Glioblastoma Multiforme: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 97 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 126
FOXM1 transcription factor network 104
Syndecan-4-mediated signaling events 95
Angiopoietin receptor Tie2-mediated signaling 81
Endothelins 79
TCGA08_p53 71
HIF-2-alpha transcription factor network 68
TCGA08_rtk_signaling 68
Thromboxane A2 receptor signaling 67
PDGFR-alpha signaling pathway 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 126 9581 76 -0.084 0.1 1000 -1000 -0.01 -1000
FOXM1 transcription factor network 104 5308 51 -0.32 0.055 1000 -1000 -0.053 -1000
Syndecan-4-mediated signaling events 95 6374 67 -0.14 0.036 1000 -1000 -0.031 -1000
Angiopoietin receptor Tie2-mediated signaling 81 7146 88 -0.28 0.051 1000 -1000 -0.052 -1000
Endothelins 79 7662 96 -0.14 0.035 1000 -1000 -0.021 -1000
TCGA08_p53 71 500 7 -0.002 0.032 1000 -1000 -0.01 -1000
HIF-2-alpha transcription factor network 68 2943 43 -0.066 0.046 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 68 1788 26 -0.026 0.087 1000 -1000 -0.004 -1000
Thromboxane A2 receptor signaling 67 7137 105 -0.061 0.043 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 67 2964 44 -0.093 0.036 1000 -1000 -0.026 -1000
EGFR-dependent Endothelin signaling events 67 1418 21 -0.004 0.093 1000 -1000 -0.01 -1000
Effects of Botulinum toxin 65 1698 26 -0.008 0.05 1000 -1000 -0.01 -1000
PLK2 and PLK4 events 63 189 3 -0.018 0.035 1000 -1000 -0.018 -1000
Arf6 signaling events 62 3852 62 -0.004 0.092 1000 -1000 -0.005 -1000
Wnt signaling 62 434 7 -0.006 0.036 1000 -1000 -0.003 -1000
Syndecan-3-mediated signaling events 61 2146 35 -0.073 0.076 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 61 3139 51 -0.1 0.068 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 60 1027 17 -0.001 0.041 1000 -1000 -0.006 -1000
Ceramide signaling pathway 59 4541 76 -0.084 0.07 1000 -1000 -0.019 -1000
LPA receptor mediated events 58 5926 102 -0.12 0.036 1000 -1000 -0.037 -1000
TCGA08_retinoblastoma 58 467 8 -0.046 0.054 1000 -1000 -0.004 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 57 1904 33 -0.049 0.066 1000 -1000 -0.012 -1000
Syndecan-1-mediated signaling events 56 1933 34 -0.009 0.035 1000 -1000 -0.017 -1000
Nongenotropic Androgen signaling 54 2830 52 -0.086 0.059 1000 -1000 -0.023 -1000
Glypican 2 network 51 206 4 0 0.006 1000 -1000 0 -1000
Syndecan-2-mediated signaling events 50 3481 69 -0.026 0.037 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 49 834 17 -0.14 0.061 1000 -1000 -0.005 -1000
EPO signaling pathway 49 2705 55 -0.001 0.083 1000 -1000 -0.013 -1000
amb2 Integrin signaling 49 4084 82 -0.018 0.076 1000 -1000 -0.014 -1000
IL2 signaling events mediated by STAT5 49 1081 22 -0.071 0.042 1000 -1000 -0.021 -1000
Fc-epsilon receptor I signaling in mast cells 48 4729 97 -0.12 0.047 1000 -1000 -0.048 -1000
S1P5 pathway 48 828 17 -0.014 0.035 1000 -1000 -0.009 -1000
IL23-mediated signaling events 47 2865 60 -0.052 0.15 1000 -1000 -0.032 -1000
S1P4 pathway 47 1186 25 -0.016 0.035 1000 -1000 -0.008 -1000
FoxO family signaling 46 2967 64 -0.16 0.042 1000 -1000 -0.016 -1000
Osteopontin-mediated events 45 1718 38 -0.065 0.049 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 43 2625 61 -0.08 0.076 1000 -1000 -0.037 -1000
Ephrin B reverse signaling 43 2089 48 -0.065 0.065 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 43 2976 68 -0.1 0.045 1000 -1000 -0.027 -1000
BCR signaling pathway 41 4144 99 -0.048 0.049 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 40 1056 26 -0.038 0.036 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 40 2377 58 -0.067 0.037 1000 -1000 -0.019 -1000
EPHB forward signaling 40 3453 85 -0.051 0.08 1000 -1000 -0.041 -1000
Signaling events mediated by VEGFR1 and VEGFR2 40 5062 125 -0.044 0.058 1000 -1000 -0.037 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 39 2146 54 -0.031 0.068 1000 -1000 -0.029 -1000
Reelin signaling pathway 39 2230 56 -0.014 0.065 1000 -1000 -0.014 -1000
E-cadherin signaling in keratinocytes 39 1702 43 -0.035 0.061 1000 -1000 -0.015 -1000
ErbB2/ErbB3 signaling events 38 2519 65 -0.039 0.036 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 38 5292 136 -0.2 0.2 1000 -1000 -0.037 -1000
IL12-mediated signaling events 38 3324 87 -0.098 0.099 1000 -1000 -0.021 -1000
Signaling events mediated by PTP1B 38 2930 76 -0.033 0.058 1000 -1000 -0.02 -1000
Glypican 1 network 38 1826 48 -0.036 0.05 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 38 1380 36 -0.058 0.055 1000 -1000 -0.045 -1000
Arf6 downstream pathway 37 1613 43 -0.027 0.051 1000 -1000 -0.029 -1000
mTOR signaling pathway 37 1969 53 -0.028 0.045 1000 -1000 -0.02 -1000
Class I PI3K signaling events 37 2763 73 -0.051 0.056 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 36 1026 28 -0.019 0.035 1000 -1000 -0.019 -1000
BMP receptor signaling 36 2981 81 -0.026 0.056 1000 -1000 -0.009 -1000
Paxillin-independent events mediated by a4b1 and a4b7 36 1361 37 -0.034 0.078 1000 -1000 -0.017 -1000
IL1-mediated signaling events 36 2247 62 -0.039 0.073 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 36 2667 74 -0.11 0.079 1000 -1000 -0.047 -1000
p38 MAPK signaling pathway 36 1609 44 0 0.041 1000 -1000 -0.006 -1000
IFN-gamma pathway 35 2437 68 -0.037 0.065 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 35 2385 68 -0.033 0.061 1000 -1000 -0.019 -1000
IL6-mediated signaling events 35 2653 75 -0.066 0.096 1000 -1000 -0.027 -1000
IGF1 pathway 35 2041 57 -0.043 0.065 1000 -1000 -0.029 -1000
PLK1 signaling events 34 2960 85 -0.043 0.056 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 34 1624 47 -0.14 0.047 1000 -1000 -0.03 -1000
Neurotrophic factor-mediated Trk receptor signaling 34 4158 120 -0.037 0.087 1000 -1000 -0.024 -1000
Hedgehog signaling events mediated by Gli proteins 33 2190 65 -0.025 0.058 1000 -1000 -0.025 -1000
S1P1 pathway 33 1218 36 -0.011 0.049 1000 -1000 -0.016 -1000
Plasma membrane estrogen receptor signaling 33 2915 86 -0.069 0.057 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 32 2754 85 -0.11 0.12 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 32 1775 54 -0.008 0.049 1000 -1000 -0.011 -1000
PDGFR-beta signaling pathway 32 3136 97 -0.053 0.067 1000 -1000 -0.041 -1000
Signaling events mediated by PRL 32 1099 34 -0.035 0.047 1000 -1000 -0.022 -1000
ErbB4 signaling events 31 2183 69 -0.081 0.059 1000 -1000 -0.019 -1000
TCR signaling in naïve CD8+ T cells 31 2971 93 -0.27 0.32 1000 -1000 -0.026 -1000
IL4-mediated signaling events 30 2801 91 -0.31 0.059 1000 -1000 -0.046 -1000
Retinoic acid receptors-mediated signaling 30 1762 58 -0.059 0.059 1000 -1000 -0.022 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 30 1371 45 -0.029 0.074 1000 -1000 -0.022 -1000
Caspase cascade in apoptosis 29 2198 74 -0.072 0.056 1000 -1000 -0.024 -1000
p75(NTR)-mediated signaling 29 3699 125 -0.025 0.083 1000 -1000 -0.041 -1000
Signaling events regulated by Ret tyrosine kinase 29 2426 82 -0.052 0.061 1000 -1000 -0.024 -1000
Signaling mediated by p38-gamma and p38-delta 29 449 15 -0.024 0.035 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 29 2277 76 -0.039 0.089 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 29 2321 78 -0.023 0.072 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 29 380 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 -0.009 -1000
Visual signal transduction: Cones 28 1068 38 -0.013 0.058 1000 -1000 -0.01 -1000
a4b1 and a4b7 Integrin signaling 28 140 5 0.027 0.052 1000 -1000 0.032 -1000
Signaling events mediated by HDAC Class III 28 1134 40 -0.05 0.05 1000 -1000 -0.049 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 28 2331 83 -0.034 0.066 1000 -1000 -0.015 -1000
Insulin Pathway 28 2092 74 -0.034 0.08 1000 -1000 -0.03 -1000
LPA4-mediated signaling events 27 330 12 -0.017 0.015 1000 -1000 -0.015 -1000
Aurora A signaling 27 1644 60 -0.026 0.057 1000 -1000 -0.018 -1000
S1P3 pathway 27 1135 42 -0.021 0.036 1000 -1000 -0.025 -1000
Integrins in angiogenesis 26 2253 84 -0.043 0.069 1000 -1000 -0.019 -1000
Aurora B signaling 26 1777 67 -0.033 0.062 1000 -1000 -0.021 -1000
Nectin adhesion pathway 25 1580 63 -0.01 0.08 1000 -1000 -0.024 -1000
Calcium signaling in the CD4+ TCR pathway 25 775 31 -0.022 0.081 1000 -1000 -0.024 -1000
Glucocorticoid receptor regulatory network 24 2753 114 -0.13 0.059 1000 -1000 -0.041 -1000
Regulation of Telomerase 24 2535 102 -0.025 0.076 1000 -1000 -0.036 -1000
BARD1 signaling events 23 1367 57 -0.062 0.081 1000 -1000 -0.056 -1000
Circadian rhythm pathway 23 526 22 -0.009 0.053 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class I 23 2406 104 -0.028 0.066 1000 -1000 -0.024 -1000
TRAIL signaling pathway 22 1070 48 -0.023 0.085 1000 -1000 -0.02 -1000
E-cadherin signaling events 22 112 5 0.032 0.061 1000 -1000 0.032 -1000
Insulin-mediated glucose transport 21 676 32 -0.018 0.041 1000 -1000 -0.018 -1000
RXR and RAR heterodimerization with other nuclear receptor 21 1131 52 -0.044 0.1 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 19 597 31 -0.021 0.036 1000 -1000 -0.018 -1000
IL27-mediated signaling events 19 1016 51 -0.011 0.05 1000 -1000 -0.031 -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 -0.015 -1000
Signaling mediated by p38-alpha and p38-beta 18 816 44 -0.013 0.075 1000 -1000 -0.014 -1000
ceramide signaling pathway 17 868 49 -0.012 0.052 1000 -1000 -0.02 -1000
Arf6 trafficking events 17 1218 71 -0.038 0.046 1000 -1000 -0.031 -1000
VEGFR1 specific signals 17 955 56 -0.027 0.04 1000 -1000 -0.021 -1000
Canonical NF-kappaB pathway 16 644 39 -0.031 0.064 1000 -1000 -0.015 -1000
Regulation of Androgen receptor activity 16 1160 70 -0.029 0.066 1000 -1000 -0.03 -1000
Sumoylation by RanBP2 regulates transcriptional repression 15 423 27 -0.032 0.074 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 15 319 20 -0.011 0.035 1000 -1000 -0.01 -1000
Arf1 pathway 15 863 54 -0.06 0.044 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 14 490 34 -0.053 0.093 1000 -1000 -0.038 -1000
Aurora C signaling 14 102 7 0 0.059 1000 -1000 -0.009 -1000
Signaling events mediated by the Hedgehog family 13 724 52 -0.017 0.078 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 10 799 76 -0.018 0.065 1000 -1000 -0.03 -1000
FOXA2 and FOXA3 transcription factor networks 9 454 46 0 0.099 1000 -1000 -0.046 -1000
Visual signal transduction: Rods 8 426 52 -0.032 0.083 1000 -1000 -0.008 -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 -0.01 -1000
Total 4924 276661 7203 -6.7 8.3 131000 -131000 -2.9 -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 0.036 0.47 0.61 88 -0.76 82 170
HDAC7 -0.001 0.005 -10000 0 -0.043 5 5
HIF1A/ARNT/Cbp/p300/Src-1 -0.03 0.38 0.57 33 -0.72 68 101
SMAD4 0.033 0.013 0.079 11 -10000 0 11
ID2 0.058 0.48 0.62 114 -0.75 82 196
AP1 0.013 0.082 -10000 0 -0.17 73 73
ABCG2 0.022 0.47 0.61 98 -0.75 85 183
HIF1A 0.045 0.13 0.23 84 -0.16 62 146
TFF3 0.051 0.47 0.62 108 -0.75 80 188
GATA2 0.038 0.013 0.074 24 -0.076 2 26
AKT1 0.053 0.14 0.24 90 -0.2 38 128
response to hypoxia 0.009 0.087 0.17 71 -0.13 37 108
MCL1 0.063 0.48 0.63 102 -0.75 81 183
NDRG1 0.003 0.46 0.61 74 -0.76 87 161
SERPINE1 -0.057 0.4 0.56 46 -0.77 79 125
FECH 0.049 0.47 0.62 107 -0.75 81 188
FURIN 0.063 0.48 0.62 115 -0.75 81 196
NCOA2 0.037 0.005 -10000 0 0 9 9
EP300 0.074 0.19 0.37 92 -0.31 33 125
HMOX1 -0.015 0.46 0.61 75 -0.78 85 160
BHLHE40 -0.056 0.41 0.54 72 -0.73 84 156
BHLHE41 -0.056 0.41 0.54 72 -0.73 84 156
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.071 0.18 0.35 47 -0.23 36 83
ENG 0.037 0.16 0.29 66 -0.25 20 86
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 -0.056 0.22 -10000 0 -0.86 26 26
TFRC 0.04 0.48 0.63 93 -0.75 84 177
CXCR4 0.022 0.47 0.62 85 -0.76 86 171
TF -0.072 0.41 0.63 47 -0.75 88 135
CITED2 0.021 0.46 0.61 90 -0.76 82 172
HIF1A/ARNT -0.084 0.44 0.65 11 -0.88 73 84
LDHA -0.066 0.28 -10000 0 -0.99 37 37
ETS1 0.065 0.48 0.62 115 -0.76 79 194
PGK1 0.057 0.49 0.63 104 -0.77 81 185
NOS2 -0.056 0.41 0.54 72 -0.73 84 156
ITGB2 0.012 0.46 0.6 89 -0.76 85 174
ALDOA 0.067 0.48 0.63 107 -0.75 82 189
Cbp/p300/CITED2 -0.026 0.45 0.6 61 -0.82 79 140
FOS 0.026 0.018 -10000 0 0 148 148
HK2 0.066 0.48 0.62 117 -0.75 82 199
SP1 0.033 0.057 0.1 33 -0.14 37 70
GCK 0.1 0.25 0.61 38 -0.63 2 40
HK1 0.016 0.46 0.63 81 -0.76 81 162
NPM1 0.062 0.48 0.62 115 -0.76 80 195
EGLN1 0.059 0.48 0.61 111 -0.76 80 191
CREB1 0.031 0.035 -10000 0 -0.1 29 29
PGM1 0.061 0.48 0.62 114 -0.76 82 196
SMAD3 0.037 0.008 0.081 11 -10000 0 11
EDN1 0.056 0.22 0.46 32 -0.52 21 53
IGFBP1 0.002 0.43 0.6 75 -0.75 75 150
VEGFA -0.018 0.34 0.48 73 -0.59 77 150
HIF1A/JAB1 0.045 0.1 0.2 58 -0.16 25 83
CP -0.027 0.45 0.61 66 -0.76 87 153
CXCL12 -0.032 0.42 0.61 50 -0.76 78 128
COPS5 0.036 0.006 -10000 0 0 12 12
SMAD3/SMAD4 0.04 0.05 0.14 5 -0.14 30 35
BNIP3 -0.006 0.45 0.64 71 -0.76 81 152
EGLN3 0.012 0.45 0.6 86 -0.75 82 168
CA9 -0.011 0.43 0.61 62 -0.76 79 141
TERT 0.059 0.48 0.63 103 -0.75 81 184
ENO1 0.057 0.48 0.64 104 -0.76 80 184
PFKL 0.064 0.48 0.63 105 -0.76 81 186
NCOA1 0.033 0.01 -10000 0 0 43 43
ADM -0.015 0.46 0.61 78 -0.76 88 166
ARNT 0.049 0.12 0.24 79 -0.14 57 136
HNF4A 0.038 0.009 -10000 0 -10000 0 0
ADFP -0.024 0.44 0.6 70 -0.77 84 154
SLC2A1 0.017 0.37 0.54 70 -0.62 75 145
LEP 0.024 0.44 0.64 77 -0.76 73 150
HIF1A/ARNT/Cbp/p300 -0.047 0.38 0.57 28 -0.72 69 97
EPO 0.032 0.32 0.55 56 -0.58 45 101
CREBBP 0.081 0.18 0.36 95 -0.26 30 125
HIF1A/ARNT/Cbp/p300/HDAC7 -0.05 0.37 0.54 28 -0.71 70 98
PFKFB3 0.015 0.46 0.62 92 -0.75 83 175
NT5E -0.017 0.45 0.63 68 -0.75 87 155
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.091 0.65 0.99 29 -1.2 93 122
PLK1 0.052 0.16 0.6 12 -0.76 8 20
BIRC5 -0.072 0.44 0.64 12 -1.2 57 69
HSPA1B -0.091 0.65 0.9 36 -1.2 99 135
MAP2K1 0.045 0.1 0.23 58 -10000 0 58
BRCA2 -0.086 0.66 1 30 -1.2 95 125
FOXM1 -0.24 0.97 1.1 32 -1.9 99 131
XRCC1 -0.082 0.66 1 31 -1.2 95 126
FOXM1B/p19 -0.32 0.57 -10000 0 -1.4 96 96
Cyclin D1/CDK4 -0.11 0.58 0.82 31 -1.1 99 130
CDC2 -0.11 0.72 1.1 34 -1.3 102 136
TGFA -0.069 0.58 0.84 39 -1 98 137
SKP2 -0.089 0.66 0.99 31 -1.2 96 127
CCNE1 0.023 0.036 0.096 21 -0.034 106 127
CKS1B -0.097 0.68 1 31 -1.2 101 132
RB1 -0.077 0.37 0.51 15 -1 48 63
FOXM1C/SP1 -0.18 0.74 0.87 21 -1.5 101 122
AURKB 0.055 0.15 0.66 10 -1 3 13
CENPF -0.11 0.7 1 32 -1.2 108 140
CDK4 0.025 0.051 0.15 29 -10000 0 29
MYC -0.11 0.56 0.77 34 -1 105 139
CHEK2 0.034 0.087 0.2 49 -10000 0 49
ONECUT1 -0.09 0.63 0.86 40 -1.1 101 141
CDKN2A 0.004 0.015 -10000 0 -0.097 3 3
LAMA4 -0.094 0.65 0.97 30 -1.2 94 124
FOXM1B/HNF6 -0.17 0.77 0.9 33 -1.5 101 134
FOS -0.14 0.7 0.98 30 -1.2 124 154
SP1 0.033 0.019 0.069 1 -0.044 23 24
CDC25B -0.096 0.67 0.96 31 -1.2 96 127
response to radiation 0.023 0.066 0.14 78 -10000 0 78
CENPB -0.085 0.66 0.95 36 -1.2 94 130
CENPA -0.094 0.66 1 29 -1.2 94 123
NEK2 -0.084 0.66 1.1 30 -1.2 97 127
HIST1H2BA -0.091 0.65 0.9 36 -1.2 99 135
CCNA2 0.022 0.031 0.09 5 -0.033 74 79
EP300 0.033 0.011 -10000 0 0 49 49
CCNB1/CDK1 -0.19 0.83 1.1 28 -1.6 104 132
CCNB2 -0.11 0.69 0.99 33 -1.3 96 129
CCNB1 -0.12 0.74 1.1 34 -1.3 103 137
ETV5 -0.12 0.69 0.97 32 -1.2 120 152
ESR1 -0.088 0.65 0.96 31 -1.2 97 128
CCND1 -0.11 0.61 0.86 37 -1.1 100 137
GSK3A 0.037 0.082 0.19 55 -10000 0 55
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 78 -10000 0 78
FOXM1B/Cbp/p300 -0.16 0.68 0.78 17 -1.4 99 116
GAS1 -0.093 0.67 0.99 33 -1.2 97 130
MMP2 -0.12 0.69 0.96 34 -1.2 111 145
RB1/FOXM1C -0.15 0.6 0.83 25 -1.2 97 122
CREBBP 0.036 0.004 -10000 0 -10000 0 0
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 -0.46 41 41
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 0.032 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 -0.42 159 159
THBS1 0.029 0.014 -10000 0 0 90 90
integrin-mediated signaling pathway -0.13 0.27 -10000 0 -0.44 166 166
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 -0.46 164 164
TFPI 0.029 0.015 -10000 0 0 97 97
F2 0.01 0.04 -10000 0 -0.042 174 174
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 0.027 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 -0.042 24 24
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 -0.46 173 173
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 -0.44 169 169
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 -0.83 132 132
NCK1/PAK1/Dok-R -0.12 0.17 -10000 0 -0.39 122 122
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 -0.081 1 90
RELA 0.035 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 -0.7 136 136
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 0.4 4 -0.6 130 134
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 -0.76 116 116
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 -1.1 98 98
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 -10000 0 -0.71 152 152
ANGPT4 0.023 0.028 -10000 0 -0.034 89 89
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 -0.83 156 156
mol:L-citrulline -0.13 0.32 0.4 4 -0.6 130 134
AGTR1 0.021 0.034 -10000 0 -0.047 88 88
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 -0.77 127 127
Angiotensin II/AT1 0.014 0.036 -10000 0 -0.061 64 64
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 -0.92 125 125
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 -0.74 135 135
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 -0.78 126 126
Tie2/Ang2 -0.28 0.51 -10000 0 -0.99 148 148
Tie2/Ang1 -0.15 0.38 -10000 0 -0.93 89 89
FOXO1 -0.22 0.39 -10000 0 -0.75 156 156
ELF1 0.028 0.036 0.1 1 -0.045 76 77
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 -0.22 125 125
FYN -0.24 0.41 -10000 0 -0.82 151 151
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.16 0.32 -10000 0 -0.63 136 136
ETS1 0 0.12 -10000 0 -0.25 86 86
PXN -0.17 0.31 -10000 0 -0.65 126 126
ITGB1 0.027 0.016 -10000 0 0 118 118
NOS3 -0.16 0.36 0.42 3 -0.68 129 132
RAC1 0.027 0.016 -10000 0 0 123 123
TNF -0.001 0.12 -10000 0 -0.25 84 84
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 -0.54 130 135
mol:Phosphatidic acid -0.14 0.35 -10000 0 -0.86 89 89
mol:Angiotensin II -0.004 0.013 0.021 1 -0.032 72 73
mol:NADP -0.13 0.32 0.4 4 -0.6 130 134
Rac1/GTP -0.17 0.34 -10000 0 -0.71 120 120
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 0.21 72 -0.26 82 154
PTK2B 0.035 0.006 -10000 0 0 15 15
mol:Ca2+ -0.097 0.25 0.39 1 -0.52 80 81
EDN1 0.004 0.09 0.15 5 -0.16 97 102
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 0.29 24 -0.36 57 81
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.12 0.2 11 -0.24 62 73
ADCY4 -0.035 0.095 0.14 32 -0.2 91 123
ADCY5 -0.035 0.095 0.14 32 -0.2 91 123
ADCY6 -0.005 0.13 0.23 36 -0.24 56 92
ADCY7 -0.011 0.13 0.21 39 -0.24 59 98
ADCY1 0 0.12 0.22 34 -0.25 41 75
ADCY2 -0.005 0.13 0.23 38 -0.24 57 95
ADCY3 -0.035 0.095 0.14 32 -0.2 91 123
ADCY8 -0.008 0.13 0.22 39 -0.24 51 90
ADCY9 -0.007 0.13 0.22 36 -0.24 58 94
arachidonic acid secretion -0.069 0.26 0.32 30 -0.49 101 131
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.11 0.18 11 -0.23 60 71
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 85 85
ETA receptor/Endothelin-1/Gs/GTP 0.005 0.12 -10000 0 -0.2 100 100
mol:GTP 0 0.006 0.024 3 -0.025 3 6
COL3A1 -0.074 0.15 0.19 8 -0.36 96 104
EDNRB 0.023 0.044 0.095 61 -0.082 45 106
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.017 0.14 0.21 69 -0.28 58 127
CYSLTR1 -0.038 0.12 0.18 32 -0.24 89 121
SLC9A1 -0.014 0.087 0.13 2 -0.19 64 66
mol:GDP -0.016 0.17 0.28 27 -0.37 56 83
SLC9A3 -0.12 0.29 -10000 0 -0.65 77 77
RAF1 -0.028 0.21 0.29 36 -0.4 83 119
JUN -0.14 0.33 0.47 1 -0.63 114 115
JAK2 -0.018 0.13 0.21 59 -0.25 76 135
mol:IP3 -0.006 0.12 0.21 17 -0.26 49 66
ETA receptor/Endothelin-1 -0.027 0.14 -10000 0 -0.27 106 106
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 -10000 0 -0.14 103 103
FOS -0.086 0.35 0.38 24 -0.83 78 102
Gai/GDP -0.07 0.27 -10000 0 -0.74 64 64
CRK 0.035 0.008 -10000 0 0 23 23
mol:Ca ++ -0.018 0.17 0.26 54 -0.33 75 129
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.002 0.12 0.23 24 -0.28 46 70
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 0.27 26 -0.34 54 80
ETA receptor/Endothelin-1/Gq/GTP -0.008 0.12 0.2 10 -0.26 65 75
MAPK14 -0.01 0.099 0.16 13 -0.25 42 55
TRPC6 -0.1 0.26 0.39 1 -0.55 79 80
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 0 245 245
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.1 0.17 15 -0.25 43 58
ETB receptor/Endothelin-2 0.018 0.071 -10000 0 -0.11 95 95
ETB receptor/Endothelin-3 0.016 0.07 -10000 0 -0.11 94 94
ETB receptor/Endothelin-1 -0.001 0.1 0.17 14 -0.16 111 125
MAPK3 -0.068 0.32 0.35 34 -0.72 80 114
MAPK1 -0.082 0.34 0.37 26 -0.77 81 107
Rac1/GDP -0.005 0.16 0.29 20 -0.36 45 65
cAMP biosynthetic process 0.017 0.12 0.22 44 -0.22 46 90
MAPK8 -0.13 0.31 0.34 3 -0.56 140 143
SRC 0.035 0.006 -10000 0 0 13 13
ETB receptor/Endothelin-1/Gi/GTP -0.035 0.14 0.15 6 -0.35 60 66
p130Cas/CRK/Src/PYK2 -0.016 0.18 0.32 22 -0.46 43 65
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.009 0.16 0.3 18 -0.36 51 69
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 17 -0.26 49 66
MAP2K2 -0.042 0.26 0.34 44 -0.56 78 122
MAP2K1 -0.056 0.26 0.32 30 -0.57 81 111
EDNRA -0.007 0.1 0.16 1 -0.19 92 93
positive regulation of muscle contraction 0.011 0.14 0.21 114 -0.24 63 177
Gq family/GDP 0.003 0.16 0.3 4 -0.34 56 60
HRAS/GTP -0.009 0.16 0.26 31 -0.34 58 89
PRKCH -0.007 0.12 0.23 17 -0.29 40 57
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.011 0.12 0.21 18 -0.28 49 67
PRKCB -0.005 0.12 0.21 22 -0.27 48 70
PRKCE -0.011 0.12 0.21 17 -0.28 48 65
PRKCD -0.008 0.12 0.24 22 -0.28 47 69
PRKCG -0.01 0.12 0.21 19 -0.29 45 64
regulation of vascular smooth muscle contraction -0.11 0.42 0.44 15 -1 78 93
PRKCQ -0.003 0.11 0.24 18 -0.28 35 53
PLA2G4A -0.079 0.28 0.33 28 -0.54 101 129
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 73 73
MMP1 0.02 0.073 0.2 26 -10000 0 26
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
HIF-2-alpha transcription factor network

