis 0.034 0.009 -10000 0 0 29 29
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.013 0.097 -10000 0 -0.2 80 80
SIN3B 0.034 0.009 -10000 0 0 35 35
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.011 0.077 0.15 1 -0.27 26 27
GLI2/Su(fu) -0.001 0.073 -10000 0 -0.31 17 17
FOXA2 0.045 0.055 -10000 0 -0.43 5 5
neural tube patterning 0.036 0.071 0.26 10 -0.38 3 13
SPOP 0.035 0.007 -10000 0 0 21 21
Su(fu)/PIAS1 0.042 0.036 0.096 115 -0.078 11 126
GNB1 0.033 0.01 -10000 0 0 37 37
CSNK1G2 0.033 0.01 -10000 0 0 37 37
CSNK1G3 0.035 0.005 -10000 0 0 11 11
MTSS1 0.041 0.013 0.12 11 -10000 0 11
embryonic limb morphogenesis 0.036 0.071 0.26 10 -0.38 3 13
SUFU 0.002 0.01 -10000 0 -0.11 4 4
LGALS3 0.028 0.015 -10000 0 0 106 106
catabolic process 0.013 0.14 0.27 2 -0.42 33 35
GLI3A/CBP 0.043 0.008 -10000 0 -10000 0 0
KIF3A 0.032 0.011 -10000 0 0 51 51
GLI1 0.036 0.072 0.27 8 -0.38 3 11
RAB23 0.034 0.009 -10000 0 0 29 29
CSNK1A1 0.035 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 0.034 0.039 0.096 93 -0.11 10 103
GNAZ 0.03 0.013 -10000 0 0 79 79
RBBP4 0.032 0.011 -10000 0 0 53 53
CSNK1G1 0.036 0.005 -10000 0 0 8 8
PIAS1 0.035 0.008 -10000 0 0 23 23
PRKACA 0.034 0.009 -10000 0 0 29 29
GLI2/SPOP 0.02 0.095 0.22 1 -0.32 22 23
STK36 0.001 0.003 0.024 5 -10000 0 5
Gi family/GNB1/GNG2/GDP -0.025 0.11 -10000 0 -0.23 77 77
PTCH1 0.035 0.067 0.24 10 -0.34 3 13
MIM/GLI1 0.058 0.076 0.33 4 -0.35 3 7
CREBBP 0.043 0.008 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.001 0.098 0.17 1 -0.31 29 30
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.013 0.18 -10000 0 -0.81 22 22
regulation of axonogenesis 0.002 0.063 0.22 29 -10000 0 29
myoblast fusion -0.016 0.093 0.34 26 -0.2 1 27
mol:GTP 0.016 0.064 -10000 0 -0.18 42 42
regulation of calcium-dependent cell-cell adhesion -0.027 0.073 0.15 56 -0.16 1 57
ARF1/GTP 0.035 0.061 -10000 0 -0.14 45 45
mol:GM1 0.004 0.046 -10000 0 -0.14 40 40
mol:Choline -0.014 0.04 0.083 4 -0.13 34 38
lamellipodium assembly -0.007 0.1 -10000 0 -0.37 32 32
MAPK3 0.014 0.079 0.15 1 -0.29 23 24
ARF6/GTP/NME1/Tiam1 0.028 0.073 0.17 1 -0.15 56 57
ARF1 0.035 0.007 -10000 0 0 21 21
ARF6/GDP 0.016 0.093 0.2 1 -0.35 26 27
ARF1/GDP 0.016 0.099 -10000 0 -0.29 40 40
ARF6 0.039 0.042 0.11 1 -0.13 24 25
RAB11A 0.035 0.006 -10000 0 0 16 16
TIAM1 0.029 0.021 -10000 0 -0.044 28 28
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.078 0.15 1 -0.3 22 23
actin filament bundle formation -0.021 0.1 0.29 42 -10000 0 42
KALRN 0.006 0.069 0.13 2 -0.26 27 29
RAB11FIP3/RAB11A 0.046 0.035 -10000 0 -0.16 12 12
RhoA/GDP 0.022 0.1 -10000 0 -0.29 42 42
NME1 -0.001 0.008 -10000 0 -0.03 23 23
Rac1/GDP 0.017 0.092 -10000 0 -0.3 30 30
substrate adhesion-dependent cell spreading 0.016 0.064 -10000 0 -0.18 42 42
cortical actin cytoskeleton organization -0.007 0.1 -10000 0 -0.38 32 32
RAC1 0.027 0.016 -10000 0 0 123 123
liver development 0.016 0.064 -10000 0 -0.18 42 42
ARF6/GTP 0.016 0.064 -10000 0 -0.18 42 42
RhoA/GTP 0.034 0.062 -10000 0 -0.15 45 45
mol:GDP -0.002 0.095 0.17 2 -0.3 38 40
ARF6/GTP/RAB11FIP3/RAB11A 0.051 0.067 -10000 0 -0.13 48 48
RHOA 0.035 0.007 -10000 0 0 21 21
PLD1 0.013 0.051 -10000 0 -0.14 40 40
RAB11FIP3 0.035 0.007 -10000 0 0 19 19
tube morphogenesis -0.007 0.1 -10000 0 -0.37 32 32
ruffle organization -0.002 0.063 -10000 0 -0.22 29 29
regulation of epithelial cell migration 0.016 0.064 -10000 0 -0.18 42 42
PLD2 0.014 0.05 -10000 0 -0.14 39 39
PIP5K1A -0.002 0.063 -10000 0 -0.22 29 29
mol:Phosphatidic acid -0.014 0.04 0.083 4 -0.13 34 38
Rac1/GTP -0.008 0.1 -10000 0 -0.38 32 32
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.035 0.005 -10000 0 0 11 11
MKNK1 0.034 0.009 -10000 0 0 31 31
mol:PIP3 -0.02 0.057 0.096 2 -0.23 21 23
FRAP1 0.024 0.1 -10000 0 -0.45 16 16
AKT1 0.004 0.1 0.17 82 -0.25 30 112
INSR 0.034 0.008 -10000 0 0 28 28
Insulin Receptor/Insulin 0.045 0.014 -10000 0 -10000 0 0
mol:GTP 0.028 0.11 0.21 39 -0.26 29 68
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.049 -10000 0 -0.18 22 22
TSC2 0.034 0.008 -10000 0 0 26 26
RHEB/GDP 0.005 0.079 -10000 0 -0.23 29 29
TSC1 0.034 0.01 -10000 0 0 36 36
Insulin Receptor/IRS1 0.02 0.062 -10000 0 -0.25 23 23
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.073 0.15 1 -0.22 15 16
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.085 0.26 11 -0.29 5 16
MAP3K5 -0.024 0.082 0.17 1 -0.23 65 66
PIK3R1 0.032 0.012 -10000 0 0 61 61
apoptosis -0.024 0.082 0.17 1 -0.23 65 66
mol:LY294002 0 0 0.001 9 -0.001 19 28
EIF4B 0.024 0.083 0.24 15 -0.27 7 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.072 0.23 9 -0.25 4 13
eIF4E/eIF4G1/eIF4A1 0.007 0.077 -10000 0 -0.3 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.082 -10000 0 -0.23 31 31
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.065 0.19 13 -0.2 11 24
FKBP1A 0.033 0.011 -10000 0 0 46 46
RHEB/GTP 0.02 0.091 0.25 7 -0.23 29 36
mol:Amino Acids 0 0 0.001 9 -0.001 19 28
FKBP12/Rapamycin 0.021 0.025 -10000 0 -0.13 11 11
PDPK1 -0.022 0.061 0.15 16 -0.22 19 35
EIF4E 0.034 0.009 -10000 0 0 35 35
ASK1/PP5C -0.03 0.23 -10000 0 -0.56 71 71
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.01 0.094 -10000 0 -0.31 31 31
TSC1/TSC2 0.031 0.12 0.23 39 -0.28 29 68
tumor necrosis factor receptor activity 0 0 0.001 19 -0.001 9 28
RPS6 0.031 0.013 -10000 0 0 72 72
PPP5C 0.033 0.01 -10000 0 0 39 39
EIF4G1 0.033 0.01 -10000 0 0 44 44
IRS1 0 0.059 -10000 0 -0.26 23 23
INS 0.035 0.006 -10000 0 0 15 15
PTEN 0.027 0.016 -10000 0 0 130 130
PDK2 -0.022 0.061 0.15 16 -0.22 19 35
EIF4EBP1 -0.028 0.26 -10000 0 -1.1 26 26
PIK3CA 0.03 0.014 -10000 0 0 85 85
PPP2R5D 0.019 0.097 0.28 2 -0.41 16 18
peptide biosynthetic process -0.019 0.017 0.18 3 -10000 0 3
RHEB 0.028 0.015 -10000 0 0 115 115
EIF4A1 0.035 0.007 -10000 0 0 20 20
mol:Rapamycin 0 0.001 0.003 29 -0.003 14 43
EEF2 -0.019 0.018 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.011 0.25 -10000 0 -1.1 26 26
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.024 0.019 -10000 0 -0.13 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.11 -10000 0 -0.27 63 63
IRAK/TOLLIP 0.029 0.032 0.18 1 -0.12 19 20
IKBKB 0.036 0.004 -10000 0 0 6 6
IKBKG 0.036 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.043 0.022 -10000 0 -10000 0 0
IL1A 0.035 0.008 -10000 0 0 23 23
IL1B -0.014 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.05 0.18 1 -0.13 27 28
IL1R2 0.03 0.014 -10000 0 0 85 85
IL1R1 0.035 0.006 -10000 0 0 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.097 -10000 0 -0.29 36 36
TOLLIP 0.034 0.009 -10000 0 0 30 30
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.004 -10000 0 0 5 5
TAK1/TAB1/TAB2 0.055 0.049 -10000 0 -0.14 21 21
IKK complex/ELKS -0.036 0.091 -10000 0 -0.26 10 10
JUN -0.039 0.041 0.15 2 -0.21 9 11
MAP3K7 0.033 0.01 -10000 0 0 38 38
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.1 -10000 0 -0.14 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88 0.064 0.068 -10000 0 -0.13 48 48
PIK3R1 0.032 0.012 -10000 0 0 61 61
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.073 0.074 -10000 0 -0.12 47 47
IL1 beta fragment/IL1R1/IL1RAP 0.023 0.08 -10000 0 -0.14 80 80
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 -0.033 0.035 0.17 2 -0.2 7 9
IRAK1 -0.018 0.011 -10000 0 -0.12 5 5
IL1RN/IL1R1 0.052 0.01 -10000 0 -10000 0 0
IRAK4 0.035 0.007 -10000 0 0 17 17
PRKCI 0.034 0.008 -10000 0 0 25 25
TRAF6 0.036 0.005 -10000 0 0 8 8
PI3K 0.016 0.075 -10000 0 -0.16 73 73
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.11 -10000 0 -0.26 63 63
CHUK 0.026 0.016 -10000 0 0 133 133
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.023 0.08 -10000 0 -0.14 80 80
IL1 beta/IL1R2 0.018 0.071 -10000 0 -0.13 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0.059 0.068 0.2 1 -0.14 34 35
NF kappa B1 p50/RelA 0.011 0.096 -10000 0 -0.15 101 101
IRAK3 0.034 0.008 -10000 0 0 26 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.038 0.082 -10000 0 -0.13 78 78
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.072 -10000 0 -0.27 12 12
IL1 alpha/IL1R1/IL1RAP 0.048 0.053 -10000 0 -0.12 32 32
RELA 0.036 0.005 -10000 0 0 10 10
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
SQSTM1 0.034 0.009 -10000 0 0 33 33
MYD88 0.034 0.009 -10000 0 0 31 31
IRAK/TRAF6/MEKK3 0.05 0.037 0.19 1 -0.12 20 21
IL1RAP 0.03 0.014 -10000 0 0 85 85
UBE2N 0.035 0.005 -10000 0 0 11 11
IRAK/TRAF6 -0.038 0.061 0.061 68 -0.19 24 92
CASP1 0.029 0.015 -10000 0 0 102 102
IL1RN/IL1R2 0.044 0.021 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.095 -10000 0 -0.14 87 87
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.092 -10000 0 -0.3 32 32
PIK3CA 0.03 0.014 -10000 0 0 85 85
IL1RN 0.036 0.004 -10000 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.065 0.06 -10000 0 -0.14 23 23
