Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression 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 71 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
Signaling events mediated by Stem cell factor receptor (c-Kit) 116
Signaling events regulated by Ret tyrosine kinase 113
Wnt signaling 99
FOXM1 transcription factor network 94
Syndecan-1-mediated signaling events 91
Endothelins 85
EGFR-dependent Endothelin signaling events 83
HIF-1-alpha transcription factor network 81
IGF1 pathway 81
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 79
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
Signaling events mediated by Stem cell factor receptor (c-Kit) 116 9125 78 -0.39 0.17 1000 -1000 -0.045 -1000
Signaling events regulated by Ret tyrosine kinase 113 9321 82 -0.23 0.018 1000 -1000 -0.057 -1000
Wnt signaling 99 694 7 -0.13 -0.011 1000 -1000 -0.009 -1000
FOXM1 transcription factor network 94 4807 51 -0.43 0.024 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 91 3109 34 -0.19 0.018 1000 -1000 -0.009 -1000
Endothelins 85 8247 96 -0.25 0.018 1000 -1000 -0.051 -1000
EGFR-dependent Endothelin signaling events 83 1757 21 -0.17 0.024 1000 -1000 -0.046 -1000
HIF-1-alpha transcription factor network 81 6163 76 -0.25 0.025 1000 -1000 -0.05 -1000
IGF1 pathway 81 4658 57 -0.14 0.057 1000 -1000 -0.058 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 79 5394 68 -0.43 0.22 1000 -1000 -0.083 -1000
Plasma membrane estrogen receptor signaling 72 6228 86 -0.2 0.19 1000 -1000 -0.062 -1000
TCGA08_retinoblastoma 70 561 8 -0.052 0.026 1000 -1000 -0.005 -1000
FAS signaling pathway (CD95) 69 3246 47 -0.16 0.072 1000 -1000 -0.027 -1000
Glucocorticoid receptor regulatory network 68 7807 114 -0.54 0.28 1000 -1000 -0.05 -1000
Noncanonical Wnt signaling pathway 67 1757 26 -0.13 0.018 1000 -1000 -0.016 -1000
IL4-mediated signaling events 67 6157 91 -0.52 0.39 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 67 6551 97 -0.15 0.038 1000 -1000 -0.056 -1000
IL27-mediated signaling events 65 3338 51 -0.27 0.17 1000 -1000 -0.053 -1000
IL6-mediated signaling events 65 4896 75 -0.18 0.043 1000 -1000 -0.029 -1000
TCR signaling in naïve CD8+ T cells 62 5789 93 -0.13 0.07 1000 -1000 -0.054 -1000
IL12-mediated signaling events 59 5182 87 -0.3 0.029 1000 -1000 -0.093 -1000
Osteopontin-mediated events 59 2262 38 -0.15 0.018 1000 -1000 -0.014 -1000
Arf6 signaling events 57 3588 62 -0.15 0.034 1000 -1000 -0.013 -1000
IL23-mediated signaling events 57 3423 60 -0.27 0.017 1000 -1000 -0.091 -1000
Thromboxane A2 receptor signaling 55 5871 105 -0.14 0.038 1000 -1000 -0.045 -1000
Stabilization and expansion of the E-cadherin adherens junction 54 4009 74 -0.14 0.03 1000 -1000 -0.06 -1000
Signaling events mediated by the Hedgehog family 52 2709 52 -0.16 0.056 1000 -1000 -0.015 -1000
Nongenotropic Androgen signaling 52 2742 52 -0.13 0.064 1000 -1000 -0.035 -1000
PLK2 and PLK4 events 49 149 3 -0.049 0.008 1000 -1000 -0.005 -1000
E-cadherin signaling events 49 249 5 -0.049 0.011 1000 -1000 -0.006 -1000
BMP receptor signaling 48 3902 81 -0.23 0.046 1000 -1000 -0.055 -1000
Syndecan-4-mediated signaling events 48 3263 67 -0.08 0.022 1000 -1000 -0.023 -1000
ErbB4 signaling events 44 3101 69 -0.17 0.097 1000 -1000 -0.058 -1000
Ephrin B reverse signaling 43 2083 48 -0.14 0.021 1000 -1000 -0.043 -1000
amb2 Integrin signaling 41 3384 82 -0.12 0.023 1000 -1000 -0.048 -1000
LPA receptor mediated events 41 4248 102 -0.13 0.018 1000 -1000 -0.045 -1000
Syndecan-2-mediated signaling events 40 2798 69 -0.072 0.022 1000 -1000 -0.018 -1000
IL2 signaling events mediated by PI3K 40 2376 58 -0.23 0.018 1000 -1000 -0.051 -1000
BCR signaling pathway 40 4036 99 -0.16 0.043 1000 -1000 -0.053 -1000
Caspase cascade in apoptosis 39 2894 74 -0.085 0.044 1000 -1000 -0.019 -1000
TCGA08_p53 39 277 7 -0.037 0.028 1000 -1000 -0.004 -1000
Signaling events mediated by PTP1B 38 2924 76 -0.15 0.055 1000 -1000 -0.046 -1000
Integrins in angiogenesis 37 3166 84 -0.18 0.031 1000 -1000 -0.057 -1000
Visual signal transduction: Rods 37 1959 52 -0.1 0.027 1000 -1000 -0.053 -1000
Canonical Wnt signaling pathway 36 1865 51 -0.25 0.098 1000 -1000 -0.032 -1000
Calcium signaling in the CD4+ TCR pathway 36 1132 31 -0.14 0.026 1000 -1000 -0.046 -1000
Ras signaling in the CD4+ TCR pathway 35 598 17 -0.038 0.013 1000 -1000 -0.017 -1000
Cellular roles of Anthrax toxin 34 1330 39 -0.14 0.018 1000 -1000 -0.012 -1000
Glypican 1 network 34 1635 48 -0.064 0.017 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 34 1532 45 -0.13 0.018 1000 -1000 -0.06 -1000
Glypican 2 network 34 138 4 -0.016 0 1000 -1000 -0.004 -1000
E-cadherin signaling in keratinocytes 34 1462 43 -0.079 0.018 1000 -1000 -0.017 -1000
Coregulation of Androgen receptor activity 33 2546 76 -0.18 0.029 1000 -1000 -0.022 -1000
IL1-mediated signaling events 33 2104 62 -0.082 0.051 1000 -1000 -0.054 -1000
Signaling mediated by p38-gamma and p38-delta 33 506 15 -0.07 0.014 1000 -1000 -0.005 -1000
Class IB PI3K non-lipid kinase events 33 99 3 -0.004 -1000 1000 -1000 -0.001 -1000
Regulation of nuclear SMAD2/3 signaling 32 4464 136 -0.2 0.066 1000 -1000 -0.024 -1000
Nectin adhesion pathway 32 2038 63 -0.11 0.024 1000 -1000 -0.054 -1000
Syndecan-3-mediated signaling events 32 1120 35 -0.099 0.033 1000 -1000 -0.024 -1000
E-cadherin signaling in the nascent adherens junction 32 2501 76 -0.078 0.024 1000 -1000 -0.054 -1000
Presenilin action in Notch and Wnt signaling 31 1941 61 -0.22 0.036 1000 -1000 -0.04 -1000
TRAIL signaling pathway 31 1523 48 -0.05 0.018 1000 -1000 -0.052 -1000
PDGFR-alpha signaling pathway 29 1294 44 -0.18 0.028 1000 -1000 -0.028 -1000
Reelin signaling pathway 29 1632 56 -0.089 0.038 1000 -1000 -0.052 -1000
Visual signal transduction: Cones 28 1097 38 -0.072 0.025 1000 -1000 -0.013 -1000
IFN-gamma pathway 27 1865 68 -0.086 0.023 1000 -1000 -0.06 -1000
Effects of Botulinum toxin 27 725 26 -0.17 0.019 1000 -1000 -0.009 -1000
IL2 signaling events mediated by STAT5 27 598 22 -0.073 0.021 1000 -1000 -0.018 -1000
Class I PI3K signaling events 27 2022 73 -0.089 0.031 1000 -1000 -0.031 -1000
Regulation of Telomerase 27 2802 102 -0.2 0.044 1000 -1000 -0.076 -1000
Insulin Pathway 27 2033 74 -0.16 0.05 1000 -1000 -0.057 -1000
Aurora B signaling 26 1787 67 -0.095 0.02 1000 -1000 -0.031 -1000
p75(NTR)-mediated signaling 25 3126 125 -0.13 0.036 1000 -1000 -0.056 -1000
FOXA2 and FOXA3 transcription factor networks 25 1178 46 -0.2 0.074 1000 -1000 -0.033 -1000
Ceramide signaling pathway 25 1967 76 -0.14 0.055 1000 -1000 -0.025 -1000
TCGA08_rtk_signaling 25 664 26 -0.079 0.039 1000 -1000 -0.006 -1000
PLK1 signaling events 24 2040 85 -0.1 0.028 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 24 1299 52 -0.11 0.037 1000 -1000 -0.036 -1000
Regulation of Androgen receptor activity 22 1601 70 -0.18 0.026 1000 -1000 -0.045 -1000
Sphingosine 1-phosphate (S1P) pathway 21 613 28 -0.079 0.021 1000 -1000 -0.014 -1000
S1P1 pathway 21 788 36 -0.061 0.018 1000 -1000 -0.045 -1000
Angiopoietin receptor Tie2-mediated signaling 21 1881 88 -0.16 0.052 1000 -1000 -0.072 -1000
ErbB2/ErbB3 signaling events 20 1329 65 -0.059 0.024 1000 -1000 -0.042 -1000
mTOR signaling pathway 20 1062 53 -0.037 0.035 1000 -1000 -0.039 -1000
VEGFR1 specific signals 20 1120 56 -0.035 0.026 1000 -1000 -0.019 -1000
Aurora A signaling 19 1146 60 -0.037 0.034 1000 -1000 -0.011 -1000
Arf6 downstream pathway 19 848 43 -0.022 0.019 1000 -1000 -0.028 -1000
HIF-2-alpha transcription factor network 19 858 43 -0.081 0.082 1000 -1000 -0.053 -1000
EPHB forward signaling 19 1645 85 -0.039 0.038 1000 -1000 -0.053 -1000
PDGFR-beta signaling pathway 19 1882 97 -0.082 0.036 1000 -1000 -0.054 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 18 1015 54 -0.092 0.031 1000 -1000 -0.06 -1000
JNK signaling in the CD4+ TCR pathway 18 308 17 -0.036 0.029 1000 -1000 -0.018 -1000
ceramide signaling pathway 18 906 49 -0.11 0.037 1000 -1000 -0.025 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 18 599 33 -0.074 0.049 1000 -1000 -0.018 -1000
p38 MAPK signaling pathway 18 812 44 -0.078 0.034 1000 -1000 -0.052 -1000
BARD1 signaling events 17 970 57 -0.041 0.04 1000 -1000 -0.018 -1000
Hedgehog signaling events mediated by Gli proteins 17 1137 65 -0.051 0.041 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class III 17 691 40 -0.077 0.034 1000 -1000 -0.014 -1000
Atypical NF-kappaB pathway 17 543 31 -0.074 0.028 1000 -1000 -0.019 -1000
Regulation of p38-alpha and p38-beta 17 964 54 -0.074 0.043 1000 -1000 -0.038 -1000
Signaling events mediated by PRL 17 602 34 -0.095 0.026 1000 -1000 -0.016 -1000
Retinoic acid receptors-mediated signaling 16 976 58 -0.085 0.04 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 16 726 44 -0.09 0.025 1000 -1000 -0.015 -1000
Signaling events mediated by VEGFR1 and VEGFR2 16 2007 125 -0.06 0.055 1000 -1000 -0.065 -1000
S1P3 pathway 16 697 42 -0.079 0.021 1000 -1000 -0.015 -1000
Neurotrophic factor-mediated Trk receptor signaling 16 1990 120 -0.12 0.053 1000 -1000 -0.052 -1000
Paxillin-independent events mediated by a4b1 and a4b7 15 576 37 -0.023 0.028 1000 -1000 -0.018 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 15 1267 83 -0.11 0.057 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 14 174 12 -0.03 0.015 1000 -1000 -0.007 -1000
a4b1 and a4b7 Integrin signaling 14 70 5 -0.007 0.018 1000 -1000 -0.005 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 14 1247 85 -0.14 0.039 1000 -1000 -0.051 -1000
EPO signaling pathway 13 745 55 -0.15 0.024 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class II 12 949 75 -0.16 0.039 1000 -1000 -0.032 -1000
Paxillin-dependent events mediated by a4b1 12 432 36 -0.032 0.035 1000 -1000 -0.047 -1000
Nephrin/Neph1 signaling in the kidney podocyte 10 352 34 -0.009 0.035 1000 -1000 -0.015 -1000
Aurora C signaling 10 70 7 -0.007 0.016 1000 -1000 -0.022 -1000
Circadian rhythm pathway 9 201 22 -0.046 0.042 1000 -1000 -0.023 -1000
S1P5 pathway 9 161 17 -0.017 0.018 1000 -1000 -0.012 -1000
FoxO family signaling 9 612 64 -0.12 0.068 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 9 117 13 0 0.034 1000 -1000 -0.008 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 8 193 23 -0.03 0.033 1000 -1000 -0.014 -1000
Canonical NF-kappaB pathway 8 344 39 -0.056 0.06 1000 -1000 -0.058 -1000
Ephrin A reverse signaling 8 60 7 0 0.015 1000 -1000 -0.004 -1000
Class I PI3K signaling events mediated by Akt 6 417 68 -0.038 0.052 1000 -1000 -0.026 -1000
Arf6 trafficking events 6 433 71 -0.021 0.031 1000 -1000 -0.045 -1000
S1P4 pathway 6 166 25 -0.017 0.021 1000 -1000 -0.015 -1000
Insulin-mediated glucose transport 5 175 32 -0.015 0.033 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 5 542 104 -0.033 0.053 1000 -1000 -0.033 -1000
Rapid glucocorticoid signaling 5 117 20 -0.005 0.02 1000 -1000 -0.007 -1000
Arf1 pathway 3 165 54 -0.001 0.036 1000 -1000 -0.019 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 40 27 -0.001 0.04 1000 -1000 -0.037 -1000
Total 4471 264204 7203 -15 -990 131000 -131000 -4.7 -131000
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.15 0.21 -10000 0 -0.41 168 168
CRKL -0.16 0.22 -10000 0 -0.45 165 165
HRAS -0.12 0.19 -10000 0 -0.38 146 146
mol:PIP3 -0.15 0.2 0.24 1 -0.42 158 159
SPRED1 -0.002 0.098 -10000 0 -0.47 21 21
SPRED2 -0.003 0.1 -10000 0 -0.5 21 21
GAB1 -0.17 0.23 -10000 0 -0.47 168 168
FOXO3 -0.14 0.2 -10000 0 -0.42 154 154
AKT1 -0.16 0.21 -10000 0 -0.44 163 163
BAD -0.14 0.2 -10000 0 -0.41 153 153
megakaryocyte differentiation -0.17 0.23 -10000 0 -0.47 166 166
GSK3B -0.14 0.2 -10000 0 -0.41 154 154
RAF1 -0.088 0.16 -10000 0 -0.31 140 140
SHC1 0.017 0.023 -10000 0 -0.52 1 1
STAT3 -0.17 0.22 -10000 0 -0.47 163 163
STAT1 -0.37 0.49 -10000 0 -0.92 206 206
HRAS/SPRED1 -0.095 0.17 -10000 0 -0.32 145 145
cell proliferation -0.17 0.22 -10000 0 -0.45 165 165
PIK3CA 0.015 0.029 -10000 0 -0.34 3 3
TEC 0.013 0.052 -10000 0 -0.52 5 5
RPS6KB1 -0.17 0.22 -10000 0 -0.46 169 169
HRAS/SPRED2 -0.095 0.17 -10000 0 -0.34 107 107
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.45 163 163
MAPK3 -0.053 0.12 -10000 0 -0.26 59 59
STAP1 -0.19 0.24 -10000 0 -0.48 174 174
GRAP2 0.012 0.042 -10000 0 -0.28 10 10
JAK2 -0.31 0.4 -10000 0 -0.75 213 213
STAT1 (dimer) -0.36 0.47 -10000 0 -0.89 206 206
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.16 0.23 -10000 0 -0.45 168 168
actin filament polymerization -0.17 0.22 -10000 0 -0.4 221 221
LYN 0.014 0.031 -10000 0 -0.25 7 7
STAP1/STAT5A (dimer) -0.24 0.31 -10000 0 -0.64 166 166
PIK3R1 -0.01 0.11 -10000 0 -0.42 33 33
CBL/CRKL/GRB2 -0.13 0.2 -10000 0 -0.41 153 153
PI3K -0.16 0.23 -10000 0 -0.45 168 168
PTEN -0.001 0.1 -10000 0 -0.52 19 19
SCF/KIT/EPO/EPOR -0.39 0.54 -10000 0 -1.2 152 152
MAPK8 -0.17 0.22 -10000 0 -0.46 165 165
STAT3 (dimer) -0.17 0.22 -10000 0 -0.46 163 163
positive regulation of transcription -0.042 0.1 0.17 1 -0.21 54 55
mol:GDP -0.12 0.2 -10000 0 -0.39 153 153
PIK3C2B -0.17 0.22 -10000 0 -0.47 164 164
CBL/CRKL -0.14 0.21 -10000 0 -0.42 165 165
FER -0.17 0.22 -10000 0 -0.47 163 163
SH2B3 -0.17 0.22 -10000 0 -0.46 163 163
PDPK1 -0.14 0.18 0.23 1 -0.39 152 153
SNAI2 -0.19 0.25 -10000 0 -0.5 177 177
positive regulation of cell proliferation -0.27 0.36 -10000 0 -0.67 213 213
KITLG -0.096 0.2 -10000 0 -0.45 123 123
cell motility -0.27 0.36 -10000 0 -0.67 213 213
PTPN6 0.023 0.037 -10000 0 -0.43 3 3
EPOR -0.091 0.16 -10000 0 -0.96 2 2
STAT5A (dimer) -0.22 0.3 -10000 0 -0.56 213 213
SOCS1 0.015 0.031 -10000 0 -0.32 4 4
cell migration 0.17 0.22 0.45 174 -10000 0 174
SOS1 0.017 0.023 -10000 0 -0.52 1 1
EPO -0.03 0.099 -10000 0 -0.26 80 80
VAV1 -0.014 0.12 -10000 0 -0.39 42 42
GRB10 -0.18 0.23 -10000 0 -0.47 167 167
PTPN11 0.022 0.024 -10000 0 -0.5 1 1
SCF/KIT -0.18 0.23 -10000 0 -0.45 197 197
GO:0007205 0.008 0.011 -10000 0 -10000 0 0
MAP2K1 -0.063 0.13 -10000 0 -0.28 58 58
CBL 0.017 0.012 -10000 0 -0.25 1 1
KIT -0.33 0.53 -10000 0 -1.2 121 121
MAP2K2 -0.064 0.13 -10000 0 -0.27 74 74
SHC/Grb2/SOS1 -0.14 0.22 -10000 0 -0.43 161 161
STAT5A -0.23 0.31 -10000 0 -0.57 212 212
GRB2 0.016 0.024 -10000 0 -0.25 4 4
response to radiation -0.19 0.24 -10000 0 -0.49 177 177
SHC/GRAP2 0.022 0.034 -10000 0 -0.37 2 2
PTPRO -0.18 0.23 -10000 0 -0.48 166 166
SH2B2 -0.18 0.22 -10000 0 -0.41 221 221
DOK1 0.002 0.083 -10000 0 -0.41 19 19
MATK -0.18 0.23 -10000 0 -0.46 174 174
CREBBP 0.003 0.059 -10000 0 -0.54 2 2
BCL2 -0.33 0.55 -10000 0 -1.3 125 125
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.057 0.13 -9999 0 -0.74 13 13
Crk/p130 Cas/Paxillin -0.17 0.18 -9999 0 -0.4 163 163
JUN -0.17 0.21 -9999 0 -0.45 142 142
HRAS 0.012 0.051 -9999 0 -0.41 7 7
RET51/GFRalpha1/GDNF/GRB10 -0.21 0.22 -9999 0 -0.38 277 277
RAP1A 0.012 0.057 -9999 0 -0.52 6 6
FRS2 0.011 0.047 -9999 0 -0.27 13 13
RAP1A/GDP 0.009 0.041 -9999 0 -0.38 6 6
RET51/GFRalpha1/GDNF/DOK1 -0.21 0.22 -9999 0 -0.39 271 271
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.033 -9999 0 -0.52 2 2
RET9/GFRalpha1/GDNF/Enigma -0.1 0.14 -9999 0 -0.28 188 188
RHOA 0.005 0.08 -9999 0 -0.52 12 12
RAP1A/GTP -0.18 0.19 -9999 0 -0.36 245 245
GRB7 -0.017 0.1 -9999 0 -0.29 59 59
RET51/GFRalpha1/GDNF -0.2 0.21 -9999 0 -0.38 265 265
MAPKKK cascade -0.18 0.19 -9999 0 -0.45 145 145
BCAR1 0.017 0.012 -9999 0 -0.25 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.14 0.19 -9999 0 -0.35 199 199
lamellipodium assembly -0.16 0.16 -9999 0 -0.34 208 208
RET51/GFRalpha1/GDNF/SHC -0.2 0.21 -9999 0 -0.38 266 266
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
RET9/GFRalpha1/GDNF/SHC -0.1 0.14 -9999 0 -0.28 189 189
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.14 -9999 0 -0.28 190 190
MAPK3 -0.16 0.18 -9999 0 -0.43 135 135
DOK1 0.002 0.083 -9999 0 -0.41 19 19
DOK6 -0.028 0.14 -9999 0 -0.44 52 52
PXN 0.018 0 -9999 0 -10000 0 0
neurite development -0.16 0.19 -9999 0 -0.41 146 146
DOK5 -0.028 0.14 -9999 0 -0.38 60 60
GFRA1 -0.22 0.24 -9999 0 -0.43 282 282
MAPK8 -0.16 0.2 -9999 0 -0.43 145 145
HRAS/GTP -0.21 0.22 -9999 0 -0.52 145 145
tube development -0.091 0.13 -9999 0 -0.26 193 193
MAPK1 -0.17 0.18 -9999 0 -0.43 135 135
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.079 0.12 -9999 0 -0.24 189 189
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.015 0.035 -9999 0 -0.43 3 3
PDLIM7 0.017 0.012 -9999 0 -0.25 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.2 0.23 -9999 0 -0.4 251 251
SHC1 0.017 0.023 -9999 0 -0.52 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.2 0.21 -9999 0 -0.38 269 269
RET51/GFRalpha1/GDNF/Dok5 -0.22 0.23 -9999 0 -0.41 277 277
PRKCA 0.014 0.033 -9999 0 -0.25 8 8
HRAS/GDP 0.009 0.036 -9999 0 -0.29 7 7
CREB1 -0.14 0.19 -9999 0 -0.38 189 189
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.083 0.14 -9999 0 -0.25 192 192
RET51/GFRalpha1/GDNF/Grb7 -0.22 0.22 -9999 0 -0.4 275 275
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.18 0.23 -9999 0 -0.41 247 247
DOK4 0.013 0.047 -9999 0 -0.37 7 7
JNK cascade -0.16 0.2 -9999 0 -0.44 142 142
RET9/GFRalpha1/GDNF/FRS2 -0.11 0.14 -9999 0 -0.28 190 190
SHANK3 0.016 0.033 -9999 0 -0.52 2 2
RASA1 0.004 0.078 -9999 0 -0.42 16 16
NCK1 0.011 0.045 -9999 0 -0.28 12 12
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.077 0.12 -9999 0 -0.23 189 189
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.16 0.19 -9999 0 -0.43 133 133
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.17 0.21 -9999 0 -0.46 143 143
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.23 -9999 0 -0.54 131 131
PI3K -0.23 0.28 -9999 0 -0.53 217 217
SOS1 0.017 0.023 -9999 0 -0.52 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.09 0.14 -9999 0 -0.26 193 193
GRB10 -0.003 0.097 -9999 0 -0.43 24 24
activation of MAPKK activity -0.13 0.16 -9999 0 -0.37 122 122
RET51/GFRalpha1/GDNF/FRS2 -0.2 0.21 -9999 0 -0.38 268 268
GAB1 0.006 0.074 -9999 0 -0.43 14 14
IRS1 -0.048 0.17 -9999 0 -0.49 68 68
IRS2 -0.026 0.13 -9999 0 -0.39 57 57
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.19 0.24 -9999 0 -0.55 136 136
RET51/GFRalpha1/GDNF/PKC alpha -0.2 0.21 -9999 0 -0.38 265 265
GRB2 0.016 0.024 -9999 0 -0.25 4 4
PRKACA 0.018 0 -9999 0 -10000 0 0
GDNF 0.014 0.042 -9999 0 -0.45 4 4
RAC1 0.018 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.23 0.26 -9999 0 -0.43 274 274
Rac1/GTP -0.19 0.2 -9999 0 -0.41 208 208
RET9/GFRalpha1/GDNF -0.12 0.15 -9999 0 -0.32 188 188
GFRalpha1/GDNF -0.15 0.18 -9999 0 -0.37 188 188
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.34 214 214
FZD6 -0.077 0.2 -9999 0 -0.45 108 108
WNT6 -0.011 0.087 -9999 0 -0.26 54 54
WNT4 -0.062 0.18 -9999 0 -0.45 90 90
FZD3 -0.03 0.15 -9999 0 -0.48 51 51
WNT5A -0.084 0.2 -9999 0 -0.43 120 120
WNT11 -0.013 0.089 -9999 0 -0.26 57 57
FOXM1 transcription factor network

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
NFATC3 -0.24 0.57 -10000 0 -1.1 118 118
PLK1 0.024 0.058 -10000 0 -10000 0 0
BIRC5 -0.092 0.39 -10000 0 -1.4 40 40
HSPA1B -0.25 0.56 -10000 0 -1.1 128 128
MAP2K1 0.018 0.047 -10000 0 -0.3 1 1
BRCA2 -0.26 0.59 -10000 0 -1.1 124 124
FOXM1 -0.4 0.94 -10000 0 -1.7 127 127
XRCC1 -0.24 0.57 -10000 0 -1.1 111 111
FOXM1B/p19 -0.42 0.55 0.45 1 -1.2 142 143
Cyclin D1/CDK4 -0.3 0.57 -10000 0 -1 160 160
CDC2 -0.27 0.62 -10000 0 -1.2 118 118
TGFA -0.29 0.55 -10000 0 -1 151 151
SKP2 -0.24 0.57 -10000 0 -1.1 118 118
CCNE1 -0.019 0.1 -10000 0 -0.29 64 64
CKS1B -0.24 0.57 -10000 0 -1.1 122 122
RB1 -0.22 0.32 -10000 0 -0.84 80 80
FOXM1C/SP1 -0.31 0.67 -10000 0 -1.3 134 134
AURKB 0.011 0.13 -10000 0 -1.4 3 3
CENPF -0.26 0.6 -10000 0 -1.2 115 115
CDK4 0.013 0.032 -10000 0 -0.26 5 5
MYC -0.22 0.52 -10000 0 -0.97 130 130
CHEK2 0.011 0.073 -10000 0 -0.41 9 9
ONECUT1 -0.28 0.57 -10000 0 -1.1 144 144
CDKN2A -0.056 0.15 -10000 0 -0.33 108 108
LAMA4 -0.24 0.58 -10000 0 -1.1 119 119
FOXM1B/HNF6 -0.37 0.71 -10000 0 -1.4 145 145
FOS -0.34 0.64 -10000 0 -1.2 149 149
SP1 0.017 0.024 -10000 0 -0.52 1 1
CDC25B -0.24 0.57 -10000 0 -1.1 112 112
response to radiation 0 0.039 -10000 0 -10000 0 0
CENPB -0.24 0.57 -10000 0 -1.1 113 113
CENPA -0.27 0.61 -10000 0 -1.2 112 112
NEK2 -0.29 0.62 -10000 0 -1.2 135 135
HIST1H2BA -0.24 0.57 -10000 0 -1.1 116 116
CCNA2 -0.027 0.14 -10000 0 -0.4 57 57
EP300 0.014 0.047 -10000 0 -0.52 4 4
CCNB1/CDK1 -0.32 0.7 -10000 0 -1.4 114 114
CCNB2 -0.25 0.59 -10000 0 -1.1 122 122
CCNB1 -0.27 0.62 -10000 0 -1.2 119 119
ETV5 -0.25 0.58 -10000 0 -1.1 114 114
ESR1 -0.43 0.71 -10000 0 -1.2 219 219
CCND1 -0.31 0.6 -10000 0 -1.1 161 161
GSK3A 0.019 0.037 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.014 0.13 -10000 0 -0.35 53 53
CDK2 0.011 0.048 -10000 0 -0.31 10 10
G2/M transition of mitotic cell cycle 0 0.046 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.38 0.53 -10000 0 -1.2 133 133
GAS1 -0.32 0.64 -10000 0 -1.2 152 152
MMP2 -0.28 0.62 -10000 0 -1.2 129 129
RB1/FOXM1C -0.31 0.6 -10000 0 -1.1 163 163
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
Syndecan-1-mediated signaling events

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
TGFB1 0.017 0.023 -9999 0 -0.52 1 1
CCL5 -0.051 0.18 -9999 0 -0.49 71 71
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
FGFR/FGF2/Syndecan-1 -0.17 0.27 -9999 0 -0.46 180 180
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.16 0.26 -9999 0 -0.54 126 126
Syndecan-1/Syntenin -0.16 0.26 -9999 0 -0.53 129 129
MAPK3 -0.13 0.24 -9999 0 -0.52 109 109
HGF/MET 0.007 0.073 -9999 0 -0.38 13 13
TGFB1/TGF beta receptor Type II 0.017 0.023 -9999 0 -0.52 1 1
BSG 0.016 0.024 -9999 0 -0.25 4 4
keratinocyte migration -0.15 0.25 -9999 0 -0.53 126 126
Syndecan-1/RANTES -0.18 0.28 -9999 0 -0.52 159 159
Syndecan-1/CD147 -0.14 0.26 -9999 0 -0.54 117 117
Syndecan-1/Syntenin/PIP2 -0.15 0.25 -9999 0 -0.52 129 129
LAMA5 0.005 0.075 -9999 0 -0.41 15 15
positive regulation of cell-cell adhesion -0.15 0.24 -9999 0 -0.5 129 129
MMP7 -0.095 0.21 -9999 0 -0.44 129 129
HGF 0.008 0.069 -9999 0 -0.45 11 11
Syndecan-1/CASK -0.16 0.26 -9999 0 -0.44 180 180
Syndecan-1/HGF/MET -0.15 0.26 -9999 0 -0.55 116 116
regulation of cell adhesion -0.12 0.23 -9999 0 -0.51 106 106
HPSE -0.015 0.12 -9999 0 -0.39 43 43
positive regulation of cell migration -0.17 0.27 -9999 0 -0.46 180 180
SDC1 -0.17 0.27 -9999 0 -0.46 180 180
Syndecan-1/Collagen -0.17 0.27 -9999 0 -0.46 180 180
PPIB 0.014 0.044 -9999 0 -0.41 5 5
MET 0 0.075 -9999 0 -0.29 31 31
PRKACA 0.018 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
MAPK1 -0.13 0.24 -9999 0 -0.52 111 111
homophilic cell adhesion -0.16 0.26 -9999 0 -0.45 180 180
MMP1 -0.19 0.22 -9999 0 -0.38 269 269
Endothelins

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
AKT1 -0.043 0.26 0.28 61 -0.44 112 173
PTK2B 0.017 0.017 -10000 0 -0.25 2 2
mol:Ca2+ -0.071 0.26 -10000 0 -0.7 50 50
EDN1 -0.065 0.24 0.23 61 -0.46 115 176
EDN3 -0.1 0.18 -10000 0 -0.32 190 190
EDN2 -0.13 0.22 -10000 0 -0.41 185 185
HRAS/GDP -0.11 0.24 -10000 0 -0.48 112 112
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.087 0.22 -10000 0 -0.43 114 114
ADCY4 -0.043 0.21 -10000 0 -0.48 69 69
ADCY5 -0.06 0.22 -10000 0 -0.46 84 84
ADCY6 -0.041 0.21 -10000 0 -0.46 71 71
ADCY7 -0.046 0.22 -10000 0 -0.52 62 62
ADCY1 -0.04 0.21 -10000 0 -0.47 66 66
ADCY2 -0.075 0.24 -10000 0 -0.44 110 110
ADCY3 -0.044 0.21 -10000 0 -0.47 73 73
ADCY8 -0.043 0.21 -10000 0 -0.47 68 68
ADCY9 -0.05 0.22 -10000 0 -0.46 80 80
arachidonic acid secretion -0.12 0.26 -10000 0 -0.52 122 122
ETB receptor/Endothelin-1/Gq/GTP -0.079 0.18 -10000 0 -0.37 105 105
GNAO1 0.016 0.024 -10000 0 -0.25 4 4
HRAS 0.011 0.051 -10000 0 -0.41 7 7
ETA receptor/Endothelin-1/G12/GTP -0.002 0.27 0.35 77 -0.47 81 158
ETA receptor/Endothelin-1/Gs/GTP -0.007 0.26 0.33 77 -0.44 87 164
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.048 0.28 -10000 0 -0.64 63 63
EDNRB -0.03 0.13 -10000 0 -0.39 52 52
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.042 0.26 -10000 0 -0.62 58 58
CYSLTR1 -0.075 0.3 -10000 0 -0.6 95 95
SLC9A1 -0.01 0.15 -10000 0 -0.3 55 55
mol:GDP -0.12 0.26 -10000 0 -0.5 121 121
SLC9A3 -0.13 0.34 -10000 0 -0.65 131 131
RAF1 -0.13 0.25 -10000 0 -0.52 116 116
JUN -0.11 0.36 -10000 0 -0.98 62 62
JAK2 -0.043 0.26 0.28 61 -0.43 116 177
mol:IP3 -0.11 0.22 -10000 0 -0.46 113 113
ETA receptor/Endothelin-1 -0.019 0.32 0.42 77 -0.51 113 190
PLCB1 -0.086 0.18 -10000 0 -0.38 138 138
PLCB2 0.014 0.027 -10000 0 -0.39 2 2
ETA receptor/Endothelin-3 -0.074 0.19 -10000 0 -0.4 100 100
FOS -0.18 0.35 -10000 0 -0.95 80 80
Gai/GDP -0.007 0.14 -10000 0 -0.82 10 10
CRK 0.016 0.033 -10000 0 -0.52 2 2
mol:Ca ++ -0.14 0.32 -10000 0 -0.6 130 130
BCAR1 0.017 0.012 -10000 0 -0.25 1 1
PRKCB1 -0.13 0.24 -10000 0 -0.47 131 131
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.001 0.088 -10000 0 -0.44 19 19
GNAL 0.011 0.052 -10000 0 -0.33 11 11
Gs family/GDP -0.12 0.22 -10000 0 -0.46 115 115
ETA receptor/Endothelin-1/Gq/GTP -0.068 0.23 -10000 0 -0.44 104 104
MAPK14 -0.084 0.17 -10000 0 -0.4 82 82
TRPC6 -0.077 0.28 -10000 0 -0.76 47 47
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.018 0 -10000 0 -10000 0 0
GNAI1 -0.017 0.12 -10000 0 -0.38 46 46
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.096 0.18 -10000 0 -0.37 116 116
ETB receptor/Endothelin-2 -0.11 0.18 -10000 0 -0.4 135 135
ETB receptor/Endothelin-3 -0.09 0.16 -10000 0 -0.38 90 90
ETB receptor/Endothelin-1 -0.068 0.21 -10000 0 -0.39 121 121
MAPK3 -0.17 0.34 -10000 0 -0.81 94 94
MAPK1 -0.17 0.34 -10000 0 -0.81 94 94
Rac1/GDP -0.1 0.24 -10000 0 -0.48 110 110
cAMP biosynthetic process -0.047 0.22 0.27 1 -0.46 82 83
MAPK8 -0.089 0.29 -10000 0 -0.66 79 79
SRC 0.015 0.035 -10000 0 -0.43 3 3
ETB receptor/Endothelin-1/Gi/GTP -0.037 0.15 -10000 0 -0.37 54 54
p130Cas/CRK/Src/PYK2 -0.1 0.25 -10000 0 -0.52 107 107
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.1 0.24 -10000 0 -0.48 110 110
COL1A2 -0.12 0.38 -10000 0 -0.81 99 99
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.095 0.22 -10000 0 -0.4 150 150
mol:DAG -0.11 0.22 -10000 0 -0.46 113 113
MAP2K2 -0.15 0.28 -10000 0 -0.62 110 110
MAP2K1 -0.15 0.28 -10000 0 -0.62 106 106
EDNRA -0.003 0.2 0.23 59 -0.54 53 112
positive regulation of muscle contraction -0.031 0.22 0.25 56 -0.49 67 123
Gq family/GDP -0.13 0.21 -10000 0 -0.51 95 95
HRAS/GTP -0.12 0.23 -10000 0 -0.48 115 115
PRKCH -0.099 0.22 -10000 0 -0.45 109 109
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCA -0.098 0.22 -10000 0 -0.45 105 105
PRKCB -0.1 0.21 -10000 0 -0.44 116 116
PRKCE -0.099 0.22 -10000 0 -0.44 112 112
PRKCD -0.098 0.22 -10000 0 -0.45 107 107
PRKCG -0.097 0.22 -10000 0 -0.45 106 106
regulation of vascular smooth muscle contraction -0.21 0.41 -10000 0 -1.1 80 80
PRKCQ -0.11 0.23 -10000 0 -0.47 112 112
PLA2G4A -0.14 0.28 -10000 0 -0.57 122 122
GNA14 -0.081 0.18 -10000 0 -0.35 140 140
GNA15 0.001 0.077 -10000 0 -0.34 23 23
GNA12 0.018 0 -10000 0 -10000 0 0
GNA11 0.012 0.047 -10000 0 -0.52 4 4
Rac1/GTP -0.002 0.27 0.35 77 -0.45 86 163
MMP1 -0.25 0.4 0.29 11 -0.66 210 221
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.051 -9999 0 -0.41 7 7
EGFR -0.079 0.18 -9999 0 -0.35 139 139
EGF/EGFR -0.17 0.21 -9999 0 -0.36 244 244
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.085 0.16 -9999 0 -0.29 169 169
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.03 0.15 -9999 0 -0.5 49 49
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.14 0.23 -9999 0 -0.42 193 193
EGF/EGFR dimer/SHC -0.12 0.18 -9999 0 -0.35 174 174
mol:GDP -0.086 0.15 -9999 0 -0.29 169 169
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.097 0.21 -9999 0 -0.43 135 135
GRB2/SOS1 0.024 0.023 -9999 0 -0.37 1 1
HRAS/GTP -0.1 0.12 -9999 0 -0.34 60 60
SHC1 0.017 0.023 -9999 0 -0.52 1 1
HRAS/GDP -0.081 0.14 -9999 0 -0.35 60 60
FRAP1 -0.078 0.14 -9999 0 -0.35 58 58
EGF/EGFR dimer -0.15 0.2 -9999 0 -0.42 173 173
SOS1 0.017 0.023 -9999 0 -0.52 1 1
GRB2 0.016 0.024 -9999 0 -0.25 4 4
ETA receptor/Endothelin-1 -0.089 0.19 -9999 0 -0.41 120 120
HIF-1-alpha transcription factor network

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
PKM2 -0.15 0.47 -9999 0 -0.91 105 105
HDAC7 0.001 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.13 0.39 -9999 0 -0.77 91 91
SMAD4 0.01 0.067 -9999 0 -0.49 9 9
ID2 -0.16 0.48 -9999 0 -0.92 107 107
AP1 -0.1 0.19 -9999 0 -0.44 107 107
ABCG2 -0.16 0.48 -9999 0 -0.92 109 109
HIF1A -0.055 0.19 -9999 0 -0.53 59 59
TFF3 -0.23 0.52 -9999 0 -0.93 145 145
GATA2 -0.013 0.096 -9999 0 -0.33 40 40
AKT1 -0.006 0.1 -9999 0 -0.45 8 8
response to hypoxia -0.02 0.084 -9999 0 -0.16 22 22
MCL1 -0.16 0.47 -9999 0 -0.9 108 108
NDRG1 -0.17 0.49 -9999 0 -0.93 110 110
SERPINE1 -0.17 0.48 -9999 0 -0.93 109 109
FECH -0.16 0.48 -9999 0 -0.91 113 113
FURIN -0.16 0.48 -9999 0 -0.92 107 107
NCOA2 0.009 0.063 -9999 0 -0.4 11 11
EP300 0.009 0.12 -9999 0 -0.38 12 12
HMOX1 -0.17 0.49 -9999 0 -0.92 113 113
BHLHE40 -0.17 0.46 -9999 0 -0.88 117 117
BHLHE41 -0.17 0.46 -9999 0 -0.88 117 117
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.008 0.16 -9999 0 -0.36 50 50
ENG 0.007 0.15 -9999 0 -0.34 46 46
JUN -0.037 0.15 -9999 0 -0.47 57 57
RORA -0.17 0.49 -9999 0 -0.92 115 115
ABCB1 -0.1 0.25 -9999 0 -1.1 26 26
TFRC -0.18 0.49 -9999 0 -0.93 115 115
CXCR4 -0.18 0.49 -9999 0 -0.93 115 115
TF -0.16 0.48 -9999 0 -0.91 108 108
CITED2 -0.16 0.48 -9999 0 -0.92 106 106
HIF1A/ARNT -0.2 0.54 -9999 0 -1.1 99 99
LDHA -0.043 0.15 -9999 0 -1.2 8 8
ETS1 -0.16 0.48 -9999 0 -0.91 110 110
PGK1 -0.16 0.47 -9999 0 -0.91 105 105
NOS2 -0.17 0.46 -9999 0 -0.88 117 117
ITGB2 -0.17 0.49 -9999 0 -0.93 114 114
ALDOA -0.16 0.48 -9999 0 -0.92 107 107
Cbp/p300/CITED2 -0.16 0.48 -9999 0 -0.95 100 100
FOS -0.11 0.2 -9999 0 -0.38 171 171
HK2 -0.16 0.47 -9999 0 -0.9 108 108
SP1 0.022 0.031 -9999 0 -0.52 1 1
GCK 0.011 0.2 -9999 0 -0.82 9 9
HK1 -0.16 0.47 -9999 0 -0.91 105 105
NPM1 -0.16 0.47 -9999 0 -0.91 105 105
EGLN1 -0.16 0.48 -9999 0 -0.92 108 108
CREB1 0.025 0.024 -9999 0 -0.52 1 1
PGM1 -0.16 0.48 -9999 0 -0.92 108 108
SMAD3 0.005 0.079 -9999 0 -0.41 17 17
EDN1 -0.22 0.48 -9999 0 -1.2 100 100
IGFBP1 -0.16 0.47 -9999 0 -0.91 108 108
VEGFA -0.086 0.36 -9999 0 -0.69 91 91
HIF1A/JAB1 -0.038 0.14 -9999 0 -0.38 63 63
CP -0.25 0.51 -9999 0 -0.95 136 136
CXCL12 -0.18 0.51 -9999 0 -0.97 115 115
COPS5 0.01 0.056 -9999 0 -0.35 11 11
SMAD3/SMAD4 0.013 0.074 -9999 0 -0.36 18 18
BNIP3 -0.16 0.48 -9999 0 -0.92 109 109
EGLN3 -0.2 0.5 -9999 0 -0.94 124 124
CA9 -0.17 0.49 -9999 0 -0.93 111 111
TERT -0.16 0.48 -9999 0 -0.92 105 105
ENO1 -0.16 0.48 -9999 0 -0.92 106 106
PFKL -0.16 0.48 -9999 0 -0.92 105 105
NCOA1 0.011 0.057 -9999 0 -0.52 6 6
ADM -0.2 0.51 -9999 0 -0.94 125 125
ARNT 0.003 0.076 -9999 0 -10000 0 0
HNF4A 0.02 0.035 -9999 0 -0.52 2 2
ADFP -0.17 0.49 -9999 0 -0.93 115 115
SLC2A1 -0.085 0.36 -9999 0 -0.69 89 89
LEP -0.18 0.48 -9999 0 -0.9 118 118
HIF1A/ARNT/Cbp/p300 -0.13 0.4 -9999 0 -0.79 91 91
EPO -0.092 0.35 -9999 0 -0.77 54 54
CREBBP 0.01 0.12 -9999 0 -0.36 10 10
HIF1A/ARNT/Cbp/p300/HDAC7 -0.13 0.39 -9999 0 -0.79 88 88
PFKFB3 -0.16 0.48 -9999 0 -0.93 107 107
NT5E -0.16 0.48 -9999 0 -0.93 106 106
IGF1 pathway

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
NCK2 0.015 0.026 -10000 0 -0.25 5 5
PTK2 0.016 0.029 -10000 0 -0.34 3 3
CRKL -0.1 0.19 -10000 0 -0.37 154 154
GRB2/SOS1/SHC 0.034 0.025 -10000 0 -0.3 2 2
HRAS 0.012 0.051 -10000 0 -0.41 7 7
IRS1/Crk -0.1 0.19 -10000 0 -0.36 154 154
IGF-1R heterotetramer/IGF1/PTP1B -0.11 0.18 -10000 0 -0.37 155 155
AKT1 -0.086 0.18 -10000 0 -0.42 84 84
BAD -0.075 0.17 -10000 0 -0.39 84 84
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.19 -10000 0 -0.36 154 154
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.1 0.19 -10000 0 -0.37 155 155
RAF1 -0.063 0.16 -10000 0 -0.39 70 70
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.088 0.19 -10000 0 -0.34 153 153
YWHAZ 0.017 0.017 -10000 0 -0.25 2 2
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.2 -10000 0 -0.38 169 169
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
RPS6KB1 -0.086 0.18 -10000 0 -0.42 85 85
GNB2L1 0.015 0.04 -10000 0 -0.52 3 3
positive regulation of MAPKKK cascade -0.058 0.14 0.22 1 -0.34 70 71
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.023 -10000 0 -0.37 1 1
HRAS/GTP -0.099 0.15 -10000 0 -0.43 73 73
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.06 0.15 -10000 0 -0.35 71 71
IGF-1R heterotetramer -0.1 0.22 -10000 0 -0.51 110 110
IGF-1R heterotetramer/IGF1/IRS/Nck -0.1 0.19 -10000 0 -0.37 152 152
Crk/p130 Cas/Paxillin -0.078 0.18 -10000 0 -0.45 72 72
IGF1R -0.1 0.22 -10000 0 -0.51 110 110
IGF1 -0.12 0.22 -10000 0 -0.44 146 146
IRS2/Crk -0.11 0.2 -10000 0 -0.36 166 166
PI3K -0.1 0.2 -10000 0 -0.36 164 164
apoptosis 0.057 0.15 0.34 84 -10000 0 84
HRAS/GDP 0.009 0.036 -10000 0 -0.29 7 7
PRKCD -0.096 0.21 -10000 0 -0.44 117 117
RAF1/14-3-3 E -0.048 0.14 -10000 0 -0.34 70 70
BAD/14-3-3 -0.061 0.16 -10000 0 -0.36 84 84
PRKCZ -0.09 0.18 -10000 0 -0.32 164 164
Crk/p130 Cas/Paxillin/FAK1 -0.087 0.14 -10000 0 -0.39 67 67
PTPN1 0.002 0.07 -10000 0 -0.28 28 28
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.11 0.22 -10000 0 -0.41 153 153
BCAR1 0.017 0.012 -10000 0 -0.25 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.086 0.17 -10000 0 -0.32 163 163
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0.023 -10000 0 -0.52 1 1
IRS1/NCK2 -0.1 0.19 -10000 0 -0.37 152 152
GRB10 -0.003 0.097 -10000 0 -0.43 24 24
PTPN11 -0.1 0.19 -10000 0 -0.37 152 152
IRS1 -0.12 0.2 -10000 0 -0.38 169 169
IRS2 -0.12 0.21 -10000 0 -0.39 165 165
IGF-1R heterotetramer/IGF1 -0.14 0.22 -10000 0 -0.46 156 156
GRB2 0.016 0.024 -10000 0 -0.25 4 4
PDPK1 -0.094 0.18 -10000 0 -0.33 164 164
YWHAE 0.016 0.029 -10000 0 -0.34 3 3
PRKD1 -0.12 0.23 -10000 0 -0.48 118 118
SHC1 0.017 0.023 -10000 0 -0.52 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.017 0.037 -10000 0 -0.43 2 2
NFATC2 -0.11 0.26 -10000 0 -0.6 77 77
NFATC3 -0.055 0.11 -10000 0 -0.24 67 67
CD40LG -0.32 0.43 -10000 0 -0.89 156 156
ITCH 0.006 0.085 -10000 0 -10000 0 0
CBLB 0.005 0.088 -10000 0 -0.59 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.38 -10000 0 -0.91 87 87
JUNB 0.011 0.055 -10000 0 -0.36 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.1 -10000 0 -0.27 48 48
T cell anergy -0.033 0.14 -10000 0 -0.39 48 48
TLE4 -0.071 0.23 -10000 0 -0.72 37 37
Jun/NFAT1-c-4/p21SNFT -0.3 0.45 -10000 0 -0.91 147 147
AP-1/NFAT1-c-4 -0.37 0.52 -10000 0 -1 156 156
IKZF1 -0.08 0.23 -10000 0 -0.71 40 40
T-helper 2 cell differentiation -0.22 0.35 -10000 0 -0.79 112 112
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.52 112 112
CALM1 0.003 0.058 -10000 0 -10000 0 0
EGR2 -0.29 0.52 -10000 0 -1.2 92 92
EGR3 -0.37 0.58 -10000 0 -1.2 141 141
NFAT1/FOXP3 -0.064 0.2 -10000 0 -0.57 39 39
EGR1 -0.1 0.2 -10000 0 -0.39 156 156
JUN -0.035 0.15 -10000 0 -0.46 57 57
EGR4 0 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.06 -10000 0 -10000 0 0
GBP3 -0.14 0.31 -10000 0 -0.75 94 94
FOSL1 0.016 0.024 -10000 0 -0.25 4 4
NFAT1-c-4/MAF/IRF4 -0.28 0.44 -10000 0 -0.86 157 157
DGKA -0.066 0.21 -10000 0 -0.68 34 34
CREM 0.016 0.017 -10000 0 -0.26 2 2
NFAT1-c-4/PPARG -0.3 0.46 -10000 0 -0.9 162 162
CTLA4 -0.052 0.18 -10000 0 -0.53 40 40
NFAT1-c-4 (dimer)/EGR1 -0.33 0.48 -10000 0 -0.95 161 161
NFAT1-c-4 (dimer)/EGR4 -0.28 0.44 -10000 0 -0.88 157 157
FOS -0.11 0.2 -10000 0 -0.39 152 152
IFNG -0.3 0.47 -10000 0 -1.1 94 94
T cell activation -0.17 0.29 -10000 0 -0.75 64 64
MAF -0.012 0.12 -10000 0 -0.44 35 35
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.22 0.38 0.73 152 -10000 0 152
TNF -0.3 0.42 -10000 0 -0.88 144 144
FASLG -0.43 0.65 -10000 0 -1.3 166 166
TBX21 -0.11 0.21 -10000 0 -0.46 137 137
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ -0.018 0.11 -10000 0 -0.32 51 51
PTPN1 -0.069 0.2 -10000 0 -0.64 36 36
NFAT1-c-4/ICER1 -0.28 0.44 -10000 0 -0.88 156 156
GATA3 -0.1 0.23 -10000 0 -0.51 124 124
T-helper 1 cell differentiation -0.28 0.44 -10000 0 -1.1 97 97
IL2RA -0.25 0.35 -10000 0 -0.87 93 93
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.058 0.19 -10000 0 -0.61 31 31
E2F1 0.013 0.071 -10000 0 -0.36 16 16
PPARG -0.036 0.14 -10000 0 -0.33 81 81
SLC3A2 -0.06 0.19 -10000 0 -0.61 32 32
IRF4 -0.01 0.085 -10000 0 -0.26 52 52
PTGS2 -0.33 0.44 -10000 0 -0.9 157 157
CSF2 -0.33 0.43 -10000 0 -0.9 156 156
JunB/Fra1/NFAT1-c-4 -0.26 0.43 -10000 0 -0.84 156 156
IL4 -0.24 0.37 -10000 0 -0.85 106 106
IL5 -0.32 0.43 -10000 0 -0.89 155 155
IL2 -0.18 0.29 -10000 0 -0.78 61 61
IL3 -0.04 0.052 -10000 0 -10000 0 0
RNF128 -0.053 0.2 -10000 0 -0.6 47 47
NFATC1 -0.22 0.39 -10000 0 -0.73 152 152
CDK4 0.14 0.22 0.57 51 -10000 0 51
PTPRK -0.12 0.3 -10000 0 -0.73 86 86
IL8 -0.36 0.44 -10000 0 -0.93 158 158
POU2F1 0.027 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.058 0.14 -10000 0 -0.26 154 154
ER alpha/Gai/GDP/Gbeta gamma -0.089 0.19 -10000 0 -0.35 156 156
AKT1 -0.2 0.35 -10000 0 -0.74 151 151
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.2 0.35 -10000 0 -0.75 151 151
mol:Ca2+ -0.1 0.18 -10000 0 -0.44 88 88
IGF1R -0.083 0.2 -10000 0 -0.47 110 110
E2/ER alpha (dimer)/Striatin -0.09 0.15 -10000 0 -0.32 155 155
SHC1 0.017 0.023 -10000 0 -0.52 1 1
apoptosis 0.19 0.33 0.7 151 -10000 0 151
RhoA/GTP -0.086 0.12 -10000 0 -0.41 27 27
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.12 0.18 -10000 0 -0.38 154 154
regulation of stress fiber formation 0.041 0.12 0.29 41 -10000 0 41
E2/ERA-ERB (dimer) -0.086 0.15 -10000 0 -0.31 150 150
KRAS 0.009 0.065 -10000 0 -0.44 10 10
G13/GTP -0.08 0.14 -10000 0 -0.29 151 151
pseudopodium formation -0.041 0.12 -10000 0 -0.29 41 41
E2/ER alpha (dimer)/PELP1 -0.086 0.15 -10000 0 -0.31 150 150
GRB2 0.016 0.024 -10000 0 -0.25 4 4
GNG2 0.016 0.029 -10000 0 -0.34 3 3
GNAO1 0.016 0.024 -10000 0 -0.25 4 4
HRAS 0.012 0.051 -10000 0 -0.41 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.11 0.22 -10000 0 -0.44 152 152
E2/ER beta (dimer) 0.013 0.008 -10000 0 -0.17 1 1
mol:GDP -0.12 0.17 -10000 0 -0.39 150 150
mol:NADP -0.11 0.22 -10000 0 -0.44 152 152
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
mol:IP3 -0.11 0.19 -10000 0 -0.46 88 88
IGF-1R heterotetramer -0.083 0.2 -10000 0 -0.47 110 110
PLCB1 -0.12 0.19 -10000 0 -0.48 87 87
PLCB2 -0.074 0.17 -10000 0 -0.53 53 53
IGF1 -0.1 0.2 -10000 0 -0.41 146 146
mol:L-citrulline -0.11 0.22 -10000 0 -0.44 152 152
RHOA 0.005 0.08 -10000 0 -0.52 12 12
Gai/GDP -0.008 0.12 -10000 0 -0.75 10 10
JNK cascade 0.013 0.008 -10000 0 -0.17 1 1
BCAR1 0.017 0.012 -10000 0 -0.25 1 1
ESR2 0.017 0.012 -10000 0 -0.25 1 1
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.16 0.24 -10000 0 -0.46 199 199
Gq family/GDP/Gbeta gamma -0.024 0.12 -10000 0 -0.49 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.044 0.13 -10000 0 -0.63 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.18 -10000 0 -0.38 155 155
GNAZ 0.001 0.088 -10000 0 -0.44 19 19
E2/ER alpha (dimer) -0.12 0.17 -10000 0 -0.33 199 199
STRN 0.011 0.056 -10000 0 -0.42 8 8
GNAL 0.011 0.052 -10000 0 -0.33 11 11
PELP1 0.018 0 -10000 0 -10000 0 0
MAPK11 0.021 0.007 -10000 0 -10000 0 0
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.018 0 -10000 0 -10000 0 0
GNAI1 -0.017 0.12 -10000 0 -0.38 46 46
HBEGF -0.093 0.19 -10000 0 -0.43 65 65
cAMP biosynthetic process -0.081 0.11 -10000 0 -0.25 152 152
SRC -0.079 0.18 -10000 0 -0.42 42 42
PI3K 0.005 0.082 -10000 0 -0.37 21 21
GNB1 0.013 0.052 -10000 0 -0.52 5 5
G13/GDP/Gbeta gamma -0.1 0.15 -10000 0 -0.33 151 151
SOS1 0.017 0.023 -10000 0 -0.52 1 1
IGF-1R heterotetramer/IGF1 -0.16 0.21 -10000 0 -0.44 167 167
Gs family/GTP -0.066 0.13 -10000 0 -0.26 152 152
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.064 -10000 0 -0.28 20 20
vasodilation -0.1 0.22 -10000 0 -0.42 152 152
mol:DAG -0.11 0.19 -10000 0 -0.46 88 88
Gs family/GDP/Gbeta gamma -0.1 0.15 -10000 0 -0.32 152 152
MSN -0.045 0.13 -10000 0 -0.32 41 41
Gq family/GTP -0.084 0.18 -10000 0 -0.57 52 52
mol:PI-3-4-5-P3 -0.19 0.34 -10000 0 -0.72 151 151
NRAS 0.005 0.076 -10000 0 -0.4 16 16
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.1 0.22 0.42 152 -10000 0 152
GRB2/SOS1 0.024 0.023 -10000 0 -0.37 1 1
RhoA/GDP -0.093 0.18 -10000 0 -0.37 151 151
NOS3 -0.11 0.23 -10000 0 -0.46 152 152
GNA11 0.014 0.047 -10000 0 -0.52 4 4
MAPKKK cascade -0.12 0.26 -10000 0 -0.53 154 154
E2/ER alpha (dimer)/PELP1/Src -0.13 0.18 -10000 0 -0.4 155 155
ruffle organization -0.041 0.12 -10000 0 -0.29 41 41
ROCK2 -0.051 0.13 -10000 0 -0.37 29 29
GNA14 -0.079 0.18 -10000 0 -0.35 140 140
GNA15 0.002 0.076 -10000 0 -0.34 23 23
GNA13 0.011 0.055 -10000 0 -0.36 10 10
MMP9 -0.095 0.18 -10000 0 -0.44 48 48
MMP2 -0.09 0.2 -10000 0 -0.45 59 59
TCGA08_retinoblastoma