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
MMP14 -0.006 0.14 -10000 0 -0.65 20 20
oxygen homeostasis 0.005 0.021 0.045 68 -0.025 30 98
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 0.27 37 -0.24 42 79
EPO -0.032 0.2 0.4 20 -0.43 54 74
FIH (dimer) 0.018 0.039 0.11 19 -0.04 57 76
APEX1 0.017 0.041 0.1 8 -0.05 40 48
SERPINE1 -0.066 0.2 0.33 11 -0.45 74 85
FLT1 -0.007 0.14 -10000 0 -0.62 21 21
ADORA2A -0.023 0.23 0.42 42 -0.42 65 107
germ cell development -0.027 0.22 0.39 38 -0.41 67 105
SLC11A2 -0.02 0.24 0.44 39 -0.44 66 105
BHLHE40 -0.03 0.23 0.4 36 -0.42 67 103
HIF1AN 0.018 0.039 0.11 19 -0.04 57 76
HIF2A/ARNT/SIRT1 -0.007 0.16 0.32 23 -0.29 52 75
ETS1 0.046 0.032 0.12 42 -0.11 11 53
CITED2 -0.053 0.26 -10000 0 -0.86 41 41
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 0.47 12 -0.48 67 79
EPAS1 0.007 0.13 0.27 48 -0.23 46 94
SP1 0.04 0.011 0.11 8 -10000 0 8
ABCG2 -0.033 0.25 0.44 36 -0.44 81 117
EFNA1 -0.028 0.24 0.41 35 -0.43 72 107
FXN -0.025 0.23 0.41 41 -0.42 67 108
POU5F1 -0.03 0.23 0.4 36 -0.42 67 103
neuron apoptosis 0.014 0.26 0.47 67 -0.46 12 79
EP300 0.033 0.011 -10000 0 0 49 49
EGLN3 0.02 0.039 0.11 16 -0.04 60 76
EGLN2 0.024 0.041 0.11 22 -0.04 50 72
EGLN1 0.025 0.041 0.11 21 -0.039 59 80
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 -0.048 50 58
SLC2A1 -0.046 0.22 0.38 30 -0.44 70 100
TWIST1 -0.063 0.2 0.36 16 -0.42 83 99
ELK1 0.037 0.036 0.11 30 -0.094 25 55
HIF2A/ARNT/Cbp/p300 0.013 0.18 0.37 32 -0.31 51 83
VEGFA -0.03 0.23 0.4 36 -0.42 67 103
CREBBP 0.036 0.004 -10000 0 0 5 5
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.024 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 0.23 111 -0.17 12 123
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 19 24
PI3K 0.033 0.08 0.19 63 -0.16 11 74
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 0.19 150 -10000 0 150
AKT2 0.034 0.008 -10000 0 0 26 26
PTEN 0.026 0.016 -10000 0 0 130 130
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.035 0.008 -10000 0 0 24 24
GNB1/GNG2 -0.045 0.076 -10000 0 -0.17 120 120
AKT1 -0.003 0.16 0.28 35 -0.3 35 70
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 -0.28 91 119
LYN -0.007 0.083 0.25 33 -0.16 7 40
RhoA/GTP -0.004 0.08 0.15 24 -0.13 94 118
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.012 0.21 0.35 33 -0.32 112 145
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 31 31
G beta5/gamma2 -0.052 0.1 -10000 0 -0.22 117 117
PRKCH -0.012 0.2 0.35 28 -0.32 112 140
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 56 -10000 0 56
PTGDR 0.035 0.007 -10000 0 0 20 20
G12 family/GTP -0.042 0.15 -10000 0 -0.29 103 103
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 28 -0.35 97 125
cell morphogenesis 0.043 0.027 -10000 0 -0.12 10 10
PLCB2 -0.032 0.27 0.43 17 -0.46 102 119
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 0.24 23 -0.17 8 31
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 27 -0.35 106 133
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 0.42 22 -0.48 118 140
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 38 -0.22 107 145
TGM2/GTP -0.012 0.24 0.4 21 -0.39 87 108
MAPK11 -0.002 0.15 0.28 37 -0.22 108 145
ARHGEF1 0.006 0.12 0.22 42 -0.18 98 140
GNAI2 0.033 0.01 -10000 0 0 42 42
JNK cascade -0.016 0.22 0.37 28 -0.36 117 145
RAB11/GDP 0.033 0.011 -10000 0 -0.011 24 24
ICAM1 0 0.18 0.31 39 -0.27 112 151
cAMP biosynthetic process -0.01 0.2 0.34 28 -0.32 86 114
Gq family/GTP/EBP50 0.011 0.055 0.25 6 -0.16 31 37
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 0.28 29 -0.23 36 65
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 31 31
platelet activation -0.004 0.19 0.35 34 -0.28 107 141
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 31 32
TXA2/TP beta/beta Arrestin2 0.004 0.054 -10000 0 -0.3 10 10
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 26 -0.38 115 141
EGFR 0.01 0.016 -10000 0 0 355 355
TXA2/TP alpha -0.024 0.26 0.43 18 -0.44 88 106
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 -0.008 0.082 0.25 30 -0.16 18 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 -0.14 3 12
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 0.34 28 -0.32 114 142
PRKCB -0.012 0.21 0.34 28 -0.33 117 145
PRKCE -0.013 0.21 0.35 27 -0.33 114 141
PRKCD -0.016 0.22 0.35 32 -0.35 116 148
PRKCG -0.016 0.22 0.36 28 -0.35 115 143
muscle contraction -0.035 0.26 0.41 23 -0.44 115 138
PRKCZ -0.011 0.2 0.35 28 -0.32 117 145
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 26 -0.33 108 134
MAPKKK cascade -0.027 0.24 0.39 23 -0.4 112 135
SELE -0.006 0.18 0.32 30 -0.28 120 150
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.056 0.18 9 -0.17 15 24
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 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
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 0.024 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 0.051 48 -0.098 56 104
PLCG1 -0.018 0.041 0.051 48 -0.098 56 104
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 0.051 48 -0.098 56 104
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 -0.13 65 65
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 0.051 48 -0.098 56 104
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 57 -10000 0 57
ELK1/SRF -0.019 0.084 0.14 69 -0.16 56 125
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 0.024 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 -0.013 0.075 -10000 0 -0.15 89 89
ITGAV 0.034 0.009 -10000 0 0 30 30
ELK1 -0.033 0.068 0.088 21 -0.16 84 105
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 57 -10000 0 57
cell proliferation -0.005 0.054 -10000 0 -0.13 65 65
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.009 -10000 0 0 32 32
EGFR 0.01 0.016 -10000 0 0 355 355
EGF/EGFR 0.002 0.052 -10000 0 -0.11 58 58
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.058 -10000 0 -0.11 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.027 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 0.056 -10000 0 -0.13 59 59
mol:GDP 0.005 0.055 -10000 0 -0.11 60 60
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.032 0.011 -10000 0 0 50 50
GRB2/SOS1 0.024 0.019 -10000 0 -0.13 7 7
HRAS/GTP -0.004 0.052 -10000 0 -0.11 68 68
SHC1 0.033 0.011 -10000 0 0 48 48
HRAS/GDP 0 0.059 -10000 0 -0.12 68 68
FRAP1 0.093 0.12 0.19 284 -0.18 4 288
EGF/EGFR dimer -0.004 0.057 -10000 0 -0.14 61 61
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
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 0 154 -10000 0 154
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 0.024 0.054 0.096 37 -0.075 92 129
RAB3GAP2/RIMS1/UNC13B 0.05 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 0.064 0.095 123 -0.089 89 212
RAB3GAP2 0.034 0.008 -10000 0 0 25 25
STX1A/SNAP25/VAMP2 0.018 0.099 0.17 15 -0.15 81 96
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.024 0.054 0.096 37 -0.075 92 129
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 0.097 15 -0.085 42 57
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 0.099 0.17 15 -0.15 81 96
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
Arf6 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
CENTA1/KIF3B 0.013 0.035 -10000 0 -0.11 38 38
ARNO/beta Arrestin1-2 0.04 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 0.057 -10000 0 -0.14 61 61
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 38 38
EGF 0.035 0.008 -10000 0 0 24 24
somatostatin receptor activity 0 0 0.001 137 0 4 141
ARAP2 0 0 0 125 0 3 128
mol:GDP 0.068 0.065 0.15 116 -0.14 3 119
mol:PI-3-4-5-P3 0 0 0 129 0 4 133
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 64 -10000 0 64
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 0.19 126 -0.2 4 130
EGFR/EGFR/EGF/EGF/ARFGEP100 0.002 0.056 -10000 0 -0.12 59 59
ADRB2 0.033 0.01 -10000 0 0 40 40
receptor agonist activity 0 0 0 122 0 4 126
actin filament binding 0 0 0 127 0 4 131
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 0.001 152 -0.001 3 155
ARF6/GDP 0.038 0.061 0.16 16 -0.19 13 29
ARF6/GDP/GULP/ACAP1 0.056 0.072 0.19 25 -0.16 2 27
alphaIIb/beta3 Integrin/paxillin/GIT1 0.092 0.01 -10000 0 -10000 0 0
ACAP1 0 0 0 52 -10000 0 52
ACAP2 0 0 0 116 0 3 119
LHCGR/beta Arrestin2 0.029 0.025 -10000 0 -0.14 7 7
EFNA1 0.033 0.011 -10000 0 0 47 47
HGF 0.025 0.017 -10000 0 0 157 157
CYTH3 0 0 0.001 136 0 4 140
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 0 132 0 3 135
endosomal lumen acidification 0 0 0 127 0 2 129
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 0 116 0 3 119
PIP3-E 0.03 0.014 -10000 0 0 86 86
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 0.001 138 -0.001 4 142
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 0.004 0.042 -10000 0 -0.092 48 48
alphaIIb/beta3 Integrin 0.053 0.005 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.006 0.088 -9999 0 -0.17 85 85
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
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.035 0.006 -9999 0 0 15 15
Syndecan-3/Src/Cortactin -0.024 0.19 -9999 0 -0.45 72 72
Syndecan-3/Neurocan -0.065 0.18 -9999 0 -0.48 73 73
POMC 0.035 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 -0.49 74 74
Syndecan-3/IL8 -0.055 0.18 -9999 0 -0.47 74 74
PSEN1 0.033 0.01 -9999 0 0 41 41
Src/Cortactin 0.05 0.015 -9999 0 -0.14 1 1
FYN 0.03 0.014 -9999 0 0 82 82
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 -0.47 74 74
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 -0.46 74 74
IL8 0.019 0.018 -9999 0 0 233 233
Syndecan-3/Fyn/Cortactin -0.033 0.21 -9999 0 -0.5 74 74
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 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
HDAC1 0.032 0.046 0.12 64 -0.038 83 147
AES 0.03 0.041 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 62 -0.34 9 71
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 -0.34 14 38
FZD1 0.025 0.017 -10000 0 0 155 155
AXIN2 -0.024 0.093 0.12 2 -0.24 64 66
AXIN1 0.036 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 -0.58 30 30
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.13 0.24 12 -0.41 19 31
Axin1/APC/GSK3 0.005 0.092 0.21 6 -0.36 18 24
Axin1/APC/GSK3/beta catenin/Macf1 0.029 0.13 0.26 13 -0.36 31 44
HNF1A 0.007 0.03 0.071 72 -0.035 4 76
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 0.034 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 0.01 0.16 0.27 5 -0.5 29 34
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 -10000 0 -0.23 7 7
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 66 -0.035 86 152
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.016 0.14 -10000 0 -0.34 30 30
MAP3K8 0.022 0.018 -10000 0 0 182 182
FOS 0.016 0.11 -10000 0 -0.33 18 18
PRKCA 0.028 0.025 -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 -0.14 50 50
MAPK3 0.033 0.057 -10000 0 -0.34 4 4
MAP2K1 0.007 0.058 0.16 1 -0.23 12 13
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 74 133
MAPK1 0.006 0.13 -10000 0 -0.43 30 30
RAF1 -0.001 0.068 -10000 0 -0.34 16 16
KRAS 0.033 0.01 -10000 0 0 37 37
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.24 110 112
SMPD1 -0.003 0.05 0.15 1 -0.19 15 16
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 0.15 3 -0.24 107 110
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 0.19 9 -0.22 99 108
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.054 0.13 0.19 10 -0.23 111 121
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 -0.25 178 180
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 0.091 1 -0.25 111 112
CTSD 0.032 0.011 -10000 0 0 55 55
regulation of nitric oxide biosynthetic process 0.049 0.025 -10000 0 -0.14 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.023 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 0.035 0.005 -10000 0 0 10 10
CYCS -0.013 0.085 0.13 6 -0.25 34 40
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 -0.29 7 8
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 -0.14 103 110
NF kappa B1/RelA/I kappa B alpha 0.07 0.045 -10000 0 -0.12 18 18
AIFM1 -0.034 0.095 0.12 2 -0.16 121 123
BCL2 0.035 0.007 -10000 0 0 17 17
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.2 42 54
AP1 -0.012 0.074 0.083 6 -0.14 92 98
mol:PIP3 -0.021 0.048 -10000 0 -0.13 66 66
AKT1 -0.006 0.093 0.21 19 -0.24 29 48
PTK2B -0.002 0.059 0.12 4 -0.15 57 61
RHOA 0.011 0.077 0.18 13 -0.34 12 25
PIK3CB 0.035 0.006 -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 0.08 44 -0.16 54 98
endothelial cell migration -0.018 0.099 -10000 0 -0.3 53 53
ADCY4 -0.016 0.083 0.15 12 -0.24 36 48
ADCY5 -0.016 0.083 0.15 12 -0.24 36 48
ADCY6 -0.003 0.09 0.17 11 -0.24 35 46
ADCY7 -0.006 0.094 0.16 11 -0.24 42 53
ADCY1 -0.01 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 -0.24 36 48
ADCY8 -0.006 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 56 61
arachidonic acid secretion -0.021 0.11 0.15 10 -0.25 64 74
GNG2 0 0.001 0.002 2 -0.003 18 20
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 -0.2 41 55
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 -0.25 64 74
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 0.065 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 -0.012 0.058 -10000 0 -0.13 75 75
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 28 -0.26 44 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 58 74
GNAQ 0.008 0.027 0.057 37 -0.058 55 92
LPAR2 0 0.001 0.002 1 -0.003 4 5
LPAR3 0 0.001 -10000 0 -0.002 6 6
LPAR1 -0.01 0.033 -10000 0 -0.1 53 53
IL8 -0.12 0.2 0.29 13 -0.39 151 164
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 0.061 27 -0.083 56 83
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 -0.24 26 26
cell migration 0.001 0.075 -10000 0 -0.25 31 31
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 -0.26 62 70
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 -0.17 5 18
Gi(beta/gamma) -0.014 0.12 0.17 9 -0.27 60 69
mol:LPA -0.01 0.033 -10000 0 -0.1 53 53
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.082 0.13 1 -0.21 44 45
MAPKKK cascade -0.021 0.11 0.15 10 -0.25 64 74
contractile ring contraction involved in cytokinesis 0.013 0.078 0.19 13 -0.34 12 25
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 0.056 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
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.026 -10000 0 -0.051 56 56
CDKN2C -0.007 0.022 -10000 0 -0.034 104 104
CDKN2A 0.006 0.016 0.086 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 0.19 148 -0.13 5 153
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 86 86
HIF1A -0.031 0.11 -9999 0 -0.28 73 73
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 19 19
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 86 86
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 88 88
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 90 90
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 0.035 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
Syndecan-1-mediated signaling 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
TGFB1 0.032 0.012 -10000 0 0 62 62
CCL5 0.032 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 0.021 0.1 0.2 28 -0.24 12 40
Syndecan-1/Syntenin 0.028 0.11 0.21 37 -0.24 14 51
MAPK3 0.005 0.099 0.18 23 -0.22 18 41
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 12 40
Syndecan-1/RANTES 0.021 0.1 0.21 28 -0.22 12 40
Syndecan-1/CD147 0.024 0.11 0.22 14 -0.23 17 31
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 0 157 157
Syndecan-1/CASK -0.009 0.078 0.15 3 -0.22 12 15
Syndecan-1/HGF/MET 0.025 0.088 0.24 9 -0.24 5 14
regulation of cell adhesion 0.003 0.11 0.23 40 -0.22 20 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 -0.26 7 33
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 19 41
homophilic cell adhesion 0.017 0.1 0.2 30 -0.23 10 40
MMP1 0.031 0.013 -10000 0 0 71 71
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.003 0 29 -10000 0 29
GNB1/GNG2 0.036 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 -0.035 0.076 0.18 14 -0.17 70 84
T-DHT/AR 0.025 0.007 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.002 54 -0.006 73 127
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 0 245 245
mol:GDP -0.021 0.035 -10000 0 -0.15 14 14
cell proliferation -0.057 0.18 0.27 14 -0.43 80 94
PIK3CA 0.03 0.014 -10000 0 0 85 85
FOS -0.086 0.28 0.33 4 -0.69 79 83
mol:Ca2+ -0.005 0.021 -10000 0 -0.054 63 63
MAPK3 -0.041 0.13 0.26 15 -0.3 76 91
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 70 127
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 70 127
HRAS/GTP 0.042 0.066 -10000 0 -0.096 67 67
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 70 127
PI3K 0.016 0.064 -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 -0.12 7 7
HRAS/GDP 0.007 0.062 -10000 0 -0.18 15 15
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 0.19 14 -0.22 14 28
RAC1-CDC42/GDP 0.025 0.057 -10000 0 -0.17 11 11
T-DHT/AR/PELP1/Src 0.059 0.032 -10000 0 -0.12 7 7
MAP2K2 -0.038 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 -0.45 58 58
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 -0.2 67 67
CDC42 0.035 0.008 -10000 0 0 22 22
Glypican 2 network

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
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
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.014 0.06 -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 0.035 0.005 -10000 0 0 10 10
positive regulation of cell-cell adhesion 0.013 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 0.082 5 -0.24 4 9
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 -0.11 57 90
MAPK1 -0.019 0.048 0.11 30 -0.12 44 74
Syndecan-2/RACK1 0.03 0.062 0.14 2 -0.11 70 72
NF1 0.036 0.003 -10000 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.024 0.082 5 -0.24 4 9
ITGA2 0.028 0.015 -10000 0 0 108 108
MAPK8 -0.004 0.038 0.12 3 -0.37 3 6
Syndecan-2/alpha2/beta1 Integrin 0.009 0.062 0.14 1 -0.11 85 86
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 0.007 0.066 0.14 1 -0.13 70 71
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 0.016 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 -0.13 72 73
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 -0.12 47 79
FN1 0.034 0.009 -10000 0 0 29 29
Syndecan-2/IL8 -0.003 0.068 -10000 0 -0.18 55 55
SDC2 0.007 0.024 0.082 5 -0.24 4 9
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 -0.12 66 66
Syndecan-2/Ezrin 0.015 0.052 -10000 0 -0.11 63 63
PRKACA -0.02 0.048 0.11 33 -0.11 58 91
angiogenesis -0.003 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
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 39 39
JUN -0.14 0.24 0.22 1 -0.51 133 134
MAP3K7 0.002 0.051 -10000 0 -0.16 35 35
GRAP2 0.034 0.009 -10000 0 0 33 33
CRK 0.035 0.008 -10000 0 0 23 23
MAP2K4 -0.013 0.069 0.15 1 -0.23 23 24
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 -0.15 40 40
LAT/GRAP2/SLP76/HPK1/HIP-55 0.061 0.054 -10000 0 -0.11 30 30
EPO signaling pathway

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
BCL2L1 0.046 0.081 0.34 2 -0.32 1 3
CRKL 0.048 0.097 0.17 168 -10000 0 168
mol:DAG 0.017 0.063 0.2 5 -0.18 26 31
HRAS 0.053 0.11 0.24 65 -0.19 2 67
MAPK8 0.015 0.074 0.16 82 -10000 0 82
RAP1A 0.05 0.098 0.17 172 -10000 0 172
GAB1 0.041 0.092 0.17 147 -10000 0 147
MAPK14 0.025 0.089 0.16 127 -10000 0 127
EPO 0.029 0.02 -10000 0 -0.032 2 2
PLCG1 0.017 0.064 0.2 5 -0.19 26 31
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 0.17 141 -0.16 3 144
STAT1 0.022 0.068 0.24 6 -0.23 7 13
STAT5B 0.02 0.064 0.22 6 -0.2 9 15
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 0.17 172 -10000 0 172
SOCS3 0.036 0.004 -10000 0 0 5 5
STAT1 (dimer) 0.022 0.067 0.24 6 -0.22 7 13
JAK2 0.035 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 39 -10000 0 39
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 0.2 5 -0.18 26 31
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 0.16 126 -0.21 1 127
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 60 60
CRKL/CBL/C3G 0.082 0.073 0.24 37 -10000 0 37
VAV2 0.049 0.097 0.17 172 -10000 0 172
CBL 0.05 0.098 0.17 174 -10000 0 174
SHC/Grb2/SOS1 0.02 0.034 -10000 0 -0.1 9 9
STAT5A 0.02 0.063 0.22 5 -0.18 23 28
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 0.17 170 -10000 0 170
BCL2 0.047 0.083 0.31 1 -0.32 1 2
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 84 84
alphaM/beta2 Integrin/GPIbA 0.049 0.068 -10000 0 -0.12 55 55
alphaM/beta2 Integrin/proMMP-9 -0.008 0.09 -10000 0 -0.13 139 139
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 53 53
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 0.076 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 0.024 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 13 13
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 -0.3 5 10
MST1R 0.035 0.007 -10000 0 0 19 19
leukocyte activation during inflammatory response 0.051 0.061 -10000 0 -0.11 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 0.032 0.011 -10000 0 0 50 50
GP1BA 0.035 0.006 -10000 0 0 12 12
alphaM/beta2 Integrin/CTGF 0.021 0.085 -10000 0 -0.13 98 98
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 -0.24 14 14
cell adhesion 0.049 0.067 -10000 0 -0.12 55 55
NFKB1 -0.002 0.078 0.21 19 -0.2 2 21
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 -0.018 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 64 64
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 0.076 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 0.2 4 -0.29 6 10
positive regulation of phagocytosis 0.016 0.1 0.17 4 -0.24 44 48
Ron/MSP 0.05 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.086 -10000 0 -0.14 64 64
alphaM/beta2 Integrin/uPAR 0.038 0.074 -10000 0 -0.13 60 60
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 0.23 3 -0.29 5 8
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 0.088 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 -0.24 14 14
VTN 0.036 0.004 -10000 0 0 5 5
alphaM/beta2 Integrin/CYR61 0.012 0.093 -10000 0 -0.14 116 116
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 -0.14 144 150
FN1 0.034 0.009 -10000 0 0 29 29
alphaM/beta2 Integrin/Thy1 0.031 0.084 -10000 0 -0.13 85 85
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 0.22 1 -0.29 6 7
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 69 69
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 0.12 -10000 0 -0.21 61 61
SELP 0.035 0.006 -10000 0 0 14 14
IL2 signaling events mediated by STAT5

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
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 93 93
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 -0.58 31 33
SHC1 0.032 0.014 -10000 0 -0.005 57 57
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 -0.029 6 6
G1/S transition of mitotic cell cycle -0.071 0.27 0.28 13 -0.57 95 108
PTPN11 0.035 0.009 -10000 0 -0.03 7 7
CCND2 -0.071 0.19 -10000 0 -0.49 82 82
LCK 0.035 0.01 -10000 0 -0.008 23 23
GRB2 0.034 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 0.39 1 -0.8 23 24
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.012 -10000 0 0 57 57
LAT2 -0.015 0.088 -10000 0 -0.26 43 43
AP1 -0.055 0.18 -10000 0 -0.38 69 69
mol:PIP3 0.021 0.13 0.24 42 -0.28 41 83
IKBKB 0.012 0.092 0.19 36 -0.19 35 71
AKT1 -0.049 0.11 0.25 13 -0.27 45 58
IKBKG 0.01 0.091 0.18 34 -0.19 35 69
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 0.2 54 -0.22 41 95
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 12 22
PTPN13 -0.03 0.18 -10000 0 -0.59 32 32
PTPN11 0.03 0.022 -10000 0 -0.034 45 45
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.031 0.11 0.24 6 -0.31 35 41
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 0.01 0.11 0.21 7 -0.27 52 59
LAT -0.019 0.11 0.18 1 -0.27 58 59
PAK2 -0.014 0.12 0.22 13 -0.33 42 55
NFATC2 -0.012 0.013 -10000 0 -0.042 65 65
HRAS -0.015 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 67 67
Antigen/IgE/Fc epsilon R1 0.042 0.059 -10000 0 -0.093 66 66
mol:GDP -0.007 0.13 0.2 11 -0.36 44 55
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 36 72
KLRG1 -0.017 0.094 0.12 2 -0.26 45 47
VAV1 -0.018 0.1 0.16 4 -0.28 53 57
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.021 0.11 0.18 1 -0.27 61 62
negative regulation of mast cell degranulation -0.021 0.088 -10000 0 -0.25 44 44
BTK -0.009 0.13 -10000 0 -0.37 40 40
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.025 0.1 -10000 0 -0.19 109 109
GAB2/PI3K/SHP2 -0.067 0.074 -10000 0 -0.2 83 83
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.004 0.071 -10000 0 -0.18 57 57
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 94 94
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 -0.55 141 141
DUSP1 0.031 0.013 -10000 0 0 75 75
NF-kappa-B/RelA 0.018 0.065 0.13 31 -0.13 35 66
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 0.16 2 -0.27 62 64
RELA 0.035 0.005 -10000 0 0 10 10
ITK 0.003 0.036 -10000 0 -0.3 2 2
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.002 0.13 0.25 14 -0.34 41 55
cytokine secretion 0.01 0.044 0.085 26 -0.093 35 61
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 45 54
EDG1 -0.01 0.003 -10000 0 -10000 0 0
mol:DAG 0.004 0.14 0.24 34 -0.3 52 86
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 -0.25 39 49
MAP2K4 0.021 0.15 -10000 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.024 0.1 -10000 0 -0.14 121 121
mol:Choline -0.031 0.069 0.3 10 -0.17 12 22
SHC/Grb2/SOS1 0.014 0.12 0.19 1 -0.27 60 61
FYN 0.03 0.014 -10000 0 0 82 82
DOK1 0.036 0.002 -10000 0 0 2 2
PXN -0.025 0.18 -10000 0 -0.58 30 30
HCLS1 -0.022 0.12 0.16 7 -0.3 62 69
PRKCB 0.014 0.11 0.21 41 -0.22 46 87
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 0.16 7 -0.29 54 61
RASA1 0.034 0.009 -10000 0 0 30 30
mol:Phosphatidic acid -0.031 0.069 0.3 10 -0.17 12 22
IKK complex 0.008 0.077 0.18 25 -0.16 21 46
WIPF1 0 0 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.003 0.11 0.28 39 -10000 0 39
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 -0.28 39 39
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.26 48 48
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 -0.27 48 48
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 0 245 245
IL23-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
CCL2 -0.052 0.6 0.75 32 -1 120 152
IL23A 0.098 0.37 0.77 20 -0.96 20 40
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 0.72 24 -0.89 19 43
IL17F 0.04 0.27 0.5 36 -0.58 25 61
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 0.082 0.41 0.75 27 -1 30 57
IL23 0.098 0.35 0.73 17 -0.93 20 37
IL23R 0.07 0.14 0.29 86 -0.15 8 94
IL1B 0.092 0.4 0.74 30 -1.1 23 53
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.097 0.35 0.74 17 -0.87 17 34
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 46 -10000 0 46
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 74 -0.19 9 83
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 0.065 2 0 17 19
RELA 0.039 0.008 0.065 2 0 10 12
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 0.63 21 -0.87 23 44
IFNG 0.019 0.033 0.097 27 -0.08 5 32
STAT3 (dimer) 0.048 0.34 0.62 22 -0.82 25 47
IL18R1 0.035 0.008 -10000 0 -0.031 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.1 0.26 0.56 46 -0.51 16 62
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 0.74 22 -0.88 21 43
STAT3/STAT4 0.077 0.35 0.61 23 -0.85 24 47
STAT4 (dimer) 0.079 0.35 0.64 25 -0.89 23 48
IL18 0.031 0.013 -10000 0 0 69 69
IL19 0.098 0.35 0.72 20 -0.87 17 37
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 0.72 20 -0.84 21 41
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 0.074 1 -0.035 103 104
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -10000 0 -0.029 43 43
CD3E 0.095 0.35 0.74 17 -0.88 17 34
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
S1P4 pathway

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
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 -0.28 39 39
PLCG1 -0.016 0.1 -10000 0 -0.25 50 50
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 0.001 0.11 -10000 0 -0.27 39 39
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.016 0.1 -10000 0 -0.2 89 89
MAPK1 -0.009 0.095 -10000 0 -0.25 43 43
S1P/S1P5/Gi -0.014 0.1 -10000 0 -0.27 48 48
GNAI1 0.018 0.018 -10000 0 0 245 245
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 0.19 101 -0.18 3 104
S1P/S1P4/Gi -0.014 0.1 -10000 0 -0.27 48 48
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
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0 0.05 -10000 0 -10000 0 0
PLK1 -0.059 0.2 -10000 0 -0.61 24 24
CDKN1B -0.1 0.21 0.43 4 -0.36 135 139
FOXO3 -0.064 0.22 0.32 5 -0.48 82 87
KAT2B -0.001 0.021 0.048 14 -0.04 85 99
FOXO1/SIRT1 0.013 0.055 -10000 0 -0.25 10 10
CAT -0.075 0.26 -10000 0 -0.88 26 26
CTNNB1 0.035 0.007 -10000 0 0 21 21
AKT1 0.021 0.042 -10000 0 -0.059 72 72
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 81 90
response to oxidative stress 0 0.023 0.051 13 -0.044 63 76
FOXO3A/SIRT1 -0.06 0.22 0.29 4 -0.46 85 89
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 0.44 1 -0.79 80 81
YWHAQ 0.036 0.005 -10000 0 0 8 8
FOXO1/14-3-3 family 0.005 0.15 -10000 0 -0.51 21 21
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 15 79
MAPK9 0.042 0.092 0.18 118 -0.14 20 138
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 -0.77 89 93
RBL2 -0.079 0.29 -10000 0 -0.92 38 38
RAL/GDP 0.02 0.051 -10000 0 -0.12 26 26
CHUK 0.013 0.039 -10000 0 -0.058 77 77
Ran/GTP 0.018 0.025 -10000 0 -0.054 21 21
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 -0.058 91 92
CCNB1 -0.16 0.41 0.49 1 -1.1 80 81
FOXO1-3a-4/beta catenin -0.043 0.21 0.36 12 -0.38 93 105
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 -0.04 85 99
CSNK1G3 0.035 0.005 -10000 0 0 11 11
Ran/GTP/Exportin 1 0.038 0.036 -10000 0 -0.14 7 7
ZFAND5 -0.028 0.16 0.24 10 -0.31 80 90
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 82 87
BCL6 -0.099 0.33 -10000 0 -0.94 51 51
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
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 -0.014 0.12 0.24 1 -0.31 42 43
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.081 -10000 0 -0.15 75 75
AP1 -0.015 0.14 0.28 3 -0.28 79 82
ILK -0.03 0.073 0.2 2 -0.24 31 33
bone resorption -0.04 0.081 0.18 7 -0.23 32 39
PTK2B 0.035 0.006 -10000 0 0 15 15
PYK2/p130Cas 0.044 0.089 -10000 0 -0.17 51 51
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 38 45
MAPK1 -0.028 0.086 0.17 12 -0.25 37 49
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 0.18 3 -0.19 30 33
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 -10000 0 -0.99 28 28
NF kappa B1 p50/RelA 0.005 0.13 0.24 2 -0.32 38 40
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.005 -10000 0 0 10 10
alphaV beta3 Integrin 0.04 0.058 -10000 0 -0.13 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.031 0.064 0.19 2 -0.23 26 28
VAV3 -0.032 0.066 0.19 1 -0.23 31 32
MAP3K14 -0.027 0.074 0.17 5 -0.21 33 38
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 -0.023 0.073 0.14 4 -0.22 31 35
MMP2 -0.061 0.12 0.18 2 -0.32 62 64
Presenilin action in Notch and Wnt 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
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 0.069 8 -0.002 50 58
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 -0.006 26 36
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 -0.46 13 13
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 0.23 17 -0.3 8 25
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 0.24 4 -0.37 1 5
CtBP/CBP/TCF1/TLE1/AES 0.013 0.073 0.17 49 -0.18 18 67
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 0.062 9 -0.01 55 64
CTNNB1 0.044 0.088 0.22 22 -0.31 5 27
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 0.033 9 -10000 0 9
CTBP1 0.034 0.012 0.071 7 -0.005 28 35
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 0.02 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 0.23 2 -0.64 26 28
DVL1 0.016 0.091 -10000 0 -0.41 15 15
CSNK2A1 0.034 0.01 -10000 0 -0.001 32 32
MAP3K7IP1 0.032 0.017 0.063 9 -0.01 48 57
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 0.13 1 -0.21 22 23
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 -0.49 53 53
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 6 -0.018 61 67
Ephrin B reverse 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
EFNB2 0.028 0.015 -10000 0 0 110 110
EPHB2 0.034 0.01 0.055 1 0 35 36
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 -0.15 9 9
Ephrin B2/EPHB1-2 0.031 0.056 -10000 0 -0.1 51 51
neuron projection morphogenesis 0.035 0.042 -10000 0 -0.13 11 11
Ephrin B1/EPHB1-2/Tiam1 0.056 0.049 -10000 0 -0.1 27 27
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 27 27
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 0.23 -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 -0.14 9 9
angiogenesis -0.045 0.17 -10000 0 -0.57 47 47
LCK -0.048 0.22 -10000 0 -0.72 48 48
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.041 0.01 -10000 0 -0.041 1 1
NFATC2 0.014 0.16 0.27 5 -0.36 40 45
NFATC3 0.02 0.13 0.26 25 -0.24 68 93
CD40LG -0.011 0.34 0.49 46 -0.69 67 113
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 0.38 13 -0.62 52 65
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 0.26 9 -0.24 1 10
TLE4 0.011 0.11 -10000 0 -0.32 21 21
Jun/NFAT1-c-4/p21SNFT -0.018 0.32 0.44 2 -0.72 67 69
AP-1/NFAT1-c-4 -0.042 0.34 -10000 0 -0.78 63 63
IKZF1 0.007 0.1 0.16 8 -0.24 38 46
T-helper 2 cell differentiation -0.079 0.23 -10000 0 -0.62 39 39
AP-1/NFAT1 0.015 0.15 0.28 19 -0.28 47 66
CALM1 0.045 0.023 0.13 2 -10000 0 2
EGR2 -0.069 0.41 0.49 13 -0.97 71 84
EGR3 -0.054 0.42 0.48 19 -0.98 67 86
NFAT1/FOXP3 0.038 0.12 0.26 2 -0.27 30 32
EGR1 0.029 0.015 0.07 1 0 103 104
JUN 0.033 0.042 0.11 36 -0.049 15 51
EGR4 0.036 0.004 0.07 1 0 5 6
mol:Ca2+ 0.005 0.003 -10000 0 -10000 0 0
GBP3 0.007 0.1 0.16 8 -0.24 38 46
FOSL1 0.032 0.012 -10000 0 0 56 56
NFAT1-c-4/MAF/IRF4 0.011 0.33 -10000 0 -0.71 70 70
DGKA 0.012 0.1 -10000 0 -0.29 23 23
CREM 0.027 0.015 -10000 0 0 121 121
NFAT1-c-4/PPARG -0.004 0.32 -10000 0 -0.72 69 69
CTLA4 0.01 0.093 -10000 0 -0.26 22 22
NFAT1-c-4 (dimer)/EGR1 -0.027 0.34 -10000 0 -0.76 70 70
NFAT1-c-4 (dimer)/EGR4 0.004 0.33 -10000 0 -0.73 69 69
FOS 0.024 0.038 0.1 32 -0.042 51 83
IFNG -0.01 0.13 -10000 0 -0.42 16 16
T cell activation -0.01 0.22 0.42 5 -0.56 28 33
MAF 0.034 0.009 -10000 0 0 34 34
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.28 0.6 67 -0.45 19 86
TNF -0.036 0.31 0.38 15 -0.7 71 86
FASLG -0.094 0.46 0.55 2 -1.1 70 72
TBX21 0.04 0.007 0.11 3 -10000 0 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.027 0.017 -10000 0 -10000 0 0
PTPN1 0.008 0.12 -10000 0 -0.34 26 26
NFAT1-c-4/ICER1 -0.026 0.32 -10000 0 -0.73 69 69
GATA3 0.027 0.017 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.004 0.14 -10000 0 -0.42 16 16
IL2RA -0.066 0.24 0.33 3 -0.6 58 61
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.009 0.11 -10000 0 -0.35 23 23
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 -0.69 63 66
CSF2 -0.011 0.34 0.49 46 -0.69 67 113
JunB/Fra1/NFAT1-c-4 -0.019 0.3 -10000 0 -0.71 66 66
IL4 -0.083 0.23 -10000 0 -0.65 38 38
IL5 -0.012 0.34 0.49 46 -0.69 67 113
IL2 -0.011 0.22 0.43 2 -0.56 28 30
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 -0.6 67 86
CDK4 -0.015 0.28 0.6 29 -1 14 43
PTPRK -0.004 0.14 -10000 0 -0.44 37 37
IL8 -0.1 0.29 0.45 8 -0.73 64 72
POU2F1 0.039 0.008 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0 0.11 0.26 3 -0.3 31 34
IKBKB 0.016 0.079 0.26 4 -0.27 10 14
AKT1 0.003 0.089 0.21 38 -0.18 17 55
IKBKG 0.011 0.073 0.23 2 -0.25 11 13
CALM1 -0.024 0.13 0.23 4 -0.37 38 42
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+ -0.022 0.13 0.24 5 -0.39 38 43
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 30 30
CAMK2G -0.016 0.12 0.22 5 -0.36 38 43
CSNK2A1 0.034 0.009 -10000 0 0 31 31
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.008 0.064 -10000 0 -0.15 52 52
GO:0007205 -0.022 0.14 0.24 5 -0.39 38 43
SYK 0.031 0.013 -10000 0 0 71 71
ELK1 -0.027 0.13 0.24 3 -0.38 38 41
NFATC1 -0.017 0.091 0.23 5 -0.26 33 38
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 0.22 4 -0.33 40 44
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 0.24 4 -0.37 39 43
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 14 16
GRB2 0.035 0.006 -10000 0 0 16 16
PI3K/BCAP/CD19 -0.033 0.16 0.37 1 -0.43 40 41
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 -0.022 0.14 0.25 4 -0.4 37 41
CSK 0.035 0.007 -10000 0 0 17 17
FOS -0.025 0.13 0.2 9 -0.37 39 48
CHUK -0.048 0.13 0.23 2 -0.26 107 109
IBTK 0.034 0.008 -10000 0 0 24 24
CARD11/BCL10/MALT1/TAK1 0.001 0.13 0.28 2 -0.34 37 39
PTPN6 -0.02 0.086 0.15 4 -0.3 29 33
RELA 0.036 0.005 -10000 0 0 10 10
BCL2A1 0.018 0.033 0.089 12 -0.091 18 30
VAV2 -0.013 0.097 -10000 0 -0.3 32 32
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 0.25 9 -0.31 23 32
SH3BP5 0.033 0.011 -10000 0 0 47 47
PIK3AP1 -0.021 0.14 0.25 4 -0.42 37 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.03 0.18 -10000 0 -0.53 43 43
RAF1 -0.026 0.11 0.21 8 -0.32 42 50
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 -0.3 34 39
MAPK1 -0.03 0.1 0.21 7 -0.31 34 41
CD72/SHP1 0.007 0.1 0.25 14 -0.28 30 44
NFKB1 0.035 0.007 -10000 0 0 17 17
MAPK8 0.019 0.11 0.25 10 -0.31 21 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 22 23
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 0.14 0.23 4 -0.37 47 51
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.02 0.14 -10000 0 -0.44 28 28
DAPP1 0 0.14 -10000 0 -0.47 27 27
cytokine secretion -0.015 0.087 0.23 5 -0.24 33 38
mol:DAG -0.022 0.14 0.25 4 -0.4 37 41
PLCG2 0.032 0.012 -10000 0 0 60 60
MAP2K1 -0.03 0.11 0.2 6 -0.31 40 46
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.072 -10000 0 -0.12 86 86
mol:PI-3-4-5-P3 -0.015 0.074 0.19 22 -0.21 15 37
ETS1 -0.024 0.11 0.21 5 -0.34 36 41
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 -0.29 31 31
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 0.23 22 -0.31 17 39
B-cell antigen/BCR complex/LYN/SYK 0.025 0.1 0.26 1 -0.27 27 28
CARD11 -0.021 0.13 0.23 5 -0.37 38 43
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 0.059 0.16 23 -0.16 13 36
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 -0.081 20 27
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.18 81 81
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 -0.17 85 85
CSNK1A1 0.035 0.006 -10000 0 0 12 12
GNAS -0.016 0.081 -10000 0 -0.17 83 83
GO:0007205 -0.02 0.084 0.18 3 -0.25 27 30
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
IL2 signaling events mediated by PI3K