MAP2K6 -0.038 0.034 0.17 3 -0.2 7 10
IGF1 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
NCK2 0.035 0.007 -10000 0 0 19 19
PTK2 0.034 0.008 -10000 0 0 28 28
CRKL -0.017 0.044 0.098 28 -0.15 23 51
GRB2/SOS1/SHC 0.04 0.03 -10000 0 -0.12 12 12
HRAS 0.034 0.009 -10000 0 0 32 32
IRS1/Crk 0.016 0.047 -10000 0 -0.14 35 35
IGF-1R heterotetramer/IGF1/PTP1B 0.051 0.056 -10000 0 -0.14 28 28
AKT1 -0.03 0.079 0.15 36 -0.22 30 66
BAD -0.035 0.075 0.14 33 -0.22 28 61
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.046 0.1 28 -0.16 24 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.025 0.05 0.22 2 -0.14 29 31
RAF1 -0.032 0.14 -10000 0 -0.54 27 27
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.043 0.055 -10000 0 -0.13 28 28
YWHAZ 0.035 0.007 -10000 0 0 17 17
IGF-1R heterotetramer/IGF1/IRS1 0.032 0.049 -10000 0 -0.16 24 24
PIK3CA 0.03 0.014 -10000 0 0 85 85
RPS6KB1 -0.029 0.076 0.16 37 -0.2 22 59
GNB2L1 0.035 0.005 -10000 0 0 11 11
positive regulation of MAPKKK cascade -0.03 0.12 0.23 4 -0.42 27 31
PXN 0.036 0.004 -10000 0 0 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
HRAS/GTP 0.015 0.053 -10000 0 -0.14 40 40
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.065 0.055 -10000 0 -0.12 31 31
IGF-1R heterotetramer 0.036 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.046 0.061 -10000 0 -0.14 34 34
Crk/p130 Cas/Paxillin 0.036 0.056 0.22 1 -0.13 35 36
IGF1R 0.036 0.014 -10000 0 -10000 0 0
IGF1 0.032 0.026 -10000 0 -0.055 33 33
IRS2/Crk -0.029 0.057 0.1 20 -0.18 30 50
PI3K 0.035 0.087 -10000 0 -0.14 77 77
apoptosis 0.033 0.081 0.21 29 -0.16 30 59
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
PRKCD 0 0.059 -10000 0 -0.21 22 22
RAF1/14-3-3 E -0.01 0.13 0.23 1 -0.47 27 28
BAD/14-3-3 -0.034 0.085 0.16 30 -0.22 29 59
PRKCZ -0.024 0.074 0.15 38 -0.19 22 60
Crk/p130 Cas/Paxillin/FAK1 -0.043 0.076 0.13 31 -0.21 30 61
PTPN1 0.034 0.008 -10000 0 0 26 26
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.06 -10000 0 -0.22 23 23
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.073 -10000 0 -0.14 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.024 0.051 0.13 2 -0.14 34 36
GRB10 0.022 0.018 -10000 0 0 185 185
PTPN11 -0.018 0.046 0.099 29 -0.15 24 53
IRS1 0.009 0.042 0.12 2 -0.16 24 26
IRS2 -0.018 0.05 0.1 22 -0.19 23 45
IGF-1R heterotetramer/IGF1 0.039 0.052 -10000 0 -0.17 24 24
GRB2 0.035 0.006 -10000 0 0 16 16
PDPK1 -0.023 0.081 0.17 37 -0.2 21 58
YWHAE 0.034 0.009 -10000 0 0 29 29
PRKD1 -0.003 0.062 -10000 0 -0.24 24 24
SHC1 0.033 0.011 -10000 0 0 48 48
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.049 0.039 -10000 0 -0.099 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.045 0.18 -10000 0 -0.48 49 49
AKT1 -0.057 0.23 -10000 0 -0.62 58 58
PIK3CA 0.03 0.014 -10000 0 0 85 85
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.052 0.24 -10000 0 -0.63 57 57
mol:Ca2+ 0.004 0.044 0.17 4 -0.21 3 7
IGF1R 0.032 0.012 -10000 0 0 56 56
E2/ER alpha (dimer)/Striatin 0.045 0.013 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 48 48
apoptosis 0.057 0.22 0.58 60 -10000 0 60
RhoA/GTP 0.011 0.055 -10000 0 -0.13 51 51
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.021 0.15 -10000 0 -0.36 56 56
regulation of stress fiber formation 0.035 0.062 0.18 21 -0.14 32 53
E2/ERA-ERB (dimer) 0.044 0.015 -10000 0 -10000 0 0
KRAS 0.033 0.01 -10000 0 0 37 37
G13/GTP 0.042 0.014 -10000 0 -10000 0 0
pseudopodium formation -0.035 0.062 0.14 32 -0.18 21 53
E2/ER alpha (dimer)/PELP1 0.042 0.024 -10000 0 -0.11 7 7
GRB2 0.035 0.006 -10000 0 0 16 16
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 0 81 81
HRAS 0.034 0.009 -10000 0 0 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.021 0.16 -10000 0 -0.41 48 48
E2/ER beta (dimer) 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.005 0.056 0.13 4 -0.19 21 25
mol:NADP -0.021 0.16 -10000 0 -0.41 48 48
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.004 0.04 -10000 0 -0.2 1 1
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 56 56
PLCB1 0.011 0.04 -10000 0 -0.2 1 1
PLCB2 0.011 0.04 -10000 0 -0.2 1 1
IGF1 0.035 0.007 -10000 0 0 20 20
mol:L-citrulline -0.021 0.16 -10000 0 -0.41 48 48
RHOA 0.035 0.007 -10000 0 0 21 21
Gai/GDP -0.069 0.24 -10000 0 -0.64 66 66
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.034 0.009 -10000 0 0 29 29
GNAQ 0.034 0.009 -10000 0 0 31 31
ESR1 0.034 0.009 -10000 0 0 34 34
Gq family/GDP/Gbeta gamma -0.008 0.16 -10000 0 -0.47 37 37
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.14 -10000 0 -0.71 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.16 0.25 4 -0.36 55 59
GNAZ 0.03 0.013 -10000 0 0 79 79
E2/ER alpha (dimer) 0.025 0.007 -10000 0 -10000 0 0
STRN 0.036 0.002 -10000 0 0 2 2
GNAL 0.035 0.006 -10000 0 0 13 13
PELP1 0.035 0.007 -10000 0 0 19 19
MAPK11 -0.015 0.006 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 0 42 42
GNAI3 0.035 0.006 -10000 0 0 12 12
GNAI1 0.018 0.018 -10000 0 0 246 246
HBEGF -0.027 0.18 0.33 10 -0.41 56 66
cAMP biosynthetic process 0.036 0.016 -10000 0 -10000 0 0
SRC -0.05 0.17 0.21 2 -0.44 52 54
PI3K 0.016 0.075 -10000 0 -0.16 73 73
GNB1 0.033 0.01 -10000 0 0 37 37
G13/GDP/Gbeta gamma 0.022 0.066 -10000 0 -0.17 28 28
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.031 0.12 -10000 0 -0.3 55 55
Gs family/GTP 0.046 0.02 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.064 -10000 0 -0.13 50 50
vasodilation -0.019 0.16 -10000 0 -0.39 48 48
mol:DAG 0.004 0.04 -10000 0 -0.2 1 1
Gs family/GDP/Gbeta gamma 0.004 0.059 -10000 0 -0.18 28 28
MSN -0.033 0.064 0.14 32 -0.19 21 53
Gq family/GTP 0.023 0.042 -10000 0 -0.2 1 1
mol:PI-3-4-5-P3 -0.05 0.22 -10000 0 -0.61 57 57
NRAS 0.032 0.012 -10000 0 0 58 58
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.019 0.16 0.39 48 -10000 0 48
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
RhoA/GDP 0.02 0.066 -10000 0 -0.19 24 24
NOS3 -0.024 0.17 -10000 0 -0.44 48 48
GNA11 0.032 0.012 -10000 0 0 60 60
MAPKKK cascade -0.004 0.15 -10000 0 -0.46 36 36
E2/ER alpha (dimer)/PELP1/Src -0.012 0.17 0.26 4 -0.38 53 57
ruffle organization -0.035 0.062 0.14 32 -0.18 21 53
ROCK2 -0.028 0.068 0.19 7 -0.19 14 21
GNA14 0.034 0.008 -10000 0 0 28 28
GNA15 0.032 0.012 -10000 0 0 59 59
GNA13 0.035 0.007 -10000 0 0 18 18
MMP9 -0.033 0.17 0.37 2 -0.4 61 63
MMP2 -0.034 0.17 0.25 6 -0.42 55 61
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0 0.009 -10000 0 -0.032 15 15
BUB1B -0.022 0.082 0.11 21 -0.22 59 80
PLK1 0.004 0.022 0.083 12 -0.074 2 14
PLK1S1 0.002 0.013 0.046 19 -0.044 1 20
KIF2A 0.004 0.02 0.073 12 -0.066 2 14
regulation of mitotic centrosome separation 0.005 0.022 0.083 12 -0.074 2 14
GOLGA2 0.034 0.008 -10000 0 0 24 24
Hec1/SPC24 -0.004 0.01 -10000 0 -0.053 5 5
WEE1 -0.03 0.13 -10000 0 -0.46 35 35
cytokinesis -0.022 0.11 0.14 11 -0.3 57 68
PP2A-alpha B56 0.056 0.067 -10000 0 -0.48 4 4
AURKA 0.002 0.015 0.052 20 -0.041 2 22
PICH/PLK1 -0.034 0.073 0.066 8 -0.18 82 90
CENPE 0.004 0.045 0.13 36 -0.1 5 41
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization 0.004 0.02 0.073 12 -0.066 2 14
PPP2CA 0.035 0.007 -10000 0 0 20 20
FZR1 0.034 0.009 -10000 0 0 33 33
TPX2 -0.026 0.089 0.12 1 -0.22 81 82
PAK1 0.035 0.007 -10000 0 0 17 17
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 20 20
CLSPN 0.01 0.027 -10000 0 -0.2 6 6
GORASP1 0.034 0.008 -10000 0 0 28 28
metaphase 0.001 0.003 0.013 11 -0.01 1 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.046 19 -0.044 1 20
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -10000 0 8
STAG2 0.035 0.007 -10000 0 0 21 21
GRASP65/GM130/RAB1/GTP -0.017 0.14 -10000 0 -0.6 23 23
spindle elongation 0.005 0.022 0.083 12 -0.074 2 14
ODF2 0.035 0.008 -10000 0 0 26 26
BUB1 0.026 0.045 -10000 0 -0.57 2 2
TPT1 -0.002 0.049 -10000 0 -0.18 31 31
CDC25C 0.012 0.026 -10000 0 -0.21 5 5
CDC25B 0.014 0.031 -10000 0 -0.029 150 150
SGOL1 0 0.009 0.032 15 -10000 0 15
RHOA 0.035 0.007 -10000 0 0 21 21
CCNB1/CDK1 -0.015 0.12 -10000 0 -0.23 93 93
CDC14B -0.011 0.004 0.011 6 -10000 0 6
CDC20 0.028 0.016 -10000 0 0 117 117
PLK1/PBIP1 -0.015 0.036 0.058 6 -0.09 75 81
mitosis -0.001 0.003 0.012 9 -10000 0 9
FBXO5 -0.015 0.06 0.11 13 -0.16 46 59
CDC2 0.017 0.023 -10000 0 -0.03 40 40
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.059 -10000 0 -0.26 22 22
ERCC6L -0.041 0.1 -10000 0 -0.22 89 89
NLP/gamma Tubulin 0.002 0.027 0.07 9 -0.1 19 28
microtubule cytoskeleton organization -0.002 0.049 -10000 0 -0.18 31 31
G2/M transition DNA damage checkpoint -0.001 0.002 0.01 4 -10000 0 4
PPP1R12A 0.035 0.008 -10000 0 0 21 21
interphase -0.001 0.002 0.01 4 -10000 0 4
PLK1/PRC1-2 0.008 0.075 -10000 0 -0.14 84 84
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.052 -10000 0 -0.14 19 19