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
CDKN2B -0.017 0.12 -10000 0 -0.38 46 46
CDKN2C 0.005 0.085 -10000 0 -0.37 23 23
CDKN2A -0.052 0.15 -10000 0 -0.32 106 106
CCND2 0.019 0.085 0.2 74 -0.15 6 80
RB1 -0.022 0.092 0.15 3 -0.22 77 80
CDK4 0.026 0.096 0.23 77 -10000 0 77
CDK6 0.019 0.093 0.23 63 -0.2 6 69
G1/S progression 0.022 0.092 0.22 77 -0.15 3 80
FAS signaling pathway (CD95)

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
SPTAN1 0.067 0.099 0.24 122 -10000 0 122
RFC1 0.067 0.099 0.23 128 -10000 0 128
PRKDC 0.064 0.1 0.24 121 -0.3 1 122
RIPK1 0.018 0.024 -10000 0 -0.52 1 1
CASP7 -0.013 0.12 0.24 2 -0.68 14 16
FASLG/FAS/FADD/FAF1 -0.012 0.13 0.22 49 -0.3 47 96
MAP2K4 -0.045 0.16 -10000 0 -0.42 45 45
mol:ceramide -0.044 0.15 -10000 0 -0.38 59 59
GSN 0.056 0.11 0.24 123 -0.3 11 134
FASLG/FAS/FADD/FAF1/Caspase 8 -0.013 0.13 -10000 0 -0.36 41 41
FAS -0.026 0.13 -10000 0 -0.42 51 51
BID 0.012 0.066 0.29 16 -0.32 8 24
MAP3K1 -0.016 0.13 0.26 2 -0.38 29 31
MAP3K7 0.015 0.021 -10000 0 -0.25 3 3
RB1 0.054 0.11 0.23 117 -0.29 9 126
CFLAR 0.01 0.065 -10000 0 -0.44 10 10
HGF/MET -0.036 0.14 -10000 0 -0.33 90 90
ARHGDIB 0.044 0.12 0.23 111 -0.29 20 131
FADD -0.003 0.068 -10000 0 -0.26 35 35
actin filament polymerization -0.056 0.11 0.3 11 -0.23 123 134
NFKB1 -0.042 0.08 -10000 0 -0.85 1 1
MAPK8 -0.06 0.19 -10000 0 -0.47 71 71
DFFA 0.066 0.099 0.24 122 -10000 0 122
DNA fragmentation during apoptosis 0.066 0.098 0.23 127 -10000 0 127
FAS/FADD/MET -0.014 0.1 -10000 0 -0.33 39 39
CFLAR/RIP1 0.02 0.05 -10000 0 -0.36 8 8
FAIM3 -0.001 0.099 -10000 0 -0.49 20 20
FAF1 0.013 0.025 -10000 0 -0.52 1 1
PARP1 0.064 0.1 0.24 122 -0.28 5 127
DFFB 0.066 0.099 0.24 125 -10000 0 125
CHUK -0.025 0.091 -10000 0 -0.43 6 6
FASLG -0.065 0.17 -10000 0 -0.38 106 106
FAS/FADD -0.02 0.11 -10000 0 -0.38 33 33
HGF 0.008 0.069 -10000 0 -0.45 11 11
LMNA 0.06 0.095 0.22 112 -0.26 8 120
CASP6 0.063 0.1 0.23 126 -0.27 4 130
CASP10 0.012 0.029 -10000 0 -0.25 6 6
CASP3 0.072 0.12 0.28 128 -10000 0 128
PTPN13 -0.071 0.2 -10000 0 -0.49 93 93
CASP8 0.013 0.068 0.37 18 -10000 0 18
IL6 -0.16 0.4 -10000 0 -1.2 59 59
MET 0 0.075 -10000 0 -0.29 31 31
ICAD/CAD 0.066 0.089 0.22 115 -10000 0 115
FASLG/FAS/FADD/FAF1/Caspase 10 -0.045 0.15 -10000 0 -0.38 59 59
activation of caspase activity by cytochrome c 0.012 0.066 0.29 16 -0.32 8 24
PAK2 0.067 0.099 0.24 123 -10000 0 123
BCL2 -0.11 0.22 -10000 0 -0.47 144 144
Glucocorticoid receptor regulatory network

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
PCK2 0.018 0.15 0.36 11 -0.84 10 21
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.012 0.051 -10000 0 -0.41 7 7
TBX21 -0.2 0.33 -10000 0 -0.66 151 151
SUMO2 0.014 0.022 -10000 0 -0.26 3 3
STAT1 (dimer) -0.023 0.13 -10000 0 -0.34 66 66
FKBP4 0.012 0.055 -10000 0 -0.44 7 7
FKBP5 -0.045 0.16 -10000 0 -0.42 75 75
GR alpha/HSP90/FKBP51/HSP90 0.073 0.16 0.28 88 -0.29 37 125
PRL -0.057 0.14 -10000 0 -0.87 3 3
cortisol/GR alpha (dimer)/TIF2 0.23 0.26 0.53 182 -0.4 2 184
RELA -0.052 0.091 -10000 0 -0.26 20 20
FGG 0.2 0.22 0.49 133 -0.39 2 135
GR beta/TIF2 0.11 0.14 0.3 112 -0.32 14 126
IFNG -0.41 0.43 -10000 0 -0.92 166 166
apoptosis -0.004 0.18 0.5 6 -0.55 5 11
CREB1 0.007 0.056 -10000 0 -0.36 5 5
histone acetylation -0.045 0.14 0.3 2 -0.33 63 65
BGLAP -0.072 0.15 -10000 0 -0.57 11 11
GR/PKAc 0.092 0.14 0.28 82 -0.31 17 99
NF kappa B1 p50/RelA -0.091 0.17 -10000 0 -0.4 63 63
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.099 0.1 0.24 134 -10000 0 134
GATA3 -0.093 0.23 -10000 0 -0.5 124 124
AKT1 0.006 0.059 0.21 4 -0.38 9 13
CSF2 -0.073 0.15 -10000 0 -0.71 11 11
GSK3B 0.016 0.008 -10000 0 -10000 0 0
NR1I3 0.009 0.18 0.48 6 -0.91 3 9
CSN2 0.17 0.18 0.41 121 -0.41 4 125
BRG1/BAF155/BAF170/BAF60A 0.041 0.034 -10000 0 -0.27 5 5
NFATC1 -0.004 0.12 -10000 0 -0.41 39 39
POU2F1 0.025 0.012 -10000 0 -0.22 1 1
CDKN1A -0.035 0.28 -10000 0 -1.5 16 16
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.007 -10000 0 -10000 0 0
SFN -0.015 0.12 -10000 0 -0.45 37 37
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.064 0.16 0.29 64 -0.3 36 100
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.086 0.33 0.5 2 -0.8 80 82
JUN -0.21 0.24 -10000 0 -0.52 150 150
IL4 -0.1 0.2 -10000 0 -0.64 33 33
CDK5R1 0.013 0.031 -10000 0 -0.25 7 7
PRKACA 0.018 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.28 0.21 46 -0.5 217 263
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.081 0.15 0.3 65 -0.29 24 89
cortisol/GR alpha (monomer) 0.28 0.32 0.63 187 -0.46 3 190
NCOA2 0.009 0.063 -10000 0 -0.4 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.21 -10000 0 -0.47 155 155
AP-1/NFAT1-c-4 -0.44 0.4 -10000 0 -0.79 244 244
AFP -0.16 0.2 -10000 0 -0.71 20 20
SUV420H1 0.014 0.037 -10000 0 -0.29 7 7
IRF1 0.11 0.25 0.45 51 -0.81 19 70
TP53 -0.015 0.17 -10000 0 -0.53 47 47
PPP5C 0.012 0.052 -10000 0 -0.39 8 8
KRT17 -0.53 0.58 -10000 0 -1.2 187 187
KRT14 -0.32 0.51 -10000 0 -1.3 104 104
TBP 0.028 0.012 -10000 0 -0.24 1 1
CREBBP 0.061 0.1 0.26 79 -0.53 2 81
HDAC1 0.011 0.025 -10000 0 -0.53 1 1
HDAC2 0.008 0.053 -10000 0 -0.29 14 14
AP-1 -0.44 0.4 -10000 0 -0.8 244 244
MAPK14 0.015 0.013 -10000 0 -0.25 1 1
MAPK10 -0.026 0.12 -10000 0 -0.36 58 58
MAPK11 0.016 0.008 -10000 0 -10000 0 0
KRT5 -0.54 0.58 -10000 0 -1.1 213 213
interleukin-1 receptor activity -0.001 0.009 -10000 0 -10000 0 0
NCOA1 0.013 0.059 -10000 0 -0.52 6 6
STAT1 -0.023 0.13 -10000 0 -0.34 66 66
CGA -0.12 0.2 -10000 0 -0.65 29 29
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.16 0.37 104 -0.39 2 106
MAPK3 0.014 0.027 -10000 0 -0.39 2 2
MAPK1 0.014 0.034 -10000 0 -0.52 2 2
ICAM1 -0.22 0.34 -10000 0 -0.8 95 95
NFKB1 -0.053 0.093 -10000 0 -0.28 18 18
MAPK8 -0.15 0.19 -10000 0 -0.42 128 128
MAPK9 -0.008 0.11 -10000 0 -0.51 24 24
cortisol/GR alpha (dimer) -0.014 0.18 0.5 6 -0.58 5 11
BAX 0.001 0.11 -10000 0 -10000 0 0
POMC -0.13 0.2 -10000 0 -1.2 6 6
EP300 0.059 0.11 0.26 79 -0.53 4 83
cortisol/GR alpha (dimer)/p53 0.21 0.28 0.55 158 -0.48 4 162
proteasomal ubiquitin-dependent protein catabolic process 0.07 0.08 0.21 77 -10000 0 77
SGK1 0.11 0.13 0.34 101 -0.26 4 105
IL13 -0.31 0.29 -10000 0 -0.62 198 198
IL6 -0.28 0.41 -10000 0 -0.84 138 138
PRKACG 0.016 0.033 -10000 0 -0.52 2 2
IL5 -0.26 0.24 -10000 0 -0.67 76 76
IL2 -0.32 0.33 -10000 0 -0.74 142 142
CDK5 0.015 0.027 -10000 0 -0.39 2 2
PRKACB -0.036 0.14 -10000 0 -0.34 79 79
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
IL8 -0.27 0.37 -10000 0 -0.85 113 113
CDK5R1/CDK5 0.02 0.03 -10000 0 -0.37 1 1
NF kappa B1 p50/RelA/PKAc -0.063 0.15 -10000 0 -0.36 56 56
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.24 0.51 180 -0.36 1 181
SMARCA4 0.015 0.031 -10000 0 -0.32 4 4
chromatin remodeling 0.16 0.16 0.36 141 -0.33 1 142
NF kappa B1 p50/RelA/Cbp -0.018 0.16 0.31 28 -0.39 26 54
JUN (dimer) -0.21 0.24 -10000 0 -0.52 150 150
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
VIPR1 -0.11 0.24 -10000 0 -0.68 55 55
NR3C1 0.16 0.21 0.42 145 -0.46 11 156
NR4A1 0.01 0.063 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.017 0.055 -10000 0 -0.42 6 6
MAPKKK cascade -0.004 0.18 0.5 6 -0.55 5 11
cortisol/GR alpha (dimer)/Src-1 0.24 0.26 0.54 175 -0.43 3 178
PBX1 0.004 0.1 -10000 0 -0.49 22 22
POU1F1 0.023 0.033 -10000 0 -0.3 5 5
SELE -0.35 0.47 -10000 0 -1 155 155
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.36 141 -0.34 1 142
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.24 0.51 180 -0.36 1 181
mol:cortisol 0.16 0.19 0.37 185 -10000 0 185
MMP1 -0.44 0.52 -10000 0 -0.99 201 201
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.013 0.048 -9999 0 -0.47 5 5
GNB1/GNG2 -0.11 0.19 -9999 0 -0.42 103 103
mol:DAG -0.093 0.18 -9999 0 -0.44 72 72
PLCG1 -0.096 0.18 -9999 0 -0.46 72 72
YES1 -0.12 0.2 -9999 0 -0.45 105 105
FZD3 -0.03 0.15 -9999 0 -0.48 51 51
FZD6 -0.077 0.2 -9999 0 -0.45 108 108
G protein -0.099 0.19 -9999 0 -0.46 76 76
MAP3K7 -0.068 0.15 -9999 0 -0.4 58 58
mol:Ca2+ -0.09 0.17 -9999 0 -0.43 72 72
mol:IP3 -0.093 0.18 -9999 0 -0.44 72 72
NLK 0.016 0.044 -9999 0 -0.9 1 1
GNB1 0.013 0.052 -9999 0 -0.52 5 5
CAMK2A -0.079 0.16 -9999 0 -0.42 61 61
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.34 214 214
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
GNAS -0.12 0.2 -9999 0 -0.44 105 105
GO:0007205 -0.092 0.17 -9999 0 -0.43 73 73
WNT6 -0.011 0.087 -9999 0 -0.26 54 54
WNT4 -0.062 0.18 -9999 0 -0.45 90 90
NFAT1/CK1 alpha -0.091 0.19 -9999 0 -0.46 75 75
GNG2 0.016 0.029 -9999 0 -0.34 3 3
WNT5A -0.084 0.2 -9999 0 -0.43 120 120
WNT11 -0.013 0.089 -9999 0 -0.26 57 57
CDC42 -0.11 0.2 -9999 0 -0.42 104 104
IL4-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
BCL2L1 -0.33 0.63 -10000 0 -1.3 115 115
STAT6 (cleaved dimer) -0.43 0.56 -10000 0 -1.2 144 144
IGHG1 -0.083 0.25 -10000 0 -0.45 60 60
IGHG3 -0.33 0.6 -10000 0 -1.2 139 139
AKT1 -0.11 0.31 -10000 0 -0.68 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.065 0.24 -10000 0 -0.6 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.34 -10000 0 -0.75 60 60
THY1 -0.35 0.65 -10000 0 -1.4 118 118
MYB -0.097 0.22 -10000 0 -0.49 119 119
HMGA1 0.014 0.039 -10000 0 -0.36 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.34 -10000 0 -0.65 91 91
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.31 -10000 0 -0.75 34 34
SP1 0.021 0.03 -10000 0 -0.53 1 1
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.016 0.055 -10000 0 -0.4 7 7
STAT6 (dimer)/ETS1 -0.34 0.63 -10000 0 -1.3 135 135
SOCS1 -0.18 0.4 -10000 0 -0.78 103 103
SOCS3 -0.12 0.33 -10000 0 -0.95 24 24
FCER2 -0.22 0.46 -10000 0 -0.94 88 88
PARP14 0.006 0.078 -10000 0 -0.43 15 15
CCL17 -0.42 0.71 -10000 0 -1.4 146 146
GRB2 0.016 0.024 -10000 0 -0.25 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.083 0.26 -10000 0 -0.64 25 25
T cell proliferation -0.35 0.65 -10000 0 -1.3 127 127
IL4R/JAK1 -0.35 0.64 -10000 0 -1.3 131 131
EGR2 -0.39 0.69 -10000 0 -1.4 134 134
JAK2 0.001 0.072 -10000 0 -0.34 12 12
JAK3 0.021 0.008 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
JAK1 0.012 0.061 -10000 0 -0.52 6 6
COL1A2 -0.22 0.54 -10000 0 -1.5 72 72
CCL26 -0.34 0.63 -10000 0 -1.3 124 124
IL4R -0.37 0.7 -10000 0 -1.4 123 123
PTPN6 0.021 0.038 -10000 0 -0.42 3 3
IL13RA2 -0.38 0.67 -10000 0 -1.3 140 140
IL13RA1 -0.002 0.089 -10000 0 -0.49 12 12
IRF4 -0.038 0.2 -10000 0 -0.99 6 6
ARG1 -0.064 0.27 -10000 0 -1 21 21
CBL -0.13 0.32 -10000 0 -0.61 88 88
GTF3A 0.02 0.032 -10000 0 -0.38 2 2
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
IL13RA1/JAK2 0.003 0.099 -10000 0 -0.36 18 18
IRF4/BCL6 -0.044 0.19 -10000 0 -0.92 6 6
CD40LG 0.012 0.07 -10000 0 -0.32 20 20
MAPK14 -0.13 0.33 -10000 0 -0.67 67 67
mitosis -0.1 0.3 -10000 0 -0.65 47 47
STAT6 -0.43 0.85 -10000 0 -1.6 139 139
SPI1 0.012 0.07 -10000 0 -0.43 11 11
RPS6KB1 -0.099 0.29 -10000 0 -0.64 40 40
STAT6 (dimer) -0.44 0.86 -10000 0 -1.6 139 139
STAT6 (dimer)/PARP14 -0.39 0.7 -10000 0 -1.4 140 140
mast cell activation 0.004 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.11 0.3 -10000 0 -0.68 47 47
FRAP1 -0.11 0.31 -10000 0 -0.68 49 49
LTA -0.33 0.63 -10000 0 -1.3 119 119
FES 0.01 0.058 -10000 0 -0.39 10 10
T-helper 1 cell differentiation 0.39 0.75 1.4 139 -10000 0 139
CCL11 -0.38 0.65 -10000 0 -1.3 141 141
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.3 -10000 0 -0.68 35 35
IL2RG 0.001 0.08 -10000 0 -0.29 35 35
IL10 -0.34 0.63 -10000 0 -1.3 120 120
IRS1 -0.048 0.17 -10000 0 -0.49 68 68
IRS2 -0.026 0.13 -10000 0 -0.39 57 57
IL4 -0.039 0.22 -10000 0 -1.4 6 6
IL5 -0.34 0.63 -10000 0 -1.3 116 116
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.24 0.5 -10000 0 -0.95 124 124
COL1A1 -0.23 0.56 -10000 0 -1.6 72 72
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.37 0.67 -10000 0 -1.4 120 120
IL2R gamma/JAK3 0.017 0.059 -10000 0 -0.33 5 5
TFF3 -0.52 0.77 -10000 0 -1.4 191 191
ALOX15 -0.35 0.64 -10000 0 -1.4 111 111
MYBL1 -0.066 0.17 -10000 0 -0.36 117 117
T-helper 2 cell differentiation -0.25 0.49 -10000 0 -0.96 125 125
SHC1 0.017 0.023 -10000 0 -0.52 1 1
CEBPB 0.008 0.075 -10000 0 -0.34 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.32 -10000 0 -0.73 44 44
mol:PI-3-4-5-P3 -0.11 0.31 -10000 0 -0.68 49 49
PI3K -0.12 0.33 -10000 0 -0.72 49 49
DOK2 -0.021 0.13 -10000 0 -0.4 48 48
ETS1 0.007 0.07 -10000 0 -0.28 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.073 0.25 -10000 0 -0.62 23 23
ITGB3 -0.34 0.63 -10000 0 -1.3 121 121
PIGR -0.5 0.76 -10000 0 -1.4 180 180
IGHE 0.022 0.086 0.21 45 -0.25 4 49
MAPKKK cascade -0.071 0.24 -10000 0 -0.6 23 23
BCL6 -0.004 0.1 -10000 0 -0.46 24 24
OPRM1 -0.34 0.63 -10000 0 -1.3 116 116
RETNLB -0.33 0.63 -10000 0 -1.3 118 118
SELP -0.46 0.75 -10000 0 -1.5 158 158
AICDA -0.35 0.61 -10000 0 -1.3 129 129
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.007 0.074 -9999 0 -0.5 11 11
LAT2 -0.089 0.18 -9999 0 -0.34 142 142
AP1 -0.14 0.22 -9999 0 -0.49 125 125
mol:PIP3 -0.099 0.22 -9999 0 -0.49 92 92
IKBKB -0.043 0.12 -9999 0 -0.26 86 86
AKT1 -0.068 0.16 -9999 0 -0.4 74 74
IKBKG -0.041 0.12 -9999 0 -0.26 86 86
MS4A2 -0.15 0.23 -9999 0 -0.43 203 203
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.029 -9999 0 -0.34 3 3
MAP3K1 -0.086 0.19 -9999 0 -0.43 97 97
mol:Ca2+ -0.071 0.16 -9999 0 -0.36 92 92
LYN 0.012 0.032 -9999 0 -0.26 7 7
CBLB -0.086 0.18 -9999 0 -0.34 139 139
SHC1 0.017 0.023 -9999 0 -0.52 1 1
RasGAP/p62DOK -0.013 0.11 -9999 0 -0.3 58 58
positive regulation of cell migration -0.013 0.089 -9999 0 -0.28 46 46
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.088 0.18 -9999 0 -0.38 103 103
PTPN13 -0.12 0.22 -9999 0 -0.55 78 78
PTPN11 0.012 0.027 -9999 0 -0.56 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.046 0.14 -9999 0 -0.32 74 74
SYK -0.025 0.14 -9999 0 -0.49 43 43
GRB2 0.015 0.024 -9999 0 -0.26 4 4
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.2 -9999 0 -0.49 100 100
LAT -0.092 0.18 -9999 0 -0.42 91 91
PAK2 -0.081 0.2 -9999 0 -0.44 92 92
NFATC2 -0.042 0.082 -9999 0 -0.62 5 5
HRAS -0.096 0.21 -9999 0 -0.48 95 95
GAB2 0.009 0.048 -9999 0 -0.25 17 17
PLA2G1B 0.038 0.026 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.2 -9999 0 -0.39 168 168
Antigen/IgE/Fc epsilon R1 -0.11 0.19 -9999 0 -0.35 168 168
mol:GDP -0.11 0.22 -9999 0 -0.51 95 95
JUN -0.034 0.15 -9999 0 -0.46 57 57
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.11 -9999 0 -0.42 33 33
FOS -0.11 0.2 -9999 0 -0.37 171 171
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.097 0.18 -9999 0 -0.36 139 139
CHUK -0.046 0.12 -9999 0 -0.26 91 91
KLRG1 -0.084 0.17 -9999 0 -0.39 87 87
VAV1 -0.1 0.2 -9999 0 -0.36 149 149
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.086 0.18 -9999 0 -0.34 139 139
negative regulation of mast cell degranulation -0.079 0.16 -9999 0 -0.36 87 87
BTK -0.11 0.23 -9999 0 -0.52 93 93
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.13 0.25 -9999 0 -0.5 122 122
GAB2/PI3K/SHP2 -0.1 0.15 -9999 0 -0.43 76 76
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.097 0.2 -9999 0 -0.44 96 96
RAF1 0.029 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.21 -9999 0 -0.36 184 184
FCER1G 0.02 0.026 -9999 0 -0.26 4 4
FCER1A -0.074 0.2 -9999 0 -0.51 91 91
Antigen/IgE/Fc epsilon R1/Fyn -0.095 0.18 -9999 0 -0.33 170 170
MAPK3 0.037 0.026 -9999 0 -10000 0 0
MAPK1 0.037 0.026 -9999 0 -10000 0 0
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 -0.02 0.11 -9999 0 -0.48 19 19
DUSP1 -0.038 0.15 -9999 0 -0.41 69 69
NF-kappa-B/RelA -0.039 0.061 -9999 0 -0.18 33 33
actin cytoskeleton reorganization -0.088 0.18 -9999 0 -0.48 65 65
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.091 0.2 -9999 0 -0.45 97 97
FER -0.086 0.18 -9999 0 -0.34 140 140
RELA 0.018 0 -9999 0 -10000 0 0
ITK -0.053 0.13 -9999 0 -0.4 52 52
SOS1 0.017 0.023 -9999 0 -0.52 1 1
PLCG1 -0.1 0.22 -9999 0 -0.51 93 93
cytokine secretion -0.029 0.044 -9999 0 -0.17 3 3
SPHK1 -0.11 0.2 -9999 0 -0.35 166 166
PTK2 -0.092 0.19 -9999 0 -0.5 65 65
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.21 -9999 0 -0.51 96 96
EDG1 -0.013 0.089 -9999 0 -0.28 46 46
mol:DAG -0.095 0.22 -9999 0 -0.48 98 98
MAP2K2 0.032 0.031 -9999 0 -0.26 2 2
MAP2K1 0.033 0.024 -9999 0 -10000 0 0
MAP2K7 0.017 0.023 -9999 0 -0.52 1 1
KLRG1/SHP2 -0.073 0.15 -9999 0 -0.37 77 77
MAP2K4 -0.011 0.16 -9999 0 -0.91 16 16
Fc epsilon R1/FcgammaRIIB -0.12 0.22 -9999 0 -0.38 184 184
mol:Choline -0.087 0.17 -9999 0 -0.38 103 103
SHC/Grb2/SOS1 -0.066 0.17 -9999 0 -0.41 73 73
FYN 0.008 0.067 -9999 0 -0.41 12 12
DOK1 0.002 0.083 -9999 0 -0.41 19 19
PXN -0.079 0.18 -9999 0 -0.46 65 65
HCLS1 -0.096 0.19 -9999 0 -0.36 145 145
PRKCB -0.069 0.16 -9999 0 -0.35 99 99
FCGR2B -0.031 0.15 -9999 0 -0.5 50 50
IGHE -0.003 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.08 0.16 -9999 0 -0.37 87 87
LCP2 -0.004 0.098 -9999 0 -0.4 27 27
PLA2G4A -0.11 0.21 -9999 0 -0.38 157 157
RASA1 0.004 0.078 -9999 0 -0.42 16 16
mol:Phosphatidic acid -0.087 0.17 -9999 0 -0.38 103 103
IKK complex -0.023 0.098 -9999 0 -0.2 70 70
WIPF1 0.005 0.076 -9999 0 -0.4 16 16
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.03 -10000 0 -0.46 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.17 0.26 0.61 102 -10000 0 102
IL27/IL27R/JAK1 -0.2 0.35 -10000 0 -0.91 75 75
TBX21 -0.22 0.3 -10000 0 -0.6 163 163
IL12B 0.001 0.075 -10000 0 -0.35 21 21
IL12A -0.01 0.064 -10000 0 -0.19 55 55
IL6ST -0.12 0.22 -10000 0 -0.47 143 143
IL27RA/JAK1 -0.11 0.33 -10000 0 -1.2 39 39
IL27 -0.082 0.2 -10000 0 -0.5 98 98
TYK2 0.011 0.011 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.006 0.11 -10000 0 -1.4 1 1
T-helper 2 cell differentiation 0.17 0.26 0.61 102 -10000 0 102
T cell proliferation during immune response 0.17 0.26 0.61 102 -10000 0 102
MAPKKK cascade -0.17 0.26 -10000 0 -0.61 102 102
STAT3 0.015 0.04 -10000 0 -0.52 3 3
STAT2 0.018 0 -10000 0 -10000 0 0
STAT1 -0.021 0.12 -10000 0 -0.33 58 58
IL12RB1 0.017 0.003 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.21 0.28 -10000 0 -0.58 158 158
IL27/IL27R/JAK2/TYK2 -0.17 0.27 -10000 0 -0.62 102 102
positive regulation of T cell mediated cytotoxicity -0.17 0.26 -10000 0 -0.61 102 102
STAT1 (dimer) -0.27 0.4 0.46 9 -0.91 104 113
JAK2 0.004 0.055 -10000 0 -0.33 12 12
JAK1 0.011 0.057 -10000 0 -0.52 6 6
STAT2 (dimer) -0.16 0.25 -10000 0 -0.59 101 101
T cell proliferation -0.2 0.27 -10000 0 -0.61 118 118
IL12/IL12R/TYK2/JAK2 -0.033 0.15 -10000 0 -0.9 8 8
IL17A -0.006 0.11 -10000 0 -1.4 1 1
mast cell activation 0.17 0.26 0.61 102 -10000 0 102
IFNG -0.031 0.047 -10000 0 -0.11 90 90
T cell differentiation -0.01 0.009 0.024 1 -0.023 140 141
STAT3 (dimer) -0.16 0.25 -10000 0 -0.6 96 96
STAT5A (dimer) -0.16 0.26 -10000 0 -0.61 98 98
STAT4 (dimer) -0.17 0.27 -10000 0 -0.6 114 114
STAT4 -0.024 0.13 -10000 0 -0.42 50 50
T cell activation 0.002 0.038 0.097 58 -10000 0 58
IL27R/JAK2/TYK2 -0.16 0.33 -10000 0 -0.98 57 57
GATA3 -0.25 0.55 -10000 0 -1.3 119 119
IL18 -0.035 0.12 -10000 0 -0.32 76 76
positive regulation of mast cell cytokine production -0.15 0.25 -10000 0 -0.59 97 97
IL27/EBI3 -0.06 0.16 -10000 0 -0.38 95 95
IL27RA -0.12 0.34 -10000 0 -1.3 38 38
IL6 -0.077 0.18 -10000 0 -0.35 147 147
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.054 0.16 0.49 38 -1.2 3 41
IL1B -0.033 0.12 -10000 0 -0.29 81 81
EBI3 0.002 0.071 -10000 0 -0.44 12 12
TNF -0.003 0.067 -10000 0 -0.25 31 31
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.11 0.3 -10000 0 -0.75 46 46
CRP -0.11 0.3 -10000 0 -0.76 44 44
cell cycle arrest -0.14 0.34 -10000 0 -0.78 80 80
TIMP1 -0.11 0.3 -10000 0 -0.76 60 60
IL6ST -0.11 0.22 -10000 0 -0.46 143 143
Rac1/GDP -0.1 0.22 0.28 2 -0.45 112 114
AP1 -0.05 0.16 -10000 0 -0.43 39 39
GAB2 0.011 0.048 -10000 0 -0.25 17 17
TNFSF11 -0.18 0.41 -10000 0 -0.97 89 89
HSP90B1 0.008 0.11 -10000 0 -0.8 6 6
GAB1 0.007 0.074 -10000 0 -0.42 14 14
MAPK14 -0.11 0.22 -10000 0 -0.52 74 74
AKT1 0.038 0.073 -10000 0 -0.47 3 3
FOXO1 0.036 0.086 -10000 0 -0.45 5 5
MAP2K6 -0.12 0.22 0.27 2 -0.41 144 146
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.1 0.25 -10000 0 -0.53 92 92
MITF -0.11 0.22 0.29 2 -0.43 124 126
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.018 0 -10000 0 -10000 0 0
A2M -0.042 0.28 -10000 0 -1.4 22 22
CEBPB 0.013 0.073 -10000 0 -0.33 20 20
GRB2/SOS1/GAB family/SHP2 -0.017 0.1 -10000 0 -0.39 10 10
STAT3 -0.15 0.37 -10000 0 -0.84 80 80
STAT1 -0.042 0.17 -10000 0 -0.95 16 16
CEBPD -0.16 0.38 -10000 0 -0.94 75 75
PIK3CA 0.017 0.029 -10000 0 -0.34 3 3
PI3K 0.008 0.083 -10000 0 -0.37 21 21
JUN -0.034 0.15 -10000 0 -0.46 57 57
PIAS3/MITF -0.095 0.21 0.27 2 -0.41 115 117
MAPK11 -0.11 0.22 -10000 0 -0.51 77 77
STAT3 (dimer)/FOXO1 -0.082 0.29 -10000 0 -0.64 68 68
GRB2/SOS1/GAB family -0.11 0.18 -10000 0 -0.46 75 75
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.22 -10000 0 -0.39 167 167
GRB2 0.017 0.024 -10000 0 -0.25 4 4
JAK2 0.01 0.053 -10000 0 -0.32 12 12
LBP -0.097 0.26 -10000 0 -0.62 50 50
PIK3R1 -0.008 0.11 -10000 0 -0.42 33 33
JAK1 0.013 0.059 -10000 0 -0.53 6 6
MYC -0.14 0.37 -10000 0 -0.93 67 67
FGG -0.11 0.3 -10000 0 -0.76 47 47
macrophage differentiation -0.14 0.34 -10000 0 -0.78 80 80
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.13 0.2 -10000 0 -0.35 204 204
JUNB -0.11 0.29 -10000 0 -0.73 50 50
FOS -0.11 0.2 -10000 0 -0.37 171 171
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.31 2 -0.42 144 146
STAT1/PIAS1 -0.11 0.22 0.32 2 -0.44 118 120
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.067 -10000 0 -0.38 4 4
STAT3 (dimer) -0.14 0.36 -10000 0 -0.83 79 79
PRKCD -0.1 0.27 -10000 0 -0.59 81 81
IL6R 0.002 0.085 -10000 0 -0.37 23 23
SOCS3 -0.1 0.23 -10000 0 -0.69 39 39
gp130 (dimer)/JAK1/JAK1/LMO4 -0.096 0.19 -10000 0 -0.35 170 170
Rac1/GTP -0.11 0.24 -10000 0 -0.47 109 109
HCK -0.005 0.11 -10000 0 -0.47 25 25
MAPKKK cascade 0.008 0.093 -10000 0 -0.55 4 4
bone resorption -0.16 0.38 -10000 0 -0.88 90 90
IRF1 -0.12 0.33 -10000 0 -0.82 61 61
mol:GDP -0.12 0.23 0.29 2 -0.44 133 135
SOS1 0.018 0.024 -10000 0 -0.52 1 1
VAV1 -0.12 0.23 0.29 2 -0.44 133 135
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.22 -10000 0 -0.46 102 102
PTPN11 0.004 0.058 -10000 0 -1.2 1 1
IL6/IL6RA -0.056 0.14 -10000 0 -0.36 77 77
gp130 (dimer)/TYK2/TYK2/LMO4 -0.095 0.18 -10000 0 -0.34 169 169
gp130 (dimer)/JAK2/JAK2/LMO4 -0.099 0.18 -10000 0 -0.35 174 174
IL6 -0.084 0.18 -10000 0 -0.36 146 146
PIAS3 0.018 0 -10000 0 -10000 0 0
PTPRE -0.002 0.088 -10000 0 -0.47 17 17
PIAS1 0.017 0.012 -10000 0 -0.25 1 1
RAC1 0.018 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.11 0.18 0.27 2 -0.35 150 152
LMO4 -0.073 0.18 -10000 0 -0.38 123 123
STAT3 (dimer)/PIAS3 -0.14 0.34 -10000 0 -0.77 80 80
MCL1 0.043 0.083 -10000 0 -0.82 2 2
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.058 0.21 -10000 0 -0.46 93 93
FYN -0.085 0.26 -10000 0 -0.56 101 101
LAT/GRAP2/SLP76 -0.098 0.21 -10000 0 -0.48 103 103
IKBKB 0.012 0.047 -10000 0 -0.31 10 10
AKT1 -0.048 0.19 -10000 0 -0.38 104 104
B2M -0.005 0.1 -10000 0 -0.45 25 25
IKBKG 0.003 0.061 -10000 0 -0.14 39 39
MAP3K8 -0.036 0.15 -10000 0 -0.39 70 70
mol:Ca2+ -0.022 0.031 -10000 0 -0.084 64 64
integrin-mediated signaling pathway 0.007 0.068 -10000 0 -0.31 20 20
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.083 0.26 -10000 0 -0.56 105 105
TRPV6 -0.11 0.19 -10000 0 -0.38 159 159
CD28 -0.044 0.16 -10000 0 -0.4 78 78
SHC1 -0.09 0.26 -10000 0 -0.56 102 102
receptor internalization -0.12 0.3 -10000 0 -0.62 114 114
PRF1 -0.079 0.24 -10000 0 -0.74 38 38
KRAS 0.009 0.065 -10000 0 -0.44 10 10
GRB2 0.016 0.024 -10000 0 -0.25 4 4
COT/AKT1 -0.047 0.16 -10000 0 -0.33 96 96
LAT -0.095 0.27 -10000 0 -0.56 112 112
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.029 0.13 -10000 0 -0.35 68 68
CD3E 0.016 0.018 -10000 0 -0.26 2 2
CD3G -0.092 0.2 -10000 0 -0.41 136 136
RASGRP2 -0.002 0.036 -10000 0 -0.17 13 13
RASGRP1 -0.061 0.2 -10000 0 -0.4 106 106
HLA-A -0.012 0.12 -10000 0 -0.43 34 34
RASSF5 -0.004 0.096 -10000 0 -0.38 29 29
RAP1A/GTP/RAPL 0.007 0.068 -10000 0 -0.31 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.064 -10000 0 -0.12 62 62
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.045 0.078 -10000 0 -0.21 72 72
PRKCA -0.043 0.1 -10000 0 -0.25 87 87
GRAP2 0.012 0.042 -10000 0 -0.28 10 10
mol:IP3 -0.051 0.18 0.22 43 -0.38 95 138
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.08 0.22 -10000 0 -0.46 97 97
ORAI1 0.07 0.11 0.3 66 -0.38 1 67
CSK -0.088 0.26 -10000 0 -0.56 99 99
B7 family/CD28 -0.11 0.3 -10000 0 -0.61 113 113
CHUK 0.005 0.081 -10000 0 -0.5 13 13
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.3 -10000 0 -0.65 103 103
PTPN6 -0.094 0.26 -10000 0 -0.57 101 101
VAV1 -0.1 0.28 -10000 0 -0.59 107 107
Monovalent TCR/CD3 -0.096 0.22 -10000 0 -0.4 144 144
CBL 0.017 0.012 -10000 0 -0.25 1 1
LCK -0.097 0.28 -10000 0 -0.61 98 98
PAG1 -0.092 0.26 -10000 0 -0.58 99 99
RAP1A 0.012 0.057 -10000 0 -0.52 6 6
TCR/CD3/MHC I/CD8/LCK -0.12 0.3 -10000 0 -0.66 102 102
CD80 0.009 0.048 -10000 0 -0.27 14 14
CD86 -0.008 0.11 -10000 0 -0.5 26 26
PDK1/CARD11/BCL10/MALT1 -0.054 0.094 -10000 0 -0.24 89 89
HRAS 0.012 0.051 -10000 0 -0.41 7 7
GO:0035030 -0.091 0.24 -10000 0 -0.5 113 113
CD8A 0 0.005 -10000 0 -10000 0 0
CD8B 0.001 0.069 -10000 0 -0.28 29 29
PTPRC -0.041 0.16 -10000 0 -0.42 71 71
PDK1/PKC theta -0.06 0.23 -10000 0 -0.48 103 103
CSK/PAG1 -0.08 0.25 -10000 0 -0.54 97 97
SOS1 0.017 0.023 -10000 0 -0.52 1 1
peptide-MHC class I -0.01 0.13 -10000 0 -0.48 31 31
GRAP2/SLP76 -0.085 0.26 -10000 0 -0.56 100 100
STIM1 0.034 0.059 -10000 0 -0.36 2 2
RAS family/GTP -0.002 0.088 -10000 0 -0.17 67 67
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.33 -10000 0 -0.67 114 114
mol:DAG -0.072 0.14 0.13 1 -0.34 99 100
RAP1A/GDP 0.003 0.031 -10000 0 -0.079 19 19
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
CD247 -0.11 0.21 -10000 0 -0.41 153 153
cytotoxic T cell degranulation -0.076 0.23 -10000 0 -0.7 39 39
RAP1A/GTP -0.005 0.014 -10000 0 -0.075 17 17
mol:PI-3-4-5-P3 -0.063 0.22 -10000 0 -0.46 105 105
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.076 0.23 0.24 38 -0.49 99 137
NRAS 0.005 0.076 -10000 0 -0.4 16 16
ZAP70 0.005 0.06 -10000 0 -0.27 24 24
GRB2/SOS1 0.024 0.023 -10000 0 -0.37 1 1
LAT/GRAP2/SLP76/VAV1 -0.1 0.21 0.16 1 -0.49 103 104
MALT1 0.011 0.053 -10000 0 -0.37 9 9
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
CD8 heterodimer 0.002 0.049 -10000 0 -0.19 29 29
CARD11 0.002 0.077 -10000 0 -0.33 24 24
PRKCB -0.048 0.1 -10000 0 -0.24 99 99
PRKCE -0.045 0.11 -10000 0 -0.25 91 91
PRKCQ -0.078 0.26 -10000 0 -0.54 105 105
LCP2 -0.004 0.097 -10000 0 -0.4 27 27
BCL10 0.017 0.012 -10000 0 -0.25 1 1
regulation of survival gene product expression -0.037 0.16 -10000 0 -0.33 103 103
IKK complex 0.012 0.059 -10000 0 -0.1 47 47
RAS family/GDP -0.008 0.015 -10000 0 -0.064 20 20
MAP3K14 -0.029 0.12 -10000 0 -0.26 87 87
PDPK1 -0.042 0.18 -10000 0 -0.36 102 102
TCR/CD3/MHC I/CD8/Fyn -0.091 0.26 -10000 0 -0.6 89 89
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.029 0.12 -10000 0 -0.35 30 30
TBX21 -0.3 0.59 -10000 0 -1.3 126 126
B2M -0.005 0.1 -10000 0 -0.45 25 25
TYK2 0.012 0.022 -10000 0 -10000 0 0
IL12RB1 0.012 0.022 -10000 0 -10000 0 0
GADD45B -0.18 0.44 -10000 0 -1.1 85 85
IL12RB2 -0.076 0.16 -10000 0 -0.32 142 142
GADD45G -0.18 0.43 -10000 0 -1 86 86
natural killer cell activation -0.005 0.024 -10000 0 -10000 0 0
RELB 0.003 0.078 -10000 0 -0.38 19 19
RELA 0.018 0 -10000 0 -10000 0 0
IL18 -0.046 0.17 -10000 0 -0.44 76 76
IL2RA -0.03 0.14 -10000 0 -0.4 60 60
IFNG -0.088 0.17 -10000 0 -0.33 161 161
STAT3 (dimer) -0.14 0.37 -10000 0 -0.77 111 111
HLA-DRB5 -0.002 0.093 -10000 0 -0.51 17 17
FASLG -0.24 0.52 -10000 0 -1.1 107 107
NF kappa B2 p52/RelB -0.24 0.41 -10000 0 -0.88 127 127
CD4 0.015 0.007 -10000 0 -10000 0 0
SOCS1 0.015 0.031 -10000 0 -0.32 4 4
EntrezGene:6955 -0.005 0.012 -10000 0 -10000 0 0
CD3D -0.033 0.13 -10000 0 -0.35 68 68
CD3E 0.013 0.021 -10000 0 -0.28 2 2
CD3G -0.097 0.2 -10000 0 -0.42 136 136
IL12Rbeta2/JAK2 -0.048 0.13 -10000 0 -0.3 80 80
CCL3 -0.2 0.44 -10000 0 -1 96 96
CCL4 -0.2 0.46 -10000 0 -1 101 101
HLA-A -0.012 0.11 -10000 0 -0.43 34 34
IL18/IL18R -0.056 0.21 -10000 0 -0.41 117 117
NOS2 -0.19 0.44 -10000 0 -0.86 124 124
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.12 -10000 0 -0.37 28 28
IL1R1 -0.25 0.51 -10000 0 -1.1 117 117
IL4 0.016 0.063 -10000 0 -0.48 7 7
JAK2 0.004 0.06 -10000 0 -0.34 12 12
EntrezGene:6957 -0.004 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.33 -10000 0 -0.81 71 71
RAB7A -0.12 0.34 -10000 0 -0.81 79 79
lysosomal transport -0.12 0.33 -10000 0 -0.76 80 80
FOS -0.29 0.5 -10000 0 -1.1 121 121
STAT4 (dimer) -0.18 0.43 -10000 0 -0.9 114 114
STAT5A (dimer) -0.27 0.42 -10000 0 -0.91 130 130
GZMA -0.2 0.43 -10000 0 -0.87 126 126
GZMB -0.28 0.57 -10000 0 -1.2 120 120
HLX 0.005 0.079 -10000 0 -0.48 13 13
LCK -0.25 0.52 -10000 0 -1 135 135
TCR/CD3/MHC II/CD4 -0.11 0.23 -10000 0 -0.5 106 106
IL2/IL2R -0.014 0.14 -10000 0 -0.33 71 71
MAPK14 -0.18 0.44 -10000 0 -0.97 98 98
CCR5 -0.19 0.46 -10000 0 -1.1 81 81
IL1B -0.053 0.17 -10000 0 -0.42 81 81
STAT6 -0.066 0.18 -10000 0 -0.37 79 79
STAT4 -0.024 0.13 -10000 0 -0.42 50 50
STAT3 0.015 0.04 -10000 0 -0.52 3 3
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
NFKB2 0.015 0.031 -10000 0 -0.32 4 4
IL12B 0 0.077 -10000 0 -0.34 21 21
CD8A -0.001 0.008 -10000 0 -10000 0 0
CD8B 0.001 0.07 -10000 0 -0.28 29 29
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.029 0.12 0.35 30 -10000 0 30
IL2RB -0.016 0.12 -10000 0 -0.43 40 40
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.38 -10000 0 -0.8 113 113
IL2RG -0.002 0.078 -10000 0 -0.28 35 35
IL12 -0.011 0.089 -10000 0 -0.36 14 14
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
CD247 -0.11 0.21 -10000 0 -0.42 153 153
IL2 0.011 0.051 -10000 0 -0.33 10 10
SPHK2 0.017 0.023 -10000 0 -0.52 1 1
FRAP1 0.018 0 -10000 0 -10000 0 0
IL12A -0.019 0.095 -10000 0 -0.28 55 55
IL12/IL12R/TYK2/JAK2 -0.25 0.54 -10000 0 -1.1 125 125
MAP2K3 -0.18 0.44 -10000 0 -0.99 97 97
RIPK2 0.013 0.04 -10000 0 -0.28 9 9
MAP2K6 -0.19 0.45 -10000 0 -0.97 106 106
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.08 -10000 0 -0.52 12 12
IL18RAP -0.071 0.19 -10000 0 -0.4 114 114
IL12Rbeta1/TYK2 0.018 0.032 -10000 0 -10000 0 0
EOMES -0.059 0.26 -10000 0 -1.3 21 21
STAT1 (dimer) -0.2 0.39 -10000 0 -0.8 124 124
T cell proliferation -0.12 0.31 -10000 0 -0.66 106 106
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.01 0.12 -10000 0 -0.41 37 37
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.3 -10000 0 -0.72 109 109
ATF2 -0.15 0.4 -10000 0 -0.89 94 94
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.062 0.17 -9999 0 -0.43 52 52
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.18 -9999 0 -0.49 44 44
alphaV/beta3 Integrin/Osteopontin/Src -0.098 0.18 -9999 0 -0.39 131 131
AP1 -0.15 0.26 -9999 0 -0.58 105 105
ILK -0.064 0.16 -9999 0 -0.41 47 47
bone resorption -0.055 0.17 -9999 0 -0.42 51 51
PTK2B 0.017 0.017 -9999 0 -0.25 2 2
PYK2/p130Cas -0.059 0.17 -9999 0 -0.39 59 59
ITGAV -0.001 0.1 -9999 0 -0.49 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.007 0.081 -9999 0 -0.37 21 21
alphaV/beta3 Integrin/Osteopontin -0.076 0.18 -9999 0 -0.34 142 142
MAP3K1 -0.09 0.18 -9999 0 -0.32 166 166
JUN -0.034 0.15 -9999 0 -0.46 57 57
MAPK3 -0.064 0.17 -9999 0 -0.46 49 49
MAPK1 -0.064 0.17 -9999 0 -0.46 50 50
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 -0.08 0.17 -9999 0 -0.41 67 67
ITGB3 0.003 0.077 -9999 0 -0.32 25 25
NFKBIA -0.063 0.19 -9999 0 -0.5 51 51
FOS -0.11 0.2 -9999 0 -0.37 171 171
CD44 -0.004 0.1 -9999 0 -0.43 26 26
CHUK 0.005 0.081 -9999 0 -0.5 13 13
PLAU -0.14 0.38 -9999 0 -1.2 56 56
NF kappa B1 p50/RelA -0.047 0.19 -9999 0 -0.52 45 45
BCAR1 0.017 0.012 -9999 0 -0.25 1 1
RELA 0.018 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.003 0.1 -9999 0 -0.42 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.085 0.18 -9999 0 -0.32 162 162
VAV3 -0.12 0.2 -9999 0 -0.43 100 100
MAP3K14 -0.069 0.17 -9999 0 -0.31 137 137
ROCK2 0.013 0.048 -9999 0 -0.47 5 5
SPP1 -0.14 0.23 -9999 0 -0.42 188 188
RAC1 0.018 0 -9999 0 -10000 0 0
Rac1/GTP -0.11 0.18 -9999 0 -0.41 92 92
MMP2 -0.13 0.24 -9999 0 -0.54 103 103
Arf6 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
CENTA1/KIF3B 0 0.058 -9999 0 -0.26 23 23
ARNO/beta Arrestin1-2 -0.013 0.089 -9999 0 -0.24 59 59
EGFR -0.079 0.18 -9999 0 -0.35 139 139
EPHA2 0.008 0.059 -9999 0 -0.33 14 14
USP6 0.012 0.04 -9999 0 -0.25 12 12
IQSEC1 0.016 0.026 -9999 0 -0.39 2 2
EGFR/EGFR/EGF/EGF -0.15 0.2 -9999 0 -0.42 173 173
ARRB2 0.011 0.052 -9999 0 -0.32 12 12
mol:GTP 0.006 0.015 -9999 0 -0.13 2 2
ARRB1 0.004 0.075 -9999 0 -0.37 18 18
FBXO8 0.015 0.04 -9999 0 -0.52 3 3
TSHR 0.008 0.071 -9999 0 -0.5 10 10
EGF -0.14 0.23 -9999 0 -0.42 193 193
somatostatin receptor activity 0 0 -9999 0 -0.001 95 95
ARAP2 0 0 -9999 0 0 110 110
mol:GDP -0.054 0.11 -9999 0 -0.25 89 89
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 96 96
ITGA2B 0.016 0.02 -9999 0 -0.25 3 3
ARF6 0.016 0.033 -9999 0 -0.52 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.071 -9999 0 -0.27 24 24
ADAP1 0 0 -9999 0 0 87 87
KIF13B -0.002 0.095 -9999 0 -0.43 23 23
HGF/MET 0.007 0.073 -9999 0 -0.38 13 13
PXN 0.018 0 -9999 0 -10000 0 0
ARF6/GTP -0.067 0.11 -9999 0 -0.27 93 93
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.12 0.18 -9999 0 -0.35 173 173
ADRB2 -0.045 0.16 -9999 0 -0.4 80 80
receptor agonist activity 0 0 -9999 0 0 92 92
actin filament binding 0 0 -9999 0 0 96 96
SRC 0.015 0.035 -9999 0 -0.43 3 3
ITGB3 0.002 0.075 -9999 0 -0.32 25 25
GNAQ 0 0 -9999 0 -0.001 88 88
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 90 90
ARF6/GDP -0.003 0.059 -9999 0 -0.3 5 5
ARF6/GDP/GULP/ACAP1 -0.058 0.13 -9999 0 -0.32 85 85
alphaIIb/beta3 Integrin/paxillin/GIT1 0.034 0.048 -9999 0 -0.26 8 8
ACAP1 0 0 -9999 0 0 21 21
ACAP2 0 0 -9999 0 0 104 104
LHCGR/beta Arrestin2 0.009 0.07 -9999 0 -0.44 12 12
EFNA1 0 0.094 -9999 0 -0.49 18 18
HGF 0.008 0.069 -9999 0 -0.45 11 11
CYTH3 0 0 -9999 0 -0.001 95 95
CYTH2 -0.001 0.002 -9999 0 -0.004 100 100
NCK1 0.011 0.045 -9999 0 -0.28 12 12
fibronectin binding 0 0 -9999 0 0 75 75
endosomal lumen acidification 0 0 -9999 0 0 82 82
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.035 0.15 -9999 0 -0.44 61 61
GNAQ/ARNO -0.001 0.003 -9999 0 -0.006 89 89
mol:Phosphatidic acid 0 0 -9999 0 0 104 104
PIP3-E 0.004 0.068 -9999 0 -0.3 23 23
MET 0 0.075 -9999 0 -0.29 31 31
GNA14 -0.08 0.18 -9999 0 -0.35 140 140
GNA15 0.002 0.076 -9999 0 -0.34 23 23
GIT1 0.014 0.035 -9999 0 -0.3 6 6
mol:PI-4-5-P2 0 0 -9999 0 -0.001 92 92
GNA11 0.013 0.047 -9999 0 -0.52 4 4
LHCGR 0.003 0.083 -9999 0 -0.46 16 16
AGTR1 -0.15 0.21 -9999 0 -0.36 231 231
desensitization of G-protein coupled receptor protein signaling pathway 0.009 0.07 -9999 0 -0.44 12 12
IPCEF1/ARNO -0.095 0.14 -9999 0 -0.28 179 179
alphaIIb/beta3 Integrin 0.014 0.056 -9999 0 -0.36 7 7
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.23 0.53 -10000 0 -1.3 83 83
IL23A -0.21 0.49 -10000 0 -1.2 73 73
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.42 -10000 0 -1 87 87
positive regulation of T cell mediated cytotoxicity -0.21 0.51 -10000 0 -1.1 90 90
ITGA3 -0.2 0.48 -10000 0 -1.1 82 82
IL17F -0.097 0.32 -10000 0 -0.68 75 75
IL12B 0.004 0.084 -10000 0 -0.35 21 21
STAT1 (dimer) -0.21 0.49 -10000 0 -1.1 91 91
CD4 -0.17 0.44 -10000 0 -1.1 58 58
IL23 -0.2 0.47 -10000 0 -1.1 73 73
IL23R -0.011 0.18 -10000 0 -1.4 7 7
IL1B -0.23 0.53 -10000 0 -1.3 82 82
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.18 0.44 -10000 0 -1.1 58 58
TYK2 0.013 0.024 -10000 0 -10000 0 0
STAT4 -0.024 0.13 -10000 0 -0.42 50 50
STAT3 0.015 0.041 -10000 0 -0.52 3 3
IL18RAP -0.075 0.18 -10000 0 -0.41 114 114
IL12RB1 0.013 0.024 -10000 0 -10000 0 0
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
IL12Rbeta1/TYK2 0.017 0.031 -10000 0 -10000 0 0
IL23R/JAK2 -0.013 0.19 -10000 0 -1.3 7 7
positive regulation of chronic inflammatory response -0.21 0.51 -10000 0 -1.1 90 90
natural killer cell activation 0.001 0.012 0.073 8 -10000 0 8
JAK2 0.011 0.065 -10000 0 -0.34 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
NFKB1 0.016 0.024 -10000 0 -0.52 1 1
RELA 0.017 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.45 -10000 0 -1.1 73 73
ALOX12B -0.17 0.44 -10000 0 -1 70 70
CXCL1 -0.27 0.54 -10000 0 -1.2 112 112
T cell proliferation -0.21 0.51 -10000 0 -1.1 90 90
NFKBIA 0.014 0.043 -10000 0 -0.46 4 4
IL17A -0.052 0.26 -10000 0 -0.54 61 61
PI3K -0.19 0.47 -10000 0 -1.1 88 88
IFNG -0.027 0.05 0.12 2 -0.13 53 55
STAT3 (dimer) -0.21 0.41 -10000 0 -0.99 89 89
IL18R1 -0.014 0.11 -10000 0 -0.41 37 37
IL23/IL23R/JAK2/TYK2/SOCS3 -0.08 0.28 -10000 0 -0.64 47 47
IL18/IL18R -0.082 0.2 -10000 0 -0.41 117 117
macrophage activation -0.015 0.017 -10000 0 -0.044 70 70
TNF -0.2 0.49 -10000 0 -1.2 75 75
STAT3/STAT4 -0.24 0.45 -10000 0 -1.1 95 95
STAT4 (dimer) -0.21 0.5 -10000 0 -1.1 95 95
IL18 -0.05 0.17 -10000 0 -0.44 76 76
IL19 -0.19 0.44 -10000 0 -1.1 70 70
STAT5A (dimer) -0.2 0.49 -10000 0 -1.1 89 89
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
SOCS3 0.005 0.074 -10000 0 -0.38 17 17
CXCL9 -0.27 0.57 -10000 0 -1.2 112 112
MPO -0.17 0.44 -10000 0 -1.1 69 69
positive regulation of humoral immune response -0.21 0.51 -10000 0 -1.1 90 90
IL23/IL23R/JAK2/TYK2 -0.22 0.54 -10000 0 -1.2 87 87
IL6 -0.26 0.55 -10000 0 -1.2 100 100
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
IL2 0.008 0.053 -10000 0 -0.34 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.012 0.073 8 -10000 0 8
CD3E -0.17 0.44 -10000 0 -1 69 69
keratinocyte proliferation -0.21 0.51 -10000 0 -1.1 90 90
NOS2 -0.18 0.44 -10000 0 -0.96 91 91
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.015 0.12 -10000 0 -0.38 44 44
GNB1/GNG2 -0.058 0.078 -10000 0 -0.18 138 138
AKT1 -0.023 0.12 -10000 0 -0.21 80 80
EGF -0.14 0.23 -10000 0 -0.42 193 193
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.03 0.061 -10000 0 -0.29 5 5
mol:Ca2+ -0.048 0.17 -10000 0 -0.29 141 141
LYN 0.029 0.062 -10000 0 -0.29 5 5
RhoA/GTP -0.041 0.056 -10000 0 -0.13 82 82
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.066 0.19 -10000 0 -0.35 142 142
GNG2 0.016 0.029 -10000 0 -0.34 3 3
ARRB2 0.018 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.004 0.1 -10000 0 -0.39 22 22
G beta5/gamma2 -0.075 0.1 -10000 0 -0.24 138 138
PRKCH -0.062 0.19 -10000 0 -0.35 138 138
DNM1 0.013 0.047 -10000 0 -0.37 7 7
TXA2/TP beta/beta Arrestin3 0.006 0.019 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.002 0.088 -10000 0 -0.35 29 29
G12 family/GTP -0.096 0.13 -10000 0 -0.3 141 141
ADRBK1 0.018 0 -10000 0 -10000 0 0
ADRBK2 0.002 0.088 -10000 0 -0.49 16 16
RhoA/GTP/ROCK1 0.016 0.05 -10000 0 -0.31 12 12
mol:GDP 0.019 0.12 0.32 24 -10000 0 24
mol:NADP 0.017 0.012 -10000 0 -0.25 1 1
RAB11A 0.016 0.029 -10000 0 -0.34 3 3
PRKG1 0.017 0.012 -10000 0 -0.25 1 1
mol:IP3 -0.067 0.2 -10000 0 -0.37 141 141
cell morphogenesis 0.016 0.05 -10000 0 -0.31 12 12
PLCB2 -0.1 0.26 -10000 0 -0.5 139 139
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.016 0.073 -10000 0 -0.31 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.02 0.085 -10000 0 -0.35 15 15
RHOA 0.005 0.08 -10000 0 -0.52 12 12
PTGIR 0.016 0.033 -10000 0 -0.52 2 2
PRKCB1 -0.081 0.22 -10000 0 -0.4 142 142
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.012 -10000 0 -0.25 1 1
TXA2/TXA2-R family -0.11 0.27 -10000 0 -0.52 140 140
LCK -0.008 0.11 -10000 0 -0.37 16 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.034 0.044 -10000 0 -0.36 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.059 -10000 0 -0.53 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.034 0.044 -10000 0 -0.36 2 2
MAPK14 -0.033 0.13 -10000 0 -0.23 137 137
TGM2/GTP -0.079 0.23 -10000 0 -0.41 147 147
MAPK11 -0.033 0.13 -10000 0 -0.23 137 137
ARHGEF1 -0.021 0.1 -10000 0 -0.17 136 136
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
JNK cascade -0.069 0.21 -10000 0 -0.38 140 140
RAB11/GDP 0.016 0.028 -10000 0 -0.34 3 3
ICAM1 -0.052 0.17 -10000 0 -0.3 139 139
cAMP biosynthetic process -0.063 0.19 -10000 0 -0.34 139 139
Gq family/GTP/EBP50 -0.038 0.11 -10000 0 -0.29 63 63
actin cytoskeleton reorganization 0.016 0.05 -10000 0 -0.31 12 12
SRC 0.029 0.062 -10000 0 -0.29 5 5
GNB5 0.005 0.081 -10000 0 -0.5 13 13
GNB1 0.013 0.052 -10000 0 -0.52 5 5
EGF/EGFR -0.028 0.11 -10000 0 -0.28 49 49
VCAM1 -0.054 0.17 -10000 0 -0.31 145 145
TP beta/Gq family/GDP/G beta5/gamma2 -0.004 0.1 -10000 0 -0.39 22 22
platelet activation -0.042 0.17 -10000 0 -0.3 139 139
PGI2/IP 0.012 0.024 -10000 0 -0.38 2 2
PRKACA 0.015 0.046 -10000 0 -0.26 12 12
Gq family/GDP/G beta5/gamma2 -0.005 0.096 -10000 0 -0.36 22 22
TXA2/TP beta/beta Arrestin2 -0.005 0.044 -10000 0 -0.56 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.021 0.044 -10000 0 -0.24 12 12
mol:DAG -0.079 0.22 -10000 0 -0.41 140 140
EGFR -0.079 0.18 -10000 0 -0.35 139 139
TXA2/TP alpha -0.09 0.25 -10000 0 -0.46 139 139
Gq family/GTP -0.038 0.078 -10000 0 -0.24 58 58
YES1 0.026 0.07 -10000 0 -0.32 7 7
GNAI2/GTP -0.015 0.055 -10000 0 -0.27 11 11
PGD2/DP -0.001 0.062 -10000 0 -0.24 29 29
SLC9A3R1 -0.043 0.16 -10000 0 -0.44 70 70
FYN 0.026 0.073 -10000 0 -0.31 12 12
mol:NO 0.017 0.012 -10000 0 -0.25 1 1
GNA15 0.002 0.076 -10000 0 -0.34 23 23
PGK/cGMP 0.023 0.01 -10000 0 -0.13 1 1
RhoA/GDP 0.006 0.079 -10000 0 -0.51 12 12
TP alpha/TGM2/GDP/G beta/gamma 0.028 0.078 -10000 0 -0.37 7 7
NOS3 0.017 0.012 -10000 0 -0.26 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCA -0.061 0.19 -10000 0 -0.34 139 139
PRKCB -0.064 0.19 -10000 0 -0.35 141 141
PRKCE -0.062 0.19 -10000 0 -0.35 139 139
PRKCD -0.068 0.2 -10000 0 -0.37 139 139
PRKCG -0.069 0.2 -10000 0 -0.37 140 140
muscle contraction -0.095 0.25 -10000 0 -0.48 140 140
PRKCZ -0.06 0.18 -10000 0 -0.34 140 140
ARR3 0.017 0.012 -10000 0 -0.25 1 1
TXA2/TP beta 0.028 0.059 -10000 0 -0.23 18 18
PRKCQ -0.068 0.2 -10000 0 -0.35 145 145
MAPKKK cascade -0.086 0.23 -10000 0 -0.44 140 140
SELE -0.077 0.2 -10000 0 -0.38 144 144
TP beta/GNAI2/GDP/G beta/gamma 0.038 0.068 -10000 0 -0.37 7 7
ROCK1 0.018 0 -10000 0 -10000 0 0
GNA14 -0.079 0.18 -10000 0 -0.35 140 140
chemotaxis -0.13 0.31 -10000 0 -0.6 140 140
GNA12 0.018 0 -10000 0 -10000 0 0
GNA13 0.011 0.055 -10000 0 -0.36 10 10
GNA11 0.014 0.047 -10000 0 -0.52 4 4
Rac1/GTP 0.013 0.002 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.027 0.13 -10000 0 -0.26 110 110
epithelial cell differentiation -0.007 0.1 -10000 0 -0.26 76 76
CYFIP2 -0.042 0.16 -10000 0 -0.47 65 65
ENAH 0.012 0.096 -10000 0 -0.31 14 14
EGFR -0.079 0.18 -10000 0 -0.35 139 139
EPHA2 0.008 0.059 -10000 0 -0.33 14 14
MYO6 -0.012 0.11 -10000 0 -0.25 90 90
CTNNB1 0.001 0.09 -10000 0 -0.45 19 19
ABI1/Sra1/Nap1 -0.004 0.11 -10000 0 -0.31 53 53
AQP5 -0.086 0.19 -10000 0 -0.46 87 87
CTNND1 0.016 0.029 -10000 0 -0.34 3 3
mol:PI-4-5-P2 -0.004 0.1 -10000 0 -0.24 78 78
regulation of calcium-dependent cell-cell adhesion -0.014 0.1 -10000 0 -0.24 82 82
EGF -0.14 0.23 -10000 0 -0.42 193 193
NCKAP1 0.015 0.031 -10000 0 -0.32 4 4
AQP3 -0.088 0.2 -10000 0 -0.49 86 86
cortical microtubule organization -0.007 0.1 -10000 0 -0.26 76 76
GO:0000145 -0.006 0.095 -10000 0 -0.23 78 78
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.11 -10000 0 -0.26 76 76
MLLT4 -0.006 0.11 -10000 0 -0.46 26 26
ARF6/GDP -0.04 0.086 -10000 0 -0.39 12 12
ARF6 0.016 0.033 -10000 0 -0.52 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.071 -10000 0 -0.27 24 24
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.006 0.12 -10000 0 -0.44 15 15
PVRL2 0.002 0.089 -10000 0 -0.52 15 15
ZYX -0.009 0.11 -10000 0 -0.24 84 84
ARF6/GTP 0.03 0.072 -10000 0 -0.27 22 22
CDH1 -0.049 0.17 -10000 0 -0.48 70 70
EGFR/EGFR/EGF/EGF -0.14 0.14 -10000 0 -0.38 92 92
RhoA/GDP -0.01 0.11 -10000 0 -0.25 85 85
actin cytoskeleton organization -0.007 0.11 -10000 0 -0.24 76 76
IGF-1R heterotetramer -0.083 0.2 -10000 0 -0.47 110 110
GIT1 0.014 0.035 -10000 0 -0.3 6 6
IGF1R -0.083 0.2 -10000 0 -0.47 110 110
IGF1 -0.1 0.2 -10000 0 -0.41 146 146
DIAPH1 -0.055 0.18 -10000 0 -0.58 53 53
Wnt receptor signaling pathway 0.007 0.1 0.26 76 -10000 0 76
RHOA 0.005 0.08 -10000 0 -0.52 12 12
RhoA/GTP -0.044 0.089 -10000 0 -0.37 16 16
CTNNA1 0.017 0.023 -10000 0 -0.52 1 1
VCL -0.007 0.11 -10000 0 -0.24 76 76
EFNA1 0 0.094 -10000 0 -0.49 18 18
LPP -0.003 0.1 -10000 0 -0.29 17 17
Ephrin A1/EPHA2 -0.044 0.094 -10000 0 -0.24 91 91
SEC6/SEC8 -0.045 0.092 -10000 0 -0.41 10 10
MGAT3 -0.014 0.11 -10000 0 -0.25 82 82
HGF/MET -0.044 0.089 -10000 0 -0.28 20 20
HGF 0.008 0.069 -10000 0 -0.45 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.027 0.13 -10000 0 -0.26 110 110
actin cable formation 0.017 0.1 -10000 0 -0.28 21 21
KIAA1543 0.001 0.1 -10000 0 -0.38 9 9
KIFC3 -0.005 0.1 -10000 0 -0.24 77 77
NCK1 0.011 0.045 -10000 0 -0.28 12 12
EXOC3 0.017 0.012 -10000 0 -0.25 1 1
ACTN1 -0.009 0.11 -10000 0 -0.24 85 85
NCK1/GIT1 0.019 0.042 -10000 0 -0.44 2 2
mol:GDP -0.007 0.1 -10000 0 -0.26 76 76
EXOC4 0.016 0.033 -10000 0 -0.52 2 2
STX4 -0.003 0.1 -10000 0 -0.24 76 76
PIP5K1C -0.004 0.1 -10000 0 -0.24 78 78
LIMA1 -0.024 0.14 -10000 0 -0.52 41 41
ABI1 0.016 0.02 -10000 0 -0.25 3 3
ROCK1 0.009 0.1 -10000 0 -0.32 16 16
adherens junction assembly 0.012 0.11 -10000 0 -0.52 5 5
IGF-1R heterotetramer/IGF1 -0.12 0.16 -10000 0 -0.3 203 203
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.1 -10000 0 -0.39 33 33
MET 0 0.075 -10000 0 -0.29 31 31
PLEKHA7 -0.003 0.099 -10000 0 -0.24 77 77
mol:GTP 0.024 0.07 -10000 0 -0.27 24 24
establishment of epithelial cell apical/basal polarity 0.006 0.11 -10000 0 -0.41 10 10
cortical actin cytoskeleton stabilization -0.027 0.13 -10000 0 -0.26 110 110
regulation of cell-cell adhesion -0.007 0.11 -10000 0 -0.24 76 76
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.027 0.13 -10000 0 -0.26 110 110
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.1 0.26 -10000 0 -0.62 82 82
IHH -0.014 0.093 -10000 0 -0.48 14 14
SHH Np/Cholesterol/GAS1 -0.057 0.14 -10000 0 -0.29 133 133
LRPAP1 0.016 0.026 -10000 0 -0.39 2 2
dorsoventral neural tube patterning 0.056 0.14 0.29 133 -10000 0 133
SMO/beta Arrestin2 -0.055 0.17 -10000 0 -0.48 45 45
SMO -0.066 0.18 -10000 0 -0.5 49 49
AKT1 -0.027 0.13 -10000 0 -0.5 22 22
ARRB2 0.018 0 -10000 0 -10000 0 0
BOC -0.02 0.12 -10000 0 -0.38 50 50
ADRBK1 0.018 0 -10000 0 -10000 0 0
heart looping -0.065 0.18 -10000 0 -0.49 49 49
STIL -0.052 0.15 -10000 0 -0.37 53 53
DHH N/PTCH2 0.026 0 -10000 0 -10000 0 0
DHH N/PTCH1 -0.028 0.13 -10000 0 -0.37 24 24
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
DHH 0.018 0 -10000 0 -10000 0 0
PTHLH -0.12 0.31 -10000 0 -0.83 66 66
determination of left/right symmetry -0.065 0.18 -10000 0 -0.49 49 49
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
skeletal system development -0.12 0.31 -10000 0 -0.82 66 66
IHH N/Hhip 0.004 0.068 -10000 0 -0.29 22 22
DHH N/Hhip 0.021 0.037 -10000 0 -0.37 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.065 0.18 -10000 0 -0.49 49 49
pancreas development 0.011 0.052 -10000 0 -0.33 11 11
HHAT -0.045 0.17 -10000 0 -0.51 63 63
PI3K 0.005 0.082 -10000 0 -0.37 21 21
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.072 0.19 -10000 0 -0.47 98 98
somite specification -0.065 0.18 -10000 0 -0.49 49 49
SHH Np/Cholesterol/PTCH1 -0.049 0.14 -10000 0 -0.36 49 49
SHH Np/Cholesterol/PTCH2 -0.007 0.098 -10000 0 -0.28 61 61
SHH Np/Cholesterol/Megalin -0.1 0.18 -10000 0 -0.33 181 181
SHH -0.021 0.13 -10000 0 -0.37 61 61
catabolic process -0.042 0.14 -10000 0 -0.33 76 76
SMO/Vitamin D3 -0.061 0.17 -10000 0 -0.4 63 63
SHH Np/Cholesterol/Hhip -0.01 0.1 -10000 0 -0.28 64 64
LRP2 -0.16 0.24 -10000 0 -0.48 183 183
receptor-mediated endocytosis -0.12 0.2 -10000 0 -0.46 90 90
SHH Np/Cholesterol/BOC -0.027 0.12 -10000 0 -0.28 85 85
SHH Np/Cholesterol/CDO -0.019 0.11 -10000 0 -0.29 74 74
mesenchymal cell differentiation 0.011 0.1 0.28 64 -10000 0 64
mol:Vitamin D3 -0.047 0.14 -10000 0 -0.36 49 49
IHH N/PTCH2 0.01 0.055 -10000 0 -0.32 11 11
CDON -0.004 0.099 -10000 0 -0.41 27 27
IHH N/PTCH1 -0.04 0.14 -10000 0 -0.33 76 76
Megalin/LRPAP1 -0.1 0.18 -10000 0 -0.37 158 158
PTCH2 0.018 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.017 0.097 -10000 0 -0.28 61 61
PTCH1 -0.043 0.14 -10000 0 -0.33 76 76
HHIP 0.011 0.052 -10000 0 -0.33 11 11
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.02 -10000 0 -0.24 3 3
GNB1/GNG2 -0.031 0.13 -10000 0 -0.28 107 107
regulation of S phase of mitotic cell cycle -0.031 0.12 -10000 0 -0.24 120 120
GNAO1 0.016 0.024 -10000 0 -0.25 4 4
HRAS 0.011 0.051 -10000 0 -0.41 7 7
SHBG/T-DHT 0.012 0 -10000 0 -10000 0 0
PELP1 0.017 0.001 -10000 0 -10000 0 0
AKT1 0.008 0.038 -10000 0 -0.26 9 9
MAP2K1 -0.032 0.12 -10000 0 -0.32 32 32
T-DHT/AR -0.064 0.16 -10000 0 -0.38 104 104
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 164 164
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.018 0 -10000 0 -10000 0 0
GNAI1 -0.017 0.12 -10000 0 -0.38 46 46
mol:GDP -0.089 0.17 -10000 0 -0.43 103 103
cell proliferation -0.066 0.18 -10000 0 -0.4 83 83
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
FOS -0.13 0.3 -10000 0 -0.81 76 76
mol:Ca2+ -0.014 0.022 -10000 0 -0.08 23 23
MAPK3 -0.05 0.14 -10000 0 -0.42 32 32
MAPK1 -0.029 0.092 -10000 0 -0.27 26 26
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
mol:IP3 -0.001 0.002 -10000 0 -0.003 166 166
cAMP biosynthetic process 0.013 0.021 -10000 0 -10000 0 0
GNG2 0.016 0.029 -10000 0 -0.34 3 3
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.003 166 166
HRAS/GTP -0.036 0.12 -10000 0 -0.26 107 107
actin cytoskeleton reorganization -0.01 0.049 -10000 0 -0.24 21 21
SRC 0.015 0.035 -10000 0 -0.43 3 3
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.003 166 166
PI3K 0.006 0.07 -10000 0 -0.31 21 21
apoptosis 0.064 0.17 0.41 82 -10000 0 82
T-DHT/AR/PELP1 -0.044 0.13 -10000 0 -0.32 103 103
HRAS/GDP -0.063 0.18 -10000 0 -0.4 105 105
CREB1 -0.069 0.18 -10000 0 -0.44 82 82
RAC1-CDC42/GTP 0.02 0.057 -10000 0 -0.24 21 21
AR -0.089 0.21 -10000 0 -0.52 104 104
GNB1 0.013 0.052 -10000 0 -0.52 5 5
RAF1 -0.033 0.12 -10000 0 -0.25 107 107
RAC1-CDC42/GDP -0.047 0.17 -10000 0 -0.38 103 103
T-DHT/AR/PELP1/Src -0.032 0.12 -10000 0 -0.28 105 105
MAP2K2 -0.033 0.12 -10000 0 -0.33 32 32
T-DHT/AR/PELP1/Src/PI3K -0.032 0.12 -10000 0 -0.24 120 120
GNAZ 0.001 0.088 -10000 0 -0.44 19 19
SHBG 0.018 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.002 0.1 -10000 0 -0.44 15 15
mol:T-DHT 0 0.001 -10000 0 -0.003 52 52
RAC1 0.018 0 -10000 0 -10000 0 0
GNRH1 0 0.057 -10000 0 -0.23 26 26
Gi family/GTP -0.022 0.092 -10000 0 -0.28 21 21
CDC42 0.018 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.049 0.17 -9999 0 -0.44 77 77
PLK4 0.008 0.065 -9999 0 -0.38 13 13
regulation of centriole replication -0.029 0.13 -9999 0 -0.37 59 59
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.02 0.13 -9999 0 -0.32 78 78
E-cadherin/beta catenin -0.034 0.14 -9999 0 -0.38 74 74
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
JUP 0.011 0.056 -9999 0 -0.42 8 8
CDH1 -0.049 0.17 -9999 0 -0.48 70 70
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.065 0.13 -9999 0 -0.28 97 97
SMAD6-7/SMURF1 0.034 0.021 -9999 0 -0.3 1 1
NOG 0.009 0.056 -9999 0 -0.31 14 14
SMAD9 -0.023 0.12 -9999 0 -0.65 12 12
SMAD4 0.009 0.067 -9999 0 -0.49 9 9
SMAD5 -0.062 0.14 -9999 0 -0.37 60 60
BMP7/USAG1 -0.18 0.18 -9999 0 -0.39 202 202
SMAD5/SKI -0.051 0.14 -9999 0 -0.37 48 48
SMAD1 0.024 0.061 -9999 0 -0.34 9 9
BMP2 -0.019 0.11 -9999 0 -0.32 58 58
SMAD1/SMAD1/SMAD4 -0.01 0.044 -9999 0 -0.33 3 3
BMPR1A 0.009 0.068 -9999 0 -0.47 10 10
BMPR1B -0.11 0.16 -9999 0 -0.29 216 216
BMPR1A-1B/BAMBI -0.13 0.17 -9999 0 -0.36 157 157
AHSG 0.016 0.024 -9999 0 -0.25 4 4
CER1 0.017 0.012 -9999 0 -0.25 1 1
BMP2-4/CER1 -0.052 0.14 -9999 0 -0.35 84 84
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.053 0.14 -9999 0 -0.35 56 56
BMP2-4 (homodimer) -0.075 0.16 -9999 0 -0.42 83 83
RGMB 0.009 0.07 -9999 0 -0.52 9 9
BMP6/BMPR2/BMPR1A-1B -0.042 0.11 -9999 0 -0.3 53 53
RGMA -0.027 0.12 -9999 0 -0.3 75 75
SMURF1 0.018 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.072 0.14 -9999 0 -0.32 96 96
BMP2-4/USAG1 -0.2 0.2 -9999 0 -0.38 245 245
SMAD6/SMURF1/SMAD5 -0.051 0.14 -9999 0 -0.38 47 47
SOSTDC1 -0.23 0.23 -9999 0 -0.39 314 314
BMP7/BMPR2/BMPR1A-1B -0.06 0.12 -9999 0 -0.3 68 68
SKI 0.017 0.017 -9999 0 -0.25 2 2
BMP6 (homodimer) -0.006 0.089 -9999 0 -0.3 40 40
HFE2 0.004 0.08 -9999 0 -0.45 15 15
ZFYVE16 0.016 0.033 -9999 0 -0.52 2 2
MAP3K7 0.016 0.02 -9999 0 -0.25 3 3
BMP2-4/CHRD -0.059 0.16 -9999 0 -0.37 84 84
SMAD5/SMAD5/SMAD4 -0.055 0.14 -9999 0 -0.36 58 58
MAPK1 0.016 0.033 -9999 0 -0.52 2 2
TAK1/TAB family -0.032 0.13 -9999 0 -0.42 26 26
BMP7 (homodimer) -0.041 0.13 -9999 0 -0.29 101 101
NUP214 0.016 0.026 -9999 0 -0.39 2 2
BMP6/FETUA 0.008 0.065 -9999 0 -0.36 8 8
SMAD1/SKI 0.032 0.06 -9999 0 -0.34 7 7
SMAD6 0.016 0.024 -9999 0 -0.25 4 4
CTDSP2 0.014 0.044 -9999 0 -0.41 5 5
BMP2-4/FETUA -0.053 0.14 -9999 0 -0.35 84 84
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
GREM1 -0.038 0.16 -9999 0 -0.45 63 63
BMPR2 (homodimer) 0.016 0.033 -9999 0 -0.52 2 2
GADD34/PP1CA 0.03 0.04 -9999 0 -0.3 5 5
BMPR1A-1B (homodimer) -0.068 0.12 -9999 0 -0.38 39 39
CHRDL1 -0.013 0.09 -9999 0 -0.27 56 56
ENDOFIN/SMAD1 0.032 0.063 -9999 0 -0.35 9 9
SMAD6-7/SMURF1/SMAD1 0.046 0.058 -9999 0 -0.31 7 7
SMAD6/SMURF1 0.018 0 -9999 0 -10000 0 0
BAMBI -0.13 0.22 -9999 0 -0.41 182 182
SMURF2 0.009 0.058 -9999 0 -0.34 13 13
BMP2-4/CHRDL1 -0.068 0.16 -9999 0 -0.36 97 97
BMP2-4/GREM1 -0.085 0.18 -9999 0 -0.37 119 119
SMAD7 0.016 0.026 -9999 0 -0.39 2 2
SMAD8A/SMAD8A/SMAD4 -0.016 0.11 -9999 0 -0.53 16 16
SMAD1/SMAD6 0.033 0.06 -9999 0 -0.34 7 7
TAK1/SMAD6 0.025 0.014 -9999 0 -10000 0 0
BMP7 -0.041 0.13 -9999 0 -0.29 101 101
BMP6 -0.006 0.089 -9999 0 -0.3 40 40
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.052 0.13 -9999 0 -0.31 67 67
PPM1A 0.016 0.026 -9999 0 -0.39 2 2
SMAD1/SMURF2 0.029 0.067 -9999 0 -0.34 9 9
SMAD7/SMURF1 0.025 0.019 -9999 0 -0.37 1 1
CTDSPL 0.011 0.062 -9999 0 -0.52 7 7
PPP1CA 0.011 0.048 -9999 0 -0.3 11 11
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.016 0.033 -9999 0 -0.52 2 2
PPP1R15A 0.016 0.029 -9999 0 -0.34 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.081 0.16 -9999 0 -0.34 106 106
CHRD 0.003 0.073 -9999 0 -0.33 22 22
BMPR2 0.016 0.033 -9999 0 -0.52 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.074 0.15 -9999 0 -0.33 96 96
BMP4 -0.092 0.19 -9999 0 -0.39 143 143
FST -0.017 0.11 -9999 0 -0.32 54 54
BMP2-4/NOG -0.056 0.15 -9999 0 -0.35 88 88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.048 0.11 -9999 0 -0.3 53 53
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.042 0.19 -9999 0 -0.51 66 66
Syndecan-4/Syndesmos -0.044 0.21 -9999 0 -0.51 71 71
positive regulation of JNK cascade -0.072 0.22 -9999 0 -0.51 88 88
Syndecan-4/ADAM12 -0.071 0.24 -9999 0 -0.54 94 94
CCL5 -0.051 0.18 -9999 0 -0.49 71 71
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DNM2 0.017 0.012 -9999 0 -0.25 1 1
ITGA5 0.015 0.035 -9999 0 -0.43 3 3
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
PLG 0.016 0.033 -9999 0 -0.51 2 2
ADAM12 -0.051 0.17 -9999 0 -0.47 74 74
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0.063 -9999 0 -0.49 8 8
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.006 0.012 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.041 0.21 -9999 0 -0.51 71 71
Syndecan-4/CXCL12/CXCR4 -0.077 0.24 -9999 0 -0.54 88 88
Syndecan-4/Laminin alpha3 -0.08 0.23 -9999 0 -0.55 77 77
MDK -0.016 0.12 -9999 0 -0.37 46 46
Syndecan-4/FZD7 -0.07 0.23 -9999 0 -0.53 85 85
Syndecan-4/Midkine -0.055 0.21 -9999 0 -0.52 76 76
FZD7 -0.049 0.16 -9999 0 -0.4 85 85
Syndecan-4/FGFR1/FGF -0.074 0.22 -9999 0 -0.49 87 87
THBS1 -0.025 0.14 -9999 0 -0.52 42 42
integrin-mediated signaling pathway -0.062 0.22 -9999 0 -0.51 84 84
positive regulation of MAPKKK cascade -0.072 0.22 -9999 0 -0.51 88 88
Syndecan-4/TACI -0.042 0.2 -9999 0 -0.51 72 72
CXCR4 -0.028 0.14 -9999 0 -0.42 55 55
cell adhesion -0.008 0.1 -9999 0 -0.29 56 56
Syndecan-4/Dynamin -0.04 0.2 -9999 0 -0.51 71 71
Syndecan-4/TSP1 -0.06 0.22 -9999 0 -0.52 81 81
Syndecan-4/GIPC -0.042 0.2 -9999 0 -0.51 71 71
Syndecan-4/RANTES -0.072 0.23 -9999 0 -0.55 78 78
ITGB1 0.014 0.044 -9999 0 -0.41 5 5
LAMA1 0.015 0.026 -9999 0 -0.25 5 5
LAMA3 -0.07 0.19 -9999 0 -0.43 103 103
RAC1 0.018 0 -9999 0 -10000 0 0
PRKCA 0.018 0.05 -9999 0 -0.24 6 6
Syndecan-4/alpha-Actinin -0.045 0.21 -9999 0 -0.52 73 73
TFPI 0.004 0.061 -9999 0 -0.26 25 25
F2 0.017 0.007 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.022 0.041 -9999 0 -0.37 5 5
positive regulation of cell adhesion -0.072 0.22 -9999 0 -0.52 77 77
ACTN1 0.005 0.079 -9999 0 -0.48 13 13
TNC -0.039 0.14 -9999 0 -0.36 79 79
Syndecan-4/CXCL12 -0.067 0.23 -9999 0 -0.54 82 82
FGF6 0.009 0.066 -9999 0 -0.52 8 8
RHOA 0.005 0.08 -9999 0 -0.52 12 12
CXCL12 -0.041 0.16 -9999 0 -0.47 64 64
TNFRSF13B 0.013 0.035 -9999 0 -0.25 9 9
FGF2 -0.064 0.16 -9999 0 -0.34 122 122
FGFR1 -0.013 0.11 -9999 0 -0.35 44 44
Syndecan-4/PI-4-5-P2 -0.05 0.2 -9999 0 -0.52 71 71
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.047 0.16 -9999 0 -0.45 73 73
cell migration 0.002 0.008 -9999 0 -10000 0 0
PRKCD 0.015 0.041 -9999 0 -0.44 4 4
vasculogenesis -0.057 0.21 -9999 0 -0.5 81 81
SDC4 -0.053 0.22 -9999 0 -0.55 71 71
Syndecan-4/Tenascin C -0.065 0.22 -9999 0 -0.53 84 84
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.009 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.047 0.21 -9999 0 -0.52 73 73
MMP9 -0.04 0.17 -9999 0 -0.5 60 60
Rac1/GTP -0.008 0.1 -9999 0 -0.3 56 56
cytoskeleton organization -0.041 0.2 -9999 0 -0.49 71 71
GIPC1 0.014 0.042 -9999 0 -0.45 4 4
Syndecan-4/TFPI -0.046 0.21 -9999 0 -0.51 73 73
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.1 0.3 -10000 0 -0.9 54 54
epithelial cell differentiation -0.1 0.23 -10000 0 -0.7 59 59
ITCH 0.019 0.028 -10000 0 -10000 0 0
WWP1 -0.13 0.4 -10000 0 -1.4 44 44
FYN 0.008 0.067 -10000 0 -0.41 12 12
EGFR -0.079 0.18 -10000 0 -0.35 139 139
PRL 0.015 0.031 -10000 0 -0.32 4 4
neuron projection morphogenesis -0.032 0.22 -10000 0 -0.71 45 45
PTPRZ1 -0.028 0.11 -10000 0 -0.29 79 79
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.047 0.25 -10000 0 -0.82 45 45
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.08 0.27 -10000 0 -0.93 45 45
ADAM17 0.017 0.037 -10000 0 -0.28 3 3
ErbB4/ErbB4 -0.11 0.32 -10000 0 -0.99 52 52
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.1 0.3 -10000 0 -0.87 57 57
NCOR1 0.016 0.033 -10000 0 -0.52 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.073 0.26 -10000 0 -0.87 47 47
GRIN2B -0.074 0.25 -10000 0 -0.8 49 49
ErbB4/ErbB2/betacellulin -0.12 0.28 -10000 0 -0.72 73 73
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
HBEGF 0.005 0.072 -10000 0 -0.36 18 18
PRLR -0.03 0.15 -10000 0 -0.49 50 50
E4ICDs/ETO2 -0.17 0.34 -10000 0 -0.79 89 89
axon guidance -0.079 0.28 -10000 0 -0.88 50 50
NEDD4 0.003 0.095 -10000 0 -0.53 15 15
Prolactin receptor/Prolactin receptor/Prolactin -0.01 0.11 -10000 0 -0.37 45 45
CBFA2T3 -0.13 0.23 -10000 0 -0.45 162 162
ErbB4/ErbB2/HBEGF -0.091 0.27 -10000 0 -0.81 54 54
MAPK3 -0.04 0.23 -10000 0 -0.75 45 45
STAT1 (dimer) -0.11 0.3 -10000 0 -0.9 56 56
MAPK1 -0.04 0.23 -10000 0 -0.75 45 45
JAK2 0.01 0.053 -10000 0 -0.32 12 12
ErbB4/ErbB2/neuregulin 1 beta -0.09 0.27 -10000 0 -0.82 53 53
NRG1 0.018 0.047 -10000 0 -0.28 6 6
NRG3 0 0.081 -10000 0 -0.34 26 26
NRG2 -0.017 0.1 -10000 0 -0.3 57 57
NRG4 0.009 0.051 -10000 0 -0.27 16 16
heart development -0.079 0.28 -10000 0 -0.88 50 50
neural crest cell migration -0.088 0.26 -10000 0 -0.8 53 53
ERBB2 -0.007 0.088 -10000 0 -0.35 18 18
WWOX/E4ICDs -0.1 0.29 -10000 0 -0.91 52 52
SHC1 0.017 0.023 -10000 0 -0.52 1 1
ErbB4/EGFR/neuregulin 4 -0.13 0.31 -10000 0 -0.85 63 63
apoptosis 0.097 0.28 0.82 57 -10000 0 57
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.31 -10000 0 -0.92 55 55
ErbB4/ErbB2/epiregulin -0.1 0.27 -10000 0 -0.78 59 59
ErbB4/ErbB4/betacellulin/betacellulin -0.13 0.3 -10000 0 -0.86 62 62
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.088 0.29 -10000 0 -0.72 74 74
MDM2 -0.096 0.3 -10000 0 -0.92 52 52
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.062 0.25 -10000 0 -0.84 44 44
STAT5A -0.072 0.27 -10000 0 -0.84 50 50
ErbB4/EGFR/neuregulin 1 beta -0.11 0.28 -10000 0 -0.78 63 63
DLG4 0.018 0 -10000 0 -10000 0 0
GRB2/SHC 0.024 0.023 -10000 0 -0.37 1 1
E4ICDs/TAB2/NCoR1 -0.081 0.28 -10000 0 -0.93 47 47
STAT5A (dimer) -0.11 0.26 -10000 0 -0.79 59 59
MAP3K7IP2 0.014 0.047 -10000 0 -0.52 4 4
STAT5B (dimer) -0.068 0.27 -10000 0 -0.83 51 51
LRIG1 -0.032 0.15 -10000 0 -0.48 53 53
EREG -0.024 0.11 -10000 0 -0.28 74 74
BTC -0.05 0.17 -10000 0 -0.42 82 82
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.081 0.28 -10000 0 -0.89 50 50
ERBB4 -0.11 0.32 -10000 0 -1 52 52
STAT5B 0.016 0.026 -10000 0 -0.39 2 2
YAP1 -0.014 0.1 -10000 0 -0.71 6 6
GRB2 0.016 0.024 -10000 0 -0.25 4 4
ErbB4/ErbB2/neuregulin 4 -0.088 0.27 -10000 0 -0.83 52 52
glial cell differentiation 0.079 0.28 0.91 47 -10000 0 47
WWOX -0.003 0.072 -10000 0 -0.25 40 40
cell proliferation -0.1 0.27 -10000 0 -0.78 58 58
Ephrin B reverse signaling