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
BCL2L1 0.004 0.093 -10000 0 -0.36 4 4
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 0.3 7 -0.41 59 66
FRAP1 -0.034 0.2 0.32 7 -0.47 59 66
FOXO3 -0.034 0.2 0.3 7 -0.46 62 69
AKT1 -0.04 0.21 0.31 4 -0.5 61 65
GAB2 0.029 0.019 -10000 0 -0.012 76 76
SMPD1 0.002 0.095 -10000 0 -0.52 13 13
SGMS1 -0.004 0.034 0.061 20 -0.07 66 86
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.029 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 0.27 10 -0.4 66 76
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 26 -0.01 44 70
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 -0.067 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 0.24 8 -0.38 48 56
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 -0.38 47 53
Rac1/GDP 0.005 0.052 0.11 4 -0.13 48 52
T cell proliferation -0.023 0.14 0.24 6 -0.35 47 53
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 0.24 6 -0.37 47 53
NF kappa B1 p50/RelA -0.013 0.19 0.31 6 -0.42 59 65
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 0.035 0.005 -10000 0 0 10 10
IL2RA 0.021 0.021 -10000 0 -0.004 189 189
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 0.007 32 -0.009 43 75
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 0.24 6 -0.35 47 53
GRB2 0.032 0.016 -10000 0 -0.018 42 42
IL2 0.035 0.016 -10000 0 -0.029 23 23
PIK3CA 0.028 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 0.33 1 -0.45 27 28
EPHB forward signaling

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
Ephrin A5/EPHB2 0.045 0.013 -10000 0 -10000 0 0
cell-cell adhesion 0.032 0.041 0.19 14 -10000 0 14
Ephrin B/EPHB2/RasGAP 0.058 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 61 61
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 15 -10000 0 15
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 -0.19 10 24
lamellipodium assembly -0.032 0.041 -10000 0 -0.19 14 14
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.071 -10000 0 -0.18 48 48
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 0.05 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 0.043 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 -0.26 16 18
MAPK1 -0.009 0.073 0.17 3 -0.26 20 23
Rac1/GDP -0.002 0.1 0.26 23 -0.23 32 55
actin cytoskeleton reorganization -0.039 0.06 -10000 0 -0.2 37 37
CDC42/GDP 0.03 0.13 0.23 88 -0.23 34 122
PI3K 0.024 0.076 -10000 0 -0.14 61 61
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 0.078 0.53 8 -0.2 14 22
MAP4K4 -0.006 0.068 0.24 18 -0.2 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 -0.18 52 52
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 0.23 2 -0.27 21 23
NRAS 0.032 0.012 -10000 0 0 58 58
SYNJ1 -0.026 0.056 0.19 12 -0.19 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 0.032 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 -0.27 4 9
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 -0.26 7 113
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 -0.21 42 42
Rac1/GTP -0.031 0.046 -10000 0 -0.2 14 14
Ephrin B/EPHB1/Src/Paxillin 0.008 0.066 -10000 0 -0.15 56 56
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.043 0.042 -10000 0 -0.14 23 23
AKT1 -0.019 0.17 0.27 12 -0.42 45 57
PTK2B -0.005 0.11 0.21 39 -0.37 12 51
VEGFR2 homodimer/Frs2 0.025 0.082 -10000 0 -0.32 16 16
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 0.28 23 -0.37 29 52
mol:Ca2+ 0.002 0.12 0.21 73 -0.32 20 93
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.022 0.091 -10000 0 -0.28 22 22
RP11-342D11.1 -0.013 0.095 0.15 45 -0.23 46 91
CDH5 0.03 0.014 -10000 0 0 83 83
VEGFA homodimer 0.035 0.034 -10000 0 -0.094 14 14
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 0.035 0.12 -10000 0 -0.27 35 35
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 0.3 15 -0.33 17 32
eNOS/Hsp90 0.023 0.11 0.28 15 -0.31 17 32
PIK3R1 0.032 0.012 -10000 0 0 61 61
mol:IP3 0.002 0.12 0.21 73 -0.32 20 93
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 -0.28 24 25
PTPN6 0.032 0.011 -10000 0 0 50 50
EPAS1 0.03 0.062 -10000 0 -0.24 15 15
mol:L-citrulline 0.025 0.12 0.3 15 -0.33 17 32
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 -0.3 19 20
VEGFR2 homodimer/VEGFA homodimer 0.012 0.098 -10000 0 -0.25 46 46
VEGFR2/3 heterodimer 0.026 0.083 -10000 0 -0.32 17 17
VEGFB 0.036 0.005 -10000 0 0 9 9
MAPK11 0.004 0.13 0.28 28 -0.33 21 49
VEGFR2 homodimer -0.003 0.083 0.18 2 -0.39 14 16
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 33 -0.3 19 52
MAPK1 0.008 0.12 0.26 38 -0.3 21 59
VEGFA145/NRP2 0.022 0.022 -10000 0 -0.046 7 7
VEGFR1/2 heterodimer 0.024 0.083 -10000 0 -0.33 16 16
KDR -0.003 0.083 0.18 2 -0.39 14 16
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 0.26 9 -0.36 36 45
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.014 0.083 0.19 1 -0.29 19 20
FES 0.002 0.12 0.24 48 -0.34 17 65
GAB1 0.01 0.12 0.23 15 -0.37 23 38
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.083 -10000 0 -0.3 19 19
CTNNB1 0.035 0.007 -10000 0 0 21 21
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.035 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 0.26 18 -0.4 43 61
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.058 0.095 -10000 0 -0.28 17 17
PRKACA 0.034 0.009 -10000 0 0 29 29
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.08 -10000 0 -0.29 15 15
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.001 0.12 0.24 46 -0.34 17 63
actin cytoskeleton reorganization 0.015 0.082 0.19 1 -0.3 18 19
PTK2 0.006 0.13 0.24 16 -0.47 18 34
EDG1 -0.005 0.13 0.22 63 -0.35 27 90
mol:DAG 0.002 0.12 0.21 73 -0.32 20 93
CaM/Ca2+ 0.019 0.12 0.25 24 -0.24 47 71
MAP2K3 -0.004 0.12 0.23 45 -0.34 16 61
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.033 0.13 0.22 73 -0.3 43 116
PLCG1 0.002 0.12 0.21 73 -0.33 20 93
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.033 0.089 -10000 0 -0.29 18 18
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 0.014 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 0.24 18 -0.4 27 45
mol:PI-3-4-5-P3 -0.006 0.13 0.25 13 -0.34 36 49
FYN 0.03 0.014 -10000 0 0 82 82
VEGFB/NRP1 0.001 0.12 0.2 72 -0.33 17 89
mol:NO 0.025 0.12 0.3 15 -0.33 17 32
PXN 0.036 0.004 -10000 0 0 5 5
HRAS/GTP -0.044 0.07 -10000 0 -0.24 45 45
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 0.32 12 -0.36 17 29
VEGFR2 homodimer/VEGFA homodimer/Sck 0.007 0.093 -10000 0 -0.29 28 28
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCA -0.004 0.12 0.22 49 -0.31 20 69
PRKCB 0 0.12 0.22 48 -0.31 20 68
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 0.022 0.022 -10000 0 -0.046 7 7
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 -0.45 18 30
MAP3K13 0.002 0.12 0.21 71 -0.35 16 87
PDPK1 -0.023 0.12 0.23 23 -0.34 31 54
Lissencephaly gene (LIS1) in neuronal migration and development

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
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 -0.24 15 15
p35/CDK5 -0.018 0.072 0.2 26 -0.22 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 32 -0.27 26 58
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 0.28 106 -0.27 16 122
LIS1/IQGAP1 0.014 0.059 -10000 0 -0.15 49 49
RHOA -0.007 0.068 -10000 0 -0.33 14 14
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 77 -0.26 22 99
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 -0.22 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 -0.19 19 19
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.032 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 82 82
ITGA3 0.032 0.011 -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 24 24
long-term memory 0.043 0.062 -10000 0 -0.12 28 28
DAB1/LIS1 0.046 0.073 -10000 0 -0.13 35 35
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 35 -0.19 1 36
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 -0.28 31 72
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
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.016 0.11 0.22 4 -0.35 30 34
adherens junction organization 0.002 0.074 0.17 2 -0.3 19 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.11 0.19 58 -0.28 20 78
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 -0.32 24 24
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.026 0.065 -10000 0 -0.44 4 4
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 4 -0.26 15 19
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 -0.27 15 16
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -10000 0 -0.12 2 2
mol:PI-3-4-5-P3 0.02 0.09 -10000 0 -0.29 23 23
PIK3CA 0.03 0.015 -10000 0 -0.002 89 89
PI3K 0.02 0.092 -10000 0 -0.29 23 23
FYN -0.035 0.13 0.22 1 -0.31 69 70
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 0.19 88 -0.28 19 107
establishment of polarity of embryonic epithelium 0.004 0.061 0.15 4 -0.26 16 20
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 23 49
RhoA/GTP 0.012 0.085 -10000 0 -0.26 25 25
AKT2 -0.004 0.076 0.14 1 -0.27 23 24
actin cable formation 0 0.06 0.15 4 -0.25 16 20
apoptosis 0.008 0.098 0.33 27 -0.22 4 31
CTNNA1 0.035 0.008 -10000 0 -0.002 19 19
mol:GDP -0.017 0.068 0.16 7 -0.28 18 25
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
ErbB2/ErbB3 signaling events

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
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 0.19 18 -0.2 4 22
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 -0.17 16 23
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.077 0.21 13 -0.12 77 90
AKT1 -0.009 0.009 0.014 39 -10000 0 39
BAD -0.015 0.007 0.011 4 -10000 0 4
MAPK10 0.004 0.074 0.17 39 -0.16 12 51
mol:GTP 0 0.001 0.003 2 -0.005 24 26
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.077 0.19 6 -0.19 14 20
RAF1 -0.015 0.1 0.23 12 -0.24 31 43
ErbB2/ErbB3/neuregulin 2 0.003 0.071 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 15 -0.004 62 77
cell proliferation -0.036 0.24 0.37 3 -0.57 57 60
FOS -0.027 0.2 0.33 10 -0.42 87 97
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 39 42
MAPK1 -0.039 0.22 0.34 3 -0.57 51 54
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 0.18 48 -0.14 5 53
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 0.011 4 -10000 0 4
RAC1-CDC42/GTP -0.023 0.046 -10000 0 -0.13 49 49
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.008 0.014 3 -10000 0 3
CHRNA1 -0.003 0.15 0.31 6 -0.37 40 46
myelination -0.025 0.082 0.23 19 -0.21 4 23
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 7 7
MAP2K2 -0.022 0.1 0.22 14 -0.24 34 48
SRC 0.035 0.006 -10000 0 0 13 13
mol:cAMP -0.001 0.001 0.003 11 -0.004 1 12
PTPN11 -0.028 0.079 0.17 14 -0.21 6 20
MAP2K1 -0.033 0.2 -10000 0 -0.57 33 33
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 39 39
nervous system development -0.03 0.07 0.17 4 -0.18 14 18
CDC42 0.035 0.008 -10000 0 0 22 22
Regulation of nuclear SMAD2/3 signaling

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
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 9 -0.16 19 28
AKT1 0.03 0.019 -10000 0 -0.029 29 29
GSC 0.004 0.031 0.096 22 -0.063 2 24
NKX2-5 0.033 0.017 0.071 9 -0.059 12 21
muscle cell differentiation -0.019 0.13 0.31 44 -10000 0 44
SMAD2-3/SMAD4/SP1 0.051 0.14 0.32 5 -0.25 44 49
SMAD4 0.021 0.056 0.14 2 -0.13 33 35
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 -0.11 138 138
SMAD3/SMAD4/VDR 0.043 0.12 -10000 0 -0.2 36 36
MYC 0.028 0.014 -10000 0 -10000 0 0
CDKN2B -0.2 0.19 -10000 0 -0.53 30 30
AP1 -0.002 0.1 0.21 2 -0.24 44 46
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.007 0.13 -10000 0 -0.39 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.081 -10000 0 -0.28 28 28
SP3 0.035 0.015 0.079 14 -0.051 8 22
CREB1 0.036 0.004 -10000 0 0 6 6
FOXH1 0.034 0.014 0.072 10 -0.053 9 19
SMAD3/SMAD4/GR 0.038 0.091 0.24 2 -0.18 21 23
GATA3 0.028 0.018 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.094 -10000 0 -0.3 27 27
MEF2C/TIF2 -0.013 0.08 0.22 20 -0.23 15 35
endothelial cell migration 0.2 0.49 1.2 98 -10000 0 98
MAX 0.027 0.042 0.084 85 -0.053 85 170
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 0.084 80 -0.053 86 166
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 13 13
SMAD2/SMAD2/SMAD4/FOXH1 0.047 0.076 0.2 2 -0.16 31 33
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 -0.16 28 29
SMAD3/SMAD4/ATF3 0.017 0.1 -10000 0 -0.18 66 66
SAP30 0.035 0.006 -10000 0 0 15 15
Cbp/p300/PIAS3 0.04 0.073 -10000 0 -0.095 89 89
JUN -0.013 0.099 0.2 10 -0.26 39 49
SMAD3/SMAD4/IRF7 0.042 0.09 0.22 1 -0.17 29 30
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 0.16 32 -0.21 1 33
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 0.23 3 -0.17 14 17
Cbp/p300/SNIP1 0.043 0.057 -10000 0 -0.068 65 65
ZBTB17 0.035 0.006 -10000 0 -10000 0 0
LAMC1 -0.033 0.1 0.16 10 -0.31 38 48
TGIF2/HDAC complex/SMAD3/SMAD4 0.039 0.085 0.22 1 -0.16 37 38
IRF7 0.034 0.01 -10000 0 -10000 0 0
ESR1 0.041 0.032 0.12 61 -0.001 35 96
HNF4A 0.035 0.006 -10000 0 0 15 15
MEF2C -0.02 0.075 0.21 22 -0.23 16 38
SMAD2-3/SMAD4 0.041 0.094 0.24 1 -0.2 27 28
Cbp/p300/Src-1 0.032 0.075 -10000 0 -0.11 70 70
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 -0.043 101 101
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 50 50
SNIP1 0.036 0.007 -10000 0 0 12 12
GCN5L2 0.021 0.034 -10000 0 -0.045 95 95
SMAD3/SMAD4/TFE3 0.031 0.12 0.26 4 -0.23 48 52
MSG1/HSC70 0.008 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 2 -0.12 41 43
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.072 -10000 0 -0.2 30 30
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 42 46
IFNB1 -0.004 0.06 0.16 8 -0.18 5 13
SMAD3/SMAD4/MEF2C 0.03 0.093 0.24 5 -0.24 17 22
CITED1 0.025 0.017 -10000 0 0 146 146
SMAD2-3/SMAD4/ARC105 0.041 0.085 0.22 2 -0.18 25 27
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.1 -10000 0 -0.35 25 25
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 0.21 2 -0.47 107 109
IL10 -0.01 0.063 0.17 10 -0.19 4 14
PIASy/HDAC complex 0.027 0.03 0.07 19 -0.03 84 103
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 0.17 11 -0.19 3 14
CDK4 0.021 0.03 -10000 0 -0.045 63 63
PIAS4 0.027 0.03 0.07 18 -0.03 84 102
ATF3 0.027 0.016 -10000 0 0 120 120
SMAD3/SMAD4/SP1 0.029 0.14 0.32 2 -0.25 52 54
FOXG1 0.001 0.007 0.023 21 -10000 0 21
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 0.21 22 -0.23 16 38
CEBPB 0.032 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.023 0.073 0.19 1 -0.14 47 48
MYOD1 0.036 0.004 -10000 0 0 6 6
SMAD3/SMAD4/HNF4 0.039 0.086 0.22 1 -0.16 28 29
SMAD3/SMAD4/GATA3 0.033 0.085 -10000 0 -0.17 21 21
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 28 29
ITGB5 -0.029 0.1 0.21 11 -0.26 39 50
TGIF/SIN3/HDAC complex/CtBP -0.005 0.097 -10000 0 -0.32 28 28
SMAD3/SMAD4/AR 0.038 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 0.17 2 -0.3 58 60
SMAD3/SMAD4/MYOD 0.041 0.086 0.22 1 -0.17 27 28
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 0.057 0.097 0.24 1 -0.19 27 28
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.097 -10000 0 -0.32 27 27
TFDP1 0.033 0.011 -10000 0 0 49 49
SMAD3/SMAD4/AP1 0.02 0.12 0.24 3 -0.25 41 44
SMAD3/SMAD4/RUNX2 0.041 0.086 0.22 1 -0.16 32 33
TGIF2 0.034 0.009 -10000 0 0 30 30
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.035 0.005 -10000 0 0 10 10
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.088 0.22 30 -0.2 12 42
TBX21 0.072 0.2 0.56 6 -0.58 3 9
B2M 0.035 0.007 -10000 0 0 19 19
TYK2 0.035 0.039 0.12 14 -0.054 11 25
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 0.11 21 -0.053 15 36
GADD45G 0.093 0.19 0.54 8 -0.55 3 11
natural killer cell activation 0.012 0.024 0.054 75 -0.036 11 86
RELB 0.034 0.009 -10000 0 0 33 33
RELA 0.035 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 0 162 162
IFNG 0.034 0.009 -10000 0 0 32 32
STAT3 (dimer) 0.076 0.22 0.45 26 -0.52 24 50
HLA-DRB5 -0.001 0.009 -10000 0 -0.023 45 45
FASLG 0.077 0.2 0.5 13 -0.52 9 22
NF kappa B2 p52/RelB 0.057 0.19 0.42 13 -0.46 16 29
CD4 0.024 0.027 -10000 0 -0.039 56 56
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 0.028 -10000 0 -0.042 64 64
CD3E 0.027 0.027 -10000 0 -0.036 74 74
CD3G 0.026 0.029 -10000 0 -0.042 67 67
IL12Rbeta2/JAK2 0.053 0.058 0.18 15 -10000 0 15
CCL3 0.074 0.2 0.45 28 -0.47 16 44
CCL4 0.044 0.33 0.56 17 -1 30 47
HLA-A 0.035 0.007 -10000 0 0 19 19
IL18/IL18R 0.088 0.064 0.21 28 -0.12 7 35
NOS2 0.076 0.19 0.42 35 -0.43 16 51
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.087 0.22 27 -0.21 11 38
IL1R1 0.074 0.2 0.53 12 -0.55 5 17
IL4 0.003 0.048 -10000 0 -0.074 74 74
JAK2 0.033 0.037 0.11 12 -0.05 20 32
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 0.096 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 31 -0.49 15 46
STAT5A (dimer) 0.079 0.19 0.42 14 -0.47 16 30
GZMA 0.072 0.2 0.54 12 -0.55 5 17
GZMB 0.071 0.2 0.56 11 -0.54 6 17
HLX 0 0 -10000 0 -10000 0 0
LCK 0.058 0.2 0.45 27 -0.49 16 43
TCR/CD3/MHC II/CD4 -0.021 0.12 0.16 22 -0.2 117 139
IL2/IL2R 0.058 0.049 -10000 0 -10000 0 0
MAPK14 0.099 0.22 0.5 21 -0.62 18 39
CCR5 0.079 0.18 0.39 39 -0.39 17 56
IL1B 0.029 0.037 0.11 7 -0.05 27 34
STAT6 0.046 0.1 0.28 16 -0.44 3 19
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 21 -0.051 27 48
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 0.2 12 -0.22 30 42
IL2RB 0.032 0.011 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.2 0.44 34 -0.46 15 49
IL2RG 0.034 0.008 -10000 0 0 24 24
IL12 0.062 0.059 0.18 22 -10000 0 22
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 -0.051 32 46
IL12/IL12R/TYK2/JAK2 0.064 0.21 0.5 24 -0.51 16 40
MAP2K3 0.093 0.22 0.48 23 -0.62 18 41
RIPK2 0.035 0.005 -10000 0 0 11 11
MAP2K6 0.097 0.22 0.49 20 -0.58 18 38
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 0.038 0.019 0.086 2 -0.04 19 21
IL12Rbeta1/TYK2 0.047 0.063 0.17 7 -0.15 15 22
EOMES -0.02 0.038 0.074 2 -0.098 48 50
STAT1 (dimer) 0.085 0.19 0.44 24 -0.44 13 37
T cell proliferation 0.08 0.18 0.4 35 -0.41 18 53
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 0.09 0.21 0.46 21 -0.59 18 39
Signaling events mediated by PTP1B

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
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 -0.25 48 48
FYN 0.03 0.014 -10000 0 0 82 82
p210 bcr-abl/PTP1B -0.011 0.11 0.17 1 -0.27 42 43
EGFR 0.009 0.017 -10000 0 -0.03 3 3
EGF/EGFR -0.033 0.09 -10000 0 -0.28 38 38
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 52 52
Insulin Receptor/Insulin 0.018 0.11 -10000 0 -0.26 33 33
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 0.026 0.024 -10000 0 -0.022 89 89
YES1 0.033 0.01 -10000 0 0 37 37
CAV1 0.005 0.14 0.22 27 -0.28 51 78
TXN 0.034 0.01 -10000 0 0 38 38
PTP1B/IRS1/GRB2 0.007 0.12 -10000 0 -0.28 40 40
cell migration 0.011 0.11 0.27 42 -0.17 1 43
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 -0.25 44 45
Crk/p130 Cas -0.002 0.11 -10000 0 -0.25 46 46
DOK1 -0.008 0.1 0.18 6 -0.29 32 38
JAK2 -0.01 0.12 -10000 0 -0.34 42 42
Jak2/Leptin Receptor/Leptin -0.009 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 -0.27 42 43
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 0.17 0.26 13 -0.37 58 71
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 -0.28 39 39
mol:H2O2 0.003 0.005 0.021 5 -10000 0 5
STAT3 (dimer) -0.007 0.11 -10000 0 -0.29 30 30
negative regulation of transcription -0.009 0.12 -10000 0 -0.33 42 42
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 5 -0.36 56 61
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 -0.27 49 49
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 0.17 1 -0.29 26 27
STAT5A -0.003 0.1 -10000 0 -0.3 25 25
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 -0.47 57 57
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 0 78 78
Glypican 1 network

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
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 0.05 0.053 -10000 0 -0.12 34 34
SERPINC1 0.035 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 -0.036 0.12 0.18 11 -0.3 58 69
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 0.035 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-dependent events mediated by a4b1

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
CRKL 0.034 0.008 -9999 0 0 25 25
Rac1/GDP 0.027 0.02 -9999 0 -0.024 14 14
DOCK1 0.023 0.017 -9999 0 0 178 178
ITGA4 0.035 0.006 -9999 0 0 12 12
RAC1 0.027 0.016 -9999 0 0 123 123
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.035 0.008 -9999 0 0 23 23
alpha4/beta1 Integrin 0.053 0.033 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.051 0.018 -9999 0 -10000 0 0
lamellipodium assembly -0.051 0.15 -9999 0 -0.36 72 72
PIK3CA 0.03 0.014 -9999 0 0 85 85
PI3K 0.016 0.075 -9999 0 -0.16 73 73
ARF6 0.035 0.007 -9999 0 0 21 21
TLN1 0.029 0.014 -9999 0 0 94 94
PXN -0.021 0.006 -9999 0 -10000 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
ARF6/GTP 0.052 0.047 -9999 0 -0.11 1 1
cell adhesion 0.046 0.049 -9999 0 -0.12 12 12
CRKL/CBL 0.05 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.026 -9999 0 -10000 0 0
ITGB1 0.027 0.016 -9999 0 0 118 118
ITGB7 0.035 0.005 -9999 0 0 10 10
ARF6/GDP 0.034 0.016 -9999 0 -0.025 16 16
alpha4/beta1 Integrin/Paxillin/VCAM1 0.014 0.077 -9999 0 -0.11 104 104
p130Cas/Crk/Dock1 0.026 0.036 -9999 0 -0.12 17 17
VCAM1 0.022 0.018 -9999 0 0 186 186
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.051 -9999 0 -0.12 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.046 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP -0.053 0.045 -9999 0 -10000 0 0
CBL 0.036 0.004 -9999 0 0 6 6
PRKACA 0.034 0.009 -9999 0 0 29 29
GIT1 0.036 0.003 -9999 0 0 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.051 -9999 0 -0.12 12 12
Rac1/GTP -0.058 0.16 -9999 0 -0.4 72 72
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.013 0.18 -10000 0 -0.81 22 22
regulation of axonogenesis 0.002 0.063 0.22 31 -10000 0 31
myoblast fusion -0.016 0.093 0.35 26 -0.18 3 29
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 57 -0.16 2 59
ARF1/GTP 0.035 0.061 -10000 0 -0.14 45 45
mol:GM1 0.004 0.046 0.088 1 -0.14 41 42
mol:Choline -0.014 0.04 0.083 4 -0.13 36 40
lamellipodium assembly -0.007 0.1 -10000 0 -0.37 32 32
MAPK3 0.014 0.079 0.14 35 -0.22 38 73
ARF6/GTP/NME1/Tiam1 0.028 0.073 0.16 2 -0.15 57 59
ARF1 0.035 0.007 -10000 0 0 21 21
ARF6/GDP 0.016 0.093 0.18 3 -0.35 26 29
ARF1/GDP 0.016 0.099 0.18 1 -0.28 42 43
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 0.14 34 -0.3 22 56
actin filament bundle formation -0.021 0.1 0.29 42 -10000 0 42
KALRN 0.006 0.069 0.12 3 -0.26 27 30
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 31 31
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 31 31
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 31 31
mol:Phosphatidic acid -0.014 0.04 0.083 4 -0.13 36 40
Rac1/GTP -0.008 0.1 -10000 0 -0.38 32 32
mTOR signaling 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
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 0.092 3 -0.22 22 25
FRAP1 0.024 0.1 0.26 1 -0.44 17 18
AKT1 0.004 0.1 0.17 81 -0.25 30 111
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 0.2 47 -0.25 30 77
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.049 -10000 0 -0.17 25 25
TSC2 0.034 0.008 -10000 0 0 26 26
RHEB/GDP 0.005 0.079 -10000 0 -0.22 32 32
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 4 -0.2 23 27
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.085 0.25 13 -0.27 7 20
MAP3K5 -0.023 0.082 0.17 1 -0.23 64 65
PIK3R1 0.032 0.012 -10000 0 0 61 61
apoptosis -0.023 0.082 0.17 1 -0.23 64 65
mol:LY294002 0 0 0.001 18 -0.001 21 39
EIF4B 0.024 0.083 0.24 16 -0.27 7 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.072 0.23 9 -0.23 6 15
eIF4E/eIF4G1/eIF4A1 0.007 0.077 -10000 0 -0.29 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.082 -10000 0 -0.21 37 37
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.065 0.19 13 -0.19 13 26
FKBP1A 0.033 0.011 -10000 0 0 46 46
RHEB/GTP 0.02 0.092 0.25 7 -0.23 29 36
mol:Amino Acids 0 0 0.001 18 -0.001 21 39
FKBP12/Rapamycin 0.021 0.025 -10000 0 -0.13 11 11
PDPK1 -0.022 0.061 0.15 16 -0.22 21 37
EIF4E 0.034 0.009 -10000 0 0 35 35
ASK1/PP5C -0.028 0.23 -10000 0 -0.56 72 72
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.01 0.094 -10000 0 -0.31 31 31
TSC1/TSC2 0.031 0.12 0.22 47 -0.27 30 77
tumor necrosis factor receptor activity 0 0 0.001 21 -0.001 18 39
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 0.06 -10000 0 -0.26 23 23
INS 0.035 0.006 -10000 0 0 15 15
PTEN 0.026 0.016 -10000 0 0 130 130
PDK2 -0.022 0.061 0.15 16 -0.22 21 37
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 -0.4 17 19
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 30 -0.002 18 48
EEF2 -0.019 0.018 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.011 0.25 -10000 0 -1.1 26 26
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.022 0.055 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 -0.046 0.19 0.24 2 -0.49 56 58
mol:DAG -0.012 0.091 0.19 21 -0.21 42 63
HRAS 0.034 0.019 0.085 1 -0.032 24 25
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 60 60
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 -0.2 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 82 82
ARF6 0.035 0.007 -10000 0 0 21 21
FGR 0.032 0.011 -10000 0 0 52 52
mol:Ca2+ 0.004 0.062 0.16 30 -0.13 11 41
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 0.18 24 -0.17 18 42
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 15 -0.21 31 46
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 21 -0.31 23 44
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 -0.051 0.16 -10000 0 -0.35 79 79
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 71 71
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 -0.2 11 29
ARAP3/RAP1A/GTP -0.023 0.056 0.16 21 -0.2 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 -0.41 43 44
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 0.23 14 -0.28 48 62
LCK 0.035 0.007 -10000 0 0 17 17
BTK -0.027 0.052 0.14 21 -0.19 11 32
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0 245 245
S1P/S1P5/G12 0.019 0.039 -10000 0 -0.16 3 3
S1P/S1P3/Gq 0.024 0.04 0.15 6 -0.22 8 14
S1P/S1P4/Gi -0.006 0.11 0.15 2 -0.29 43 45
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 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
BMP7/BMPR2/BMPR1A-1B/FS 0.065 0.064 -10000 0 -0.12 13 13
SMAD6-7/SMURF1 0.048 0.036 -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 0.025 -10000 0 -10000 0 0
SMAD5/SKI -0.015 0.1 -10000 0 -0.3 38 38
SMAD1 -0.026 0.15 -10000 0 -0.39 46 46
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 0.016 -10000 0 0 142 142
BMPR1B 0.035 0.005 -10000 0 0 11 11
BMPR1A-1B/BAMBI 0.02 0.062 -10000 0 -0.13 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 -0.24 29 29
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 -0.29 33 33
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 -0.39 44 45
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 -0.4 45 46
SMAD6-7/SMURF1/SMAD1 0.008 0.14 0.24 1 -0.41 33 34
SMAD6/SMURF1 0.026 0.016 -10000 0 0 136 136
BAMBI 0.018 0.018 -10000 0 0 237 237
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 43 44
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 -0.22 26 26
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
Paxillin-independent events mediated by a4b1 and a4b7

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
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 -0.33 21 21
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 0.075 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 0.035 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 -0.35 20 20
IL1-mediated signaling events