RAB1A 0.035 0.007 -10000 0 0 17 17
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.002 0.018 0.064 16 -0.051 1 17
mitotic prometaphase 0 0.005 0.021 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.098 0.17 2 -0.21 96 98
microtubule-based process 0.019 0.024 0.095 4 -0.064 1 5
Golgi organization 0.005 0.022 0.083 12 -0.074 2 14
Cohesin/SA2 0.02 0.032 0.096 4 -0.095 20 24
PPP1CB/MYPT1 0.046 0.036 -10000 0 -0.15 14 14
KIF20A 0.029 0.015 -10000 0 0 101 101
APC/C/CDC20 0.02 0.024 0.1 5 -10000 0 5
PPP2R1A 0.032 0.012 -10000 0 0 61 61
chromosome segregation -0.015 0.036 0.057 6 -0.089 75 81
PRC1 0.028 0.015 -10000 0 0 113 113
ECT2 0 0.057 0.14 45 -0.11 25 70
C13orf34 0.003 0.019 0.067 15 -0.062 1 16
NUDC 0.001 0.059 -10000 0 -0.26 22 22
regulation of attachment of spindle microtubules to kinetochore -0.021 0.082 0.11 22 -0.21 59 81
spindle assembly 0.002 0.024 0.075 14 -0.078 13 27
spindle stabilization 0.002 0.013 0.046 19 -0.044 1 20
APC/C/HCDH1 0.023 0.027 0.087 1 -0.12 15 16
MKLP2/PLK1 0.019 0.024 0.095 4 -0.065 1 5
CCNB1 0.016 0.027 -10000 0 -0.028 94 94
PPP1CB 0.036 0.006 -10000 0 0 12 12
BTRC 0.027 0.016 -10000 0 0 124 124
ROCK2 0.016 0.029 -10000 0 -0.21 3 3
TUBG1 0.002 0.049 0.099 1 -0.22 20 21
G2/M transition of mitotic cell cycle -0.043 0.1 0.13 16 -0.23 89 105
MLF1IP -0.008 0.006 0.009 3 -10000 0 3
INCENP 0.036 0.003 -10000 0 0 4 4
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 0.051 0.071 -10000 0 -0.12 35 35
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.034 0.008 -10000 0 0 25 25
STAT1 (dimer)/Cbp/p300 0.028 0.084 0.25 8 -0.22 16 24
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.043 0.06 -10000 0 -0.14 35 35
antigen processing and presentation of peptide antigen via MHC class I -0.029 0.078 -10000 0 -0.18 66 66
CaM/Ca2+ 0.048 0.077 -10000 0 -0.14 37 37
RAP1A 0.036 0.005 -10000 0 0 8 8
STAT1 (dimer)/SHP2 -0.019 0.063 0.16 23 -0.19 8 31
AKT1 -0.023 0.092 0.26 14 -0.22 30 44
MAP2K1 -0.022 0.063 0.21 11 -0.19 8 19
MAP3K11 -0.016 0.066 0.23 10 -0.18 5 15
IFNGR1 0.032 0.018 -10000 0 -0.035 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.035 0.13 -10000 0 -0.3 61 61
Rap1/GTP -0.038 0.035 -10000 0 -0.16 7 7
CRKL/C3G 0.049 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.065 0.074 -10000 0 -0.13 31 31
CEBPB -0.003 0.12 0.33 5 -0.41 23 28
STAT3 0.033 0.01 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.059 0.09 -10000 0 -0.74 3 3
STAT1 -0.019 0.066 0.23 11 -0.19 8 19
CALM1 0.033 0.011 -10000 0 0 49 49
IFN-gamma (dimer) 0.03 0.021 -10000 0 -0.036 34 34
PIK3CA 0.03 0.014 -10000 0 0 85 85
STAT1 (dimer)/PIAS1 -0.02 0.076 0.24 11 -0.21 12 23
CEBPB/PTGES2/Cbp/p300 0.009 0.091 -10000 0 -0.29 22 22
mol:Ca2+ 0.047 0.068 -10000 0 -0.12 35 35
MAPK3 0.012 0.086 0.34 2 -0.73 2 4
STAT1 (dimer) -0.029 0.11 0.19 6 -0.25 54 60
MAPK1 -0.037 0.21 -10000 0 -0.74 34 34
JAK2 0.026 0.022 -10000 0 -0.036 31 31
PIK3R1 0.032 0.012 -10000 0 0 61 61
JAK1 0.033 0.017 -10000 0 -0.035 16 16
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.004 0.1 0.32 5 -0.43 9 14
SMAD7 -0.008 0.064 0.16 25 -0.14 15 40
CBL/CRKL/C3G 0.027 0.074 0.25 8 -0.18 5 13
PI3K 0.027 0.091 -10000 0 -0.14 71 71
IFNG 0.03 0.021 -10000 0 -0.036 34 34
apoptosis 0.015 0.092 0.3 5 -0.44 8 13
CAMK2G 0.025 0.017 -10000 0 0 155 155
STAT3 (dimer) 0.033 0.01 -10000 0 0 37 37
CAMK2A 0.036 0.004 -10000 0 0 7 7
CAMK2B 0.019 0.018 -10000 0 0 236 236
FRAP1 -0.03 0.085 0.22 15 -0.21 30 45
PRKCD -0.023 0.089 0.27 14 -0.2 22 36
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.029 0.078 -10000 0 -0.18 66 66
PTPN2 0.035 0.006 -10000 0 0 16 16
EP300 0.033 0.012 -10000 0 -0.001 50 50
IRF1 -0.03 0.062 0.21 7 -0.29 9 16
STAT1 (dimer)/PIASy -0.018 0.071 0.24 11 -0.19 7 18
SOCS1 0.017 0.085 -10000 0 -1 3 3
mol:GDP -0.016 0.072 0.22 11 -0.19 3 14
CASP1 -0.018 0.077 0.17 21 -0.16 58 79
PTGES2 0.035 0.007 -10000 0 0 18 18
IRF9 0 0.046 0.13 17 -0.12 19 36
mol:PI-3-4-5-P3 0.013 0.079 -10000 0 -0.14 72 72
RAP1/GDP -0.027 0.054 0.11 22 -0.16 6 28
CBL -0.016 0.066 0.23 10 -0.18 5 15
MAP3K1 -0.016 0.065 0.23 9 -0.18 4 13
PIAS1 0.035 0.008 -10000 0 0 23 23
PIAS4 0.034 0.009 -10000 0 0 32 32
antigen processing and presentation of peptide antigen via MHC class II -0.029 0.078 -10000 0 -0.18 66 66
PTPN11 -0.01 0.068 0.17 36 -0.18 5 41
CREBBP 0.036 0.005 -10000 0 -0.005 6 6
RAPGEF1 0.035 0.007 -10000 0 0 18 18
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.02 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.047 0.034 -10000 0 -0.12 12 12
CDKN1B -0.026 0.12 0.2 5 -0.33 56 61
CDKN1A -0.026 0.12 -10000 0 -0.33 58 58
FRAP1 0.035 0.006 -10000 0 0 14 14
PRKDC 0.033 0.01 -10000 0 0 42 42
FOXO3 -0.022 0.11 -10000 0 -0.31 60 60
AKT1 -0.022 0.12 -10000 0 -0.33 59 59
BAD 0.035 0.006 -10000 0 0 16 16
AKT3 0.015 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.022 0.11 -10000 0 -0.31 60 60
AKT1/ASK1 -0.011 0.13 -10000 0 -0.32 59 59
BAD/YWHAZ 0.061 0.038 -10000 0 -0.13 12 12
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.034 0.009 -10000 0 0 31 31
JNK cascade 0.011 0.12 0.31 59 -10000 0 59
TSC1 -0.027 0.12 -10000 0 -0.33 55 55
YWHAZ 0.035 0.007 -10000 0 0 17 17
AKT1/RAF1 -0.005 0.13 -10000 0 -0.33 61 61
EP300 0.033 0.011 -10000 0 0 49 49
mol:GDP -0.021 0.12 -10000 0 -0.32 59 59
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.03 0.12 -10000 0 -0.33 61 61
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.002 0.016 0.1 11 -10000 0 11
MAP3K5 0.03 0.014 -10000 0 0 82 82
MAPKAP1 0.034 0.008 -10000 0 0 26 26
negative regulation of cell cycle 0.007 0.11 0.37 21 -10000 0 21
YWHAH 0.031 0.013 -10000 0 0 74 74
AKT1S1 -0.022 0.11 -10000 0 -0.31 60 60
CASP9 -0.024 0.12 0.2 1 -0.32 57 58
YWHAB 0.035 0.007 -10000 0 0 21 21
p27Kip1/KPNA1 -0.01 0.13 0.27 4 -0.32 59 63
GBL 0.035 0.005 -10000 0 0 11 11
PDK1/Src/Hsp90 0.047 0.009 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
SRC 0.035 0.006 -10000 0 0 13 13
AKT2/p21CIP1 -0.026 0.11 0.24 1 -0.28 58 59
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.063 -10000 0 -0.47 5 5
CHUK -0.025 0.11 -10000 0 -0.32 50 50
BAD/BCL-XL 0 0.12 -10000 0 -0.31 59 59
mTORC2 0.061 0.03 -10000 0 -0.12 7 7
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.009 0.13 -10000 0 -0.44 23 23
PDPK1 0.036 0.003 -10000 0 0 4 4
MDM2 -0.01 0.12 0.2 33 -0.32 53 86
MAPKKK cascade 0.005 0.13 0.33 61 -10000 0 61
MDM2/Cbp/p300 0.019 0.13 0.26 2 -0.31 53 55
TSC1/TSC2 -0.033 0.13 0.24 7 -0.34 60 67
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.13 0.24 2 -0.3 53 55
glucose import -0.008 0.02 0.2 2 -10000 0 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.081 0.19 1 -0.36 8 9
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.021 0.2 2 -10000 0 2
GSK3A -0.023 0.12 0.2 9 -0.32 55 64
FOXO1 -0.022 0.11 -10000 0 -0.31 60 60
GSK3B -0.028 0.12 0.2 2 -0.34 59 61
SFN 0.031 0.013 -10000 0 0 74 74
G1/S transition of mitotic cell cycle -0.029 0.13 0.25 9 -0.33 61 70
p27Kip1/14-3-3 family 0.009 0.11 -10000 0 -0.53 12 12
PRKACA 0.034 0.009 -10000 0 0 29 29
KPNA1 0.035 0.007 -10000 0 0 21 21
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.028 0.015 -10000 0 0 115 115
CREBBP 0.036 0.004 -10000 0 0 5 5
Signaling events mediated by PRL

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
CCNE1 0.032 0.012 -10000 0 0 61 61
mol:Halofuginone -0.002 0.03 -10000 0 -0.18 14 14
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.033 0.16 -10000 0 -0.4 62 62
PRL-3/alpha Tubulin 0.018 0.03 -10000 0 -0.13 18 18
mol:Ca2+ -0.018 0.041 0.26 9 -10000 0 9
AGT 0.029 0.015 -10000 0 0 100 100
CCNA2 -0.034 0.11 -10000 0 -0.61 13 13
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.058 -10000 0 -0.33 14 14
CDK2/Cyclin E1 -0.008 0.15 -10000 0 -0.37 58 58
MAPK3 -0.019 0.008 0 69 -10000 0 69
PRL-2 /Rab GGTase beta 0.047 0.034 -10000 0 -0.16 11 11
MAPK1 -0.017 0.009 0 108 -10000 0 108
PTP4A1 -0.024 0.1 -10000 0 -0.63 13 13
PTP4A3 0.031 0.012 -10000 0 0 66 66
PTP4A2 0.035 0.006 -10000 0 0 16 16
ITGB1 -0.015 0.011 0 168 -10000 0 168
SRC 0.035 0.006 -10000 0 0 13 13
RAC1 -0.002 0.09 -10000 0 -0.39 21 21
Rab GGTase beta/Rab GGTase alpha 0.046 0.031 -10000 0 -0.14 10 10
PRL-1/ATF-5 -0.035 0.1 -10000 0 -0.56 14 14
RABGGTA 0.034 0.009 -10000 0 0 30 30
BCAR1 -0.01 0.052 0.25 18 -10000 0 18
RHOC -0.006 0.11 -10000 0 -0.4 30 30
RHOA -0.009 0.13 -10000 0 -0.45 31 31
cell motility -0.004 0.12 -10000 0 -0.41 27 27
PRL-1/alpha Tubulin -0.035 0.1 -10000 0 -0.57 14 14
PRL-3/alpha1 Integrin 0.018 0.03 -10000 0 -0.13 18 18
ROCK1 -0.004 0.12 -10000 0 -0.41 28 28
RABGGTB 0.035 0.007 -10000 0 0 19 19
CDK2 0.033 0.01 -10000 0 0 40 40
mitosis -0.023 0.1 -10000 0 -0.62 13 13
ATF5 0.033 0.01 -10000 0 0 38 38