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
EFNB2 -0.008 0.11 -10000 0 -0.4 33 33
EPHB2 0.008 0.062 -10000 0 -0.32 16 16
EFNB1 0.017 0.051 -10000 0 -0.4 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.082 -10000 0 -0.37 7 7
Ephrin B2/EPHB1-2 -0.006 0.089 -10000 0 -0.28 34 34
neuron projection morphogenesis -0.023 0.061 -10000 0 -0.34 8 8
Ephrin B1/EPHB1-2/Tiam1 0.015 0.087 -10000 0 -0.29 22 22
DNM1 0.013 0.047 -10000 0 -0.37 7 7
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.084 0.23 -10000 0 -0.55 95 95
YES1 -0.13 0.3 -10000 0 -0.84 81 81
Ephrin B1/EPHB1-2/NCK2 0.019 0.078 -10000 0 -0.27 18 18
PI3K -0.081 0.24 -10000 0 -0.56 97 97
mol:GDP 0.013 0.086 -10000 0 -0.29 22 22
ITGA2B 0.016 0.02 -10000 0 -0.25 3 3
endothelial cell proliferation -0.01 0.1 -10000 0 -0.33 40 40
FYN -0.13 0.3 -10000 0 -0.82 82 82
MAP3K7 -0.084 0.23 -10000 0 -0.63 81 81
FGR -0.11 0.3 -10000 0 -0.82 81 81
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
RGS3 0.017 0.012 -10000 0 -0.25 1 1
cell adhesion -0.069 0.22 -10000 0 -0.55 87 87
LYN -0.12 0.3 -10000 0 -0.83 81 81
Ephrin B1/EPHB1-2/Src Family Kinases -0.12 0.28 -10000 0 -0.77 81 81
Ephrin B1/EPHB1-2 -0.11 0.25 -10000 0 -0.68 81 81
SRC -0.11 0.3 -10000 0 -0.82 81 81
ITGB3 0.002 0.075 -10000 0 -0.32 25 25
EPHB1 -0.022 0.1 -10000 0 -0.28 72 72
EPHB4 -0.013 0.12 -10000 0 -0.43 36 36
RAC1 0.018 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.01 0.1 -10000 0 -0.34 40 40
alphaIIb/beta3 Integrin 0.014 0.056 -10000 0 -0.36 7 7
BLK -0.13 0.3 -10000 0 -0.83 81 81
HCK -0.13 0.3 -10000 0 -0.82 82 82
regulation of stress fiber formation -0.018 0.076 0.27 18 -10000 0 18
MAPK8 -0.074 0.22 -10000 0 -0.51 97 97
Ephrin B1/EPHB1-2/RGS3 0.02 0.075 -10000 0 -0.27 15 15
endothelial cell migration -0.09 0.22 -10000 0 -0.47 114 114
NCK2 0.015 0.026 -10000 0 -0.25 5 5
PTPN13 -0.089 0.24 -10000 0 -0.59 93 93
regulation of focal adhesion formation -0.018 0.076 0.27 18 -10000 0 18
chemotaxis -0.019 0.074 0.27 15 -10000 0 15
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
Rac1/GTP 0.015 0.078 -10000 0 -0.36 7 7
angiogenesis -0.11 0.24 -10000 0 -0.68 81 81
LCK -0.14 0.31 -10000 0 -0.82 84 84
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.029 0.15 -9999 0 -0.4 63 63
alphaM/beta2 Integrin/GPIbA -0.011 0.11 -9999 0 -0.34 40 40
alphaM/beta2 Integrin/proMMP-9 -0.036 0.15 -9999 0 -0.36 80 80
PLAUR -0.016 0.13 -9999 0 -0.47 37 37
HMGB1 0.011 0.021 -9999 0 -0.27 1 1
alphaM/beta2 Integrin/Talin 0 0.1 -9999 0 -0.36 30 30
AGER 0.01 0.031 -9999 0 -0.39 2 2
RAP1A 0.012 0.057 -9999 0 -0.52 6 6
SELPLG -0.003 0.097 -9999 0 -0.43 24 24
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.012 0.13 -9999 0 -0.36 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
CYR61 -0.042 0.16 -9999 0 -0.42 72 72
TLN1 0.017 0.023 -9999 0 -0.52 1 1
Rap1/GTP -0.036 0.1 -9999 0 -0.42 25 25
RHOA 0.005 0.08 -9999 0 -0.52 12 12
P-selectin oligomer -0.12 0.22 -9999 0 -0.44 156 156
MYH2 -0.003 0.13 -9999 0 -0.44 25 25
MST1R -0.039 0.16 -9999 0 -0.51 57 57
leukocyte activation during inflammatory response 0.008 0.086 -9999 0 -0.31 30 30
APOB 0.018 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.032 0.15 -9999 0 -0.47 54 54
JAM3 -0.006 0.11 -9999 0 -0.5 24 24
GP1BA -0.002 0.071 -9999 0 -0.25 39 39
alphaM/beta2 Integrin/CTGF -0.031 0.14 -9999 0 -0.39 59 59
alphaM/beta2 Integrin -0.008 0.13 -9999 0 -0.45 27 27
JAM3 homodimer -0.006 0.11 -9999 0 -0.5 24 24
ICAM2 0.007 0.068 -9999 0 -0.4 13 13
ICAM1 -0.019 0.12 -9999 0 -0.39 47 47
phagocytosis triggered by activation of immune response cell surface activating receptor -0.008 0.13 -9999 0 -0.44 27 27
cell adhesion -0.011 0.11 -9999 0 -0.34 40 40
NFKB1 -0.032 0.17 -9999 0 -0.38 76 76
THY1 -0.007 0.11 -9999 0 -0.5 25 25
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
Lipoprotein(a) 0.023 0.016 -9999 0 -0.31 1 1
alphaM/beta2 Integrin/LRP/tPA -0.049 0.14 -9999 0 -0.32 93 93
IL6 -0.087 0.27 -9999 0 -0.69 75 75
ITGB2 -0.022 0.12 -9999 0 -0.43 40 40
elevation of cytosolic calcium ion concentration -0.044 0.18 -9999 0 -0.41 82 82
alphaM/beta2 Integrin/JAM2/JAM3 -0.02 0.15 -9999 0 -0.38 64 64
JAM2 -0.019 0.13 -9999 0 -0.43 43 43
alphaM/beta2 Integrin/ICAM1 -0.028 0.16 -9999 0 -0.33 91 91
alphaM/beta2 Integrin/uPA/Plg -0.027 0.14 -9999 0 -0.34 75 75
RhoA/GTP -0.008 0.14 -9999 0 -0.44 30 30
positive regulation of phagocytosis -0.007 0.16 -9999 0 -0.5 35 35
Ron/MSP -0.017 0.12 -9999 0 -0.37 55 55
alphaM/beta2 Integrin/uPAR/uPA -0.044 0.18 -9999 0 -0.41 82 82
alphaM/beta2 Integrin/uPAR -0.019 0.14 -9999 0 -0.4 52 52
PLAU -0.052 0.17 -9999 0 -0.43 83 83
PLAT -0.093 0.19 -9999 0 -0.37 150 150
actin filament polymerization -0.001 0.13 -9999 0 -0.42 25 25
MST1 0.016 0.02 -9999 0 -0.25 3 3
alphaM/beta2 Integrin/lipoprotein(a) 0.011 0.088 -9999 0 -0.31 30 30
TNF -0.035 0.19 -9999 0 -0.64 29 29
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
alphaM/beta2 Integrin/uPA -0.041 0.15 -9999 0 -0.38 74 74
fibrinolysis -0.028 0.14 -9999 0 -0.34 75 75
HCK -0.005 0.11 -9999 0 -0.47 25 25
dendritic cell antigen processing and presentation -0.008 0.13 -9999 0 -0.44 27 27
VTN 0.016 0.02 -9999 0 -0.25 3 3
alphaM/beta2 Integrin/CYR61 -0.035 0.14 -9999 0 -0.37 69 69
LPA 0.016 0.026 -9999 0 -0.39 2 2
LRP1 0.017 0.023 -9999 0 -0.52 1 1
cell migration -0.051 0.18 -9999 0 -0.36 106 106
FN1 -0.048 0.17 -9999 0 -0.46 73 73
alphaM/beta2 Integrin/Thy1 -0.014 0.12 -9999 0 -0.37 48 48
MPO 0.008 0.05 -9999 0 -0.25 19 19
KNG1 0.017 0.017 -9999 0 -0.25 2 2
RAP1/GDP 0.017 0.044 -9999 0 -0.31 8 8
ROCK1 0 0.13 -9999 0 -0.44 25 25
ELA2 0.017 0.017 -9999 0 -0.25 2 2
PLG 0.016 0.033 -9999 0 -0.52 2 2
CTGF -0.035 0.15 -9999 0 -0.42 63 63
alphaM/beta2 Integrin/Hck -0.012 0.14 -9999 0 -0.43 41 41
ITGAM 0.002 0.071 -9999 0 -0.48 10 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.072 0.18 -9999 0 -0.35 131 131
HP 0.013 0.049 -9999 0 -0.43 6 6
leukocyte adhesion -0.034 0.18 -9999 0 -0.54 43 43
SELP -0.12 0.22 -9999 0 -0.44 156 156
LPA receptor 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
GNB1/GNG2 0.005 0.08 -9999 0 -0.24 48 48
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.086 -9999 0 -0.3 16 16
AP1 -0.092 0.14 -9999 0 -0.3 133 133
mol:PIP3 -0.067 0.11 -9999 0 -0.28 85 85
AKT1 0.007 0.11 -9999 0 -0.34 29 29
PTK2B -0.009 0.064 -9999 0 -0.2 47 47
RHOA -0.007 0.093 -9999 0 -0.41 17 17
PIK3CB 0.012 0.055 -9999 0 -0.44 7 7
mol:Ca2+ -0.025 0.094 -9999 0 -0.27 53 53
MAGI3 -0.014 0.12 -9999 0 -0.46 35 35
RELA 0.018 0 -9999 0 -10000 0 0
apoptosis -0.004 0.067 -9999 0 -0.22 44 44
HRAS/GDP 0.009 0.036 -9999 0 -0.29 7 7
positive regulation of microtubule depolymerization -0.045 0.12 -9999 0 -0.26 117 117
NF kappa B1 p50/RelA -0.04 0.092 -9999 0 -0.32 28 28
endothelial cell migration -0.036 0.18 -9999 0 -0.55 54 54
ADCY4 -0.005 0.11 -9999 0 -0.3 48 48
ADCY5 -0.014 0.11 -9999 0 -0.31 48 48
ADCY6 -0.004 0.1 -9999 0 -0.29 47 47
ADCY7 -0.007 0.11 -9999 0 -0.32 47 47
ADCY1 -0.003 0.1 -9999 0 -0.29 47 47
ADCY2 -0.025 0.12 -9999 0 -0.34 53 53
ADCY3 -0.006 0.1 -9999 0 -0.29 49 49
ADCY8 -0.005 0.1 -9999 0 -0.29 47 47
ADCY9 -0.01 0.11 -9999 0 -0.29 48 48
GSK3B -0.002 0.061 -9999 0 -0.18 45 45
arachidonic acid secretion 0.001 0.1 -9999 0 -0.28 49 49
GNG2 0.016 0.029 -9999 0 -0.34 3 3
TRIP6 0 0.088 -9999 0 -0.4 23 23
GNAO1 -0.004 0.078 -9999 0 -0.24 48 48
HRAS 0.012 0.051 -9999 0 -0.41 7 7
NFKBIA -0.014 0.091 -9999 0 -0.27 33 33
GAB1 0.006 0.074 -9999 0 -0.43 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.006 0.15 -9999 0 -0.89 15 15
JUN -0.034 0.15 -9999 0 -0.46 57 57
LPA/LPA2/NHERF2 -0.024 0.1 -9999 0 -0.31 52 52
TIAM1 -0.025 0.18 -9999 0 -1 15 15
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
mol:IP3 -0.025 0.095 -9999 0 -0.27 53 53
PLCB3 -0.016 0.094 -9999 0 -0.3 49 49
FOS -0.11 0.2 -9999 0 -0.37 171 171
positive regulation of mitosis 0.001 0.1 -9999 0 -0.28 49 49
LPA/LPA1-2-3 -0.015 0.068 -9999 0 -0.21 54 54
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.017 0.012 -9999 0 -0.25 1 1
stress fiber formation 0.001 0.063 -9999 0 -0.19 45 45
GNAZ -0.013 0.096 -9999 0 -0.28 55 55
EGFR/PI3K-beta/Gab1 -0.069 0.12 -9999 0 -0.3 85 85
positive regulation of dendritic cell cytokine production -0.015 0.068 -9999 0 -0.21 54 54
LPA/LPA2/MAGI-3 -0.013 0.08 -9999 0 -0.28 35 35
ARHGEF1 0.009 0.074 -9999 0 -0.21 46 46
GNAI2 -0.01 0.095 -9999 0 -0.29 49 49
GNAI3 -0.003 0.077 -9999 0 -0.25 44 44
GNAI1 -0.023 0.11 -9999 0 -0.31 58 58
LPA/LPA3 -0.011 0.033 -9999 0 -0.11 54 54
LPA/LPA2 -0.011 0.033 -9999 0 -0.1 54 54
LPA/LPA1 -0.019 0.09 -9999 0 -0.28 54 54
HB-EGF/EGFR -0.069 0.16 -9999 0 -0.35 104 104
HBEGF -0.027 0.13 -9999 0 -0.38 64 64
mol:DAG -0.025 0.095 -9999 0 -0.27 53 53
cAMP biosynthetic process -0.007 0.11 -9999 0 -0.3 51 51
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
SRC 0.015 0.035 -9999 0 -0.43 3 3
GNB1 0.013 0.052 -9999 0 -0.52 5 5
LYN -0.013 0.088 -9999 0 -0.27 29 29
GNAQ -0.005 0.027 -9999 0 -0.082 54 54
LPAR2 0 0.001 -9999 0 -10000 0 0
LPAR3 0 0.001 -9999 0 -10000 0 0
LPAR1 -0.012 0.052 -9999 0 -0.16 54 54
IL8 -0.13 0.19 -9999 0 -0.42 120 120
PTK2 -0.003 0.067 -9999 0 -0.21 45 45
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
CASP3 -0.004 0.068 -9999 0 -0.22 44 44
EGFR -0.079 0.18 -9999 0 -0.35 139 139
PLCG1 -0.014 0.056 -9999 0 -0.14 66 66
PLD2 -0.004 0.071 -9999 0 -0.22 47 47
G12/G13 0.005 0.08 -9999 0 -0.24 46 46
PI3K-beta -0.039 0.098 -9999 0 -0.36 30 30
cell migration 0.016 0.062 -9999 0 -0.25 17 17
SLC9A3R2 -0.032 0.15 -9999 0 -0.49 52 52
PXN 0.001 0.064 -9999 0 -0.2 45 45
HRAS/GTP 0.001 0.1 -9999 0 -0.28 49 49
RAC1 0.018 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
PRKCE 0.01 0.061 -9999 0 -0.43 9 9
PRKCD -0.019 0.094 -9999 0 -0.26 54 54
Gi(beta/gamma) 0 0.11 -9999 0 -0.29 48 48
mol:LPA -0.012 0.052 -9999 0 -0.16 54 54
TRIP6/p130 Cas/FAK1/Paxillin 0.012 0.086 -9999 0 -0.33 14 14
MAPKKK cascade 0.001 0.1 -9999 0 -0.28 49 49
contractile ring contraction involved in cytokinesis -0.007 0.092 -9999 0 -0.4 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.043 0.096 -9999 0 -0.29 56 56
GNA15 -0.003 0.051 -9999 0 -0.27 11 11
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.011 0.055 -9999 0 -0.36 10 10
MAPT -0.047 0.13 -9999 0 -0.27 117 117
GNA11 0.002 0.038 -9999 0 -0.3 4 4
Rac1/GTP 0.005 0.16 -9999 0 -0.94 15 15
MMP2 -0.036 0.18 -9999 0 -0.55 54 54
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.042 0.15 -9999 0 -0.38 76 76
EPHB2 0.007 0.061 -9999 0 -0.32 16 16
Syndecan-2/TACI -0.006 0.092 -9999 0 -0.3 38 38
LAMA1 0.015 0.026 -9999 0 -0.25 5 5
Syndecan-2/alpha2 ITGB1 -0.062 0.17 -9999 0 -0.31 143 143
HRAS 0.012 0.051 -9999 0 -0.41 7 7
Syndecan-2/CASK -0.016 0.089 -9999 0 -0.31 38 38
ITGA5 0.015 0.035 -9999 0 -0.43 3 3
BAX 0.01 0.085 -9999 0 -10000 0 0
EPB41 0.016 0.026 -9999 0 -0.39 2 2
positive regulation of cell-cell adhesion -0.011 0.094 -9999 0 -0.28 49 49
LAMA3 -0.07 0.19 -9999 0 -0.43 103 103
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.019 0.12 -9999 0 -0.39 48 48
Syndecan-2/MMP2 -0.033 0.14 -9999 0 -0.38 65 65
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.024 0.13 -9999 0 -0.37 58 58
dendrite morphogenesis -0.009 0.095 -9999 0 -0.3 42 42
Syndecan-2/GM-CSF -0.014 0.099 -9999 0 -0.31 43 43
determination of left/right symmetry -0.017 0.11 -9999 0 -0.27 70 70
Syndecan-2/PKC delta -0.006 0.094 -9999 0 -0.3 41 41
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
MAPK3 -0.005 0.09 -9999 0 -0.27 44 44
MAPK1 -0.005 0.092 -9999 0 -0.28 44 44
Syndecan-2/RACK1 0.004 0.087 -9999 0 -0.26 44 44
NF1 0.015 0.035 -9999 0 -0.43 3 3
FGFR/FGF/Syndecan-2 -0.017 0.11 -9999 0 -0.27 70 70
ITGA2 -0.048 0.17 -9999 0 -0.46 73 73
MAPK8 0.001 0.094 -9999 0 -0.3 41 41
Syndecan-2/alpha2/beta1 Integrin -0.018 0.13 -9999 0 -0.3 86 86
Syndecan-2/Kininogen -0.004 0.091 -9999 0 -0.3 38 38
ITGB1 0.014 0.044 -9999 0 -0.41 5 5
SRC 0.007 0.085 -9999 0 -0.25 45 45
Syndecan-2/CASK/Protein 4.1 -0.004 0.083 -9999 0 -0.27 39 39
extracellular matrix organization -0.004 0.091 -9999 0 -0.3 39 39
actin cytoskeleton reorganization -0.042 0.15 -9999 0 -0.38 76 76
Syndecan-2/Caveolin-2/Ras -0.014 0.12 -9999 0 -0.33 55 55
Syndecan-2/Laminin alpha3 -0.055 0.15 -9999 0 -0.34 99 99
Syndecan-2/RasGAP 0.006 0.094 -9999 0 -0.25 52 52
alpha5/beta1 Integrin 0.022 0.041 -9999 0 -0.37 5 5
PRKCD 0.014 0.042 -9999 0 -0.45 4 4
Syndecan-2 dimer -0.009 0.096 -9999 0 -0.3 42 42
GO:0007205 0.004 0.005 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.012 0.094 -9999 0 -0.24 53 53
RHOA 0.005 0.08 -9999 0 -0.52 12 12
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
TNFRSF13B 0.013 0.035 -9999 0 -0.25 9 9
RASA1 0.004 0.078 -9999 0 -0.42 16 16
alpha2/beta1 Integrin -0.024 0.13 -9999 0 -0.37 58 58
Syndecan-2/Synbindin -0.003 0.091 -9999 0 -0.3 38 38
TGFB1 0.017 0.023 -9999 0 -0.52 1 1
CASP3 0.003 0.085 -9999 0 -0.27 41 41
FN1 -0.048 0.17 -9999 0 -0.46 73 73
Syndecan-2/IL8 -0.055 0.14 -9999 0 -0.33 87 87
SDC2 -0.017 0.11 -9999 0 -0.27 70 70
KNG1 0.017 0.017 -9999 0 -0.25 2 2
Syndecan-2/Neurofibromin -0.005 0.093 -9999 0 -0.3 40 40
TRAPPC4 0.018 0 -9999 0 -10000 0 0
CSF2 -0.001 0.074 -9999 0 -0.28 33 33
Syndecan-2/TGFB1 -0.004 0.092 -9999 0 -0.3 39 39
Syndecan-2/Syntenin/PI-4-5-P2 -0.011 0.094 -9999 0 -0.28 49 49
Syndecan-2/Ezrin -0.01 0.092 -9999 0 -0.28 50 50
PRKACA 0.004 0.084 -9999 0 -0.27 40 40
angiogenesis -0.055 0.14 -9999 0 -0.33 87 87
MMP2 -0.032 0.15 -9999 0 -0.47 54 54
IL8 -0.072 0.17 -9999 0 -0.34 135 135
calcineurin-NFAT signaling pathway -0.006 0.092 -9999 0 -0.3 38 38
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.005 0.13 -10000 0 -0.54 6 6
UGCG -0.11 0.27 -10000 0 -0.77 74 74
AKT1/mTOR/p70S6K/Hsp90/TERT -0.07 0.19 -10000 0 -0.38 100 100
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.11 0.27 -10000 0 -0.76 74 74
mol:DAG -0.014 0.12 -10000 0 -0.95 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.14 0.2 -10000 0 -0.42 149 149
FRAP1 -0.12 0.26 -10000 0 -0.47 159 159
FOXO3 -0.064 0.19 -10000 0 -0.42 77 77
AKT1 -0.073 0.21 -10000 0 -0.44 89 89
GAB2 0.007 0.048 -10000 0 -0.25 17 17
SMPD1 -0.004 0.079 -10000 0 -0.8 4 4
SGMS1 -0.01 0.099 -10000 0 -0.73 8 8
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 0.069 -10000 0 -0.31 21 21
CALM1 0.018 0 -10000 0 -10000 0 0
cell proliferation -0.088 0.2 -10000 0 -0.45 103 103
EIF3A 0.017 0.012 -10000 0 -0.25 1 1
PI3K 0.006 0.083 -10000 0 -0.37 21 21
RPS6KB1 -0.034 0.1 -10000 0 -0.37 1 1
mol:sphingomyelin -0.014 0.12 -10000 0 -0.95 8 8
natural killer cell activation -0.002 0.004 -10000 0 -0.013 28 28
JAK3 0.018 0.004 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
JAK1 0.012 0.057 -10000 0 -0.52 6 6
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MYC -0.091 0.28 -10000 0 -0.96 37 37
MYB -0.23 0.5 -10000 0 -1.2 108 108
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.043 0.16 -10000 0 -0.37 59 59
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.014 0.099 -10000 0 -0.46 2 2
mol:PI-3-4-5-P3 -0.042 0.16 -10000 0 -0.37 59 59
Rac1/GDP 0.011 0.064 -10000 0 -0.28 21 21
T cell proliferation -0.038 0.15 -10000 0 -0.34 59 59
SHC1 0.015 0.024 -10000 0 -0.52 1 1
RAC1 0.017 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.009 0.029 -10000 0 -0.061 118 118
PRKCZ -0.04 0.15 -10000 0 -0.36 59 59
NF kappa B1 p50/RelA -0.085 0.23 -10000 0 -0.46 108 108
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.14 -10000 0 -0.49 28 28
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
RELA 0.018 0 -10000 0 -10000 0 0
IL2RA -0.032 0.14 -10000 0 -0.41 60 60
IL2RB -0.016 0.12 -10000 0 -0.43 40 40
TERT 0.013 0.042 -10000 0 -0.33 7 7
E2F1 -0.076 0.19 -10000 0 -0.44 113 113
SOS1 0.015 0.024 -10000 0 -0.53 1 1
RPS6 0.015 0.037 -10000 0 -0.39 4 4
mol:cAMP 0.004 0.014 0.029 119 -10000 0 119
PTPN11 0.015 0.024 -10000 0 -0.52 1 1
IL2RG -0.002 0.078 -10000 0 -0.28 35 35
actin cytoskeleton organization -0.038 0.15 -10000 0 -0.34 59 59
GRB2 0.014 0.024 -10000 0 -0.25 4 4
IL2 0.011 0.051 -10000 0 -0.33 10 10
PIK3CA 0.016 0.03 -10000 0 -0.35 3 3
Rac1/GTP 0.013 0.064 -10000 0 -0.26 21 21
LCK -0.073 0.18 -10000 0 -0.4 117 117
BCL2 -0.19 0.39 -10000 0 -0.83 129 129
BCR signaling pathway