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
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 -0.28 54 54
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 -0.28 38 38
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 -0.27 57 57
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 -0.14 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 0.037 0.082 -10000 0 -0.13 78 78
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.072 -10000 0 -0.18 48 48
IL1 alpha/IL1R1/IL1RAP 0.048 0.053 -10000 0 -0.12 32 32
RELA 0.035 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 -0.29 33 33
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
Stabilization and expansion of the E-cadherin adherens junction

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
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 0.18 1 -0.28 7 8
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 -10000 0 -0.3 28 28
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 -0.23 10 10
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
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.025 0.082 0.17 8 -0.3 27 35
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 0.001 0.057 -10000 0 -0.12 59 59
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 -0.5 130 130
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 0 157 157
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 -0.3 29 41
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 0 126 126
ROCK1 -0.026 0.091 0.27 21 -0.27 6 27
adherens junction assembly -0.018 0.07 0.21 5 -0.3 13 18
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 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
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 0.01 0.099 -10000 0 -0.29 29 29
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 0.029 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 81 81
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
IFN-gamma 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
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 62 62
CaM/Ca2+ 0.048 0.077 -10000 0 -0.14 35 35
RAP1A 0.036 0.005 -10000 0 0 8 8
STAT1 (dimer)/SHP2 -0.019 0.063 0.16 27 -0.19 8 35
AKT1 -0.023 0.092 0.2 28 -0.22 29 57
MAP2K1 -0.022 0.063 0.15 33 -0.19 8 41
MAP3K11 -0.016 0.067 0.17 31 -0.18 6 37
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 -0.31 60 60
Rap1/GTP -0.037 0.035 -10000 0 -0.16 6 6
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 0.32 6 -0.41 23 29
STAT3 0.033 0.01 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.06 0.09 -10000 0 -0.74 3 3
STAT1 -0.019 0.066 0.18 25 -0.19 8 33
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 -0.019 0.076 0.19 27 -0.2 13 40
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 -0.26 53 59
MAPK1 -0.037 0.21 0.35 1 -0.74 34 35
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 0.003 0.1 0.3 7 -0.4 11 18
SMAD7 -0.008 0.064 0.16 25 -0.14 14 39
CBL/CRKL/C3G 0.027 0.073 0.25 8 -0.18 5 13
PI3K 0.027 0.091 -10000 0 -0.19 30 30
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 0.18 29 -0.21 30 59
PRKCD -0.023 0.09 0.21 27 -0.2 22 49
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.029 0.078 -10000 0 -0.18 62 62
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 0.2 8 -0.29 9 17
STAT1 (dimer)/PIASy -0.018 0.071 0.22 13 -0.19 7 20
SOCS1 0.017 0.085 -10000 0 -1 3 3
mol:GDP -0.016 0.072 0.18 29 -0.19 3 32
CASP1 -0.018 0.077 0.16 26 -0.16 58 84
PTGES2 0.035 0.007 -10000 0 0 18 18
IRF9 0 0.046 0.13 18 -0.12 22 40
mol:PI-3-4-5-P3 0.014 0.079 -10000 0 -0.16 47 47
RAP1/GDP -0.027 0.054 0.11 21 -0.18 4 25
CBL -0.016 0.066 0.17 31 -0.18 5 36
MAP3K1 -0.016 0.065 0.17 29 -0.18 5 34
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 62 62
PTPN11 -0.01 0.068 0.17 37 -0.18 5 42
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 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
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 81 81
MAPKAP1 0.034 0.008 -10000 0 0 26 26
negative regulation of cell cycle 0.007 0.11 0.33 26 -10000 0 26
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 -0.4 27 27
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 -10000 0 -0.36 8 8
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 0.24 10 -0.33 61 71
p27Kip1/14-3-3 family 0.009 0.11 -10000 0 -0.54 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
IL6-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
BCL2L1 0.058 0.26 0.54 17 -0.69 23 40
CRP 0.054 0.26 0.57 10 -0.72 19 29
cell cycle arrest 0.047 0.29 0.52 15 -0.75 29 44
TIMP1 -0.001 0.37 0.56 13 -0.79 69 82
IL6ST 0.028 0.032 0.089 1 -0.045 38 39
Rac1/GDP 0.05 0.11 0.3 18 -0.3 10 28
AP1 0.017 0.19 -10000 0 -0.52 38 38
GAB2 0.034 0.012 -10000 0 -0.041 1 1
TNFSF11 0.053 0.26 0.56 8 -0.73 19 27
HSP90B1 0.002 0.22 0.34 1 -0.84 27 28
GAB1 0.031 0.014 -10000 0 -0.041 1 1
MAPK14 0.03 0.065 0.21 1 -0.32 2 3
AKT1 -0.013 0.17 -10000 0 -0.55 29 29
FOXO1 -0.009 0.16 -10000 0 -0.52 30 30
MAP2K6 0.032 0.072 0.18 4 -0.24 8 12
mol:GTP 0 0.004 -10000 0 -0.023 2 2
MAP2K4 0.041 0.14 0.33 26 -0.34 17 43
MITF 0.034 0.083 0.21 14 -0.27 9 23
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 0.53 13 -0.8 29 42
STAT1 0.022 0.068 -10000 0 -0.74 3 3
CEBPD 0.02 0.33 0.57 7 -0.89 41 48
PIK3CA 0.03 0.015 -10000 0 -0.041 1 1
PI3K 0.017 0.076 -10000 0 -0.16 73 73
JUN 0.033 0.01 -10000 0 0 39 39
PIAS3/MITF 0.075 0.11 0.26 23 -0.27 10 33
MAPK11 0.026 0.063 0.21 2 -0.32 2 4
STAT3 (dimer)/FOXO1 -0.014 0.26 0.44 10 -0.61 52 62
GRB2/SOS1/GAB family 0.04 0.11 0.22 3 -0.26 31 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.005 0.1 0.18 10 -0.25 43 53
GRB2 0.036 0.008 -10000 0 -0.041 1 1
JAK2 0.03 0.014 -10000 0 0 86 86
LBP 0.06 0.25 0.5 18 -0.61 26 44
PIK3R1 0.032 0.013 -10000 0 -0.041 1 1
JAK1 0.029 0.026 -10000 0 -0.041 47 47
MYC 0.009 0.36 0.58 11 -0.88 54 65
FGG 0.053 0.26 0.57 7 -0.75 18 25
macrophage differentiation 0.047 0.29 0.52 15 -0.75 29 44
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.055 0.073 -10000 0 -0.16 7 7
JUNB 0.052 0.29 0.53 22 -0.84 24 46
FOS 0.025 0.017 -10000 0 0 147 147
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.036 0.086 0.22 18 -0.27 9 27
STAT1/PIAS1 0.073 0.12 0.28 17 -0.32 7 24
GRB2/SOS1/GAB family/SHP2/PI3K -0.001 0.17 -10000 0 -0.51 31 31
STAT3 (dimer) 0.032 0.29 0.52 15 -0.79 29 44
PRKCD 0.096 0.22 0.4 83 -0.42 25 108
IL6R 0.03 0.026 -10000 0 -0.04 56 56
SOCS3 0.057 0.083 0.42 3 -10000 0 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.043 0.088 0.18 1 -0.17 42 43
Rac1/GTP 0.042 0.12 0.3 10 -0.32 11 21
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 0.53 10 -0.69 19 29
IRF1 0.046 0.29 0.54 15 -0.86 24 39
mol:GDP 0.033 0.088 0.22 20 -0.26 9 29
SOS1 0.001 0.005 0.025 11 -0.022 1 12
VAV1 0.031 0.087 0.22 18 -0.27 9 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.024 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 21 21
PIAS3 0.035 0.007 -10000 0 0 17 17
PTPRE 0.009 0.029 -10000 0 -0.049 52 52
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 6 -0.22 5 11
LMO4 0.029 0.032 0.089 1 -0.047 35 36
STAT3 (dimer)/PIAS3 0.02 0.27 0.46 5 -0.73 30 35
MCL1 -0.005 0.17 0.4 1 -0.77 13 14
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 32 -0.22 28 60
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 0.15 39 -0.2 22 61
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 41 41
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 35 35
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 0.086 34 -0.19 30 64
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 -0.001 0.059 0.13 4 -0.21 22 26
RAF1/14-3-3 E -0.01 0.13 -10000 0 -0.47 27 27
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 32 -0.21 30 62
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 0.038 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 40 -0.21 21 61
YWHAE 0.034 0.009 -10000 0 0 29 29
PRKD1 -0.003 0.063 0.13 2 -0.24 24 26
SHC1 0.033 0.011 -10000 0 0 48 48
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0 0.009 -10000 0 -0.034 13 13
BUB1B -0.022 0.083 0.12 18 -0.22 59 77
PLK1 0.004 0.022 0.083 12 -0.069 3 15
PLK1S1 0.002 0.013 0.048 16 -0.039 2 18
KIF2A 0.004 0.02 0.073 12 -0.062 3 15
regulation of mitotic centrosome separation 0.005 0.022 0.083 12 -0.069 3 15
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 0.055 16 -0.041 2 18
PICH/PLK1 -0.034 0.073 0.066 8 -0.18 82 90
CENPE 0.004 0.046 0.12 46 -0.1 11 57
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
positive regulation of microtubule depolymerization 0.004 0.02 0.073 12 -0.062 3 15
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 0.048 16 -0.039 2 18
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 -0.069 3 15
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 0.034 13 -10000 0 13
RHOA 0.035 0.007 -10000 0 0 21 21
CCNB1/CDK1 -0.015 0.12 -10000 0 -0.22 99 99
CDC14B -0.011 0.004 0.011 6 -10000 0 6
CDC20 0.027 0.016 -10000 0 0 117 117
PLK1/PBIP1 -0.015 0.036 0.059 5 -0.09 75 80
mitosis -0.001 0.003 0.012 9 -10000 0 9
FBXO5 -0.015 0.06 0.11 13 -0.16 47 60
CDC2 0.017 0.023 -10000 0 -0.03 40 40
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.001 0.059 -10000 0 -0.26 22 22
ERCC6L -0.041 0.1 -10000 0 -0.22 93 93
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 0.053 -10000 0 -0.12 29 29
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 0.065 15 -0.051 1 16
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 97 99
microtubule-based process 0.019 0.024 0.095 4 -0.061 3 7
Golgi organization 0.005 0.022 0.083 12 -0.069 3 15
Cohesin/SA2 0.02 0.032 0.092 6 -0.093 21 27
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 -0.059 2 7
PPP2R1A 0.032 0.012 -10000 0 0 61 61
chromosome segregation -0.015 0.036 0.059 5 -0.089 75 80
PRC1 0.028 0.015 -10000 0 0 113 113
ECT2 0 0.057 0.14 47 -0.1 31 78
C13orf34 0.003 0.019 0.069 14 -0.056 2 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 18 -0.21 59 77
spindle assembly 0.002 0.024 0.075 14 -0.078 13 27
spindle stabilization 0.002 0.013 0.048 16 -0.039 2 18
APC/C/HCDH1 0.023 0.027 0.087 1 -0.12 15 16
MKLP2/PLK1 0.019 0.024 0.095 4 -0.061 3 7
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
FAS signaling pathway (CD95)

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
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 -0.58 138 138
FASLG/FAS/FADD/FAF1 -0.006 0.085 0.16 32 -0.18 40 72
MAP2K4 -0.035 0.14 0.21 1 -0.33 35 36
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 -0.26 24 36
FAS 0.022 0.02 -10000 0 -10000 0 0
BID -0.03 0.033 0.077 9 -0.13 20 29
MAP3K1 -0.087 0.19 -10000 0 -0.36 140 140
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 0.23 1 -0.36 21 22
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 0 157 157
LMNA -0.02 0.052 0.2 6 -0.2 24 30
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 -0.69 4 4
MET 0.023 0.018 -10000 0 0 183 183
ICAD/CAD -0.023 0.05 0.27 3 -0.21 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 0.077 9 -0.13 20 29
PAK2 -0.012 0.057 0.21 8 -0.21 23 31
BCL2 0.035 0.007 -10000 0 0 17 17
Neurotrophic factor-mediated Trk receptor signaling

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
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 40 -0.21 1 41
SHC 2-3/Grb2 0.006 0.13 -10000 0 -0.33 40 40
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 29 29
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 0.18 4 -0.22 23 27
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 0.014 -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 0.024 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 0.22 10 -0.31 23 33
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 0.19 8 -0.22 24 32
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 -0.17 25 25
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 -0.053 39 39
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 -0.14 74 74
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 -0.2 21 21
STAT3 0.02 0.087 -10000 0 -0.28 35 35
axon guidance 0.005 0.07 -10000 0 -0.14 76 76
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 0.18 9 -0.21 23 32
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.024 -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 -0.35 23 24
Rac1/GDP 0.011 0.071 0.19 9 -0.22 19 28
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 0.086 -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 44 44
NGF (dimer)/TRKA 0.008 0.039 0.15 4 -0.13 2 6
Rac1/GTP -0.014 0.058 -10000 0 -0.21 26 26
FRS2 family/SHP2/CRK family 0.087 0.055 -10000 0 -0.12 17 17
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC2 0.032 0.011 -10000 0 0 50 50
GNB1/GNG2 0.029 0.035 -10000 0 -0.12 16 16
forebrain development 0.036 0.071 0.26 7 -0.38 3 10
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 0 134 134
ARRB2 0.034 0.008 -10000 0 0 27 27
GLI3/SPOP 0.004 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 0 245 245
XPO1 0.037 0.005 -10000 0 0 5 5
GLI1/Su(fu) 0.012 0.05 0.24 1 -0.28 5 6
SAP30 0.035 0.006 -10000 0 0 15 15
mol:GDP 0.026 0.016 -10000 0 0 134 134
MIM/GLI2A 0.041 0.013 0.12 11 -10000 0 11
IFT88 0.034 0.009 -10000 0 0 29 29
GNAI3 0.035 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 -0.28 41 41
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 -0.014 0.097 -10000 0 -0.26 43 43
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 0.14 2 -0.27 27 29
GLI2/Su(fu) -0.001 0.073 -10000 0 -0.31 17 17
FOXA2 0.045 0.055 -10000 0 -0.49 1 1
neural tube patterning 0.036 0.071 0.26 7 -0.38 3 10
SPOP 0.035 0.007 -10000 0 0 21 21
Su(fu)/PIAS1 0.042 0.036 0.096 115 -0.12 4 119
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 7 -0.38 3 10
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 -0.41 34 36
GLI3A/CBP 0.043 0.008 -10000 0 -10000 0 0
KIF3A 0.032 0.011 -10000 0 0 51 51
GLI1 0.035 0.071 0.27 6 -0.38 3 9
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 -0.13 8 101
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 0.019 0.096 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 -0.34 40 40
PTCH1 0.034 0.066 0.24 8 -0.34 3 11
MIM/GLI1 0.058 0.076 0.35 3 -0.35 3 6
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
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.05 -10000 0 -0.18 25 25
PDGFRB 0.035 0.009 -10000 0 -0.001 26 26
SPHK1 0.018 0.021 -10000 0 -10000 0 0
mol:S1P 0.019 0.028 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.005 0.14 0.24 11 -0.44 29 40
GNAO1 0.032 0.015 0.063 1 0 81 82
PDGFB-D/PDGFRB/PLCgamma1 0.023 0.14 0.25 21 -0.36 33 54
PLCG1 -0.011 0.13 0.22 13 -0.39 31 44
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.009 -10000 0 -0.001 26 26
GNAI2 0.035 0.012 -10000 0 0 42 42
GNAI3 0.037 0.007 -10000 0 0 12 12
GNAI1 0.019 0.019 -10000 0 0 245 245
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.011 0.072 0.12 11 -0.27 25 36
S1P1/S1P 0.026 0.073 0.21 4 -0.27 14 18
negative regulation of cAMP metabolic process -0.004 0.14 0.24 11 -0.43 29 40
MAPK3 -0.006 0.14 0.27 8 -0.42 28 36
calcium-dependent phospholipase C activity 0 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
KDR 0.028 0.033 0.086 9 -0.13 15 24
PLCB2 0.033 0.082 0.22 13 -0.25 14 27
RAC1 0.027 0.016 -10000 0 0 123 123
RhoA/GTP 0.018 0.063 -10000 0 -0.23 15 15
receptor internalization 0.024 0.069 0.2 4 -0.25 14 18
PTGS2 0.028 0.15 0.36 8 -0.46 15 23
Rac1/GTP 0.013 0.055 -10000 0 -0.25 10 10
RHOA 0.035 0.007 -10000 0 0 21 21
VEGFA -0.001 0.021 -10000 0 -0.098 20 20
negative regulation of T cell proliferation -0.004 0.14 0.24 11 -0.43 29 40
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.015 -10000 0 0 79 79
MAPK1 -0.002 0.13 0.27 10 -0.44 24 34
S1P1/S1P/PDGFB-D/PDGFRB 0.049 0.096 0.26 7 -0.28 19 26
ABCC1 0.036 0.008 -10000 0 0 19 19
Plasma membrane estrogen receptor signaling

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.049 0.039 -10000 0 -0.099 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.046 0.18 -10000 0 -0.47 50 50
AKT1 -0.058 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 61 -10000 0 61
RhoA/GTP 0.01 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 -0.18 6 27
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 0.18 6 -0.18 21 27
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 -0.022 0.16 -10000 0 -0.42 47 47
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 -0.022 0.16 -10000 0 -0.42 47 47
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 -0.022 0.16 -10000 0 -0.42 47 47
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 -0.38 51 55
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 0 245 245
HBEGF -0.027 0.18 0.32 11 -0.43 52 63
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 0.021 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 -0.31 53 53
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 -0.4 47 47
mol:DAG 0.004 0.04 -10000 0 -0.2 1 1
Gs family/GDP/Gbeta gamma 0.003 0.059 -10000 0 -0.18 28 28
MSN -0.033 0.064 0.18 6 -0.19 21 27
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 0.4 47 -10000 0 47
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 47 47
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 0.25 6 -0.39 52 58
ruffle organization -0.035 0.062 0.18 6 -0.18 21 27
ROCK2 -0.028 0.068 0.19 7 -0.19 13 20
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 -0.034 0.17 0.37 2 -0.4 61 63
MMP2 -0.035 0.17 0.23 8 -0.42 55 63
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
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 -10000 0 -0.69 13 13
PTK2B 0.035 0.006 -10000 0 0 15 15
RAPGEF1 0.036 0.1 0.26 11 -0.39 16 27
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 0.27 5 -0.39 16 21
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 -0.21 17 17
GAB1/CRKL/SHP2/PI3K 0.053 0.12 0.27 2 -0.41 16 18
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 0.026 0.016 -10000 0 0 130 130
ELK1 0.12 0.18 0.35 172 -10000 0 172
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 0.24 8 -0.4 15 23
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 0.26 25 -0.33 12 37
GRB2/SHC 0.075 0.059 0.16 92 -0.12 1 93
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 0.34 172 -10000 0 172
HGF/MET/MUC20 0.028 0.024 -10000 0 -10000 0 0
cell migration 0.074 0.058 0.16 92 -0.12 1 93
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 -0.17 17 17
MET/MUC20 0.017 0.013 -10000 0 -10000 0 0
RAP1B 0.036 0.099 0.25 11 -0.36 16 27
RAP1A 0.031 0.1 0.25 12 -0.37 16 28
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 -0.22 17 17
cell proliferation 0.036 0.075 0.23 15 -0.3 6 21
RPS6KB1 0.014 0.021 -10000 0 -0.26 1 1
MAPK3 0.086 0.17 0.39 30 -10000 0 30
MAPK1 0.12 0.21 0.52 63 -10000 0 63
RANBP9 0.035 0.006 -10000 0 0 15 15
MAPK8 -0.049 0.16 0.25 2 -0.33 72 74
SRC 0.01 0.045 -10000 0 -0.17 17 17
PI3K 0.057 0.069 0.16 74 -0.15 7 81
MET/Glomulin 0.017 0.024 -10000 0 -0.094 11 11
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.024 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 -0.4 11 25
BAD -0.032 0.12 -10000 0 -0.66 13 13
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 0 157 157
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 0.079 0.053 0.16 95 -0.097 5 100
PDPK1 -0.021 0.13 -10000 0 -0.72 13 13
HGF/MET/SHIP 0.028 0.024 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 82 82
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 36 38
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 -0.25 36 36
apoptosis 0.013 0.1 0.18 2 -0.25 36 38
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 -0.32 44 47
BLK 0.035 0.007 -10000 0 0 17 17
HCK 0.027 0.016 -10000 0 0 123 123
MAP2K3 0.035 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 5 -0.26 42 47
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 0.14 0.2 3 -0.33 47 50
p38alpha-beta/MKP5 0.008 0.14 0.23 2 -0.33 44 46
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
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.03 0.11 0.33 11 -0.32 21 32
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 0.27 16 -0.24 15 31
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.021 0.11 0.31 9 -0.35 20 29
PIK3CA 0.03 0.014 -10000 0 0 85 85
FGR 0.004 0.096 0.27 2 -0.51 11 13
mol:Ca2+ 0.012 0.1 0.26 11 -0.38 20 31
MYC -0.003 0.26 0.39 24 -0.67 50 74
SHC1 0.033 0.011 -10000 0 0 48 48
HRAS/GDP 0.013 0.064 0.17 20 -0.17 16 36
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 0.012 0.11 0.26 11 -0.38 20 31
PTEN 0.026 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 0.24 18 -0.24 14 32
GAB1 0.009 0.12 0.29 10 -0.38 28 38
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.01 0.12 0.28 23 -0.32 31 54
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 -0.28 35 39
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 0.26 11 -0.39 20 31
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 0.32 1 -0.45 6 7
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 -0.41 44 58
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 0.014 0.063 0.26 3 -0.34 5 8
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 0.27 10 -0.35 27 37
PDGFB-D/PDGFRB/CBL 0.008 0.13 0.29 7 -0.44 26 33
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 27 -0.6 51 78
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 38 38
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 0.32 9 -0.36 20 29
LYN -0.034 0.16 0.22 2 -0.47 49 51
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 0.26 11 -0.39 20 31
PLCG1 0.011 0.11 0.26 11 -0.4 20 31
NHERF/PDGFRB 0.062 0.037 -10000 0 -0.12 12 12
YES1 -0.009 0.13 0.23 3 -0.53 24 27
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 -10000 0 -0.45 75 75
DOK1 -0.018 0.05 0.17 21 -0.13 2 23
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 0.33 29 -0.43 51 80
PRKCD -0.015 0.051 0.18 21 -0.13 2 23
FER -0.016 0.051 0.18 20 -0.13 3 23
MAPKKK cascade -0.011 0.064 0.16 44 -0.17 5 49
RASA1 -0.016 0.052 0.18 21 -0.17 6 27
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 0.26 11 -0.34 27 38
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 PRL

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
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 0.031 -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 0.11 4 -0.33 14 18
CDK2/Cyclin E1 -0.008 0.15 -10000 0 -0.37 58 58
MAPK3 -0.019 0.008 -10000 0 -10000 0 0
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 -0.39 31 31
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 0.031 -10000 0 -0.13 18 18
ROCK1 -0.004 0.12 -10000 0 -0.42 27 27
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
ErbB4 signaling events

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
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 -0.098 22 23
WWP1 -0.023 0.21 -10000 0 -1.1 17 17
FYN 0.03 0.014 -10000 0 0 82 82
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 0.24 6 -0.47 18 24
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 -0.098 22 22
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 -0.1 20 21
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 0.21 1 -0.55 17 18
MAPK3 -0.016 0.11 0.26 5 -0.49 17 22
STAT1 (dimer) 0.02 0.13 -10000 0 -0.62 17 17
MAPK1 -0.018 0.11 0.26 5 -0.48 18 23
JAK2 0.03 0.014 -10000 0 0 86 86
ErbB4/ErbB2/neuregulin 1 beta 0.004 0.11 0.21 1 -0.55 17 18
NRG1 -0.022 0.018 0.042 7 -0.083 17 24
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 0.2 1 -0.54 17 18
ERBB2 -0.022 0.02 0.056 10 -0.083 17 27
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 0.28 1 -0.77 17 18
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
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.028 0.069 0.18 28 -0.23 9 37
FYN -0.009 0.097 0.21 10 -0.29 28 38
LAT/GRAP2/SLP76 0.021 0.07 0.21 5 -0.26 11 16
IKBKB 0.036 0.004 -10000 0 0 6 6
AKT1 0.005 0.084 0.2 15 -0.24 20 35
B2M 0.036 0.008 -10000 0 0 19 19
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 15 -0.28 23 38
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 -0.27 7 36
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 0.19 5 -0.21 17 22
LAT 0.011 0.065 0.19 13 -0.28 8 21
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 0 6 6
CD3G 0.037 0.007 -10000 0 -10000 0 0
RASGRP2 0.007 0.019 0.074 2 -0.15 4 6
RASGRP1 -0.024 0.13 0.21 28 -0.24 90 118
HLA-A 0.036 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 43 -0.097 20 63
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.036 -10000 0 -0.12 25 25
PRKCA -0.001 0.056 0.16 23 -0.17 6 29
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 -0.16 5 17
ORAI1 -0.27 0.48 0.38 4 -1.1 123 127
CSK 0.012 0.064 0.19 12 -0.28 8 20
B7 family/CD28 0.06 0.091 0.25 19 -0.27 8 27
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 -0.28 9 18
PTPN6 0.01 0.071 0.22 15 -0.29 9 24
VAV1 0.021 0.076 0.2 37 -0.28 7 44
Monovalent TCR/CD3 0.022 0.017 0.11 1 -10000 0 1
CBL 0.036 0.004 -10000 0 0 6 6
LCK 0.007 0.082 0.21 14 -0.26 16 30
PAG1 0.014 0.064 0.2 11 -0.28 8 19
RAP1A 0.036 0.005 -10000 0 0 8 8
TCR/CD3/MHC I/CD8/LCK 0.016 0.069 0.2 12 -0.28 10 22
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 -0.14 22 22
HRAS 0.034 0.009 -10000 0 0 32 32
GO:0035030 0.012 0.068 0.18 24 -0.21 12 36
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 -0.28 12 36
CSK/PAG1 0.01 0.063 0.2 9 -0.27 8 17
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.049 0.033 -10000 0 -0.15 11 11
GRAP2/SLP76 0.03 0.078 0.23 4 -0.28 12 16
STIM1 -0.047 0.16 1.2 5 -10000 0 5
RAS family/GTP 0.004 0.071 0.15 24 -0.16 35 59
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 0.068 32 -0.05 17 49
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 -0.58 132 132
RAP1A/GTP 0.004 0.007 -10000 0 -0.055 4 4
mol:PI-3-4-5-P3 0.011 0.09 0.22 17 -0.24 22 39
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.015 0.068 0.17 1 -0.25 10 11
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 9 -0.26 9 18
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 11 11
PRKCE -0.001 0.056 0.16 22 -0.17 6 28
PRKCQ 0.009 0.094 0.22 25 -0.29 13 38
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 18 33
IKK complex 0.001 0.038 0.12 16 -0.093 2 18
RAS family/GDP -0.004 0.015 -10000 0 -0.038 41 41
MAP3K14 0.008 0.063 0.17 24 -0.17 17 41
PDPK1 0.006 0.079 0.2 16 -0.23 17 33
TCR/CD3/MHC I/CD8/Fyn 0.01 0.062 -10000 0 -0.27 10 10
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.051 0.38 0.75 2 -0.99 24 26
STAT6 (cleaved dimer) -0.066 0.34 -10000 0 -0.9 32 32
IGHG1 -0.009 0.25 0.42 20 -0.76 20 40
IGHG3 -0.06 0.36 0.62 1 -0.88 33 34
AKT1 -0.022 0.27 0.5 5 -0.7 31 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.018 0.19 0.45 5 -0.56 7 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.006 0.26 0.51 3 -0.72 20 23
THY1 -0.12 0.5 0.77 2 -1.2 63 65
MYB 0.032 0.011 -10000 0 0 50 50
HMGA1 0.035 0.006 -10000 0 0 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.002 0.26 0.52 11 -0.56 20 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.004 0.25 0.51 2 -0.77 15 17
SP1 0.029 0.075 0.12 92 -0.14 66 158
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.008 0.044 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.046 0.36 -10000 0 -0.92 29 29
SOCS1 -0.033 0.29 0.51 3 -0.66 30 33
SOCS3 -0.002 0.22 -10000 0 -0.6 5 5
FCER2 -0.024 0.32 0.65 1 -0.76 15 16
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.059 0.38 0.71 1 -1 23 24
GRB2 0.035 0.006 -10000 0 0 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.006 0.22 0.46 7 -0.56 17 24
T cell proliferation -0.064 0.37 0.66 1 -0.94 32 33
IL4R/JAK1 -0.064 0.38 0.66 1 -0.98 27 28
EGR2 -0.11 0.49 0.71 1 -1.2 52 53
JAK2 0.02 0.064 0.15 17 -10000 0 17
JAK3 0.032 0.019 -10000 0 -0.036 17 17
PIK3R1 0.032 0.012 -10000 0 0 61 61
JAK1 0.027 0.039 0.11 7 -10000 0 7
COL1A2 -0.11 0.47 0.52 2 -1.2 70 72
CCL26 -0.057 0.38 0.67 2 -0.91 33 35
IL4R -0.053 0.4 0.79 3 -1 24 27
PTPN6 0.015 0.036 -10000 0 -0.055 10 10
IL13RA2 -0.31 0.65 0.75 3 -1.1 172 175
IL13RA1 0.024 0.066 0.15 16 -10000 0 16
IRF4 0.043 0.12 -10000 0 -0.56 1 1
ARG1 0.007 0.21 0.51 2 -0.81 8 10
CBL -0.007 0.24 0.48 6 -0.54 20 26
GTF3A 0.048 0.034 0.12 69 -0.15 3 72
PIK3CA 0.03 0.014 -10000 0 0 85 85
IL13RA1/JAK2 0.024 0.1 0.23 10 -0.16 20 30
IRF4/BCL6 0.037 0.12 -10000 0 -0.46 1 1
CD40LG 0.041 0.004 0.13 1 -10000 0 1
MAPK14 -0.004 0.24 0.48 5 -0.56 15 20
mitosis -0.018 0.26 0.5 5 -0.66 31 36
STAT6 -0.061 0.42 0.81 4 -1 33 37
SPI1 0.037 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.021 0.25 0.48 5 -0.64 30 35
STAT6 (dimer) -0.061 0.42 0.81 4 -1 33 37
STAT6 (dimer)/PARP14 -0.078 0.37 -10000 0 -0.95 33 33
mast cell activation -0.002 0.016 -10000 0 -0.04 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.008 0.21 0.48 4 -0.53 8 12
FRAP1 -0.022 0.27 0.5 5 -0.7 31 36
LTA -0.059 0.38 0.71 1 -1 23 24
FES 0.035 0.006 -10000 0 0 14 14
T-helper 1 cell differentiation 0.059 0.42 0.99 33 -0.78 5 38
CCL11 -0.061 0.36 -10000 0 -0.96 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.012 0.22 0.49 5 -0.55 6 11
IL2RG 0.032 0.018 -10000 0 -0.035 18 18
IL10 -0.054 0.38 0.7 3 -1 23 26
IRS1 0.032 0.011 -10000 0 0 51 51
IRS2 0.029 0.014 -10000 0 0 93 93
IL4 0.026 0.18 0.56 1 -0.87 5 6
IL5 -0.059 0.38 0.71 1 -1 23 24
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.052 0.38 0.65 11 -0.87 36 47
COL1A1 0.02 0.26 0.6 5 -0.94 9 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.068 0.38 -10000 0 -1 23 23
IL2R gamma/JAK3 0.051 0.021 -10000 0 -10000 0 0
TFF3 -0.054 0.38 0.71 1 -0.99 23 24
ALOX15 -0.059 0.38 0.71 1 -1 22 23
MYBL1 0.029 0.014 -10000 0 0 92 92
T-helper 2 cell differentiation -0.041 0.34 0.63 4 -0.76 32 36
SHC1 0.033 0.011 -10000 0 0 48 48
CEBPB 0.035 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.014 0.26 0.52 4 -0.75 19 23
mol:PI-3-4-5-P3 -0.021 0.27 0.51 5 -0.7 31 36
PI3K -0.026 0.28 0.51 5 -0.74 31 36
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.004 0.046 -10000 0 -0.086 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.007 0.21 0.44 8 -0.54 21 29
ITGB3 -0.059 0.38 0.71 1 -1 23 24
PIGR -0.054 0.38 0.71 2 -1 23 25
IGHE -0.008 0.077 0.17 32 -0.18 14 46
MAPKKK cascade 0.009 0.21 0.43 10 -0.53 21 31
BCL6 0.03 0.013 -10000 0 0 72 72
OPRM1 -0.058 0.38 0.71 1 -1 23 24
RETNLB -0.057 0.38 0.67 2 -0.91 33 35
SELP -0.055 0.38 0.77 2 -1 23 25
AICDA -0.058 0.36 -10000 0 -0.94 24 24
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC3 0.036 0.005 -10000 0 0 8 8
VDR 0.035 0.007 -10000 0 0 17 17
Cbp/p300/PCAF 0.041 0.026 -10000 0 -0.12 9 9
EP300 0.033 0.011 -10000 0 0 49 49
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.001 0.055 -10000 0 -0.22 11 11
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.004 -10000 0 0 6 6
AKT1 0.007 0.079 0.2 5 -0.22 10 15
RAR alpha/9cRA/Cyclin H -0.026 0.13 -10000 0 -0.29 41 41
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.005 0.059 -10000 0 -0.21 24 24
CDC2 0.02 0.02 -10000 0 -0.002 214 214
response to UV -0.001 0.007 0.02 1 -0.026 33 34
RAR alpha/Jnk1 0.018 0.033 -10000 0 -10000 0 0
NCOR2 0.036 0.003 -10000 0 0 4 4
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.034 0.16 -10000 0 -0.53 35 35
NCOA2 0.036 0.005 -10000 0 0 9 9
NCOA3 0.035 0.008 -10000 0 0 22 22
NCOA1 0.033 0.01 -10000 0 0 43 43
VDR/VDR/DNA 0.035 0.007 -10000 0 0 17 17
RARG 0.032 0.017 -10000 0 -0.024 41 41
RAR gamma1/9cRA 0.045 0.013 -10000 0 -10000 0 0
MAPK3 0.031 0.018 -10000 0 -0.035 33 33
MAPK1 0.033 0.011 -10000 0 0 48 48
MAPK8 0.023 0.022 -10000 0 -0.006 155 155
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.028 0.12 -10000 0 -0.34 45 45
RARA 0.005 0.038 -10000 0 -0.2 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.003 0.044 -10000 0 -0.18 12 12
PRKCA 0.03 0.028 0.078 3 -0.071 33 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.036 0.17 -10000 0 -0.57 38 38
RXRG 0.016 0.029 -10000 0 -10000 0 0
RXRA -0.017 0.084 -10000 0 -0.28 28 28
RXRB 0.016 0.027 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RBP1 0.026 0.016 -10000 0 0 132 132
CRBP1/9-cic-RA -0.004 0.06 -10000 0 -0.13 88 88
RARB 0.031 0.022 0.074 1 -0.046 33 34
PRKCG 0.028 0.029 0.076 4 -0.071 33 37
MNAT1 0.034 0.009 -10000 0 0 35 35
RAR alpha/RXRs -0.02 0.13 0.27 2 -0.4 30 32
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.096 -10000 0 -0.3 28 28
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.061 -10000 0 -0.18 25 25
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.17 -10000 0 -0.6 35 35
positive regulation of DNA binding -0.03 0.12 -10000 0 -0.27 42 42
NRIP1 -0.059 0.28 -10000 0 -1.1 33 33
RXRs/RARs -0.017 0.12 -10000 0 -0.4 37 37
RXRs/RXRs/DNA/9cRA -0.04 0.12 -10000 0 -0.34 47 47
PRKACA 0.034 0.009 -10000 0 0 29 29
CDK7 0.035 0.008 -10000 0 0 22 22
TFIIH 0.059 0.051 -10000 0 -0.17 18 18
RAR alpha/9cRA 0.019 0.09 -10000 0 -0.18 26 26
CCNH 0.035 0.006 -10000 0 0 16 16
CREBBP 0.036 0.004 -10000 0 0 5 5
RAR gamma2/9cRA 0.055 0.05 -10000 0 -0.16 16 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.035 0.005 -10000 0 0 11 11
Caspase 8 (4 units) -0.004 0.093 -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 9 9
protein ubiquitination 0.011 0.067 0.21 2 -0.23 8 10
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 81 81
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 9 9
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 12 12
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 0.016 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 -0.029 0.14 0.28 10 -0.31 38 48
RELA 0.042 0.016 0.079 71 -10000 0 71
CASP2 0.026 0.016 -10000 0 0 130 130
CASP3 0.002 0.11 0.26 14 -0.31 19 33
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 -0.25 12 15
APAF-1/Caspase 9 0.001 0.086 0.17 7 -0.21 21 28
BCL2 -0.015 0.092 0.27 2 -0.33 9 11
Caspase cascade in apoptosis