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.098 -10000 0 -0.25 26 26
mol:DAG -0.013 0.088 0.19 3 -0.25 26 29
PLCG1 -0.013 0.09 0.19 3 -0.25 26 29
YES1 -0.016 0.084 -10000 0 -0.27 20 20
FZD3 0.028 0.015 -10000 0 0 104 104
FZD6 0.027 0.016 -10000 0 0 121 121
G protein -0.005 0.098 0.21 6 -0.27 26 32
MAP3K7 -0.035 0.075 0.14 7 -0.23 31 38
mol:Ca2+ -0.012 0.086 0.19 3 -0.24 26 29
mol:IP3 -0.013 0.088 0.19 3 -0.25 26 29
NLK -0.038 0.25 -10000 0 -0.77 49 49
GNB1 0.033 0.01 -10000 0 0 37 37
CAMK2A -0.03 0.078 0.18 5 -0.24 26 31
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
Noncanonical Wnts/FZD -0.006 0.088 -10000 0 -0.28 16 16
CSNK1A1 0.035 0.006 -10000 0 0 12 12
GNAS -0.016 0.081 -10000 0 -0.27 18 18
GO:0007205 -0.02 0.084 0.18 3 -0.25 26 29
WNT6 0.036 0.002 -10000 0 0 2 2
WNT4 0.035 0.007 -10000 0 0 18 18
NFAT1/CK1 alpha -0.005 0.098 0.24 3 -0.26 27 30
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.03 0.014 -10000 0 0 89 89
WNT11 0.035 0.006 -10000 0 0 15 15
CDC42 -0.026 0.08 0.16 2 -0.27 22 24
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.047 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 0 18 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.003 -10000 0 0 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.035 0.007 -10000 0 0 20 20
RAC1-CDC42/GTP/PAK family -0.002 0.051 -10000 0 -0.14 47 47
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.033 0.01 -10000 0 0 37 37
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.036 0.004 -10000 0 0 5 5
FYN 0.03 0.014 -10000 0 0 83 83
MAP3K12 0.036 0.005 -10000 0 0 9 9
FGR 0.032 0.011 -10000 0 0 52 52
p38 alpha/TAB1 0.014 0.11 0.18 2 -0.26 37 39
PRKG1 0.027 0.016 -10000 0 0 124 124
DUSP8 0.033 0.01 -10000 0 0 38 38
PGK/cGMP/p38 alpha 0.002 0.098 -10000 0 -0.24 40 40
apoptosis 0.013 0.1 0.18 2 -0.25 38 40
RAL/GTP 0.029 0.038 -10000 0 -0.12 20 20
LYN 0.031 0.013 -10000 0 0 72 72
DUSP1 0.031 0.013 -10000 0 0 75 75
PAK1 0.035 0.007 -10000 0 0 17 17
SRC 0.035 0.006 -10000 0 0 13 13
RAC1/OSM/MEKK3/MKK3 0.049 0.036 -10000 0 -0.11 6 6
TRAF6 0.036 0.005 -10000 0 0 8 8
RAC1 0.027 0.016 -10000 0 0 123 123
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 0.034 0.027 -10000 0 -0.12 6 6
MAPK11 -0.008 0.13 0.2 3 -0.3 49 52
BLK 0.035 0.007 -10000 0 0 17 17
HCK 0.027 0.016 -10000 0 0 123 123
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 47 47
TRAF6/MEKK3 0.045 0.01 -10000 0 -0.1 1 1
MAP3K7IP1 0.034 0.009 -10000 0 0 33 33
MAPK14 0.005 0.11 0.18 4 -0.26 44 48
positive regulation of innate immune response -0.005 0.14 0.21 3 -0.34 47 50
LCK 0.035 0.007 -10000 0 0 17 17
p38alpha-beta/MKP7 -0.007 0.13 0.2 4 -0.33 47 51
p38alpha-beta/MKP5 0.008 0.14 0.22 3 -0.33 44 47
PGK/cGMP 0.02 0.012 -10000 0 -10000 0 0
PAK2 0.034 0.009 -10000 0 0 35 35
p38alpha-beta/MKP1 -0.001 0.14 0.23 2 -0.34 48 50
CDC42 0.035 0.008 -10000 0 0 22 22
RALB 0.035 0.006 -10000 0 0 15 15
RALA 0.026 0.017 -10000 0 0 143 143
PAK3 0.026 0.016 -10000 0 0 134 134
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.034 0.008 -10000 0 0 25 25
RAS family/GTP/Tiam1 -0.006 0.086 -10000 0 -0.2 63 63
NT3 (dimer)/TRKC 0.046 0.026 -10000 0 -0.14 6 6
NT3 (dimer)/TRKB 0.027 0.068 -10000 0 -0.12 67 67
SHC/Grb2/SOS1/GAB1/PI3K -0.008 0.091 -10000 0 -0.21 66 66
RAPGEF1 0.035 0.007 -10000 0 0 18 18
BDNF 0.032 0.012 -10000 0 0 61 61
PIK3CA 0.03 0.014 -10000 0 0 85 85
DYNLT1 0.033 0.01 -10000 0 0 41 41
NTRK1 0.035 0.006 -10000 0 0 12 12
NTRK2 0.027 0.016 -10000 0 0 126 126
NTRK3 0.034 0.009 -10000 0 0 32 32
NT-4/5 (dimer)/TRKB 0.014 0.057 -10000 0 -0.12 70 70
neuron apoptosis -0.007 0.12 0.31 39 -0.21 1 40
SHC 2-3/Grb2 0.006 0.13 -10000 0 -0.34 39 39
SHC1 0.033 0.011 -10000 0 0 48 48
SHC2 -0.011 0.12 -10000 0 -0.43 29 29
SHC3 -0.012 0.12 -10000 0 -0.41 28 28
STAT3 (dimer) 0.02 0.087 -10000 0 -0.28 35 35
NT3 (dimer)/TRKA 0.059 0.029 -10000 0 -10000 0 0
RIN/GDP 0.003 0.071 0.2 2 -0.24 18 20
GIPC1 0.034 0.009 -10000 0 0 30 30
KRAS 0.033 0.01 -10000 0 0 37 37
DNAJA3 -0.004 0.04 0.14 3 -0.13 1 4
RIN/GTP 0.011 0.036 -10000 0 -0.13 26 26
CCND1 -0.012 0.11 -10000 0 -0.49 25 25
MAGED1 0.034 0.008 -10000 0 0 26 26
PTPN11 0.036 0.005 -10000 0 0 9 9
RICS 0.033 0.01 -10000 0 0 41 41
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.04 0.03 -10000 0 -0.12 12 12
GRB2 0.035 0.006 -10000 0 0 16 16
NGF (dimer)/TRKA/MATK 0.044 0.015 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.047 0.019 -10000 0 -0.14 1 1
ELMO1 0.02 0.018 -10000 0 0 219 219
RhoG/GTP/ELMO1/DOCK1 0.009 0.046 -10000 0 -0.12 43 43
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.009 -10000 0 0 32 32
DOCK1 0.023 0.017 -10000 0 0 178 178
GAB2 0.033 0.01 -10000 0 0 44 44
RIT2 0.025 0.017 -10000 0 0 157 157
RIT1 0.032 0.012 -10000 0 0 61 61
FRS2 0.035 0.008 -10000 0 0 22 22
DNM1 0.035 0.008 -10000 0 0 23 23
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 0.012 0.048 0.16 2 -0.17 11 13
mol:GDP 0.001 0.1 0.24 6 -0.33 19 25
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.003 0.044 -10000 0 -0.13 43 43
RIT1/GDP 0.011 0.08 0.2 7 -0.25 17 24
TIAM1 0.033 0.01 -10000 0 0 43 43
PIK3R1 0.032 0.012 -10000 0 0 61 61
BDNF (dimer)/TRKB 0.028 0.069 -10000 0 -0.13 67 67
KIDINS220/CRKL/C3G 0.049 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.051 -10000 0 -0.15 29 29
FRS2 family/SHP2 0.067 0.027 -10000 0 -0.12 6 6
SHC/GRB2/SOS1/GAB1 0.046 0.044 -10000 0 -0.11 19 19
RIT1/GTP 0.014 0.042 -10000 0 -0.13 36 36
NT3 (dimer) 0.034 0.008 -10000 0 0 23 23
RAP1/GDP 0 0.059 -10000 0 -0.18 21 21
KIDINS220/CRKL 0.034 0.008 -10000 0 0 25 25
BDNF (dimer) 0.032 0.012 -10000 0 0 61 61
ubiquitin-dependent protein catabolic process 0.042 0.017 -10000 0 -0.12 1 1
Schwann cell development -0.011 0.016 -10000 0 -0.055 34 34
EHD4 0.033 0.01 -10000 0 0 37 37
FRS2 family/GRB2/SOS1 0.063 0.027 -10000 0 -0.11 7 7
FRS2 family/SHP2/CRK family/C3G/GAB2 0.01 0.068 -10000 0 -0.26 16 16
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 8 8
CDC42/GTP 0.017 0.08 -10000 0 -0.2 25 25
ABL1 0.031 0.013 -10000 0 0 67 67
SH2B family/GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
Rap1/GTP 0.007 0.065 -10000 0 -0.22 11 11
STAT3 0.02 0.086 -10000 0 -0.28 35 35
axon guidance 0.005 0.07 -10000 0 -0.14 70 70
MAPK3 -0.005 0.058 0.18 41 -10000 0 41
MAPK1 -0.005 0.054 0.18 35 -10000 0 35
CDC42/GDP 0.012 0.078 0.19 8 -0.23 17 25
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.024 -10000 0 -0.12 8 8
PI3K 0.016 0.075 -10000 0 -0.16 73 73
FRS3 0.036 0.002 -10000 0 0 2 2
FAIM 0.034 0.008 -10000 0 0 27 27
GAB1 0.031 0.013 -10000 0 0 75 75
RASGRF1 -0.004 0.041 0.14 2 -0.13 2 4
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.018 0.021 0.089 11 -0.12 2 13
RGS19 0.034 0.008 -10000 0 0 24 24
CDC42 0.035 0.008 -10000 0 0 22 22
RAS family/GTP 0.013 0.097 0.23 1 -0.38 18 19
Rac1/GDP 0.011 0.071 0.19 8 -0.26 13 21
NGF (dimer)/TRKA/GRIT 0.039 0.035 -10000 0 -0.12 21 21
neuron projection morphogenesis -0.037 0.24 -10000 0 -0.86 35 35
NGF (dimer)/TRKA/NEDD4-2 0.043 0.017 -10000 0 -0.12 1 1
MAP2K1 0.002 0.074 0.18 48 -0.19 5 53
NGFR 0.031 0.013 -10000 0 0 67 67
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.047 -10000 0 -0.22 10 10
RAS family/GTP/PI3K -0.024 0.1 -10000 0 -0.21 96 96
FRS2 family/SHP2/GRB2/SOS1 0.076 0.038 -10000 0 -0.14 9 9
NRAS 0.032 0.012 -10000 0 0 58 58
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
PRKCI 0.034 0.008 -10000 0 0 25 25
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.014 0.085 -10000 0 -0.49 11 11
RASA1 0.034 0.009 -10000 0 0 30 30
TRKA/c-Abl 0.031 0.058 -10000 0 -0.14 47 47
SQSTM1 0.034 0.009 -10000 0 0 33 33
BDNF (dimer)/TRKB/GIPC 0.049 0.072 -10000 0 -0.12 58 58
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.033 -10000 0 -0.1 14 14
MATK 0.034 0.009 -10000 0 0 35 35
NEDD4L 0.033 0.011 -10000 0 0 47 47
RAS family/GDP -0.019 0.055 -10000 0 -0.16 41 41
NGF (dimer)/TRKA 0.008 0.039 0.15 4 -0.13 2 6
Rac1/GTP -0.014 0.058 -10000 0 -0.21 25 25
FRS2 family/SHP2/CRK family 0.087 0.055 -10000 0 -0.12 17 17
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.03 0.034 -10000 0 -0.14 8 8
CRKL 0.039 0.11 0.26 6 -0.41 16 22
mol:PIP3 -0.018 0.13 0.34 1 -0.78 13 14
AKT1 -0.027 0.12 0.25 1 -0.69 13 14
PTK2B 0.035 0.006 -10000 0 0 15 15
RAPGEF1 0.036 0.1 0.27 9 -0.39 16 25
RANBP10 0.036 0.004 -10000 0 0 6 6
PIK3CA 0.03 0.014 -10000 0 0 85 85
HGF/MET/SHIP2 0.041 0.038 -10000 0 -0.12 2 2
MAP3K5 0.039 0.11 0.28 4 -0.39 16 20
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.035 -10000 0 -10000 0 0
AP1 0.034 0.08 0.15 84 -0.14 46 130
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 48 48
apoptosis -0.11 0.35 -10000 0 -0.78 99 99
STAT3 (dimer) 0.012 0.056 -10000 0 -0.29 8 8
GAB1/CRKL/SHP2/PI3K 0.053 0.12 0.28 1 -0.41 16 17