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
JUN -0.061 0.16 -10000 0 -0.39 72 72
IKBKB 0.005 0.077 -10000 0 -0.26 9 9
AKT1 -0.017 0.098 0.21 10 -0.22 55 65
IKBKG 0.008 0.078 -10000 0 -0.26 10 10
CALM1 -0.03 0.13 0.21 11 -0.36 46 57
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
MAP3K1 -0.075 0.19 -10000 0 -0.47 69 69
MAP3K7 0.016 0.02 -10000 0 -0.25 3 3
mol:Ca2+ -0.039 0.14 0.21 11 -0.37 51 62
DOK1 0.002 0.083 -10000 0 -0.41 19 19
AP-1 -0.045 0.1 0.18 1 -0.23 75 76
LYN 0.014 0.031 -10000 0 -0.25 7 7
BLNK -0.012 0.12 -10000 0 -0.51 30 30
SHC1 0.017 0.023 -10000 0 -0.52 1 1
BCR complex -0.033 0.13 -10000 0 -0.34 71 71
CD22 -0.055 0.19 -10000 0 -0.48 63 63
CAMK2G -0.022 0.12 -10000 0 -0.33 45 45
CSNK2A1 0.017 0.023 -10000 0 -0.52 1 1
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.057 0.11 -10000 0 -0.44 21 21
GO:0007205 -0.04 0.14 0.21 11 -0.38 51 62
SYK -0.023 0.14 -10000 0 -0.48 43 43
ELK1 -0.032 0.13 0.21 11 -0.36 49 60
NFATC1 -0.04 0.16 -10000 0 -0.38 64 64
B-cell antigen/BCR complex -0.033 0.13 -10000 0 -0.34 71 71
PAG1/CSK 0.009 0.074 -10000 0 -0.37 16 16
NFKBIB 0.014 0.031 0.097 1 -0.12 2 3
HRAS -0.028 0.13 -10000 0 -0.34 50 50
NFKBIA 0.015 0.03 0.097 1 -0.13 1 2
NF-kappa-B/RelA/I kappa B beta 0.02 0.027 -10000 0 -0.16 1 1
RasGAP/Csk -0.026 0.14 -10000 0 -0.31 77 77
mol:GDP -0.038 0.13 0.21 11 -0.36 51 62
PTEN -0.002 0.1 -10000 0 -0.52 19 19
CD79B -0.042 0.15 -10000 0 -0.36 84 84
NF-kappa-B/RelA/I kappa B alpha 0.02 0.027 -10000 0 -0.16 1 1
GRB2 0.016 0.024 -10000 0 -0.25 4 4
PI3K/BCAP/CD19 -0.063 0.18 -10000 0 -0.48 60 60
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
mol:IP3 -0.041 0.14 0.21 11 -0.38 51 62
CSK 0.015 0.031 -10000 0 -0.32 4 4
FOS -0.078 0.15 -10000 0 -0.39 64 64
CHUK 0.001 0.094 -10000 0 -0.32 21 21
IBTK 0.016 0.033 -10000 0 -0.52 2 2
CARD11/BCL10/MALT1/TAK1 -0.023 0.12 0.2 1 -0.37 37 38
PTPN6 -0.046 0.18 -10000 0 -0.45 64 64
RELA 0.018 0 -10000 0 -10000 0 0
BCL2A1 0.013 0.03 -10000 0 -0.099 7 7
VAV2 -0.065 0.19 -10000 0 -0.51 60 60
ubiquitin-dependent protein catabolic process 0.019 0.03 0.1 1 -0.11 2 3
BTK -0.036 0.2 -10000 0 -1.1 18 18
CD19 -0.073 0.2 -10000 0 -0.44 91 91
MAP4K1 0.012 0.04 -10000 0 -0.25 12 12
CD72 -0.03 0.14 -10000 0 -0.37 65 65
PAG1 -0.005 0.097 -10000 0 -0.38 30 30
MAPK14 -0.057 0.16 -10000 0 -0.42 61 61
SH3BP5 -0.005 0.1 -10000 0 -0.44 26 26
PIK3AP1 -0.045 0.16 0.23 11 -0.41 60 71
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.055 0.19 -10000 0 -0.44 71 71
RAF1 -0.02 0.12 -10000 0 -0.31 49 49
RasGAP/p62DOK/SHIP -0.036 0.15 -10000 0 -0.32 79 79
CD79A -0.011 0.084 -10000 0 -0.26 54 54
re-entry into mitotic cell cycle -0.045 0.1 0.17 2 -0.23 74 76
RASA1 0.004 0.078 -10000 0 -0.42 16 16
MAPK3 -0.003 0.1 -10000 0 -0.32 26 26
MAPK1 -0.003 0.1 -10000 0 -0.32 27 27
CD72/SHP1 -0.055 0.19 -10000 0 -0.51 61 61
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MAPK8 -0.058 0.17 -10000 0 -0.41 65 65
actin cytoskeleton organization -0.049 0.17 -10000 0 -0.44 59 59
NF-kappa-B/RelA 0.043 0.054 0.19 1 -0.23 3 4
Calcineurin -0.023 0.12 -10000 0 -0.36 39 39
PI3K -0.087 0.14 -10000 0 -0.39 74 74
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.15 0.24 11 -0.41 51 62
SOS1 0.017 0.023 -10000 0 -0.52 1 1
Bam32/HPK1 -0.13 0.31 -10000 0 -0.75 96 96
DAPP1 -0.16 0.35 -10000 0 -0.86 95 95
cytokine secretion -0.037 0.15 -10000 0 -0.35 64 64
mol:DAG -0.041 0.14 0.21 11 -0.38 51 62
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
MAP2K1 -0.011 0.11 -10000 0 -0.35 28 28
B-cell antigen/BCR complex/FcgammaRIIB -0.045 0.15 -10000 0 -0.32 106 106
mol:PI-3-4-5-P3 -0.058 0.11 0.25 13 -0.29 63 76
ETS1 -0.019 0.12 -10000 0 -0.36 36 36
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.031 0.15 -10000 0 -0.31 86 86
B-cell antigen/BCR complex/LYN -0.077 0.18 -10000 0 -0.54 50 50
MALT1 0.011 0.053 -10000 0 -0.37 9 9
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
RAC1 -0.053 0.18 -10000 0 -0.47 57 57
B-cell antigen/BCR complex/LYN/SYK -0.053 0.19 -10000 0 -0.5 60 60
CARD11 -0.038 0.14 0.21 11 -0.37 55 66
FCGR2B -0.031 0.15 -10000 0 -0.5 50 50
PPP3CA 0.006 0.073 -10000 0 -0.44 13 13
BCL10 0.017 0.012 -10000 0 -0.25 1 1
IKK complex 0.012 0.04 0.11 1 -0.11 8 9
PTPRC -0.04 0.15 -10000 0 -0.41 71 71
PDPK1 -0.017 0.091 0.2 9 -0.2 55 64
PPP3CB 0.016 0.026 -10000 0 -0.39 2 2
PPP3CC -0.001 0.098 -10000 0 -0.51 19 19
POU2F2 0.019 0.021 -10000 0 -0.098 1 1
Caspase cascade in apoptosis

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
TOP1 -0.002 0.11 0.2 9 -0.25 59 68
ACTA1 -0.03 0.14 0.24 8 -0.34 63 71
NUMA1 -0.005 0.11 0.22 3 -0.26 45 48
SPTAN1 -0.01 0.13 0.24 11 -0.32 55 66
LIMK1 -0.029 0.15 0.23 9 -0.33 78 87
BIRC3 -0.085 0.19 -10000 0 -0.41 128 128
BIRC2 0.016 0.02 -10000 0 -0.25 3 3
BAX 0.016 0.02 -10000 0 -0.25 3 3
CASP10 -0.042 0.13 -10000 0 -0.31 100 100
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.003 0.12 0.2 9 -0.27 53 62
DIABLO 0.018 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.13 0.23 11 -0.32 55 66
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0.063 -10000 0 -0.49 8 8
GSN -0.019 0.14 0.23 9 -0.34 64 73
MADD 0.018 0 -10000 0 -10000 0 0
TFAP2A -0.009 0.14 -10000 0 -0.56 27 27
BID -0.022 0.089 -10000 0 -0.2 95 95
MAP3K1 -0.029 0.13 -10000 0 -0.42 41 41
TRADD 0.016 0.026 -10000 0 -0.39 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.022 0.041 -10000 0 -0.37 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.029 0.14 0.23 5 -0.33 69 74
CASP9 0.017 0.023 -10000 0 -0.52 1 1
DNA repair -0.02 0.075 0.29 8 -0.19 37 45
neuron apoptosis -0.026 0.17 -10000 0 -0.64 36 36
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.005 0.13 0.25 3 -0.3 52 55
APAF1 0.012 0.051 -10000 0 -0.41 7 7
CASP6 0.003 0.11 -10000 0 -0.7 7 7
TRAF2 0.014 0.042 -10000 0 -0.45 4 4
ICAD/CAD -0.003 0.13 0.23 11 -0.31 55 66
CASP7 0.044 0.12 0.29 68 -0.4 11 79
KRT18 -0.071 0.21 -10000 0 -0.57 76 76
apoptosis -0.005 0.13 0.26 8 -0.3 56 64
DFFA -0.01 0.13 0.24 11 -0.32 55 66
DFFB -0.01 0.13 0.24 11 -0.32 55 66
PARP1 0.02 0.075 0.19 37 -0.3 8 45
actin filament polymerization 0.026 0.14 0.33 62 -0.22 9 71
TNF -0.004 0.094 -10000 0 -0.36 31 31
CYCS -0.012 0.062 -10000 0 -0.15 42 42
SATB1 -0.019 0.13 -10000 0 -0.45 25 25
SLK -0.01 0.13 0.24 11 -0.32 56 67
p15 BID/BAX -0.011 0.081 -10000 0 -0.28 11 11
CASP2 0.011 0.089 -10000 0 -0.38 11 11
JNK cascade 0.029 0.13 0.42 41 -10000 0 41
CASP3 -0.017 0.14 0.25 11 -0.35 55 66
LMNB2 0.018 0.068 -10000 0 -0.29 7 7
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
CASP4 -0.005 0.11 -10000 0 -0.49 24 24
Mammalian IAPs/DIABLO -0.024 0.11 -10000 0 -0.28 76 76
negative regulation of DNA binding -0.009 0.14 -10000 0 -0.56 27 27
stress fiber formation -0.01 0.13 0.23 11 -0.32 56 67
GZMB -0.058 0.16 -10000 0 -0.37 98 98
CASP1 -0.038 0.16 -10000 0 -0.42 60 60
LMNB1 -0.032 0.12 -10000 0 -0.29 36 36
APP -0.027 0.17 -10000 0 -0.65 36 36
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.013 0 -10000 0 -10000 0 0
VIM -0.009 0.13 0.26 8 -0.3 56 64
LMNA 0.014 0.076 -10000 0 -0.3 11 11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.094 -10000 0 -0.41 11 11
LRDD 0.018 0 -10000 0 -10000 0 0
SREBF1 -0.036 0.15 0.24 10 -0.32 85 95
APAF-1/Caspase 9 0.014 0.068 -10000 0 -0.57 2 2
nuclear fragmentation during apoptosis -0.005 0.11 0.22 3 -0.26 45 48
CFL2 -0.027 0.15 0.23 4 -0.34 62 66
GAS2 -0.035 0.15 0.24 10 -0.32 82 92
positive regulation of apoptosis -0.002 0.08 -10000 0 -0.26 19 19
PRF1 -0.008 0.091 -10000 0 -0.3 43 43
TCGA08_p53

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
CDKN2A -0.037 0.11 -10000 0 -0.23 108 108
TP53 -0.036 0.1 0.28 2 -0.36 37 39
Senescence -0.036 0.1 0.28 2 -0.36 37 39
Apoptosis -0.036 0.1 0.28 2 -0.36 37 39
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.072 0.24 31 -0.18 13 44
MDM4 0.013 0.044 -10000 0 -0.32 8 8
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.066 -10000 0 -0.52 8 8
Jak2/Leptin Receptor -0.039 0.12 0.21 1 -0.34 50 51
PTP1B/AKT1 -0.043 0.12 0.29 2 -0.32 50 52
FYN 0.008 0.067 -10000 0 -0.41 12 12
p210 bcr-abl/PTP1B -0.055 0.12 0.32 2 -0.32 63 65
EGFR -0.085 0.18 -10000 0 -0.36 139 139
EGF/EGFR -0.14 0.2 -10000 0 -0.37 193 193
CSF1 0.014 0.037 -10000 0 -0.29 7 7
AKT1 0.011 0.054 -10000 0 -0.38 9 9
INSR 0.015 0.037 -10000 0 -0.39 4 4
PTP1B/N-cadherin -0.065 0.15 0.28 2 -0.35 74 76
Insulin Receptor/Insulin -0.02 0.1 -10000 0 -0.33 25 25
HCK -0.005 0.11 -10000 0 -0.47 25 25
CRK 0.016 0.033 -10000 0 -0.52 2 2
TYK2 -0.046 0.12 0.3 2 -0.32 55 57
EGF -0.15 0.23 -10000 0 -0.43 193 193
YES1 0.007 0.07 -10000 0 -0.43 12 12
CAV1 -0.074 0.14 0.29 2 -0.36 65 67
TXN 0.013 0.017 -10000 0 -0.26 2 2
PTP1B/IRS1/GRB2 -0.067 0.15 -10000 0 -0.35 92 92
cell migration 0.055 0.12 0.32 63 -0.32 2 65
STAT3 0.014 0.041 -10000 0 -0.52 3 3
PRLR -0.027 0.15 -10000 0 -0.49 50 50
ITGA2B 0.015 0.02 -10000 0 -0.25 3 3
CSF1R 0.017 0.017 -10000 0 -0.25 2 2
Prolactin Receptor/Prolactin -0.002 0.12 -10000 0 -0.36 47 47
FGR 0.017 0.017 -10000 0 -0.25 2 2
PTP1B/p130 Cas -0.044 0.12 0.28 2 -0.31 57 59
Crk/p130 Cas -0.036 0.12 -10000 0 -0.3 56 56
DOK1 -0.039 0.13 0.3 2 -0.38 42 44
JAK2 -0.037 0.12 -10000 0 -0.32 52 52
Jak2/Leptin Receptor/Leptin -0.069 0.13 -10000 0 -0.37 51 51
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
PTPN1 -0.056 0.12 0.32 2 -0.32 64 66
LYN 0.014 0.031 -10000 0 -0.25 7 7
CDH2 -0.027 0.13 -10000 0 -0.34 66 66
SRC -0.005 0.07 -10000 0 -0.68 3 3
ITGB3 0.001 0.076 -10000 0 -0.32 25 25
CAT1/PTP1B -0.085 0.17 0.25 2 -0.44 67 69
CAPN1 0.003 0.078 -10000 0 -0.44 15 15
CSK 0.015 0.031 -10000 0 -0.32 4 4
PI3K -0.036 0.1 -10000 0 -0.33 36 36
mol:H2O2 -0.003 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.062 0.12 -10000 0 -0.38 39 39
negative regulation of transcription -0.037 0.11 -10000 0 -0.32 52 52
FCGR2A -0.003 0.099 -10000 0 -0.45 23 23
FER 0.013 0.027 -10000 0 -0.4 2 2
alphaIIb/beta3 Integrin 0.011 0.056 -10000 0 -0.37 7 7
BLK -0.019 0.1 -10000 0 -0.29 63 63
Insulin Receptor/Insulin/Shc 0.032 0.032 -10000 0 -0.31 4 4
RHOA 0.004 0.081 -10000 0 -0.53 12 12
LEPR -0.005 0.093 -10000 0 -0.34 34 34
BCAR1 0.017 0.012 -10000 0 -0.25 1 1
p210 bcr-abl/Grb2 0.016 0.023 -10000 0 -0.25 4 4
mol:NADPH -0.003 0.004 -10000 0 -10000 0 0
TRPV6 -0.06 0.16 -10000 0 -0.43 57 57
PRL 0.018 0.033 -10000 0 -0.32 4 4
SOCS3 -0.005 0.17 -10000 0 -1.3 8 8
SPRY2 -0.036 0.15 -10000 0 -0.43 60 60
Insulin Receptor/Insulin/IRS1 -0.008 0.12 -10000 0 -0.32 62 62
CSF1/CSF1R -0.037 0.12 -10000 0 -0.34 39 39
Ras protein signal transduction 0.029 0.039 -10000 0 -0.19 3 3
IRS1 -0.048 0.17 -10000 0 -0.49 68 68
INS 0.017 0.024 -10000 0 -0.53 1 1
LEP -0.051 0.15 -10000 0 -0.34 101 101
STAT5B -0.043 0.11 0.25 2 -0.28 64 66
STAT5A -0.044 0.11 0.25 2 -0.28 65 67
GRB2 0.016 0.024 -10000 0 -0.25 4 4
PDGFB-D/PDGFRB -0.048 0.13 0.28 2 -0.35 56 58
CSN2 0.02 0.1 -10000 0 -1.4 2 2
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
LAT -0.025 0.12 -10000 0 -0.55 19 19
YBX1 0.007 0.072 -10000 0 -0.33 16 16
LCK -0.074 0.18 -10000 0 -0.4 117 117
SHC1 0.017 0.023 -10000 0 -0.52 1 1
NOX4 -0.059 0.18 -10000 0 -0.49 78 78
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.064 -9999 0 -0.37 9 9
alphaV beta3 Integrin -0.034 0.13 -9999 0 -0.33 62 62
PTK2 -0.008 0.14 -9999 0 -0.47 26 26
IGF1R -0.083 0.2 -9999 0 -0.47 110 110
PI4KB 0.016 0.033 -9999 0 -0.52 2 2
MFGE8 -0.018 0.12 -9999 0 -0.36 50 50
SRC 0.015 0.035 -9999 0 -0.43 3 3
CDKN1B -0.022 0.13 -9999 0 -0.49 29 29
VEGFA 0 0.075 -9999 0 -0.29 31 31
ILK 0.002 0.072 -9999 0 -0.75 2 2
ROCK1 0.018 0 -9999 0 -10000 0 0
AKT1 0.007 0.075 -9999 0 -0.45 6 6
PTK2B 0.012 0.091 -9999 0 -0.32 27 27
alphaV/beta3 Integrin/JAM-A -0.014 0.12 -9999 0 -0.28 60 60
CBL 0.017 0.012 -9999 0 -0.25 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.01 0.087 -9999 0 -0.33 27 27
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.22 -9999 0 -0.39 169 169
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.021 0.086 -9999 0 -0.37 14 14
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.13 -9999 0 -0.33 67 67
PI4KA 0.018 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.18 0.24 -9999 0 -0.53 131 131
PI4 Kinase 0.025 0.024 -9999 0 -0.37 2 2
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
alphaV/beta3 Integrin/Osteopontin -0.082 0.16 -9999 0 -0.33 141 141
RPS6KB1 -0.15 0.23 -9999 0 -0.49 135 135
TLN1 0.017 0.023 -9999 0 -0.52 1 1
MAPK3 -0.092 0.22 -9999 0 -0.65 57 57
GPR124 0 0.095 -9999 0 -0.52 17 17
MAPK1 -0.092 0.22 -9999 0 -0.64 58 58
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
alphaV/beta3 Integrin/Tumstatin 0.011 0.087 -9999 0 -0.35 24 24
cell adhesion -0.008 0.12 -9999 0 -0.42 24 24
ANGPTL3 0.011 0.056 -9999 0 -0.42 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.021 0.059 -9999 0 -0.3 11 11
IGF-1R heterotetramer -0.083 0.2 -9999 0 -0.47 110 110
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
TGFBR2 0.013 0.049 -9999 0 -0.43 6 6
ITGB3 0.002 0.075 -9999 0 -0.32 25 25
IGF1 -0.1 0.2 -9999 0 -0.41 146 146
RAC1 0.018 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.004 0.11 -9999 0 -0.38 33 33
apoptosis -0.002 0.099 -9999 0 -0.48 21 21
CD47 -0.005 0.11 -9999 0 -0.47 25 25
alphaV/beta3 Integrin/CD47 0 0.1 -9999 0 -0.32 42 42
VCL 0.016 0.029 -9999 0 -0.34 3 3
alphaV/beta3 Integrin/Del1 -0.066 0.17 -9999 0 -0.35 115 115
CSF1 0.014 0.037 -9999 0 -0.29 7 7
PIK3C2A -0.003 0.096 -9999 0 -0.74 6 6
PI4 Kinase/Pyk2 -0.042 0.092 -9999 0 -0.4 18 18
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.013 0.099 -9999 0 -0.34 29 29
FAK1/Vinculin 0.004 0.11 -9999 0 -0.37 26 26
alphaV beta3/Integrin/ppsTEM5 0.004 0.11 -9999 0 -0.38 33 33
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VTN 0.016 0.02 -9999 0 -0.25 3 3
BCAR1 0.017 0.012 -9999 0 -0.25 1 1
FGF2 -0.064 0.16 -9999 0 -0.34 122 122
F11R -0.037 0.12 -9999 0 -0.37 41 41
alphaV/beta3 Integrin/Lactadherin -0.006 0.12 -9999 0 -0.39 38 38
alphaV/beta3 Integrin/TGFBR2 0.011 0.089 -9999 0 -0.35 26 26
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.031 0.062 -9999 0 -0.27 19 19
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
alphaV/beta3 Integrin/Talin 0.014 0.075 -9999 0 -0.31 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.048 0.17 -9999 0 -0.46 73 73
alphaV/beta3 Integrin/Pyk2 0.018 0.094 -9999 0 -0.32 27 27
SDC1 -0.038 0.16 -9999 0 -0.46 62 62
VAV3 -0.024 0.13 -9999 0 -0.27 102 102
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
IRS1 -0.048 0.17 -9999 0 -0.49 68 68
FAK1/Paxillin 0.004 0.11 -9999 0 -0.37 25 25
cell migration 0.011 0.1 -9999 0 -0.34 23 23
ITGAV -0.002 0.1 -9999 0 -0.48 21 21
PI3K -0.016 0.12 -9999 0 -0.41 22 22
SPP1 -0.14 0.23 -9999 0 -0.43 188 188
KDR 0.013 0.052 -9999 0 -0.52 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.002 0.099 -9999 0 -0.48 21 21
COL4A3 0.013 0.047 -9999 0 -0.37 7 7
angiogenesis -0.081 0.22 -9999 0 -0.65 56 56
Rac1/GTP -0.013 0.12 -9999 0 -0.42 11 11
EDIL3 -0.11 0.22 -9999 0 -0.44 152 152
cell proliferation 0.011 0.089 -9999 0 -0.34 26 26
Visual signal transduction: Rods

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
mol:K + 0.011 0.056 -9999 0 -0.42 8 8
GNAT1/GTP 0.01 0.035 -9999 0 -0.34 5 5
Metarhodopsin II/Arrestin -0.045 0.12 -9999 0 -0.31 64 64
PDE6G/GNAT1/GTP 0.02 0.033 -9999 0 -0.31 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.013 0.048 -9999 0 -0.47 5 5
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.082 0.12 -9999 0 -0.27 137 137
mol:Na + -0.04 0.088 -9999 0 -0.43 14 14
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.056 0.15 -9999 0 -0.34 96 96
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.002 0.11 -9999 0 -0.44 14 14
CNGB1 0.018 0 -9999 0 -10000 0 0
RDH5 -0.003 0.072 -9999 0 -0.25 40 40
SAG -0.098 0.19 -9999 0 -0.36 162 162
mol:Ca2+ 0.001 0.11 -9999 0 -0.39 17 17
Na + (4 Units) -0.039 0.085 -9999 0 -0.38 17 17
RGS9 -0.033 0.13 -9999 0 -0.31 81 81
GNB1/GNGT1 -0.033 0.1 -9999 0 -0.37 18 18
GNAT1/GDP -0.04 0.13 -9999 0 -0.29 99 99
GUCY2D 0.018 0 -9999 0 -10000 0 0
GNGT1 -0.063 0.14 -9999 0 -0.28 144 144
GUCY2F 0.006 0.076 -9999 0 -0.46 13 13
GNB5 0.005 0.081 -9999 0 -0.5 13 13
mol:GMP (4 units) -0.034 0.12 -9999 0 -0.26 118 118
mol:11-cis-retinal -0.003 0.072 -9999 0 -0.25 40 40
mol:cGMP 0.026 0.087 -9999 0 -0.3 30 30
GNB1 0.013 0.052 -9999 0 -0.52 5 5
Rhodopsin 0.012 0.049 -9999 0 -10000 0 0
SLC24A1 0.011 0.056 -9999 0 -0.42 8 8
CNGA1 -0.061 0.15 -9999 0 -0.32 123 123
Metarhodopsin II 0.011 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.027 0.075 -9999 0 -0.29 24 24
RGS9BP -0.072 0.18 -9999 0 -0.41 111 111
Metarhodopsin II/Transducin -0.005 0.064 -9999 0 -0.25 22 22
GCAP Family/Ca ++ 0.016 0.074 -9999 0 -0.3 24 24
PDE6A/B -0.066 0.17 -9999 0 -0.37 115 115
mol:Pi -0.056 0.15 -9999 0 -0.34 96 96
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.014 0.083 -9999 0 -0.29 22 22
PDE6B -0.1 0.22 -9999 0 -0.5 123 123
PDE6A 0.011 0.048 -9999 0 -0.3 11 11
PDE6G 0.016 0.024 -9999 0 -0.25 4 4
RHO 0.018 0 -9999 0 -10000 0 0
PDE6 -0.088 0.17 -9999 0 -0.41 63 63
GUCA1A 0.001 0.092 -9999 0 -0.48 18 18
GC2/GCAP Family 0.02 0.092 -9999 0 -0.32 30 30
GUCA1C 0.005 0.078 -9999 0 -0.43 15 15
GUCA1B 0.014 0.035 -9999 0 -0.3 6 6
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.05 0.22 3 -0.53 1 4
AES 0.033 0.037 0.2 1 -10000 0 1
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.009 0.076 -10000 0 -0.36 19 19
SMAD4 0.009 0.067 -10000 0 -0.49 9 9
DKK2 -0.026 0.14 -10000 0 -0.42 52 52
TLE1 -0.017 0.16 0.2 2 -0.48 50 52
MACF1 0.016 0.026 -10000 0 -0.39 2 2
CTNNB1 -0.006 0.098 0.28 2 -0.36 13 15
WIF1 -0.024 0.098 -10000 0 -0.25 81 81
beta catenin/RanBP3 0.069 0.19 0.38 108 -0.46 2 110
KREMEN2 -0.19 0.23 -10000 0 -0.41 257 257
DKK1 -0.12 0.19 -10000 0 -0.34 199 199
beta catenin/beta TrCP1 0.005 0.096 0.3 1 -0.37 11 12
FZD1 0.003 0.082 -10000 0 -0.43 17 17
AXIN2 -0.097 0.33 -10000 0 -1.3 31 31
AXIN1 0.017 0.012 -10000 0 -0.25 1 1
RAN 0.018 0.012 -10000 0 -0.25 1 1
Axin1/APC/GSK3/beta catenin 0.034 0.036 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.16 -10000 0 -0.43 34 34
Axin1/APC/GSK3 0.049 0.042 0.25 3 -10000 0 3
Axin1/APC/GSK3/beta catenin/Macf1 0.037 0.067 -10000 0 -0.3 2 2
HNF1A 0.031 0.044 0.2 1 -0.24 3 4
CTBP1 0.033 0.041 0.21 2 -0.26 1 3
MYC -0.12 0.36 -10000 0 -1.4 36 36
RANBP3 0.018 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.12 0.16 -10000 0 -0.33 186 186
NKD1 0.009 0.059 -10000 0 -0.38 11 11
TCF4 0.008 0.12 0.2 2 -0.49 26 28
TCF3 0.029 0.057 0.21 2 -0.36 5 7
WNT1/LRP6/FZD1/Axin1 0.031 0.062 -10000 0 -0.27 20 20
Ran/GTP 0.014 0.009 -10000 0 -0.17 1 1
CtBP/CBP/TCF/TLE1/AES 0.098 0.25 0.5 118 -0.48 8 126
LEF1 -0.007 0.13 0.18 16 -0.31 64 80
DVL1 0.045 0.042 -10000 0 -0.31 3 3
CSNK2A1 0.017 0.023 -10000 0 -0.52 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.038 0.17 -10000 0 -0.49 35 35
DKK1/LRP6/Kremen 2 -0.17 0.17 -10000 0 -0.33 249 249
LRP6 0.008 0.065 -10000 0 -0.38 13 13
CSNK1A1 0.035 0.048 0.21 4 -0.46 1 5
NLK 0.008 0.044 -10000 0 -0.28 11 11
CCND1 -0.25 0.54 -10000 0 -1.4 87 87
WNT1 0.016 0.023 -10000 0 -0.52 1 1
GSK3A 0.018 0.001 -10000 0 -10000 0 0
GSK3B 0.017 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.068 -10000 0 -0.47 10 10
PPP2R5D 0.028 0.035 0.25 6 -10000 0 6
APC 0.026 0.062 -10000 0 -0.24 23 23
WNT1/LRP6/FZD1 0.037 0.06 -10000 0 -0.24 10 10
CREBBP 0.032 0.051 0.21 2 -0.52 2 4
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.002 0.077 -10000 0 -0.3 26 26
NFATC2 0.013 0.043 -10000 0 -0.3 5 5
NFATC3 0.015 0.03 -10000 0 -10000 0 0
CD40LG -0.097 0.25 -10000 0 -0.55 86 86
PTGS2 -0.11 0.26 -10000 0 -0.56 87 87
JUNB 0.011 0.055 -10000 0 -0.36 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.018 -10000 0 -10000 0 0
CALM1 0.016 0.009 -10000 0 -10000 0 0
JUN -0.035 0.15 -10000 0 -0.46 57 57
mol:Ca2+ -0.004 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.011 -10000 0 -0.14 2 2
FOSL1 0.016 0.024 -10000 0 -0.25 4 4
CREM 0.016 0.017 -10000 0 -0.26 2 2
Jun/NFAT1-c-4/p21SNFT -0.024 0.15 -10000 0 -0.35 53 53
FOS -0.11 0.2 -10000 0 -0.37 171 171
IFNG -0.14 0.3 -10000 0 -0.6 113 113
AP-1/NFAT1-c-4 -0.1 0.3 -10000 0 -0.62 95 95
FASLG -0.12 0.3 -10000 0 -0.62 108 108
NFAT1-c-4/ICER1 0.008 0.095 0.24 1 -0.31 14 15
IL2RA -0.11 0.28 -10000 0 -0.58 97 97
FKBP12/FK506 0.012 0.011 -10000 0 -0.17 2 2
CSF2 -0.099 0.26 -10000 0 -0.55 90 90
JunB/Fra1/NFAT1-c-4 0.016 0.1 -10000 0 -0.31 18 18
IL4 -0.095 0.25 -10000 0 -0.54 86 86
IL2 -0.005 0.1 -10000 0 -1.3 3 3
IL3 0.008 0.021 -10000 0 -10000 0 0
FKBP1A 0.017 0.017 -10000 0 -0.25 2 2
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.034 0.14 -9999 0 -0.33 76 76
MAP3K8 -0.038 0.15 -9999 0 -0.39 70 70
FOS -0.014 0.092 -9999 0 -0.3 11 11
PRKCA 0.01 0.034 -9999 0 -0.26 8 8
PTPN7 0.006 0.049 -9999 0 -0.28 14 14
HRAS 0.011 0.051 -9999 0 -0.41 7 7
PRKCB -0.003 0.007 -9999 0 -0.013 169 169
NRAS 0.004 0.076 -9999 0 -0.41 16 16
RAS family/GTP 0.013 0.064 -9999 0 -0.28 20 20
MAPK3 0.002 0.057 -9999 0 -0.45 2 2
MAP2K1 -0.005 0.064 -9999 0 -0.23 11 11
ELK1 0.01 0.038 -9999 0 -0.39 4 4
BRAF 0.004 0.057 -9999 0 -0.41 7 7
mol:GTP -0.001 0.002 -9999 0 -0.004 170 170
MAPK1 0.001 0.06 -9999 0 -0.43 3 3
RAF1 0.011 0.028 -9999 0 -10000 0 0
KRAS 0.008 0.065 -9999 0 -0.44 10 10
Cellular roles of Anthrax toxin

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
ANTXR1 -0.024 0.14 -10000 0 -0.46 46 46
ANTXR2 0.002 0.09 -10000 0 -0.5 16 16
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.021 -10000 0 -0.074 44 44
monocyte activation -0.022 0.12 -10000 0 -0.41 41 41
MAP2K2 0.007 0.06 -10000 0 -0.77 3 3
MAP2K1 0.005 0.021 -10000 0 -10000 0 0
MAP2K7 0.005 0.024 -10000 0 -0.27 1 1
MAP2K6 -0.009 0.063 -10000 0 -0.2 39 39
CYAA -0.014 0.092 -10000 0 -0.3 44 44
MAP2K4 -0.006 0.056 -10000 0 -0.21 31 31
IL1B -0.03 0.095 -10000 0 -0.25 68 68
Channel -0.009 0.1 -10000 0 -0.32 44 44
NLRP1 0.002 0.036 -10000 0 -0.2 9 9
CALM1 0.018 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.007 0.027 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.021 0.074 44 -10000 0 44
MAPK3 0.005 0.024 -10000 0 -0.19 2 2
MAPK1 0.004 0.027 -10000 0 -0.27 2 2
PGR -0.14 0.12 -10000 0 -0.2 365 365
PA/Cellular Receptors -0.011 0.11 -10000 0 -0.35 44 44
apoptosis -0.007 0.021 -10000 0 -0.074 44 44
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.008 0.094 -10000 0 -0.3 44 44
macrophage activation 0.011 0.028 -10000 0 -0.25 3 3
TNF -0.004 0.094 -10000 0 -0.36 31 31
VCAM1 -0.022 0.12 -10000 0 -0.42 41 41
platelet activation 0.007 0.027 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.034 0.12 18 -10000 0 18
IL18 -0.031 0.11 -10000 0 -0.28 70 70
negative regulation of macrophage activation -0.007 0.021 -10000 0 -0.074 44 44
LEF -0.007 0.021 -10000 0 -0.074 44 44
CASP1 -0.006 0.042 -10000 0 -0.098 60 60
mol:cAMP 0.007 0.027 -10000 0 -10000 0 0
necrosis -0.007 0.021 -10000 0 -0.074 44 44
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.095 -10000 0 -0.3 44 44
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.045 0.14 -10000 0 -0.37 67 67
fibroblast growth factor receptor signaling pathway -0.045 0.14 -10000 0 -0.36 67 67
LAMA1 0.015 0.026 -10000 0 -0.25 5 5
PRNP 0.006 0.073 -10000 0 -0.44 13 13
GPC1/SLIT2 -0.025 0.14 -10000 0 -0.39 60 60
SMAD2 0.012 0.084 -10000 0 -0.28 36 36
GPC1/PrPc/Cu2+ 0.002 0.083 -10000 0 -0.33 30 30
GPC1/Laminin alpha1 0.007 0.082 -10000 0 -0.37 22 22
TDGF1 0.017 0.012 -10000 0 -0.25 1 1
CRIPTO/GPC1 0.009 0.08 -10000 0 -0.37 22 22
APP/GPC1 -0.025 0.13 -10000 0 -0.38 57 57
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.01 0.081 -10000 0 -0.31 30 30
FLT1 0.004 0.08 -10000 0 -0.45 15 15
GPC1/TGFB/TGFBR1/TGFBR2 0.009 0.093 -10000 0 -0.32 35 35
SERPINC1 0.007 0.054 -10000 0 -0.27 19 19
FYN 0.01 0.079 -10000 0 -0.31 29 29
FGR 0.015 0.068 -10000 0 -0.3 22 22
positive regulation of MAPKKK cascade -0.012 0.12 -10000 0 -0.36 42 42
SLIT2 -0.029 0.15 -10000 0 -0.48 50 50
GPC1/NRG 0.002 0.089 -10000 0 -0.38 23 23
NRG1 0.008 0.053 -10000 0 -0.27 18 18
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.002 0.097 -10000 0 -0.32 37 37
LYN 0.014 0.071 -10000 0 -0.31 22 22
mol:Spermine -0.005 0.079 -10000 0 -0.35 25 25
cell growth -0.045 0.14 -10000 0 -0.36 67 67
BMP signaling pathway 0.006 0.11 0.49 25 -10000 0 25
SRC 0.015 0.073 -10000 0 -0.32 23 23
TGFBR1 0.003 0.082 -10000 0 -0.42 18 18
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.054 0.14 -10000 0 -0.3 122 122
GPC1 -0.006 0.11 -10000 0 -0.49 25 25
TGFBR1 (dimer) 0.003 0.082 -10000 0 -0.42 18 18
VEGFA 0 0.075 -10000 0 -0.29 31 31
BLK -0.005 0.092 -10000 0 -0.33 30 30
HCK 0.002 0.095 -10000 0 -0.32 41 41
FGF2 -0.064 0.16 -10000 0 -0.34 122 122
FGFR1 -0.013 0.11 -10000 0 -0.35 44 44
VEGFR1 homodimer 0.004 0.08 -10000 0 -0.45 15 15
TGFBR2 0.013 0.049 -10000 0 -0.43 6 6
cell death -0.025 0.13 -10000 0 -0.38 57 57
ATIII/GPC1 0.002 0.088 -10000 0 -0.38 23 23
PLA2G2A/GPC1 -0.041 0.12 -10000 0 -0.39 41 41
LCK -0.039 0.13 -10000 0 -0.32 82 82
neuron differentiation 0.002 0.089 -10000 0 -0.38 23 23
PrPc/Cu2+ 0.005 0.053 -10000 0 -0.31 13 13
APP -0.029 0.14 -10000 0 -0.43 56 56
TGFBR2 (dimer) 0.013 0.049 -10000 0 -0.43 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.002 0.07 -9999 0 -0.28 28 28
Caspase 8 (4 units) -0.034 0.14 -9999 0 -0.42 31 31
NEF -0.014 0.042 -9999 0 -0.18 10 10
NFKBIA -0.004 0.061 -9999 0 -0.52 4 4
BIRC3 -0.064 0.21 -9999 0 -0.55 74 74
CYCS -0.04 0.14 -9999 0 -0.41 37 37
RIPK1 0.017 0.023 -9999 0 -0.52 1 1
CD247 -0.13 0.24 -9999 0 -0.47 153 153
MAP2K7 -0.023 0.13 -9999 0 -0.5 16 16
protein ubiquitination 0.018 0.095 -9999 0 -0.33 13 13
CRADD 0.01 0.063 -9999 0 -0.49 8 8
DAXX 0.017 0.012 -9999 0 -0.25 1 1
FAS -0.024 0.13 -9999 0 -0.42 51 51
BID -0.048 0.14 -9999 0 -0.42 40 40
NF-kappa-B/RelA/I kappa B alpha -0.014 0.12 -9999 0 -0.27 76 76
TRADD 0.016 0.026 -9999 0 -0.39 2 2
MAP3K5 -0.022 0.13 -9999 0 -0.42 47 47
CFLAR 0.009 0.065 -9999 0 -0.44 10 10
FADD 0 0.067 -9999 0 -0.25 35 35
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.014 0.12 -9999 0 -0.27 76 76
MAPK8 -0.016 0.12 -9999 0 -0.5 14 14
APAF1 0.012 0.051 -9999 0 -0.41 7 7
TRAF1 0.013 0.04 -9999 0 -0.28 9 9
TRAF2 0.014 0.042 -9999 0 -0.45 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.052 0.15 -9999 0 -0.35 69 69
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.01 0.1 -9999 0 -0.37 15 15
CHUK 0.017 0.1 -9999 0 -0.36 13 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0.11 -9999 0 -0.29 55 55
TCRz/NEF -0.11 0.21 -9999 0 -0.43 133 133
TNF -0.004 0.094 -9999 0 -0.36 31 31
FASLG -0.12 0.26 -9999 0 -0.5 133 133
NFKB1 -0.001 0.046 -9999 0 -0.52 1 1
TNFR1A/BAG4/TNF-alpha 0.012 0.074 -9999 0 -0.31 18 18
CASP6 -0.02 0.14 -9999 0 -0.55 18 18
CASP7 -0.072 0.23 -9999 0 -0.54 80 80
RELA 0 0.04 -9999 0 -10000 0 0
CASP2 0.018 0 -9999 0 -10000 0 0
CASP3 -0.066 0.22 -9999 0 -0.54 78 78
TNFRSF1A 0.016 0.033 -9999 0 -0.52 2 2
TNFR1A/BAG4 0.014 0.054 -9999 0 -0.37 5 5
CASP8 0.018 0 -9999 0 -10000 0 0
CASP9 0.017 0.023 -9999 0 -0.52 1 1
MAP3K14 0.015 0.1 -9999 0 -0.41 11 11
APAF-1/Caspase 9 -0.097 0.15 -9999 0 -0.4 86 86
BCL2 -0.066 0.15 -9999 0 -0.44 36 36
Glypican 2 network