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.008 0.087 -10000 0 -0.28 30 30
ACTA1 -0.032 0.086 -10000 0 -0.3 25 25
NUMA1 -0.002 0.084 -10000 0 -0.32 19 19
SPTAN1 -0.041 0.087 0.21 4 -0.3 28 32
LIMK1 0.009 0.11 0.19 65 -0.36 12 77
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 -0.28 31 31
DIABLO 0.036 0.004 -10000 0 0 5 5
apoptotic nuclear changes -0.041 0.086 0.21 4 -0.29 28 32
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 -0.32 24 29
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 29 41
CASP9 0.034 0.009 -10000 0 0 31 31
DNA repair 0.03 0.066 0.23 21 -10000 0 21
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 0.29 2 -0.3 24 26
CASP7 -0.072 0.1 -10000 0 -0.23 125 125
KRT18 0.024 0.052 -10000 0 -0.47 4 4
apoptosis -0.033 0.091 -10000 0 -0.35 19 19
DFFA -0.04 0.082 0.2 1 -0.3 25 26
DFFB -0.039 0.081 0.2 1 -0.31 23 24
PARP1 -0.03 0.067 -10000 0 -0.24 21 21
actin filament polymerization -0.014 0.1 0.33 12 -0.18 66 78
TNF 0.036 0.004 -10000 0 0 6 6
CYCS 0.01 0.039 0.14 6 -0.24 3 9
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 -0.31 25 25
LMNB2 0.051 0.088 0.22 17 -0.27 8 25
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 0.23 13 -0.3 32 45
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 22 22
LMNA 0.056 0.088 0.23 11 -0.34 5 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.057 -10000 0 -0.22 13 13
LRDD 0.035 0.007 -10000 0 0 18 18
SREBF1 -0.038 0.083 0.18 1 -0.31 24 25
APAF-1/Caspase 9 0.012 0.1 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.002 0.083 -10000 0 -0.31 19 19
CFL2 0.014 0.1 0.18 65 -0.34 12 77
GAS2 -0.03 0.086 0.23 1 -0.3 24 25
positive regulation of apoptosis 0.051 0.1 0.22 21 -0.35 8 29
PRF1 0.023 0.017 -10000 0 0 174 174
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.05 0.022 -10000 0 -0.14 5 5
Necdin/E2F1 -0.016 0.084 -10000 0 -0.14 142 142
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.071 0.047 -10000 0 -0.12 22 22
NGF (dimer)/p75(NTR)/BEX1 0.01 0.063 -10000 0 -0.12 93 93
NT-4/5 (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
IKBKB 0.036 0.004 -10000 0 0 6 6
AKT1 -0.011 0.083 0.19 36 -0.2 22 58
IKBKG 0.036 0 -10000 0 -10000 0 0
BDNF 0.032 0.012 -10000 0 0 61 61
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.008 -10000 0 -10000 0 0
FURIN 0.036 0.005 -10000 0 0 9 9
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.034 -10000 0 -0.12 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.021 0.068 -10000 0 -0.16 45 45
proBDNF (dimer) 0.032 0.012 -10000 0 0 61 61
NTRK1 0.035 0.006 -10000 0 0 12 12
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.005 0.12 -10000 0 -0.35 39 39
IRAK1 0.035 0.006 -10000 0 0 16 16
SHC1 -0.003 0.035 0.091 58 -10000 0 58
ARHGDIA 0.035 0.007 -10000 0 0 19 19
RhoA/GTP 0.024 0.019 -10000 0 -0.13 7 7
Gamma Secretase 0.076 0.072 -10000 0 -0.15 29 29
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.056 -10000 0 -0.11 47 47
MAGEH1 0.032 0.012 -10000 0 0 63 63
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.002 0.073 -10000 0 -0.11 131 131
Mammalian IAPs/DIABLO 0.056 0.035 -10000 0 -0.15 6 6
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.034 0.008 -10000 0 0 26 26
APP 0.035 0.007 -10000 0 0 19 19
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.031 0.013 -10000 0 0 69 69
RhoA/GDP/RHOGDI 0.05 0.03 0.17 1 -0.1 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.005 0.053 0.19 8 -10000 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.056 -10000 0 -0.18 32 32
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.041 0.019 -10000 0 -0.12 1 1
NCSTN 0.034 0.008 -10000 0 0 28 28
mol:GTP 0.031 0.041 -10000 0 -0.12 29 29
PSENEN 0.034 0.009 -10000 0 0 33 33
mol:ceramide -0.006 0.043 0.099 63 -10000 0 63
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.052 -10000 0 -0.27 9 9
p75(NTR)/beta APP 0.042 0.032 -10000 0 -0.14 9 9
BEX1 0.028 0.015 -10000 0 0 111 111
mol:GDP -0.008 0.003 -10000 0 -10000 0 0
NGF (dimer) 0.046 0.033 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.039 0.017 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
RAC1/GTP 0.026 0.024 -10000 0 -0.095 6 6
MYD88 0.034 0.009 -10000 0 0 31 31
CHUK 0.026 0.016 -10000 0 0 133 133
NGF (dimer)/p75(NTR)/PKA 0.031 0.041 -10000 0 -0.12 29 29
RHOB 0.031 0.013 -10000 0 0 72 72
RHOA 0.035 0.007 -10000 0 0 21 21
MAGE-G1/E2F1 0.026 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.034 0.008 -10000 0 0 23 23
TP53 -0.007 0.074 0.2 24 -0.2 6 30
PRDM4 -0.006 0.045 0.099 69 -10000 0 69
BDNF (dimer) 0.076 0.033 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
SORT1 0.035 0.005 -10000 0 0 11 11
activation of caspase activity 0.064 0.045 -10000 0 -0.12 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.03 -10000 0 -0.11 4 4
RHOC 0.035 0.006 -10000 0 0 16 16
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.012 0.11 0.23 34 -0.32 17 51
DIABLO 0.036 0.004 -10000 0 0 5 5
SMPD2 -0.006 0.043 0.1 63 -10000 0 63
APH1B 0.035 0.006 -10000 0 0 14 14
APH1A 0.035 0.006 -10000 0 0 16 16
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.021 -10000 0 -0.12 3 3
PSEN1 0.033 0.01 -10000 0 0 41 41
APAF-1/Pro-Caspase 9 0.049 0.018 -10000 0 -0.14 2 2
NT3 (dimer)/p75(NTR) 0.044 0.021 -10000 0 -10000 0 0
MAPK8 -0.003 0.078 0.22 16 -0.26 8 24
MAPK9 0.023 0.096 0.23 37 -0.27 11 48
APAF1 0.036 0.003 -10000 0 0 4 4
NTF3 0.035 0.008 -10000 0 0 23 23
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.018 0.018 -10000 0 0 247 247
RAC1/GDP 0.018 0.02 -10000 0 -0.13 6 6
RhoA-B-C/GDP 0.046 0.073 -10000 0 -0.15 52 52
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.057 -10000 0 -0.12 29 29
RhoA-B-C/GTP 0.03 0.041 -10000 0 -0.12 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.079 0.06 -10000 0 -0.12 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.083 0.027 -10000 0 -0.12 2 2
PRKACB 0.033 0.011 -10000 0 0 45 45
proBDNF (dimer)/p75 ECD 0.046 0.019 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.03 0.013 -10000 0 0 77 77
BIRC2 0.035 0.005 -10000 0 0 11 11
neuron projection morphogenesis -0.013 0.069 0.13 29 -0.16 24 53
BAD 0.007 0.098 0.23 25 -0.29 15 40
RIPK2 0.035 0.005 -10000 0 0 11 11
NGFR 0.031 0.013 -10000 0 0 67 67
CYCS -0.011 0.044 0.18 5 -0.19 3 8
ADAM17 0.035 0.006 -10000 0 0 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.057 0.029 -10000 0 -0.11 3 3
BCL2L11 0.007 0.097 0.23 24 -0.29 14 38
BDNF (dimer)/p75(NTR) 0.041 0.023 -10000 0 -10000 0 0
PI3K 0.025 0.068 -10000 0 -0.12 71 71
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.02 -10000 0 -0.1 3 3
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
PRKCI 0.034 0.008 -10000 0 0 25 25
NGF (dimer)/p75(NTR) 0.023 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.049 0.047 -10000 0 -0.12 26 26
TRAF6 0.036 0.005 -10000 0 0 8 8
RAC1 0.027 0.016 -10000 0 0 123 123
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.009 -10000 0 0 34 34
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.032 0.034 0.14 15 -0.15 2 17
SQSTM1 0.034 0.009 -10000 0 0 33 33
NGFRAP1 0.035 0.006 -10000 0 0 13 13
CASP3 0.007 0.095 0.22 25 -0.28 16 41
E2F1 0.035 0.006 -10000 0 0 16 16
CASP9 0.034 0.009 -10000 0 0 31 31
IKK complex 0.041 0.066 -10000 0 -0.26 8 8
NGF (dimer)/TRKA 0.026 0.004 -10000 0 -10000 0 0
MMP7 0.026 0.016 -10000 0 0 131 131
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.064 0.052 -10000 0 -0.11 28 28
MMP3 0.035 0.007 -10000 0 0 21 21
APAF-1/Caspase 9 -0.025 0.04 -10000 0 -0.2 6 6
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.092 -10000 0 -0.39 23 23
Crk/p130 Cas/Paxillin -0.052 0.089 -10000 0 -0.19 103 103
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 0.032 -10000 0 -10000 0 0
RHOA 0.035 0.007 -10000 0 0 21 21
RAP1A/GTP 0.054 0.048 -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 -0.11 23 23
lamellipodium assembly -0.027 0.085 -10000 0 -0.19 67 67
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 0.23 4 -0.21 10 14
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 -0.17 23 23
HRAS/GTP 0.021 0.091 -10000 0 -0.18 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 -0.19 113 113
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.045 -10000 0 -0.16 14 14
PI3K -0.045 0.13 0.2 3 -0.26 94 97
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 -0.25 10 10
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 0.052 0.057 -10000 0 -0.11 22 22
Rac1/GTP -0.027 0.1 0.19 1 -0.22 62 63
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 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
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 10 14
MAP2K3 0.035 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 72 75
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
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.071 -10000 0 -0.29 22 22
KLHL20 0.041 0.092 0.2 61 -0.19 21 82
CYFIP2 0.031 0.013 -10000 0 0 73 73
Rac1/GDP 0.008 0.063 0.2 2 -0.25 14 16
ENAH 0.007 0.074 -10000 0 -0.31 20 20
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 57 0 10 67
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 -0.21 16 27
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 -10000 0 -0.28 21 21
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 0.2 1 -0.29 21 22
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 67 0 26 93
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 0.13 15 -0.17 25 40
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 17 20
actin cytoskeleton organization 0.034 0.073 0.16 62 -0.14 21 83
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 0.035 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 0.22 4 -0.26 16 20
CDC42/GTP/IQGAP1 0.035 0.042 -10000 0 -0.12 32 32
JUP 0.032 0.011 -10000 0 0 50 50
p120 catenin/RhoA/GDP 0.025 0.077 0.25 3 -0.24 17 20
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 31 40
NME1 0 0 -10000 0 0 30 30
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 -0.17 22 22
WASF2 -0.009 0.02 -10000 0 -0.074 31 31
Rap1/GTP -0.022 0.058 0.15 16 -0.25 13 29
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 -0.15 31 39
VAV2 0.016 0.12 -10000 0 -0.56 11 11
RAP1/GDP -0.008 0.064 0.17 17 -0.25 12 29
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 0 126 126
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 -0.096 6 6
mol:GTP 0 0 0.001 60 0 30 90
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
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 0.032 0.12 0.28 26 -0.36 20 46
CRKL 0.028 0.11 0.25 14 -0.37 20 34
HRAS 0.036 0.1 0.26 8 -0.32 20 28
mol:PIP3 0.036 0.15 0.31 29 -0.37 33 62
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.036 0.004 -10000 0 0 7 7
GAB1 0.025 0.1 0.23 9 -0.39 20 29
FOXO3 0.037 0.16 0.3 25 -0.38 40 65
AKT1 0.037 0.17 0.31 24 -0.4 40 64
BAD 0.032 0.17 0.31 24 -0.38 40 64
megakaryocyte differentiation 0.026 0.099 0.23 10 -0.39 18 28
GSK3B 0.03 0.17 0.31 23 -0.4 41 64
RAF1 0.024 0.09 0.25 12 -0.28 20 32
SHC1 0.033 0.011 -10000 0 0 48 48
STAT3 0.019 0.1 0.24 4 -0.4 20 24
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 0.27 13 -0.38 18 31
HRAS/SPRED2 0.046 0.098 0.26 10 -0.28 20 30
LYN/TEC/p62DOK 0.065 0.12 0.28 2 -0.4 20 22
MAPK3 0.024 0.088 0.26 21 -0.22 17 38
STAP1 0.026 0.099 0.23 3 -0.39 20 23
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 0.072 0.11 0.29 2 -0.38 20 22
actin filament polymerization 0.028 0.099 0.24 4 -0.38 20 24
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 0.32 10 -0.36 19 29
PI3K 0.054 0.13 0.3 9 -0.38 19 28
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 0.24 4 -0.39 20 24
positive regulation of transcription 0.024 0.078 0.24 22 -0.18 16 38
mol:GDP 0.042 0.096 0.26 2 -0.34 19 21
PIK3C2B 0.019 0.099 0.26 5 -0.38 20 25
CBL/CRKL 0.054 0.11 0.31 11 -0.37 19 30
FER 0.024 0.1 0.26 5 -0.39 20 25
SH2B3 0.026 0.099 0.23 3 -0.39 20 23
PDPK1 0.031 0.14 0.3 27 -0.33 34 61
SNAI2 0.029 0.1 0.24 9 -0.39 19 28
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 0.31 3 -0.54 19 22
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 -0.035 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 0.24 3 -0.4 20 23
GO:0007205 -0.002 0.007 0.021 17 -0.02 4 21
MAP2K1 0.018 0.081 0.22 14 -0.22 22 36
CBL 0.036 0.004 -10000 0 0 6 6
KIT 0.013 0.24 -10000 0 -1.1 19 19
MAP2K2 0.023 0.091 0.3 20 -0.23 18 38
SHC/Grb2/SOS1 0.055 0.1 0.27 2 -0.36 20 22
STAT5A 0.034 0.14 0.32 3 -0.56 19 22
GRB2 0.035 0.006 -10000 0 0 16 16
response to radiation 0.029 0.1 0.24 9 -0.38 19 28
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 0.23 3 -0.39 20 23
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 -0.84 5 5
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.027 -9999 0 -0.14 2 2
FBXW11 0.035 0.007 -9999 0 0 20 20
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 20 20
CHUK 0.026 0.016 -9999 0 0 133 133
NF kappa B2 p100/RelB 0.067 0.061 -9999 0 -0.12 11 11
NFKB1 0.035 0.007 -9999 0 0 17 17
MAP3K14 0.035 0.006 -9999 0 0 12 12
NF kappa B1 p50/RelB 0.047 0.025 -9999 0 -0.14 5 5
RELB 0.034 0.009 -9999 0 0 33 33
NFKB2 0.027 0.016 -9999 0 0 127 127
NF kappa B2 p52/RelB 0.035 0.022 -9999 0 -10000 0 0
regulation of B cell activation 0.034 0.022 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.011 -10000 0 0 53 53
SMAD2 -0.017 0.068 0.17 2 -0.25 17 19
SMAD3 0.011 0.064 -10000 0 -0.34 6 6
SMAD3/SMAD4 -0.004 0.16 -10000 0 -0.49 41 41
SMAD4/Ubc9/PIASy 0.053 0.051 -10000 0 -0.12 30 30
SMAD2/SMAD2/SMAD4 0.024 0.1 -10000 0 -0.25 25 25
PPM1A 0.034 0.008 -10000 0 0 25 25
CALM1 0.033 0.011 -10000 0 0 49 49
SMAD2/SMAD4 0 0.07 -10000 0 -0.21 27 27
MAP3K1 0.035 0.007 -10000 0 0 18 18
TRAP-1/SMAD4 0.037 0.051 -10000 0 -0.14 34 34
MAPK3 0.036 0.003 -10000 0 0 4 4
MAPK1 0.033 0.011 -10000 0 0 48 48
NUP214 0.035 0.008 -10000 0 0 23 23
CTDSP1 0.035 0.006 -10000 0 0 14 14
CTDSP2 0.03 0.013 -10000 0 0 77 77
CTDSPL 0.034 0.009 -10000 0 0 29 29
KPNB1 0.035 0.008 -10000 0 0 23 23
TGFBRAP1 0.035 0.005 -10000 0 0 10 10
UBE2I 0.036 0.003 -10000 0 0 3 3
NUP153 0.034 0.008 -10000 0 0 28 28
KPNA2 0.034 0.009 -10000 0 0 34 34
PIAS4 0.034 0.009 -10000 0 0 32 32
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.041 0.01 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.01 0.06 -10000 0 -0.12 83 83
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.036 0.004 -10000 0 0 6 6
RGS9-1/Gbeta5/R9AP 0.045 0.014 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.046 0.011 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.036 0.004 -10000 0 0 7 7
Cone Metarhodopsin II/X-Arrestin 0.027 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.056 0.093 73 -0.11 68 141
Cone PDE6 0.055 0.046 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.016 0.064 -10000 0 -0.11 82 82
GNAT2/GDP 0.058 0.02 -10000 0 -0.1 1 1
GNB5 0.035 0.007 -10000 0 0 18 18
mol:GMP (4 units) -0.011 0.034 0.18 13 -10000 0 13
Cone Transducin 0.044 0.01 -10000 0 -10000 0 0
SLC24A2 0.029 0.014 -10000 0 0 92 92
GNB3/GNGT2 0.026 0.005 -10000 0 -10000 0 0
GNB3 0.035 0.007 -10000 0 0 20 20
GNAT2/GTP 0.026 0.003 -10000 0 -10000 0 0
CNGA3 0.022 0.018 -10000 0 0 187 187
ARR3 0.036 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.01 0.06 -10000 0 -0.12 83 83
mol:Pi 0.045 0.014 -10000 0 -0.12 1 1
Cone CNG Channel 0.028 0.074 -10000 0 -0.11 78 78
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.029 0.014 -10000 0 0 92 92
RGS9 0.035 0.006 -10000 0 0 15 15
PDE6C 0.027 0.016 -10000 0 0 127 127
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.035 0.007 -10000 0 0 20 20
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.016 -9999 0 0 118 118
ITGB7 0.035 0.005 -9999 0 0 10 10
ITGA4 0.035 0.006 -9999 0 0 12 12
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.04 0.024 -9999 0 -9999 0 0
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.033 0.011 -10000 0 0 49 49
HDAC4 0.034 0.008 -10000 0 0 24 24
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.001 0.037 -10000 0 -0.12 38 38
CDKN1A -0.037 0.12 -10000 0 -0.46 34 34
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.033 0.011 -10000 0 0 46 46
FOXO3 0.001 0.036 0.26 8 -10000 0 8
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.026 -10000 0 -0.18 9 9
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.033 0.01 -10000 0 0 37 37
TAT 0.035 0.005 -10000 0 0 11 11
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.001 -10000 0 -10000 0 0
PPARGC1A 0.031 0.013 -10000 0 0 75 75
FHL2 0.027 0.016 -10000 0 0 118 118
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.041 0.044 0.16 27 -0.17 4 31
HIST2H4A 0.001 0.037 0.12 38 -10000 0 38
SIRT1/FOXO3a 0.028 0.043 0.15 41 -0.18 1 42
SIRT1 0.033 0.046 0.18 38 -10000 0 38
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.049 0.053 0.17 23 -0.13 14 37
SIRT1/Histone H1b 0.027 0.047 0.16 3 -0.16 7 10
apoptosis -0.05 0.048 0.13 6 -0.17 24 30
SIRT1/PGC1A 0.031 0.042 0.14 25 -0.12 13 38
p53/SIRT1 0.038 0.083 0.34 26 -0.15 19 45
SIRT1/FOXO4 0.024 0.046 0.14 27 -0.14 16 43
FOXO1/FHL2/SIRT1 0.024 0.042 0.14 21 -0.1 20 41
HIST1H1E 0.012 0.026 -10000 0 -0.18 8 8
SIRT1/p300 0.038 0.049 0.16 30 -0.15 11 41
muscle cell differentiation 0.004 0.037 0.12 4 -0.11 38 42
TP53 0.039 0.045 0.18 39 -10000 0 39
KU70/SIRT1/BAX 0.05 0.049 0.17 24 -0.13 6 30
CREBBP 0.036 0.004 -10000 0 0 5 5
MEF2D 0.035 0.006 -10000 0 0 13 13
HIV-1 Tat/SIRT1 0.042 0.043 0.16 30 -0.14 4 34
ACSS2 0.001 0.037 0.12 38 -10000 0 38
SIRT1/PCAF/MYOD -0.004 0.037 0.11 38 -0.12 4 42
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.034 0.009 -10000 0 0 30 30
NFATC1 0.001 0.1 0.22 2 -0.41 21 23
NFATC2 -0.034 0.081 0.12 1 -0.17 100 101
NFATC3 0.009 0.018 -10000 0 -0.1 12 12
YWHAE 0.034 0.009 -10000 0 0 29 29
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.081 0.16 5 -0.21 42 47
Exportin 1/Ran/NUP214 0.066 0.031 -10000 0 -0.15 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.021 0.093 -10000 0 -0.21 26 26
BCL2/BAX 0.046 0.023 -10000 0 -0.14 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.13 12 12
CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
BAX 0.033 0.011 -10000 0 0 46 46
MAPK14 0.036 0.004 -10000 0 0 6 6
BAD 0.035 0.006 -10000 0 0 16 16
CABIN1/MEF2D 0.007 0.086 0.18 1 -0.2 40 41
Calcineurin A alpha-beta B1/BCL2 0.035 0.007 -10000 0 0 17 17
FKBP8 0.033 0.01 -10000 0 0 37 37
activation-induced cell death of T cells -0.007 0.085 0.2 40 -0.18 1 41
KPNB1 0.035 0.008 -10000 0 0 23 23
KPNA2 0.034 0.009 -10000 0 0 34 34
XPO1 0.036 0.004 -10000 0 0 5 5
SFN 0.031 0.013 -10000 0 0 74 74
MAP3K8 0.023 0.018 -10000 0 0 182 182
NFAT4/CK1 alpha 0.025 0.042 0.17 1 -0.16 15 16
MEF2D/NFAT1/Cbp/p300 0.008 0.11 0.23 1 -0.21 38 39
CABIN1 -0.006 0.081 0.16 5 -0.21 41 46
CALM1 0.033 0.011 -10000 0 0 49 49
RAN 0.035 0.006 -10000 0 0 13 13
MAP3K1 0.035 0.007 -10000 0 0 18 18
CAMK4 0.036 0.004 -10000 0 0 7 7
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.036 0.003 -10000 0 0 4 4
YWHAH 0.031 0.013 -10000 0 0 74 74
Calcineurin A alpha-beta B1/AKAP79/PKA 0.048 0.017 -10000 0 -10000 0 0
YWHAB 0.035 0.007 -10000 0 0 21 21
MAPK8 0.026 0.016 -10000 0 0 133 133
MAPK9 0.035 0.006 -10000 0 0 12 12
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.033 0.011 -10000 0 0 46 46
NFAT1-c-4/YWHAQ 0 0.11 0.2 2 -0.36 21 23
PRKCH 0.033 0.01 -10000 0 0 38 38
CABIN1/Cbp/p300 0.046 0.03 -10000 0 -0.14 9 9
CASP3 0.034 0.009 -10000 0 0 30 30
PIM1 0.035 0.005 -10000 0 0 10 10
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.02 -10000 0 -0.11 11 11
apoptosis 0.018 0.036 -10000 0 -0.17 12 12
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.096 -10000 0 -0.33 24 24
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.036 0.004 -10000 0 0 7 7
JNK2/NFAT4 0.027 0.034 -10000 0 -0.12 17 17
BAD/BCL-XL 0.047 0.026 -10000 0 -0.14 6 6
PRKCD 0.034 0.01 -10000 0 0 36 36
NUP214 0.035 0.008 -10000 0 0 23 23
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.036 0.004 -10000 0 0 5 5
PRKCG 0.033 0.01 -10000 0 0 38 38
PRKCQ 0.025 0.017 -10000 0 0 146 146
FKBP38/BCL2 0.048 0.017 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 0 49 49
PRKCB1 0.03 0.013 -10000 0 0 80 80
CSNK2A1 0.034 0.009 -10000 0 0 31 31
NFATc/JNK1 0.009 0.1 -10000 0 -0.39 21 21
CaM/Ca2+/FKBP38 0.038 0.03 -10000 0 -0.12 12 12
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 11 11
CSNK1A1 -0.015 0.021 0.087 12 -0.12 8 20
CaM/Ca2+/CAMK IV 0.041 0.028 -10000 0 -0.12 12 12
NFATc/ERK1 0.019 0.11 -10000 0 -0.39 21 21
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.021 0.094 -10000 0 -0.21 28 28
NR4A1 -0.025 0.079 0.16 8 -0.2 33 41
GSK3B 0.034 0.009 -10000 0 0 35 35
positive T cell selection 0.01 0.019 -10000 0 -0.1 12 12
NFAT1/CK1 alpha -0.02 0.069 0.093 1 -0.17 45 46
RCH1/ KPNB1 0.035 0.057 -10000 0 -0.15 41 41
YWHAQ 0.036 0.005 -10000 0 0 8 8
PRKACA 0.034 0.009 -10000 0 0 29 29
AKAP5 0.034 0.008 -10000 0 0 24 24
MEF2D 0.035 0.006 -10000 0 0 13 13
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.035 0.007 -10000 0 0 17 17
NFATc/p38 alpha 0.02 0.11 0.25 1 -0.39 21 22
CREBBP 0.036 0.004 -10000 0 0 5 5
BCL2 0.035 0.007 -10000 0 0 17 17
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.032 0.049 -10000 0 -0.11 23 23
TC10/GTP 0.029 0.046 -10000 0 -0.12 19 19
Insulin Receptor/Insulin/IRS1/Shp2 0.072 0.058 -10000 0 -0.13 28 28
HRAS 0.034 0.009 -10000 0 0 32 32
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.031 0.013 -10000 0 0 67 67
FOXO3 -0.009 0.016 0.02 3 -0.054 32 35
AKT1 -0.019 0.091 0.22 17 -0.21 23 40
INSR 0.031 0.021 0.074 4 -0.037 34 38
Insulin Receptor/Insulin 0.056 0.061 0.22 4 -0.14 34 38
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.018 -10000 0 0 185 185
SORBS1 0.027 0.016 -10000 0 0 126 126
CRK 0.035 0.008 -10000 0 0 23 23
PTPN1 -0.022 0.048 0.14 21 -0.25 6 27
CAV1 -0.011 0.041 0.17 9 -0.19 8 17
CBL/APS/CAP/Crk-II/C3G 0.052 0.053 -10000 0 -0.11 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.069 0.063 -10000 0 -0.14 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.03 0.078 -10000 0 -0.13 76 76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.02 0.066 -10000 0 -0.32 11 11
RPS6KB1 -0.026 0.084 0.2 18 -0.2 23 41
PARD6A 0.035 0.007 -10000 0 0 17 17
CBL 0.036 0.004 -10000 0 0 6 6
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.023 0.018 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.031 0.085 0.17 30 -0.21 24 54
HRAS/GTP -0.034 0.032 0.033 6 -0.12 39 45
Insulin Receptor 0.031 0.021 0.074 4 -0.037 34 38
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.08 0.066 -10000 0 -0.13 30 30
PRKCI 0.026 0.084 -10000 0 -0.43 14 14
Insulin Receptor/Insulin/GRB14/PDK1 0.012 0.066 -10000 0 -0.13 72 72
SHC1 0.033 0.011 -10000 0 0 48 48
negative regulation of MAPKKK cascade 0.036 0.053 -10000 0 -10000 0 0
PI3K 0.041 0.085 -10000 0 -0.13 76 76
NCK2 0.035 0.007 -10000 0 0 19 19
RHOQ 0.035 0.006 -10000 0 0 14 14
mol:H2O2 -0.004 0.006 -10000 0 -0.034 6 6
HRAS/GDP 0.021 0.029 -10000 0 -0.13 16 16
AKT2 -0.022 0.081 0.22 12 -0.19 12 24
PRKCZ 0.004 0.073 -10000 0 -0.41 13 13
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.014 0.052 0.16 25 -0.15 4 29
F2RL2 0.036 0.004 -10000 0 0 6 6
TRIP10 0.033 0.01 -10000 0 0 39 39
Insulin Receptor/Insulin/Shc 0.056 0.036 -10000 0 -0.12 8 8
TC10/GTP/CIP4/Exocyst 0.041 0.029 -10000 0 -0.12 13 13
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.071 0.044 -10000 0 -0.13 11 11
RAPGEF1 0.035 0.007 -10000 0 0 18 18
RASA1 0.034 0.009 -10000 0 0 30 30
NCK1 0.034 0.008 -10000 0 0 26 26
CBL/APS/CAP/Crk-II 0.046 0.04 -10000 0 -0.11 13 13
TC10/GDP 0.023 0.023 -10000 0 -0.13 10 10
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.066 -10000 0 -0.13 32 32
INPP5D -0.02 0.028 0.065 20 -0.11 23 43
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.005 0.005 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.005 -10000 0 0 9 9
IRS1 0.032 0.011 -10000 0 0 51 51
p62DOK/RasGAP 0.036 0.053 -10000 0 -10000 0 0
INS 0.033 0.022 0.087 14 -0.037 34 48
mol:PI-3-4-P2 -0.02 0.028 0.065 20 -0.11 23 43
GRB2 0.035 0.006 -10000 0 0 16 16
EIF4EBP1 -0.028 0.083 0.2 17 -0.21 22 39
PTPRA 0.034 0.015 0.074 2 -0.047 6 8
PIK3CA 0.03 0.014 -10000 0 0 85 85
TC10/GTP/CIP4 0.041 0.029 -10000 0 -0.12 13 13
PDPK1 0.036 0.003 -10000 0 0 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.051 -10000 0 -0.16 30 30
Insulin Receptor/Insulin/IRS1 0.052 0.046 -10000 0 -0.11 25 25
Insulin Receptor/Insulin/IRS3 0.045 0.03 -10000 0 -0.069 5 5
Par3/Par6 0.072 0.04 -10000 0 -0.11 15 15