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.054 0.11 0.27 2 -0.4 16 18
PTPN11 0.036 0.005 -10000 0 0 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.035 0.007 -10000 0 0 20 20
PTEN 0.027 0.016 -10000 0 0 130 130
ELK1 0.12 0.18 0.35 171 -10000 0 171
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.011 0.032 0.14 1 -0.14 12 13
PAK1 -0.03 0.12 -10000 0 -0.66 13 13
HGF/MET/RANBP10 0.042 0.036 -10000 0 -10000 0 0
HRAS 0.012 0.079 -10000 0 -0.47 9 9
DOCK1 0.028 0.1 0.25 6 -0.4 15 21
GAB1 0.04 0.1 -10000 0 -0.43 15 15
CRK 0.038 0.11 0.27 2 -0.41 16 18
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.062 -10000 0 -0.41 8 8
JUN 0.033 0.01 -10000 0 0 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.011 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
cell morphogenesis 0.026 0.11 0.27 22 -0.34 11 33
GRB2/SHC 0.075 0.059 0.16 93 -0.12 1 94
FOS 0.025 0.017 -10000 0 0 147 147
GLMN 0.004 0.004 0.068 2 -10000 0 2
cell motility 0.12 0.18 0.34 171 -10000 0 171
HGF/MET/MUC20 0.028 0.024 -10000 0 -10000 0 0
cell migration 0.074 0.058 0.16 93 -0.12 1 94
GRB2 0.035 0.006 -10000 0 0 16 16
CBL 0.036 0.004 -10000 0 0 6 6
MET/RANBP10 0.033 0.026 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.044 -10000 0 -0.27 4 4
MET/MUC20 0.017 0.013 -10000 0 -10000 0 0
RAP1B 0.036 0.099 0.26 9 -0.36 16 25
RAP1A 0.031 0.1 0.27 8 -0.37 16 24
HGF/MET/RANBP9 0.039 0.041 -10000 0 -0.12 7 7
RAF1 0.031 0.096 -10000 0 -0.44 12 12
STAT3 0.012 0.056 -10000 0 -0.29 8 8
cell proliferation 0.036 0.075 0.26 8 -0.3 6 14
RPS6KB1 0.014 0.021 -10000 0 -0.26 1 1
MAPK3 0.086 0.17 0.33 121 -10000 0 121
MAPK1 0.12 0.21 0.61 43 -10000 0 43
RANBP9 0.035 0.006 -10000 0 0 15 15
MAPK8 -0.048 0.16 0.26 1 -0.34 65 66
SRC 0.01 0.045 -10000 0 -0.26 4 4
PI3K 0.057 0.069 0.16 74 -0.14 10 84
MET/Glomulin 0.017 0.024 -10000 0 -0.094 11 11
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.025 0.098 0.28 2 -0.42 13 15
MET 0.023 0.018 -10000 0 0 183 183
MAP4K1 0.048 0.11 0.28 3 -0.4 16 19
PTK2 0.034 0.008 -10000 0 0 28 28
MAP2K2 0.036 0.1 0.29 14 -0.42 10 24
BAD -0.032 0.12 -10000 0 -0.63 14 14
MAP2K4 0.033 0.1 0.27 7 -0.36 16 23
SHP2/GRB2/SOS1/GAB1 0.016 0.081 -10000 0 -0.34 17 17
INPPL1 0.035 0.006 -10000 0 0 12 12
PXN 0.036 0.004 -10000 0 0 5 5
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.002 0.017 0.074 17 -10000 0 17
PLCgamma1/PKC 0.025 0.013 -10000 0 -0.13 3 3
HGF 0.024 0.017 -10000 0 0 158 158
RASA1 0.034 0.009 -10000 0 0 30 30
NCK1 0.034 0.008 -10000 0 0 26 26
PTPRJ 0.036 0.005 -10000 0 0 8 8
NCK/PLCgamma1 0.08 0.053 0.16 96 -0.097 5 101
PDPK1 -0.021 0.13 0.27 3 -0.72 13 16
HGF/MET/SHIP 0.028 0.024 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.021 0.13 -10000 0 -0.63 17 17
epithelial cell differentiation -0.006 0.14 -10000 0 -0.64 17 17
ITCH 0.03 0.031 0.11 1 -0.1 20 21
WWP1 -0.02 0.22 -10000 0 -1.1 17 17
FYN 0.03 0.014 -10000 0 0 83 83
EGFR 0.01 0.016 -10000 0 0 355 355
PRL 0.035 0.006 -10000 0 0 14 14
neuron projection morphogenesis -0.025 0.1 0.26 4 -0.48 17 21
PTPRZ1 0.022 0.018 -10000 0 0 184 184
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.053 0.12 -10000 0 -0.52 17 17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.11 -10000 0 -0.57 17 17
ADAM17 0.03 0.03 -10000 0 -0.11 19 19
ErbB4/ErbB4 -0.002 0.13 -10000 0 -0.68 17 17
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.12 -10000 0 -0.62 17 17
NCOR1 0.034 0.008 -10000 0 0 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.12 -10000 0 -0.57 17 17
GRIN2B -0.008 0.11 0.23 2 -0.54 17 19
ErbB4/ErbB2/betacellulin 0.026 0.11 -10000 0 -0.55 17 17
STAT1 0.033 0.01 -10000 0 0 40 40
HBEGF 0.035 0.008 -10000 0 0 22 22
PRLR 0.036 0.004 -10000 0 0 7 7
E4ICDs/ETO2 0.021 0.13 -10000 0 -0.62 17 17
axon guidance -0.028 0.16 -10000 0 -0.79 17 17
NEDD4 0.028 0.031 0.11 1 -0.11 19 20
Prolactin receptor/Prolactin receptor/Prolactin 0.052 0.011 -10000 0 -10000 0 0
CBFA2T3 0.034 0.008 -10000 0 0 26 26
ErbB4/ErbB2/HBEGF 0.024 0.11 -10000 0 -0.55 17 17
MAPK3 -0.016 0.11 0.28 3 -0.49 17 20
STAT1 (dimer) 0.02 0.13 -10000 0 -0.62 17 17
MAPK1 -0.018 0.11 0.28 3 -0.49 17 20
JAK2 0.03 0.014 -10000 0 0 86 86
ErbB4/ErbB2/neuregulin 1 beta 0.004 0.11 -10000 0 -0.55 17 17
NRG1 -0.022 0.018 0.097 1 -0.083 17 18
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.036 0.005 -10000 0 0 9 9
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.028 0.16 -10000 0 -0.79 17 17
neural crest cell migration 0.004 0.11 -10000 0 -0.54 17 17
ERBB2 -0.022 0.02 0.11 3 -0.083 17 20
WWOX/E4ICDs 0.011 0.11 -10000 0 -0.54 17 17
SHC1 0.033 0.011 -10000 0 0 48 48
ErbB4/EGFR/neuregulin 4 -0.012 0.095 -10000 0 -0.46 17 17
apoptosis -0.006 0.12 0.58 17 -10000 0 17
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.023 0.13 -10000 0 -0.63 17 17
ErbB4/ErbB2/epiregulin 0.024 0.11 -10000 0 -0.55 17 17
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.13 -10000 0 -0.63 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.059 0.13 -10000 0 -0.55 17 17
MDM2 0.01 0.14 0.26 37 -0.6 17 54
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.021 0.1 -10000 0 -0.5 17 17
STAT5A -0.033 0.15 -10000 0 -0.77 17 17
ErbB4/EGFR/neuregulin 1 beta -0.002 0.085 -10000 0 -0.42 17 17
DLG4 0.035 0.006 -10000 0 0 13 13
GRB2/SHC 0.043 0.035 -10000 0 -0.15 12 12
E4ICDs/TAB2/NCoR1 0.031 0.13 -10000 0 -0.62 17 17
STAT5A (dimer) 0.002 0.16 -10000 0 -0.7 17 17
MAP3K7IP2 0.033 0.01 -10000 0 0 42 42
STAT5B (dimer) -0.013 0.16 -10000 0 -0.77 17 17
LRIG1 0.03 0.014 -10000 0 0 81 81
EREG 0.035 0.007 -10000 0 0 21 21
BTC 0.036 0.005 -10000 0 0 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.029 0.16 -10000 0 -0.8 17 17
ERBB4 -0.002 0.13 -10000 0 -0.68 17 17
STAT5B 0.036 0.004 -10000 0 0 6 6
YAP1 -0.081 0.2 -10000 0 -0.51 85 85
GRB2 0.035 0.006 -10000 0 0 16 16
ErbB4/ErbB2/neuregulin 4 0.002 0.11 -10000 0 -0.54 17 17
glial cell differentiation -0.031 0.13 0.61 17 -10000 0 17
WWOX 0.024 0.017 -10000 0 0 160 160
cell proliferation -0.011 0.11 -10000 0 -0.57 17 17
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.03 0.11 0.34 10 -0.35 17 27
PDGFB-D/PDGFRB/SLAP 0.018 0.073 -10000 0 -0.16 67 67
PDGFB-D/PDGFRB/APS/CBL 0.044 0.024 -10000 0 -0.12 8 8
AKT1 -0.022 0.095 0.24 24 -0.22 20 44
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.021 0.11 0.31 9 -0.37 17 26
PIK3CA 0.03 0.014 -10000 0 0 85 85
FGR 0.005 0.098 0.31 3 -0.51 11 14
mol:Ca2+ 0.012 0.1 0.27 8 -0.42 16 24
MYC -0.003 0.26 0.39 23 -0.67 50 73
SHC1 0.033 0.011 -10000 0 0 48 48
HRAS/GDP 0.013 0.064 0.17 20 -0.16 18 38
LRP1/PDGFRB/PDGFB 0.047 0.056 -10000 0 -0.14 31 31
GRB10 0.022 0.018 -10000 0 0 185 185
PTPN11 0.036 0.005 -10000 0 0 9 9
GO:0007205 0.011 0.11 0.27 8 -0.42 16 24
PTEN 0.027 0.016 -10000 0 0 130 130
GRB2 0.035 0.006 -10000 0 0 16 16
GRB7 0.035 0.006 -10000 0 0 13 13
PDGFB-D/PDGFRB/SHP2 0.046 0.035 -10000 0 -0.14 14 14
PDGFB-D/PDGFRB/GRB10 0.021 0.054 -10000 0 -0.15 36 36
cell cycle arrest 0.018 0.073 -10000 0 -0.16 67 67
HRAS 0.034 0.009 -10000 0 0 32 32
HIF1A -0.027 0.088 0.21 24 -0.22 19 43
GAB1 0.009 0.12 0.29 10 -0.39 26 36
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.01 0.12 0.32 15 -0.34 26 41
PDGFB-D/PDGFRB 0.054 0.053 -10000 0 -0.14 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.043 0.041 -10000 0 -0.14 20 20
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.025 0.12 0.3 4 -0.29 29 33
positive regulation of MAPKKK cascade 0.046 0.035 -10000 0 -0.14 14 14
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.012 0.11 0.27 8 -0.43 16 24
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -0.01 25 25
PDGFB-D/PDGFRB/GRB7 0.049 0.024 -10000 0 -0.14 5 5
SHB 0.033 0.011 -10000 0 0 48 48
BLK 0.012 0.075 0.26 3 -0.42 7 10
PTPN2 0.033 0.015 -10000 0 -0.017 36 36
PDGFB-D/PDGFRB/SNX15 0.049 0.027 -10000 0 -0.14 8 8
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.005 0.16 0.29 14 -0.42 41 55
CBL 0.036 0.004 -10000 0 0 6 6
PDGFB-D/PDGFRB/DEP1 0.048 0.028 -10000 0 -0.14 8 8
LCK 0.015 0.065 0.29 4 -0.34 5 9
PDGFRB 0.031 0.021 0.062 1 -0.018 68 69
ACP1 0.034 0.008 -10000 0 0 28 28
HCK -0.043 0.18 -10000 0 -0.51 57 57
ABL1 0.004 0.12 0.28 9 -0.36 26 35
PDGFB-D/PDGFRB/CBL 0.008 0.13 0.3 6 -0.44 25 31
PTPN1 0.032 0.016 -10000 0 -0.013 46 46
SNX15 0.036 0.004 -10000 0 0 6 6
STAT3 0.033 0.01 -10000 0 0 37 37
STAT1 0.033 0.01 -10000 0 0 40 40
cell proliferation 0.005 0.24 0.37 26 -0.6 50 76
SLA 0.027 0.016 -10000 0 0 122 122
actin cytoskeleton reorganization -0.016 0.069 0.2 29 -0.19 7 36
SRC 0.017 0.049 0.31 1 -10000 0 1
PI3K -0.047 0.045 -10000 0 -0.17 37 37
PDGFB-D/PDGFRB/GRB7/SHC 0.06 0.037 -10000 0 -0.12 10 10
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.021 0.11 0.31 9 -0.38 17 26
LYN -0.034 0.16 -10000 0 -0.47 49 49
LRP1 0.031 0.013 -10000 0 0 68 68