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
MDK -0.016 0.12 -9999 0 -0.37 46 46
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.011 0.083 -9999 0 -0.26 46 46
neuron projection morphogenesis -0.011 0.083 -9999 0 -0.26 46 46
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.011 0.088 -10000 0 -0.29 23 23
adherens junction organization -0.013 0.11 -10000 0 -0.25 78 78
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.11 -10000 0 -0.34 21 21
FMN1 -0.008 0.1 -10000 0 -0.24 78 78
mol:IP3 0.006 0.081 -10000 0 -0.33 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.11 -10000 0 -0.25 78 78
CTNNB1 0.002 0.09 -10000 0 -0.45 19 19
AKT1 0.007 0.092 -10000 0 -0.33 11 11
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.018 0.15 -10000 0 -0.38 76 76
CTNND1 0.016 0.029 -10000 0 -0.34 3 3
mol:PI-4-5-P2 0 0.1 -10000 0 -0.23 78 78
VASP -0.007 0.11 -10000 0 -0.24 84 84
ZYX -0.006 0.11 -10000 0 -0.36 13 13
JUB -0.023 0.13 -10000 0 -0.29 50 50
EGFR(dimer) -0.043 0.13 -10000 0 -0.35 32 32
E-cadherin/beta catenin-gamma catenin -0.019 0.12 -10000 0 -0.3 78 78
mol:PI-3-4-5-P3 0.003 0.092 -10000 0 -0.26 28 28
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
PI3K 0.004 0.093 -10000 0 -0.26 28 28
FYN 0.015 0.085 -10000 0 -0.3 15 15
mol:Ca2+ 0.006 0.08 -10000 0 -0.32 6 6
JUP 0.012 0.056 -10000 0 -0.42 8 8
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
mol:DAG 0.006 0.081 -10000 0 -0.33 6 6
CDH1 -0.049 0.17 -10000 0 -0.48 70 70
RhoA/GDP -0.025 0.12 -10000 0 -0.35 28 28
establishment of polarity of embryonic epithelium -0.006 0.11 -10000 0 -0.24 84 84
SRC 0.015 0.035 -10000 0 -0.43 3 3
RAC1 0.018 0 -10000 0 -10000 0 0
RHOA 0.005 0.08 -10000 0 -0.52 12 12
EGFR -0.079 0.18 -10000 0 -0.35 139 139
CASR 0.012 0.078 -10000 0 -0.31 7 7
RhoA/GTP 0.008 0.086 -10000 0 -0.32 11 11
AKT2 0.009 0.087 -10000 0 -0.36 5 5
actin cable formation -0.007 0.1 -10000 0 -0.23 84 84
apoptosis -0.006 0.089 0.26 26 -10000 0 26
CTNNA1 0.017 0.024 -10000 0 -0.52 1 1
mol:GDP -0.03 0.12 -10000 0 -0.36 22 22
PIP5K1A -0.001 0.1 -10000 0 -0.23 78 78
PLCG1 0.006 0.082 -10000 0 -0.34 6 6
Rac1/GTP -0.034 0.12 -10000 0 -0.32 31 31
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.042 0.16 -9999 0 -0.46 67 67
SVIL -0.004 0.1 -9999 0 -0.43 27 27
ZNF318 0.014 0.005 -9999 0 -10000 0 0
JMJD2C 0.023 0.032 -9999 0 -0.32 4 4
T-DHT/AR/Ubc9 -0.065 0.14 -9999 0 -0.33 103 103
CARM1 0.014 0.039 -9999 0 -0.36 5 5
PRDX1 0.012 0.05 -9999 0 -0.43 6 6
PELP1 0.017 0.001 -9999 0 -10000 0 0
CTNNB1 0.002 0.09 -9999 0 -0.45 19 19
AKT1 0.01 0.053 -9999 0 -0.37 9 9
PTK2B 0.017 0.017 -9999 0 -0.25 2 2
MED1 -0.001 0.066 -9999 0 -0.25 34 34
MAK -0.018 0.094 -9999 0 -0.28 57 57
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.019 0.012 -9999 0 -0.25 1 1
GSN 0 0.095 -9999 0 -0.43 23 23
NCOA2 0.009 0.063 -9999 0 -0.4 11 11
NCOA6 0.019 0.012 -9999 0 -0.25 1 1
DNA-PK 0.029 0.029 -9999 0 -0.31 2 2
NCOA4 0.008 0.069 -9999 0 -0.45 11 11
PIAS3 0.019 0.002 -9999 0 -10000 0 0
cell proliferation -0.043 0.092 -9999 0 -0.67 7 7
XRCC5 0.017 0.001 -9999 0 -10000 0 0
UBE3A 0.018 0.033 -9999 0 -0.52 2 2
T-DHT/AR/SNURF -0.076 0.14 -9999 0 -0.32 118 118
FHL2 -0.15 0.34 -9999 0 -0.95 73 73
RANBP9 0.019 0.012 -9999 0 -0.25 1 1
JMJD1A -0.002 0.055 -9999 0 -10000 0 0
CDK6 -0.019 0.1 -9999 0 -0.29 63 63
TGFB1I1 -0.003 0.1 -9999 0 -0.48 23 23
T-DHT/AR/CyclinD1 -0.12 0.21 -9999 0 -0.43 149 149
XRCC6 0.016 0.012 -9999 0 -0.26 1 1
T-DHT/AR -0.085 0.17 -9999 0 -0.33 138 138
CTDSP1 0.016 0.033 -9999 0 -0.52 2 2
CTDSP2 0.011 0.044 -9999 0 -0.42 5 5
BRCA1 0.001 0.094 -9999 0 -0.48 19 19
TCF4 -0.01 0.12 -9999 0 -0.51 26 26
CDKN2A -0.055 0.15 -9999 0 -0.33 108 108
SRF 0 0.054 -9999 0 -0.28 4 4
NKX3-1 -0.056 0.11 -9999 0 -0.25 97 97
KLK3 0.022 0.055 -9999 0 -10000 0 0
TMF1 0.018 0.001 -9999 0 -10000 0 0
HNRNPA1 0.015 0.023 -9999 0 -0.52 1 1
AOF2 0.018 0.026 -9999 0 -0.39 2 2
APPL1 0.015 0.054 -9999 0 -0.37 9 9
T-DHT/AR/Caspase 8 -0.066 0.14 -9999 0 -0.33 103 103
AR -0.11 0.21 -9999 0 -0.53 104 104
UBA3 0 0.001 -9999 0 -10000 0 0
PATZ1 0.003 0.084 -9999 0 -0.5 14 14
PAWR 0.001 0.091 -9999 0 -0.44 20 20
PRKDC 0.011 0.045 -9999 0 -0.31 9 9
PA2G4 0.016 0.012 -9999 0 -0.26 1 1
UBE2I 0.018 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.059 0.13 -9999 0 -0.3 103 103
RPS6KA3 0.011 0.057 -9999 0 -0.34 12 12
T-DHT/AR/ARA70 -0.071 0.15 -9999 0 -0.34 109 109
LATS2 0.004 0.078 -9999 0 -0.48 13 13
T-DHT/AR/PRX1 -0.062 0.13 -9999 0 -0.31 106 106
Cyclin D3/CDK11 p58 0.013 0.008 -9999 0 -0.17 1 1
VAV3 -0.082 0.2 -9999 0 -0.48 108 108
KLK2 -0.013 0.075 -9999 0 -0.4 1 1
CASP8 0.017 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.054 0.14 -9999 0 -0.3 111 111
TMPRSS2 -0.18 0.38 -9999 0 -0.96 97 97
CCND1 -0.089 0.2 -9999 0 -0.44 124 124
PIAS1 0.019 0.012 -9999 0 -0.25 1 1
mol:T-DHT -0.018 0.037 -9999 0 -0.077 130 130
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.016 0.05 -9999 0 -0.43 6 6
T-DHT/AR/CDK6 -0.085 0.17 -9999 0 -0.37 118 118
CMTM2 0.016 0.023 -9999 0 -0.52 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.003 0.049 -9999 0 -0.31 6 6
CCND3 0.017 0.012 -9999 0 -0.25 1 1
TGIF1 0.006 0.073 -9999 0 -0.52 10 10
FKBP4 0.013 0.055 -9999 0 -0.44 7 7
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.012 0.011 -9999 0 -0.17 2 2
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
ERC1 0.011 0.056 -9999 0 -0.42 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.024 0.11 -9999 0 -0.32 40 40
IRAK/TOLLIP 0.029 0.019 -9999 0 -0.23 1 1
IKBKB 0.012 0.047 -9999 0 -0.31 10 10
IKBKG 0.018 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.025 0.12 -9999 0 -0.36 46 46
IL1A 0.006 0.063 -9999 0 -0.31 18 18
IL1B -0.067 0.18 -9999 0 -0.43 86 86
IRAK/TRAF6/p62/Atypical PKCs 0.031 0.053 -9999 0 -0.23 18 18
IL1R2 -0.045 0.15 -9999 0 -0.35 89 89
IL1R1 -0.046 0.16 -9999 0 -0.4 80 80
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.018 0.12 -9999 0 -0.29 61 61
TOLLIP 0.017 0.012 -9999 0 -0.25 1 1
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0.012 -9999 0 -0.25 1 1
TAK1/TAB1/TAB2 0.033 0.034 -9999 0 -0.34 4 4
IKK complex/ELKS 0.051 0.075 -9999 0 -0.45 3 3
JUN 0.014 0.093 -9999 0 -0.44 4 4
MAP3K7 0.016 0.02 -9999 0 -0.25 3 3
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.059 0.18 -9999 0 -0.34 120 120
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.002 0.1 -9999 0 -0.28 57 57
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.005 0.1 -9999 0 -0.26 57 57
IL1 beta fragment/IL1R1/IL1RAP -0.069 0.18 -9999 0 -0.36 120 120
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 0.032 0.063 -9999 0 -0.37 2 2
IRAK1 0.019 0.018 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.061 0.17 -9999 0 -0.41 87 87
IRAK4 0.014 0.044 -9999 0 -0.41 5 5
PRKCI 0.002 0.085 -9999 0 -0.43 18 18
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
PI3K 0.005 0.082 -9999 0 -0.37 21 21
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.032 0.13 -9999 0 -0.36 47 47
CHUK 0.005 0.081 -9999 0 -0.5 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.069 0.18 -9999 0 -0.36 120 120
IL1 beta/IL1R2 -0.082 0.18 -9999 0 -0.36 128 128
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.033 -9999 0 -0.33 1 1
NF kappa B1 p50/RelA -0.082 0.14 -9999 0 -0.44 54 54
IRAK3 -0.018 0.099 -9999 0 -0.28 64 64
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.056 0.17 -9999 0 -0.34 110 110
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.089 -9999 0 -0.38 4 4
IL1 alpha/IL1R1/IL1RAP -0.013 0.11 -9999 0 -0.31 53 53
RELA 0.018 0 -9999 0 -10000 0 0
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
SQSTM1 0.012 0.053 -9999 0 -0.48 6 6
MYD88 0.013 0.048 -9999 0 -0.47 5 5
IRAK/TRAF6/MEKK3 0.038 0.021 -9999 0 -0.25 1 1
IL1RAP 0.012 0.044 -9999 0 -0.28 11 11
UBE2N 0.017 0.017 -9999 0 -0.25 2 2
IRAK/TRAF6 -0.069 0.12 -9999 0 -0.39 49 49
CASP1 -0.051 0.17 -9999 0 -0.42 84 84
IL1RN/IL1R2 -0.06 0.16 -9999 0 -0.39 82 82
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.057 0.17 -9999 0 -0.35 111 111
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.1 -9999 0 -0.3 50 50
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
IL1RN -0.043 0.16 -9999 0 -0.4 76 76
TRAF6/TAK1/TAB1/TAB2 0.04 0.031 -9999 0 -0.26 5 5
MAP2K6 0.028 0.063 -9999 0 -0.24 24 24
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.018 0.062 -9999 0 -0.31 17 17
SNTA1 0.011 0.058 -9999 0 -0.48 7 7
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.004 0.086 -9999 0 -0.32 31 31
MAPK12 -0.004 0.092 -9999 0 -0.28 47 47
CCND1 -0.07 0.17 -9999 0 -0.42 91 91
p38 gamma/SNTA1 0.002 0.093 -9999 0 -0.26 51 51
MAP2K3 0.014 0.037 -9999 0 -0.29 7 7
PKN1 0.013 0.045 -9999 0 -0.39 6 6
G2/M transition checkpoint -0.004 0.091 -9999 0 -0.27 47 47
MAP2K6 -0.005 0.091 -9999 0 -0.3 43 43
MAPT -0.054 0.15 -9999 0 -0.32 120 120
MAPK13 0.011 0.071 -9999 0 -0.38 16 16
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.003 0.072 -9999 0 -0.33 23 23
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.004 0.088 0.33 33 -10000 0 33
PI3K Class IB/PDE3B -0.004 0.088 -10000 0 -0.33 33 33
PDE3B -0.004 0.088 -10000 0 -0.33 33 33
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.019 0.049 -10000 0 -0.51 4 4
HSPA8 0.001 0.09 -10000 0 -0.52 15 15
SMAD3/SMAD4/ER alpha -0.091 0.2 0.23 4 -0.37 158 162
AKT1 0.01 0.056 -10000 0 -0.37 9 9
GSC -0.2 0.49 -10000 0 -1.4 77 77
NKX2-5 -0.018 0.093 -10000 0 -0.26 67 67
muscle cell differentiation 0.066 0.16 0.43 58 -10000 0 58
SMAD2-3/SMAD4/SP1 -0.006 0.18 -10000 0 -0.42 59 59
SMAD4 -0.015 0.1 -10000 0 -0.32 33 33
CBFB 0.015 0.037 -10000 0 -0.39 4 4
SAP18 0.017 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.014 0.075 -10000 0 -0.29 8 8
SMAD3/SMAD4/VDR 0.027 0.12 -10000 0 -0.37 25 25
MYC -0.024 0.14 -10000 0 -0.45 46 46
CDKN2B -0.047 0.3 -10000 0 -1.3 25 25
AP1 -0.068 0.23 -10000 0 -0.54 76 76
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.037 0.066 -10000 0 -0.28 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.004 0.12 -10000 0 -0.34 37 37
SP3 0.014 0.02 -10000 0 -10000 0 0
CREB1 0.017 0.023 -10000 0 -0.52 1 1
FOXH1 -0.001 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.004 0.13 -10000 0 -0.36 47 47
GATA3 -0.099 0.22 -10000 0 -0.5 124 124
SKI/SIN3/HDAC complex/NCoR1 0.042 0.037 -10000 0 -10000 0 0
MEF2C/TIF2 -0.028 0.17 -10000 0 -0.5 42 42
endothelial cell migration 0.018 0.24 1.3 16 -10000 0 16
MAX 0.018 0.009 -10000 0 -10000 0 0
RBBP7 0.01 0.051 -10000 0 -0.3 13 13
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
RUNX2 0.013 0.049 -10000 0 -0.43 6 6
RUNX3 -0.062 0.18 -10000 0 -0.4 101 101
RUNX1 -0.027 0.14 -10000 0 -0.42 54 54
CTBP1 0.017 0.017 -10000 0 -0.25 2 2
NR3C1 -0.001 0.099 -10000 0 -0.51 19 19
VDR -0.003 0.1 -10000 0 -0.51 21 21
CDKN1A -0.03 0.27 -10000 0 -1.2 21 21
KAT2B 0.001 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.016 0.13 -10000 0 -0.3 61 61
DCP1A 0.017 0.023 -10000 0 -0.52 1 1
SKI 0.016 0.017 -10000 0 -0.25 2 2
SERPINE1 -0.019 0.24 -10000 0 -1.3 16 16
SMAD3/SMAD4/ATF2 0.006 0.11 -10000 0 -0.32 31 31
SMAD3/SMAD4/ATF3 -0.017 0.14 -10000 0 -0.35 57 57
SAP30 0.012 0.053 -10000 0 -0.48 6 6
Cbp/p300/PIAS3 0.047 0.053 -10000 0 -0.29 6 6
JUN -0.07 0.22 -10000 0 -0.54 75 75
SMAD3/SMAD4/IRF7 0.002 0.13 -10000 0 -0.36 40 40
TFE3 0.018 0.026 -10000 0 -10000 0 0
COL1A2 -0.1 0.37 -10000 0 -1 72 72
mesenchymal cell differentiation -0.003 0.11 0.36 32 -10000 0 32
DLX1 -0.009 0.081 -10000 0 -0.25 53 53
TCF3 0.013 0.044 -10000 0 -0.32 8 8
FOS -0.11 0.2 -10000 0 -0.38 171 171
SMAD3/SMAD4/Max 0.008 0.11 -10000 0 -0.33 30 30
Cbp/p300/SNIP1 0.035 0.046 -10000 0 -0.3 9 9
ZBTB17 0.019 0.012 -10000 0 -10000 0 0
LAMC1 0.003 0.15 -10000 0 -0.53 30 30
TGIF2/HDAC complex/SMAD3/SMAD4 0.001 0.12 -10000 0 -0.35 35 35
IRF7 0.007 0.079 -10000 0 -0.49 12 12
ESR1 -0.15 0.24 -10000 0 -0.46 181 181
HNF4A 0.016 0.033 -10000 0 -0.52 2 2
MEF2C -0.035 0.18 -10000 0 -0.51 45 45
SMAD2-3/SMAD4 -0.008 0.12 -10000 0 -0.33 44 44
Cbp/p300/Src-1 0.036 0.055 -10000 0 -0.28 12 12
IGHV3OR16-13 -0.017 0.039 -10000 0 -0.52 1 1
TGIF2/HDAC complex 0.009 0.066 -10000 0 -0.42 11 11
CREBBP 0.019 0.034 -10000 0 -0.51 2 2
SKIL 0.005 0.07 -10000 0 -0.34 19 19
HDAC1 0.016 0.023 -10000 0 -0.52 1 1
HDAC2 0.008 0.053 -10000 0 -0.29 15 15
SNIP1 0.014 0.041 -10000 0 -0.52 3 3
GCN5L2 0.018 0.044 -10000 0 -0.46 4 4
SMAD3/SMAD4/TFE3 0.014 0.12 -10000 0 -0.35 38 38
MSG1/HSC70 -0.019 0.097 -10000 0 -0.41 16 16
SMAD2 -0.002 0.051 -10000 0 -0.51 1 1
SMAD3 -0.004 0.1 -10000 0 -0.4 23 23
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.097 -10000 0 -0.29 28 28
SMAD2/SMAD2/SMAD4 -0.007 0.055 -10000 0 -0.28 11 11
NCOR1 0.015 0.033 -10000 0 -0.52 2 2
NCOA2 0.009 0.063 -10000 0 -0.4 11 11
NCOA1 0.012 0.057 -10000 0 -0.52 6 6
MYOD/E2A -0.001 0.097 -10000 0 -0.37 31 31
SMAD2-3/SMAD4/SP1/MIZ-1 0.007 0.17 -10000 0 -0.4 54 54
IFNB1 0.005 0.13 -10000 0 -0.43 28 28
SMAD3/SMAD4/MEF2C -0.027 0.2 -10000 0 -0.53 50 50
CITED1 -0.029 0.1 -10000 0 -0.26 89 89
SMAD2-3/SMAD4/ARC105 0.009 0.12 -10000 0 -0.33 28 28
RBL1 0.01 0.048 -10000 0 -0.27 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.15 -10000 0 -0.47 36 36
RUNX1-3/PEBPB2 -0.042 0.14 -10000 0 -0.34 86 86
SMAD7 -0.042 0.23 -10000 0 -0.57 56 56
MYC/MIZ-1 -0.003 0.1 -10000 0 -0.37 33 33
SMAD3/SMAD4 0.046 0.14 0.31 29 -0.4 15 44
IL10 -0.046 0.18 -10000 0 -0.39 78 78
PIASy/HDAC complex 0.009 0.051 -10000 0 -0.44 6 6
PIAS3 0.019 0.005 -10000 0 -10000 0 0
CDK2 0.015 0.048 -10000 0 -0.3 10 10
IL5 -0.047 0.18 -10000 0 -0.4 70 70
CDK4 0.019 0.029 -10000 0 -0.25 5 5
PIAS4 0.009 0.051 -10000 0 -0.44 6 6
ATF3 -0.02 0.13 -10000 0 -0.41 47 47
SMAD3/SMAD4/SP1 -0.01 0.18 -10000 0 -0.42 60 60
FOXG1 -0.007 0.083 -10000 0 -0.27 45 45
FOXO3 0.015 0.061 -10000 0 -0.4 8 8
FOXO1 0.007 0.081 -10000 0 -0.37 20 20
FOXO4 0.019 0.047 -10000 0 -0.37 5 5
heart looping -0.034 0.17 -10000 0 -0.51 45 45
CEBPB 0.004 0.073 -10000 0 -0.34 20 20
SMAD3/SMAD4/DLX1 -0.01 0.12 -10000 0 -0.31 43 43
MYOD1 -0.015 0.13 -10000 0 -0.47 36 36
SMAD3/SMAD4/HNF4 0.005 0.11 -10000 0 -0.32 35 35
SMAD3/SMAD4/GATA3 -0.062 0.2 -10000 0 -0.38 127 127
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.07 -10000 0 -0.34 19 19
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.036 0.17 -10000 0 -0.34 100 100
SMAD3/SMAD4/SP1-3 -0.001 0.19 -10000 0 -0.48 51 51
MED15 0.018 0 -10000 0 -10000 0 0
SP1 -0.002 0.069 -10000 0 -0.29 7 7
SIN3B 0.017 0.012 -10000 0 -0.25 1 1
SIN3A 0.017 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.02 0.15 -10000 0 -0.36 53 53
ITGB5 -0.032 0.23 -10000 0 -0.64 58 58
TGIF/SIN3/HDAC complex/CtBP 0.041 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.061 0.19 -10000 0 -0.39 117 117
AR -0.088 0.21 -10000 0 -0.52 104 104
negative regulation of cell growth -0.002 0.12 -10000 0 -0.37 31 31
SMAD3/SMAD4/MYOD -0.016 0.13 -10000 0 -0.31 64 64
E2F5 -0.014 0.12 -10000 0 -0.39 41 41
E2F4 0.017 0.017 -10000 0 -0.25 2 2
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.01 0.11 -10000 0 -0.32 19 19
SMAD2-3/SMAD4/FOXO1-3a-4 0.005 0.13 -10000 0 -0.35 42 42
TFDP1 0.011 0.042 -10000 0 -0.25 13 13
SMAD3/SMAD4/AP1 -0.064 0.24 -10000 0 -0.55 75 75
SMAD3/SMAD4/RUNX2 0.003 0.12 -10000 0 -0.36 32 32
TGIF2 0.009 0.066 -10000 0 -0.42 11 11
TGIF1 0.008 0.073 -10000 0 -0.52 10 10
ATF2 0.018 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
alphaV beta3 Integrin 0.001 0.094 -9999 0 -0.4 22 22
PTK2 -0.001 0.15 -9999 0 -0.46 42 42
positive regulation of JNK cascade -0.028 0.086 -9999 0 -0.31 43 43
CDC42/GDP 0.021 0.13 -9999 0 -0.42 41 41
Rac1/GDP 0.023 0.13 -9999 0 -0.41 41 41
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
RAP1A 0.012 0.057 -9999 0 -0.52 6 6
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
CDC42/GTP -0.033 0.11 -9999 0 -0.38 43 43
nectin-3/I-afadin -0.016 0.12 -9999 0 -0.41 41 41
RAPGEF1 0.009 0.15 -9999 0 -0.47 41 41
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.001 0.17 -9999 0 -0.54 41 41
PDGFB-D/PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
TLN1 0.004 0.099 -9999 0 -0.4 20 20
Rap1/GTP -0.031 0.093 -9999 0 -0.33 42 42
IQGAP1 0.018 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.015 0.073 -9999 0 -0.28 28 28
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.016 0.12 -9999 0 -0.41 41 41
PVR 0.008 0.059 -9999 0 -0.33 14 14
Necl-5(dimer) 0.008 0.059 -9999 0 -0.33 14 14
mol:GDP 0.011 0.16 -9999 0 -0.51 41 41
MLLT4 -0.006 0.11 -9999 0 -0.46 26 26
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
PI3K 0.001 0.13 -9999 0 -0.32 59 59
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
positive regulation of lamellipodium assembly -0.028 0.088 -9999 0 -0.32 41 41
PVRL1 0.014 0.035 -9999 0 -0.3 6 6
PVRL3 -0.019 0.12 -9999 0 -0.4 46 46
PVRL2 0.002 0.089 -9999 0 -0.52 15 15
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
CDH1 -0.049 0.17 -9999 0 -0.48 70 70
CLDN1 -0.11 0.21 -9999 0 -0.4 165 165
JAM-A/CLDN1 -0.065 0.16 -9999 0 -0.32 128 128
SRC -0.01 0.18 -9999 0 -0.61 41 41
ITGB3 0.002 0.075 -9999 0 -0.32 25 25
nectin-1(dimer)/I-afadin/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
FARP2 0.006 0.16 -9999 0 -0.51 43 43
RAC1 0.018 0 -9999 0 -10000 0 0
CTNNA1 0.017 0.023 -9999 0 -0.52 1 1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.006 0.11 -9999 0 -0.35 44 44
nectin-1/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
nectin-2/I-afadin -0.002 0.1 -9999 0 -0.39 33 33
RAC1/GTP/IQGAP1/filamentous actin 0.024 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.002 0.11 -9999 0 -0.34 43 43
CDC42/GTP/IQGAP1/filamentous actin 0.024 0 -9999 0 -10000 0 0
F11R 0.011 0.055 -9999 0 -0.36 10 10
positive regulation of filopodium formation -0.028 0.086 -9999 0 -0.31 43 43
alphaV/beta3 Integrin/Talin 0.006 0.13 -9999 0 -0.48 20 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.1 -9999 0 -0.39 33 33
nectin-2(dimer)/I-afadin/I-afadin -0.002 0.1 -9999 0 -0.39 33 33
PIP5K1C -0.004 0.1 -9999 0 -0.42 21 21
VAV2 0.006 0.16 -9999 0 -0.52 41 41
RAP1/GDP 0.019 0.13 -9999 0 -0.39 41 41
ITGAV -0.002 0.1 -9999 0 -0.48 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.01 0.12 -9999 0 -0.35 53 53
nectin-3(dimer)/I-afadin/I-afadin -0.016 0.12 -9999 0 -0.41 41 41
Rac1/GTP -0.032 0.11 -9999 0 -0.4 41 41
PTPRM -0.011 0.11 -9999 0 -0.31 47 47
E-cadherin/beta catenin/alpha catenin -0.012 0.13 -9999 0 -0.25 104 104
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.018 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.003 0.068 -9999 0 -0.28 26 26
Syndecan-3/Src/Cortactin -0.046 0.16 -9999 0 -0.52 35 35
Syndecan-3/Neurocan -0.007 0.13 -9999 0 -0.57 24 24
POMC 0.001 0.072 -9999 0 -0.28 30 30
EGFR -0.079 0.18 -9999 0 -0.35 139 139
Syndecan-3/EGFR -0.049 0.16 -9999 0 -0.39 68 68
AGRP 0.016 0.029 -9999 0 -0.34 3 3
NCSTN 0.017 0.023 -9999 0 -0.52 1 1
PSENEN 0.017 0.012 -9999 0 -0.25 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.001 0.093 -9999 0 -0.51 17 17
APH1A 0.003 0.067 -9999 0 -0.29 25 25
NCAN 0.007 0.053 -9999 0 -0.25 21 21
long-term memory -0.003 0.13 -9999 0 -0.48 32 32
Syndecan-3/IL8 -0.045 0.16 -9999 0 -0.42 58 58
PSEN1 0.013 0.052 -9999 0 -0.52 5 5
Src/Cortactin 0.014 0.054 -9999 0 -0.37 5 5
FYN 0.008 0.067 -9999 0 -0.41 12 12
limb bud formation -0.031 0.12 -9999 0 -0.59 24 24
MC4R 0.014 0.039 -9999 0 -0.36 5 5
SRC 0.015 0.035 -9999 0 -0.43 3 3
PTN -0.099 0.19 -9999 0 -0.37 158 158
FGFR/FGF/Syndecan-3 -0.032 0.12 -9999 0 -0.6 24 24
neuron projection morphogenesis -0.045 0.16 -9999 0 -0.47 40 40
Syndecan-3/AgRP -0.003 0.13 -9999 0 -0.56 25 25
Syndecan-3/AgRP/MC4R 0.006 0.13 -9999 0 -0.53 26 26
Fyn/Cortactin 0.009 0.068 -9999 0 -0.38 10 10
SDC3 -0.032 0.13 -9999 0 -0.61 24 24
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.044 0.15 -9999 0 -0.41 58 58
IL8 -0.072 0.17 -9999 0 -0.34 135 135
Syndecan-3/Fyn/Cortactin -0.003 0.13 -9999 0 -0.49 32 32
Syndecan-3/CASK -0.03 0.12 -9999 0 -0.58 24 24
alpha-MSH/MC4R 0.012 0.057 -9999 0 -0.37 5 5
Gamma Secretase 0.033 0.069 -9999 0 -0.25 25 25
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.037 0.17 -9999 0 -0.45 74 74
KLHL20 -0.015 0.099 -9999 0 -0.26 21 21
CYFIP2 -0.042 0.16 -9999 0 -0.47 65 65
Rac1/GDP 0.006 0.11 -9999 0 -0.3 21 21
ENAH -0.036 0.18 -9999 0 -0.45 76 76
AP1M1 0.017 0.023 -9999 0 -0.52 1 1
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
RAP1A 0.012 0.057 -9999 0 -0.52 6 6
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
CDC42/GTP -0.032 0.069 -9999 0 -0.3 10 10
ABI1/Sra1/Nap1 -0.042 0.054 -9999 0 -0.17 36 36
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.12 -9999 0 -0.28 79 79
RAPGEF1 -0.015 0.15 -9999 0 -0.38 74 74
CTNND1 0.016 0.029 -9999 0 -0.34 3 3
regulation of calcium-dependent cell-cell adhesion -0.039 0.17 -9999 0 -0.46 74 74
CRK -0.024 0.16 -9999 0 -0.41 75 75
E-cadherin/gamma catenin/alpha catenin -0.01 0.12 -9999 0 -0.31 65 65
alphaE/beta7 Integrin 0.023 0.038 -9999 0 -0.37 5 5
IQGAP1 0.018 0 -9999 0 -10000 0 0
NCKAP1 0.015 0.031 -9999 0 -0.32 4 4
Rap1/GTP/I-afadin 0.014 0.073 -9999 0 -0.28 28 28
DLG1 -0.031 0.17 -9999 0 -0.44 74 74
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.028 0.055 -9999 0 -0.22 14 14
MLLT4 -0.006 0.11 -9999 0 -0.46 26 26
ARF6/GTP/NME1/Tiam1 0.023 0.052 -9999 0 -0.3 10 10
PI3K -0.036 0.07 -9999 0 -0.29 13 13
ARF6 0.016 0.033 -9999 0 -0.52 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.027 0.13 -9999 0 -0.37 64 64
TIAM1 0.006 0.073 -9999 0 -0.44 13 13
E-cadherin(dimer)/Ca2+ -0.005 0.11 -9999 0 -0.26 76 76
AKT1 -0.022 0.043 -9999 0 -0.18 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
CDH1 -0.049 0.17 -9999 0 -0.48 70 70
RhoA/GDP 0.003 0.12 -9999 0 -0.32 27 27
actin cytoskeleton organization -0.009 0.075 -9999 0 -0.19 21 21
CDC42/GDP 0.008 0.11 -9999 0 -0.29 22 22
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.007 0.09 -9999 0 -0.24 66 66
ITGB7 0.018 0 -9999 0 -10000 0 0
RAC1 0.018 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.005 0.11 -9999 0 -0.28 76 76
E-cadherin/Ca2+/beta catenin/alpha catenin -0.014 0.1 -9999 0 -0.27 75 75
mol:GDP -0.004 0.13 -9999 0 -0.3 75 75
CDC42/GTP/IQGAP1 0.024 0 -9999 0 -10000 0 0
JUP 0.011 0.056 -9999 0 -0.42 8 8
p120 catenin/RhoA/GDP 0.002 0.12 -9999 0 -0.34 20 20
RAC1/GTP/IQGAP1 0.024 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.023 0.035 -9999 0 -0.37 4 4
RHOA 0.005 0.08 -9999 0 -0.52 12 12
CDC42 0.018 0 -9999 0 -10000 0 0
CTNNA1 0.017 0.023 -9999 0 -0.52 1 1
positive regulation of S phase of mitotic cell cycle -0.027 0.094 -9999 0 -0.2 99 99
NME1 0.012 0.039 -9999 0 -0.25 11 11
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.033 0.17 -9999 0 -0.44 75 75
regulation of cell-cell adhesion -0.029 0.061 -9999 0 -0.26 10 10
WASF2 -0.021 0.031 -9999 0 -0.2 1 1
Rap1/GTP -0.038 0.08 -9999 0 -0.34 10 10
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.009 0.1 -9999 0 -0.25 70 70
CCND1 -0.035 0.12 -9999 0 -0.25 99 99
VAV2 -0.022 0.16 -9999 0 -0.4 74 74
RAP1/GDP 0.005 0.11 -9999 0 -0.36 9 9
adherens junction assembly -0.031 0.17 -9999 0 -0.43 75 75
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0.02 -9999 0 -0.25 3 3
PIP5K1C 0.014 0.042 -9999 0 -0.45 4 4
regulation of heterotypic cell-cell adhesion 0.006 0.11 -9999 0 -0.24 84 84
E-cadherin/beta catenin -0.045 0.11 -9999 0 -0.35 61 61
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.033 0.17 -9999 0 -0.44 75 75
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
Rac1/GTP -0.078 0.12 -9999 0 -0.42 27 27
E-cadherin/beta catenin/alpha catenin -0.017 0.12 -9999 0 -0.31 75 75
ITGAE 0.013 0.052 -9999 0 -0.52 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.04 0.18 -9999 0 -0.47 74 74
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.025 0.076 -10000 0 -0.64 6 6
HDAC1 0.022 0.03 -10000 0 -0.53 1 1
AES 0.019 0.006 -10000 0 -10000 0 0
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
DTX1 0.012 0.049 -10000 0 -0.34 9 9
LRP6/FZD1 0.009 0.076 -10000 0 -0.36 19 19
TLE1 -0.031 0.15 -10000 0 -0.45 56 56
AP1 -0.05 0.13 -10000 0 -0.3 82 82
NCSTN 0.017 0.023 -10000 0 -0.52 1 1
ADAM10 0.013 0.045 -10000 0 -0.39 6 6
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.041 0.13 -10000 0 -0.42 8 8
NICD/RBPSUH 0.027 0.076 -10000 0 -0.63 6 6
WIF1 -0.024 0.098 -10000 0 -0.25 81 81
NOTCH1 -0.003 0.077 -10000 0 -0.67 6 6
PSENEN 0.017 0.012 -10000 0 -0.25 1 1
KREMEN2 -0.19 0.23 -10000 0 -0.41 257 257
DKK1 -0.12 0.19 -10000 0 -0.34 199 199
beta catenin/beta TrCP1 0.004 0.084 0.24 4 -0.35 17 21
APH1B 0.001 0.093 -10000 0 -0.51 17 17
APH1A 0.003 0.067 -10000 0 -0.29 25 25
AXIN1 0.006 0.04 0.24 8 -0.24 2 10
CtBP/CBP/TCF1/TLE1/AES 0.036 0.1 0.29 5 -0.26 1 6
PSEN1 0.013 0.052 -10000 0 -0.52 5 5
FOS -0.11 0.2 -10000 0 -0.37 171 171
JUN -0.034 0.15 -10000 0 -0.46 57 57
MAP3K7 0.019 0.022 -10000 0 -0.26 3 3
CTNNB1 -0.005 0.084 0.23 7 -0.38 15 22
MAPK3 0.016 0.026 -10000 0 -0.39 2 2
DKK2/LRP6/Kremen 2 -0.12 0.16 -10000 0 -0.33 186 186
HNF1A 0.017 0.026 -10000 0 -0.24 5 5
CTBP1 0.018 0.018 -10000 0 -0.26 2 2
MYC -0.086 0.34 -10000 0 -1.4 34 34
NKD1 0.01 0.059 -10000 0 -0.38 11 11
FZD1 0.003 0.082 -10000 0 -0.43 17 17
NOTCH1 precursor/Deltex homolog 1 0.024 0.085 -10000 0 -0.69 6 6
apoptosis -0.05 0.12 -10000 0 -0.3 82 82
Delta 1/NOTCHprecursor 0.027 0.076 -10000 0 -0.63 6 6
DLL1 0.017 0.012 -10000 0 -0.25 1 1
PPARD 0.004 0.045 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.069 -10000 0 -0.25 25 25
APC 0.002 0.055 0.24 7 -0.35 7 14
DVL1 0.022 0.038 -10000 0 -0.38 3 3
CSNK2A1 0.016 0.023 -10000 0 -0.52 1 1
MAP3K7IP1 0.02 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.17 0.17 -10000 0 -0.34 249 249
LRP6 0.008 0.065 -10000 0 -0.38 13 13
CSNK1A1 0.016 0.024 -10000 0 -0.52 1 1
NLK 0.032 0.03 -10000 0 -0.26 1 1
CCND1 -0.22 0.51 -10000 0 -1.4 87 87
WNT1 0.017 0.023 -10000 0 -0.52 1 1
Axin1/APC/beta catenin 0.017 0.074 0.28 4 -0.35 6 10
DKK2 -0.026 0.14 -10000 0 -0.42 52 52
NOTCH1 precursor/DVL1 0.036 0.077 -10000 0 -0.57 6 6
GSK3B 0.018 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.068 -10000 0 -0.47 10 10
NOTCH/Deltex homolog 1 0.022 0.085 -10000 0 -0.7 6 6
PPP2R5D 0.013 0.036 0.27 5 -10000 0 5
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
WNT1/LRP6/FZD1 0.009 0.079 -10000 0 -0.27 23 23
RBPJ 0.018 0 -10000 0 -10000 0 0
CREBBP 0.013 0.035 -10000 0 -0.52 2 2
TRAIL 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
TNFSF10 -0.042 0.16 -10000 0 -0.46 67 67
positive regulation of NF-kappaB transcription factor activity -0.019 0.12 -10000 0 -0.37 52 52
MAP2K4 -0.013 0.12 -10000 0 -0.4 23 23
IKBKB 0.012 0.047 -10000 0 -0.31 10 10
TNFRSF10B 0.005 0.079 -10000 0 -0.46 14 14
TNFRSF10A -0.004 0.1 -10000 0 -0.47 24 24
SMPD1 -0.008 0.086 -10000 0 -0.23 58 58
IKBKG 0.018 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.015 0.031 -10000 0 -0.32 4 4
TRAIL/TRAILR2 -0.026 0.14 -10000 0 -0.4 57 57
TRAIL/TRAILR3 -0.032 0.13 -10000 0 -0.37 54 54
TRAIL/TRAILR1 -0.032 0.14 -10000 0 -0.4 64 64
TRAIL/TRAILR4 -0.019 0.12 -10000 0 -0.37 52 52
TRAIL/TRAILR1/DAP3/GTP -0.013 0.12 -10000 0 -0.3 65 65
IKK complex -0.028 0.082 -10000 0 -0.42 15 15
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.012 0.019 -10000 0 -0.27 2 2
MAPK3 -0.019 0.12 -10000 0 -0.37 52 52
MAP3K1 -0.01 0.12 -10000 0 -0.4 23 23
TRAILR4 (trimer) 0.015 0.031 -10000 0 -0.32 4 4
TRADD 0.016 0.026 -10000 0 -0.39 2 2
TRAILR1 (trimer) -0.004 0.1 -10000 0 -0.46 24 24
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.004 0.11 -10000 0 -0.43 13 13
CFLAR 0.009 0.065 -10000 0 -0.44 10 10
MAPK1 -0.02 0.12 -10000 0 -0.37 53 53
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.12 -10000 0 -0.29 64 64
mol:ceramide -0.008 0.086 -10000 0 -0.23 58 58
FADD 0 0.067 -10000 0 -0.25 35 35
MAPK8 -0.007 0.12 -10000 0 -0.41 20 20
TRAF2 0.014 0.042 -10000 0 -0.45 4 4
TRAILR3 (trimer) -0.004 0.075 -10000 0 -0.26 41 41
CHUK 0.005 0.081 -10000 0 -0.5 13 13
TRAIL/TRAILR1/FADD -0.025 0.13 -10000 0 -0.34 65 65
DAP3 0.016 0.026 -10000 0 -0.39 2 2
CASP10 -0.05 0.12 0.26 1 -0.36 54 55
JNK cascade -0.019 0.12 -10000 0 -0.37 52 52
TRAIL (trimer) -0.042 0.16 -10000 0 -0.46 67 67
TNFRSF10C -0.004 0.075 -10000 0 -0.26 41 41
TRAIL/TRAILR1/DAP3/GTP/FADD -0.011 0.12 -10000 0 -0.29 66 66
TRAIL/TRAILR2/FADD -0.019 0.13 -10000 0 -0.34 58 58
cell death -0.008 0.086 -10000 0 -0.23 58 58
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0.11 -10000 0 -0.46 11 11
TRAILR2 (trimer) 0.005 0.079 -10000 0 -0.46 14 14
CASP8 0.01 0.042 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.003 0.12 -10000 0 -0.29 56 56
PDGFR-alpha signaling 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
PDGFRA -0.025 0.13 -9999 0 -0.5 37 37
PDGF/PDGFRA/CRKL -0.006 0.1 -9999 0 -0.37 36 36
positive regulation of JUN kinase activity 0.019 0.077 -9999 0 -0.26 34 34
CRKL 0.014 0.047 -9999 0 -0.52 4 4
PDGF/PDGFRA/Caveolin-3 -0.004 0.097 -9999 0 -0.37 33 33
AP1 -0.18 0.34 -9999 0 -0.91 84 84
mol:IP3 -0.015 0.1 -9999 0 -0.39 33 33
PLCG1 -0.015 0.1 -9999 0 -0.39 33 33
PDGF/PDGFRA/alphaV Integrin -0.017 0.12 -9999 0 -0.4 47 47
RAPGEF1 0.018 0 -9999 0 -10000 0 0
CRK 0.016 0.033 -9999 0 -0.52 2 2
mol:Ca2+ -0.015 0.1 -9999 0 -0.39 33 33
CAV3 0.016 0.029 -9999 0 -0.34 3 3
CAV1 -0.001 0.083 -9999 0 -0.33 29 29
SHC/Grb2/SOS1 0.02 0.077 -9999 0 -0.27 34 34
PDGF/PDGFRA/Shf -0.009 0.1 -9999 0 -0.37 35 35
FOS -0.17 0.34 -9999 0 -0.89 84 84
JUN -0.051 0.11 -9999 0 -0.38 52 52
oligodendrocyte development -0.017 0.12 -9999 0 -0.4 47 47
GRB2 0.016 0.024 -9999 0 -0.25 4 4
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
mol:DAG -0.015 0.1 -9999 0 -0.39 33 33
PDGF/PDGFRA -0.025 0.13 -9999 0 -0.5 37 37
actin cytoskeleton reorganization -0.01 0.11 -9999 0 -0.39 38 38
SRF 0.028 0.025 -9999 0 -0.35 1 1
SHC1 0.017 0.023 -9999 0 -0.52 1 1
PI3K -0.007 0.11 -9999 0 -0.34 49 49
PDGF/PDGFRA/Crk/C3G 0.01 0.085 -9999 0 -0.31 33 33
JAK1 -0.009 0.1 -9999 0 -0.38 37 37
ELK1/SRF 0.012 0.083 -9999 0 -0.29 34 34
SHB 0.008 0.067 -9999 0 -0.41 12 12
SHF 0.01 0.049 -9999 0 -0.27 15 15
CSNK2A1 0.025 0.029 -9999 0 -0.49 1 1
GO:0007205 -0.018 0.11 -9999 0 -0.42 33 33
SOS1 0.017 0.023 -9999 0 -0.52 1 1
Ras protein signal transduction 0.019 0.077 -9999 0 -0.26 34 34
PDGF/PDGFRA/SHB -0.01 0.11 -9999 0 -0.39 38 38
PDGF/PDGFRA/Caveolin-1 -0.016 0.12 -9999 0 -0.41 36 36
ITGAV -0.002 0.1 -9999 0 -0.48 21 21
ELK1 -0.018 0.1 -9999 0 -0.36 35 35
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
PDGF/PDGFRA/Crk -0.004 0.1 -9999 0 -0.38 33 33
JAK-STAT cascade -0.009 0.1 -9999 0 -0.38 37 37
cell proliferation -0.009 0.1 -9999 0 -0.37 35 35
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.023 0.028 -9999 0 -0.37 1 1
VLDLR -0.061 0.17 -9999 0 -0.4 100 100
CRKL 0.014 0.047 -9999 0 -0.52 4 4
LRPAP1 0.016 0.026 -9999 0 -0.39 2 2
FYN 0.008 0.067 -9999 0 -0.41 12 12
ITGA3 -0.003 0.096 -9999 0 -0.41 25 25
RELN/VLDLR/Fyn -0.023 0.12 -9999 0 -0.32 64 64
MAPK8IP1/MKK7/MAP3K11/JNK1 0.038 0.061 -9999 0 -0.26 18 18
AKT1 -0.011 0.11 -9999 0 -0.42 15 15
MAP2K7 0.017 0.023 -9999 0 -0.52 1 1
RAPGEF1 0.018 0 -9999 0 -10000 0 0
DAB1 0.018 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.011 0.094 -9999 0 -0.28 42 42
LRPAP1/LRP8 -0.027 0.11 -9999 0 -0.37 37 37
RELN/LRP8/DAB1/Fyn -0.006 0.096 -9999 0 -0.26 48 48
DAB1/alpha3/beta1 Integrin -0.067 0.11 -9999 0 -0.37 26 26
long-term memory -0.002 0.1 -9999 0 -0.24 65 65
DAB1/LIS1 -0.028 0.12 -9999 0 -0.38 15 15
DAB1/CRLK/C3G -0.059 0.097 -9999 0 -0.37 16 16
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
DAB1/NCK2 -0.029 0.12 -9999 0 -0.36 16 16
ARHGEF2 0.004 0.079 -9999 0 -0.41 17 17
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.017 0.012 -9999 0 -0.25 1 1
CDK5R1 0.014 0.031 -9999 0 -0.25 7 7
RELN 0.01 0.059 -9999 0 -0.38 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
RELN/LRP8/Fyn -0.02 0.11 -9999 0 -0.32 48 48
GRIN2A/RELN/LRP8/DAB1/Fyn 0.004 0.097 -9999 0 -0.26 47 47
MAPK8 0.015 0.04 -9999 0 -0.52 3 3
RELN/VLDLR/DAB1 -0.014 0.1 -9999 0 -0.28 59 59
ITGB1 0.014 0.044 -9999 0 -0.41 5 5
MAP1B -0.058 0.15 -9999 0 -0.3 111 111
RELN/LRP8 -0.015 0.1 -9999 0 -0.31 43 43
GRIN2B/RELN/LRP8/DAB1/Fyn -0.009 0.11 -9999 0 -0.26 65 65
PI3K 0.005 0.082 -9999 0 -0.37 21 21
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.009 0.078 -9999 0 -0.39 17 17
RAP1A -0.019 0.12 -9999 0 -0.36 17 17
PAFAH1B1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8IP1 0.011 0.048 -9999 0 -0.3 11 11
CRLK/C3G 0.023 0.034 -9999 0 -0.37 4 4
GRIN2B -0.007 0.1 -9999 0 -0.44 28 28
NCK2 0.015 0.026 -9999 0 -0.25 5 5
neuron differentiation 0.011 0.079 -9999 0 -0.25 13 13
neuron adhesion -0.016 0.12 -9999 0 -0.33 28 28
LRP8 -0.057 0.16 -9999 0 -0.34 110 110
GSK3B -0.004 0.1 -9999 0 -0.4 14 14
RELN/VLDLR/DAB1/Fyn -0.009 0.11 -9999 0 -0.27 64 64
MAP3K11 0.015 0.035 -9999 0 -0.43 3 3
RELN/VLDLR/DAB1/P13K -0.016 0.11 -9999 0 -0.26 74 74
CDK5 0.016 0.026 -9999 0 -0.39 2 2
MAPT -0.089 0.2 -9999 0 -0.48 107 107
neuron migration -0.013 0.12 -9999 0 -0.35 27 27
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.011 0.079 -9999 0 -0.25 13 13
RELN/VLDLR -0.045 0.14 -9999 0 -0.28 113 113
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.019 0.061 -9999 0 -0.27 21 21
RGS9BP -0.072 0.18 -9999 0 -0.41 111 111
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.016 0.089 -9999 0 -0.33 24 24
mol:ADP 0.011 0.025 -9999 0 -0.38 2 2
GNAT2 -0.004 0.1 -9999 0 -0.49 23 23
RGS9-1/Gbeta5/R9AP -0.056 0.15 -9999 0 -0.34 96 96
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.089 -9999 0 -0.33 33 33
GRK7 0.015 0.035 -9999 0 -0.43 3 3
CNGB3 -0.006 0.086 -9999 0 -0.3 39 39
Cone Metarhodopsin II/X-Arrestin 0.013 0.008 -9999 0 -0.17 1 1
mol:Ca2+ -0.009 0.083 -9999 0 -0.29 27 27
Cone PDE6 -0.043 0.14 -9999 0 -0.29 105 105
Cone Metarhodopsin II 0.01 0.019 -9999 0 -0.29 2 2
Na + (4 Units) -0.005 0.085 -9999 0 -0.29 27 27
GNAT2/GDP -0.049 0.14 -9999 0 -0.29 112 112
GNB5 0.005 0.081 -9999 0 -0.5 13 13
mol:GMP (4 units) 0.001 0.091 -9999 0 -0.31 37 37
Cone Transducin 0.02 0.065 -9999 0 -0.29 21 21
SLC24A2 0.014 0.044 -9999 0 -0.41 5 5
GNB3/GNGT2 0.025 0.026 -9999 0 -0.37 2 2
GNB3 0.017 0.012 -9999 0 -0.25 1 1
GNAT2/GTP -0.003 0.076 -9999 0 -0.35 23 23
CNGA3 -0.028 0.12 -9999 0 -0.31 73 73
ARR3 0.017 0.012 -9999 0 -0.25 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.016 0.089 -9999 0 -0.33 24 24
mol:Pi -0.056 0.15 -9999 0 -0.34 96 96
Cone CNG Channel -0.014 0.11 -9999 0 -0.3 53 53
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.014 0.044 -9999 0 -0.41 5 5
RGS9 -0.033 0.13 -9999 0 -0.31 81 81
PDE6C 0.008 0.065 -9999 0 -0.38 13 13
GNGT2 0.016 0.033 -9999 0 -0.52 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.093 -9999 0 -0.44 21 21
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.012 0.1 -10000 0 -0.26 56 56
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.014 0.047 -10000 0 -0.52 4 4
STAT1 (dimer)/Cbp/p300 -0.01 0.15 -10000 0 -0.43 31 31
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.015 0.061 -10000 0 -0.35 10 10
antigen processing and presentation of peptide antigen via MHC class I -0.055 0.1 -10000 0 -0.29 60 60
CaM/Ca2+ -0.007 0.097 -10000 0 -0.31 17 17
RAP1A 0.012 0.057 -10000 0 -0.52 6 6
STAT1 (dimer)/SHP2 -0.027 0.13 -10000 0 -0.33 48 48
AKT1 -0.012 0.11 -10000 0 -0.36 19 19
MAP2K1 -0.024 0.12 -10000 0 -0.36 32 32
MAP3K11 -0.011 0.098 -10000 0 -0.3 24 24
IFNGR1 0.01 0.034 -10000 0 -0.27 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.03 0.14 -10000 0 -0.38 46 46
Rap1/GTP -0.03 0.07 -10000 0 -0.35 11 11
CRKL/C3G 0.023 0.034 -10000 0 -0.37 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.009 0.11 -10000 0 -0.27 52 52
CEBPB -0.01 0.16 -10000 0 -0.45 32 32
STAT3 0.015 0.04 -10000 0 -0.52 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.001 0.11 -10000 0 -0.91 2 2
STAT1 -0.029 0.13 -10000 0 -0.33 48 48
CALM1 0.018 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.086 0.17 -10000 0 -0.33 161 161
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
STAT1 (dimer)/PIAS1 -0.019 0.12 -10000 0 -0.37 29 29
CEBPB/PTGES2/Cbp/p300 -0.043 0.11 -10000 0 -0.4 29 29
mol:Ca2+ -0.014 0.1 -10000 0 -0.26 56 56
MAPK3 -0.016 0.14 -10000 0 -0.48 14 14
STAT1 (dimer) -0.07 0.15 -10000 0 -0.43 55 55
MAPK1 -0.017 0.14 -10000 0 -0.49 17 17
JAK2 0.007 0.056 -10000 0 -0.34 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
JAK1 0.008 0.059 -10000 0 -0.54 6 6
CAMK2D -0.005 0.1 -10000 0 -0.4 29 29
DAPK1 0 0.14 -10000 0 -0.51 20 20
SMAD7 0.004 0.073 -10000 0 -0.18 22 22
CBL/CRKL/C3G 0.005 0.095 -10000 0 -0.35 11 11
PI3K -0.022 0.11 -10000 0 -0.36 21 21
IFNG -0.086 0.17 -10000 0 -0.33 161 161
apoptosis -0.007 0.12 0.27 2 -0.39 21 23
CAMK2G 0.017 0.017 -10000 0 -0.25 2 2
STAT3 (dimer) 0.015 0.04 -10000 0 -0.52 3 3
CAMK2A 0.017 0.023 -10000 0 -0.52 1 1
CAMK2B -0.078 0.18 -10000 0 -0.36 133 133
FRAP1 -0.004 0.1 -10000 0 -0.34 17 17
PRKCD -0.01 0.11 -10000 0 -0.36 18 18
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
negative regulation of cell growth -0.055 0.1 -10000 0 -0.29 60 60
PTPN2 0.016 0.024 -10000 0 -0.25 4 4
EP300 0.014 0.047 -10000 0 -0.52 4 4
IRF1 -0.007 0.15 -10000 0 -0.47 35 35
STAT1 (dimer)/PIASy -0.024 0.13 -10000 0 -0.41 25 25
SOCS1 0.01 0.064 -10000 0 -1.4 1 1
mol:GDP 0.003 0.091 -10000 0 -0.33 11 11
CASP1 -0.017 0.12 -10000 0 -0.28 68 68
PTGES2 0.017 0.012 -10000 0 -0.25 1 1
IRF9 0.017 0.085 -10000 0 -0.32 19 19
mol:PI-3-4-5-P3 -0.048 0.089 -10000 0 -0.34 22 22
RAP1/GDP -0.03 0.071 -10000 0 -0.37 10 10
CBL -0.01 0.097 -10000 0 -0.28 30 30
MAP3K1 -0.033 0.12 -10000 0 -0.32 54 54
PIAS1 0.017 0.012 -10000 0 -0.25 1 1
PIAS4 0.012 0.05 -10000 0 -0.43 6 6
antigen processing and presentation of peptide antigen via MHC class II -0.055 0.1 -10000 0 -0.29 60 60
PTPN11 -0.019 0.1 -10000 0 -0.26 56 56
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
RAPGEF1 0.018 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.009 0.027 -9999 0 -0.17 12 12
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.007 0.062 -9999 0 -0.4 3 3
STXBP1 0.017 0.017 -9999 0 -0.25 2 2
ACh/CHRNA1 0.008 0.046 -9999 0 -0.3 9 9
RAB3GAP2/RIMS1/UNC13B 0.019 0.054 -9999 0 -0.32 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.003 0.073 -9999 0 -0.25 41 41
mol:ACh 0.002 0.026 -9999 0 -0.1 24 24
RAB3GAP2 0.017 0.023 -9999 0 -0.52 1 1
STX1A/SNAP25/VAMP2 0.018 0.053 -9999 0 -0.23 5 5
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.008 0.046 -9999 0 -0.29 9 9
UNC13B 0.011 0.049 -9999 0 -0.3 12 12
CHRNA1 0.01 0.064 -9999 0 -0.46 9 9
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.1 0.14 -9999 0 -0.22 265 265
SNAP25 -0.008 0.055 -9999 0 -0.14 57 57
VAMP2 0.007 0.011 -9999 0 -0.26 1 1
SYT1 -0.17 0.21 -9999 0 -0.36 265 265
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0.026 -9999 0 -0.27 1 1
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.053 -9999 0 -0.23 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.048 -9999 0 -0.25 17 17
ELF1 -0.012 0.12 -9999 0 -0.37 43 43
CCNA2 -0.026 0.13 -9999 0 -0.39 57 57
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
JAK3 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
JAK1 0.012 0.057 -9999 0 -0.52 6 6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.01 0.14 -9999 0 -0.38 38 38
SHC1 0.018 0.023 -9999 0 -0.52 1 1
SP1 0.015 0.07 -9999 0 -0.36 16 16
IL2RA -0.035 0.2 -9999 0 -0.73 37 37
IL2RB -0.016 0.12 -9999 0 -0.43 40 40
SOS1 0.017 0.023 -9999 0 -0.52 1 1
IL2RG -0.001 0.078 -9999 0 -0.28 35 35
G1/S transition of mitotic cell cycle -0.026 0.2 -9999 0 -0.57 47 47
PTPN11 0.018 0.023 -9999 0 -0.52 1 1
CCND2 0.009 0.14 -9999 0 -0.77 16 16
LCK -0.073 0.18 -9999 0 -0.4 117 117
GRB2 0.016 0.024 -9999 0 -0.25 4 4
IL2 0.012 0.051 -9999 0 -0.33 10 10
CDK6 -0.019 0.1 -9999 0 -0.29 63 63
CCND3 0.021 0.12 -9999 0 -0.45 13 13
Class I PI3K signaling events

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
ARF5/GTP 0.019 0.071 0.24 15 -0.23 28 43
DAPP1 -0.038 0.14 -10000 0 -0.42 43 43
Src family/SYK family/BLNK-LAT/BTK-ITK -0.051 0.22 -10000 0 -0.54 64 64
mol:DAG 0.001 0.1 0.19 9 -0.23 49 58
HRAS 0.012 0.051 -10000 0 -0.41 7 7
RAP1A 0.012 0.057 -10000 0 -0.52 6 6
ARF5/GDP -0.016 0.11 -10000 0 -0.31 31 31
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
ARF5 0.015 0.04 -10000 0 -0.52 3 3
mol:GTP -0.006 0.068 0.22 15 -0.25 25 40
ARF1/GTP -0.006 0.067 0.22 15 -0.24 25 40
RHOA 0.005 0.08 -10000 0 -0.52 12 12
YES1 0.007 0.07 -10000 0 -0.43 12 12
RAP1A/GTP 0.015 0.069 0.22 15 -0.25 25 40
ADAP1 -0.006 0.065 0.21 15 -0.24 25 40
ARAP3 -0.006 0.067 0.22 15 -0.25 25 40
INPPL1 0.012 0.055 -10000 0 -0.44 7 7
PREX1 -0.089 0.2 -10000 0 -0.44 124 124
ARHGEF6 -0.019 0.13 -10000 0 -0.41 45 45
ARHGEF7 0.016 0.02 -10000 0 -0.25 3 3
ARF1 0.017 0.023 -10000 0 -0.52 1 1
NRAS 0.005 0.076 -10000 0 -0.4 16 16
FYN 0.008 0.067 -10000 0 -0.41 12 12
ARF6 0.016 0.033 -10000 0 -0.52 2 2
FGR 0.017 0.017 -10000 0 -0.25 2 2
mol:Ca2+ 0.006 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
ZAP70 0.005 0.06 -10000 0 -0.26 24 24
mol:IP3 0.004 0.073 -10000 0 -0.18 24 24
LYN 0.014 0.031 -10000 0 -0.25 7 7
ARF1/GDP -0.015 0.1 -10000 0 -0.32 28 28
RhoA/GDP 0.003 0.099 0.23 6 -0.34 25 31
PDK1/Src/Hsp90 0.031 0.039 -10000 0 -0.3 6 6
BLNK -0.012 0.12 -10000 0 -0.51 30 30
actin cytoskeleton reorganization -0.006 0.12 0.23 6 -0.41 23 29
SRC 0.015 0.035 -10000 0 -0.43 3 3
PLEKHA2 0.014 0.043 -10000 0 -0.31 8 8
RAC1 0.018 0 -10000 0 -10000 0 0
PTEN -0.003 0.096 -10000 0 -0.5 19 19
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
ARF6/GTP 0.019 0.069 0.24 14 -0.33 3 17
RhoA/GTP 0.015 0.082 0.22 14 -0.26 32 46
Src family/SYK family/BLNK-LAT -0.032 0.17 -10000 0 -0.47 47 47
BLK -0.019 0.1 -10000 0 -0.29 63 63
PDPK1 0.016 0.026 -10000 0 -0.39 2 2
CYTH1 -0.006 0.065 0.21 15 -0.24 25 40
HCK -0.005 0.11 -10000 0 -0.47 25 25
CYTH3 -0.006 0.065 0.21 15 -0.24 25 40
CYTH2 -0.006 0.065 0.21 15 -0.24 25 40
KRAS 0.009 0.065 -10000 0 -0.44 10 10
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.025 0.052 0.18 12 -0.22 5 17
SGK1 -0.004 0.047 0.18 13 -0.21 6 19
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.025 0.11 -10000 0 -0.29 41 41
SOS1 0.017 0.023 -10000 0 -0.52 1 1
SYK -0.023 0.14 -10000 0 -0.48 43 43
ARF6/GDP 0.005 0.085 0.24 6 -0.3 20 26
mol:PI-3-4-5-P3 -0.004 0.074 0.25 19 -0.25 25 44
ARAP3/RAP1A/GTP 0.014 0.07 0.22 15 -0.25 25 40
VAV1 -0.014 0.12 -10000 0 -0.39 42 42
mol:PI-3-4-P2 0.008 0.039 -10000 0 -0.32 7 7
RAS family/GTP/PI3K Class I 0.022 0.069 -10000 0 -0.25 25 25
PLEKHA1 0.012 0.052 -10000 0 -0.32 12 12
Rac1/GDP -0.014 0.1 -10000 0 -0.32 27 27
LAT 0.002 0.068 -10000 0 -0.27 29 29
Rac1/GTP -0.03 0.14 -10000 0 -0.4 42 42
ITK -0.008 0.1 0.22 14 -0.25 61 75
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.008 0.13 0.22 8 -0.32 50 58
LCK -0.074 0.18 -10000 0 -0.4 117 117
BTK 0.007 0.091 0.22 14 -0.27 37 51
Regulation of Telomerase

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
Telomerase catalytic core complex -0.1 0.22 -10000 0 -0.63 43 43
RAD9A 0.018 0 -10000 0 -10000 0 0
AP1 -0.1 0.19 -10000 0 -0.43 107 107
IFNAR2 0.013 0.036 -10000 0 -0.3 6 6
AKT1 -0.053 0.12 -10000 0 -0.26 75 75
ER alpha/Oestrogen -0.12 0.18 -10000 0 -0.33 199 199
NFX1/SIN3/HDAC complex 0.038 0.048 -10000 0 -0.31 2 2
EGF -0.14 0.23 -10000 0 -0.42 193 193
SMG5 0.016 0.029 -10000 0 -0.34 3 3
SMG6 0.017 0.023 -10000 0 -0.52 1 1
SP3/HDAC2 0.019 0.041 -10000 0 -0.37 2 2
TERT/c-Abl -0.089 0.21 -10000 0 -0.59 42 42
SAP18 0.017 0.001 -10000 0 -10000 0 0
MRN complex 0.03 0.045 -10000 0 -0.3 9 9
WT1 -0.1 0.19 -10000 0 -0.35 172 172
WRN 0.012 0.049 -10000 0 -0.34 9 9
SP1 0.016 0.025 -10000 0 -0.53 1 1
SP3 0.017 0.003 -10000 0 -10000 0 0
TERF2IP 0.018 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.099 0.17 -10000 0 -0.55 35 35
Mad/Max 0.021 0.023 -10000 0 -10000 0 0
TERT -0.1 0.23 -10000 0 -0.66 40 40
CCND1 -0.2 0.44 -10000 0 -1.1 89 89
MAX 0.017 0.004 -10000 0 -10000 0 0
RBBP7 0.01 0.051 -10000 0 -0.3 13 13
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
TERF2 0.014 0.036 -10000 0 -0.46 3 3
PTGES3 0.016 0.026 -10000 0 -0.39 2 2
SIN3A 0.017 0.001 -10000 0 -10000 0 0
Telomerase/911 0.026 0.046 -10000 0 -0.35 2 2
CDKN1B -0.072 0.19 -10000 0 -0.65 33 33
RAD1 0.016 0.033 -10000 0 -0.52 2 2
XRCC5 0.018 0 -10000 0 -10000 0 0
XRCC6 0.017 0.012 -10000 0 -0.25 1 1
SAP30 0.012 0.053 -10000 0 -0.48 6 6
TRF2/PARP2 0.024 0.03 -10000 0 -0.36 3 3
UBE3A 0.015 0.033 -10000 0 -0.52 2 2
JUN -0.034 0.15 -10000 0 -0.46 57 57
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.011 0.025 -10000 0 -0.38 2 2
FOS -0.11 0.2 -10000 0 -0.37 171 171
IFN-gamma/IRF1 -0.075 0.16 -10000 0 -0.36 103 103
PARP2 0.017 0.012 -10000 0 -0.25 1 1
BLM -0.021 0.13 -10000 0 -0.4 48 48
Telomerase 0.025 0.06 -10000 0 -0.34 3 3
IRF1 -0.017 0.12 -10000 0 -0.37 40 40
ESR1 -0.16 0.24 -10000 0 -0.46 199 199
KU/TER 0.026 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.025 0.023 -10000 0 -0.26 3 3
ubiquitin-dependent protein catabolic process 0.043 0.051 -10000 0 -0.35 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.052 -10000 0 -0.36 2 2
HDAC1 0.016 0.023 -10000 0 -0.52 1 1
HDAC2 0.008 0.055 -10000 0 -0.3 15 15
ATM 0.001 0.017 0.21 3 -10000 0 3
SMAD3 0.015 0.059 -10000 0 -0.36 11 11
ABL1 0.018 0 -10000 0 -10000 0 0
MXD1 0.014 0.031 -10000 0 -0.25 7 7
MRE11A 0.018 0 -10000 0 -10000 0 0
HUS1 0.016 0.02 -10000 0 -0.25 3 3
RPS6KB1 0.008 0.049 -10000 0 -0.25 18 18
TERT/NF kappa B1/14-3-3 -0.091 0.22 -10000 0 -0.61 45 45
NR2F2 -0.05 0.17 -10000 0 -0.44 79 79
MAPK3 0.019 0.041 -10000 0 -0.37 4 4
MAPK1 0.018 0.044 -10000 0 -0.37 5 5
TGFB1/TGF beta receptor Type II 0.017 0.023 -10000 0 -0.52 1 1
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
HNRNPC 0.018 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.001 0.017 0.21 3 -10000 0 3
NBN 0.015 0.035 -10000 0 -0.43 3 3
EGFR -0.079 0.18 -10000 0 -0.35 139 139
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.15 0.2 -10000 0 -0.42 173 173
MYC -0.027 0.14 -10000 0 -0.43 52 52
IL2 0.01 0.052 -10000 0 -0.34 10 10
KU 0.026 0.008 -10000 0 -10000 0 0
RAD50 0.011 0.062 -10000 0 -0.52 7 7
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
TGFB1 0.017 0.024 -10000 0 -0.52 1 1
TRF2/BLM -0.002 0.091 -10000 0 -0.35 30 30
FRAP1 0.018 0 -10000 0 -10000 0 0
KU/TERT -0.08 0.21 -10000 0 -0.6 37 37
SP1/HDAC2 0.019 0.048 -10000 0 -0.42 3 3
PINX1 0.016 0.02 -10000 0 -0.25 3 3
Telomerase/EST1A -0.1 0.17 -10000 0 -0.55 36 36
Smad3/Myc -0.003 0.099 -10000 0 -0.31 46 46
911 complex 0.034 0.024 -10000 0 -0.3 2 2
IFNG -0.092 0.18 -10000 0 -0.33 161 161
Telomerase/PinX1 -0.099 0.17 -10000 0 -0.56 35 35
Telomerase/AKT1/mTOR/p70S6K -0.008 0.092 -10000 0 -0.42 7 7
SIN3B 0.017 0.012 -10000 0 -0.25 1 1
YWHAE 0.016 0.029 -10000 0 -0.34 3 3
Telomerase/EST1B -0.1 0.17 -10000 0 -0.55 36 36
response to DNA damage stimulus 0.004 0.005 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.044 0.047 -10000 0 -0.27 11 11
TRF2/WRN 0.02 0.043 -10000 0 -0.35 6 6
Telomerase/hnRNP C1/C2 -0.099 0.17 -10000 0 -0.56 33 33
E2F1 0.005 0.071 -10000 0 -0.37 16 16
ZNFX1 0.007 0.071 -10000 0 -0.42 13 13
PIF1 0.015 0.026 -10000 0 -0.25 5 5
NCL 0.018 0 -10000 0 -10000 0 0
DKC1 0.016 0.02 -10000 0 -0.25 3 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP -0.048 0.1 -9999 0 -0.26 88 88
TC10/GTP -0.022 0.063 -9999 0 -0.23 39 39
Insulin Receptor/Insulin/IRS1/Shp2 0.005 0.11 -9999 0 -0.29 63 63
HRAS 0.012 0.051 -9999 0 -0.41 7 7
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.16 0.21 -9999 0 -0.36 247 247
FOXO3 -0.021 0.065 -9999 0 -0.71 4 4
AKT1 -0.068 0.14 -9999 0 -0.37 44 44
INSR 0.015 0.038 -9999 0 -0.38 4 4
Insulin Receptor/Insulin 0.036 0.079 -9999 0 -0.49 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 -0.003 0.097 -9999 0 -0.43 24 24
SORBS1 -0.032 0.14 -9999 0 -0.39 65 65
CRK 0.016 0.033 -9999 0 -0.52 2 2
PTPN1 0.023 0.075 -9999 0 -0.48 4 4
CAV1 -0.012 0.11 -9999 0 -0.27 69 69
CBL/APS/CAP/Crk-II/C3G 0.014 0.078 -9999 0 -0.25 35 35
Insulin Receptor/Insulin/IRS1/NCK2 0.004 0.11 -9999 0 -0.29 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.11 -9999 0 -0.25 80 80
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.09 -9999 0 -0.46 6 6
RPS6KB1 -0.06 0.13 -9999 0 -0.33 50 50
PARD6A 0.004 0.081 -9999 0 -0.44 16 16
CBL 0.017 0.012 -9999 0 -0.25 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.014 0.11 -9999 0 -0.78 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.082 0.11 -9999 0 -0.33 51 51
HRAS/GTP -0.028 0.073 -9999 0 -0.33 7 7
Insulin Receptor 0.015 0.037 -9999 0 -0.38 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.014 0.1 -9999 0 -0.26 62 62
PRKCI -0.033 0.1 -9999 0 -0.52 21 21
Insulin Receptor/Insulin/GRB14/PDK1 -0.098 0.12 -9999 0 -0.36 50 50
SHC1 0.017 0.023 -9999 0 -0.52 1 1
negative regulation of MAPKKK cascade 0.009 0.12 -9999 0 -0.7 11 11
PI3K -0.005 0.11 -9999 0 -0.26 80 80
NCK2 0.015 0.026 -9999 0 -0.25 5 5
RHOQ 0.012 0.053 -9999 0 -0.48 6 6
mol:H2O2 -0.002 0.008 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.036 -9999 0 -0.29 7 7
AKT2 -0.065 0.13 -9999 0 -0.36 42 42
PRKCZ -0.028 0.074 -9999 0 -0.53 9 9
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.002 0.093 -9999 0 -0.25 63 63
F2RL2 -0.074 0.19 -9999 0 -0.44 105 105
TRIP10 0.013 0.048 -9999 0 -0.47 5 5
Insulin Receptor/Insulin/Shc 0.032 0.029 -9999 0 -0.27 4 4
TC10/GTP/CIP4/Exocyst 0.018 0.045 -9999 0 -0.31 9 9
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.05 0.036 -9999 0 -0.3 4 4
RAPGEF1 0.018 0 -9999 0 -10000 0 0
RASA1 0.004 0.078 -9999 0 -0.42 16 16
NCK1 0.011 0.045 -9999 0 -0.28 12 12
CBL/APS/CAP/Crk-II 0.005 0.082 -9999 0 -0.28 35 35
TC10/GDP 0.009 0.039 -9999 0 -0.34 6 6
Insulin Receptor/Insulin/SHC/GRB10 0.032 0.064 -9999 0 -0.27 20 20
INPP5D -0.014 0.096 -9999 0 -0.27 62 62
SOS1 0.017 0.023 -9999 0 -0.52 1 1
SGK1 -0.01 0.012 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
IRS1 -0.048 0.17 -9999 0 -0.49 68 68
p62DOK/RasGAP 0.009 0.12 -9999 0 -0.71 11 11
INS 0.017 0.025 -9999 0 -0.52 1 1
mol:PI-3-4-P2 -0.013 0.096 -9999 0 -0.27 62 62
GRB2 0.016 0.024 -9999 0 -0.25 4 4
EIF4EBP1 -0.067 0.13 -9999 0 -0.34 57 57
PTPRA 0.017 0.028 -9999 0 -0.4 2 2
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
TC10/GTP/CIP4 0.018 0.045 -9999 0 -0.31 9 9
PDPK1 0.016 0.026 -9999 0 -0.39 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.095 -9999 0 -0.4 6 6
Insulin Receptor/Insulin/IRS1 -0.006 0.11 -9999 0 -0.29 62 62
Insulin Receptor/Insulin/IRS3 0.024 0.034 -9999 0 -0.37 3 3
Par3/Par6 -0.02 0.13 -9999 0 -0.29 86 86
Aurora B 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
Condensin I complex 0.01 0.079 -9999 0 -0.26 32 32
STMN1 0.002 0.088 -9999 0 -0.38 22 22
Aurora B/RasGAP/Survivin -0.011 0.12 -9999 0 -0.34 53 53
Chromosomal passenger complex/Cul3 protein complex -0.052 0.14 -9999 0 -0.32 67 67
BIRC5 -0.038 0.16 -9999 0 -0.43 67 67
DES -0.026 0.13 -9999 0 -0.68 16 16
Aurora C/Aurora B/INCENP 0.015 0.062 -9999 0 -0.29 14 14
Aurora B/TACC1 -0.005 0.088 -9999 0 -0.32 32 32
Aurora B/PP2A 0.019 0.042 -9999 0 -0.39 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.011 0.033 -9999 0 -0.21 9 9
mitotic metaphase/anaphase transition 0 0.005 -9999 0 -10000 0 0
NDC80 -0.014 0.12 -9999 0 -0.4 39 39
Cul3 protein complex -0.048 0.14 -9999 0 -0.33 93 93
KIF2C -0.061 0.24 -9999 0 -0.65 59 59
PEBP1 0.013 0.047 -9999 0 -0.53 4 4
KIF20A -0.027 0.14 -9999 0 -0.46 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.011 0.07 -9999 0 -0.38 13 13
SEPT1 0.008 0.052 -9999 0 -0.27 17 17
SMC2 0.003 0.077 -9999 0 -0.36 20 20
SMC4 0.014 0.04 -9999 0 -0.34 6 6
NSUN2/NPM1/Nucleolin 0.015 0.082 -9999 0 -0.87 3 3
PSMA3 0.017 0.012 -9999 0 -0.25 1 1
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B 0.013 0.04 -9999 0 -0.33 5 5
AURKB 0.009 0.058 -9999 0 -0.32 14 14
AURKC 0.008 0.053 -9999 0 -0.27 18 18
CDCA8 -0.016 0.12 -9999 0 -0.4 42 42
cytokinesis -0.049 0.26 -9999 0 -0.72 51 51
Aurora B/Septin1 -0.036 0.23 -9999 0 -0.65 51 51
AURKA -0.012 0.11 -9999 0 -0.41 36 36
INCENP 0.001 0.082 -9999 0 -0.37 22 22
KLHL13 -0.095 0.2 -9999 0 -0.39 146 146
BUB1 -0.052 0.17 -9999 0 -0.44 81 81
hSgo1/Aurora B/Survivin -0.016 0.14 -9999 0 -0.38 52 52
EVI5 0.013 0.047 -9999 0 -0.52 4 4
RhoA/GTP -0.045 0.24 -9999 0 -0.6 65 65
SGOL1 -0.01 0.11 -9999 0 -0.38 37 37
CENPA -0.041 0.21 -9999 0 -0.59 51 51
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.02 0.041 -9999 0 -0.39 3 3
NCAPD2 0.012 0.04 -9999 0 -0.25 12 12
Aurora B/PP1-gamma 0.018 0.05 -9999 0 -0.38 6 6
RHOA 0.005 0.08 -9999 0 -0.52 12 12
NCAPH -0.008 0.11 -9999 0 -0.46 29 29
NPM1 0.012 0.052 -9999 0 -0.6 3 3
RASA1 0.004 0.078 -9999 0 -0.42 16 16
KLHL9 -0.001 0.096 -9999 0 -0.49 19 19
mitotic prometaphase -0.001 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.041 -9999 0 -0.38 3 3
PPP1CC 0.015 0.04 -9999 0 -0.52 3 3
Centraspindlin -0.053 0.27 -9999 0 -0.69 60 60
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
NSUN2 0.012 0.054 -9999 0 -0.5 4 4
MYLK 0.003 0.07 -9999 0 -0.33 20 20
KIF23 -0.024 0.14 -9999 0 -0.45 47 47
VIM -0.01 0.11 -9999 0 -0.38 34 34
RACGAP1 -0.004 0.1 -9999 0 -0.5 22 22
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.013 0.052 -9999 0 -0.6 3 3
Chromosomal passenger complex -0.045 0.22 -9999 0 -0.56 58 58
Chromosomal passenger complex/EVI5 -0.012 0.15 -9999 0 -0.35 66 66
TACC1 -0.022 0.13 -9999 0 -0.41 49 49
PPP2R5D 0.016 0.02 -9999 0 -0.25 3 3
CUL3 0.01 0.06 -9999 0 -0.43 9 9
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.019 0.05 -10000 0 -0.37 8 8
Necdin/E2F1 -0.027 0.14 -10000 0 -0.38 62 62
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.01 0.11 -10000 0 -0.27 78 78
NGF (dimer)/p75(NTR)/BEX1 -0.016 0.075 -10000 0 -0.29 12 12
NT-4/5 (dimer)/p75(NTR) 0.004 0.045 -10000 0 -0.2 23 23
IKBKB 0.012 0.047 -10000 0 -0.31 10 10
AKT1 0.01 0.072 -10000 0 -0.25 30 30
IKBKG 0.018 0 -10000 0 -10000 0 0
BDNF -0.016 0.091 -10000 0 -0.26 64 64
MGDIs/NGR/p75(NTR)/LINGO1 -0.003 0.086 -10000 0 -0.31 22 22
FURIN 0.004 0.076 -10000 0 -0.37 19 19
proBDNF (dimer)/p75(NTR)/Sortilin 0.004 0.075 -10000 0 -0.33 11 11
LINGO1 -0.019 0.095 -10000 0 -0.26 69 69
Sortilin/TRAF6/NRIF -0.017 0.056 -10000 0 -0.33 5 5
proBDNF (dimer) -0.016 0.09 -10000 0 -0.26 64 64
NTRK1 0.01 0.053 -10000 0 -0.32 12 12
RTN4R 0.001 0.087 -10000 0 -0.41 21 21
neuron apoptosis 0.003 0.1 -10000 0 -0.47 7 7
IRAK1 0.015 0.029 -10000 0 -0.25 6 6
SHC1 0.013 0.04 -10000 0 -0.31 4 4
ARHGDIA 0.016 0.029 -10000 0 -0.34 3 3
RhoA/GTP 0.004 0.058 -10000 0 -0.38 12 12
Gamma Secretase 0.033 0.069 -10000 0 -0.25 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.001 0.095 -10000 0 -0.3 43 43
MAGEH1 -0.019 0.14 -10000 0 -0.52 36 36
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.11 -10000 0 -0.3 65 65
Mammalian IAPs/DIABLO -0.024 0.11 -10000 0 -0.28 76 76
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 -0.008 0.11 -10000 0 -0.48 27 27
APP -0.029 0.14 -10000 0 -0.43 56 56
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.013 0.044 -10000 0 -0.32 8 8
RhoA/GDP/RHOGDI 0.017 0.057 -10000 0 -0.27 16 16
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.006 0.054 0.15 3 -0.26 10 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.026 0.04 -10000 0 -0.23 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.016 0.041 -10000 0 -0.31 4 4
NCSTN 0.017 0.023 -10000 0 -0.52 1 1
mol:GTP -0.016 0.089 -10000 0 -0.31 31 31
PSENEN 0.017 0.012 -10000 0 -0.25 1 1
mol:ceramide 0.014 0.056 -10000 0 -0.29 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.022 0.049 -10000 0 -0.26 1 1
p75(NTR)/beta APP -0.017 0.11 -10000 0 -0.37 39 39
BEX1 -0.039 0.11 -10000 0 -0.26 108 108
mol:GDP 0.002 0.037 -10000 0 -0.32 3 3
NGF (dimer) -0.038 0.13 -10000 0 -0.29 101 101
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.009 0.081 -10000 0 -0.28 23 23
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
RAC1/GTP 0.015 0.032 -10000 0 -0.27 3 3
MYD88 0.013 0.048 -10000 0 -0.47 5 5
CHUK 0.005 0.081 -10000 0 -0.5 13 13
NGF (dimer)/p75(NTR)/PKA -0.016 0.09 -10000 0 -0.31 31 31
RHOB -0.041 0.17 -10000 0 -0.52 58 58
RHOA 0.005 0.08 -10000 0 -0.52 12 12
MAGE-G1/E2F1 0.018 0.051 -10000 0 -0.37 7 7
NT3 (dimer) -0.021 0.11 -10000 0 -0.28 68 68
TP53 -0.001 0.098 -10000 0 -0.37 12 12
PRDM4 0.017 0.049 -10000 0 -0.28 10 10
BDNF (dimer) -0.12 0.2 -10000 0 -0.37 173 173
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
SORT1 0.009 0.065 -10000 0 -0.44 10 10
activation of caspase activity -0.013 0.11 -10000 0 -0.27 78 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.052 -10000 0 -0.28 11 11
RHOC 0.015 0.04 -10000 0 -0.52 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0 0.095 -10000 0 -0.3 16 16
DIABLO 0.018 0 -10000 0 -10000 0 0
SMPD2 0.014 0.056 -10000 0 -0.3 12 12
APH1B 0.001 0.093 -10000 0 -0.51 17 17
APH1A 0.003 0.067 -10000 0 -0.29 25 25
proNGF (dimer)/p75(NTR)/Sortilin 0.011 0.055 -10000 0 -0.31 10 10
PSEN1 0.013 0.052 -10000 0 -0.52 5 5
APAF-1/Pro-Caspase 9 0.022 0.041 -10000 0 -0.37 5 5
NT3 (dimer)/p75(NTR) -0.009 0.09 -10000 0 -0.4 13 13
MAPK8 0.014 0.08 -10000 0 -0.3 6 6
MAPK9 0.005 0.096 -10000 0 -0.37 10 10
APAF1 0.012 0.051 -10000 0 -0.41 7 7
NTF3 -0.021 0.11 -10000 0 -0.28 68 68
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.044 0.17 -10000 0 -0.49 65 65
RAC1/GDP 0.013 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.028 0.12 -10000 0 -0.25 96 96
p75 CTF/Sortilin/TRAF6/NRIF 0.036 0.048 -10000 0 -0.27 10 10
RhoA-B-C/GTP -0.016 0.089 -10000 0 -0.31 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.021 0.07 -10000 0 -0.26 14 14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.015 0.071 -10000 0 -0.29 12 12
PRKACB -0.036 0.14 -10000 0 -0.34 79 79
proBDNF (dimer)/p75 ECD 0.002 0.064 -10000 0 -0.34 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.085 0.19 -10000 0 -0.41 128 128
BIRC2 0.016 0.02 -10000 0 -0.25 3 3
neuron projection morphogenesis -0.033 0.11 0.2 2 -0.35 36 38
BAD 0.008 0.091 -10000 0 -0.31 11 11
RIPK2 0.013 0.04 -10000 0 -0.28 9 9
NGFR 0.004 0.065 -10000 0 -0.29 23 23
CYCS 0.01 0.074 -10000 0 -0.25 34 34
ADAM17 0.016 0.024 -10000 0 -0.25 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.024 0.044 -10000 0 -0.27 6 6
BCL2L11 0.008 0.091 -10000 0 -0.31 11 11
BDNF (dimer)/p75(NTR) -0.006 0.075 -10000 0 -0.4 4 4
PI3K 0.011 0.072 -10000 0 -0.28 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.022 0.05 -10000 0 -0.28 10 10
NDNL2 0.018 0 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.34 3 3
PRKCI 0.002 0.085 -10000 0 -0.43 18 18
NGF (dimer)/p75(NTR) 0.004 0.045 -10000 0 -0.2 23 23
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.008 0.08 -10000 0 -0.28 33 33
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.016 0.033 -10000 0 -0.52 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.005 0.07 -10000 0 -0.29 17 17
SQSTM1 0.012 0.053 -10000 0 -0.48 6 6
NGFRAP1 -0.055 0.18 -10000 0 -0.52 72 72
CASP3 0.01 0.087 -10000 0 -0.29 11 11
E2F1 0.006 0.07 -10000 0 -0.37 16 16
CASP9 0.017 0.023 -10000 0 -0.52 1 1
IKK complex -0.013 0.047 -10000 0 -0.34 3 3
NGF (dimer)/TRKA 0.008 0.037 -10000 0 -0.22 12 12
MMP7 -0.095 0.21 -10000 0 -0.44 129 129
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.028 0.054 -10000 0 -0.25 13 13
MMP3 -0.13 0.22 -10000 0 -0.42 177 177
APAF-1/Caspase 9 -0.046 0.077 -10000 0 -0.31 10 10
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.019 0.27 -9999 0 -0.76 29 29
PCK1 0.019 0.2 -9999 0 -0.88 7 7
HNF4A 0.033 0.27 -9999 0 -0.76 23 23
KCNJ11 -0.015 0.38 -9999 0 -1 49 49
AKT1 0.011 0.17 -9999 0 -0.43 30 30
response to starvation 0.006 0.003 -9999 0 -10000 0 0
DLK1 0.019 0.3 -9999 0 -0.77 30 30
NKX2-1 0.074 0.14 -9999 0 -10000 0 0
ACADM 0.01 0.29 -9999 0 -0.77 36 36
TAT 0.018 0.17 -9999 0 -0.6 3 3
CEBPB 0.01 0.071 -9999 0 -0.33 20 20
CEBPA 0.011 0.085 -9999 0 -0.5 14 14
TTR -0.041 0.28 -9999 0 -0.68 55 55
PKLR 0.022 0.26 -9999 0 -0.72 28 28
APOA1 0.032 0.3 -9999 0 -0.83 25 25
CPT1C 0 0.3 -9999 0 -0.83 37 37
ALAS1 0.039 0.19 -9999 0 -1.6 2 2
TFRC -0.047 0.39 -9999 0 -1.1 47 47
FOXF1 -0.002 0.062 -9999 0 -0.3 19 19
NF1 0.023 0.039 -9999 0 -0.46 3 3
HNF1A (dimer) 0.03 0.047 -9999 0 -0.24 6 6
CPT1A 0.007 0.3 -9999 0 -0.84 33 33
HMGCS1 0.018 0.27 -9999 0 -0.72 30 30
NR3C1 0.007 0.1 -9999 0 -0.5 19 19
CPT1B 0.022 0.26 -9999 0 -0.73 27 27
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.02 0.04 -9999 0 -0.26 7 7
GCK 0.017 0.27 -9999 0 -0.72 32 32
CREB1 0.02 0.036 -9999 0 -0.36 2 2
IGFBP1 0.028 0.16 -9999 0 -0.73 4 4
PDX1 0.035 0.26 -9999 0 -1.1 14 14
UCP2 -0.025 0.35 -9999 0 -0.88 54 54
ALDOB 0.024 0.29 -9999 0 -0.77 29 29
AFP -0.049 0.15 -9999 0 -0.66 6 6
BDH1 0.011 0.28 -9999 0 -0.74 36 36
HADH 0.021 0.3 -9999 0 -0.81 29 29
F2 0.032 0.3 -9999 0 -0.84 23 23
HNF1A 0.03 0.047 -9999 0 -0.24 6 6
G6PC 0.035 0.096 -9999 0 -1.3 1 1
SLC2A2 0.042 0.22 -9999 0 -1 6 6
INS 0.002 0.028 -9999 0 -0.53 1 1
FOXA1 -0.081 0.21 -9999 0 -0.49 108 108
FOXA3 -0.016 0.13 -9999 0 -0.38 31 31
FOXA2 0.032 0.35 -9999 0 -0.82 37 37
ABCC8 -0.2 0.52 -9999 0 -0.91 168 168
ALB -0.055 0.17 -9999 0 -0.76 12 12
Ceramide 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
SPHK2 0.01 0.074 -10000 0 -0.37 18 18
MAP4K4 -0.003 0.11 -10000 0 -0.45 12 12
BAG4 0.002 0.07 -10000 0 -0.28 28 28
PKC zeta/ceramide -0.025 0.04 0.13 8 -0.12 1 9
NFKBIA 0.014 0.042 -10000 0 -0.45 4 4
BIRC3 -0.085 0.19 -10000 0 -0.41 128 128
BAX -0.003 0.022 -10000 0 -10000 0 0
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
AKT1 0.017 0.051 -10000 0 -0.34 9 9
BAD -0.018 0.041 0.15 8 -0.18 1 9
SMPD1 0.008 0.06 -10000 0 -0.24 19 19
RB1 -0.028 0.07 0.15 8 -0.32 20 28
FADD/Caspase 8 0.007 0.1 -10000 0 -0.43 11 11
MAP2K4 -0.043 0.092 0.15 1 -0.28 55 56
NSMAF 0.009 0.065 -10000 0 -0.44 10 10
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.04 0.15 8 -0.18 1 9
EGF -0.14 0.23 -10000 0 -0.42 193 193
mol:ceramide -0.027 0.044 0.15 8 -0.12 1 9
MADD 0.018 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.028 0.13 -10000 0 -0.38 56 56
ASAH1 -0.036 0.15 -10000 0 -0.42 65 65
negative regulation of cell cycle -0.027 0.069 0.15 8 -0.31 20 28
cell proliferation -0.036 0.097 -10000 0 -0.23 83 83
BID -0.013 0.12 -10000 0 -0.55 17 17
MAP3K1 -0.041 0.084 0.15 7 -0.3 38 45
EIF2A -0.013 0.059 -10000 0 -0.26 15 15
TRADD 0.016 0.026 -10000 0 -0.39 2 2
CRADD 0.01 0.063 -10000 0 -0.49 8 8
MAPK3 0.002 0.039 -10000 0 -0.19 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.04 0.16 1 -0.19 1 2
Cathepsin D/ceramide -0.022 0.055 0.14 7 -0.23 11 18
FADD -0.006 0.11 -10000 0 -0.38 19 19
KSR1 -0.017 0.042 0.15 8 -0.2 1 9
MAPK8 -0.03 0.069 0.14 5 -0.2 51 56
PRKRA -0.017 0.042 0.15 8 -10000 0 8
PDGFA -0.003 0.099 -10000 0 -0.44 24 24
TRAF2 0.014 0.042 -10000 0 -0.45 4 4
IGF1 -0.1 0.2 -10000 0 -0.41 146 146
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.026 0.044 0.15 8 -0.12 1 9
CTSD 0.002 0.075 -10000 0 -0.32 24 24
regulation of nitric oxide biosynthetic process 0.026 0.017 -10000 0 -0.37 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.035 0.11 -10000 0 -0.25 81 81
PRKCD 0.014 0.042 -10000 0 -0.45 4 4
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.028 0.13 -10000 0 -0.38 56 56
RelA/NF kappa B1 0.026 0.017 -10000 0 -0.37 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0.091 -10000 0 -0.44 20 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.005 0.11 -10000 0 -0.45 13 13
TNFR1A/BAG4/TNF-alpha 0.012 0.074 -10000 0 -0.31 18 18
mol:Sphingosine-1-phosphate 0.01 0.074 -10000 0 -0.37 18 18
MAP2K1 -0.002 0.039 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.018 0 -10000 0 -10000 0 0
CYCS 0.027 0.065 0.16 76 -10000 0 76
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
TNFR1A/BAG4 0.014 0.054 -10000 0 -0.37 5 5
EIF2AK2 -0.02 0.061 0.15 4 -0.26 18 22
TNF-alpha/TNFR1A/FAN 0.016 0.073 -10000 0 -0.31 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.062 -10000 0 -0.31 1 1
MAP2K2 -0.003 0.043 -10000 0 -0.24 4 4
SMPD3 0.005 0.072 -10000 0 -0.3 14 14
TNF -0.004 0.094 -10000 0 -0.36 31 31
PKC zeta/PAR4 0.001 0.065 -10000 0 -0.32 20 20
mol:PHOSPHOCHOLINE 0.055 0.1 0.22 129 -10000 0 129
NF kappa B1/RelA/I kappa B alpha 0.03 0.055 -10000 0 -0.25 18 18
AIFM1 0.027 0.065 0.16 75 -10000 0 75
BCL2 -0.11 0.22 -10000 0 -0.47 144 144
TCGA08_rtk_signaling