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -10000 0 -9999 0 0
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.015 0.044 0.16 16 -9999 0 16
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.023 0.056 0.16 1 -0.2 23 24
BIRC5 0.029 0.015 -10000 0 0 102 102
NFKBIA -0.007 0.04 0.14 8 -0.18 13 21
CPEB1 0.032 0.011 -10000 0 0 54 54
AKT1 -0.005 0.029 0.18 2 -0.18 4 6
NDEL1 0.035 0.007 -10000 0 0 19 19
Aurora A/BRCA1 0.023 0.041 -10000 0 -0.15 19 19
NDEL1/TACC3 0.037 0.056 0.15 1 -0.17 21 22
GADD45A 0.031 0.013 -10000 0 0 74 74
GSK3B 0.034 0.015 0.088 23 0 35 58
PAK1/Aurora A 0.03 0.047 0.16 1 -0.16 20 21
MDM2 0.033 0.011 -10000 0 0 49 49
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.016 0.01 -10000 0 -10000 0 0
TP53 0.002 0.069 -10000 0 -0.23 30 30
DLG7 -0.003 0.041 0.1 38 -0.18 11 49
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.012 -10000 0 0 56 56
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.059 0.16 1 -0.16 32 33
G2/M transition of mitotic cell cycle 0.023 0.04 -10000 0 -0.15 19 19
AURKA 0.007 0.047 0.13 22 -0.21 16 38
AURKB 0.008 0.035 -10000 0 -0.14 25 25
CDC25B 0 0.074 0.12 1 -0.29 25 26
G2/M transition checkpoint 0.002 0.034 0.076 22 -0.14 20 42
mRNA polyadenylation 0.015 0.049 -10000 0 -0.13 42 42
Aurora A/CPEB 0.015 0.049 -10000 0 -0.13 42 42
Aurora A/TACC1/TRAP/chTOG 0.05 0.079 -10000 0 -0.17 43 43
BRCA1 0.035 0.006 -10000 0 0 16 16
centrosome duplication 0.03 0.047 0.16 1 -0.16 20 21
regulation of centrosome cycle 0.035 0.055 0.15 1 -0.17 21 22
spindle assembly 0.048 0.078 -10000 0 -0.17 43 43
TDRD7 0.033 0.01 -10000 0 0 40 40
Aurora A/RasGAP/Survivin 0.035 0.072 -10000 0 -0.19 22 22
CENPA 0.003 0.061 -10000 0 -0.26 22 22
Aurora A/PP2A 0.031 0.047 0.16 1 -0.16 21 22
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.006 0.049 0.14 1 -0.21 14 15
negative regulation of DNA binding 0 0.072 -10000 0 -0.24 33 33
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.045 -10000 0 -0.14 26 26
RASA1 0.034 0.009 -10000 0 0 30 30
Ajuba/Aurora A 0.002 0.034 0.076 22 -0.14 20 42
mitotic prometaphase -0.004 0.01 0.067 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.047 0.13 22 -0.21 16 38
TACC1 0.035 0.008 -10000 0 0 22 22
TACC3 0.032 0.011 -10000 0 0 55 55
Aurora A/Antizyme1 0.023 0.041 -10000 0 -0.15 19 19
Aurora A/RasGAP 0.028 0.057 0.16 1 -0.22 19 20
OAZ1 0.033 0.01 -10000 0 0 41 41
RAN 0.035 0.006 -10000 0 0 13 13
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.035 0.015 0.088 25 0 29 54
GIT1 0.036 0.003 -10000 0 0 4 4
GIT1/beta-PIX/PAK1 0.057 0.047 -10000 0 -0.12 25 25
Importin alpha/Importin beta/TPX2 -0.016 0.01 -10000 0 -10000 0 0
PPP2R5D 0.036 0.004 -10000 0 0 6 6
Aurora A/TPX2 -0.026 0.052 0.093 2 -0.22 18 20
PAK1 0.035 0.007 -10000 0 0 17 17
CKAP5 0.034 0.009 -10000 0 0 33 33
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.36 34 34
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 -10000 0 0
GNAI3 0.036 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 0.02 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 -0.29 38 39
MAPK3 -0.011 0.1 0.18 1 -0.29 38 39
MAPK1 -0.004 0.095 0.18 1 -0.29 30 31
JAK2 -0.016 0.11 0.17 1 -0.31 41 42
CXCR4 -0.009 0.1 0.18 1 -0.29 37 38
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 -0.29 37 38
S1P/S1P3/Gi -0.008 0.1 0.2 1 -0.3 38 39
RAC1 0.027 0.016 -10000 0 0 123 123
RhoA/GTP 0.008 0.11 0.19 1 -0.28 39 40
VEGFA 0.002 0.002 0.028 4 -10000 0 4
S1P/S1P2/Gi -0.012 0.1 0.16 1 -0.3 38 39
VEGFR1 homodimer/VEGFA homodimer 0.029 0.009 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 -10000 0 0
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 -0.29 31 31
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.024 -10000 0 -0.13 10 10
alphaV beta3 Integrin 0.059 0.048 -10000 0 -0.13 25 25
PTK2 0.005 0.085 0.22 4 -0.29 20 24
IGF1R 0.032 0.012 -10000 0 0 56 56
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.035 0.006 -10000 0 0 13 13
SRC 0.035 0.006 -10000 0 0 13 13
CDKN1B 0.002 0.089 -10000 0 -0.32 32 32
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.01 0.072 -10000 0 -0.3 23 23
ROCK1 0.035 0.006 -10000 0 0 14 14
AKT1 -0.004 0.069 -10000 0 -0.31 20 20
PTK2B -0.008 0.066 0.18 35 -0.19 4 39
alphaV/beta3 Integrin/JAM-A 0.069 0.047 -10000 0 -0.12 20 20
CBL 0.036 0.004 -10000 0 0 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.061 0.044 -10000 0 -0.12 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.066 0.068 -10000 0 -0.13 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.057 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Syndecan-1 0.054 0.043 -10000 0 -0.12 15 15
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.047 0.083 -10000 0 -0.15 65 65
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
alphaV/beta3 Integrin/Osteopontin 0.047 0.069 -10000 0 -0.14 55 55
RPS6KB1 -0.043 0.066 0.24 3 -0.21 18 21
TLN1 0.029 0.014 -10000 0 0 94 94
MAPK3 0.002 0.086 -10000 0 -0.33 25 25
GPR124 0.034 0.008 -10000 0 0 24 24
MAPK1 -0.001 0.087 -10000 0 -0.35 23 23
PXN 0.036 0.004 -10000 0 0 5 5
PIK3R1 0.032 0.012 -10000 0 0 61 61
alphaV/beta3 Integrin/Tumstatin 0.062 0.043 -10000 0 -0.12 23 23
cell adhesion 0.047 0.054 -10000 0 -0.16 27 27
ANGPTL3 0.036 0.005 -10000 0 0 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.037 0.029 -10000 0 -0.12 10 10
IGF-1R heterotetramer 0.032 0.012 -10000 0 0 56 56
Rac1/GDP 0.018 0.02 -10000 0 -0.13 6 6
TGFBR2 0.034 0.008 -10000 0 0 27 27
ITGB3 0.036 0.004 -10000 0 0 5 5
IGF1 0.035 0.007 -10000 0 0 20 20
RAC1 0.027 0.016 -10000 0 0 123 123
regulation of cell-matrix adhesion 0.058 0.045 -10000 0 -0.12 23 23
apoptosis 0.034 0.009 -10000 0 0 30 30
CD47 0.034 0.008 -10000 0 0 25 25
alphaV/beta3 Integrin/CD47 0.058 0.048 -10000 0 -0.13 26 26
VCL 0.027 0.016 -10000 0 0 127 127
alphaV/beta3 Integrin/Del1 0.062 0.043 -10000 0 -0.12 23 23
CSF1 0.036 0.004 -10000 0 0 5 5
PIK3C2A 0.01 0.018 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.026 0.041 -10000 0 -0.12 27 27
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.05 -10000 0 -0.12 27 27
FAK1/Vinculin 0.013 0.074 0.22 3 -0.26 17 20
alphaV beta3/Integrin/ppsTEM5 0.059 0.045 -10000 0 -0.12 23 23
RHOA 0.035 0.007 -10000 0 0 21 21
VTN 0.036 0.004 -10000 0 0 5 5
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.034 0.008 -10000 0 0 25 25
F11R -0.019 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.06 0.046 -10000 0 -0.13 24 24
alphaV/beta3 Integrin/TGFBR2 0.058 0.047 -10000 0 -0.12 26 26
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.04 -10000 0 -0.11 23 23
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.045 0.051 -10000 0 -0.12 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.034 0.009 -10000 0 0 29 29
alphaV/beta3 Integrin/Pyk2 0.059 0.058 0.19 29 -0.12 27 56
SDC1 0.03 0.014 -10000 0 0 81 81
VAV3 -0.025 0.03 0.18 2 -0.19 5 7
PTPN11 0.036 0.005 -10000 0 0 9 9
IRS1 0.032 0.011 -10000 0 0 51 51
FAK1/Paxillin 0.023 0.079 0.22 4 -0.25 20 24
cell migration -0.004 0.068 0.2 4 -0.28 11 15
ITGAV 0.034 0.009 -10000 0 0 30 30
PI3K 0.051 0.085 -10000 0 -0.14 59 59
SPP1 0.032 0.011 -10000 0 0 51 51
KDR 0.03 0.014 -10000 0 0 86 86
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.009 -10000 0 0 30 30
COL4A3 0.036 0 -10000 0 -10000 0 0
angiogenesis 0 0.096 0.22 1 -0.38 24 25
Rac1/GTP -0.028 0.036 0.18 1 -0.19 7 8
EDIL3 0.036 0.003 -10000 0 0 4 4
cell proliferation 0.057 0.047 -10000 0 -0.12 26 26
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.001 0.012 -10000 0 -0.093 8 8
STMN1 -0.019 0.01 0.059 2 -10000 0 2
Aurora B/RasGAP/Survivin 0.033 0.075 -10000 0 -0.14 70 70
Chromosomal passenger complex/Cul3 protein complex -0.033 0.077 -10000 0 -0.2 61 61
BIRC5 0.029 0.015 -10000 0 0 102 102
DES 0.025 0.091 -10000 0 -0.64 8 8
Aurora C/Aurora B/INCENP 0.057 0.026 -10000 0 -10000 0 0
Aurora B/TACC1 0.041 0.025 -10000 0 -0.12 8 8
Aurora B/PP2A 0.049 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.004 0.052 -10000 0 -0.19 31 31
mitotic metaphase/anaphase transition -0.001 0.003 0.009 19 -0.009 1 20
NDC80 -0.01 0.006 0.014 2 -10000 0 2
Cul3 protein complex 0.026 0.034 -10000 0 -0.13 10 10
KIF2C -0.018 0.12 -10000 0 -0.45 31 31
PEBP1 -0.001 0.003 0.009 14 -0.009 9 23
KIF20A 0.028 0.015 -10000 0 0 101 101
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.039 0.045 -10000 0 -0.14 24 24
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.002 0.078 -10000 0 -0.48 8 8
PSMA3 0.034 0.009 -10000 0 0 32 32
G2/M transition of mitotic cell cycle -0.001 0.002 0.009 8 -0.006 1 9
H3F3B 0.009 0.032 -10000 0 -0.2 11 11
AURKB 0.032 0.015 -10000 0 -0.008 52 52
AURKC 0.033 0.011 -10000 0 0 47 47
CDCA8 0.032 0.013 -10000 0 -0.003 53 53
cytokinesis -0.025 0.14 0.18 5 -0.41 49 54
Aurora B/Septin1 -0.013 0.14 0.2 1 -0.41 42 43
AURKA -0.001 0.002 0.009 8 -0.006 1 9
INCENP 0.034 0.014 0.057 1 -0.025 22 23
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.036 0.006 0.058 1 0 11 12
hSgo1/Aurora B/Survivin 0.022 0.05 -10000 0 -0.11 55 55
EVI5 0.035 0.006 -10000 0 0 11 11
RhoA/GTP 0.009 0.13 -10000 0 -0.32 50 50
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.006 0.077 0.12 1 -0.28 29 30
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.044 0.031 -10000 0 -0.14 9 9
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.047 0.026 -10000 0 -0.15 6 6
RHOA 0.035 0.007 -10000 0 0 21 21
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 0.006 0.065 -10000 0 -0.32 14 14
RASA1 0.034 0.009 -10000 0 0 30 30
KLHL9 0.022 0.018 -10000 0 0 196 196
mitotic prometaphase -0.001 0.003 0.009 14 -0.009 9 23
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.031 -10000 0 -0.14 9 9
PPP1CC 0.036 0.005 -10000 0 0 8 8
Centraspindlin 0.002 0.13 -10000 0 -0.34 50 50
RhoA/GDP 0.024 0.019 -10000 0 -0.13 7 7
NSUN2 0.002 0.041 -10000 0 -0.29 8 8
MYLK -0.013 0.067 -10000 0 -0.2 56 56
KIF23 0.028 0.017 -10000 0 -0.005 93 93
VIM -0.015 0.011 0.016 1 -10000 0 1
RACGAP1 0.031 0.015 -10000 0 -0.003 77 77
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.002 0.066 -10000 0 -0.29 22 22
Chromosomal passenger complex -0.015 0.097 0.13 4 -0.24 59 63
Chromosomal passenger complex/EVI5 0.062 0.084 -10000 0 -0.15 54 54
TACC1 0.035 0.008 -10000 0 0 22 22
PPP2R5D 0.036 0.004 -10000 0 0 6 6
CUL3 0.036 0.002 -10000 0 0 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.008 -10000 0 0 25 25
alphaV beta3 Integrin 0.043 0.042 -10000 0 -0.14 23 23
PTK2 0.015 0.11 -10000 0 -0.33 27 27
positive regulation of JNK cascade 0.023 0.09 -10000 0 -0.28 21 21
CDC42/GDP 0.038 0.12 -10000 0 -0.35 34 34
Rac1/GDP 0.029 0.11 -10000 0 -0.36 20 20
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.036 0.005 -10000 0 0 8 8
CTNNB1 0.035 0.007 -10000 0 0 21 21
CDC42/GTP 0.031 0.11 -10000 0 -0.34 20 20
nectin-3/I-afadin 0.043 0.026 -10000 0 -0.14 4 4
RAPGEF1 0.006 0.12 -10000 0 -0.36 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.006 0.13 -10000 0 -0.39 37 37
PDGFB-D/PDGFRB 0.034 0.008 -10000 0 0 25 25
TLN1 -0.01 0.052 0.093 38 -0.24 13 51
Rap1/GTP -0.002 0.085 -10000 0 -0.27 38 38
IQGAP1 0.033 0.01 -10000 0 0 43 43
Rap1/GTP/I-afadin 0.042 0.015 -10000 0 -0.1 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.043 0.026 -10000 0 -0.14 4 4
PVR 0.034 0.009 -10000 0 0 30 30
Necl-5(dimer) 0.034 0.009 -10000 0 0 30 30
mol:GDP 0.023 0.14 -10000 0 -0.41 33 33
MLLT4 0.034 0.009 -10000 0 0 35 35
PIK3CA 0.03 0.014 -10000 0 0 85 85
PI3K 0.053 0.088 -10000 0 -0.13 70 70
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.049 0.015 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.019 0.087 -10000 0 -0.28 22 22
PVRL1 0.036 0.004 -10000 0 0 5 5
PVRL3 0.032 0.012 -10000 0 0 56 56
PVRL2 0.034 0.01 -10000 0 0 36 36
PIK3R1 0.032 0.012 -10000 0 0 61 61
CDH1 0.033 0.01 -10000 0 0 37 37
CLDN1 0.034 0.008 -10000 0 0 27 27
JAM-A/CLDN1 0.073 0.043 -10000 0 -0.11 8 8
SRC 0.013 0.14 -10000 0 -0.42 37 37
ITGB3 0.036 0.004 -10000 0 0 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.049 0.015 -10000 0 -10000 0 0
FARP2 0.029 0.14 -10000 0 -0.44 21 21
RAC1 0.027 0.016 -10000 0 0 123 123
CTNNA1 0.035 0.007 -10000 0 0 18 18
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.034 -10000 0 -0.12 4 4
nectin-1/I-afadin 0.049 0.015 -10000 0 -10000 0 0
nectin-2/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.026 0.044 -10000 0 -0.12 32 32
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.059 0.032 -10000 0 -0.12 4 4
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.042 -10000 0 -0.12 32 32
F11R 0.032 0.011 -10000 0 0 52 52
positive regulation of filopodium formation 0.023 0.09 -10000 0 -0.28 21 21
alphaV/beta3 Integrin/Talin 0.032 0.091 0.21 38 -0.21 27 65
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.046 0.023 -10000 0 -0.14 3 3
PIP5K1C -0.01 0.04 0.091 5 -0.22 13 18
VAV2 0.025 0.14 -10000 0 -0.46 23 23
RAP1/GDP 0.027 0.11 0.26 1 -0.32 35 36
ITGAV 0.034 0.009 -10000 0 0 30 30
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.056 0.037 -10000 0 -0.14 6 6
nectin-3(dimer)/I-afadin/I-afadin 0.043 0.026 -10000 0 -0.14 4 4
Rac1/GTP 0.025 0.1 -10000 0 -0.35 19 19
PTPRM 0.008 0.044 -10000 0 -0.23 14 14
E-cadherin/beta catenin/alpha catenin 0.08 0.058 -10000 0 -0.12 11 11
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 0 22 22
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.001 0.038 0.096 27 -0.098 9 36
NFATC2 0 0.027 0.084 16 -0.095 9 25
NFATC3 -0.002 0.038 0.096 27 -0.1 10 37
CD40LG 0.012 0.12 0.28 38 -0.24 2 40
PTGS2 -0.022 0.066 0.23 7 -0.24 2 9
JUNB 0.03 0.014 -10000 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.026 -10000 0 -0.12 11 11
CaM/Ca2+ 0.026 0.026 -10000 0 -0.12 11 11
CALM1 0.035 0.013 0.065 4 0 49 53
JUN 0.036 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.021 0.021 -10000 0 -0.11 11 11
FOSL1 0.032 0.012 -10000 0 0 56 56
CREM 0.027 0.016 -10000 0 0 121 121
Jun/NFAT1-c-4/p21SNFT 0.058 0.07 0.26 13 -0.18 3 16
FOS 0.027 0.019 -10000 0 -10000 0 0
IFNG 0.009 0.11 0.29 32 -0.24 2 34
AP-1/NFAT1-c-4 0.081 0.11 0.35 7 -0.26 2 9
FASLG 0.01 0.11 0.28 35 -0.24 2 37
NFAT1-c-4/ICER1 0.04 0.051 0.21 12 -10000 0 12
IL2RA 0.002 0.087 0.25 20 -0.24 2 22
FKBP12/FK506 0.021 0.024 -10000 0 -0.13 11 11
CSF2 0.011 0.11 0.28 37 -0.24 2 39
JunB/Fra1/NFAT1-c-4 0.047 0.056 0.22 6 -0.18 1 7
IL4 0.011 0.11 0.28 37 -0.24 2 39
IL2 0.014 0.079 -10000 0 -0.83 4 4
IL3 0.031 0.075 -10000 0 -0.59 6 6
FKBP1A 0.033 0.011 -10000 0 0 46 46
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.038 0.008 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.023 0.1 -10000 0 -0.48 16 16
SMARCC2 0.033 0.011 -10000 0 0 45 45
SMARCC1 0.034 0.009 -10000 0 0 33 33
TBX21 0.031 0.052 -10000 0 -10000 0 0
SUMO2 0.033 0.018 0.073 1 -0.029 30 31
STAT1 (dimer) 0.035 0.037 -10000 0 -0.17 12 12
FKBP4 0.034 0.009 -10000 0 0 34 34
FKBP5 0.028 0.015 -10000 0 0 115 115
GR alpha/HSP90/FKBP51/HSP90 -0.024 0.064 -10000 0 -0.18 10 10
PRL 0.039 0.052 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.041 0.12 -10000 0 -0.32 1 1
RELA 0.017 0.11 0.17 33 -0.16 115 148
FGG -0.049 0.1 -10000 0 -0.32 2 2
GR beta/TIF2 -0.024 0.074 -10000 0 -0.22 2 2
IFNG 0.035 0.078 0.34 1 -10000 0 1
apoptosis -0.024 0.19 0.42 23 -0.51 31 54
CREB1 0.042 0.009 -10000 0 -10000 0 0
histone acetylation 0.021 0.053 -10000 0 -0.24 1 1
BGLAP 0.039 0.059 -10000 0 -10000 0 0
GR/PKAc 0.019 0.089 -10000 0 -0.18 19 19
NF kappa B1 p50/RelA 0.031 0.18 0.28 30 -0.26 110 140
SMARCD1 0.035 0.007 -10000 0 0 17 17
MDM2 -0.008 0.035 -10000 0 -10000 0 0
GATA3 0.032 0.02 -10000 0 -10000 0 0
AKT1 0.028 0.029 0.16 8 -0.086 17 25
CSF2 0.006 0.033 -10000 0 -10000 0 0
GSK3B 0.032 0.019 0.073 1 -0.03 26 27
NR1I3 -0.016 0.18 0.46 14 -0.5 17 31
CSN2 -0.045 0.087 -10000 0 -0.29 2 2
BRG1/BAF155/BAF170/BAF60A 0.059 0.074 -10000 0 -0.17 36 36
NFATC1 0.04 0.008 -10000 0 -10000 0 0
POU2F1 0.039 0.012 -10000 0 -10000 0 0
CDKN1A -0.13 0.42 -10000 0 -1.2 57 57
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 0.028 29 -10000 0 29
SFN 0.031 0.013 -10000 0 0 74 74
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.007 0.065 -10000 0 -0.15 7 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.071 0.27 0.43 14 -0.66 68 82
JUN 0.025 0.053 0.32 4 -10000 0 4
IL4 0.036 0.051 -10000 0 -10000 0 0
CDK5R1 0.035 0.008 -10000 0 0 21 21
PRKACA 0.034 0.009 -10000 0 0 29 29
cortisol/GR alpha (monomer)/AP-1 -0.048 0.053 -10000 0 -0.21 15 15
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.001 0.071 -10000 0 -0.16 15 15
cortisol/GR alpha (monomer) -0.056 0.12 -10000 0 -0.37 2 2
NCOA2 0.036 0.005 -10000 0 0 9 9
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.039 0.031 0.16 7 -10000 0 7
AP-1/NFAT1-c-4 0.051 0.073 0.42 2 -10000 0 2
AFP 0.023 0.066 -10000 0 -10000 0 0
SUV420H1 0.032 0.011 -10000 0 0 52 52
IRF1 -0.029 0.12 -10000 0 -0.63 14 14
TP53 -0.015 0.17 -10000 0 -0.49 54 54
PPP5C 0.033 0.01 -10000 0 0 39 39
KRT17 0.04 0.079 0.43 1 -10000 0 1
KRT14 0.031 0.067 -10000 0 -10000 0 0
TBP 0.042 0.017 -10000 0 -10000 0 0
CREBBP 0.029 0.018 -10000 0 -0.09 10 10
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.011 -10000 0 -10000 0 0
AP-1 0.051 0.073 0.43 2 -10000 0 2
MAPK14 0.034 0.018 0.073 1 -0.03 28 29
MAPK10 0.029 0.02 0.072 1 -0.03 23 24
MAPK11 0.03 0.02 0.073 1 -0.03 28 29
KRT5 0.039 0.077 0.43 1 -10000 0 1
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.032 0.019 0.077 3 -0.067 10 13
STAT1 0.035 0.037 -10000 0 -0.17 12 12
CGA 0.037 0.053 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.033 0.07 -10000 0 -0.36 8 8
MAPK3 0.033 0.019 0.074 2 -0.03 33 35
MAPK1 0.03 0.019 -10000 0 -0.03 27 27
ICAM1 0.029 0.13 0.33 14 -10000 0 14
NFKB1 0.017 0.11 0.17 31 -0.16 113 144
MAPK8 0.034 0.058 0.28 2 -10000 0 2
MAPK9 0.033 0.018 0.073 1 -0.029 28 29
cortisol/GR alpha (dimer) -0.028 0.2 0.43 22 -0.52 34 56
BAX -0.033 0.18 -10000 0 -0.88 9 9
POMC 0.032 0.071 0.5 1 -10000 0 1
EP300 0.026 0.019 -10000 0 -0.09 10 10
cortisol/GR alpha (dimer)/p53 -0.071 0.13 -10000 0 -0.42 18 18
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.069 0.24 29 -10000 0 29
SGK1 -0.017 0.062 -10000 0 -0.24 15 15
IL13 0.027 0.064 -10000 0 -10000 0 0
IL6 0.03 0.13 0.33 16 -10000 0 16
PRKACG 0.035 0.006 -10000 0 0 14 14
IL5 0.018 0.075 0.4 1 -10000 0 1
IL2 0.04 0.075 -10000 0 -10000 0 0
CDK5 0.026 0.017 -10000 0 0 137 137
PRKACB 0.033 0.011 -10000 0 0 45 45
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.11 0.39 0.32 18 -0.78 117 135
CDK5R1/CDK5 0.033 0.042 -10000 0 -0.14 18 18
NF kappa B1 p50/RelA/PKAc 0.055 0.16 0.3 23 -0.21 99 122
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.037 0.1 -10000 0 -0.37 1 1
SMARCA4 0.031 0.013 -10000 0 0 76 76
chromatin remodeling -0.036 0.1 -10000 0 -0.36 26 26
NF kappa B1 p50/RelA/Cbp 0.045 0.16 0.29 16 -0.22 106 122
JUN (dimer) 0.025 0.053 0.32 4 -10000 0 4
YWHAH 0.031 0.013 -10000 0 0 74 74
VIPR1 0.034 0.062 0.37 4 -10000 0 4
NR3C1 -0.039 0.083 -10000 0 -0.35 1 1
NR4A1 0.039 0.008 -10000 0 -10000 0 0
TIF2/SUV420H1 0.036 0.053 -10000 0 -0.14 38 38
MAPKKK cascade -0.024 0.19 0.42 23 -0.51 31 54
cortisol/GR alpha (dimer)/Src-1 -0.047 0.12 -10000 0 -0.39 2 2
PBX1 0.04 0.01 -10000 0 -10000 0 0
POU1F1 0.041 0.011 -10000 0 -10000 0 0
SELE 0.026 0.13 0.33 2 -10000 0 2
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.036 0.1 -10000 0 -0.37 24 24
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.037 0.1 -10000 0 -0.37 1 1
mol:cortisol -0.034 0.059 -10000 0 -10000 0 0
MMP1 0.036 0.072 0.34 1 -0.49 3 4
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.026 0.15 -10000 0 -0.57 8 8
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 -0.031 18 18
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 -0.52 16 16
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 -0.5 17 17
Mad/Max 0.047 0.027 -10000 0 -10000 0 0
TERT 0.022 0.16 -10000 0 -0.58 8 8
CCND1 -0.015 0.29 -10000 0 -0.95 38 38
MAX 0.031 0.018 -10000 0 -0.029 30 30
RBBP7 0.036 0.005 -10000 0 0 8 8
RBBP4 0.032 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 -0.32 28 63
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 -0.029 10 10
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 -0.11 29 29
ESR1 0.034 0.009 -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 0.023 -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 -0.56 13 13
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 -10000 0 0
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.004 0.057 -10000 0 -0.14 61 61
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 -0.53 11 11
SP1/HDAC2 0.042 0.045 -10000 0 -0.14 11 11
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.02 0.14 -10000 0 -0.47 16 16
Smad3/Myc 0.012 0.049 -10000 0 -0.13 41 41
911 complex 0.05 0.037 -10000 0 -0.12 4 4
IFNG 0.027 0.039 -10000 0 -0.11 33 33
Telomerase/PinX1 0.02 0.14 -10000 0 -0.47 16 16
Telomerase/AKT1/mTOR/p70S6K 0.022 0.096 -10000 0 -0.48 9 9
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 -0.47 16 16
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 -0.47 16 16
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
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.046 0.036 -10000 0 -0.14 16 16
ATM 0.034 0.01 -10000 0 0 36 36
UBE2D3 0.035 0.005 -10000 0 0 11 11
PRKDC 0.033 0.01 -10000 0 0 42 42
ATR 0.034 0.008 -10000 0 0 24 24
UBE2L3 0.034 0.009 -10000 0 0 33 33
FANCD2 0.008 0.035 -10000 0 -0.2 13 13
protein ubiquitination 0.074 0.054 -10000 0 -0.13 18 18
XRCC5 0.036 0.004 -10000 0 0 7 7
XRCC6 0.033 0.01 -10000 0 0 37 37
M/R/N Complex 0.068 0.024 -10000 0 -0.12 4 4
MRE11A 0.036 0.004 -10000 0 0 7 7
DNA-PK 0.057 0.047 -10000 0 -0.14 19 19
FA complex/FANCD2/Ubiquitin 0.002 0.085 -10000 0 -0.29 23 23
FANCF 0.035 0.007 -10000 0 0 20 20
BRCA1 0.035 0.006 -10000 0 0 16 16
CCNE1 0.032 0.012 -10000 0 0 61 61
CDK2/Cyclin E1 0.044 0.024 -10000 0 -0.14 2 2
FANCG 0.03 0.014 -10000 0 0 81 81
BRCA1/BACH1/BARD1 0.045 0.036 -10000 0 -0.14 16 16
FANCE 0.036 0.004 -10000 0 0 6 6
FANCC 0.035 0.006 -10000 0 0 16 16
NBN 0.035 0.005 -10000 0 0 11 11
FANCA 0.035 0.007 -10000 0 0 18 18
DNA repair -0.016 0.085 0.22 8 -0.3 13 21
BRCA1/BARD1/ubiquitin 0.045 0.036 -10000 0 -0.14 16 16
BARD1/DNA-PK 0.069 0.063 -10000 0 -0.14 30 30
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.045 0.036 0.14 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.064 -10000 0 -0.22 23 23
BRCA1/BACH1/BARD1/TopBP1 0.051 0.061 -10000 0 -0.14 42 42
BRCA1/BARD1/P53 0.064 0.067 -10000 0 -0.13 41 41
BARD1/CSTF1/BRCA1 0.062 0.039 -10000 0 -0.12 16 16
BRCA1/BACH1 0.035 0.006 -10000 0 0 16 16
BARD1 0.035 0.007 -10000 0 0 18 18
PCNA 0.033 0.01 -10000 0 0 44 44
BRCA1/BARD1/UbcH5C 0.063 0.041 -10000 0 -0.13 17 17
BRCA1/BARD1/UbcH7 0.059 0.044 -10000 0 -0.13 19 19
BRCA1/BARD1/RAD51/PCNA 0.069 0.061 -10000 0 -0.13 32 32
BARD1/DNA-PK/P53 0.066 0.081 -10000 0 -0.13 51 51
BRCA1/BARD1/Ubiquitin 0.045 0.036 -10000 0 -0.14 16 16
BRCA1/BARD1/CTIP 0.039 0.058 -10000 0 -0.14 41 41
FA complex 0.013 0.056 -10000 0 -0.2 21 21
BARD1/EWS 0.043 0.037 -10000 0 -0.14 16 16
RBBP8 -0.019 0.008 -10000 0 -10000 0 0
TP53 0.031 0.013 -10000 0 0 75 75
TOPBP1 0.033 0.011 -10000 0 0 48 48
G1/S transition of mitotic cell cycle -0.062 0.066 0.13 41 -10000 0 41
BRCA1/BARD1 0.081 0.058 -10000 0 -0.13 18 18
CSTF1 0.035 0.006 -10000 0 0 14 14
BARD1/EWS-Fli1 0.021 0.028 -10000 0 -0.13 16 16
CDK2 0.033 0.01 -10000 0 0 40 40
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.007 -10000 0 0 17 17
RAD50 0.035 0.006 -10000 0 0 12 12
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.045 0.036 -10000 0 -0.14 16 16
EWSR1 0.033 0.01 -10000 0 0 37 37
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.029 0.16 -10000 0 -0.99 10 10
CLOCK 0.033 0.019 -10000 0 -0.066 10 10
TIMELESS/CRY2 0.023 0.16 -10000 0 -1 10 10
DEC1/BMAL1 0.032 0.057 -10000 0 -0.13 49 49
ATR 0.034 0.008 -10000 0 0 24 24
NR1D1 0.013 0.064 -10000 0 -0.38 2 2
ARNTL 0.031 0.02 -10000 0 -0.069 8 8
TIMELESS -0.002 0.16 -10000 0 -1.1 10 10
NPAS2 0.036 0.017 -10000 0 -0.066 10 10
CRY2 0.035 0.007 -10000 0 0 21 21
mol:CO -0.009 0.027 0.13 10 -0.069 44 54
CHEK1 0.033 0.011 -10000 0 0 49 49
mol:HEME 0.009 0.027 0.069 44 -0.13 10 54
PER1 0.032 0.011 -10000 0 0 51 51
BMAL/CLOCK/NPAS2 0.053 0.075 0.23 1 -0.14 48 49
BMAL1/CLOCK 0.008 0.12 -10000 0 -0.51 18 18
S phase of mitotic cell cycle 0.029 0.16 -10000 0 -0.99 10 10
TIMELESS/CHEK1/ATR 0.029 0.16 -10000 0 -1 10 10
mol:NADPH 0.009 0.027 0.069 44 -0.13 10 54
PER1/TIMELESS 0.021 0.16 -10000 0 -1 10 10