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.036 0.004 -10000 0 0 6 6
STAT5A 0.036 0.004 -10000 0 0 6 6
NCK1-2/p130 Cas 0.065 0.065 -10000 0 -0.14 25 25
SPHK1 0.033 0.011 0.059 2 0 47 49
EDG1 0.034 0.011 0.059 2 0 38 40
mol:DAG 0.012 0.11 0.27 8 -0.43 16 24
PLCG1 0.011 0.11 0.28 8 -0.44 16 24
NHERF/PDGFRB 0.062 0.037 -10000 0 -0.12 12 12
YES1 -0.008 0.13 0.29 3 -0.54 23 26
cell migration 0.061 0.037 -10000 0 -0.12 12 12
SHC/Grb2/SOS1 0.067 0.06 -10000 0 -0.14 18 18
SLC9A3R2 0.036 0.004 -10000 0 0 5 5
SLC9A3R1 0.034 0.009 -10000 0 0 34 34
NHERF1-2/PDGFRB/PTEN 0.059 0.054 -10000 0 -0.12 13 13
FYN -0.053 0.19 0.22 1 -0.45 75 76
DOK1 -0.018 0.05 0.16 24 -0.13 3 27
HRAS/GTP 0.021 0.029 -10000 0 -0.13 16 16
PDGFB 0.034 0.009 -10000 0 0 35 35
RAC1 0.017 0.19 0.34 26 -0.43 50 76
PRKCD -0.015 0.051 0.18 22 -0.13 3 25
FER -0.016 0.051 0.16 24 -0.13 6 30
MAPKKK cascade -0.011 0.064 0.16 44 -0.17 5 49
RASA1 -0.016 0.052 0.16 25 -0.16 9 34
NCK1 0.034 0.008 -10000 0 0 26 26
NCK2 0.035 0.007 -10000 0 0 19 19
p62DOK/Csk -0.013 0.059 0.18 22 -0.2 3 25
PDGFB-D/PDGFRB/SHB 0.045 0.028 -10000 0 -0.14 6 6
chemotaxis 0.004 0.11 0.27 9 -0.35 26 35
STAT1-3-5/STAT1-3-5 0.06 0.072 -10000 0 -0.14 30 30
Bovine Papilomavirus E5/PDGFRB 0.02 0.026 -10000 0 -0.14 8 8
PTPRJ 0.036 0.005 -10000 0 0 8 8
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.032 0.12 0.26 35 -0.36 20 55
CRKL 0.028 0.11 0.22 26 -0.37 20 46
HRAS 0.036 0.1 0.26 9 -0.32 20 29
mol:PIP3 0.036 0.15 0.3 34 -0.35 41 75
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.036 0.004 -10000 0 0 7 7
GAB1 0.025 0.1 0.22 12 -0.39 20 32
FOXO3 0.037 0.16 0.29 29 -0.38 40 69
AKT1 0.037 0.17 0.31 24 -0.4 40 64
BAD 0.032 0.17 0.3 27 -0.38 40 67
megakaryocyte differentiation 0.026 0.099 0.23 10 -0.39 18 28
GSK3B 0.03 0.17 0.3 24 -0.4 41 65
RAF1 0.024 0.09 0.24 13 -0.28 20 33
SHC1 0.033 0.011 -10000 0 0 48 48
STAT3 0.019 0.1 0.23 5 -0.4 20 25
STAT1 0.011 0.19 -10000 0 -0.87 19 19
HRAS/SPRED1 0.026 0.087 0.22 7 -0.27 21 28
cell proliferation 0.011 0.093 0.25 3 -0.38 20 23
PIK3CA 0.03 0.014 -10000 0 0 85 85
TEC 0.036 0.004 -10000 0 0 6 6
RPS6KB1 0.049 0.12 0.26 18 -0.38 18 36
HRAS/SPRED2 0.046 0.098 0.26 10 -0.27 21 31
LYN/TEC/p62DOK 0.065 0.12 0.27 3 -0.4 20 23
MAPK3 0.024 0.088 0.25 22 -0.21 22 44
STAP1 0.026 0.099 0.21 7 -0.39 20 27
GRAP2 0.034 0.009 -10000 0 0 33 33
JAK2 0.013 0.17 -10000 0 -0.74 19 19
STAT1 (dimer) 0.019 0.19 -10000 0 -0.85 19 19
mol:Gleevec -0.003 0.006 -10000 0 -0.022 2 2
GRB2/SOCS1/VAV1 0.073 0.11 0.28 3 -0.38 20 23
actin filament polymerization 0.028 0.099 0.23 6 -0.38 20 26
LYN 0.031 0.013 -10000 0 0 72 72
STAP1/STAT5A (dimer) 0.026 0.13 0.28 1 -0.54 19 20
PIK3R1 0.032 0.012 -10000 0 0 61 61
CBL/CRKL/GRB2 0.066 0.11 0.3 15 -0.36 19 34
PI3K 0.054 0.13 0.29 15 -0.38 19 34
PTEN 0.026 0.016 -10000 0 0 130 130
SCF/KIT/EPO/EPOR 0.027 0.22 -10000 0 -0.99 19 19
MAPK8 0.01 0.094 0.25 3 -0.39 20 23
STAT3 (dimer) 0.02 0.099 0.23 5 -0.39 20 25
positive regulation of transcription 0.024 0.078 0.24 22 -0.17 22 44
mol:GDP 0.042 0.096 0.26 2 -0.33 20 22
PIK3C2B 0.019 0.099 0.24 8 -0.38 20 28
CBL/CRKL 0.054 0.11 0.27 20 -0.37 19 39
FER 0.024 0.1 0.24 7 -0.39 20 27
SH2B3 0.026 0.099 0.21 7 -0.39 20 27
PDPK1 0.031 0.14 0.28 32 -0.32 38 70
SNAI2 0.029 0.1 0.23 12 -0.38 20 32
positive regulation of cell proliferation 0.03 0.16 0.35 2 -0.66 19 21
KITLG 0.039 0.02 -10000 0 -0.05 18 18
cell motility 0.03 0.16 0.35 2 -0.66 19 21
PTPN6 0.022 0.025 -10000 0 -0.032 70 70
EPOR 0.048 0.08 -10000 0 -10000 0 0
STAT5A (dimer) 0.034 0.14 0.3 4 -0.54 19 23
SOCS1 0.036 0.004 -10000 0 0 7 7
cell migration -0.023 0.098 0.37 20 -0.3 4 24
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.027 0.021 -10000 0 -0.036 13 13
VAV1 0.033 0.01 -10000 0 0 38 38
GRB10 0.016 0.086 0.24 4 -0.35 17 21
PTPN11 0.027 0.021 -10000 0 -0.032 53 53
SCF/KIT 0.03 0.1 0.22 7 -0.4 20 27
GO:0007205 -0.002 0.007 0.021 17 -0.021 1 18
MAP2K1 0.018 0.081 0.22 15 -0.22 23 38
CBL 0.036 0.004 -10000 0 0 6 6
KIT 0.013 0.24 -10000 0 -1 21 21
MAP2K2 0.023 0.091 0.28 23 -0.22 20 43
SHC/Grb2/SOS1 0.055 0.1 0.26 3 -0.36 20 23
STAT5A 0.034 0.14 0.3 4 -0.56 19 23
GRB2 0.035 0.006 -10000 0 0 16 16
response to radiation 0.029 0.1 0.23 12 -0.38 19 31
SHC/GRAP2 0.043 0.029 -10000 0 -0.14 7 7
PTPRO 0.025 0.099 0.23 9 -0.4 18 27
SH2B2 0.026 0.099 0.21 7 -0.39 20 27
DOK1 0.036 0.002 -10000 0 0 2 2
MATK 0.02 0.097 0.24 2 -0.38 20 22
CREBBP 0.052 0.043 0.14 1 -0.12 19 20
BCL2 0.042 0.12 -10000 0 -1 3 3
Caspase cascade in apoptosis

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
TOP1 -0.008 0.087 -10000 0 -0.28 30 30
ACTA1 -0.032 0.086 0.16 1 -0.29 27 28
NUMA1 -0.002 0.084 -10000 0 -0.32 18 18
SPTAN1 -0.041 0.087 0.2 6 -0.29 29 35
LIMK1 0.009 0.11 0.19 68 -0.34 13 81
BIRC3 0.031 0.013 -10000 0 0 77 77
BIRC2 0.036 0.005 -10000 0 0 11 11
BAX 0.033 0.011 -10000 0 0 46 46
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 -0.009 0.088 -10000 0 -0.29 26 26
DIABLO 0.036 0.004 -10000 0 0 5 5
apoptotic nuclear changes -0.041 0.086 0.2 6 -0.29 29 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.035 0.006 -10000 0 0 12 12
GSN -0.032 0.092 0.21 5 -0.31 25 30
MADD 0.035 0.006 -10000 0 0 13 13
TFAP2A 0.041 0.071 -10000 0 -0.54 6 6
BID -0.002 0.04 -10000 0 -0.19 18 18
MAP3K1 -0.001 0.048 -10000 0 -0.38 4 4
TRADD 0.036 0.004 -10000 0 0 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.018 -10000 0 -0.14 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.038 0.094 0.2 12 -0.3 31 43
CASP9 0.034 0.009 -10000 0 0 31 31
DNA repair 0.03 0.067 0.24 20 -10000 0 20
neuron apoptosis 0.016 0.11 -10000 0 -0.61 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.022 0.086 -10000 0 -0.32 23 23
APAF1 0.036 0.003 -10000 0 0 4 4
CASP6 0.021 0.12 -10000 0 -0.86 6 6
TRAF2 0.035 0.006 -10000 0 0 14 14
ICAD/CAD -0.043 0.082 0.25 3 -0.3 24 27
CASP7 -0.072 0.1 -10000 0 -0.23 123 123
KRT18 0.024 0.052 -10000 0 -0.47 4 4
apoptosis -0.032 0.092 -10000 0 -0.34 21 21
DFFA -0.04 0.082 0.18 2 -0.3 26 28
DFFB -0.039 0.081 0.2 1 -0.31 24 25
PARP1 -0.03 0.067 -10000 0 -0.24 20 20
actin filament polymerization -0.014 0.1 0.32 13 -0.18 68 81
TNF 0.036 0.004 -10000 0 0 6 6
CYCS 0.01 0.039 0.14 4 -0.24 3 7
SATB1 0.014 0.11 -10000 0 -0.75 6 6
SLK -0.025 0.08 -10000 0 -0.3 25 25
p15 BID/BAX -0.001 0.069 0.15 2 -0.18 47 49
CASP2 0.046 0.096 0.22 92 -0.24 8 100
JNK cascade 0.001 0.047 0.38 4 -10000 0 4
CASP3 -0.036 0.086 -10000 0 -0.3 27 27
LMNB2 0.051 0.088 0.23 11 -0.28 7 18
RIPK1 0.035 0.007 -10000 0 0 18 18
CASP4 0.03 0.014 -10000 0 0 86 86
Mammalian IAPs/DIABLO 0.056 0.035 -10000 0 -0.15 6 6
negative regulation of DNA binding 0.041 0.071 -10000 0 -0.54 6 6
stress fiber formation -0.034 0.08 -10000 0 -0.29 25 25
GZMB -0.013 0.011 0 194 -10000 0 194
CASP1 -0.01 0.066 -10000 0 -0.2 51 51
LMNB1 0.033 0.12 0.22 19 -0.3 32 51
APP 0.016 0.11 -10000 0 -0.62 14 14
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.011 0.002 0 13 -10000 0 13
VIM -0.032 0.094 -10000 0 -0.34 23 23
LMNA 0.056 0.088 0.23 13 -0.34 5 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.057 -10000 0 -0.22 12 12
LRDD 0.035 0.007 -10000 0 0 18 18
SREBF1 -0.038 0.083 0.18 1 -0.3 25 26
APAF-1/Caspase 9 0.012 0.1 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.002 0.083 -10000 0 -0.32 18 18
CFL2 0.014 0.1 0.18 68 -0.33 13 81
GAS2 -0.03 0.086 0.2 2 -0.3 24 26
positive regulation of apoptosis 0.051 0.1 0.22 22 -0.35 8 30
PRF1 0.023 0.017 -10000 0 0 174 174
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0.001 0 7 -9999 0 7
ADCY5 -0.009 0.001 0 7 -9999 0 7
ADCY6 -0.017 0.004 0 22 -9999 0 22
ADCY7 -0.016 0.005 0 44 -9999 0 44
ADCY1 -0.013 0.008 0 126 -9999 0 126
ADCY2 -0.017 0.004 0 20 -9999 0 20
ADCY3 -0.009 0.001 0 7 -9999 0 7
ADCY8 -0.015 0.006 0 74 -9999 0 74
PRKCE -0.011 0.001 0 7 -9999 0 7
ADCY9 -0.017 0.003 0 18 -9999 0 18
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.015 0.044 0.16 16 -9999 0 16
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.092 -10000 0 -0.39 23 23
Crk/p130 Cas/Paxillin -0.052 0.089 -10000 0 -0.19 101 101
JUN -0.015 0.05 -10000 0 -0.24 13 13
HRAS 0.034 0.009 -10000 0 0 32 32
RET51/GFRalpha1/GDNF/GRB10 0.037 0.06 -10000 0 -0.11 30 30
RAP1A 0.036 0.005 -10000 0 0 8 8
FRS2 0.035 0.008 -10000 0 0 22 22
RAP1A/GDP 0.026 0.008 -10000 0 -0.13 1 1
RET51/GFRalpha1/GDNF/DOK1 0.061 0.046 -10000 0 -10000 0 0
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.035 0.008 -10000 0 0 23 23
RET9/GFRalpha1/GDNF/Enigma 0.048 0.033 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
RAP1A/GTP 0.054 0.049 -10000 0 -0.11 1 1
GRB7 0.035 0.006 -10000 0 0 13 13
RET51/GFRalpha1/GDNF 0.059 0.047 -10000 0 -10000 0 0
MAPKKK cascade -0.005 0.072 -10000 0 -0.17 12 12