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
PDGFRA -0.017 0.13 -10000 0 -0.48 37 37
HRAS 0.012 0.051 -10000 0 -0.41 7 7
EGFR -0.079 0.18 -10000 0 -0.35 139 139
AKT 0.014 0.079 -10000 0 -0.32 16 16
FOXO3 0.011 0.053 -10000 0 -0.37 9 9
AKT1 0.011 0.053 -10000 0 -0.37 9 9
FOXO1 0 0.092 -10000 0 -0.46 19 19
AKT3 -0.006 0.084 -10000 0 -0.28 43 43
FOXO4 0.017 0.023 -10000 0 -0.52 1 1
MET 0 0.075 -10000 0 -0.29 31 31
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
PIK3CB 0.012 0.055 -10000 0 -0.44 7 7
NRAS 0.005 0.076 -10000 0 -0.4 16 16
PIK3CG -0.007 0.1 -10000 0 -0.41 31 31
PIK3R3 0 0.091 -10000 0 -0.43 21 21
PIK3R2 0.018 0 -10000 0 -10000 0 0
NF1 0.015 0.035 -10000 0 -0.43 3 3
RAS -0.027 0.097 0.21 1 -0.27 47 48
ERBB2 -0.027 0.12 -10000 0 -0.31 72 72
proliferation/survival/translation -0.028 0.057 0.23 10 -0.17 3 13
PI3K -0.019 0.099 0.18 6 -0.23 65 71
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
KRAS 0.009 0.065 -10000 0 -0.44 10 10
FOXO 0.039 0.038 0.18 3 -0.18 2 5
AKT2 0.017 0.012 -10000 0 -0.25 1 1
PTEN -0.002 0.1 -10000 0 -0.52 19 19
PLK1 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
regulation of centriole-centriole cohesion 0.001 0.05 0.26 17 -10000 0 17
BUB1B -0.017 0.12 -10000 0 -0.41 40 40
PLK1 0.002 0.041 -10000 0 -0.12 46 46
PLK1S1 0.002 0.019 -10000 0 -0.053 45 45
KIF2A 0.005 0.054 -10000 0 -0.19 23 23
regulation of mitotic centrosome separation 0.002 0.041 -10000 0 -0.12 46 46
GOLGA2 0.016 0.026 -10000 0 -0.39 2 2
Hec1/SPC24 -0.012 0.094 -10000 0 -0.32 37 37
WEE1 -0.003 0.093 -10000 0 -0.35 25 25
cytokinesis -0.025 0.16 -10000 0 -0.52 44 44
PP2A-alpha B56 -0.059 0.27 -10000 0 -0.76 62 62
AURKA -0.002 0.064 -10000 0 -0.29 22 22
PICH/PLK1 -0.023 0.18 -10000 0 -0.48 53 53
CENPE -0.011 0.096 -10000 0 -0.32 40 40
RhoA/GTP 0.004 0.058 -10000 0 -0.38 12 12
positive regulation of microtubule depolymerization 0.005 0.054 -10000 0 -0.19 23 23
PPP2CA 0.011 0.062 -10000 0 -0.52 7 7
FZR1 0.018 0 -10000 0 -10000 0 0
TPX2 -0.013 0.083 -10000 0 -0.29 40 40
PAK1 -0.023 0.13 -10000 0 -0.38 54 54
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
CLSPN 0.002 0.057 -10000 0 -0.38 10 10
GORASP1 0.017 0.023 -10000 0 -0.52 1 1
metaphase 0 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 -10000 0 -0.053 45 45
G2 phase of mitotic cell cycle -0.001 0.003 0.016 1 -0.013 21 22
STAG2 0.017 0.023 -10000 0 -0.52 1 1
GRASP65/GM130/RAB1/GTP 0.021 0.04 -10000 0 -0.74 1 1
spindle elongation 0.002 0.041 -10000 0 -0.12 46 46
ODF2 0.016 0.024 -10000 0 -0.53 1 1
BUB1 -0.1 0.28 -10000 0 -0.85 60 60
TPT1 0.009 0.019 -10000 0 -10000 0 0
CDC25C -0.016 0.11 -10000 0 -0.43 35 35
CDC25B 0.004 0.069 -10000 0 -0.3 23 23
SGOL1 -0.001 0.051 -10000 0 -0.26 17 17
RHOA 0.005 0.08 -10000 0 -0.52 12 12
CCNB1/CDK1 -0.013 0.15 -10000 0 -0.48 42 42
CDC14B 0.01 0.03 -10000 0 -0.38 3 3
CDC20 -0.02 0.12 -10000 0 -0.37 51 51
PLK1/PBIP1 -0.011 0.083 -10000 0 -0.24 49 49
mitosis 0.002 0.007 0.035 21 -10000 0 21
FBXO5 0.003 0.054 -10000 0 -0.19 20 20
CDC2 -0.012 0.12 -10000 0 -0.45 34 34
NDC80 -0.029 0.14 -10000 0 -0.41 57 57
metaphase plate congression 0.009 0.023 -10000 0 -10000 0 0
ERCC6L -0.026 0.19 -10000 0 -0.57 46 46
NLP/gamma Tubulin 0.005 0.022 -10000 0 -0.075 5 5
microtubule cytoskeleton organization 0.009 0.019 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.002 0.01 22 -10000 0 22
PPP1R12A 0.015 0.031 -10000 0 -0.32 4 4
interphase 0 0.002 0.01 22 -10000 0 22
PLK1/PRC1-2 -0.017 0.14 -10000 0 -0.42 48 48
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.039 -10000 0 -0.22 3 3
RAB1A 0.017 0.023 -10000 0 -0.52 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.039 -10000 0 -0.14 22 22
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.058 -10000 0 -0.29 8 8
microtubule-based process -0.011 0.1 -10000 0 -0.34 41 41
Golgi organization 0.002 0.041 -10000 0 -0.12 46 46
Cohesin/SA2 0.009 0.036 -10000 0 -0.17 4 4
PPP1CB/MYPT1 0.023 0.026 -10000 0 -0.37 1 1
KIF20A -0.027 0.14 -10000 0 -0.46 49 49
APC/C/CDC20 -0.007 0.089 -10000 0 -0.31 32 32
PPP2R1A 0.017 0.012 -10000 0 -0.25 1 1
chromosome segregation -0.011 0.082 -10000 0 -0.24 49 49
PRC1 -0.019 0.13 -10000 0 -0.43 43 43
ECT2 -0.001 0.07 -10000 0 -0.24 29 29
C13orf34 0.006 0.037 -10000 0 -0.13 21 21
NUDC 0.009 0.023 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.016 0.12 -10000 0 -0.4 40 40
spindle assembly 0.005 0.031 -10000 0 -0.086 41 41
spindle stabilization 0.002 0.019 -10000 0 -0.052 45 45
APC/C/HCDH1 0.02 0.025 -10000 0 -0.32 3 3
MKLP2/PLK1 -0.011 0.1 -10000 0 -0.34 41 41
CCNB1 -0.016 0.13 -10000 0 -0.5 35 35
PPP1CB 0.016 0.02 -10000 0 -0.25 3 3
BTRC 0.008 0.054 -10000 0 -0.29 16 16
ROCK2 0.008 0.055 -10000 0 -0.24 16 16
TUBG1 0.008 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.046 0.14 -10000 0 -0.48 40 40
MLF1IP -0.018 0.1 -10000 0 -0.32 49 49
INCENP 0.001 0.081 -10000 0 -0.37 22 22
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.003 0.062 -9999 0 -1.2 1 1
VDR -0.003 0.1 -9999 0 -0.51 21 21
FAM120B 0.016 0.033 -9999 0 -0.52 2 2
RXRs/LXRs/DNA/9cRA 0.012 0.13 -9999 0 -0.41 22 22
RXRs/LXRs/DNA/Oxysterols -0.001 0.18 -9999 0 -0.44 68 68
MED1 0 0.067 -9999 0 -0.25 34 34
mol:9cRA -0.001 0.021 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.003 0.11 -9999 0 -0.43 16 16
RXRs/NUR77 0.031 0.076 -9999 0 -0.28 19 19
RXRs/PPAR 0.008 0.093 -9999 0 -0.33 19 19
NCOR2 0.018 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.075 -9999 0 -0.37 21 21
RARs/VDR/DNA/Vit D3 0.004 0.095 -9999 0 -0.27 47 47
RARA 0.011 0.057 -9999 0 -0.4 9 9
NCOA1 0.012 0.057 -9999 0 -0.52 6 6
VDR/VDR/DNA -0.003 0.1 -9999 0 -0.51 21 21
RARs/RARs/DNA/9cRA 0.005 0.077 -9999 0 -0.27 29 29
RARG 0.017 0.023 -9999 0 -0.52 1 1
RPS6KB1 0.004 0.055 -9999 0 -0.4 1 1
RARs/THRs/DNA/SMRT 0 0.1 -9999 0 -0.27 57 57
THRA -0.01 0.11 -9999 0 -0.38 37 37
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.075 -9999 0 -0.37 21 21
RXRs/PPAR/9cRA/PGJ2/DNA 0.022 0.084 -9999 0 -0.29 18 18
NR1H4 0.015 0.031 -9999 0 -0.32 4 4
RXRs/LXRs/DNA 0.037 0.11 -9999 0 -0.42 10 10
NR1H2 0.018 0.017 -9999 0 -10000 0 0
NR1H3 0.008 0.07 -9999 0 -0.44 11 11
RXRs/VDR/DNA/Vit D3 0.021 0.088 -9999 0 -0.27 37 37
NR4A1 0.01 0.049 -9999 0 -0.27 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.063 -9999 0 -0.26 9 9
RXRG 0.004 0.084 -9999 0 -0.47 15 15
RXR alpha/CCPG 0.023 0.041 -9999 0 -0.38 5 5
RXRA 0.014 0.045 -9999 0 -0.54 3 3
RXRB 0.014 0.045 -9999 0 -0.52 3 3
THRB -0.001 0.097 -9999 0 -0.48 20 20
PPARG -0.036 0.14 -9999 0 -0.33 81 81
PPARD 0.017 0.017 -9999 0 -0.25 2 2
TNF -0.01 0.23 -9999 0 -0.8 28 28
mol:Oxysterols 0 0.018 -9999 0 -10000 0 0
cholesterol transport 0 0.18 -9999 0 -0.43 68 68
PPARA 0.012 0.047 -9999 0 -0.31 10 10
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.025 0.13 -9999 0 -0.36 60 60
RXRs/NUR77/BCL2 -0.04 0.12 -9999 0 -0.24 130 130
SREBF1 -0.052 0.33 -9999 0 -1 51 51
RXRs/RXRs/DNA/9cRA 0.022 0.084 -9999 0 -0.29 18 18
ABCA1 -0.01 0.24 -9999 0 -0.84 28 28
RARs/THRs 0.001 0.12 -9999 0 -0.29 57 57
RXRs/FXR 0.034 0.074 -9999 0 -0.28 20 20
BCL2 -0.11 0.22 -9999 0 -0.47 144 144
Regulation of Androgen receptor activity

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
HDAC1 0.025 0.017 -9999 0 -0.37 1 1
SMARCC1 -0.003 0.12 -9999 0 -1.3 4 4
REL 0 0.087 -9999 0 -0.41 21 21
HDAC7 -0.025 0.13 -9999 0 -0.39 30 30
JUN -0.033 0.15 -9999 0 -0.46 57 57
EP300 0.014 0.047 -9999 0 -0.52 4 4
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.002 0.084 -9999 0 -0.38 20 20
FOXO1 0.001 0.092 -9999 0 -0.46 19 19
T-DHT/AR -0.019 0.15 -9999 0 -0.41 30 30
MAP2K6 -0.013 0.11 -9999 0 -0.4 37 37
BRM/BAF57 0.026 0.028 -9999 0 -0.37 2 2
MAP2K4 -0.007 0.1 -9999 0 -0.39 31 31
SMARCA2 0.016 0.033 -9999 0 -0.52 2 2
PDE9A -0.026 0.16 -9999 0 -0.71 14 14
NCOA2 0.01 0.063 -9999 0 -0.4 11 11
CEBPA 0.004 0.084 -9999 0 -0.5 14 14
EHMT2 0.018 0.001 -9999 0 -10000 0 0
cell proliferation 0.007 0.13 -9999 0 -0.37 20 20
NR0B1 -0.01 0.087 -9999 0 -0.27 51 51
EGR1 -0.1 0.2 -9999 0 -0.39 156 156
RXRs/9cRA 0.025 0.057 -9999 0 -0.28 18 18
AR/RACK1/Src 0.003 0.1 -9999 0 -0.34 20 20
AR/GR -0.038 0.13 -9999 0 -0.29 73 73
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
PKN1 0.013 0.045 -9999 0 -0.39 6 6
RCHY1 0.002 0.09 -9999 0 -0.5 16 16
epidermal growth factor receptor activity 0 0.001 -9999 0 -0.005 6 6
MAPK8 0.004 0.08 -9999 0 -0.38 18 18
T-DHT/AR/TIF2/CARM1 0 0.11 -9999 0 -0.36 22 22
SRC 0.005 0.09 -9999 0 -0.32 18 18
NR3C1 -0.001 0.098 -9999 0 -0.51 19 19
KLK3 -0.038 0.11 -9999 0 -0.49 2 2
APPBP2 0.009 0.042 -9999 0 -0.25 13 13
TRIM24 0.017 0.024 -9999 0 -0.25 4 4
T-DHT/AR/TIP60 -0.021 0.1 -9999 0 -0.31 42 42
TMPRSS2 -0.18 0.43 -9999 0 -1.1 95 95
RXRG 0.004 0.083 -9999 0 -0.47 15 15
mol:9cRA 0 0 -9999 0 -0.003 2 2
RXRA 0.015 0.04 -9999 0 -0.52 3 3
RXRB 0.015 0.04 -9999 0 -0.52 3 3
CARM1 0.015 0.039 -9999 0 -0.36 5 5
NR2C2 0.016 0.02 -9999 0 -0.25 3 3
KLK2 0.021 0.095 -9999 0 -0.4 4 4
AR -0.04 0.13 -9999 0 -0.28 104 104
SENP1 0.018 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
MDM2 0.009 0.044 -9999 0 -0.26 14 14
SRY 0.001 0.085 -9999 0 -0.43 18 18
GATA2 -0.007 0.093 -9999 0 -0.31 40 40
MYST2 0.011 0.047 -9999 0 -0.31 10 10
HOXB13 -0.074 0.13 -9999 0 -0.25 182 182
T-DHT/AR/RACK1/Src -0.002 0.11 -9999 0 -0.35 20 20
positive regulation of transcription -0.007 0.093 -9999 0 -0.31 40 40
DNAJA1 0.012 0.043 -9999 0 -0.46 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.06 -9999 0 -0.31 16 16
NCOA1 0.016 0.063 -9999 0 -0.55 6 6
SPDEF -0.081 0.21 -9999 0 -0.52 98 98
T-DHT/AR/TIF2 0.009 0.08 -9999 0 -0.3 11 11
T-DHT/AR/Hsp90 -0.012 0.11 -9999 0 -0.36 21 21
GSK3B 0.018 0.003 -9999 0 -10000 0 0
NR2C1 0.01 0.062 -9999 0 -0.52 7 7
mol:T-DHT -0.002 0.095 -9999 0 -0.3 36 36
SIRT1 0.016 0.029 -9999 0 -0.34 3 3
ZMIZ2 0.016 0.002 -9999 0 -10000 0 0
POU2F1 0.014 0.038 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.022 0.12 -9999 0 -0.36 26 26
CREBBP 0.016 0.033 -9999 0 -0.52 2 2
SMARCE1 0.017 0.021 -9999 0 -0.26 3 3
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.017 0.023 -9999 0 -0.52 1 1
SPHK1 -0.027 0.14 -9999 0 -0.42 54 54
GNAI2 0.006 0.075 -9999 0 -0.48 12 12
mol:S1P -0.001 0.087 -9999 0 -0.3 35 35
GNAO1 0.016 0.024 -9999 0 -0.25 4 4
mol:Sphinganine-1-P -0.007 0.1 -9999 0 -0.38 33 33
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.015 0.075 -9999 0 -0.39 8 8
GNAI3 0.018 0 -9999 0 -10000 0 0
G12/G13 0.021 0.039 -9999 0 -0.37 4 4
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.019 0.12 -9999 0 -0.4 46 46
S1P1/S1P -0.012 0.11 -9999 0 -0.29 57 57
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.017 0.12 -9999 0 -0.38 46 46
S1P/S1P5/G12 0.008 0.07 -9999 0 -0.23 35 35
S1P/S1P3/Gq -0.026 0.11 -9999 0 -0.28 61 61
S1P/S1P4/Gi 0.006 0.087 -9999 0 -0.36 14 14
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.088 -9999 0 -0.44 19 19
GNA14 -0.079 0.18 -9999 0 -0.35 140 140
GNA15 0.002 0.076 -9999 0 -0.34 23 23
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.011 0.055 -9999 0 -0.36 10 10
GNA11 0.014 0.047 -9999 0 -0.52 4 4
ABCC1 0.012 0.051 -9999 0 -0.41 7 7
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0 0.1 -9999 0 -0.36 30 30
PDGFRB 0.01 0.067 -9999 0 -0.53 8 8
SPHK1 -0.054 0.19 -9999 0 -0.76 33 33
mol:S1P -0.049 0.17 -9999 0 -0.65 35 35
S1P1/S1P/Gi -0.002 0.15 -9999 0 -0.52 22 22
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
PDGFB-D/PDGFRB/PLCgamma1 0.008 0.14 -9999 0 -0.51 19 19
PLCG1 0.004 0.14 -9999 0 -0.49 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.067 -9999 0 -0.53 8 8
GNAI2 0.007 0.076 -9999 0 -0.48 12 12
GNAI3 0.018 0.003 -9999 0 -10000 0 0
GNAI1 -0.016 0.12 -9999 0 -0.38 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.012 0.16 -9999 0 -0.6 30 30
S1P1/S1P -0.026 0.19 -9999 0 -0.51 56 56
negative regulation of cAMP metabolic process -0.001 0.14 -9999 0 -0.5 22 22
MAPK3 0.002 0.16 -9999 0 -0.54 21 21
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
KDR 0.006 0.076 -9999 0 -0.65 5 5
PLCB2 -0.015 0.17 -9999 0 -0.45 55 55
RAC1 0.018 0 -9999 0 -10000 0 0
RhoA/GTP -0.061 0.14 -9999 0 -0.42 58 58
receptor internalization -0.024 0.17 -9999 0 -0.47 56 56
PTGS2 -0.001 0.17 -9999 0 -0.77 12 12
Rac1/GTP -0.056 0.14 -9999 0 -0.42 55 55
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VEGFA -0.006 0.085 -9999 0 -0.29 31 31
negative regulation of T cell proliferation -0.001 0.14 -9999 0 -0.5 22 22
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.088 -9999 0 -0.44 19 19
MAPK1 0.002 0.16 -9999 0 -0.54 21 21
S1P1/S1P/PDGFB-D/PDGFRB -0.016 0.2 -9999 0 -0.5 56 56
ABCC1 0.012 0.051 -9999 0 -0.41 7 7
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.041 0.17 -10000 0 -0.9 12 12
NCK1/PAK1/Dok-R -0.032 0.083 -10000 0 -0.43 13 13
NCK1/Dok-R 0.029 0.18 -10000 0 -1.1 11 11
PIK3CA 0.015 0.029 -10000 0 -0.34 3 3
mol:beta2-estradiol -0.009 0.02 0.24 1 -10000 0 1
RELA 0.018 0 -10000 0 -10000 0 0
SHC1 0.017 0.024 -10000 0 -0.52 1 1
Rac/GDP 0.013 0 -10000 0 -10000 0 0
F2 0.006 0.021 0.26 1 -10000 0 1
TNIP2 0.012 0.052 -10000 0 -0.39 8 8
NF kappa B/RelA 0.052 0.15 -10000 0 -0.9 11 11
FN1 -0.048 0.17 -10000 0 -0.46 73 73
PLD2 0.037 0.16 -10000 0 -1 11 11
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
GRB14 -0.16 0.21 -10000 0 -0.36 247 247
ELK1 0.046 0.15 -10000 0 -0.92 11 11
GRB7 -0.017 0.1 -10000 0 -0.29 59 59
PAK1 -0.022 0.13 -10000 0 -0.37 54 54
Tie2/Ang1/alpha5/beta1 Integrin 0.022 0.19 -10000 0 -0.98 12 12
CDKN1A 0.02 0.2 -10000 0 -0.76 28 28
ITGA5 0.015 0.035 -10000 0 -0.43 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.026 0.18 -10000 0 -1 12 12
CRK 0.016 0.033 -10000 0 -0.52 2 2
mol:NO 0.05 0.14 -10000 0 -0.66 12 12
PLG 0.039 0.16 -10000 0 -1 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.048 0.16 -10000 0 -0.87 11 11
GRB2 0.016 0.024 -10000 0 -0.25 4 4
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
ANGPT2 -0.018 0.16 -10000 0 -0.82 8 8
BMX 0.012 0.19 -10000 0 -1.2 11 11
ANGPT1 0.021 0.085 -10000 0 -1.2 1 1
tube development 0.026 0.17 -10000 0 -0.71 18 18
ANGPT4 0.017 0.026 -10000 0 -0.39 2 2
response to hypoxia 0.003 0.011 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.045 0.19 -10000 0 -1.1 11 11
alpha5/beta1 Integrin 0.022 0.041 -10000 0 -0.37 5 5
FGF2 -0.065 0.16 -10000 0 -0.34 122 122
STAT5A (dimer) 0.026 0.21 -10000 0 -0.78 26 26
mol:L-citrulline 0.05 0.14 -10000 0 -0.66 12 12
AGTR1 -0.15 0.21 -10000 0 -0.36 231 231
MAPK14 0.035 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.027 0.16 -10000 0 -1 11 11
TEK 0.024 0.18 -10000 0 -0.94 14 14
RPS6KB1 0.04 0.16 -10000 0 -0.88 11 11
Angiotensin II/AT1 -0.099 0.15 -10000 0 -0.25 231 231
Tie2/Ang1/GRB2 0.04 0.16 -10000 0 -1 11 11
MAPK3 0.043 0.15 -10000 0 -0.92 11 11
MAPK1 0.042 0.15 -10000 0 -0.92 11 11
Tie2/Ang1/GRB7 0.025 0.17 -10000 0 -1 11 11
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MAPK8 0.038 0.16 -10000 0 -1 11 11
PI3K 0.035 0.19 -10000 0 -1.1 11 11
FES 0.031 0.19 -10000 0 -1.1 12 12
Crk/Dok-R 0.031 0.18 -10000 0 -1 11 11
Tie2/Ang1/ABIN2 0.038 0.16 -10000 0 -1 11 11
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.043 0.16 -10000 0 -0.8 12 12
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.043 0.16 -10000 0 -0.88 11 11
Tie2/Ang2 0.015 0.22 -10000 0 -1 16 16
Tie2/Ang1 0.034 0.17 -10000 0 -1.1 11 11
FOXO1 0.043 0.17 -10000 0 -0.77 16 16
ELF1 0.017 0.073 -10000 0 -0.49 10 10
ELF2 0.037 0.16 -10000 0 -1 11 11
mol:Choline 0.038 0.16 -10000 0 -0.96 11 11
cell migration -0.023 0.051 -10000 0 -0.22 20 20
FYN 0.023 0.19 -10000 0 -0.83 17 17
DOK2 -0.021 0.13 -10000 0 -0.4 48 48
negative regulation of cell cycle 0.024 0.18 -10000 0 -0.67 28 28
ETS1 0.011 0.075 -10000 0 -0.3 24 24
PXN 0.05 0.14 -10000 0 -0.72 11 11
ITGB1 0.014 0.044 -10000 0 -0.41 5 5
NOS3 0.049 0.15 -10000 0 -0.75 12 12
RAC1 0.018 0 -10000 0 -10000 0 0
TNF 0.004 0.097 -10000 0 -0.35 32 32
MAPKKK cascade 0.038 0.16 -10000 0 -0.96 11 11
RASA1 0.004 0.078 -10000 0 -0.42 16 16
Tie2/Ang1/Shc 0.041 0.16 -10000 0 -1 11 11
NCK1 0.011 0.045 -10000 0 -0.28 12 12
vasculogenesis 0.051 0.13 -10000 0 -0.59 12 12
mol:Phosphatidic acid 0.038 0.16 -10000 0 -0.96 11 11
mol:Angiotensin II 0.002 0.002 -10000 0 -10000 0 0
mol:NADP 0.05 0.14 -10000 0 -0.66 12 12
Rac1/GTP -0.011 0.14 -10000 0 -0.82 11 11
MMP2 0.016 0.19 -10000 0 -1.1 11 11
ErbB2/ErbB3 signaling events

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
USP8 0.015 0.034 -10000 0 -0.32 4 4
RAS family/GTP 0.002 0.099 -10000 0 -0.31 28 28
NFATC4 0.007 0.079 -10000 0 -0.32 11 11
ERBB2IP 0.017 0.023 -10000 0 -0.52 1 1
HSP90 (dimer) 0.013 0.045 -10000 0 -0.39 6 6
mammary gland morphogenesis -0.01 0.094 -10000 0 -0.28 38 38
JUN 0.02 0.072 -10000 0 -10000 0 0
HRAS 0.012 0.051 -10000 0 -0.41 7 7
DOCK7 -0.002 0.092 -10000 0 -0.37 11 11
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.013 0.1 -10000 0 -0.3 48 48
AKT1 0.008 0.038 -10000 0 -0.26 9 9
BAD 0.016 0.035 -10000 0 -0.31 5 5
MAPK10 0.003 0.069 -10000 0 -0.21 22 22
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.01 0.1 -10000 0 -0.3 38 38
RAF1 0.006 0.1 -10000 0 -0.32 25 25
ErbB2/ErbB3/neuregulin 2 -0.037 0.12 -10000 0 -0.34 57 57
STAT3 0.016 0.095 -10000 0 -0.95 5 5
cell migration 0.009 0.07 -10000 0 -0.21 16 16
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.045 0.24 -10000 0 -0.6 59 59
FOS -0.059 0.22 -10000 0 -0.45 105 105
NRAS 0.005 0.076 -10000 0 -0.4 16 16
mol:Ca2+ -0.01 0.094 -10000 0 -0.28 38 38
MAPK3 -0.021 0.19 -10000 0 -0.47 54 54
MAPK1 -0.021 0.19 -10000 0 -0.46 57 57
JAK2 -0.004 0.096 -10000 0 -0.32 24 24
NF2 0.003 0.01 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.001 0.082 -10000 0 -0.27 39 39
NRG1 0.007 0.053 -10000 0 -0.27 18 18
GRB2/SOS1 0.024 0.023 -10000 0 -0.37 1 1
MAPK8 -0.001 0.089 -10000 0 -0.26 40 40
MAPK9 0.008 0.067 -10000 0 -0.22 17 17
ERBB2 -0.03 0.082 -10000 0 -0.22 71 71
ERBB3 -0.019 0.14 -10000 0 -0.52 36 36
SHC1 0.016 0.023 -10000 0 -0.52 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
apoptosis -0.01 0.041 0.35 5 -10000 0 5
STAT3 (dimer) 0.016 0.093 -10000 0 -0.93 5 5
RNF41 0.02 0.031 -10000 0 -0.28 4 4
FRAP1 0.016 0.032 -10000 0 -0.31 4 4
RAC1-CDC42/GTP -0.022 0.055 -10000 0 -0.27 10 10
ErbB2/ErbB2/HSP90 (dimer) -0.015 0.074 -10000 0 -0.32 18 18
CHRNA1 -0.008 0.16 -10000 0 -0.4 50 50
myelination 0.014 0.079 -10000 0 -0.32 11 11
PPP3CB -0.001 0.086 -10000 0 -0.37 9 9
KRAS 0.009 0.065 -10000 0 -0.44 10 10
RAC1-CDC42/GDP 0.021 0.074 -10000 0 -0.29 10 10
NRG2 -0.017 0.1 -10000 0 -0.3 57 57
mol:GDP 0.001 0.082 -10000 0 -0.27 39 39
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MAP2K2 0.006 0.11 -10000 0 -0.33 25 25
SRC 0.015 0.035 -10000 0 -0.43 3 3
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0 0.091 -10000 0 -0.29 22 22
MAP2K1 -0.024 0.17 -10000 0 -0.52 17 17
heart morphogenesis -0.01 0.094 -10000 0 -0.28 38 38
RAS family/GDP 0.013 0.099 -10000 0 -0.3 27 27
GRB2 0.015 0.024 -10000 0 -0.25 4 4
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.016 0.019 -10000 0 -10000 0 0
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
activation of caspase activity -0.008 0.038 0.26 9 -10000 0 9
nervous system development -0.01 0.094 -10000 0 -0.28 38 38
CDC42 0.018 0 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0.015 0.035 -10000 0 -0.43 3 3
MKNK1 0.018 0 -10000 0 -10000 0 0
mol:PIP3 -0.037 0.11 0.25 10 -0.28 70 80
FRAP1 0.015 0.034 -10000 0 -10000 0 0
AKT1 -0.011 0.1 0.22 8 -0.25 70 78
INSR 0.015 0.037 -10000 0 -0.39 4 4
Insulin Receptor/Insulin 0.021 0.027 -10000 0 -0.31 3 3
mol:GTP 0.004 0.085 -10000 0 -0.3 14 14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.01 0.027 -10000 0 -0.18 1 1
TSC2 0.016 0.026 -10000 0 -0.39 2 2
RHEB/GDP -0.026 0.062 -10000 0 -0.27 14 14
TSC1 0.018 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.022 0.12 -10000 0 -0.33 62 62
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.011 0.031 -10000 0 -0.19 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.017 0.012 -10000 0 -0.25 1 1
RPS6KB1 0.01 0.065 -10000 0 -0.26 5 5
MAP3K5 -0.014 0.089 -10000 0 -0.28 47 47
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
apoptosis -0.014 0.089 -10000 0 -0.28 47 47
mol:LY294002 0 0.001 0.001 1 -0.001 57 58
EIF4B 0.016 0.062 -10000 0 -0.24 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.02 0.057 -10000 0 -0.26 2 2
eIF4E/eIF4G1/eIF4A1 -0.002 0.014 -10000 0 -10000 0 0
KIAA1303 0.015 0.031 -10000 0 -0.32 4 4
PI3K -0.02 0.12 -10000 0 -0.3 79 79
mTOR/RHEB/GTP/Raptor/GBL 0.032 0.054 0.18 8 -0.3 2 10
FKBP1A 0.017 0.017 -10000 0 -0.25 2 2
RHEB/GTP 0.009 0.076 -10000 0 -0.27 14 14
mol:Amino Acids 0 0.001 0.001 1 -0.001 57 58
FKBP12/Rapamycin 0.012 0.011 -10000 0 -0.17 2 2
PDPK1 -0.014 0.1 0.23 8 -0.26 70 78
EIF4E 0.018 0 -10000 0 -10000 0 0
ASK1/PP5C -0.011 0.15 -10000 0 -0.59 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.035 0.056 -10000 0 -0.56 4 4
TSC1/TSC2 0.009 0.095 0.22 8 -0.32 14 22
tumor necrosis factor receptor activity 0 0.001 0.001 57 -0.001 1 58
RPS6 0.015 0.037 -10000 0 -0.39 4 4
PPP5C 0.012 0.052 -10000 0 -0.39 8 8
EIF4G1 0.014 0.047 -10000 0 -0.52 4 4
IRS1 -0.034 0.12 -10000 0 -0.36 61 61
INS 0.017 0.023 -10000 0 -0.52 1 1
PTEN -0.002 0.1 -10000 0 -0.52 19 19
PDK2 -0.02 0.11 0.23 8 -0.27 76 84
EIF4EBP1 -0.012 0.16 -10000 0 -1.1 10 10
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
PPP2R5D 0.021 0.033 -10000 0 -10000 0 0
peptide biosynthetic process 0.025 0.03 -10000 0 -0.28 5 5
RHEB 0.016 0.026 -10000 0 -0.39 2 2
EIF4A1 0.018 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 15 -0.002 7 22
EEF2 0.025 0.031 -10000 0 -0.28 5 5
eIF4E/4E-BP1 -0.001 0.14 -10000 0 -1 10 10
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.009 0.14 -9999 0 -0.38 56 56
VEGFR1 homodimer/NRP1 -0.021 0.14 -9999 0 -0.39 56 56
mol:DAG -0.004 0.14 -9999 0 -0.61 14 14
VEGFR1 homodimer/NRP1/VEGFR 121 -0.017 0.14 -9999 0 -0.35 59 59
CaM/Ca2+ 0.006 0.13 -9999 0 -0.63 12 12
HIF1A -0.035 0.17 -9999 0 -0.46 67 67
GAB1 0.006 0.074 -9999 0 -0.43 14 14
AKT1 -0.001 0.14 -9999 0 -0.54 19 19
PLCG1 -0.004 0.14 -9999 0 -0.62 14 14
NOS3 0.018 0.12 -9999 0 -0.54 14 14
CBL 0.017 0.012 -9999 0 -0.25 1 1
mol:NO 0.019 0.12 -9999 0 -0.52 14 14
FLT1 -0.021 0.16 -9999 0 -0.45 56 56
PGF 0.012 0.051 -9999 0 -0.41 7 7
VEGFR1 homodimer/NRP2/VEGFR121 -0.01 0.14 -9999 0 -0.64 15 15
CALM1 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
eNOS/Hsp90 0.026 0.12 -9999 0 -0.5 14 14
endothelial cell proliferation 0 0.13 -9999 0 -0.6 14 14
mol:Ca2+ -0.004 0.13 -9999 0 -0.61 14 14
MAPK3 0.007 0.12 -9999 0 -0.57 13 13
MAPK1 0.007 0.12 -9999 0 -0.58 12 12
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
PLGF homodimer 0.012 0.051 -9999 0 -0.41 7 7
PRKACA 0.018 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.001 0.083 -9999 0 -0.33 29 29
VEGFA homodimer 0 0.075 -9999 0 -0.29 31 31
VEGFR1 homodimer/VEGFA homodimer -0.019 0.15 -9999 0 -0.38 59 59
platelet activating factor biosynthetic process 0.012 0.12 -9999 0 -0.55 13 13
PI3K -0.004 0.15 -9999 0 -0.59 17 17
PRKCA 0.001 0.13 -9999 0 -0.61 12 12
PRKCB -0.005 0.13 -9999 0 -0.57 14 14
VEGFR1 homodimer/PLGF homodimer -0.012 0.15 -9999 0 -0.38 59 59
VEGFA 0 0.075 -9999 0 -0.29 31 31
VEGFB 0.017 0.023 -9999 0 -0.52 1 1
mol:IP3 -0.004 0.14 -9999 0 -0.61 14 14
RASA1 -0.008 0.14 -9999 0 -0.62 15 15
NRP2 0.011 0.052 -9999 0 -0.33 11 11
VEGFR1 homodimer -0.021 0.16 -9999 0 -0.45 56 56
VEGFB homodimer 0.017 0.023 -9999 0 -0.52 1 1
NCK1 0.011 0.045 -9999 0 -0.28 12 12
eNOS/Caveolin-1 0.02 0.13 -9999 0 -0.53 16 16
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
mol:PI-3-4-5-P3 -0.005 0.14 -9999 0 -0.58 17 17
mol:L-citrulline 0.019 0.12 -9999 0 -0.52 14 14
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.004 0.13 -9999 0 -0.6 14 14
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.009 0.14 -9999 0 -0.65 14 14
CD2AP 0.016 0.029 -9999 0 -0.34 3 3
PI3K/GAB1 -0.001 0.14 -9999 0 -0.56 17 17
PDPK1 -0.003 0.13 -9999 0 -0.56 16 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.14 -9999 0 -0.63 14 14
mol:NADP 0.019 0.12 -9999 0 -0.52 14 14
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
ubiquitin-dependent protein catabolic process 0.003 0.13 -9999 0 -0.59 14 14
VEGFR1 homodimer/NRP2 -0.013 0.15 -9999 0 -0.39 57 57
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.008 0.081 -9999 0 -0.3 22 22
BIRC5 -0.037 0.15 -9999 0 -0.41 67 67
NFKBIA 0.024 0.054 -9999 0 -0.33 3 3
CPEB1 0.003 0.071 -9999 0 -0.31 23 23
AKT1 0.022 0.057 -9999 0 -0.3 4 4
NDEL1 0.018 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.013 0.067 -9999 0 -0.28 16 16
NDEL1/TACC3 0.021 0.079 -9999 0 -0.36 16 16
GADD45A -0.011 0.11 -9999 0 -0.39 38 38
GSK3B 0.021 0.015 -9999 0 -10000 0 0
PAK1/Aurora A 0.002 0.087 -9999 0 -0.3 25 25
MDM2 0.011 0.044 -9999 0 -0.25 14 14
JUB -0.027 0.15 -9999 0 -0.49 47 47
TPX2 -0.009 0.11 -9999 0 -0.37 40 40
TP53 0.004 0.089 -9999 0 -0.29 37 37
DLG7 -0.005 0.11 -9999 0 -0.35 43 43
AURKAIP1 0.016 0.029 -9999 0 -0.34 3 3
ARHGEF7 0.016 0.02 -9999 0 -0.25 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.022 0.083 -9999 0 -0.38 16 16
G2/M transition of mitotic cell cycle 0.013 0.066 -9999 0 -0.28 16 16
AURKA 0.021 0.058 -9999 0 -0.23 3 3
AURKB -0.007 0.078 -9999 0 -0.22 46 46
CDC25B 0.011 0.069 -9999 0 -0.37 5 5
G2/M transition checkpoint -0.002 0.088 -9999 0 -0.27 41 41
mRNA polyadenylation 0.015 0.054 -9999 0 -0.26 6 6
Aurora A/CPEB 0.016 0.055 -9999 0 -0.26 6 6
Aurora A/TACC1/TRAP/chTOG 0.016 0.093 -9999 0 -0.27 34 34
BRCA1 0 0.094 -9999 0 -0.48 19 19
centrosome duplication 0.002 0.087 -9999 0 -0.3 25 25
regulation of centrosome cycle 0.02 0.078 -9999 0 -0.35 16 16
spindle assembly 0.015 0.092 -9999 0 -0.27 34 34
TDRD7 0.004 0.084 -9999 0 -0.5 14 14
Aurora A/RasGAP/Survivin -0.001 0.12 -9999 0 -0.3 57 57
CENPA -0.016 0.12 -9999 0 -0.36 46 46
Aurora A/PP2A 0.025 0.047 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.008 0.088 -9999 0 -0.34 20 20
negative regulation of DNA binding 0.004 0.089 -9999 0 -0.29 37 37
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.023 0.028 -9999 0 -0.37 1 1
RASA1 0.004 0.078 -9999 0 -0.42 16 16
Ajuba/Aurora A -0.002 0.089 -9999 0 -0.27 41 41
mitotic prometaphase -0.001 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.058 -9999 0 -0.23 3 3
TACC1 -0.022 0.13 -9999 0 -0.41 49 49
TACC3 -0.006 0.11 -9999 0 -0.47 26 26
Aurora A/Antizyme1 0.034 0.044 -9999 0 -0.27 1 1
Aurora A/RasGAP 0.018 0.066 -9999 0 -0.3 11 11
OAZ1 0.018 0 -9999 0 -10000 0 0
RAN 0.017 0.012 -9999 0 -0.25 1 1
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.021 0.015 -9999 0 -10000 0 0
GIT1 0.014 0.035 -9999 0 -0.3 6 6
GIT1/beta-PIX/PAK1 0.009 0.084 -9999 0 -0.32 24 24
Importin alpha/Importin beta/TPX2 -0.009 0.11 -9999 0 -0.37 40 40
PPP2R5D 0.016 0.02 -9999 0 -0.25 3 3
Aurora A/TPX2 0.006 0.1 -9999 0 -0.4 26 26
PAK1 -0.022 0.13 -9999 0 -0.37 54 54
CKAP5 0.017 0.017 -9999 0 -0.25 2 2
Arf6 downstream pathway

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

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

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 -0.022 0.26 -10000 0 -1.1 30 30
regulation of axonogenesis -0.012 0.065 0.35 8 -10000 0 8
myoblast fusion 0.003 0.1 0.4 31 -10000 0 31
mol:GTP -0.002 0.062 -10000 0 -0.24 32 32
regulation of calcium-dependent cell-cell adhesion -0.018 0.082 0.33 13 -10000 0 13
ARF1/GTP 0.012 0.05 -10000 0 -0.32 3 3
mol:GM1 0 0.047 -10000 0 -0.25 4 4
mol:Choline 0.007 0.075 -10000 0 -0.34 16 16
lamellipodium assembly -0.001 0.11 -10000 0 -0.43 32 32
MAPK3 0.009 0.089 -10000 0 -0.33 33 33
ARF6/GTP/NME1/Tiam1 0.019 0.083 -10000 0 -0.33 13 13
ARF1 0.017 0.023 -10000 0 -0.52 1 1
ARF6/GDP -0.003 0.1 -10000 0 -0.4 31 31
ARF1/GDP 0.006 0.097 -10000 0 -0.36 33 33
ARF6 0.007 0.05 -10000 0 -0.62 2 2
RAB11A 0.016 0.029 -10000 0 -0.34 3 3
TIAM1 0.007 0.074 -10000 0 -0.44 13 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.09 -10000 0 -0.33 34 34
actin filament bundle formation 0.001 0.11 0.35 41 -10000 0 41
KALRN -0.022 0.078 -10000 0 -0.31 32 32
RAB11FIP3/RAB11A 0.019 0.05 -10000 0 -0.37 8 8
RhoA/GDP -0.001 0.11 -10000 0 -0.36 41 41
NME1 0.012 0.039 -10000 0 -0.25 11 11
Rac1/GDP 0.005 0.096 -10000 0 -0.36 32 32
substrate adhesion-dependent cell spreading -0.002 0.062 -10000 0 -0.24 32 32
cortical actin cytoskeleton organization -0.002 0.11 -10000 0 -0.43 32 32
RAC1 0.018 0 -10000 0 -10000 0 0
liver development -0.002 0.062 -10000 0 -0.24 32 32
ARF6/GTP -0.002 0.062 -10000 0 -0.24 32 32
RhoA/GTP 0.004 0.074 -10000 0 -0.36 14 14
mol:GDP -0.003 0.1 -10000 0 -0.4 32 32
ARF6/GTP/RAB11FIP3/RAB11A 0.019 0.058 -10000 0 -0.28 10 10
RHOA 0.005 0.08 -10000 0 -0.52 12 12
PLD1 0.001 0.078 -10000 0 -0.37 13 13
RAB11FIP3 0.01 0.063 -10000 0 -0.49 8 8
tube morphogenesis -0.001 0.11 -10000 0 -0.43 32 32
ruffle organization 0.012 0.065 -10000 0 -0.35 8 8
regulation of epithelial cell migration -0.002 0.062 -10000 0 -0.24 32 32
PLD2 0.01 0.06 -10000 0 -0.38 6 6
PIP5K1A 0.012 0.065 -10000 0 -0.35 8 8
mol:Phosphatidic acid 0.007 0.075 -10000 0 -0.34 16 16
Rac1/GTP -0.002 0.11 -10000 0 -0.44 32 32
HIF-2-alpha transcription factor network