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.006 -10000 0 0 13 13
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.052 0.095 -10000 0 -0.2 50 50
Ran/GTP/Exportin 1/HDAC1 -0.028 0.022 -10000 0 -0.11 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.11 -10000 0 -0.26 52 52
SUMO1 0.036 0.003 -10000 0 0 3 3
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.033 -10000 0 -0.15 20 20
FKBP3 0.034 0.009 -10000 0 0 30 30
Histones 0.034 0.075 -10000 0 -0.24 22 22
YY1/LSF 0.013 0.065 -10000 0 -0.14 65 65
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 0 13 13
I kappa B alpha/HDAC3 0.001 0.077 -10000 0 -0.2 49 49
I kappa B alpha/HDAC1 0.011 0.094 -10000 0 -0.23 52 52
SAP18 0.033 0.01 -10000 0 0 39 39
RELA -0.004 0.081 0.19 1 -0.28 18 19
HDAC1/Smad7 0.045 0.04 -10000 0 -0.12 7 7
RANGAP1 0.033 0.01 -10000 0 0 43 43
HDAC3/TR2 0.026 0.07 -10000 0 -0.26 19 19
NuRD/MBD3 Complex -0.009 0.12 -10000 0 -0.34 37 37
NF kappa B1 p50/RelA 0.01 0.09 -10000 0 -0.32 16 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.035 0.006 -10000 0 0 14 14
GATA1 0.036 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.11 -10000 0 -0.34 34 34
RBBP7 0.036 0.005 -10000 0 0 8 8
NPC 0.017 0.021 -10000 0 -0.088 18 18
RBBP4 0.032 0.011 -10000 0 0 53 53
MAX 0.034 0.008 -10000 0 0 24 24
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.035 0.007 -10000 0 0 20 20
NFKBIA 0.002 0.078 -10000 0 -0.33 21 21
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.087 -10000 0 -0.29 27 27
SIN3 complex 0.054 0.042 -10000 0 -0.12 18 18
SMURF1 0.026 0.016 -10000 0 0 136 136
CHD3 0.035 0.006 -10000 0 0 12 12
SAP30 0.035 0.006 -10000 0 0 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.034 0.008 -10000 0 0 25 25
YY1/HDAC3 -0.003 0.078 -10000 0 -0.25 28 28
YY1/HDAC2 0.013 0.063 -10000 0 -0.14 59 59
YY1/HDAC1 0.015 0.064 -10000 0 -0.22 20 20
NuRD/MBD2 Complex (MeCP1) -0.002 0.096 -10000 0 -0.28 34 34
PPARG -0.001 0.08 -10000 0 -0.21 54 54
HDAC8/hEST1B 0.023 0.006 -10000 0 -10000 0 0
UBE2I 0.036 0.003 -10000 0 0 3 3
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 20 20
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
HDAC3/SMRT (N-CoR2) 0.025 0.071 -10000 0 -0.26 19 19
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.04 -10000 0 -0.12 7 7
CREBBP 0.036 0.004 -10000 0 0 5 5
NuRD/MBD3/MBD3L2 Complex -0.005 0.11 -10000 0 -0.3 41 41
HDAC1 0.035 0.007 -10000 0 0 20 20
HDAC3 0.007 0.061 -10000 0 -0.3 13 13
HDAC2 0.032 0.011 -10000 0 0 50 50
YY1 0.009 0.035 -10000 0 -0.23 9 9
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.034 0.01 -10000 0 0 36 36
NCOR2 0.036 0.003 -10000 0 0 4 4
MXD1 0.036 0.003 -10000 0 0 4 4
STAT3 0.004 0.066 -10000 0 -0.22 34 34
NFKB1 0.035 0.007 -10000 0 0 17 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.008 -10000 0 0 24 24
YY1/LSF/HDAC1 0.028 0.072 -10000 0 -0.21 20 20
YY1/SAP30/HDAC1 0.029 0.071 -10000 0 -0.21 20 20
EP300 0.033 0.011 -10000 0 0 49 49
STAT3 (dimer non-phopshorylated) 0.004 0.066 -10000 0 -0.22 34 34
proteasomal ubiquitin-dependent protein catabolic process 0 0.081 -10000 0 -0.32 24 24
histone deacetylation -0.003 0.097 -10000 0 -0.27 38 38
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.095 -10000 0 -0.32 26 26
nuclear export -0.023 0.006 -10000 0 -10000 0 0
PRKACA 0.034 0.009 -10000 0 0 29 29
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.032 0.012 -10000 0 0 59 59
GATA2/HDAC3 0.025 0.07 -10000 0 -0.26 19 19
GATA1/HDAC1 0.05 0.023 -10000 0 -0.14 6 6
GATA1/HDAC3 0.026 0.071 -10000 0 -0.26 19 19
CHD4 0.033 0.01 -10000 0 0 38 38
TNF-alpha/TNFR1A 0.035 0.055 -10000 0 -0.14 41 41
SIN3/HDAC complex/Mad/Max -0.001 0.085 -10000 0 -0.3 23 23
NuRD Complex -0.003 0.11 -10000 0 -0.34 33 33
positive regulation of chromatin silencing 0.032 0.074 -10000 0 -0.23 22 22
SIN3B 0.034 0.009 -10000 0 0 35 35
MTA2 0.036 0.004 -10000 0 0 7 7
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.036 0.004 -10000 0 0 5 5
SUMO1/HDAC1 0.036 0.054 -10000 0 -0.22 5 5
HDAC complex 0.066 0.07 -10000 0 -0.15 36 36
GATA1/Fog1 0.027 0 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.055 0.047 -10000 0 -0.14 18 18
TNF 0.036 0.004 -10000 0 0 6 6
negative regulation of cell growth -0.001 0.084 -10000 0 -0.29 24 24
NuRD/MBD2/PRMT5 Complex -0.002 0.096 -10000 0 -0.28 34 34
Ran/GTP/Exportin 1 0.035 0.058 -10000 0 -0.16 20 20
NF kappa B/RelA/I kappa B alpha -0.008 0.097 -10000 0 -0.26 51 51
SIN3/HDAC complex/NCoR1 -0.001 0.093 -10000 0 -0.32 24 24
TFCP2 0.035 0.008 -10000 0 0 22 22
NR2C1 0.036 0.004 -10000 0 0 5 5
MBD3 0.032 0.011 -10000 0 0 51 51
MBD2 0.035 0.006 -10000 0 0 15 15
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.029 0.015 -10000 0 0 97 97
positive regulation of NF-kappaB transcription factor activity 0.035 0.044 -10000 0 -0.14 23 23
MAP2K4 0.014 0.054 0.21 2 -0.25 6 8
IKBKB 0.036 0.004 -10000 0 0 6 6
TNFRSF10B 0.034 0.008 -10000 0 0 24 24
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.014 0.027 -10000 0 -0.11 18 18
IKBKG 0.036 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.035 0.005 -10000 0 0 11 11
TRAIL/TRAILR2 0.035 0.044 -10000 0 -0.14 22 22
TRAIL/TRAILR3 0.035 0.044 -10000 0 -0.14 23 23
TRAIL/TRAILR1 0.015 0.035 -10000 0 -0.13 24 24
TRAIL/TRAILR4 0.035 0.044 -10000 0 -0.14 23 23
TRAIL/TRAILR1/DAP3/GTP 0.029 0.039 -10000 0 -0.1 31 31
IKK complex -0.023 0.11 -10000 0 -0.22 106 106
RIPK1 0.035 0.007 -10000 0 0 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.022 0.024 -10000 0 -0.13 11 11
MAPK3 -0.018 0.009 -10000 0 -10000 0 0
MAP3K1 0.022 0.053 -10000 0 -0.24 7 7
TRAILR4 (trimer) 0.035 0.005 -10000 0 0 11 11
TRADD 0.036 0.004 -10000 0 0 7 7
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.048 -10000 0 -0.16 23 23
CFLAR 0.036 0.005 -10000 0 0 9 9
MAPK1 -0.016 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.069 0.046 -10000 0 -0.11 24 24
mol:ceramide 0.014 0.027 -10000 0 -0.1 18 18
FADD 0.035 0.006 -10000 0 0 13 13
MAPK8 0.008 0.041 0.19 1 -0.25 5 6
TRAF2 0.035 0.006 -10000 0 0 14 14
TRAILR3 (trimer) 0.035 0.006 -10000 0 0 15 15
CHUK 0.026 0.016 -10000 0 0 133 133
TRAIL/TRAILR1/FADD 0.033 0.038 -10000 0 -0.12 24 24
DAP3 0.034 0.008 -10000 0 0 28 28
CASP10 -0.005 0.05 0.14 14 -0.16 21 35
JNK cascade 0.035 0.044 -10000 0 -0.14 23 23
TRAIL (trimer) 0.029 0.014 -10000 0 0 97 97
TNFRSF10C 0.035 0.006 -10000 0 0 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.041 0.047 -10000 0 -0.11 31 31
TRAIL/TRAILR2/FADD 0.05 0.048 -10000 0 -0.12 22 22
cell death 0.014 0.027 -10000 0 -0.1 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.051 -10000 0 -0.22 6 6
TRAILR2 (trimer) 0.034 0.008 -10000 0 0 24 24
CASP8 0.015 0.029 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.085 0.055 -10000 0 -0.11 22 22
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -9999 0 -0.12 2 2
E-cadherin/beta catenin 0.047 0.021 -9999 0 -0.14 2 2
CTNNB1 0.035 0.007 -9999 0 0 21 21
JUP 0.032 0.011 -9999 0 0 50 50
CDH1 0.033 0.01 -9999 0 0 37 37
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.026 0.078 -10000 0 -0.22 25 25
CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
AKT1 0.032 0.011 -10000 0 0 53 53
AKT2 0.034 0.008 -10000 0 0 26 26
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.006 0.075 0.17 1 -0.23 27 28
YWHAZ 0.035 0.007 -10000 0 0 17 17
CALM1 0.033 0.011 -10000 0 0 49 49
YWHAQ 0.036 0.005 -10000 0 0 8 8
TBC1D4 -0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.013 -10000 0 0 74 74
YWHAB 0.035 0.007 -10000 0 0 21 21
SNARE/Synip 0.02 0.018 -10000 0 -0.11 8 8
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.035 0.006 -10000 0 0 16 16
PRKCI 0.034 0.008 -10000 0 0 25 25
AS160/CaM/Ca2+ 0.021 0.025 -10000 0 -0.13 12 12
RHOQ 0.035 0.006 -10000 0 0 14 14
GYS1 0.001 0.036 0.25 1 -0.21 5 6
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 0.01 -10000 0 0 39 39
TC10/GTP/CIP4/Exocyst 0.041 0.029 -10000 0 -0.12 13 13
AS160/14-3-3 -0.006 0.098 -10000 0 -0.4 18 18
VAMP2 0.033 0.011 -10000 0 0 47 47
SLC2A4 0.005 0.08 0.17 1 -0.25 27 28
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.004 0.077 -10000 0 -0.31 25 25
SFN 0.031 0.013 -10000 0 0 74 74
LNPEP 0.036 0.005 -10000 0 0 9 9
YWHAE 0.034 0.009 -10000 0 0 29 29
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.012 0.15 0.35 21 -1 8 29
VDR 0.035 0.007 -10000 0 0 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.098 0.24 2 -0.27 39 41
RXRs/LXRs/DNA/Oxysterols 0.005 0.14 0.3 2 -0.39 44 46
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0 0.016 0.045 3 -0.047 43 46
RARs/THRs/DNA/Src-1 0.018 0.051 -10000 0 -0.16 35 35
RXRs/NUR77 0.077 0.065 -10000 0 -0.11 31 31
RXRs/PPAR 0.018 0.048 -10000 0 -0.18 5 5
NCOR2 0.036 0.003 -10000 0 0 4 4
VDR/VDR/Vit D3 0.026 0.005 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.081 0.022 -10000 0 -10000 0 0
RARA 0.036 0.003 -10000 0 0 3 3
NCOA1 0.033 0.01 -10000 0 0 43 43
VDR/VDR/DNA 0.035 0.007 -10000 0 0 17 17
RARs/RARs/DNA/9cRA 0.055 0.032 -10000 0 -10000 0 0
RARG 0.036 0.005 -10000 0 0 8 8
RPS6KB1 -0.005 0.081 0.5 6 -0.4 8 14
RARs/THRs/DNA/SMRT 0.03 0.024 -10000 0 -0.18 5 5
THRA 0.035 0.005 -10000 0 0 11 11
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.026 0.005 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.057 0.074 0.28 3 -0.15 39 42
NR1H4 0.036 0.003 -10000 0 0 3 3
RXRs/LXRs/DNA 0.081 0.1 0.3 2 -0.21 39 41
NR1H2 0.028 0.031 0.088 2 -0.06 45 47
NR1H3 0.03 0.032 0.089 2 -0.067 42 44
RXRs/VDR/DNA/Vit D3 0.07 0.061 0.2 1 -0.1 36 37
NR4A1 0.035 0.006 -10000 0 0 12 12
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.04 0.13 1 -0.15 4 5
RXRG 0.03 0.029 0.087 2 -0.058 44 46
RXR alpha/CCPG 0.022 0.021 -10000 0 -0.062 6 6
RXRA 0.03 0.03 0.087 2 -0.059 44 46
RXRB 0.031 0.032 0.088 1 -0.064 47 48
THRB 0.036 0.004 -10000 0 0 6 6
PPARG 0.034 0.008 -10000 0 0 24 24
PPARD 0.036 0.003 -10000 0 0 3 3
TNF 0 0.13 -10000 0 -0.38 39 39
mol:Oxysterols 0 0.015 0.045 3 -0.041 47 50
cholesterol transport 0.005 0.14 0.3 2 -0.39 44 46
PPARA 0.033 0.01 -10000 0 0 44 44
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.035 0.005 -10000 0 0 10 10
RXRs/NUR77/BCL2 0.02 0.03 -10000 0 -0.16 1 1
SREBF1 -0.01 0.16 -10000 0 -0.47 40 40
RXRs/RXRs/DNA/9cRA 0.057 0.074 0.28 3 -0.15 39 42
ABCA1 -0.044 0.26 -10000 0 -0.82 45 45
RARs/THRs 0.1 0.025 -10000 0 -0.12 1 1
RXRs/FXR 0.078 0.065 -10000 0 -0.11 31 31
BCL2 0.035 0.007 -10000 0 0 17 17
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.049 0.019 -10000 0 -0.14 2 2
FBXW11 0.035 0.007 -10000 0 0 20 20
NF kappa B1 p50/c-Rel 0.032 0.018 -10000 0 -0.12 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.065 -10000 0 -0.26 11 11
NFKBIA 0.004 0.053 -10000 0 -0.17 24 24
MAPK14 0.036 0.004 -10000 0 0 6 6
NF kappa B1 p105/p50 0.028 0.031 -10000 0 -0.13 16 16
ARRB2 0.011 0.026 -10000 0 -0.2 7 7
REL 0.036 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.019 -10000 0 -0.12 5 5
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.021 -10000 0 -0.12 7 7
PIK3CA 0.03 0.014 -10000 0 0 85 85
NF kappa B1 p50 dimer 0.023 0.025 0.17 6 -0.14 5 11
PIK3R1 0.032 0.012 -10000 0 0 61 61
NFKB1 -0.021 0.005 -10000 0 -10000 0 0
RELA 0.035 0.005 -10000 0 0 10 10
positive regulation of anti-apoptosis 0.013 0.036 -10000 0 -0.14 18 18
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.069 -10000 0 -0.25 12 12
SRC 0.035 0.006 -10000 0 0 13 13
PI3K 0.016 0.075 -10000 0 -0.16 73 73
NF kappa B1 p50/RelA 0.013 0.036 -10000 0 -0.14 18 18
IKBKB 0.036 0.004 -10000 0 0 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -10000 0 0 20 20
SYK 0.031 0.013 -10000 0 0 71 71
I kappa B alpha/PIK3R1 0.016 0.067 -10000 0 -0.2 29 29
cell death 0.024 0.067 -10000 0 -0.24 12 12
NF kappa B1 p105/c-Rel 0.032 0.018 -10000 0 -0.12 5 5
LCK 0.035 0.007 -10000 0 0 17 17
BCL3 0.034 0.009 -10000 0 0 31 31
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.012 -10000 0 0 62 62
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.005 0.058 0.41 2 -10000 0 2
IL27/IL27R/JAK1 0.041 0.064 -10000 0 -10000 0 0
TBX21 -0.007 0.099 0.34 19 -10000 0 19
IL12B 0.036 0.004 -10000 0 0 6 6
IL12A -0.011 0.002 0.013 2 -10000 0 2
IL6ST 0.034 0.011 -10000 0 -0.032 1 1
IL27RA/JAK1 0.03 0.051 -10000 0 -10000 0 0
IL27 0 0.004 -10000 0 -10000 0 0
TYK2 0.033 0.012 -10000 0 -0.032 1 1
T-helper cell lineage commitment 0.05 0.074 0.17 109 -0.18 2 111
T-helper 2 cell differentiation -0.005 0.058 0.41 2 -10000 0 2
T cell proliferation during immune response -0.005 0.058 0.41 2 -10000 0 2
MAPKKK cascade 0.005 0.058 -10000 0 -0.41 2 2
STAT3 0.033 0.01 -10000 0 0 37 37
STAT2 0.035 0.007 -10000 0 0 17 17
STAT1 0.033 0.01 -10000 0 0 40 40
IL12RB1 0.034 0.009 -10000 0 0 30 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.007 0.099 0.35 19 -10000 0 19
IL27/IL27R/JAK2/TYK2 0.005 0.058 -10000 0 -0.41 2 2
positive regulation of T cell mediated cytotoxicity 0.005 0.058 -10000 0 -0.41 2 2
STAT1 (dimer) 0.046 0.08 -10000 0 -10000 0 0
JAK2 0.029 0.014 -10000 0 -0.031 1 1
JAK1 0.033 0.01 -10000 0 0 37 37
STAT2 (dimer) 0.021 0.096 -10000 0 -0.33 10 10
T cell proliferation 0.007 0.06 -10000 0 -0.31 4 4
IL12/IL12R/TYK2/JAK2 0.005 0.18 -10000 0 -0.76 25 25
IL17A 0.043 0.07 0.18 88 -0.12 7 95
mast cell activation -0.005 0.058 0.41 2 -10000 0 2
IFNG 0.004 0.028 -10000 0 -0.089 19 19
T cell differentiation -0.001 0.003 -10000 0 -0.017 10 10
STAT3 (dimer) 0.017 0.1 -10000 0 -0.38 11 11
STAT5A (dimer) 0.022 0.097 -10000 0 -0.33 10 10
STAT4 (dimer) 0.021 0.095 -10000 0 -0.34 7 7
STAT4 0.034 0.009 -10000 0 0 30 30
T cell activation -0.004 0.005 -10000 0 -0.083 1 1
IL27R/JAK2/TYK2 0.035 0.064 -10000 0 -10000 0 0
GATA3 0.003 0.073 0.63 6 -10000 0 6
IL18 -0.01 0.004 0 69 -10000 0 69
positive regulation of mast cell cytokine production 0.017 0.1 -10000 0 -0.37 11 11
IL27/EBI3 0.024 0.012 -10000 0 -10000 0 0
IL27RA 0.005 0.037 -10000 0 -10000 0 0
IL6 0.021 0.018 -10000 0 0 199 199
STAT5A 0.036 0.004 -10000 0 0 6 6
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.028 -10000 0 -10000 0 0
IL1B -0.009 0.004 0 99 -10000 0 99
EBI3 0.033 0.012 -10000 0 -0.032 1 1
TNF -0.011 0.001 0 6 -10000 0 6
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.057 0.04 -10000 0 -0.11 19 19
HDAC3 0.036 0.005 -10000 0 0 8 8
Ran/GTP/Exportin 1/HDAC4 -0.029 0.023 -10000 0 -0.11 33 33
GATA1/HDAC4 0.047 0.032 -10000 0 -0.14 13 13
GATA1/HDAC5 0.052 0.013 -10000 0 -0.14 1 1
GATA2/HDAC5 0.05 0.015 -10000 0 -0.14 1 1
HDAC5/BCL6/BCoR 0.05 0.052 -10000 0 -0.13 29 29
HDAC9 0.023 0.017 -10000 0 0 178 178
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.029 -10000 0 -0.12 15 15
HDAC4/ANKRA2 0.044 0.038 -10000 0 -0.14 18 18
HDAC5/YWHAB 0.048 0.027 -10000 0 -0.16 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.033 -10000 0 -0.15 20 20
GATA2 0.035 0.006 -10000 0 0 14 14
HDAC4/RFXANK 0.038 0.047 -10000 0 -0.15 27 27
BCOR 0.034 0.009 -10000 0 0 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.035 0.006 -10000 0 0 15 15
GNB1/GNG2 0.019 0.032 -10000 0 -0.13 20 20
Histones 0.019 0.064 -10000 0 -0.16 39 39
ADRBK1 0.035 0.006 -10000 0 0 14 14
HDAC4 0.034 0.008 -10000 0 0 24 24
XPO1 0.036 0.004 -10000 0 0 5 5
HDAC5/ANKRA2 0.049 0.024 -10000 0 -0.14 6 6
HDAC4/Ubc9 0.047 0.033 -10000 0 -0.14 13 13
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.031 -10000 0 -0.14 11 11
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.036 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.042 0.037 -10000 0 -0.14 16 16
CAMK4 0.036 0.004 -10000 0 0 7 7
Tubulin/HDAC6 0.036 0.044 -10000 0 -0.12 37 37
SUMO1 0.036 0.003 -10000 0 0 3 3
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.035 0.007 -10000 0 0 21 21
GATA1 0.036 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.034 0.009 -10000 0 0 29 29
NR3C1 0.034 0.008 -10000 0 0 24 24
SUMO1/HDAC4 0.034 0.056 -10000 0 -0.22 5 5
SRF 0.036 0.002 -10000 0 0 2 2
HDAC4/YWHAB 0.044 0.04 -10000 0 -0.15 17 17
Tubulin 0.014 0.042 -10000 0 -0.13 37 37
HDAC4/14-3-3 E 0.042 0.043 -10000 0 -0.15 22 22
GNB1 0.033 0.01 -10000 0 0 37 37
RANGAP1 0.033 0.01 -10000 0 0 43 43
BCL6/BCoR 0.034 0.048 -10000 0 -0.14 29 29
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.036 -10000 0 -0.12 14 14
HDAC4/SRF 0.066 0.033 -10000 0 -0.12 12 12
HDAC4/ER alpha 0.044 0.034 -10000 0 -0.14 13 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.019 0.064 -10000 0 -0.16 39 39
cell motility 0.035 0.044 -10000 0 -0.12 37 37
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.036 0.003 -10000 0 0 3 3
HDAC7/HDAC3 0.026 0.008 -10000 0 -0.13 1 1
BCL6 0.031 0.013 -10000 0 0 72 72
HDAC4/CaMK II delta B 0.034 0.008 -10000 0 0 24 24
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 0.034 0.009 -10000 0 0 34 34
HDAC6/HDAC11 0.053 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.058 -10000 0 -0.16 20 20
NPC 0.017 0.021 -10000 0 -0.088 18 18
MEF2C 0.034 0.008 -10000 0 0 27 27
RAN 0.035 0.006 -10000 0 0 13 13
HDAC4/MEF2C 0.092 0.053 -10000 0 -0.12 24 24
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.036 0.003 -10000 0 0 4 4
TUBB2A 0.033 0.011 -10000 0 0 45 45
HDAC11 0.036 0.004 -10000 0 0 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.008 -10000 0 0 24 24
ANKRA2 0.035 0.006 -10000 0 0 12 12
RFXANK 0.033 0.011 -10000 0 0 46 46
nuclear import -0.029 0.057 0.21 23 -10000 0 23
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.035 0.007 -10000 0 0 17 17
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -10000 0 -10000 0 0
monocyte activation -0.07 0.16 -10000 0 -0.34 130 130
MAP2K2 0.018 0.04 -10000 0 -0.59 2 2
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.008 0.003 -10000 0 -10000 0 0
MAP2K6 -0.008 0.002 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -10000 0 0
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B 0.001 0.04 0.083 69 -0.075 53 122
Channel 0.022 0.004 -10000 0 -10000 0 0
NLRP1 -0.001 0 -10000 0 -10000 0 0
CALM1 0.033 0.011 -10000 0 0 49 49
negative regulation of phagocytosis -0.017 0.12 -10000 0 -0.41 38 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -10000 0 -10000 0 0
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.003 -10000 0 -10000 0 0
PGR -0.008 0.002 -10000 0 -10000 0 0
PA/Cellular Receptors 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.001 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
macrophage activation -0.012 0.012 0.07 8 -10000 0 8
TNF 0.036 0.004 -10000 0 0 6 6
VCAM1 -0.073 0.16 -10000 0 -0.34 128 128
platelet activation -0.017 0.12 -10000 0 -0.41 38 38
MAPKKK cascade 0.002 0.022 0.064 3 -0.07 33 36
IL18 -0.005 0.035 0.085 38 -0.075 56 94
negative regulation of macrophage activation -0.001 0 -10000 0 -10000 0 0
LEF -0.001 0 -10000 0 -10000 0 0
CASP1 0.003 0.004 0.025 12 -10000 0 12
mol:cAMP -0.017 0.12 -10000 0 -0.41 38 38
necrosis -0.001 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.004 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 0.045 0.063 -10000 0 -10000 0 0
MKNK1 0.034 0.009 -10000 0 0 31 31
MAPK14 0.046 0.037 0.16 3 -0.082 22 25
ATF2/c-Jun 0 0.093 -10000 0 -0.32 31 31
MAPK11 0.043 0.038 0.16 3 -0.082 22 25
MITF 0.032 0.048 0.19 2 -0.2 6 8
MAPKAPK5 0.034 0.038 0.18 3 -10000 0 3
KRT8 0.035 0.039 0.2 2 -10000 0 2
MAPKAPK3 0.035 0.006 -10000 0 0 16 16
MAPKAPK2 0.035 0.006 -10000 0 0 14 14
p38alpha-beta/CK2 0.061 0.056 0.22 3 -10000 0 3
CEBPB 0.025 0.068 0.22 2 -0.21 24 26
SLC9A1 0.032 0.041 0.16 1 -0.26 2 3
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.032 0.054 0.26 4 -0.26 1 5
p38alpha-beta/MNK1 0.064 0.067 -10000 0 -0.14 17 17
JUN -0.004 0.091 -10000 0 -0.32 30 30
PPARGC1A 0.032 0.057 0.18 6 -0.21 13 19
USF1 0.028 0.037 0.17 3 -10000 0 3
RAB5/GDP/GDI1 0.013 0.076 -10000 0 -0.21 26 26
NOS2 0.028 0.037 0.17 3 -10000 0 3
DDIT3 0.025 0.058 0.18 3 -0.2 17 20
RAB5A 0.034 0.009 -10000 0 0 29 29
HSPB1 0.075 0.13 0.28 119 -0.15 5 124
p38alpha-beta/HBP1 0.055 0.058 0.22 2 -10000 0 2
CREB1 0.024 0.068 0.22 1 -0.18 32 33
RAB5/GDP 0.019 0.034 -10000 0 -0.13 23 23
EIF4E -0.013 0.057 0.19 10 -0.19 7 17
RPS6KA4 0.034 0.038 0.18 3 -10000 0 3
PLA2G4A -0.012 0.052 0.19 5 -0.19 9 14
GDI1 0.023 0.061 0.22 1 -0.23 18 19
TP53 0.01 0.05 0.17 11 -10000 0 11
RPS6KA5 0.035 0.039 0.18 4 -10000 0 4
ESR1 0.032 0.038 0.19 2 -10000 0 2
HBP1 0.026 0.016 -10000 0 0 138 138
MEF2C 0.031 0.049 0.19 2 -0.22 7 9
MEF2A 0.03 0.048 0.22 1 -0.22 7 8
EIF4EBP1 0.021 0.073 0.22 1 -0.2 29 30
KRT19 0.035 0.039 0.19 3 -10000 0 3
ELK4 0.033 0.037 -10000 0 -10000 0 0
ATF6 0.033 0.037 0.16 2 -10000 0 2
ATF1 0.02 0.071 0.22 1 -0.19 28 29
p38alpha-beta/MAPKAPK2 0.072 0.055 0.21 2 -10000 0 2
p38alpha-beta/MAPKAPK3 0.072 0.056 0.22 3 -0.13 1 4
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.081 -10000 0 -0.29 17 17
BAG4 0.035 0.005 -10000 0 0 11 11
BAD -0.002 0.034 0.14 3 -0.14 9 12
NFKBIA 0.033 0.011 -10000 0 0 47 47
BIRC3 0.03 0.013 -10000 0 0 77 77
BAX 0.004 0.048 0.19 18 -0.13 7 25
EnzymeConsortium:3.1.4.12 0.004 0.021 -10000 0 -0.078 9 9
IKBKB -0.004 0.082 0.21 5 -0.29 16 21
MAP2K2 -0.004 0.058 0.17 36 -0.16 6 42
MAP2K1 -0.012 0.042 0.16 10 -0.16 7 17
SMPD1 0.003 0.027 -10000 0 -0.12 9 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.012 0.076 -10000 0 -0.32 8 8
MAP2K4 -0.006 0.034 0.18 2 -0.15 2 4
protein ubiquitination -0.005 0.081 0.21 1 -0.3 15 16
EnzymeConsortium:2.7.1.37 -0.01 0.05 0.16 13 -0.16 6 19
response to UV 0 0 0.002 15 -0.002 2 17
RAF1 -0.007 0.042 0.17 10 -0.14 8 18
CRADD 0.035 0.006 -10000 0 0 12 12
mol:ceramide 0.003 0.031 -10000 0 -0.12 10 10
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.031 -10000 0 -0.11 15 15
MADD 0.035 0.006 -10000 0 0 13 13
MAP3K1 -0.001 0.032 0.16 2 -0.14 4 6
TRADD 0.036 0.004 -10000 0 0 7 7
RELA/p50 0.035 0.005 -10000 0 0 10 10
MAPK3 -0.003 0.051 0.16 16 -0.16 6 22
MAPK1 -0.01 0.061 0.16 15 -0.2 14 29
p50/RELA/I-kappa-B-alpha 0.044 0.036 -10000 0 -0.14 15 15
FADD 0.009 0.071 -10000 0 -0.3 6 6
KSR1 -0.003 0.03 -10000 0 -0.13 6 6
MAPK8 -0.009 0.029 0.17 2 -0.16 1 3
TRAF2 0.035 0.006 -10000 0 0 14 14
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.007 0.077 0.21 1 -0.29 14 15
TNF R/SODD 0.034 0.054 -10000 0 -0.14 40 40
TNF 0.036 0.004 -10000 0 0 6 6
CYCS 0.014 0.052 0.15 22 -0.14 4 26
IKBKG -0.005 0.079 0.21 1 -0.29 16 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.015 0.082 -10000 0 -0.33 9 9
RELA 0.035 0.005 -10000 0 0 10 10
RIPK1 0.035 0.007 -10000 0 0 18 18
AIFM1 -0.002 0.04 0.12 18 -0.12 9 27
TNF/TNF R/SODD 0.052 0.055 -10000 0 -0.12 39 39
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.035 0.081 -10000 0 -0.6 7 7
NSMAF 0.007 0.081 0.22 6 -0.3 14 20
response to hydrogen peroxide 0 0 0.002 15 -0.002 2 17
BCL2 0.035 0.007 -10000 0 0 17 17
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.035 0.006 -10000 0 0 13 13
CLTC 0.013 0.087 -10000 0 -0.35 20 20
calcium ion-dependent exocytosis 0.014 0.063 0.13 1 -0.22 15 16
Dynamin 2/GTP 0.025 0.011 -10000 0 -0.1 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.004 0.076 -10000 0 -0.29 22 22
CPE -0.014 0.008 -10000 0 -0.12 1 1
CTNNB1 0.035 0.007 -10000 0 0 21 21
membrane fusion 0.017 0.062 -10000 0 -0.16 28 28
CTNND1 -0.018 0.011 0.087 1 -0.18 1 2
DNM2 0.034 0.009 -10000 0 0 34 34
mol:PI-4-5-P2 0.011 0.068 0.16 2 -0.23 19 21
TSHR -0.016 0.008 0.091 1 -0.12 1 2
INS 0.01 0.083 -10000 0 -0.43 15 15
BIN1 0.031 0.013 -10000 0 0 73 73
mol:Choline 0.017 0.062 -10000 0 -0.16 28 28
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.005 -10000 0 -0.11 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.007 -10000 0 0 21 21
mol:Ca2+ 0.025 0.011 -10000 0 -0.1 1 1
JUP 0.012 0.068 -10000 0 -0.28 19 19
ASAP2/amphiphysin II 0.028 0.045 -10000 0 -0.1 46 46
ARF6/GTP 0.025 0.009 -10000 0 -0.13 1 1
CDH1 0.01 0.068 -10000 0 -0.28 19 19
clathrin-independent pinocytosis 0.025 0.009 -10000 0 -0.13 1 1
MAPK8IP3 0.036 0.004 -10000 0 0 5 5
positive regulation of endocytosis 0.025 0.009 -10000 0 -0.13 1 1
EXOC2 0.035 0.008 -10000 0 0 22 22
substrate adhesion-dependent cell spreading 0.001 0.052 -10000 0 -0.29 5 5
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.034 0.009 -10000 0 0 32 32
regulation of calcium-dependent cell-cell adhesion -0.038 0.073 0.29 17 -10000 0 17
positive regulation of phagocytosis -0.015 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.046 0.013 -10000 0 -0.12 1 1
ACAP1 0.018 0.059 -10000 0 -0.22 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.006 0.062 -10000 0 -0.28 14 14
clathrin heavy chain/ACAP1 0.017 0.084 0.19 7 -0.27 20 27