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.038 0.046 -10000 0 -0.1 23 23
lamellipodium assembly -0.027 0.085 -10000 0 -0.19 61 61
RET51/GFRalpha1/GDNF/SHC 0.056 0.05 -10000 0 -0.12 7 7
PIK3CA 0.03 0.014 -10000 0 0 85 85
RET9/GFRalpha1/GDNF/SHC 0.041 0.038 -10000 0 -0.11 7 7
RET9/GFRalpha1/GDNF/Shank3 0.032 0.022 -10000 0 -10000 0 0
MAPK3 -0.022 0.046 0.18 17 -10000 0 17
DOK1 0.036 0.002 -10000 0 0 2 2
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.036 0.004 -10000 0 0 5 5
neurite development -0.019 0.048 0.17 16 -0.21 10 26
DOK5 0.03 0.014 -10000 0 0 85 85
GFRA1 0.025 0.017 -10000 0 0 147 147
MAPK8 0.001 0.047 -10000 0 -0.23 7 7
HRAS/GTP 0.021 0.091 -10000 0 -0.17 9 9
tube development 0.027 0.03 0.2 5 -0.1 7 12
MAPK1 -0.02 0.045 0.19 16 -10000 0 16
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.01 0.061 -10000 0 -0.22 11 11
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
SRC 0.035 0.006 -10000 0 0 13 13
PDLIM7 0.036 0.004 -10000 0 0 7 7
RET51/GFRalpha1/GDNF/Dok6 0.056 0.043 -10000 0 -10000 0 0
SHC1 0.033 0.011 -10000 0 0 48 48
RET51/GFRalpha1/GDNF/Dok4 0.061 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.038 0.071 -10000 0 -0.11 60 60
PRKCA 0.036 0.004 -10000 0 0 5 5
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
CREB1 -0.028 0.094 -10000 0 -0.19 105 105
PIK3R1 0.032 0.012 -10000 0 0 61 61
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.008 0.06 -10000 0 -0.16 21 21
RET51/GFRalpha1/GDNF/Grb7 0.06 0.046 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.027 0.016 -10000 0 0 127 127
DOK4 0.036 0.005 -10000 0 0 9 9
JNK cascade -0.016 0.05 -10000 0 -0.23 15 15
RET9/GFRalpha1/GDNF/FRS2 0.047 0.033 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.034 0.009 -10000 0 0 30 30
NCK1 0.034 0.008 -10000 0 0 26 26
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.056 -10000 0 -0.16 14 14
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.09 -10000 0 -0.19 99 99
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.03 0.095 -10000 0 -0.19 97 97
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.045 -10000 0 -0.16 14 14
PI3K -0.045 0.13 0.19 4 -0.26 89 93
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.039 0.038 -10000 0 -0.1 7 7
GRB10 0.022 0.018 -10000 0 0 185 185
activation of MAPKK activity 0.013 0.045 -10000 0 -0.28 8 8
RET51/GFRalpha1/GDNF/FRS2 0.059 0.047 -10000 0 -10000 0 0
GAB1 0.031 0.013 -10000 0 0 75 75
IRS1 0.032 0.011 -10000 0 0 51 51
IRS2 0.029 0.014 -10000 0 0 93 93
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.01 0.048 -10000 0 -0.16 19 19
RET51/GFRalpha1/GDNF/PKC alpha 0.06 0.046 -10000 0 -10000 0 0
GRB2 0.035 0.006 -10000 0 0 16 16
PRKACA 0.034 0.009 -10000 0 0 29 29
GDNF 0.036 0.004 -10000 0 0 6 6
RAC1 0.027 0.016 -10000 0 0 123 123
RET51/GFRalpha1/GDNF/IRS1 0.053 0.057 -10000 0 -0.11 22 22
Rac1/GTP -0.027 0.1 0.19 1 -0.22 61 62
RET9/GFRalpha1/GDNF 0.034 0.023 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.037 0.025 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.005 0 46 -10000 0 46
SNTA1 0.032 0.012 -10000 0 0 57 57
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.013 0.034 0.083 52 -10000 0 52
MAPK12 -0.01 0.032 0.2 4 -0.17 10 14
CCND1 -0.022 0.11 -10000 0 -0.37 40 40
p38 gamma/SNTA1 -0.008 0.041 0.2 4 -0.16 11 15
MAP2K3 0.036 0.005 -10000 0 0 10 10
PKN1 0.032 0.012 -10000 0 0 58 58
G2/M transition checkpoint -0.01 0.032 0.2 4 -0.16 10 14
MAP2K6 -0.007 0.028 0.1 1 -0.18 11 12
MAPT -0.024 0.077 0.16 3 -0.2 71 74
MAPK13 -0.02 0.007 0 46 -10000 0 46
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.009 0.032 -10000 0 -0.2 11 11
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.028 0.069 0.19 20 -0.26 6 26
FYN -0.009 0.097 0.22 9 -0.31 25 34
LAT/GRAP2/SLP76 0.021 0.07 0.22 4 -0.27 10 14
IKBKB 0.036 0.004 -10000 0 0 6 6
AKT1 0.005 0.084 0.2 15 -0.26 17 32
B2M 0.036 0.008 -10000 0 -10000 0 0
IKBKG -0.003 0.034 0.094 13 -0.11 5 18
MAP3K8 0.023 0.018 -10000 0 0 182 182
mol:Ca2+ -0.011 0.009 -10000 0 -0.04 4 4
integrin-mediated signaling pathway 0.024 0.007 -10000 0 -0.11 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.009 0.099 0.24 13 -0.3 17 30
TRPV6 0.32 0.56 1.3 123 -10000 0 123
CD28 0.037 0.001 -10000 0 -10000 0 0
SHC1 0.018 0.07 0.19 29 -0.29 6 35
receptor internalization 0.02 0.054 0.17 9 -0.26 6 15
PRF1 -0.13 0.3 -10000 0 -0.61 130 130
KRAS 0.033 0.01 -10000 0 0 37 37
GRB2 0.035 0.006 -10000 0 0 16 16
COT/AKT1 0.006 0.064 0.2 4 -0.22 14 18
LAT 0.011 0.065 0.2 10 -0.29 7 17
EntrezGene:6955 0.001 0.004 0.014 40 -10000 0 40
CD3D 0.034 0.011 -10000 0 -10000 0 0
CD3E 0.037 0.006 -10000 0 -10000 0 0
CD3G 0.037 0.007 -10000 0 -10000 0 0
RASGRP2 0.007 0.019 0.076 1 -0.15 4 5
RASGRP1 -0.024 0.13 0.22 26 -0.24 90 116
HLA-A 0.037 0.009 -10000 0 -10000 0 0
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.024 0.007 -10000 0 -0.11 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.054 0.13 37 -0.1 14 51
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.036 -10000 0 -0.13 16 16
PRKCA -0.001 0.057 0.18 18 -0.17 6 24
GRAP2 0.034 0.009 -10000 0 0 33 33
mol:IP3 0.005 0.054 -10000 0 -0.22 10 10
EntrezGene:6957 0.001 0.004 0.014 40 -10000 0 40
TCR/CD3/MHC I/CD8 0.019 0.044 0.15 12 -0.29 1 13
ORAI1 -0.27 0.48 0.38 4 -1.1 123 127
CSK 0.012 0.064 0.2 10 -0.29 7 17
B7 family/CD28 0.06 0.091 0.26 17 -0.3 6 23
CHUK 0.026 0.016 -10000 0 0 133 133
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.016 0.066 0.19 9 -0.3 8 17
PTPN6 0.009 0.07 0.22 14 -0.29 9 23
VAV1 0.021 0.076 0.2 35 -0.3 6 41
Monovalent TCR/CD3 0.022 0.017 0.1 5 -10000 0 5
CBL 0.036 0.004 -10000 0 0 6 6
LCK 0.007 0.082 0.22 12 -0.32 9 21
PAG1 0.014 0.064 0.2 11 -0.29 7 18
RAP1A 0.036 0.005 -10000 0 0 8 8
TCR/CD3/MHC I/CD8/LCK 0.016 0.069 0.2 11 -0.29 9 20
CD80 0.036 0.006 -10000 0 0 12 12
CD86 0.032 0.012 -10000 0 0 59 59
PDK1/CARD11/BCL10/MALT1 0.001 0.046 -10000 0 -0.15 18 18
HRAS 0.034 0.009 -10000 0 0 32 32
GO:0035030 0.012 0.068 0.19 20 -0.25 7 27
CD8A 0.001 0.004 0.014 40 -10000 0 40
CD8B 0.001 0.004 0.015 40 -10000 0 40
PTPRC 0.029 0.015 -10000 0 0 103 103
PDK1/PKC theta 0.007 0.09 0.22 24 -0.3 10 34
CSK/PAG1 0.01 0.063 0.2 9 -0.28 7 16
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.049 0.033 -10000 0 -0.14 11 11
GRAP2/SLP76 0.03 0.078 0.23 4 -0.29 11 15
STIM1 -0.047 0.16 1.2 5 -10000 0 5
RAS family/GTP 0.004 0.071 0.16 19 -0.17 30 49
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.02 0.053 0.16 8 -0.27 6 14
mol:DAG -0.019 0.036 -10000 0 -0.19 10 10
RAP1A/GDP 0.008 0.028 0.071 27 -0.052 14 41
PLCG1 0.035 0.007 -10000 0 0 20 20
CD247 0.001 0.004 0.014 40 -10000 0 40
cytotoxic T cell degranulation -0.12 0.29 -10000 0 -0.59 130 130
RAP1A/GTP 0.004 0.007 -10000 0 -0.055 4 4
mol:PI-3-4-5-P3 0.011 0.09 0.23 15 -0.28 15 30
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.015 0.068 -10000 0 -0.26 9 9
NRAS 0.032 0.012 -10000 0 0 58 58
ZAP70 0.036 0.003 -10000 0 0 3 3
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
LAT/GRAP2/SLP76/VAV1 0.014 0.068 0.19 8 -0.28 7 15
MALT1 0.034 0.009 -10000 0 0 29 29
TRAF6 0.036 0.005 -10000 0 0 8 8
CD8 heterodimer 0.003 0.008 0.027 41 -10000 0 41
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.027 -10000 0 -0.14 10 10
PRKCE -0.001 0.056 0.18 18 -0.17 6 24
PRKCQ 0.009 0.094 0.23 23 -0.3 12 35
LCP2 0.031 0.013 -10000 0 0 71 71
BCL10 0.035 0.006 -10000 0 0 15 15
regulation of survival gene product expression 0.006 0.077 0.2 15 -0.22 17 32
IKK complex 0.001 0.038 0.12 16 -0.11 1 17
RAS family/GDP -0.004 0.015 -10000 0 -0.041 34 34
MAP3K14 0.008 0.063 0.18 22 -0.18 14 36
PDPK1 0.006 0.079 0.2 16 -0.24 14 30
TCR/CD3/MHC I/CD8/Fyn 0.01 0.061 -10000 0 -0.29 8 8
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.035 0.005 -10000 0 0 11 11
Caspase 8 (4 units) -0.004 0.094 -10000 0 -0.23 22 22
NEF 0.002 0 -10000 0 -10000 0 0
NFKBIA 0.039 0.019 0.078 62 -10000 0 62
BIRC3 -0.024 0.031 0.18 4 -0.2 2 6
CYCS -0.004 0.081 0.18 46 -0.23 13 59
RIPK1 0.035 0.007 -10000 0 0 18 18
CD247 0.002 0 -10000 0 -10000 0 0
MAP2K7 -0.01 0.1 -10000 0 -0.37 10 10
protein ubiquitination 0.011 0.066 0.21 2 -0.24 7 9
CRADD 0.035 0.006 -10000 0 0 12 12
DAXX 0.036 0.004 -10000 0 0 7 7
FAS 0.021 0.018 -10000 0 0 207 207
BID -0.001 0.053 0.12 1 -0.16 37 38
NF-kappa-B/RelA/I kappa B alpha 0.074 0.053 -10000 0 -0.14 15 15
TRADD 0.036 0.004 -10000 0 0 7 7
MAP3K5 0.03 0.014 -10000 0 0 82 82
CFLAR 0.036 0.005 -10000 0 0 9 9
FADD 0.035 0.006 -10000 0 0 13 13
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.074 0.053 -10000 0 -0.14 15 15
MAPK8 -0.007 0.093 -10000 0 -0.35 10 10
APAF1 0.036 0.003 -10000 0 0 4 4
TRAF1 0.034 0.008 -10000 0 0 24 24
TRAF2 0.035 0.006 -10000 0 0 14 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.004 0.058 -10000 0 -0.16 43 43