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
MMP14 -0.054 0.27 -10000 0 -1.2 28 28
oxygen homeostasis 0.007 0.013 -10000 0 -10000 0 0
TCEB2 0.018 0 -10000 0 -10000 0 0
TCEB1 0.014 0.035 -10000 0 -0.3 6 6
VHL/Elongin B/Elongin C/HIF2A 0.035 0.13 -10000 0 -0.36 24 24
EPO 0.051 0.23 -10000 0 -0.58 27 27
FIH (dimer) 0.024 0.027 -10000 0 -0.52 1 1
APEX1 0.024 0.019 -10000 0 -0.26 1 1
SERPINE1 0.051 0.26 -10000 0 -0.7 31 31
FLT1 -0.023 0.2 -10000 0 -1.1 15 15
ADORA2A 0.041 0.25 -10000 0 -0.67 32 32
germ cell development 0.066 0.23 -10000 0 -0.62 26 26
SLC11A2 0.064 0.24 -10000 0 -0.66 27 27
BHLHE40 0.056 0.23 -10000 0 -0.62 31 31
HIF1AN 0.024 0.027 -10000 0 -0.53 1 1
HIF2A/ARNT/SIRT1 0.039 0.17 -10000 0 -0.43 30 30
ETS1 0.018 0.075 -10000 0 -0.3 24 24
CITED2 -0.013 0.15 -10000 0 -1.1 9 9
KDR -0.01 0.15 -10000 0 -1.1 9 9
PGK1 0.066 0.23 -10000 0 -0.65 25 25
SIRT1 0.015 0.029 -10000 0 -0.35 3 3
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.082 0.27 -10000 0 -0.72 31 31
EPAS1 0.018 0.15 -10000 0 -0.38 36 36
SP1 0.023 0.027 -10000 0 -0.52 1 1
ABCG2 0.058 0.25 -10000 0 -0.69 30 30
EFNA1 0.056 0.25 -10000 0 -0.63 34 34
FXN 0.057 0.23 -10000 0 -0.65 25 25
POU5F1 0.066 0.23 -10000 0 -0.65 26 26
neuron apoptosis -0.081 0.27 0.7 31 -10000 0 31
EP300 0.014 0.047 -10000 0 -0.52 4 4
EGLN3 -0.066 0.18 -10000 0 -0.39 116 116
EGLN2 0.018 0.054 -10000 0 -0.36 9 9
EGLN1 0.008 0.084 -10000 0 -0.35 24 24
VHL/Elongin B/Elongin C 0.032 0.027 -10000 0 -0.3 1 1
VHL 0.015 0.029 -10000 0 -0.25 6 6
ARNT 0.025 0.014 -10000 0 -10000 0 0
SLC2A1 0.051 0.24 -10000 0 -0.64 31 31
TWIST1 0.035 0.27 -10000 0 -0.71 41 41
ELK1 0.022 0.038 -10000 0 -0.38 4 4
HIF2A/ARNT/Cbp/p300 0.052 0.17 -10000 0 -0.44 28 28
VEGFA 0.058 0.24 -10000 0 -0.65 28 28
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
EPHB forward 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
Ephrin A5/EPHB2 0.011 0.056 -10000 0 -0.3 12 12
cell-cell adhesion 0.038 0.084 0.37 18 -10000 0 18
Ephrin B/EPHB2/RasGAP 0.023 0.087 -10000 0 -0.28 32 32
ITSN1 0.015 0.035 -10000 0 -0.43 3 3
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
SHC1 0.017 0.023 -10000 0 -0.52 1 1
Ephrin B1/EPHB3 0.006 0.072 -10000 0 -0.32 21 21
Ephrin B1/EPHB1 -0.003 0.07 -10000 0 -0.3 13 13
HRAS/GDP -0.034 0.081 -10000 0 -0.3 28 28
Ephrin B/EPHB1/GRB7 -0.003 0.097 -10000 0 -0.27 34 34
Endophilin/SYNJ1 0.018 0.065 -10000 0 -0.23 25 25
KRAS 0.009 0.065 -10000 0 -0.44 10 10
Ephrin B/EPHB1/Src 0.013 0.089 -10000 0 -0.28 26 26
endothelial cell migration -0.006 0.11 -10000 0 -0.28 59 59
GRB2 0.016 0.024 -10000 0 -0.25 4 4
GRB7 -0.017 0.1 -10000 0 -0.29 59 59
PAK1 0.002 0.093 -10000 0 -0.26 29 29
HRAS 0.012 0.051 -10000 0 -0.41 7 7
RRAS 0.015 0.075 -10000 0 -0.25 32 32
DNM1 0.013 0.047 -10000 0 -0.37 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.005 0.079 -10000 0 -0.26 27 27
lamellipodium assembly -0.038 0.084 -10000 0 -0.37 18 18
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.077 -10000 0 -0.47 5 5
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
EPHB2 0.007 0.061 -10000 0 -0.32 16 16
EPHB3 -0.005 0.1 -10000 0 -0.45 26 26
EPHB1 -0.022 0.1 -10000 0 -0.28 72 72
EPHB4 -0.013 0.12 -10000 0 -0.43 36 36
mol:GDP 0 0.1 -10000 0 -0.33 25 25
Ephrin B/EPHB2 0.019 0.07 -10000 0 -0.25 26 26
Ephrin B/EPHB3 0.012 0.086 -10000 0 -0.27 38 38
JNK cascade 0.006 0.082 -10000 0 -0.28 23 23
Ephrin B/EPHB1 0.005 0.084 -10000 0 -0.26 33 33
RAP1/GDP 0.013 0.099 -10000 0 -0.29 29 29
EFNB2 -0.008 0.11 -10000 0 -0.4 33 33
EFNB3 0.018 0 -10000 0 -10000 0 0
EFNB1 0.01 0.051 -10000 0 -0.3 13 13
Ephrin B2/EPHB1-2 -0.007 0.089 -10000 0 -0.28 34 34
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
RAP1A 0.012 0.057 -10000 0 -0.52 6 6
CDC42/GTP -0.031 0.076 -10000 0 -0.39 11 11
Rap1/GTP -0.03 0.079 -10000 0 -0.4 14 14
axon guidance 0.011 0.056 -10000 0 -0.3 12 12
MAPK3 0.027 0.07 -10000 0 -0.42 5 5
MAPK1 0.027 0.071 -10000 0 -0.39 6 6
Rac1/GDP 0.01 0.095 -10000 0 -0.3 24 24
actin cytoskeleton reorganization -0.035 0.074 -10000 0 -0.29 23 23
CDC42/GDP 0.01 0.095 -10000 0 -0.3 24 24
PI3K -0.003 0.11 -10000 0 -0.28 59 59
EFNA5 0.006 0.068 -10000 0 -0.35 17 17
Ephrin B2/EPHB4 -0.01 0.1 -10000 0 -0.33 40 40
Ephrin B/EPHB2/Intersectin/N-WASP 0.02 0.069 -10000 0 -0.23 34 34
CDC42 0.018 0 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.077 -10000 0 -0.34 17 17
PTK2 0.006 0.034 -10000 0 -0.34 3 3
MAP4K4 0.006 0.083 -10000 0 -0.28 23 23
SRC 0.015 0.035 -10000 0 -0.43 3 3
KALRN 0.006 0.057 -10000 0 -0.27 21 21
Intersectin/N-WASP 0.019 0.054 -10000 0 -0.37 10 10
neuron projection morphogenesis 0.009 0.11 -10000 0 -0.34 23 23
MAP2K1 0.022 0.073 -10000 0 -0.44 5 5
WASL 0.01 0.066 -10000 0 -0.52 8 8
Ephrin B1/EPHB1-2/NCK1 0.011 0.081 -10000 0 -0.27 26 26
cell migration 0.026 0.077 -10000 0 -0.45 5 5
NRAS 0.005 0.076 -10000 0 -0.4 16 16
SYNJ1 0.019 0.066 -10000 0 -0.24 25 25
PXN 0.018 0 -10000 0 -10000 0 0
TF 0.019 0.066 -10000 0 -0.32 1 1
HRAS/GTP 0.004 0.092 -10000 0 -0.38 12 12
Ephrin B1/EPHB1-2 0.004 0.074 -10000 0 -0.27 22 22
cell adhesion mediated by integrin 0.012 0.062 0.26 23 -10000 0 23
RAC1 0.018 0 -10000 0 -10000 0 0
mol:GTP 0.008 0.097 -10000 0 -0.28 33 33
RAC1-CDC42/GTP -0.034 0.08 -10000 0 -0.35 18 18
RASA1 0.004 0.078 -10000 0 -0.42 16 16
RAC1-CDC42/GDP 0.017 0.093 -10000 0 -0.29 23 23
ruffle organization 0.008 0.11 -10000 0 -0.38 17 17
NCK1 0.011 0.045 -10000 0 -0.28 12 12
receptor internalization 0.022 0.067 -10000 0 -0.32 2 2
Ephrin B/EPHB2/KALRN 0.024 0.078 -10000 0 -0.27 24 24
ROCK1 0.012 0.064 -10000 0 -0.28 21 21
RAS family/GDP -0.035 0.077 -10000 0 -0.31 21 21
Rac1/GTP -0.039 0.089 -10000 0 -0.39 18 18
Ephrin B/EPHB1/Src/Paxillin 0.013 0.077 -10000 0 -0.49 4 4
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.012 0.14 -9999 0 -0.46 30 30
PDGFB-D/PDGFRB/SLAP 0.01 0.074 -9999 0 -0.38 17 17
PDGFB-D/PDGFRB/APS/CBL 0.018 0.042 -9999 0 -0.32 8 8
AKT1 -0.021 0.14 -9999 0 -0.39 34 34
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.006 0.13 -9999 0 -0.49 22 22
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
FGR -0.008 0.065 -9999 0 -0.39 10 10
mol:Ca2+ 0.004 0.11 -9999 0 -0.62 11 11
MYC -0.029 0.22 -9999 0 -0.75 41 41
SHC1 0.017 0.023 -9999 0 -0.52 1 1
HRAS/GDP 0.02 0.069 -9999 0 -0.25 25 25
LRP1/PDGFRB/PDGFB 0.024 0.064 -9999 0 -0.35 13 13
GRB10 -0.003 0.097 -9999 0 -0.43 24 24
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
GO:0007205 0.003 0.11 -9999 0 -0.63 11 11
PTEN -0.002 0.1 -9999 0 -0.52 19 19
GRB2 0.016 0.024 -9999 0 -0.25 4 4
GRB7 -0.017 0.1 -9999 0 -0.29 59 59
PDGFB-D/PDGFRB/SHP2 0.019 0.052 -9999 0 -0.37 9 9
PDGFB-D/PDGFRB/GRB10 0.005 0.086 -9999 0 -0.37 24 24
cell cycle arrest 0.01 0.074 -9999 0 -0.37 17 17
HRAS 0.012 0.051 -9999 0 -0.41 7 7
HIF1A -0.035 0.14 -9999 0 -0.35 44 44
GAB1 -0.011 0.13 -9999 0 -0.61 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.008 0.13 -9999 0 -0.59 14 14
PDGFB-D/PDGFRB 0.019 0.067 -9999 0 -0.35 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.016 0.062 -9999 0 -0.37 13 13
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.017 0.15 -9999 0 -0.47 32 32
positive regulation of MAPKKK cascade 0.019 0.052 -9999 0 -0.37 9 9
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
mol:IP3 0.003 0.11 -9999 0 -0.64 11 11
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.015 0.031 -9999 0 -0.32 4 4
PDGFB-D/PDGFRB/GRB7 -0.004 0.085 -9999 0 -0.37 16 16
SHB 0.008 0.067 -9999 0 -0.41 12 12
BLK -0.024 0.091 -9999 0 -0.45 18 18
PTPN2 0.015 0.024 -9999 0 -0.26 4 4
PDGFB-D/PDGFRB/SNX15 0.019 0.05 -9999 0 -0.37 8 8
BCAR1 0.017 0.012 -9999 0 -0.25 1 1
VAV2 -0.011 0.14 -9999 0 -0.57 18 18
CBL 0.017 0.012 -9999 0 -0.25 1 1
PDGFB-D/PDGFRB/DEP1 0.015 0.063 -9999 0 -0.37 13 13
LCK -0.082 0.2 -9999 0 -0.57 68 68
PDGFRB 0.009 0.067 -9999 0 -0.53 8 8
ACP1 0.013 0.052 -9999 0 -0.52 5 5
HCK -0.029 0.14 -9999 0 -0.55 28 28
ABL1 -0.005 0.11 -9999 0 -0.49 17 17
PDGFB-D/PDGFRB/CBL -0.01 0.14 -9999 0 -0.64 16 16
PTPN1 0.001 0.07 -9999 0 -0.28 28 28
SNX15 0.017 0.012 -9999 0 -0.25 1 1
STAT3 0.015 0.04 -9999 0 -0.52 3 3
STAT1 -0.02 0.12 -9999 0 -0.33 58 58
cell proliferation -0.022 0.2 -9999 0 -0.65 42 42
SLA 0.004 0.078 -9999 0 -0.39 18 18
actin cytoskeleton reorganization 0.032 0.07 -9999 0 -0.37 7 7
SRC -0.009 0.083 -9999 0 -0.47 11 11
PI3K -0.066 0.12 -9999 0 -0.44 31 31
PDGFB-D/PDGFRB/GRB7/SHC 0.01 0.074 -9999 0 -0.31 17 17
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.007 0.14 -9999 0 -0.52 21 21
LYN -0.007 0.066 -9999 0 -0.38 11 11
LRP1 0.017 0.023 -9999 0 -0.52 1 1
SOS1 0.017 0.023 -9999 0 -0.52 1 1
STAT5B 0.016 0.026 -9999 0 -0.39 2 2
STAT5A 0.011 0.056 -9999 0 -0.42 8 8
NCK1-2/p130 Cas 0.033 0.062 -9999 0 -0.29 11 11
SPHK1 -0.027 0.14 -9999 0 -0.42 54 54
EDG1 -0.019 0.12 -9999 0 -0.4 46 46
mol:DAG 0.003 0.11 -9999 0 -0.64 11 11
PLCG1 0.003 0.11 -9999 0 -0.66 11 11
NHERF/PDGFRB -0.038 0.15 -9999 0 -0.35 91 91
YES1 -0.016 0.096 -9999 0 -0.46 19 19
cell migration -0.038 0.15 -9999 0 -0.35 91 91
SHC/Grb2/SOS1 0.036 0.06 -9999 0 -0.28 10 10
SLC9A3R2 -0.032 0.15 -9999 0 -0.49 52 52
SLC9A3R1 -0.043 0.16 -9999 0 -0.44 70 70
NHERF1-2/PDGFRB/PTEN -0.033 0.16 -9999 0 -0.32 103 103
FYN -0.017 0.14 -9999 0 -0.73 13 13
DOK1 0.013 0.074 -9999 0 -0.3 22 22
HRAS/GTP 0.009 0.036 -9999 0 -0.29 7 7
PDGFB 0.009 0.064 -9999 0 -0.39 12 12
RAC1 -0.011 0.16 -9999 0 -0.49 40 40
PRKCD 0.019 0.065 -9999 0 -0.32 14 14
FER 0.02 0.06 -9999 0 -0.3 13 13
MAPKKK cascade -0.006 0.05 -9999 0 -0.29 8 8
RASA1 0.013 0.072 -9999 0 -0.29 22 22
NCK1 0.011 0.045 -9999 0 -0.28 12 12
NCK2 0.015 0.026 -9999 0 -0.25 5 5
p62DOK/Csk 0.023 0.071 -9999 0 -0.27 23 23
PDGFB-D/PDGFRB/SHB 0.013 0.071 -9999 0 -0.4 14 14
chemotaxis -0.004 0.11 -9999 0 -0.47 17 17
STAT1-3-5/STAT1-3-5 -0.021 0.071 -9999 0 -0.4 6 6
Bovine Papilomavirus E5/PDGFRB 0.006 0.049 -9999 0 -0.39 8 8
PTPRJ 0.012 0.055 -9999 0 -0.44 7 7
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.018 0 -9999 0 -10000 0 0
VLDLR -0.061 0.17 -9999 0 -0.4 100 100
LRPAP1 0.016 0.026 -9999 0 -0.39 2 2
NUDC 0.018 0 -9999 0 -10000 0 0
RELN/LRP8 -0.015 0.1 -9999 0 -0.31 43 43
CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
KATNA1 0.015 0.033 -9999 0 -0.31 5 5
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.008 0.093 -9999 0 -0.28 43 43
IQGAP1/CaM 0.026 0 -9999 0 -10000 0 0
DAB1 0.018 0 -9999 0 -10000 0 0
IQGAP1 0.018 0 -9999 0 -10000 0 0
PLA2G7 -0.092 0.2 -9999 0 -0.41 137 137
CALM1 0.018 0 -9999 0 -10000 0 0
DYNLT1 0.018 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.027 0.11 -9999 0 -0.37 37 37
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.015 0.037 -9999 0 -0.39 4 4
CDK5R1 0.014 0.031 -9999 0 -0.25 7 7
LIS1/Poliovirus Protein 3A 0.018 0.02 -9999 0 -0.31 2 2
CDK5R2 0.017 0.017 -9999 0 -0.25 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.017 0.11 -9999 0 -0.31 59 59
YWHAE 0.016 0.029 -9999 0 -0.34 3 3
NDEL1/14-3-3 E 0.024 0.079 -9999 0 -0.29 4 4
MAP1B -0.015 0.075 -9999 0 -0.29 34 34
RAC1 0.024 0.01 -9999 0 -10000 0 0
p35/CDK5 0.007 0.085 -9999 0 -0.33 3 3
RELN 0.01 0.059 -9999 0 -0.38 11 11
PAFAH/LIS1 -0.036 0.12 -9999 0 -0.3 80 80
LIS1/CLIP170 0.029 0.031 -9999 0 -0.3 4 4
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.016 0.043 -9999 0 -0.29 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.002 0.096 -9999 0 -0.24 62 62
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.016 0.08 -9999 0 -0.31 3 3
LIS1/IQGAP1 0.031 0.021 -9999 0 -0.3 2 2
RHOA 0.014 0.067 -9999 0 -0.42 12 12
PAFAH1B1 0.024 0.024 -9999 0 -0.37 2 2
PAFAH1B3 0.009 0.067 -9999 0 -0.49 9 9
PAFAH1B2 0.017 0.012 -9999 0 -0.25 1 1
MAP1B/LIS1/Dynein heavy chain 0.013 0.055 -9999 0 -0.31 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.031 0.078 -9999 0 -10000 0 0
LRP8 -0.057 0.16 -9999 0 -0.34 110 110
NDEL1/Katanin 60 0.024 0.079 -9999 0 -0.29 3 3
P39/CDK5 0.008 0.084 -9999 0 -0.33 3 3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0.021 -9999 0 -0.3 2 2
CDK5 -0.001 0.087 -9999 0 -0.25 43 43
PPP2R5D 0.016 0.02 -9999 0 -0.25 3 3
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.026 -9999 0 -0.26 4 4
CSNK2A1 0.017 0.023 -9999 0 -0.52 1 1
RELN/VLDLR/DAB1/LIS1 0.003 0.1 -9999 0 -0.25 59 59
RELN/VLDLR -0.045 0.14 -9999 0 -0.28 113 113
CDC42 0.024 0.01 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.02 0.089 -9999 0 -0.3 33 33
MAP4K1 0.012 0.04 -9999 0 -0.25 12 12
MAP3K8 -0.036 0.15 -9999 0 -0.39 70 70
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.014 0.039 -9999 0 -0.36 5 5
CRKL 0.014 0.047 -9999 0 -0.52 4 4
MAP3K1 0.006 0.099 -9999 0 -0.35 12 12
JUN -0.008 0.092 -9999 0 -0.28 47 47
MAP3K7 0.029 0.065 -9999 0 -0.28 6 6
GRAP2 0.012 0.042 -9999 0 -0.28 10 10
CRK 0.016 0.033 -9999 0 -0.52 2 2
MAP2K4 0.006 0.094 -9999 0 -0.35 15 15
LAT 0.002 0.068 -9999 0 -0.27 29 29
LCP2 -0.004 0.097 -9999 0 -0.4 27 27
MAPK8 0.011 0.052 -9999 0 -0.58 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0.069 -9999 0 -0.3 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.026 0.087 -9999 0 -0.3 27 27
ceramide signaling pathway

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
MAP4K4 -0.009 0.13 -10000 0 -0.51 12 12
BAG4 0.002 0.07 -10000 0 -0.28 28 28
BAD 0.012 0.045 -10000 0 -0.19 8 8
NFKBIA 0.014 0.042 -10000 0 -0.45 4 4
BIRC3 -0.085 0.19 -10000 0 -0.41 128 128
BAX 0.011 0.045 -10000 0 -0.19 7 7
EnzymeConsortium:3.1.4.12 0.002 0.03 -10000 0 -0.11 12 12
IKBKB -0.003 0.12 -10000 0 -0.44 16 16
MAP2K2 0.023 0.046 -10000 0 -0.24 6 6
MAP2K1 0.024 0.043 -10000 0 -0.23 4 4
SMPD1 0.006 0.039 -10000 0 -0.19 9 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.002 0.12 -10000 0 -0.42 19 19
MAP2K4 -0.011 0.089 -10000 0 -0.24 55 55
protein ubiquitination -0.003 0.12 -10000 0 -0.44 15 15
EnzymeConsortium:2.7.1.37 0.02 0.052 -10000 0 -0.24 5 5
response to UV 0 0 -10000 0 -0.002 4 4
RAF1 0.018 0.044 -10000 0 -0.22 4 4
CRADD 0.01 0.063 -10000 0 -0.49 8 8
mol:ceramide 0.005 0.046 -10000 0 -0.17 13 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.022 0.026 -10000 0 -0.31 3 3
MADD 0.018 0 -10000 0 -10000 0 0
MAP3K1 -0.009 0.083 -10000 0 -0.24 44 44
TRADD 0.016 0.026 -10000 0 -0.39 2 2
RELA/p50 0.018 0 -10000 0 -10000 0 0
MAPK3 0.027 0.044 -10000 0 -0.2 6 6
MAPK1 0.026 0.044 -10000 0 -0.2 6 6
p50/RELA/I-kappa-B-alpha 0.024 0.031 -10000 0 -0.37 3 3
FADD -0.011 0.13 -10000 0 -0.44 19 19
KSR1 0.012 0.045 -10000 0 -0.19 7 7
MAPK8 -0.004 0.086 -10000 0 -0.22 54 54
TRAF2 0.014 0.042 -10000 0 -0.45 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK -0.007 0.13 -10000 0 -0.46 16 16
TNF R/SODD 0.014 0.054 -10000 0 -0.37 5 5
TNF -0.004 0.094 -10000 0 -0.36 31 31
CYCS 0.036 0.056 0.14 65 -0.17 5 70
IKBKG -0.001 0.12 -10000 0 -0.47 12 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.011 0.13 -10000 0 -0.52 12 12
RELA 0.018 0 -10000 0 -10000 0 0
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
AIFM1 0.037 0.056 0.14 65 -0.17 5 70
TNF/TNF R/SODD 0.012 0.074 -10000 0 -0.31 18 18
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.021 0.032 -10000 0 -10000 0 0
NSMAF -0.007 0.13 -10000 0 -0.48 14 14
response to hydrogen peroxide 0 0 -10000 0 -0.002 4 4
BCL2 -0.11 0.22 -10000 0 -0.47 144 144
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.015 0.029 -9999 0 -0.25 6 6
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.018 0 -9999 0 -10000 0 0
TCEB1 0.014 0.035 -9999 0 -0.3 6 6
HIF1A/p53 -0.02 0.11 -9999 0 -0.32 37 37
HIF1A -0.011 0.087 -9999 0 -0.32 20 20
COPS5 0.01 0.056 -9999 0 -0.35 11 11
VHL/Elongin B/Elongin C/RBX1/CUL2 0.049 0.025 -9999 0 -0.24 1 1
FIH (dimer) 0.017 0.023 -9999 0 -0.52 1 1
CDKN2A -0.053 0.15 -9999 0 -0.33 108 108
ARNT/IPAS 0.024 0.02 -9999 0 -10000 0 0
HIF1AN 0.017 0.023 -9999 0 -0.52 1 1
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
HIF1A/ARNT 0 0.084 -9999 0 -0.3 20 20
CUL2 0.017 0.017 -9999 0 -0.25 2 2
OS9 0.014 0.04 -9999 0 -0.34 6 6
RACK1/Elongin B/Elongin C 0.032 0.033 -9999 0 -0.3 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.002 0.089 -9999 0 -0.31 22 22
PHD1-3/OS9 -0.021 0.12 -9999 0 -0.28 80 80
HIF1A/RACK1/Elongin B/Elongin C 0.013 0.083 -9999 0 -0.34 5 5
VHL 0.015 0.029 -9999 0 -0.25 6 6
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
HIF1A/JAB1 -0.004 0.087 -9999 0 -0.29 22 22
EGLN3 -0.074 0.18 -9999 0 -0.4 116 116
EGLN2 0.011 0.053 -9999 0 -0.37 9 9
EGLN1 0.001 0.082 -9999 0 -0.35 24 24
TP53 -0.023 0.14 -9999 0 -0.48 43 43
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.034 0.033 -9999 0 -0.5 1 1
ARNT 0.018 0 -9999 0 -10000 0 0
ARD1A 0.016 0.02 -9999 0 -0.25 3 3
RBX1 0.018 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.032 0.11 -9999 0 -0.32 36 36
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.001 0.073 -9999 0 -0.26 34 34
TRAF2/ASK1 -0.002 0.085 -9999 0 -0.31 33 33
ATM 0.017 0.012 -9999 0 -0.25 1 1
MAP2K3 -0.011 0.12 -9999 0 -0.37 38 38
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.016 0.12 -9999 0 -0.3 54 54
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.003 0.083 -9999 0 -0.45 16 16
TXN 0.009 0.007 -9999 0 -10000 0 0
CALM1 0.018 0 -9999 0 -10000 0 0
GADD45A -0.011 0.11 -9999 0 -0.39 38 38
GADD45B -0.002 0.097 -9999 0 -0.44 23 23
MAP3K1 -0.03 0.14 -9999 0 -0.42 58 58
MAP3K6 0.015 0.035 -9999 0 -0.43 3 3
MAP3K7 0.016 0.02 -9999 0 -0.25 3 3
MAP3K4 0.018 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.004 0.099 -9999 0 -0.37 33 33
TAK1/TAB family 0.01 0.038 -9999 0 -0.42 4 4
RAC1/OSM/MEKK3 0.034 0.006 -9999 0 -10000 0 0
TRAF2 0.014 0.042 -9999 0 -0.45 4 4
RAC1/OSM/MEKK3/MKK3 -0.029 0.079 -9999 0 -0.28 37 37
TRAF6 0.017 0.033 -9999 0 -0.32 5 5
RAC1 0.018 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.078 0.18 -9999 0 -0.36 133 133
CCM2 0.018 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.034 0.11 -9999 0 -0.31 55 55
MAPK11 0.018 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.04 0.12 -9999 0 -0.29 87 87
OSM/MEKK3 0.026 0.008 -9999 0 -10000 0 0
TAOK1 0.012 0.044 -9999 0 -0.32 7 7
TAOK2 0.02 0.005 -9999 0 -10000 0 0
TAOK3 0.019 0.016 -9999 0 -0.32 1 1
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.017 0.012 -9999 0 -0.25 1 1
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
MAP3K5 -0.022 0.13 -9999 0 -0.42 47 47
MAP3K10 -0.001 0.097 -9999 0 -0.48 20 20
MAP3K3 0.017 0.012 -9999 0 -0.25 1 1
TRX/ASK1 -0.003 0.079 -9999 0 -0.31 30 30
GADD45/MTK1/MTK1 0.009 0.097 -9999 0 -0.29 42 42
BARD1 signaling events

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
BARD1/CSTF1 0.021 0.042 -10000 0 -0.37 5 5
ATM 0.017 0.012 -10000 0 -0.25 1 1
UBE2D3 0.018 0 -10000 0 -10000 0 0
PRKDC 0.012 0.045 -10000 0 -0.31 9 9
ATR 0.017 0.012 -10000 0 -0.25 1 1
UBE2L3 0.018 0 -10000 0 -10000 0 0
FANCD2 0.029 0.012 -10000 0 -10000 0 0
protein ubiquitination 0.016 0.083 -10000 0 -0.28 26 26
XRCC5 0.018 0 -10000 0 -10000 0 0
XRCC6 0.017 0.012 -10000 0 -0.25 1 1
M/R/N Complex 0.03 0.045 -10000 0 -0.3 9 9
MRE11A 0.018 0 -10000 0 -10000 0 0
DNA-PK 0.032 0.028 -10000 0 -0.3 2 2
FA complex/FANCD2/Ubiquitin 0.028 0.075 -10000 0 -0.35 8 8
FANCF 0.012 0.057 -10000 0 -0.52 6 6
BRCA1 0 0.094 -10000 0 -0.48 19 19
CCNE1 -0.018 0.099 -10000 0 -0.28 64 64
CDK2/Cyclin E1 -0.002 0.08 -10000 0 -0.37 11 11
FANCG 0.016 0.024 -10000 0 -0.25 4 4
BRCA1/BACH1/BARD1 0.01 0.076 -10000 0 -0.37 20 20
FANCE 0.006 0.061 -10000 0 -0.3 19 19
FANCC 0.013 0.042 -10000 0 -0.33 7 7
NBN 0.015 0.035 -10000 0 -0.43 3 3
FANCA -0.032 0.12 -10000 0 -0.31 80 80
DNA repair 0.012 0.12 -10000 0 -0.38 26 26
BRCA1/BARD1/ubiquitin 0.01 0.076 -10000 0 -0.37 20 20
BARD1/DNA-PK 0.04 0.038 -10000 0 -0.27 6 6
FANCL 0.014 0.031 -10000 0 -0.25 7 7
mRNA polyadenylation -0.021 0.042 0.37 5 -10000 0 5
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.057 -10000 0 -0.32 2 2
BRCA1/BACH1/BARD1/TopBP1 0.022 0.068 -10000 0 -0.31 20 20
BRCA1/BARD1/P53 0.01 0.11 -10000 0 -0.3 51 51
BARD1/CSTF1/BRCA1 0.02 0.069 -10000 0 -0.3 21 21
BRCA1/BACH1 0 0.094 -10000 0 -0.48 19 19
BARD1 0.014 0.047 -10000 0 -0.52 4 4
PCNA 0.009 0.064 -10000 0 -0.39 12 12
BRCA1/BARD1/UbcH5C 0.022 0.066 -10000 0 -0.3 20 20
BRCA1/BARD1/UbcH7 0.022 0.066 -10000 0 -0.3 20 20
BRCA1/BARD1/RAD51/PCNA -0.006 0.12 -10000 0 -0.28 74 74
BARD1/DNA-PK/P53 0.025 0.085 -10000 0 -0.25 43 43
BRCA1/BARD1/Ubiquitin 0.01 0.076 -10000 0 -0.37 20 20
BRCA1/BARD1/CTIP 0.015 0.081 -10000 0 -0.28 32 32
FA complex 0.017 0.073 -10000 0 -0.25 24 24
BARD1/EWS 0.023 0.034 -10000 0 -0.37 4 4
RBBP8 0.007 0.07 -10000 0 -0.37 12 12
TP53 -0.023 0.14 -10000 0 -0.48 43 43
TOPBP1 0.017 0.017 -10000 0 -0.25 2 2
G1/S transition of mitotic cell cycle -0.008 0.11 0.3 51 -10000 0 51
BRCA1/BARD1 0.02 0.085 -10000 0 -0.28 26 26
CSTF1 0.014 0.035 -10000 0 -0.3 6 6
BARD1/EWS-Fli1 0.01 0.034 -10000 0 -0.38 4 4
CDK2 0.012 0.047 -10000 0 -0.31 10 10
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.041 0.16 -10000 0 -0.47 64 64
RAD50 0.011 0.062 -10000 0 -0.52 7 7
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.076 -10000 0 -0.37 20 20
EWSR1 0.018 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.023 -9999 0 -0.52 1 1
HDAC2 0.009 0.053 -9999 0 -0.29 15 15
GNB1/GNG2 -0.008 0.11 -9999 0 -0.31 55 55
forebrain development 0.005 0.14 -9999 0 -0.58 15 15
GNAO1 0.017 0.024 -9999 0 -0.25 4 4
SMO/beta Arrestin2 -0.018 0.12 -9999 0 -0.37 49 49
SMO -0.047 0.16 -9999 0 -0.41 82 82
ARRB2 0.019 0.001 -9999 0 -10000 0 0
GLI3/SPOP 0.011 0.13 -9999 0 -0.43 21 21
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.018 0 -9999 0 -10000 0 0
GNAI2 0.007 0.075 -9999 0 -0.48 12 12
SIN3/HDAC complex 0.041 0.032 -9999 0 -0.27 5 5
GNAI1 -0.016 0.12 -9999 0 -0.38 46 46
XPO1 0.021 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) -0.006 0.17 -9999 0 -0.58 25 25
SAP30 0.012 0.053 -9999 0 -0.48 6 6
mol:GDP -0.047 0.16 -9999 0 -0.41 82 82
MIM/GLI2A -0.022 0.14 -9999 0 -0.4 61 61
IFT88 -0.001 0.097 -9999 0 -0.48 20 20
GNAI3 0.019 0.001 -9999 0 -10000 0 0
GLI2 0.035 0.055 -9999 0 -0.41 1 1
GLI3 0.004 0.14 -9999 0 -0.38 30 30
CSNK1D 0.018 0 -9999 0 -10000 0 0
CSNK1E 0.017 0.012 -9999 0 -0.25 1 1
SAP18 0.017 0 -9999 0 -10000 0 0
embryonic digit morphogenesis -0.001 0.097 -9999 0 -0.48 20 20
GNG2 0.016 0.029 -9999 0 -0.34 3 3
Gi family/GTP -0.008 0.12 -9999 0 -0.38 25 25
SIN3B 0.017 0.012 -9999 0 -0.25 1 1
SIN3A 0.017 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.009 0.14 -9999 0 -0.43 35 35
GLI2/Su(fu) 0.026 0.1 -9999 0 -0.45 6 6
FOXA2 -0.051 0.18 -9999 0 -0.73 34 34
neural tube patterning 0.005 0.14 -9999 0 -0.58 15 15
SPOP 0.013 0.042 -9999 0 -0.33 7 7
Su(fu)/PIAS1 0.004 0.093 -9999 0 -0.34 21 21
GNB1 0.013 0.052 -9999 0 -0.52 5 5
CSNK1G2 0.016 0.033 -9999 0 -0.52 2 2
CSNK1G3 0.013 0.052 -9999 0 -0.52 5 5
MTSS1 -0.023 0.14 -9999 0 -0.4 61 61
embryonic limb morphogenesis 0.005 0.14 -9999 0 -0.58 15 15
SUFU -0.006 0.1 -9999 0 -0.38 21 21
LGALS3 -0.041 0.16 -9999 0 -0.48 63 63
catabolic process 0.031 0.12 -9999 0 -0.36 24 24
GLI3A/CBP 0.006 0.07 -9999 0 -0.36 10 10
KIF3A 0.007 0.074 -9999 0 -0.5 11 11
GLI1 0.005 0.14 -9999 0 -0.6 15 15
RAB23 0.008 0.065 -9999 0 -0.38 13 13
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
IFT172 0.013 0.049 -9999 0 -0.43 6 6
RBBP7 0.01 0.051 -9999 0 -0.3 13 13
Su(fu)/Galectin3 -0.028 0.14 -9999 0 -0.34 71 71
GNAZ 0.002 0.088 -9999 0 -0.44 19 19
RBBP4 0.016 0.026 -9999 0 -0.39 2 2
CSNK1G1 0.017 0.012 -9999 0 -0.25 1 1
PIAS1 0.017 0.012 -9999 0 -0.25 1 1
PRKACA 0.018 0 -9999 0 -10000 0 0
GLI2/SPOP 0.04 0.057 -9999 0 -0.39 2 2
STK36 0 0.11 -9999 0 -0.52 21 21
Gi family/GNB1/GNG2/GDP 0 0.11 -9999 0 -0.4 20 20
PTCH1 0.014 0.13 -9999 0 -0.66 7 7
MIM/GLI1 0 0.16 -9999 0 -0.56 19 19
CREBBP 0.006 0.07 -9999 0 -0.36 10 10
Su(fu)/SIN3/HDAC complex 0.036 0.047 -9999 0 -0.26 1 1
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.047 -10000 0 -0.52 4 4
HDAC4 0.017 0.023 -10000 0 -0.52 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.027 0.24 3 -0.13 10 13
CDKN1A -0.018 0.13 -10000 0 -0.71 16 16
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.016 0.02 -10000 0 -0.25 3 3
FOXO3 0.001 0.043 0.41 4 -0.25 4 8
FOXO1 0 0.092 -10000 0 -0.46 19 19
FOXO4 0.022 0.034 -10000 0 -0.27 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0.012 -10000 0 -0.25 1 1
TAT -0.007 0.078 -10000 0 -0.25 48 48
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.091 -10000 0 -0.34 36 36
PPARGC1A -0.012 0.1 -10000 0 -0.31 48 48
FHL2 -0.077 0.19 -10000 0 -0.41 117 117
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.024 0.029 -10000 0 -0.37 1 1
HIST2H4A 0.011 0.027 0.13 10 -0.24 3 13
SIRT1/FOXO3a 0.005 0.041 0.32 4 -0.19 7 11
SIRT1 0.016 0.04 0.2 10 -0.35 3 13
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.034 0.029 -10000 0 -0.31 2 2
SIRT1/Histone H1b 0.004 0.072 -10000 0 -0.23 38 38
apoptosis -0.033 0.028 0.31 1 -10000 0 1
SIRT1/PGC1A 0.005 0.064 -10000 0 -0.32 11 11
p53/SIRT1 -0.016 0.11 0.4 10 -0.37 32 42
SIRT1/FOXO4 0.027 0.038 -10000 0 -0.24 7 7
FOXO1/FHL2/SIRT1 -0.03 0.12 -10000 0 -0.3 79 79
HIST1H1E -0.005 0.08 -10000 0 -0.27 39 39
SIRT1/p300 0.022 0.043 -10000 0 -0.36 5 5
muscle cell differentiation 0.002 0.081 0.31 30 -10000 0 30
TP53 -0.022 0.14 -10000 0 -0.47 43 43
KU70/SIRT1/BAX 0.033 0.028 -10000 0 -0.31 1 1
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
MEF2D 0.018 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.008 0.06 -10000 0 -0.37 1 1
ACSS2 0.023 0.029 -10000 0 -0.37 1 1
SIRT1/PCAF/MYOD -0.002 0.081 -10000 0 -0.32 30 30
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.019 0.052 -9999 0 -0.37 9 9
FBXW11 0.015 0.035 -9999 0 -0.43 3 3
NF kappa B1 p50/c-Rel 0.018 0.062 -9999 0 -0.31 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0 0.11 -9999 0 -0.44 18 18
NFKBIA -0.024 0.12 -9999 0 -0.26 87 87
MAPK14 0.017 0.012 -9999 0 -0.25 1 1
NF kappa B1 p105/p50 0.026 0.038 -9999 0 -0.3 5 5
ARRB2 0.02 0.005 -9999 0 -10000 0 0
REL 0.001 0.087 -9999 0 -0.41 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.054 -9999 0 -0.3 12 12
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.031 -9999 0 -0.3 3 3
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
NF kappa B1 p50 dimer 0.019 0.037 -9999 0 -0.37 3 3
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
NFKB1 0.02 0.037 -9999 0 -0.37 3 3
RELA 0.018 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.014 0.1 -9999 0 -0.4 16 16
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.005 0.11 -9999 0 -0.44 17 17
SRC 0.015 0.035 -9999 0 -0.43 3 3
PI3K 0.005 0.082 -9999 0 -0.37 21 21
NF kappa B1 p50/RelA -0.014 0.1 -9999 0 -0.4 16 16
IKBKB 0.012 0.047 -9999 0 -0.31 10 10
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.035 -9999 0 -0.43 3 3
SYK -0.023 0.14 -9999 0 -0.48 43 43
I kappa B alpha/PIK3R1 -0.027 0.13 -9999 0 -0.37 39 39
cell death 0.005 0.1 -9999 0 -0.42 17 17
NF kappa B1 p105/c-Rel 0.018 0.062 -9999 0 -0.31 15 15
LCK -0.074 0.18 -9999 0 -0.4 117 117
BCL3 0.008 0.071 -9999 0 -0.5 10 10
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.023 0.016 -9999 0 -0.31 1 1
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.017 0.023 -9999 0 -0.52 1 1
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.011 0.11 -9999 0 -0.4 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.006 0.1 -9999 0 -0.38 31 31
RAC1-CDC42/GTP/PAK family -0.001 0.072 -9999 0 -0.22 41 41
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.007 0.07 -9999 0 -0.43 12 12
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0.012 -9999 0 -0.25 1 1
FYN 0.008 0.067 -9999 0 -0.41 12 12
MAP3K12 0.018 0 -9999 0 -10000 0 0
FGR 0.017 0.017 -9999 0 -0.25 2 2
p38 alpha/TAB1 0.01 0.094 -9999 0 -0.28 29 29
PRKG1 0.017 0.012 -9999 0 -0.25 1 1
DUSP8 -0.005 0.1 -9999 0 -0.48 24 24
PGK/cGMP/p38 alpha -0.028 0.071 -9999 0 -0.27 29 29
apoptosis 0.009 0.09 -9999 0 -0.27 29 29
RAL/GTP 0.022 0.029 -9999 0 -0.31 4 4
LYN 0.014 0.031 -9999 0 -0.25 7 7
DUSP1 -0.038 0.15 -9999 0 -0.41 69 69
PAK1 -0.022 0.13 -9999 0 -0.37 54 54
SRC 0.015 0.035 -9999 0 -0.43 3 3
RAC1/OSM/MEKK3/MKK3 0.043 0.021 -9999 0 -0.27 1 1
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
RAC1 0.018 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.018 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.024 0 -9999 0 -10000 0 0
MAPK11 0.002 0.11 -9999 0 -0.32 34 34
BLK -0.019 0.1 -9999 0 -0.29 63 63
HCK -0.005 0.11 -9999 0 -0.47 25 25
MAP2K3 0.014 0.037 -9999 0 -0.29 7 7
DUSP16 0.005 0.078 -9999 0 -0.43 15 15
DUSP10 -0.017 0.12 -9999 0 -0.39 44 44
TRAF6/MEKK3 0.022 0.015 -9999 0 -0.28 1 1
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.003 0.1 -9999 0 -0.3 33 33
positive regulation of innate immune response 0.002 0.12 -9999 0 -0.37 31 31
LCK -0.074 0.18 -9999 0 -0.4 117 117
p38alpha-beta/MKP7 0.006 0.13 -9999 0 -0.36 36 36
p38alpha-beta/MKP5 -0.003 0.13 -9999 0 -0.35 39 39
PGK/cGMP 0.013 0.008 -9999 0 -0.17 1 1
PAK2 0.018 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.013 0.14 -9999 0 -0.36 45 45
CDC42 0.018 0 -9999 0 -10000 0 0
RALB 0.014 0.047 -9999 0 -0.52 4 4
RALA 0.018 0 -9999 0 -10000 0 0
PAK3 -0.033 0.13 -9999 0 -0.32 80 80
Signaling events mediated by PRL

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
CCNE1 -0.018 0.099 -10000 0 -0.28 64 64
mol:Halofuginone 0.004 0.012 -10000 0 -0.16 1 1
ITGA1 0 0.096 -10000 0 -0.51 18 18
CDKN1A -0.017 0.12 -10000 0 -0.47 24 24
PRL-3/alpha Tubulin 0.024 0.026 -10000 0 -0.37 1 1
mol:Ca2+ -0.076 0.13 0.38 1 -0.38 63 64
AGT -0.095 0.19 -10000 0 -0.36 158 158
CCNA2 -0.044 0.13 -10000 0 -0.42 19 19
TUBA1B 0.018 0 -10000 0 -10000 0 0
EGR1 -0.06 0.15 -10000 0 -0.37 82 82
CDK2/Cyclin E1 -0.016 0.12 -10000 0 -0.43 29 29
MAPK3 0.022 0.032 -10000 0 -0.37 2 2
PRL-2 /Rab GGTase beta 0.017 0.053 -10000 0 -0.37 8 8
MAPK1 0.021 0.035 -10000 0 -0.37 3 3
PTP4A1 -0.031 0.12 -10000 0 -0.59 5 5
PTP4A3 0.014 0.037 -10000 0 -0.29 7 7
PTP4A2 0.006 0.072 -10000 0 -0.4 15 15
ITGB1 0.02 0.041 -10000 0 -0.23 12 12
SRC 0.015 0.035 -10000 0 -0.43 3 3
RAC1 0.004 0.066 -10000 0 -0.57 2 2
Rab GGTase beta/Rab GGTase alpha 0.026 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.022 0.12 -10000 0 -0.56 5 5
RABGGTA 0.018 0 -10000 0 -10000 0 0
BCAR1 0.002 0.023 0.38 1 -0.18 1 2
RHOC 0.001 0.075 -10000 0 -0.5 5 5
RHOA -0.006 0.089 -10000 0 -0.42 14 14
cell motility 0.002 0.075 -10000 0 -0.36 6 6
PRL-1/alpha Tubulin -0.02 0.12 -10000 0 -0.61 4 4
PRL-3/alpha1 Integrin 0.011 0.077 -10000 0 -0.39 17 17
ROCK1 0.002 0.075 -10000 0 -0.36 6 6
RABGGTB 0.017 0.017 -10000 0 -0.25 2 2
CDK2 0.012 0.047 -10000 0 -0.31 10 10
mitosis -0.031 0.12 -10000 0 -0.59 5 5
ATF5 0.013 0.04 -10000 0 -0.28 9 9
Retinoic acid receptors-mediated signaling