JIP4/KLC1 0.036 0.034 -10000 0 -0.1 24 24
EXOC1 0.033 0.01 -10000 0 0 42 42
exocyst 0.001 0.053 -10000 0 -0.3 5 5
RALA/GTP 0.014 0.03 -10000 0 -0.13 17 17
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.038 -10000 0 -0.12 24 24
receptor recycling 0.025 0.009 -10000 0 -0.13 1 1
CTNNA1 -0.019 0.011 0.087 1 -0.18 1 2
NME1 -0.009 0.005 -10000 0 -0.11 1 1
clathrin coat assembly 0.014 0.086 -10000 0 -0.34 20 20
IL2RA 0.006 0.068 -10000 0 -0.34 13 13
VAMP3 -0.015 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.031 0.082 -10000 0 -0.24 24 24
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0 0.041 -10000 0 -0.21 12 12
PLD2 0 0.041 -10000 0 -0.21 12 12
EXOC5 0.03 0.014 -10000 0 0 81 81
PIP5K1C 0.009 0.063 -10000 0 -0.24 16 16
SDC1 0.014 0.07 -10000 0 -0.28 19 19
ARF6/GDP 0.026 0.005 -10000 0 0 21 21
EXOC7 0.036 0.004 -10000 0 0 5 5
E-cadherin/beta catenin 0.041 0.076 -10000 0 -0.29 17 17
mol:Phosphatidic acid 0.017 0.062 -10000 0 -0.16 28 28
endocytosis -0.027 0.044 0.1 46 -10000 0 46
SCAMP2 0.034 0.008 -10000 0 0 24 24
ADRB2 0.013 0.086 0.23 1 -0.34 19 20
EXOC3 0.035 0.006 -10000 0 0 16 16
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.022 0.01 0.088 1 -0.1 1 2
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.007 0.083 -10000 0 -0.34 20 20
RALA 0.026 0.017 -10000 0 0 143 143
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.022 0.08 0.22 2 -0.29 18 20
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.033 0.028 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.009 0.019 -10000 0 -10000 0 0
mol:DAG -0.018 0.033 0.19 1 -10000 0 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.017 -10000 0 -10000 0 0
CaM/Ca2+ -0.022 0.042 0.19 1 -0.19 2 3
HIF1A 0.04 0.012 -10000 0 -10000 0 0
GAB1 0.031 0.013 -10000 0 0 75 75
AKT1 -0.025 0.091 0.2 6 -0.31 22 28
PLCG1 -0.018 0.033 0.19 1 -10000 0 1
NOS3 0.005 0.069 -10000 0 -0.3 5 5
CBL 0.036 0.004 -10000 0 0 6 6
mol:NO 0.01 0.072 -10000 0 -0.29 5 5
FLT1 0.016 0.008 -10000 0 -10000 0 0
PGF 0.032 0.012 -10000 0 0 61 61
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.025 -10000 0 -10000 0 0
CALM1 0.033 0.011 -10000 0 0 49 49
PIK3CA 0.03 0.014 -10000 0 0 85 85
eNOS/Hsp90 0.002 0.068 -10000 0 -0.28 5 5
endothelial cell proliferation -0.003 0.046 0.19 2 -0.25 2 4
mol:Ca2+ -0.018 0.033 0.19 1 -10000 0 1
MAPK3 -0.027 0.031 0.15 1 -10000 0 1
MAPK1 -0.026 0.035 0.15 1 -0.19 2 3
PIK3R1 0.032 0.012 -10000 0 0 61 61
PLGF homodimer 0.032 0.012 -10000 0 0 61 61
PRKACA 0.034 0.009 -10000 0 0 29 29
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.018 -10000 0 0 269 269
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.009 0.019 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.027 0.044 -10000 0 -0.19 2 2
PI3K 0.034 0.078 -10000 0 -0.2 15 15
PRKCA -0.023 0.032 0.17 1 -10000 0 1
PRKCB -0.016 0.03 0.17 1 -10000 0 1
VEGFR1 homodimer/PLGF homodimer 0.03 0.028 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.036 0.005 -10000 0 0 9 9
mol:IP3 -0.018 0.033 0.19 1 -10000 0 1
RASA1 -0.025 0.027 0.19 1 -0.2 5 6
NRP2 0.036 0.005 -10000 0 0 9 9
VEGFR1 homodimer 0.016 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.036 0.005 -10000 0 0 9 9
NCK1 0.034 0.008 -10000 0 0 26 26
eNOS/Caveolin-1 0.006 0.07 -10000 0 -0.28 11 11
PTPN11 0.036 0.005 -10000 0 0 9 9
mol:PI-3-4-5-P3 0.032 0.077 -10000 0 -0.2 15 15
mol:L-citrulline 0.01 0.072 -10000 0 -0.29 5 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.04 0.043 -10000 0 -0.19 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.029 -10000 0 -0.19 1 1
CD2AP 0.033 0.01 -10000 0 0 43 43
PI3K/GAB1 0.037 0.086 -10000 0 -0.2 21 21
PDPK1 -0.026 0.072 0.24 4 -0.26 2 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.029 -10000 0 -0.19 1 1
mol:NADP 0.01 0.072 -10000 0 -0.29 5 5
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.042 -10000 0 -0.19 3 3
VEGFR1 homodimer/NRP2 0.032 0.028 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.033 0.019 0.079 9 -0.055 14 23
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.08 -10000 0 -0.24 17 17
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.011 -10000 0 -0.13 2 2
NFKBIA -0.031 0.047 0.2 3 -0.28 12 15
BIRC2 0.035 0.005 -10000 0 0 11 11
IKBKB 0.036 0.004 -10000 0 0 6 6
RIPK2 0.035 0.005 -10000 0 0 11 11
IKBKG 0.019 0.05 -10000 0 -0.25 11 11
IKK complex/A20 0.058 0.073 -10000 0 -0.27 5 5
NEMO/A20/RIP2 0.035 0.005 -10000 0 0 11 11
XPO1 0.036 0.004 -10000 0 0 5 5
NEMO/ATM 0.037 0.057 -10000 0 -0.31 6 6
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 0 13 13
Exportin 1/RanGTP 0.046 0.023 -10000 0 -0.15 6 6
IKK complex/ELKS 0.03 0.052 -10000 0 -0.25 4 4
BCL10/MALT1/TRAF6 0.063 0.034 -10000 0 -0.12 10 10
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.034 0.019 0.079 10 -0.056 15 25
RELA 0.034 0.019 0.079 10 -0.055 16 26
MALT1 0.034 0.009 -10000 0 0 29 29
cIAP1/UbcH5C 0.049 0.028 -10000 0 -0.18 6 6
ATM 0.034 0.01 -10000 0 0 36 36
TNF/TNFR1A 0.035 0.055 -10000 0 -0.14 41 41
TRAF6 0.036 0.005 -10000 0 0 8 8
PRKCA 0.036 0.004 -10000 0 0 5 5
CHUK 0.026 0.016 -10000 0 0 133 133
UBE2D3 0.035 0.005 -10000 0 0 11 11
TNF 0.036 0.004 -10000 0 0 6 6
NF kappa B1 p50/RelA 0.064 0.059 -10000 0 -0.17 25 25
BCL10 0.035 0.006 -10000 0 0 15 15
proteasomal ubiquitin-dependent protein catabolic process -0.031 0.047 0.2 3 -0.28 12 15
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.019 0.079 9 -0.055 14 23
TNFRSF1A 0.032 0.012 -10000 0 0 61 61
IKK complex 0.041 0.06 -10000 0 -0.27 4 4
CYLD 0.035 0.006 -10000 0 0 15 15
IKK complex/PKC alpha 0.051 0.067 -10000 0 -0.27 4 4
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.01 0.002 0.012 1 -10000 0 1
SMARCC1 -0.005 0.12 -10000 0 -1.2 4 4
REL 0.035 0.004 -10000 0 -0.01 3 3
HDAC7 -0.029 0.057 0.17 5 -0.21 18 23
JUN 0.034 0.01 -10000 0 0 39 39
EP300 0.033 0.011 -10000 0 0 49 49
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.017 0.018 0.044 11 -10000 0 11
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR 0.018 0.078 0.24 3 -0.22 18 21
MAP2K6 0.035 0.011 -10000 0 -0.035 10 10
BRM/BAF57 0.046 0.024 -10000 0 -0.14 3 3
MAP2K4 0.034 0.013 -10000 0 -0.034 11 11
SMARCA2 0.032 0.012 -10000 0 -10000 0 0
PDE9A -0.013 0.19 -10000 0 -0.79 26 26
NCOA2 0.036 0.005 -10000 0 0 9 9
CEBPA 0.028 0.015 -10000 0 0 115 115
EHMT2 0.036 0.004 -10000 0 0 5 5
cell proliferation -0.024 0.086 0.25 2 -0.32 12 14
NR0B1 0.03 0.014 -10000 0 0 83 83
EGR1 0.029 0.015 -10000 0 -10000 0 0
RXRs/9cRA 0.066 0.019 -10000 0 -0.11 1 1
AR/RACK1/Src -0.021 0.05 0.17 7 -0.22 2 9
AR/GR 0.002 0.06 0.16 1 -0.2 24 25
GNB2L1 0.036 0.005 -10000 0 0 11 11
PKN1 0.032 0.012 -10000 0 0 58 58
RCHY1 0.035 0.006 -10000 0 0 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.012 0.016 0.032 15 -0.053 1 16
T-DHT/AR/TIF2/CARM1 0.014 0.054 0.2 3 -0.19 4 7
SRC -0.022 0.029 0.18 3 -10000 0 3
NR3C1 0.034 0.008 -10000 0 0 24 24
KLK3 -0.011 0.077 0.42 1 -10000 0 1
APPBP2 0.034 0.014 -10000 0 -0.033 14 14
TRIM24 0.025 0.017 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.023 0.029 0.083 2 -0.15 8 10
TMPRSS2 0.015 0.081 -10000 0 -0.56 7 7
RXRG 0.035 0.006 -10000 0 0 13 13
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.035 0.007 -10000 0 0 18 18
RXRB 0.036 0.002 -10000 0 0 2 2
CARM1 0.034 0.01 -10000 0 0 36 36
NR2C2 0.036 0.004 -10000 0 0 6 6
KLK2 0.001 0.041 -10000 0 -0.24 2 2
AR -0.004 0.043 0.14 3 -0.19 18 21
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -0.001 50 50
SRY 0.035 0.004 -10000 0 -0.009 4 4
GATA2 0.035 0.006 -10000 0 0 14 14
MYST2 0.034 0.009 -10000 0 0 32 32
HOXB13 0.037 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.023 0.051 0.17 9 -0.23 2 11
positive regulation of transcription 0.035 0.006 -10000 0 0 14 14
DNAJA1 0.031 0.016 -10000 0 -0.033 14 14
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.033 -10000 0 -0.27 6 6
NCOA1 0.039 0.023 0.13 5 -0.18 2 7
SPDEF 0.037 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.027 0.082 0.17 1 -0.25 37 38
T-DHT/AR/Hsp90 -0.023 0.029 0.083 2 -0.15 8 10
GSK3B 0.034 0.01 -10000 0 0 35 35
NR2C1 0.036 0.004 -10000 0 0 5 5
mol:T-DHT -0.019 0.025 0.077 8 -0.12 4 12
SIRT1 0.026 0.017 -10000 0 0 143 143
ZMIZ2 -0.001 0.001 -10000 0 -0.019 1 1
POU2F1 0.037 0.033 0.12 12 -0.11 19 31
T-DHT/AR/DAX-1 -0.021 0.036 0.18 1 -0.19 2 3
CREBBP 0.036 0.004 -10000 0 0 5 5
SMARCE1 0.036 0.004 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.007 -10000 0 0 20 20
Ran/GTP/Exportin 1/HDAC4 -0.032 0.03 -10000 0 -0.13 33 33
MDM2/SUMO1 0.033 0.052 -10000 0 -0.22 4 4
HDAC4 0.034 0.008 -10000 0 0 24 24
Ran/GTP/Exportin 1/HDAC1 -0.031 0.03 -10000 0 -0.14 25 25
SUMO1 0.036 0.003 -10000 0 0 3 3
NPC/RanGAP1/SUMO1 0.005 0.033 -10000 0 -0.15 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.008 0.041 -10000 0 -0.16 20 20
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 0 13 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.008 -10000 0 0 24 24
SUMO1/HDAC4 0.034 0.056 -10000 0 -0.22 5 5
SUMO1/HDAC1 0.036 0.054 -10000 0 -0.22 5 5
RANGAP1 0.033 0.01 -10000 0 0 43 43
MDM2/SUMO1/SUMO1 0.074 0.047 -10000 0 -0.12 14 14
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.007 0.033 -10000 0 -0.15 20 20
Ran/GTP 0.019 0.049 -10000 0 -0.15 20 20
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.011 -10000 0 0 49 49
UBE2I 0.036 0.003 -10000 0 0 3 3
Ran/GTP/Exportin 1 0.013 0.052 0.21 2 -0.16 20 22
NPC 0.017 0.021 -10000 0 -0.088 18 18
PIAS2 0.035 0.006 -10000 0 0 15 15
PIAS1 0.035 0.008 -10000 0 0 23 23
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.035 0.029 -9999 0 -0.095 20 20
MAPK9 0.008 0.001 -9999 0 0 12 12
adrenocorticotropin secretion -0.011 0.002 0 15 -10000 0 15
GNB1/GNG2 0.018 0.026 -9999 0 -0.11 20 20
GNB1 0.033 0.01 -9999 0 0 37 37
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.008 0.001 -9999 0 0 6 6
Gs family/GTP 0.023 0.004 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.002 0 -9999 0 -10000 0 0
GNAL 0.035 0.006 -9999 0 0 13 13
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.035 0.006 -9999 0 0 15 15
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.006 0.003 -9999 0 0 133 133
MAPK11 0.007 0.002 -9999 0 0 48 48
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.004 0.026 0.14 11 -0.18 3 14
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.044 0.12 3 -0.15 10 13
AP2 0.021 0.027 -10000 0 -0.13 14 14
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.037 -10000 0 -0.12 17 17
CLTB 0.036 0.005 -10000 0 0 8 8
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.031 -10000 0 -0.18 11 11
CD4 0.031 0.013 -10000 0 0 71 71
CLTA 0.033 0.01 -10000 0 0 38 38
mol:GTP -0.003 0.002 0.007 1 -0.018 7 8
ARFGAP1 -0.011 0.002 0 17 -10000 0 17
mol:PI-4-5-P2 0.008 0.018 0.1 11 -10000 0 11
ARF1/GTP 0.018 0.017 -10000 0 -0.11 7 7
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.033 -10000 0 -0.18 10 10
mol:Choline 0.007 0.018 0.1 14 -10000 0 14
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.035 0.008 -10000 0 0 21 21
DDEF1 0.005 0.017 0.097 12 -10000 0 12
ARF1/GDP 0.006 0.014 -10000 0 -0.087 7 7
AP2M1 0.034 0.01 -10000 0 0 36 36
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.019 0.065 1 -0.11 10 11
Rac/GTP 0.018 0.021 -10000 0 -0.14 6 6
ARF1/GTP/GGA3/ARF-GAP1 0.043 0.023 -10000 0 -0.1 8 8
ARFIP2 0.031 0.016 -10000 0 -0.037 17 17
COPA 0.035 0.006 -10000 0 0 13 13
RAC1 0.027 0.016 -10000 0 0 123 123
ARF1/GTP/coatomer protein complex 0.005 0.042 -10000 0 -0.18 10 10
ARF1/GTP/ARHGAP10 0.021 0.016 -10000 0 -0.11 6 6
GGA3 0.036 0.004 -10000 0 0 7 7
ARF1/GTP/Membrin 0.028 0.023 -10000 0 -0.25 2 2
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.037 -10000 0 -0.18 11 11
ARF1/GDP/Membrin 0.031 0.026 -10000 0 -0.28 2 2
Arfaptin 2/Rac/GDP 0.03 0.036 -10000 0 -0.12 17 17
CYTH2 -0.003 0.002 0.007 1 -0.018 7 8
ARF1/GTP/GGA3 0.044 0.021 -10000 0 -0.12 6 6
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.02 -10000 0 -0.13 6 6
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.003 0.059 -10000 0 -0.19 31 31
PLD2 0.007 0.018 0.1 14 -10000 0 14
ARF-GAP1/v-SNARE -0.011 0.002 0 17 -10000 0 17
PIP5K1A 0.008 0.018 0.1 11 -10000 0 11
ARF1/GTP/Membrin/GBF1/p115 0.005 0.034 -10000 0 -0.11 6 6
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.018 0.1 14 -10000 0 14
KDEL Receptor/Ligand/ARF-GAP1 -0.011 0.002 0 17 -10000 0 17
GOSR2 0.015 0.018 -10000 0 -0.32 1 1
USO1 0.001 0.005 0.034 5 -0.03 4 9
GBF1 -0.06 0.14 -10000 0 -0.31 112 112
ARF1/GTP/Arfaptin 2 0.041 0.034 -10000 0 -0.12 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.045 -10000 0 -0.12 32 32
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.053 0.018 -10000 0 -10000 0 0
KIRREL 0.038 0.009 -10000 0 -0.041 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.053 0.018 -10000 0 -10000 0 0
PLCG1 0.035 0.007 -10000 0 0 20 20
ARRB2 0.034 0.008 -10000 0 0 27 27
WASL 0.025 0.017 -10000 0 0 155 155
Nephrin/NEPH1/podocin/CD2AP 0.081 0.049 -10000 0 -0.12 15 15
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.015 0.034 -10000 0 -0.19 6 6
FYN -0.005 0.049 0.17 30 -10000 0 30
mol:Ca2+ 0.084 0.036 -10000 0 -0.12 3 3
mol:DAG 0.086 0.037 -10000 0 -0.13 3 3
NPHS2 0.039 0.008 -10000 0 -0.041 1 1
mol:IP3 0.086 0.037 -10000 0 -0.13 3 3
regulation of endocytosis 0.051 0.05 -10000 0 -0.14 5 5
Nephrin/NEPH1/podocin/Cholesterol 0.068 0.027 -10000 0 -10000 0 0
establishment of cell polarity 0.053 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.093 0.058 -10000 0 -0.14 16 16
Nephrin/NEPH1/beta Arrestin2 0.053 0.052 -10000 0 -0.14 5 5
NPHS1 0.038 0.011 0.076 6 -10000 0 6
Nephrin/NEPH1/podocin 0.051 0.044 -10000 0 -0.11 1 1
TJP1 0.034 0.009 -10000 0 0 34 34
NCK1 0.034 0.008 -10000 0 0 26 26
NCK2 0.035 0.007 -10000 0 0 19 19
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.087 0.037 -10000 0 -0.13 3 3
CD2AP 0.033 0.01 -10000 0 0 43 43
Nephrin/NEPH1/podocin/GRB2 0.086 0.04 -10000 0 -0.13 5 5
GRB2 0.035 0.006 -10000 0 0 16 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.011 0.054 0.17 33 -10000 0 33
cytoskeleton organization -0.01 0.03 0.2 4 -0.2 2 6
Nephrin/NEPH1 0.045 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.063 0.037 -10000 0 -0.14 8 8
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.036 0.003 -9999 0 0 4 4
Aurora C/Aurora B/INCENP 0.059 0.026 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.004 0.064 -9999 0 -0.39 12 12
AURKB 0.033 0.01 -9999 0 0 39 39
AURKC 0.033 0.011 -9999 0 0 47 47
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 0.033 0.03 -10000 0 -10000 0 0
IHH 0.051 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 0.017 0.027 -10000 0 -0.11 15 15
LRPAP1 0.035 0.006 -10000 0 0 16 16
dorsoventral neural tube patterning -0.017 0.027 0.11 15 -10000 0 15
SMO/beta Arrestin2 0.078 0.055 0.25 5 -10000 0 5
SMO 0.027 0.031 -10000 0 -10000 0 0
AKT1 -0.014 0.14 -10000 0 -0.46 30 30
ARRB2 0.034 0.008 -10000 0 0 27 27
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.035 0.006 -10000 0 0 14 14
heart looping 0.027 0.031 -10000 0 -10000 0 0
STIL 0.031 0.079 0.18 89 -10000 0 89
DHH N/PTCH2 0.027 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.016 0.019 -10000 0 -10000 0 0
PIK3CA 0.03 0.014 -10000 0 0 85 85
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.023 0.01 -10000 0 -10000 0 0
determination of left/right symmetry 0.027 0.031 -10000 0 -10000 0 0
PIK3R1 0.032 0.012 -10000 0 0 61 61
skeletal system development 0.03 0.033 -10000 0 -10000 0 0
IHH N/Hhip 0.033 0.007 -10000 0 -10000 0 0
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.027 0.031 -10000 0 -10000 0 0
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.035 0.007 -10000 0 0 20 20
PI3K 0.016 0.075 -10000 0 -0.16 73 73
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.03 0.014 -10000 0 0 83 83
somite specification 0.027 0.031 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH1 0.021 0.027 0.16 2 -10000 0 2
SHH Np/Cholesterol/PTCH2 0.024 0.014 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.024 0.014 -10000 0 -10000 0 0
SHH -0.017 0.01 -10000 0 -10000 0 0
catabolic process 0.02 0.025 0.14 21 -10000 0 21
SMO/Vitamin D3 0.023 0.035 0.18 12 -10000 0 12
SHH Np/Cholesterol/Hhip -0.012 0.007 -10000 0 -10000 0 0
LRP2 0.035 0.006 -10000 0 0 12 12
receptor-mediated endocytosis 0.024 0.038 0.25 3 -10000 0 3
SHH Np/Cholesterol/BOC -0.012 0.007 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.024 0.014 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.012 0.007 -10000 0 -10000 0 0
mol:Vitamin D3 0.055 0.074 0.19 102 -10000 0 102
IHH N/PTCH2 0.06 0.01 -10000 0 -10000 0 0
CDON 0.036 0.003 -10000 0 0 4 4
IHH N/PTCH1 0.046 0.027 -10000 0 -10000 0 0
Megalin/LRPAP1 0.048 0.028 -10000 0 -0.14 9 9
PTCH2 0.036 0.004 -10000 0 0 5 5
SHH Np/Cholesterol 0.014 0.008 -10000 0 -10000 0 0
PTCH1 0.02 0.025 0.14 21 -10000 0 21
HHIP 0 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.033 0.012 -10000 0 -10000 0 0
SVIL 0.024 0.018 -10000 0 -10000 0 0
ZNF318 0.034 0.005 -10000 0 -0.045 1 1
JMJD2C 0.035 0.014 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.052 0.04 -10000 0 -10000 0 0
CARM1 0.034 0.01 -10000 0 -10000 0 0
PRDX1 0.035 0.007 -10000 0 0 19 19
PELP1 0.035 0.007 -10000 0 0 19 19
CTNNB1 0.035 0.007 -10000 0 -10000 0 0
AKT1 0.032 0.012 -10000 0 -0.031 1 1
PTK2B 0.036 0.006 -10000 0 -10000 0 0
MED1 0 0 -10000 0 -10000 0 0
MAK 0.033 0.008 -10000 0 -0.045 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.022 0.018 -10000 0 -10000 0 0
GSN 0.032 0.013 -10000 0 -10000 0 0
NCOA2 0.036 0.005 -10000 0 -10000 0 0
NCOA6 0.034 0.01 -10000 0 -10000 0 0
DNA-PK 0.055 0.047 -10000 0 -0.14 19 19
NCOA4 0.027 0.016 -10000 0 0 121 121
PIAS3 0.035 0.007 -10000 0 -10000 0 0
cell proliferation 0.021 0.046 -10000 0 -0.44 4 4
XRCC5 0.035 0.004 -10000 0 0 7 7
UBE3A 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.031 0.032 0.11 1 -0.071 31 32
FHL2 -0.018 0.18 -10000 0 -0.68 31 31
RANBP9 0.036 0.006 -10000 0 -10000 0 0
JMJD1A 0.044 0.011 -10000 0 -10000 0 0
CDK6 0.024 0.017 -10000 0 0 156 156
TGFB1I1 0.033 0.012 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.033 0.056 -10000 0 -0.11 29 29
XRCC6 0.033 0.01 -10000 0 0 37 37
T-DHT/AR 0.047 0.058 0.21 1 -0.13 31 32
CTDSP1 0.035 0.006 -10000 0 -10000 0 0
CTDSP2 0.029 0.013 -10000 0 -0.039 1 1
BRCA1 0.036 0.007 -10000 0 -10000 0 0
TCF4 0.031 0.012 -10000 0 -0.035 1 1
CDKN2A 0.005 0.012 -10000 0 -10000 0 0
SRF 0.039 0.054 -10000 0 -0.15 31 31
NKX3-1 0.026 0.068 -10000 0 -0.3 14 14
KLK3 0.014 0.05 -10000 0 -10000 0 0
TMF1 0.035 0.007 -10000 0 -10000 0 0
HNRNPA1 -0.001 0 -10000 0 -10000 0 0
AOF2 0.034 0.011 -10000 0 -10000 0 0
APPL1 -0.011 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.05 0.04 -10000 0 -10000 0 0
AR 0.035 0.03 -10000 0 -0.068 31 31
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 -0.001 0 -10000 0 -10000 0 0
PAWR 0.035 0.006 -10000 0 -10000 0 0
PRKDC 0.033 0.01 -10000 0 0 42 42
PA2G4 0.034 0.008 -10000 0 -0.032 1 1
UBE2I 0.036 0.003 -10000 0 0 3 3
T-DHT/AR/Cyclin D3/CDK11 p58 0.044 0.044 -10000 0 -0.1 11 11
RPS6KA3 0.036 0.007 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.04 0.045 -10000 0 -0.1 5 5
LATS2 -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.045 0.042 -10000 0 -0.12 8 8
Cyclin D3/CDK11 p58 0.021 0.028 -10000 0 -0.13 16 16
VAV3 0.029 0.015 -10000 0 -10000 0 0
KLK2 0.025 0.054 -10000 0 -0.32 9 9
CASP8 0.035 0.006 -10000 0 0 13 13
T-DHT/AR/TIF2/CARM1 0.065 0.048 -10000 0 -0.11 1 1
TMPRSS2 0.024 0.068 -10000 0 -0.3 14 14
CCND1 0.028 0.015 -10000 0 -10000 0 0
PIAS1 0.036 0.008 -10000 0 -10000 0 0
mol:T-DHT 0.004 0.016 0.051 1 -0.049 31 32
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.035 0.009 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.038 0.039 -10000 0 -10000 0 0
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.016 0.051 1 -0.049 31 32
CCND3 0.034 0.008 -10000 0 0 25 25
TGIF1 -0.001 0 -10000 0 -10000 0 0
FKBP4 0.034 0.009 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL 0.043 0.18 0.46 2 -0.66 15 17
PCK1 0.048 0.12 0.48 3 -0.59 3 6
HNF4A 0.055 0.16 0.57 2 -0.67 6 8
KCNJ11 0.064 0.17 0.46 3 -0.58 13 16
AKT1 0.062 0.12 0.36 1 -0.38 11 12
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.076 0.18 0.58 2 -0.67 7 9
NKX2-1 0.031 0.1 0.27 3 -0.35 8 11
ACADM 0.049 0.17 0.52 1 -0.75 8 9
TAT 0.046 0.13 0.55 1 -0.64 5 6
CEBPB 0.034 0.014 0.12 1 -10000 0 1
CEBPA 0.031 0.017 -10000 0 -10000 0 0
TTR 0.028 0.17 0.45 10 -0.6 11 21
PKLR 0.055 0.16 0.52 1 -0.68 6 7
APOA1 0.073 0.2 0.62 3 -0.82 6 9
CPT1C 0.052 0.15 0.44 3 -0.56 11 14
ALAS1 0.033 0.23 -10000 0 -1.3 12 12
TFRC 0.018 0.29 0.57 2 -0.97 33 35
FOXF1 0.031 0.013 -10000 0 -10000 0 0
NF1 0.035 0.033 -10000 0 -0.17 12 12
HNF1A (dimer) 0.006 0.005 0.11 1 -10000 0 1
CPT1A 0.051 0.15 0.52 1 -0.69 5 6
HMGCS1 0.055 0.16 0.51 3 -0.68 6 9
NR3C1 0.046 0.02 -10000 0 -10000 0 0
CPT1B 0.043 0.15 0.46 2 -0.68 6 8
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.005 -10000 0 -10000 0 0
GCK 0.08 0.17 0.49 8 -0.62 6 14
CREB1 0.043 0.013 0.15 1 -10000 0 1
IGFBP1 0.053 0.13 0.52 1 -0.63 5 6
PDX1 0.053 0.1 0.32 3 -0.33 6 9
UCP2 0.026 0.23 0.5 3 -0.66 37 40
ALDOB 0.068 0.18 0.49 2 -0.73 6 8
AFP 0.015 0.031 0.3 1 -10000 0 1
BDH1 0.046 0.18 0.51 2 -0.67 15 17
HADH 0.064 0.17 0.46 3 -0.58 13 16
F2 0.072 0.2 0.76 1 -0.84 6 7
HNF1A 0.006 0.005 0.11 1 -10000 0 1
G6PC 0.008 0.081 0.41 1 -10000 0 1
SLC2A2 0.06 0.12 0.43 1 -0.46 1 2
INS 0.024 0.041 0.18 12 -0.092 35 47
FOXA1 0.014 0.012 0.14 2 -10000 0 2
FOXA3 0.019 0.056 0.25 2 -0.18 23 25
FOXA2 0.099 0.21 0.62 3 -0.67 13 16
ABCC8 0.065 0.18 0.52 1 -0.63 10 11
ALB 0.016 0.032 0.3 1 -10000 0 1
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.036 0.005 -10000 0 0 8 8
GNAT1/GTP 0.026 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.047 0.01 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.047 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.035 0.006 -10000 0 0 12 12
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.068 0.023 -10000 0 -10000 0 0
mol:Na + 0.043 0.015 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.045 0.014 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.054 0.018 -10000 0 -10000 0 0
CNGB1 0.035 0.006 -10000 0 0 12 12
RDH5 0.034 0.008 -10000 0 0 24 24
SAG 0.036 0.005 -10000 0 0 9 9
mol:Ca2+ -0.032 0.028 0.16 9 -10000 0 9
Na + (4 Units) 0.041 0.017 -10000 0 -10000 0 0
RGS9 0.035 0.006 -10000 0 0 15 15
GNB1/GNGT1 0.03 0.039 -10000 0 -0.14 14 14
GNAT1/GDP 0.058 0.02 -10000 0 -0.1 1 1
GUCY2D 0.035 0.005 -10000 0 0 11 11
GNGT1 0.025 0.017 -10000 0 0 148 148
GUCY2F 0.036 0 -10000 0 -10000 0 0
GNB5 0.035 0.007 -10000 0 0 18 18
mol:GMP (4 units) 0.028 0.008 -10000 0 -10000 0 0
mol:11-cis-retinal 0.034 0.008 -10000 0 0 24 24
mol:cGMP 0.028 0.006 -10000 0 -10000 0 0
GNB1 0.033 0.01 -10000 0 0 37 37
Rhodopsin 0.05 0.014 -10000 0 -10000 0 0
SLC24A1 0.036 0.005 -10000 0 0 8 8
CNGA1 0.036 0.004 -10000 0 0 7 7
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.045 0.008 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.006 0.037 -10000 0 -0.16 16 16
GCAP Family/Ca ++ 0.023 0.002 -10000 0 -10000 0 0
PDE6A/B 0.052 0.01 -10000 0 -10000 0 0
mol:Pi 0.045 0.014 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.041 0.042 -10000 0 -0.11 14 14
PDE6B 0.035 0.006 -10000 0 0 12 12
PDE6A 0.036 0.004 -10000 0 0 6 6
PDE6G 0.036 0.003 -10000 0 0 3 3
RHO 0.035 0.006 -10000 0 0 12 12
PDE6 0.083 0.026 -10000 0 -0.11 1 1
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.004 -10000 0 -10000 0 0
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.036 0.003 -10000 0 0 3 3
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.036 0.005 0 8 -9999 0 8
PI3K Class IB/PDE3B 0.036 0.005 -9999 0 0 8 8
PDE3B 0.036 0.005 -9999 0 0 8 8
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.047 0.007 -10000 0 -9999 0 0
EFNA5 0.036 0.003 -10000 0 0 4 4
FYN -0.019 0.013 0.18 1 -9999 0 1
neuron projection morphogenesis 0.047 0.007 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.048 0.007 -10000 0 -9999 0 0
EPHA5 0.036 0.005 -10000 0 0 8 8
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/407045/1.GDAC_MergeDataFiles.Finished/GBM.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/GBM/868470/1.GetReducedSegments.Finished/GBM.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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

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