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.027 0.076 -10000 0 -0.26 10 10
CHUK 0.012 0.069 0.22 2 -0.25 7 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.043 0.081 -10000 0 -0.12 54 54
TCRz/NEF 0.007 0.001 -10000 0 -10000 0 0
TNF 0.036 0.004 -10000 0 0 6 6
FASLG 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.041 0.017 0.078 69 -10000 0 69
TNFR1A/BAG4/TNF-alpha 0.053 0.055 -10000 0 -0.12 39 39
CASP6 0.009 0.11 -10000 0 -0.56 6 6
CASP7 -0.03 0.14 0.28 10 -0.33 27 37
RELA 0.042 0.016 0.079 71 -10000 0 71
CASP2 0.027 0.016 -10000 0 0 130 130
CASP3 0.002 0.11 0.26 11 -0.35 12 23
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
TNFR1A/BAG4 0.034 0.054 -10000 0 -0.14 40 40
CASP8 0.035 0.006 -10000 0 0 13 13
CASP9 0.034 0.009 -10000 0 0 31 31
MAP3K14 0.022 0.079 0.2 3 -0.27 9 12
APAF-1/Caspase 9 0.001 0.086 0.19 2 -0.21 19 21
BCL2 -0.015 0.093 0.27 2 -0.33 10 12
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.071 -10000 0 -0.29 22 22
KLHL20 0.041 0.092 0.2 60 -0.19 21 81
CYFIP2 0.031 0.013 -10000 0 0 73 73
Rac1/GDP 0.008 0.063 0.21 1 -0.24 15 16
ENAH 0.007 0.073 -10000 0 -0.31 20 20
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 35 0 7 42
RAP1A 0.036 0.005 -10000 0 0 8 8
CTNNB1 0.035 0.007 -10000 0 0 21 21
CDC42/GTP -0.024 0.05 0.12 11 -0.2 19 30
ABI1/Sra1/Nap1 -0.016 0.036 -10000 0 -0.14 31 31
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.081 0.038 -10000 0 -0.13 6 6
RAPGEF1 -0.005 0.073 0.19 1 -0.28 21 22
CTNND1 0.034 0.009 -10000 0 0 30 30
regulation of calcium-dependent cell-cell adhesion 0.019 0.076 -10000 0 -0.29 23 23
CRK 0.002 0.075 0.18 12 -0.29 21 33
E-cadherin/gamma catenin/alpha catenin 0.061 0.035 -10000 0 -0.12 8 8
alphaE/beta7 Integrin 0.049 0.024 -10000 0 -0.14 6 6
IQGAP1 0.033 0.01 -10000 0 0 43 43
NCKAP1 0.036 0.002 -10000 0 0 1 1
Rap1/GTP/I-afadin 0.042 0.015 -10000 0 -0.1 1 1
DLG1 0.006 0.075 -10000 0 -0.29 23 23
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.032 0.043 -10000 0 -0.18 28 28
MLLT4 0.034 0.009 -10000 0 0 35 35
ARF6/GTP/NME1/Tiam1 0.036 0.033 -10000 0 -0.1 23 23
PI3K -0.039 0.056 -10000 0 -0.22 28 28
ARF6 0.035 0.007 -10000 0 0 21 21
mol:Ca2+ 0 0 0.001 66 0 25 91
E-cadherin/gamma catenin 0.047 0.018 -10000 0 -10000 0 0
TIAM1 0.033 0.01 -10000 0 0 43 43
E-cadherin(dimer)/Ca2+ 0.07 0.051 -10000 0 -0.14 20 20
AKT1 -0.017 0.057 0.14 11 -0.17 24 35
PIK3R1 0.032 0.012 -10000 0 0 61 61
CDH1 0.034 0.01 -10000 0 0 37 37
RhoA/GDP 0.012 0.071 0.24 3 -0.23 18 21
actin cytoskeleton organization 0.034 0.073 0.16 61 -0.14 21 82
CDC42/GDP 0.011 0.067 0.2 2 -0.23 16 18
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.048 -10000 0 -0.2 19 19
ITGB7 0.036 0.005 -10000 0 0 10 10
RAC1 0.027 0.016 -10000 0 0 123 123
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.075 0.055 -10000 0 -0.15 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin 0.053 0.032 -10000 0 -0.11 9 9
mol:GDP -0.005 0.072 0.24 3 -0.26 16 19
CDC42/GTP/IQGAP1 0.035 0.042 -10000 0 -0.12 32 32
JUP 0.033 0.011 -10000 0 0 50 50
p120 catenin/RhoA/GDP 0.025 0.077 0.25 3 -0.24 18 21
RAC1/GTP/IQGAP1 0.026 0.044 -10000 0 -0.12 32 32
PIP5K1C/AP1M1 0.018 0.031 -10000 0 -0.13 19 19
RHOA 0.035 0.007 -10000 0 0 21 21
CDC42 0.035 0.008 -10000 0 0 22 22
CTNNA1 0.035 0.007 -10000 0 0 18 18
positive regulation of S phase of mitotic cell cycle 0.01 0.046 0.11 9 -0.12 33 42
NME1 0 0 -10000 0 0 28 28
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.008 0.073 -10000 0 -0.3 21 21
regulation of cell-cell adhesion -0.026 0.039 -10000 0 -0.16 23 23
WASF2 -0.009 0.02 -10000 0 -0.074 31 31
Rap1/GTP -0.022 0.058 0.15 16 -0.22 19 35
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.089 0.05 -10000 0 -0.13 12 12
CCND1 0.012 0.054 0.13 8 -0.14 33 41
VAV2 0.016 0.12 -10000 0 -0.56 11 11
RAP1/GDP -0.008 0.064 0.17 17 -0.24 14 31
adherens junction assembly 0.008 0.071 -10000 0 -0.29 21 21
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.016 -10000 0 0 127 127
PIP5K1C 0.032 0.012 -10000 0 0 58 58
regulation of heterotypic cell-cell adhesion 0.062 0.046 0.2 2 -0.14 12 14
E-cadherin/beta catenin 0.008 0.019 -10000 0 -0.092 7 7
mol:GTP 0 0 0.001 59 0 30 89
SRC 0.006 0.072 -10000 0 -0.29 23 23
PIK3CA 0.03 0.014 -10000 0 0 85 85
Rac1/GTP -0.009 0.077 0.18 2 -0.3 21 23
E-cadherin/beta catenin/alpha catenin 0.061 0.037 -10000 0 -0.13 9 9
ITGAE 0.035 0.007 -10000 0 0 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.077 -10000 0 -0.29 23 23
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.026 0.15 -10000 0 -0.49 18 18
RAD9A 0.035 0.006 -10000 0 0 12 12
AP1 0.009 0.082 -10000 0 -0.17 72 72
IFNAR2 0.033 0.02 -10000 0 -0.035 35 35
AKT1 0.011 0.056 -10000 0 -0.25 19 19
ER alpha/Oestrogen 0.023 0.014 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.005 0.086 -10000 0 -0.27 33 33
EGF 0.033 0.015 -10000 0 -0.014 42 42
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.052 -10000 0 -0.17 19 19
TERT/c-Abl 0.033 0.16 -10000 0 -0.49 21 21
SAP18 0.034 0.01 -10000 0 0 39 39
MRN complex 0.068 0.024 -10000 0 -0.12 4 4
WT1 0.032 0.02 -10000 0 -0.034 36 36
WRN 0.034 0.009 -10000 0 0 31 31
SP1 0.033 0.023 -10000 0 -0.042 37 37
SP3 0.033 0.016 -10000 0 -0.03 25 25
TERF2IP 0.034 0.009 -10000 0 0 34 34
Telomerase/Nucleolin 0.038 0.16 -10000 0 -0.45 26 26
Mad/Max 0.047 0.027 -10000 0 -10000 0 0
TERT 0.022 0.16 -10000 0 -0.5 18 18
CCND1 -0.015 0.29 -10000 0 -0.95 38 38
MAX 0.032 0.018 -10000 0 -0.029 30 30
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.033 0.011 -10000 0 0 53 53
TERF2 0.028 0.011 0.084 5 -10000 0 5
PTGES3 0.035 0.008 -10000 0 0 22 22
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.04 0.1 -10000 0 -0.42 13 13
CDKN1B -0.025 0.083 0.098 35 -0.34 25 60
RAD1 0.035 0.007 -10000 0 0 18 18
XRCC5 0.036 0.004 -10000 0 0 7 7
XRCC6 0.033 0.01 -10000 0 0 37 37
SAP30 0.035 0.006 -10000 0 0 15 15
TRF2/PARP2 0.03 0.057 -10000 0 -0.14 43 43
UBE3A 0.034 0.012 -10000 0 -0.01 29 29
JUN 0.032 0.016 -10000 0 -0.03 19 19
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.02 -10000 0 -0.13 3 3
FOS 0.024 0.02 -10000 0 -0.03 18 18
IFN-gamma/IRF1 0.033 0.069 -10000 0 -0.19 36 36
PARP2 0.033 0.01 -10000 0 0 41 41
BLM 0.029 0.015 -10000 0 0 98 98
Telomerase 0.014 0.056 -10000 0 -0.32 9 9
IRF1 0.025 0.039 -10000 0 -0.12 26 26
ESR1 0.034 0.01 -10000 0 0 34 34
KU/TER 0.047 0.026 -10000 0 -0.14 6 6
ATM/TRF2 0.043 0.028 -10000 0 -0.11 8 8
ubiquitin-dependent protein catabolic process 0.001 0.083 -10000 0 -0.28 25 25
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.001 0.085 -10000 0 -0.28 25 25
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.03 0.024 -10000 0 -0.041 35 35
ATM 0.021 0.038 0.13 36 -0.18 5 41
SMAD3 -0.018 0.012 0.022 24 -10000 0 24
ABL1 0.031 0.013 -10000 0 0 67 67
MXD1 0.033 0.017 -10000 0 -0.029 30 30
MRE11A 0.036 0.004 -10000 0 0 7 7
HUS1 0.027 0.016 -10000 0 0 125 125
RPS6KB1 0.036 0.005 -10000 0 0 8 8
TERT/NF kappa B1/14-3-3 0.042 0.17 -10000 0 -0.51 19 19
NR2F2 0.022 0.023 -10000 0 -0.029 48 48
MAPK3 -0.017 0.015 0.021 62 -10000 0 62
MAPK1 -0.014 0.017 0.024 59 -10000 0 59
TGFB1/TGF beta receptor Type II 0.031 0.012 -10000 0 0 62 62
NFKB1 0.035 0.007 -10000 0 0 17 17
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.021 0.038 0.13 36 -0.18 5 41
NBN 0.035 0.005 -10000 0 0 11 11
EGFR 0.01 0.016 -10000 0 0 355 355
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.004 0.056 -10000 0 -0.14 60 60
MYC 0.028 0.019 -10000 0 -0.029 20 20
IL2 0.033 0.022 -10000 0 -0.042 35 35
KU 0.047 0.026 -10000 0 -0.14 6 6
RAD50 0.035 0.006 -10000 0 0 12 12
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.031 0.012 -10000 0 0 62 62
TRF2/BLM 0.012 0.077 -10000 0 -0.15 86 86
FRAP1 0.035 0.006 -10000 0 0 14 14
KU/TERT 0.05 0.16 -10000 0 -0.46 22 22
SP1/HDAC2 0.042 0.045 -10000 0 -0.099 23 23
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.02 0.14 -10000 0 -0.43 26 26
Smad3/Myc 0.012 0.049 -10000 0 -0.13 40 40
911 complex 0.051 0.037 -10000 0 -0.12 4 4
IFNG 0.027 0.039 -10000 0 -0.1 34 34
Telomerase/PinX1 0.02 0.14 -10000 0 -0.43 26 26
Telomerase/AKT1/mTOR/p70S6K 0.022 0.096 -10000 0 -0.43 11 11
SIN3B 0.034 0.01 -10000 0 0 35 35
YWHAE 0.034 0.009 -10000 0 0 29 29
Telomerase/EST1B 0.02 0.14 -10000 0 -0.43 26 26
response to DNA damage stimulus 0.009 0.018 -10000 0 -0.082 10 10
MRN complex/TRF2/Rap1 0.076 0.071 -10000 0 -0.14 39 39
TRF2/WRN 0.034 0.045 -10000 0 -0.11 38 38
Telomerase/hnRNP C1/C2 0.02 0.14 -10000 0 -0.43 26 26
E2F1 0.033 0.02 -10000 0 -0.034 34 34
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 0.007 -10000 0 0 17 17
DKC1 0.035 0.007 -10000 0 0 18 18
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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.