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
HDAC1 0.017 0.023 -10000 0 -0.52 1 1
HDAC3 0.018 0 -10000 0 -10000 0 0
VDR -0.003 0.1 -10000 0 -0.51 21 21
Cbp/p300/PCAF 0.02 0.036 -10000 0 -0.31 6 6
EP300 0.014 0.047 -10000 0 -0.52 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.022 0.059 -10000 0 -0.28 3 3
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.017 0.012 -10000 0 -0.25 1 1
AKT1 0.03 0.093 0.22 53 -0.25 19 72
RAR alpha/9cRA/Cyclin H -0.024 0.062 -10000 0 -0.4 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.014 0.07 -10000 0 -0.29 9 9
CDC2 -0.012 0.12 -10000 0 -0.44 34 34
response to UV -0.002 0.009 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.015 0.049 -10000 0 -0.37 5 5
NCOR2 0.018 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.075 -10000 0 -0.37 21 21
RXRs/RARs/NRIP1/9cRA -0.009 0.19 -10000 0 -0.54 54 54
NCOA2 0.009 0.063 -10000 0 -0.4 11 11
NCOA3 0.013 0.047 -10000 0 -0.37 7 7
NCOA1 0.012 0.057 -10000 0 -0.52 6 6
VDR/VDR/DNA -0.003 0.1 -10000 0 -0.51 21 21
RARG 0.016 0.024 -10000 0 -0.52 1 1
RAR gamma1/9cRA 0.022 0.016 -10000 0 -0.31 1 1
MAPK3 0.015 0.027 -10000 0 -0.39 2 2
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
MAPK8 0.013 0.041 -10000 0 -0.52 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.002 0.12 -10000 0 -0.45 11 11
RARA 0.019 0.047 -10000 0 -0.25 8 8
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.014 0.067 -10000 0 -0.26 7 7
PRKCA 0.011 0.038 -10000 0 -0.26 8 8
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.026 0.21 -10000 0 -0.6 54 54
RXRG 0.014 0.063 -10000 0 -0.33 12 12
RXRA 0.011 0.08 -10000 0 -0.29 8 8
RXRB 0.021 0.041 -10000 0 -0.3 3 3
VDR/Vit D3/DNA -0.002 0.075 -10000 0 -0.37 21 21
RBP1 -0.076 0.19 -10000 0 -0.42 112 112
CRBP1/9-cic-RA -0.053 0.14 -10000 0 -0.3 112 112
RARB -0.025 0.13 -10000 0 -0.36 60 60
PRKCG 0.016 0.017 -10000 0 -10000 0 0
MNAT1 0.017 0.012 -10000 0 -0.25 1 1
RAR alpha/RXRs 0.02 0.15 -10000 0 -0.42 19 19
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.023 0.11 -10000 0 -0.33 14 14
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.064 -10000 0 -0.27 4 4
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.026 0.21 -10000 0 -0.6 54 54
positive regulation of DNA binding -0.023 0.059 -10000 0 -0.38 5 5
NRIP1 -0.085 0.38 -10000 0 -1.2 53 53
RXRs/RARs -0.011 0.15 -10000 0 -0.42 55 55
RXRs/RXRs/DNA/9cRA 0.003 0.12 -10000 0 -0.31 51 51
PRKACA 0.018 0 -10000 0 -10000 0 0
CDK7 0.017 0.012 -10000 0 -0.25 1 1
TFIIH 0.033 0.031 -10000 0 -0.3 4 4
RAR alpha/9cRA 0.04 0.041 -10000 0 -0.27 3 3
CCNH 0.014 0.047 -10000 0 -0.52 4 4
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
RAR gamma2/9cRA -0.002 0.022 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.002 0.14 -9999 0 -1.1 5 5
MKNK1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.006 0.055 -9999 0 -0.29 6 6
ATF2/c-Jun -0.028 0.19 -9999 0 -0.6 49 49
MAPK11 0.006 0.053 -9999 0 -0.28 5 5
MITF 0.014 0.071 -9999 0 -0.34 11 11
MAPKAPK5 0.018 0.059 -9999 0 -0.33 5 5
KRT8 -0.004 0.1 -9999 0 -0.34 31 31
MAPKAPK3 0.017 0.017 -9999 0 -0.25 2 2
MAPKAPK2 0.014 0.047 -9999 0 -0.52 4 4
p38alpha-beta/CK2 0.009 0.074 -9999 0 -0.39 6 6
CEBPB 0.011 0.072 -9999 0 -0.32 11 11
SLC9A1 0.018 0.059 -9999 0 -0.33 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.013 0.079 -9999 0 -0.31 6 6
p38alpha-beta/MNK1 0.023 0.059 -9999 0 -0.32 5 5
JUN -0.028 0.19 -9999 0 -0.6 49 49
PPARGC1A 0.003 0.088 -9999 0 -0.35 15 15
USF1 0.006 0.084 -9999 0 -0.36 14 14
RAB5/GDP/GDI1 0.019 0.042 -9999 0 -0.23 5 5
NOS2 0.008 0.059 -9999 0 -0.34 5 5
DDIT3 0.014 0.066 -9999 0 -0.37 6 6
RAB5A 0.018 0 -9999 0 -10000 0 0
HSPB1 -0.012 0.12 -9999 0 -0.33 54 54
p38alpha-beta/HBP1 0.021 0.066 -9999 0 -0.34 8 8
CREB1 0.014 0.075 -9999 0 -0.29 14 14
RAB5/GDP 0.013 0 -9999 0 -10000 0 0
EIF4E 0.025 0.049 -9999 0 -0.27 5 5
RPS6KA4 0.018 0.061 -9999 0 -0.32 6 6
PLA2G4A -0.006 0.1 -9999 0 -0.31 30 30
GDI1 0.017 0.061 -9999 0 -0.32 6 6
TP53 -0.001 0.096 -9999 0 -0.35 20 20
RPS6KA5 0 0.1 -9999 0 -0.34 33 33
ESR1 -0.09 0.17 -9999 0 -0.33 155 155
HBP1 0.015 0.04 -9999 0 -0.52 3 3
MEF2C -0.001 0.1 -9999 0 -0.34 32 32
MEF2A 0.017 0.062 -9999 0 -0.33 6 6
EIF4EBP1 0.008 0.08 -9999 0 -0.3 14 14
KRT19 -0.014 0.12 -9999 0 -0.34 53 53
ELK4 0.016 0.065 -9999 0 -0.31 9 9
ATF6 0.018 0.06 -9999 0 -0.32 6 6
ATF1 0.014 0.076 -9999 0 -0.29 14 14
p38alpha-beta/MAPKAPK2 0.02 0.069 -9999 0 -0.37 8 8
p38alpha-beta/MAPKAPK3 0.022 0.059 -9999 0 -0.32 5 5
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.001 0.094 -9999 0 -0.4 22 22
AKT1 0.029 0.15 -9999 0 -0.5 22 22
PTK2B 0.015 0.13 -9999 0 -0.56 15 15
VEGFR2 homodimer/Frs2 0.02 0.098 -9999 0 -0.56 10 10
CAV1 -0.001 0.083 -9999 0 -0.33 29 29
CALM1 0.018 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.019 0.11 -9999 0 -0.55 11 11
endothelial cell proliferation 0.046 0.13 -9999 0 -0.47 17 17
mol:Ca2+ 0.014 0.14 -9999 0 -0.57 17 17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.033 0.1 -9999 0 -0.54 10 10
RP11-342D11.1 0.005 0.14 -9999 0 -0.58 16 16
CDH5 0.013 0.052 -9999 0 -0.52 5 5
VEGFA homodimer 0.003 0.099 -9999 0 -0.27 52 52
SHC1 0.017 0.023 -9999 0 -0.52 1 1
SHC2 -0.06 0.19 -9999 0 -0.51 77 77
HRAS/GDP -0.036 0.099 -9999 0 -0.51 15 15
SH2D2A -0.039 0.15 -9999 0 -0.38 76 76
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.044 0.12 -9999 0 -0.46 16 16
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.008 0.14 -9999 0 -0.56 14 14
VEGFR1 homodimer 0.004 0.08 -9999 0 -0.45 15 15
SHC/GRB2/SOS1 0.026 0.13 -9999 0 -0.56 15 15
GRB10 0.005 0.17 -9999 0 -0.61 28 28
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
GRB2 0.016 0.024 -9999 0 -0.25 4 4
PAK1 -0.022 0.13 -9999 0 -0.37 54 54
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.029 0.12 -9999 0 -0.52 15 15
HRAS 0.012 0.051 -9999 0 -0.41 7 7
VEGF/Rho/ROCK1/Integrin Complex 0.018 0.12 -9999 0 -0.56 13 13
HIF1A -0.037 0.16 -9999 0 -0.46 61 61
FRS2 0.011 0.047 -9999 0 -0.27 13 13
oxygen and reactive oxygen species metabolic process 0.031 0.1 -9999 0 -0.53 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.018 0 -9999 0 -10000 0 0
Nck/Pak -0.007 0.095 -9999 0 -0.37 25 25
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.018 0.12 -9999 0 -0.63 11 11
mol:GDP -0.038 0.1 -9999 0 -0.53 16 16
mol:NADP 0.042 0.11 -9999 0 -0.4 17 17
eNOS/Hsp90 0.047 0.11 -9999 0 -0.38 16 16
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
mol:IP3 0.014 0.14 -9999 0 -0.58 17 17
HIF1A/ARNT -0.014 0.12 -9999 0 -0.37 47 47
SHB 0.008 0.067 -9999 0 -0.41 12 12
VEGFA -0.002 0.076 -9999 0 -0.28 31 31
VEGFC -0.001 0.095 -9999 0 -0.47 20 20
FAK1/Vinculin 0.034 0.13 -9999 0 -0.61 12 12
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.015 0.14 -9999 0 -0.6 15 15
PTPN6 0.015 0.035 -9999 0 -0.43 3 3
EPAS1 0.012 0.088 -9999 0 -0.44 18 18
mol:L-citrulline 0.042 0.11 -9999 0 -0.4 17 17
ITGAV -0.002 0.1 -9999 0 -0.48 21 21
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.028 0.11 -9999 0 -0.52 11 11
VEGFR2 homodimer/VEGFA homodimer 0.013 0.15 -9999 0 -0.64 16 16
VEGFR2/3 heterodimer 0.024 0.095 -9999 0 -0.56 10 10
VEGFB 0.017 0.023 -9999 0 -0.52 1 1
MAPK11 0.015 0.14 -9999 0 -0.59 17 17
VEGFR2 homodimer 0.018 0.11 -9999 0 -0.55 15 15
FLT1 0.004 0.08 -9999 0 -0.45 15 15
NEDD4 0.001 0.093 -9999 0 -0.53 15 15
MAPK3 0.017 0.13 -9999 0 -0.52 17 17
MAPK1 0.016 0.13 -9999 0 -0.52 17 17
VEGFA145/NRP2 0.009 0.065 -9999 0 -0.37 8 8
VEGFR1/2 heterodimer 0.016 0.11 -9999 0 -0.59 12 12
KDR 0.018 0.11 -9999 0 -0.55 15 15
VEGFA165/NRP1/VEGFR2 homodimer 0.017 0.14 -9999 0 -0.59 17 17
SRC 0.015 0.035 -9999 0 -0.43 3 3
platelet activating factor biosynthetic process 0.018 0.13 -9999 0 -0.54 17 17
PI3K 0.02 0.16 -9999 0 -0.58 22 22
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.02 0.11 -9999 0 -0.57 10 10
FES 0.011 0.15 -9999 0 -0.62 16 16
GAB1 0.02 0.15 -9999 0 -0.58 17 17
VEGFR2 homodimer/VEGFA homodimer/Src 0.022 0.11 -9999 0 -0.57 10 10
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
SOS1 0.017 0.023 -9999 0 -0.52 1 1
ARNT 0.018 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.041 0.12 -9999 0 -0.42 18 18
VEGFR2 homodimer/VEGFA homodimer/Yes 0.018 0.12 -9999 0 -0.54 13 13
PI3K/GAB1 0.027 0.16 -9999 0 -0.49 23 23
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.013 0.12 -9999 0 -0.44 18 18
PRKACA 0.018 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.024 0.12 -9999 0 -0.54 15 15
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
CDC42 0.015 0.14 -9999 0 -0.6 16 16
actin cytoskeleton reorganization -0.008 0.13 -9999 0 -0.55 14 14
PTK2 0.026 0.14 -9999 0 -0.66 12 12
EDG1 -0.003 0.19 -9999 0 -0.64 31 31
mol:DAG 0.014 0.14 -9999 0 -0.58 17 17
CaM/Ca2+ 0.021 0.13 -9999 0 -0.53 17 17
MAP2K3 0.015 0.14 -9999 0 -0.55 19 19
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.011 0.18 -9999 0 -0.62 28 28
PLCG1 0.014 0.14 -9999 0 -0.59 17 17
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.11 -9999 0 -0.5 13 13
IQGAP1 0.018 0 -9999 0 -10000 0 0
YES1 0.007 0.07 -9999 0 -0.43 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.023 0.11 -9999 0 -0.57 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.022 0.11 -9999 0 -0.57 10 10
cell migration 0.055 0.12 -9999 0 -0.64 8 8
mol:PI-3-4-5-P3 0.021 0.15 -9999 0 -0.54 22 22
FYN 0.008 0.067 -9999 0 -0.41 12 12
VEGFB/NRP1 0.014 0.13 -9999 0 -0.56 16 16
mol:NO 0.042 0.11 -9999 0 -0.4 17 17
PXN 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.036 0.098 -9999 0 -0.51 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.009 0.17 -9999 0 -0.62 28 28
VHL 0.015 0.029 -9999 0 -0.25 6 6
ITGB3 0.002 0.075 -9999 0 -0.32 25 25
NOS3 0.041 0.12 -9999 0 -0.45 17 17
VEGFR2 homodimer/VEGFA homodimer/Sck -0.021 0.15 -9999 0 -0.49 24 24
RAC1 0.018 0 -9999 0 -10000 0 0
PRKCA 0.019 0.13 -9999 0 -0.54 17 17
PRKCB 0.012 0.13 -9999 0 -0.54 17 17
VCL 0.016 0.029 -9999 0 -0.34 3 3
VEGFA165/NRP1 0.008 0.14 -9999 0 -0.59 16 16
VEGFR1/2 heterodimer/VEGFA homodimer 0.016 0.12 -9999 0 -0.59 13 13
VEGFA165/NRP2 0.009 0.065 -9999 0 -0.37 8 8
MAPKKK cascade 0.031 0.15 -9999 0 -0.51 28 28
NRP2 0.011 0.052 -9999 0 -0.33 11 11
VEGFC homodimer -0.001 0.095 -9999 0 -0.47 20 20
NCK1 0.011 0.045 -9999 0 -0.28 12 12
ROCK1 0.018 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.035 0.13 -9999 0 -0.6 12 12
MAP3K13 0.01 0.15 -9999 0 -0.58 19 19
PDPK1 0.027 0.14 -9999 0 -0.47 23 23
S1P3 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
PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
mol:S1P 0 0.005 -9999 0 -0.015 43 43
S1P1/S1P/Gi 0 0.1 -9999 0 -0.4 16 16
GNAO1 0.016 0.024 -9999 0 -0.25 4 4
S1P/S1P3/G12/G13 0.02 0.031 -9999 0 -0.29 4 4
AKT1 0.012 0.097 -9999 0 -0.58 12 12
AKT3 0.004 0.14 -9999 0 -1.2 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
GNAI2 0.007 0.075 -9999 0 -0.48 12 12
GNAI3 0.018 0.004 -9999 0 -10000 0 0
GNAI1 -0.016 0.12 -9999 0 -0.38 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.005 -9999 0 -0.017 43 43
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.019 0.12 -9999 0 -0.4 46 46
mol:Ca2+ 0.01 0.081 -9999 0 -0.36 8 8
MAPK3 0.016 0.078 -9999 0 -0.36 7 7
MAPK1 0.016 0.078 -9999 0 -0.36 7 7
JAK2 0.006 0.095 -9999 0 -0.35 17 17
CXCR4 -0.006 0.11 -9999 0 -0.41 18 18
FLT1 0.006 0.08 -9999 0 -0.45 15 15
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.015 0.08 -9999 0 -0.36 9 9
S1P/S1P3/Gi 0.01 0.082 -9999 0 -0.36 8 8
RAC1 0.018 0 -9999 0 -10000 0 0
RhoA/GTP 0.011 0.087 -9999 0 -0.38 9 9
VEGFA 0.001 0.076 -9999 0 -0.29 31 31
S1P/S1P2/Gi 0.009 0.076 -9999 0 -0.29 14 14
VEGFR1 homodimer/VEGFA homodimer 0.01 0.083 -9999 0 -0.34 19 19
RHOA 0.005 0.08 -9999 0 -0.52 12 12
S1P/S1P3/Gq -0.027 0.094 -9999 0 -0.27 58 58
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.088 -9999 0 -0.44 19 19
G12/G13 0.021 0.039 -9999 0 -0.37 4 4
GNA14 -0.079 0.18 -9999 0 -0.35 140 140
GNA15 0.002 0.076 -9999 0 -0.34 23 23
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.011 0.055 -9999 0 -0.36 10 10
GNA11 0.014 0.047 -9999 0 -0.52 4 4
Rac1/GTP 0.018 0.075 -9999 0 -0.34 7 7
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.014 0.047 -10000 0 -0.52 4 4
RAS family/GTP/Tiam1 0.003 0.08 -10000 0 -0.37 12 12
NT3 (dimer)/TRKC -0.019 0.093 -10000 0 -0.35 17 17
NT3 (dimer)/TRKB -0.015 0.1 -10000 0 -0.32 37 37
SHC/Grb2/SOS1/GAB1/PI3K 0.023 0.065 -10000 0 -10000 0 0
RAPGEF1 0.018 0 -10000 0 -10000 0 0
BDNF -0.016 0.091 -10000 0 -0.26 64 64
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
DYNLT1 0.018 0 -10000 0 -10000 0 0
NTRK1 0.01 0.053 -10000 0 -0.32 12 12
NTRK2 -0.017 0.11 -10000 0 -0.34 52 52
NTRK3 -0.009 0.081 -10000 0 -0.25 53 53
NT-4/5 (dimer)/TRKB -0.004 0.079 -10000 0 -0.31 23 23
neuron apoptosis 0.036 0.15 0.34 79 -10000 0 79
SHC 2-3/Grb2 -0.039 0.16 -10000 0 -0.38 77 77
SHC1 0.017 0.023 -10000 0 -0.52 1 1
SHC2 -0.061 0.2 -10000 0 -0.5 78 78
SHC3 -0.007 0.11 -10000 0 -0.47 17 17
STAT3 (dimer) -0.045 0.14 -10000 0 -0.34 89 89
NT3 (dimer)/TRKA 0.001 0.083 -10000 0 -0.33 17 17
RIN/GDP 0.047 0.05 -10000 0 -0.31 1 1
GIPC1 0.014 0.042 -10000 0 -0.45 4 4
KRAS 0.009 0.065 -10000 0 -0.44 10 10
DNAJA3 0.017 0.066 0.23 20 -0.26 6 26
RIN/GTP 0.011 0.025 -10000 0 -0.31 3 3
CCND1 -0.12 0.29 -10000 0 -0.75 89 89
MAGED1 -0.008 0.11 -10000 0 -0.48 27 27
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
RICS 0.003 0.083 -10000 0 -0.45 16 16
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.034 0.025 -10000 0 -0.3 2 2
GRB2 0.016 0.024 -10000 0 -0.25 4 4
NGF (dimer)/TRKA/MATK 0.008 0.054 -10000 0 -0.3 7 7
TRKA/NEDD4-2 -0.01 0.11 -10000 0 -0.37 39 39
ELMO1 0.017 0.017 -10000 0 -0.25 2 2
RhoG/GTP/ELMO1/DOCK1 0.016 0.049 -10000 0 -0.31 11 11
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.051 -10000 0 -0.41 7 7
DOCK1 0.006 0.078 -10000 0 -0.5 12 12
GAB2 0.009 0.048 -10000 0 -0.25 17 17
RIT2 0.015 0.035 -10000 0 -0.43 3 3
RIT1 0.016 0.033 -10000 0 -0.52 2 2
FRS2 0.011 0.047 -10000 0 -0.27 13 13
DNM1 0.013 0.047 -10000 0 -0.37 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0.033 -10000 0 -0.52 2 2
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.018 0.064 0.22 21 -0.25 6 27
mol:GDP 0.053 0.065 -10000 0 -0.4 2 2
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.012 0.011 -10000 0 -0.17 2 2
RIT1/GDP 0.048 0.049 -10000 0 -0.31 1 1
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
BDNF (dimer)/TRKB -0.007 0.09 -10000 0 -0.32 24 24
KIDINS220/CRKL/C3G 0.023 0.034 -10000 0 -0.37 4 4
SHC/RasGAP 0.016 0.059 -10000 0 -0.37 11 11
FRS2 family/SHP2 0.031 0.032 -10000 0 -0.3 2 2
SHC/GRB2/SOS1/GAB1 0.037 0.049 -10000 0 -0.26 12 12
RIT1/GTP 0.012 0.024 -10000 0 -0.38 2 2
NT3 (dimer) -0.021 0.11 -10000 0 -0.28 68 68
RAP1/GDP -0.006 0.028 -10000 0 -0.26 2 2
KIDINS220/CRKL 0.014 0.047 -10000 0 -0.52 4 4
BDNF (dimer) -0.016 0.09 -10000 0 -0.26 64 64
ubiquitin-dependent protein catabolic process -0.007 0.091 -10000 0 -0.31 39 39
Schwann cell development -0.008 0.017 -10000 0 -10000 0 0
EHD4 0.013 0.052 -10000 0 -0.52 5 5
FRS2 family/GRB2/SOS1 0.04 0.037 -10000 0 -0.39 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.038 0.037 -10000 0 -0.23 6 6
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
RAP1A 0.012 0.057 -10000 0 -0.52 6 6
CDC42/GTP -0.043 0.077 -10000 0 -0.35 14 14
ABL1 0.018 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.024 0.023 -10000 0 -0.37 1 1
Rap1/GTP 0.032 0.072 -10000 0 -0.41 7 7
STAT3 -0.045 0.14 -10000 0 -0.34 89 89
axon guidance -0.041 0.074 -10000 0 -0.34 14 14
MAPK3 0.013 0.05 -10000 0 -0.26 8 8
MAPK1 0.013 0.052 -10000 0 -0.27 9 9
CDC42/GDP 0.048 0.048 -10000 0 -0.26 2 2
NTF3 -0.021 0.11 -10000 0 -0.28 68 68
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.018 0.036 -10000 0 -0.31 4 4
PI3K 0.005 0.082 -10000 0 -0.37 21 21
FRS3 0.017 0.012 -10000 0 -0.25 1 1
FAIM 0.016 0.029 -10000 0 -0.34 3 3
GAB1 0.006 0.074 -10000 0 -0.43 14 14
RASGRF1 0.007 0.076 0.23 20 -0.27 11 31
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MCF2L -0.009 0.083 -10000 0 -0.3 21 21
RGS19 0.014 0.039 -10000 0 -0.36 5 5
CDC42 0.018 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.07 -10000 0 -0.38 7 7
Rac1/GDP 0.048 0.048 -10000 0 -0.26 2 2
NGF (dimer)/TRKA/GRIT 0.011 0.06 -10000 0 -0.31 15 15
neuron projection morphogenesis -0.013 0.13 -10000 0 -0.65 6 6
NGF (dimer)/TRKA/NEDD4-2 -0.007 0.091 -10000 0 -0.31 39 39
MAP2K1 0.034 0.045 -10000 0 -0.24 11 11
NGFR 0.004 0.065 -10000 0 -0.29 23 23
NGF (dimer)/TRKA/GIPC/GAIP 0.028 0.047 -10000 0 -0.27 10 10
RAS family/GTP/PI3K 0.011 0.077 -10000 0 -0.25 39 39
FRS2 family/SHP2/GRB2/SOS1 0.047 0.037 -10000 0 -0.38 2 2
NRAS 0.005 0.076 -10000 0 -0.4 16 16
GRB2/SOS1 0.024 0.023 -10000 0 -0.37 1 1
PRKCI 0.002 0.085 -10000 0 -0.43 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.052 -10000 0 -0.48 4 4
RASA1 0.004 0.078 -10000 0 -0.42 16 16
TRKA/c-Abl 0.021 0.038 -10000 0 -0.37 3 3
SQSTM1 0.012 0.053 -10000 0 -0.48 6 6
BDNF (dimer)/TRKB/GIPC 0.007 0.081 -10000 0 -0.28 22 22
NGF (dimer)/TRKA/p62/Atypical PKCs 0.017 0.059 -10000 0 -0.26 20 20
MATK -0.003 0.075 -10000 0 -0.27 38 38
NEDD4L -0.025 0.14 -10000 0 -0.45 48 48
RAS family/GDP -0.01 0.033 -10000 0 -0.28 1 1
NGF (dimer)/TRKA 0.009 0.07 0.24 21 -0.28 6 27
Rac1/GTP -0.02 0.052 -10000 0 -0.23 18 18
FRS2 family/SHP2/CRK family 0.045 0.043 -10000 0 -0.26 8 8
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.079 -9999 0 -0.37 18 18
CRKL 0.014 0.047 -9999 0 -0.52 4 4
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DOCK1 0.006 0.078 -9999 0 -0.5 12 12
ITGA4 -0.007 0.1 -9999 0 -0.39 32 32
alpha4/beta7 Integrin/MAdCAM1 0.023 0.079 -9999 0 -0.29 27 27
EPO -0.023 0.097 -9999 0 -0.25 80 80
alpha4/beta7 Integrin 0.009 0.074 -9999 0 -0.37 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.033 -9999 0 -0.52 2 2
alpha4/beta1 Integrin 0.006 0.084 -9999 0 -0.41 17 17
EPO/EPOR (dimer) -0.003 0.069 -9999 0 -0.32 2 2
lamellipodium assembly 0.022 0.069 -9999 0 -0.35 6 6
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
PI3K 0.005 0.082 -9999 0 -0.37 21 21
ARF6 0.016 0.033 -9999 0 -0.52 2 2
JAK2 0.007 0.079 -9999 0 -0.32 19 19
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 33 33
MADCAM1 0.014 0.033 -9999 0 -0.25 8 8
cell adhesion 0.021 0.079 -9999 0 -0.29 27 27
CRKL/CBL 0.023 0.035 -9999 0 -0.37 4 4
ITGB1 0.014 0.044 -9999 0 -0.41 5 5
SRC -0.001 0.11 -9999 0 -0.31 48 48
ITGB7 0.018 0 -9999 0 -10000 0 0
RAC1 0.018 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.005 0.12 -9999 0 -0.35 46 46
p130Cas/Crk/Dock1 0.018 0.1 -9999 0 -0.46 8 8
VCAM1 -0.022 0.13 -9999 0 -0.42 48 48
RHOA 0.005 0.08 -9999 0 -0.52 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.028 0.07 -9999 0 -0.3 18 18
BCAR1 0.006 0.1 -9999 0 -0.29 42 42
EPOR 0.016 0.02 -9999 0 -0.25 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.017 0.012 -9999 0 -0.25 1 1
GIT1 0.014 0.035 -9999 0 -0.3 6 6
Rac1/GTP 0.022 0.071 -9999 0 -0.36 6 6
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.018 0 -10000 0 -10000 0 0
NFATC1 0.033 0.073 -10000 0 -0.26 24 24
NFATC2 0.027 0.041 -10000 0 -0.25 1 1
NFATC3 0.017 0.006 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.34 3 3
Calcineurin A alpha-beta B1/CABIN1 0.003 0.094 -10000 0 -0.38 13 13
Exportin 1/Ran/NUP214 0.035 0.018 -10000 0 -0.3 1 1
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.021 0.09 -10000 0 -0.42 9 9
BCL2/BAX -0.071 0.16 -10000 0 -0.37 115 115
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
BAX 0.016 0.02 -10000 0 -0.25 3 3
MAPK14 0.018 0.012 -10000 0 -0.25 1 1
BAD 0.017 0.023 -10000 0 -0.52 1 1
CABIN1/MEF2D 0.012 0.09 -10000 0 -0.39 11 11
Calcineurin A alpha-beta B1/BCL2 -0.11 0.22 -10000 0 -0.47 144 144
FKBP8 0.017 0.012 -10000 0 -0.25 1 1
activation-induced cell death of T cells -0.012 0.089 0.38 11 -10000 0 11
KPNB1 0.012 0.057 -10000 0 -0.52 6 6
KPNA2 -0.001 0.084 -10000 0 -0.34 27 27
XPO1 0.018 0 -10000 0 -10000 0 0
SFN -0.015 0.12 -10000 0 -0.45 37 37
MAP3K8 -0.036 0.15 -10000 0 -0.39 70 70
NFAT4/CK1 alpha 0.011 0.074 -10000 0 -0.24 37 37
MEF2D/NFAT1/Cbp/p300 0.057 0.059 -10000 0 -0.38 2 2
CABIN1 0.003 0.095 -10000 0 -0.39 13 13
CALM1 0.018 0.001 -10000 0 -10000 0 0
RAN 0.017 0.012 -10000 0 -0.25 1 1
MAP3K1 -0.03 0.14 -10000 0 -0.42 58 58
CAMK4 0.011 0.052 -10000 0 -0.33 11 11
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.016 0.026 -10000 0 -0.39 2 2
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.11 -10000 0 -0.37 39 39
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
MAPK8 0.015 0.041 -10000 0 -0.52 3 3
MAPK9 -0.006 0.11 -10000 0 -0.51 24 24
YWHAG 0.017 0.017 -10000 0 -0.25 2 2
FKBP1A 0.017 0.017 -10000 0 -0.25 2 2
NFAT1-c-4/YWHAQ 0.051 0.067 -10000 0 -0.28 1 1
PRKCH 0.011 0.056 -10000 0 -0.42 8 8
CABIN1/Cbp/p300 0.023 0.042 -10000 0 -0.37 6 6
CASP3 0.018 0.001 -10000 0 -10000 0 0
PIM1 0.013 0.035 -10000 0 -0.25 9 9
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.009 -10000 0 -0.14 2 2
apoptosis -0.026 0.046 -10000 0 -0.32 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.052 -10000 0 -0.33 1 1
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.01 0.06 -10000 0 -0.43 9 9
JNK2/NFAT4 0.013 0.062 -10000 0 -0.28 23 23
BAD/BCL-XL 0.026 0.017 -10000 0 -0.37 1 1
PRKCD 0.014 0.042 -10000 0 -0.45 4 4
NUP214 0.016 0.026 -10000 0 -0.39 2 2
PRKCZ 0 0.001 -10000 0 -10000 0 0
PRKCA 0.014 0.033 -10000 0 -0.25 8 8
PRKCG 0.018 0 -10000 0 -10000 0 0
PRKCQ -0.014 0.1 -10000 0 -0.31 51 51
FKBP38/BCL2 -0.07 0.16 -10000 0 -0.37 115 115
EP300 0.014 0.047 -10000 0 -0.52 4 4
PRKCB1 -0.052 0.16 -10000 0 -0.39 90 90
CSNK2A1 0.017 0.023 -10000 0 -0.52 1 1
NFATc/JNK1 0.041 0.073 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.025 0.007 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0.011 -10000 0 -0.17 2 2
CSNK1A1 0.022 0.015 -10000 0 -0.31 1 1
CaM/Ca2+/CAMK IV 0.021 0.032 -10000 0 -0.31 3 3
NFATc/ERK1 0.041 0.073 -10000 0 -0.49 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.019 0.091 -10000 0 -0.42 10 10
NR4A1 0.052 0.066 -10000 0 -0.51 2 2
GSK3B 0.018 0.001 -10000 0 -10000 0 0
positive T cell selection 0.017 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.027 0.036 -10000 0 -0.25 2 2
RCH1/ KPNB1 0.009 0.074 -10000 0 -0.38 15 15
YWHAQ 0.014 0.039 -10000 0 -0.36 5 5
PRKACA 0.018 0.001 -10000 0 -10000 0 0
AKAP5 -0.033 0.15 -10000 0 -0.42 61 61
MEF2D 0.018 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0.017 -10000 0 -0.25 2 2
NFATc/p38 alpha 0.042 0.07 -10000 0 -10000 0 0
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
BCL2 -0.11 0.22 -10000 0 -0.47 144 144
LPA4-mediated signaling events

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
ADCY4 0.011 0.053 -9999 0 -0.31 13 13
ADCY5 -0.01 0.074 -9999 0 -0.32 15 15
ADCY6 0.014 0.042 -9999 0 -0.31 8 8
ADCY7 0.007 0.06 -9999 0 -0.32 14 14
ADCY1 0.015 0.038 -9999 0 -0.31 6 6
ADCY2 -0.03 0.11 -9999 0 -0.33 51 51
ADCY3 0.01 0.054 -9999 0 -0.31 13 13
ADCY8 0.011 0.046 -9999 0 -0.31 7 7
PRKCE 0.007 0.044 -9999 0 -0.31 9 9
ADCY9 0.002 0.075 -9999 0 -0.33 24 24
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.002 0.072 -9999 0 -0.31 14 14
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.014 0.044 -9999 0 -0.41 5 5
ITGB7 0.018 0 -9999 0 -10000 0 0
ITGA4 -0.007 0.1 -9999 0 -0.39 32 32
alpha4/beta7 Integrin 0.009 0.074 -9999 0 -0.37 16 16
alpha4/beta1 Integrin 0.006 0.084 -9999 0 -0.41 17 17
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.014 0.053 -10000 0 -0.37 4 4
CRKL 0.02 0.086 -10000 0 -0.45 11 11
mol:PIP3 -0.004 0.091 0.46 19 -10000 0 19
AKT1 0.007 0.068 0.34 18 -0.28 4 22
PTK2B 0.017 0.017 -10000 0 -0.25 2 2
RAPGEF1 0.026 0.082 -10000 0 -0.44 10 10
RANBP10 0.018 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
HGF/MET/SHIP2 0.016 0.071 -10000 0 -0.31 18 18
MAP3K5 0.018 0.099 -10000 0 -0.4 15 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.021 0.079 -10000 0 -0.29 24 24
AP1 -0.087 0.16 -10000 0 -0.37 107 107
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0.023 -10000 0 -0.52 1 1
apoptosis -0.14 0.3 -10000 0 -0.74 100 100
STAT3 (dimer) 0.029 0.058 -10000 0 -0.29 2 2
GAB1/CRKL/SHP2/PI3K 0.029 0.098 -10000 0 -0.42 13 13
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.03 0.081 -10000 0 -0.46 9 9
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
PTEN -0.002 0.1 -10000 0 -0.52 19 19
ELK1 -0.005 0.036 0.25 3 -0.17 6 9
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.023 0.045 -10000 0 -0.23 7 7
PAK1 -0.005 0.089 0.31 18 -0.26 29 47
HGF/MET/RANBP10 0.02 0.063 -10000 0 -0.31 13 13
HRAS 0.025 0.077 -10000 0 -0.52 6 6
DOCK1 0.021 0.093 -10000 0 -0.49 10 10
GAB1 0.016 0.087 -10000 0 -0.48 11 11
CRK 0.021 0.084 -10000 0 -0.47 10 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.083 -10000 0 -0.49 12 12
JUN -0.034 0.15 -10000 0 -0.46 57 57
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.005 0.05 -10000 0 -0.24 17 17
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
cell morphogenesis 0.039 0.088 -10000 0 -0.36 9 9
GRB2/SHC 0.024 0.049 -10000 0 -0.23 11 11
FOS -0.11 0.2 -10000 0 -0.37 171 171
GLMN -0.001 0.014 -10000 0 -0.25 1 1
cell motility -0.005 0.036 0.25 3 -0.17 6 9
HGF/MET/MUC20 0.008 0.062 -10000 0 -0.32 13 13
cell migration 0.024 0.048 -10000 0 -0.23 11 11
GRB2 0.016 0.024 -10000 0 -0.25 4 4
CBL 0.017 0.012 -10000 0 -0.25 1 1
MET/RANBP10 0.014 0.053 -10000 0 -0.37 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.025 0.059 -10000 0 -0.3 2 2
MET/MUC20 0.001 0.052 -10000 0 -0.2 31 31
RAP1B 0.03 0.08 -10000 0 -0.41 10 10
RAP1A 0.03 0.087 -10000 0 -0.44 12 12
HGF/MET/RANBP9 0.019 0.063 -10000 0 -0.31 13 13
RAF1 0.031 0.073 -10000 0 -0.52 5 5
STAT3 0.029 0.059 -10000 0 -0.29 2 2
cell proliferation 0.037 0.07 -10000 0 -0.32 13 13
RPS6KB1 0.009 0.023 -10000 0 -10000 0 0
MAPK3 -0.01 0.04 0.66 1 -10000 0 1
MAPK1 -0.009 0.055 0.76 2 -10000 0 2
RANBP9 0.017 0.012 -10000 0 -0.25 1 1
MAPK8 0.025 0.093 -10000 0 -0.4 8 8
SRC 0.029 0.058 -10000 0 -0.28 2 2
PI3K 0.011 0.077 -10000 0 -0.26 29 29
MET/Glomulin 0.005 0.047 -10000 0 -0.17 32 32
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MAP2K1 0.037 0.069 -10000 0 -0.51 4 4
MET 0 0.075 -10000 0 -0.29 31 31
MAP4K1 0.03 0.081 -10000 0 -0.46 9 9
PTK2 0.016 0.029 -10000 0 -0.34 3 3
MAP2K2 0.036 0.073 -10000 0 -0.5 5 5
BAD 0.013 0.064 0.32 18 -0.26 5 23
MAP2K4 0.015 0.1 -10000 0 -0.35 17 17
SHP2/GRB2/SOS1/GAB1 -0.016 0.067 -10000 0 -0.39 12 12
INPPL1 0.012 0.055 -10000 0 -0.44 7 7
PXN 0.018 0 -10000 0 -10000 0 0
SH3KBP1 0 0.086 -10000 0 -0.38 23 23
HGS 0.012 0.048 -10000 0 -0.25 11 11
PLCgamma1/PKC 0.012 0.019 -10000 0 -0.27 2 2
HGF 0.008 0.069 -10000 0 -0.45 11 11
RASA1 0.004 0.078 -10000 0 -0.42 16 16
NCK1 0.011 0.045 -10000 0 -0.28 12 12
PTPRJ 0.012 0.055 -10000 0 -0.44 7 7
NCK/PLCgamma1 0.024 0.055 -10000 0 -0.24 11 11
PDPK1 0.003 0.07 0.37 18 -10000 0 18
HGF/MET/SHIP 0.008 0.062 -10000 0 -0.32 13 13
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.029 0.17 -10000 0 -0.46 9 9
CRKL 0.006 0.074 -10000 0 -0.3 8 8
mol:DAG 0.006 0.083 -10000 0 -0.28 3 3
HRAS 0.024 0.075 -10000 0 -0.41 2 2
MAPK8 0.009 0.058 -10000 0 -0.28 4 4
RAP1A 0.005 0.077 -10000 0 -0.32 9 9
GAB1 0.002 0.08 -10000 0 -0.31 9 9
MAPK14 0.011 0.054 -10000 0 -0.24 1 1
EPO -0.025 0.098 -10000 0 -0.26 80 80
PLCG1 0.006 0.084 -10000 0 -0.29 3 3
EPOR/TRPC2/IP3 Receptors 0.013 0.024 -10000 0 -0.27 3 3
RAPGEF1 0.018 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.001 0.073 -10000 0 -0.32 10 10
GAB1/SHC/GRB2/SOS1 0.02 0.074 -10000 0 -0.43 2 2
EPO/EPOR (dimer) -0.005 0.071 -10000 0 -0.32 2 2
IRS2 -0.013 0.1 -10000 0 -0.33 26 26
STAT1 -0.026 0.14 -10000 0 -0.33 52 52
STAT5B -0.002 0.1 -10000 0 -0.32 3 3
cell proliferation 0.016 0.054 -10000 0 -0.27 3 3
GAB1/SHIP/PIK3R1/SHP2/SHC -0.031 0.066 -10000 0 -0.31 12 12
TEC 0.005 0.074 -10000 0 -0.27 11 11
SOCS3 0.005 0.074 -10000 0 -0.38 17 17
STAT1 (dimer) -0.026 0.14 -10000 0 -0.32 52 52
JAK2 0.008 0.054 -10000 0 -0.32 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
EPO/EPOR (dimer)/JAK2 0.015 0.083 -10000 0 -0.29 6 6
EPO/EPOR -0.005 0.071 -10000 0 -0.32 2 2
LYN 0.012 0.033 -10000 0 -0.26 7 7
TEC/VAV2 0.014 0.076 -10000 0 -0.29 6 6
elevation of cytosolic calcium ion concentration 0.013 0.023 -10000 0 -0.27 3 3
SHC1 0.017 0.023 -10000 0 -0.52 1 1
EPO/EPOR (dimer)/LYN 0.009 0.066 -10000 0 -0.26 2 2
mol:IP3 0.006 0.083 -10000 0 -0.28 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.017 0.11 -10000 0 -0.32 39 39
SH2B3 0.015 0.024 -10000 0 -0.52 1 1
NFKB1 0.01 0.055 -10000 0 -0.27 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.004 0.05 0.26 1 -0.23 11 12
PTPN6 0 0.072 -10000 0 -0.29 6 6
TEC/VAV2/GRB2 0.021 0.074 -10000 0 -0.28 6 6
EPOR 0.013 0.024 -10000 0 -0.27 3 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.075 -10000 0 -0.44 2 2
SOS1 0.017 0.023 -10000 0 -0.52 1 1
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
CRKL/CBL/C3G 0.023 0.073 -10000 0 -0.36 3 3
VAV2 0.007 0.071 -10000 0 -0.3 4 4
CBL 0.008 0.07 -10000 0 -0.3 4 4
SHC/Grb2/SOS1 -0.021 0.044 -10000 0 -0.28 4 4
STAT5A -0.005 0.11 -10000 0 -0.31 9 9
GRB2 0.016 0.024 -10000 0 -0.25 4 4
STAT5 (dimer) -0.013 0.15 -10000 0 -0.35 38 38
LYN/PLCgamma2 -0.002 0.082 -10000 0 -0.36 16 16
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
BTK -0.005 0.092 -10000 0 -0.31 22 22
BCL2 -0.15 0.38 -10000 0 -0.86 117 117
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 0.041 0.037 -10000 0 -0.27 7 7
HDAC3 0.018 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.011 -10000 0 -0.22 1 1
GATA1/HDAC4 0.026 0.017 -10000 0 -0.37 1 1
GATA1/HDAC5 0.026 0.017 -10000 0 -0.37 1 1
GATA2/HDAC5 0.008 0.068 -10000 0 -0.37 10 10
HDAC5/BCL6/BCoR 0.016 0.078 -10000 0 -0.3 28 28
HDAC9 0.011 0.045 -10000 0 -0.28 12 12
Glucocorticoid receptor/Hsp90/HDAC6 0.021 0.068 -10000 0 -0.3 21 21
HDAC4/ANKRA2 0.013 0.072 -10000 0 -0.37 18 18
HDAC5/YWHAB 0.023 0.032 -10000 0 -0.37 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.023 0.013 -10000 0 -0.2 1 1
GATA2 -0.007 0.093 -10000 0 -0.31 40 40
HDAC4/RFXANK 0.025 0.019 -10000 0 -0.37 1 1
BCOR 0.009 0.07 -10000 0 -0.52 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.015 0.037 -10000 0 -0.39 4 4
HDAC5 0.017 0.023 -10000 0 -0.52 1 1
GNB1/GNG2 0.021 0.043 -10000 0 -0.37 6 6
Histones 0.02 0.07 -10000 0 -0.25 29 29
ADRBK1 0.018 0 -10000 0 -10000 0 0
HDAC4 0.017 0.023 -10000 0 -0.52 1 1
XPO1 0.018 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.013 0.072 -10000 0 -0.37 18 18
HDAC4/Ubc9 0.026 0.017 -10000 0 -0.37 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.024 0.027 -10000 0 -0.37 2 2
TUBA1B 0.018 0 -10000 0 -10000 0 0
HDAC6 0.018 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.025 0.019 -10000 0 -0.37 1 1
CAMK4 0.011 0.052 -10000 0 -0.33 11 11
Tubulin/HDAC6 0.022 0.063 -10000 0 -0.3 17 17
SUMO1 0.018 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
GATA1 0.018 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.34 3 3
NR3C1 -0.001 0.098 -10000 0 -0.51 19 19
SUMO1/HDAC4 0.036 0.019 -10000 0 -0.31 1 1
SRF 0.016 0.024 -10000 0 -0.25 4 4
HDAC4/YWHAB 0.023 0.032 -10000 0 -0.37 3 3
Tubulin 0.011 0.073 -10000 0 -0.37 17 17
HDAC4/14-3-3 E 0.024 0.03 -10000 0 -0.44 2 2
GNB1 0.013 0.052 -10000 0 -0.52 5 5
RANGAP1 0.014 0.037 -10000 0 -0.29 7 7
BCL6/BCoR 0.004 0.089 -10000 0 -0.37 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.035 0.015 -10000 0 -0.3 1 1
HDAC4/SRF 0.03 0.037 -10000 0 -0.3 4 4
HDAC4/ER alpha -0.1 0.18 -10000 0 -0.37 151 151
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.02 0.069 -10000 0 -0.25 29 29
cell motility 0.022 0.063 -10000 0 -0.3 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.018 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.013 0 -10000 0 -10000 0 0
BCL6 -0.004 0.1 -10000 0 -0.45 24 24
HDAC4/CaMK II delta B 0.017 0.023 -10000 0 -0.52 1 1
Hsp90/HDAC6 0.023 0.033 -10000 0 -0.37 3 3
ESR1 -0.16 0.24 -10000 0 -0.46 199 199
HDAC6/HDAC11 0.004 0.089 -10000 0 -0.37 28 28
Ran/GTP/Exportin 1 0.039 0.013 -10000 0 -10000 0 0
NPC 0.01 0.008 -10000 0 -10000 0 0
MEF2C -0.014 0.12 -10000 0 -0.45 36 36
RAN 0.017 0.012 -10000 0 -0.25 1 1
HDAC4/MEF2C 0.035 0.069 -10000 0 -0.24 28 28
GNG2 0.016 0.029 -10000 0 -0.34 3 3
NCOR2 0.018 0 -10000 0 -10000 0 0
TUBB2A -0.004 0.1 -10000 0 -0.43 26 26
HDAC11 -0.012 0.12 -10000 0 -0.5 31 31
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
RANBP2 0.017 0.017 -10000 0 -0.25 2 2
ANKRA2 0 0.095 -10000 0 -0.52 17 17
RFXANK 0.017 0.012 -10000 0 -0.25 1 1
nuclear import -0.032 0.035 0.31 5 -10000 0 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.014 0.047 -10000 0 -0.52 4 4
Rac1/GDP 0.003 0.012 -10000 0 -10000 0 0
DOCK1 0.006 0.078 -10000 0 -0.5 12 12
ITGA4 -0.007 0.1 -10000 0 -0.39 32 32
RAC1 0.018 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.074 -10000 0 -0.37 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0.033 -10000 0 -0.52 2 2
alpha4/beta1 Integrin 0.019 0.073 -10000 0 -0.34 17 17
alpha4/beta7 Integrin/Paxillin 0.028 0.058 -10000 0 -0.27 16 16
lamellipodium assembly 0.028 0.091 -10000 0 -0.35 22 22
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
PI3K 0.005 0.082 -10000 0 -0.37 21 21
ARF6 0.016 0.033 -10000 0 -0.52 2 2
TLN1 0.017 0.023 -10000 0 -0.52 1 1
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 33 33
ARF6/GTP 0.031 0.061 -10000 0 -0.47 2 2
cell adhesion 0.033 0.064 -10000 0 -0.27 18 18
CRKL/CBL 0.023 0.035 -10000 0 -0.37 4 4
alpha4/beta1 Integrin/Paxillin 0.026 0.067 -10000 0 -0.3 17 17
ITGB1 0.014 0.044 -10000 0 -0.41 5 5
ITGB7 0.018 0 -10000 0 -10000 0 0
ARF6/GDP 0.001 0.034 -10000 0 -0.51 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.015 0.1 -10000 0 -0.3 40 40
p130Cas/Crk/Dock1 0.027 0.054 -10000 0 -0.3 13 13
VCAM1 -0.022 0.13 -10000 0 -0.42 48 48
alpha4/beta1 Integrin/Paxillin/Talin 0.035 0.065 -10000 0 -0.28 18 18
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.066 -10000 0 -0.28 18 18
BCAR1 0.017 0.012 -10000 0 -0.25 1 1
mol:GDP -0.032 0.065 0.27 18 -10000 0 18
CBL 0.017 0.012 -10000 0 -0.25 1 1
PRKACA 0.018 0 -10000 0 -10000 0 0
GIT1 0.014 0.035 -10000 0 -0.3 6 6
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.035 0.065 -10000 0 -0.28 18 18
Rac1/GTP -0.019 0.087 -10000 0 -0.38 22 22
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.009 0.07 0.39 11 -10000 0 11
KIRREL 0.007 0.075 -10000 0 -0.53 10 10
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.01 0.07 -10000 0 -0.39 11 11
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
ARRB2 0.018 0 -10000 0 -10000 0 0
WASL 0.01 0.066 -10000 0 -0.52 8 8
Nephrin/NEPH1/podocin/CD2AP 0.028 0.059 -10000 0 -0.27 14 14
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.025 0.06 -10000 0 -0.29 5 5
FYN 0.014 0.059 -10000 0 -0.25 20 20
mol:Ca2+ 0.027 0.06 -10000 0 -0.29 13 13
mol:DAG 0.028 0.06 -10000 0 -0.29 13 13
NPHS2 0.015 0.036 -10000 0 -0.43 3 3
mol:IP3 0.028 0.06 -10000 0 -0.29 13 13
regulation of endocytosis 0.028 0.058 -10000 0 -0.25 13 13
Nephrin/NEPH1/podocin/Cholesterol 0.018 0.056 -10000 0 -0.28 13 13
establishment of cell polarity 0.009 0.07 -10000 0 -0.39 11 11
Nephrin/NEPH1/podocin/NCK1-2 0.035 0.06 -10000 0 -0.25 14 14
Nephrin/NEPH1/beta Arrestin2 0.029 0.059 -10000 0 -0.26 13 13
NPHS1 0.004 0.061 -10000 0 -0.26 25 25
Nephrin/NEPH1/podocin 0.02 0.061 -10000 0 -0.25 20 20
TJP1 0.013 0.052 -10000 0 -0.52 5 5
NCK1 0.011 0.045 -10000 0 -0.28 12 12
NCK2 0.015 0.026 -10000 0 -0.25 5 5
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.029 0.061 -10000 0 -0.3 13 13
CD2AP 0.016 0.029 -10000 0 -0.34 3 3
Nephrin/NEPH1/podocin/GRB2 0.028 0.058 -10000 0 -0.27 13 13
GRB2 0.016 0.024 -10000 0 -0.25 4 4
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.068 -10000 0 -0.27 24 24
cytoskeleton organization 0.029 0.063 -10000 0 -0.27 14 14
Nephrin/NEPH1 0.011 0.049 -10000 0 -0.27 11 11
Nephrin/NEPH1/ZO-1 0.019 0.066 -10000 0 -0.31 16 16
Aurora C signaling

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
INCENP 0.002 0.081 -9999 0 -0.36 22 22
Aurora C/Aurora B/INCENP 0.016 0.061 -9999 0 -0.28 14 14
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.007 0.037 -9999 0 -0.52 2 2
AURKB 0.009 0.056 -9999 0 -0.31 14 14
AURKC 0.008 0.053 -9999 0 -0.27 18 18
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.017 0.1 -10000 0 -1.3 1 1
CLOCK 0.02 0.024 -10000 0 -0.52 1 1
TIMELESS/CRY2 0.041 0.06 -10000 0 -1.2 1 1
DEC1/BMAL1 0.015 0.072 -10000 0 -0.39 15 15
ATR 0.017 0.012 -10000 0 -0.25 1 1
NR1D1 0.036 0.045 -10000 0 -10000 0 0
ARNTL 0.009 0.078 -10000 0 -0.49 12 12
TIMELESS 0.036 0.065 -10000 0 -1.3 1 1
NPAS2 -0.004 0.094 -10000 0 -0.32 39 39
CRY2 0.017 0.012 -10000 0 -0.25 1 1
mol:CO -0.014 0.012 0.14 1 -10000 0 1
CHEK1 -0.046 0.16 -10000 0 -0.38 84 84
mol:HEME 0.014 0.012 -10000 0 -0.14 1 1
PER1 0.014 0.037 -10000 0 -0.29 7 7
BMAL/CLOCK/NPAS2 0.03 0.082 -10000 0 -0.32 21 21
BMAL1/CLOCK 0.042 0.076 -10000 0 -0.54 2 2
S phase of mitotic cell cycle 0.017 0.1 -10000 0 -1.3 1 1
TIMELESS/CHEK1/ATR 0.017 0.1 -10000 0 -1.4 1 1
mol:NADPH 0.014 0.012 -10000 0 -0.14 1 1
PER1/TIMELESS 0.039 0.063 -10000 0 -1.2 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.011 0.057 -10000 0 -0.4 9 9
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.01 0.078 0.29 16 -10000 0 16
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
S1P/S1P5/G12 0.012 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.024 -10000 0 -0.25 4 4
RhoA/GTP 0.01 0.08 -10000 0 -0.29 16 16
negative regulation of cAMP metabolic process 0.008 0.072 -10000 0 -0.29 12 12
GNAZ 0.001 0.088 -10000 0 -0.44 19 19
GNAI3 0.018 0 -10000 0 -10000 0 0
GNA12 0.018 0 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.008 0.072 -10000 0 -0.29 12 12
RhoA/GDP 0.004 0.058 -10000 0 -0.38 12 12
RHOA 0.005 0.08 -10000 0 -0.52 12 12
GNAI1 -0.017 0.12 -10000 0 -0.38 46 46
FoxO family signaling

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
G6PC 0.04 0.082 -9999 0 -1.3 1 1
PLK1 0.03 0.18 -9999 0 -0.68 9 9
CDKN1B 0.062 0.17 -9999 0 -0.49 29 29
FOXO3 0.022 0.19 -9999 0 -0.57 21 21
KAT2B 0.003 0.02 -9999 0 -0.051 16 16
FOXO1/SIRT1 0.035 0.067 -9999 0 -0.37 5 5
CAT 0.024 0.2 -9999 0 -0.86 12 12
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
AKT1 0.019 0.057 -9999 0 -0.36 9 9
FOXO1 0.035 0.067 -9999 0 -0.36 5 5
MAPK10 0.014 0.073 -9999 0 -0.26 27 27
mol:GTP 0.001 0.003 -9999 0 -10000 0 0
FOXO4 0.061 0.1 -9999 0 -0.4 5 5
response to oxidative stress 0.008 0.022 -9999 0 -0.052 17 17
FOXO3A/SIRT1 0.035 0.16 -9999 0 -0.49 19 19
XPO1 0.018 0.001 -9999 0 -10000 0 0
EP300 0.017 0.047 -9999 0 -0.52 4 4
BCL2L11 0.027 0.038 -9999 0 -10000 0 0
FOXO1/SKP2 0.035 0.071 -9999 0 -0.42 5 5
mol:GDP 0.008 0.022 -9999 0 -0.052 17 17
RAN 0.018 0.012 -9999 0 -0.25 1 1
GADD45A 0.038 0.22 -9999 0 -0.9 21 21
YWHAQ 0.014 0.039 -9999 0 -0.36 5 5
FOXO1/14-3-3 family 0.066 0.061 -9999 0 -0.34 2 2
MST1 0.02 0.03 -9999 0 -0.29 3 3
CSNK1D 0.018 0 -9999 0 -10000 0 0
CSNK1E 0.017 0.012 -9999 0 -0.25 1 1
FOXO4/14-3-3 family 0.04 0.081 -9999 0 -0.56 1 1
YWHAB 0.015 0.037 -9999 0 -0.39 4 4
MAPK8 0.034 0.038 -9999 0 -0.26 7 7
MAPK9 0.023 0.067 -9999 0 -0.25 27 27
YWHAG 0.017 0.017 -9999 0 -0.25 2 2
YWHAE 0.016 0.029 -9999 0 -0.34 3 3
YWHAZ 0.017 0.017 -9999 0 -0.25 2 2
SIRT1 0.018 0.035 -9999 0 -0.35 3 3
SOD2 0.066 0.17 -9999 0 -0.66 8 8
RBL2 0.046 0.16 -9999 0 -0.82 6 6
RAL/GDP 0.031 0.034 -9999 0 -0.31 4 4
CHUK 0.009 0.083 -9999 0 -0.5 13 13
Ran/GTP 0.016 0.009 -9999 0 -0.16 1 1
CSNK1G2 0.016 0.033 -9999 0 -0.52 2 2
RAL/GTP 0.036 0.035 -9999 0 -0.28 4 4
CSNK1G1 0.017 0.012 -9999 0 -0.25 1 1
FASLG -0.12 0.41 -9999 0 -1.4 49 49
SKP2 0.007 0.052 -9999 0 -0.25 20 20
USP7 0.018 0.012 -9999 0 -0.26 1 1
IKBKB 0.015 0.051 -9999 0 -0.31 10 10
CCNB1 -0.02 0.32 -9999 0 -1.1 38 38
FOXO1-3a-4/beta catenin 0.068 0.17 -9999 0 -0.41 22 22
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.071 -9999 0 -0.41 5 5
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
SGK1 0.003 0.02 -9999 0 -0.051 16 16
CSNK1G3 0.013 0.052 -9999 0 -0.52 5 5
Ran/GTP/Exportin 1 0.028 0.011 -9999 0 -10000 0 0
ZFAND5 0.067 0.09 -9999 0 -0.39 1 1
SFN -0.015 0.12 -9999 0 -0.45 37 37
CDK2 0.015 0.047 -9999 0 -0.3 10 10
FOXO3A/14-3-3 0.043 0.08 -9999 0 -0.42 3 3
CREBBP 0.019 0.033 -9999 0 -0.52 2 2
FBXO32 -0.007 0.3 -9999 0 -1.2 23 23
BCL6 0.016 0.26 -9999 0 -1.2 19 19
RALB 0.015 0.047 -9999 0 -0.52 4 4
RALA 0.019 0.002 -9999 0 -10000 0 0
YWHAH 0.013 0.048 -9999 0 -0.47 5 5
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.015 0.065 -9999 0 -0.37 14 14
FBXW11 0.015 0.035 -9999 0 -0.43 3 3
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.035 -9999 0 -0.43 3 3
CHUK 0.005 0.081 -9999 0 -0.5 13 13
NF kappa B2 p100/RelB 0.034 0.074 -9999 0 -0.28 24 24
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAP3K14 0.015 0.037 -9999 0 -0.39 4 4
NF kappa B1 p50/RelB 0.015 0.059 -9999 0 -0.37 10 10
RELB 0.003 0.078 -9999 0 -0.38 19 19
NFKB2 0.015 0.031 -9999 0 -0.32 4 4
NF kappa B2 p52/RelB 0.014 0.052 -9999 0 -0.31 11 11
regulation of B cell activation 0.014 0.052 -9999 0 -0.31 11 11
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.009 0.067 -10000 0 -0.49 9 9
SMAD2 0.021 0.048 0.24 1 -0.23 9 10
SMAD3 0.032 0.056 -10000 0 -0.39 2 2
SMAD3/SMAD4 0.033 0.069 -10000 0 -0.34 9 9
SMAD4/Ubc9/PIASy 0.027 0.052 -10000 0 -0.3 12 12
SMAD2/SMAD2/SMAD4 0.031 0.061 -10000 0 -0.27 1 1
PPM1A 0.016 0.026 -10000 0 -0.39 2 2
CALM1 0.018 0 -10000 0 -10000 0 0
SMAD2/SMAD4 0.024 0.056 0.2 1 -0.23 17 18
MAP3K1 -0.03 0.14 -10000 0 -0.42 58 58
TRAP-1/SMAD4 0.02 0.049 -10000 0 -0.37 8 8
MAPK3 0.016 0.026 -10000 0 -0.39 2 2
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
NUP214 0.016 0.026 -10000 0 -0.39 2 2
CTDSP1 0.016 0.033 -10000 0 -0.52 2 2
CTDSP2 0.014 0.044 -10000 0 -0.41 5 5
CTDSPL 0.011 0.062 -10000 0 -0.52 7 7
KPNB1 0.012 0.057 -10000 0 -0.52 6 6
TGFBRAP1 0.017 0.012 -10000 0 -0.25 1 1
UBE2I 0.018 0 -10000 0 -10000 0 0
NUP153 0.016 0.024 -10000 0 -0.25 4 4
KPNA2 -0.001 0.084 -10000 0 -0.34 27 27
PIAS4 0.013 0.049 -10000 0 -0.43 6 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.018 0.036 -9999 0 -0.43 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.078 -9999 0 -0.38 4 4
ERC1 0.011 0.056 -9999 0 -0.42 8 8
RIP2/NOD2 -0.031 0.13 -9999 0 -0.37 66 66
NFKBIA 0.042 0.051 -9999 0 -0.54 3 3
BIRC2 0.016 0.02 -9999 0 -0.25 3 3
IKBKB 0.012 0.047 -9999 0 -0.31 10 10
RIPK2 0.013 0.04 -9999 0 -0.28 9 9
IKBKG 0.016 0.091 -9999 0 -0.51 5 5
IKK complex/A20 0.027 0.1 -9999 0 -0.44 9 9
NEMO/A20/RIP2 0.013 0.04 -9999 0 -0.28 9 9
XPO1 0.018 0 -9999 0 -10000 0 0
NEMO/ATM 0.024 0.088 -9999 0 -0.48 5 5
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.017 0.012 -9999 0 -0.25 1 1
Exportin 1/RanGTP 0.024 0.007 -9999 0 -10000 0 0
IKK complex/ELKS -0.028 0.077 -9999 0 -0.42 10 10
BCL10/MALT1/TRAF6 0.031 0.041 -9999 0 -0.38 4 4
NOD2 -0.056 0.18 -9999 0 -0.46 81 81
NFKB1 0.019 0.025 -9999 0 -0.52 1 1
RELA 0.02 0.009 -9999 0 -10000 0 0
MALT1 0.011 0.053 -9999 0 -0.37 9 9
cIAP1/UbcH5C 0.025 0.014 -9999 0 -10000 0 0
ATM 0.017 0.012 -9999 0 -0.25 1 1
TNF/TNFR1A 0.009 0.071 -9999 0 -0.37 14 14
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
PRKCA 0.014 0.033 -9999 0 -0.25 8 8
CHUK 0.005 0.081 -9999 0 -0.5 13 13
UBE2D3 0.018 0 -9999 0 -10000 0 0
TNF -0.004 0.094 -9999 0 -0.36 31 31
NF kappa B1 p50/RelA 0.045 0.036 -9999 0 -0.28 6 6
BCL10 0.017 0.012 -9999 0 -0.25 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.051 -9999 0 -0.54 3 3
beta TrCP1/SCF ubiquitin ligase complex 0.018 0.036 -9999 0 -0.42 3 3
TNFRSF1A 0.016 0.033 -9999 0 -0.52 2 2
IKK complex 0.025 0.1 -9999 0 -0.46 9 9
CYLD 0.014 0.044 -9999 0 -0.41 5 5
IKK complex/PKC alpha 0.03 0.1 -9999 0 -0.49 7 7
Ephrin A reverse signaling

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
MAPKKK cascade 0.015 0.047 -9999 0 -0.31 8 8
EFNA5 0.006 0.068 -9999 0 -0.35 17 17
FYN 0.015 0.055 -9999 0 -0.28 15 15
neuron projection morphogenesis 0.015 0.047 -9999 0 -0.31 8 8
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.015 0.047 -9999 0 -0.31 8 8
EPHA5 0.015 0.037 -9999 0 -0.39 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.025 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.04 0.016 -10000 0 -0.27 1 1
CDKN1B 0.021 0.079 -10000 0 -0.37 8 8
CDKN1A 0.025 0.072 -10000 0 -0.44 6 6
FRAP1 0.018 0 -10000 0 -10000 0 0
PRKDC 0.012 0.045 -10000 0 -0.31 9 9
FOXO3 0.033 0.062 -10000 0 -0.46 6 6
AKT1 0.03 0.053 -10000 0 -0.43 6 6
BAD 0.017 0.023 -10000 0 -0.52 1 1
AKT3 0.007 0.046 -10000 0 -0.32 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.035 0.053 -10000 0 -0.39 7 7
AKT1/ASK1 0.018 0.081 -10000 0 -0.36 10 10
BAD/YWHAZ 0.035 0.018 -10000 0 -0.3 1 1
RICTOR 0.018 0 -10000 0 -10000 0 0
RAF1 0.017 0.012 -10000 0 -0.25 1 1
JNK cascade -0.017 0.079 0.35 10 -10000 0 10
TSC1 0.036 0.051 -10000 0 -0.4 6 6
YWHAZ 0.017 0.017 -10000 0 -0.25 2 2
AKT1/RAF1 0.038 0.052 -10000 0 -0.4 6 6
EP300 0.014 0.047 -10000 0 -0.52 4 4
mol:GDP 0.03 0.053 -10000 0 -0.42 6 6
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.035 0.056 -10000 0 -0.44 6 6
YWHAQ 0.014 0.039 -10000 0 -0.36 5 5
TBC1D4 0.011 0.063 -10000 0 -0.3 19 19
MAP3K5 -0.022 0.13 -10000 0 -0.42 47 47
MAPKAP1 0.016 0.026 -10000 0 -0.39 2 2
negative regulation of cell cycle -0.034 0.048 0.24 3 -10000 0 3
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
AKT1S1 0.032 0.063 -10000 0 -0.4 9 9
CASP9 0.035 0.053 -10000 0 -0.39 7 7
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
p27Kip1/KPNA1 0.03 0.076 -10000 0 -0.36 7 7
GBL 0.015 0.035 -10000 0 -0.43 3 3
PDK1/Src/Hsp90 0.031 0.039 -10000 0 -0.3 6 6
YWHAE 0.016 0.029 -10000 0 -0.34 3 3
SRC 0.015 0.035 -10000 0 -0.43 3 3
AKT2/p21CIP1 0.03 0.068 -10000 0 -0.39 6 6
KIAA1303 0.015 0.031 -10000 0 -0.32 4 4
mTOR/RHEB/GTP/Raptor/GBL 0.038 0.041 -10000 0 -0.39 4 4
CHUK 0.03 0.068 -10000 0 -0.42 7 7
BAD/BCL-XL 0.052 0.051 -10000 0 -0.37 6 6
mTORC2 0.043 0.025 -10000 0 -0.27 3 3
AKT2 0.019 0.017 -10000 0 -0.32 1 1
FOXO1-3a-4/14-3-3 family 0.046 0.064 -10000 0 -0.28 5 5
PDPK1 0.016 0.026 -10000 0 -0.39 2 2
MDM2 0.033 0.054 -10000 0 -0.4 6 6
MAPKKK cascade -0.038 0.051 0.39 6 -10000 0 6
MDM2/Cbp/p300 0.047 0.061 -10000 0 -0.4 6 6
TSC1/TSC2 0.041 0.055 -10000 0 -0.42 6 6
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.058 -10000 0 -0.38 6 6
glucose import 0.011 0.064 -10000 0 -0.26 21 21
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.044 0.053 -10000 0 -0.38 5 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.011 0.064 -10000 0 -0.26 21 21
GSK3A 0.036 0.051 -10000 0 -0.4 6 6
FOXO1 0.027 0.068 -10000 0 -0.39 7 7
GSK3B 0.036 0.051 -10000 0 -0.4 6 6
SFN -0.015 0.12 -10000 0 -0.45 37 37
G1/S transition of mitotic cell cycle 0.042 0.05 -10000 0 -0.38 6 6
p27Kip1/14-3-3 family 0.034 0.063 -10000 0 -0.37 4 4
PRKACA 0.018 0 -10000 0 -10000 0 0
KPNA1 0.018 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
YWHAG 0.017 0.017 -10000 0 -0.25 2 2
RHEB 0.016 0.026 -10000 0 -0.39 2 2
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
Arf6 trafficking events

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
SLC2A4 0.005 0.06 -10000 0 -0.26 24 24
CLTC 0.025 0.05 -10000 0 -0.49 3 3
calcium ion-dependent exocytosis 0.021 0.039 -10000 0 -0.28 4 4
Dynamin 2/GTP 0.025 0.027 -10000 0 -0.28 2 2
EXOC4 0.016 0.033 -10000 0 -0.52 2 2
CD59 0.021 0.05 -10000 0 -0.42 4 4
CPE -0.021 0.11 -10000 0 -0.32 53 53
CTNNB1 0.001 0.09 -10000 0 -0.45 19 19
membrane fusion 0.021 0.041 -10000 0 -0.29 4 4
CTNND1 0.029 0.029 -10000 0 -0.25 3 3
DNM2 0.017 0.012 -10000 0 -0.25 1 1
mol:PI-4-5-P2 0.027 0.039 -10000 0 -0.35 3 3
TSHR 0.014 0.048 -10000 0 -0.31 11 11
INS 0.02 0.026 -10000 0 -0.51 1 1
BIN1 0.014 0.04 -10000 0 -0.34 6 6
mol:Choline 0.021 0.041 -10000 0 -0.29 4 4
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.03 -10000 0 -0.31 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0.033 -10000 0 -0.52 2 2
mol:Ca2+ 0.025 0.027 -10000 0 -0.27 2 2
JUP 0.023 0.046 -10000 0 -0.48 3 3
ASAP2/amphiphysin II 0.019 0.029 -10000 0 -0.28 4 4
ARF6/GTP 0.012 0.024 -10000 0 -0.38 2 2
CDH1 0 0.078 -10000 0 -0.46 3 3
clathrin-independent pinocytosis 0.012 0.024 -10000 0 -0.38 2 2
MAPK8IP3 0.006 0.075 -10000 0 -0.48 12 12
positive regulation of endocytosis 0.012 0.024 -10000 0 -0.38 2 2
EXOC2 -0.004 0.085 -10000 0 -0.31 35 35
substrate adhesion-dependent cell spreading 0.023 0.078 -10000 0 -0.24 37 37
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0.035 -10000 0 -0.3 6 6
regulation of calcium-dependent cell-cell adhesion -0.011 0.077 0.61 2 -10000 0 2
positive regulation of phagocytosis 0.018 0.032 -10000 0 -0.31 5 5
ARF6/GTP/JIP3 0.016 0.051 -10000 0 -0.31 12 12
ACAP1 0.019 0.035 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.016 0.046 -10000 0 -0.52 2 2
clathrin heavy chain/ACAP1 0.028 0.048 -10000 0 -0.46 3 3
JIP4/KLC1 0.031 0.027 -10000 0 -0.28 3 3
EXOC1 0.018 0 -10000 0 -10000 0 0
exocyst 0.023 0.078 -10000 0 -0.25 37 37
RALA/GTP 0.013 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.021 0.029 -10000 0 -0.31 3 3
receptor recycling 0.012 0.024 -10000 0 -0.38 2 2
CTNNA1 0.03 0.028 -10000 0 -0.25 3 3
NME1 0.017 0.03 -10000 0 -0.31 2 2
clathrin coat assembly 0.025 0.05 -10000 0 -0.48 3 3
IL2RA 0.008 0.069 -10000 0 -0.35 7 7
VAMP3 0.018 0.032 -10000 0 -0.31 5 5
GLUT4/clathrin heavy chain/ACAP1 -0.008 0.04 -10000 0 -0.43 3 3
EXOC6 -0.012 0.12 -10000 0 -0.5 30 30
PLD1 0.015 0.05 -10000 0 -0.29 11 11
PLD2 0.021 0.033 -10000 0 -0.26 6 6
EXOC5 0.016 0.033 -10000 0 -0.52 2 2
PIP5K1C 0.028 0.039 -10000 0 -0.35 3 3
SDC1 0.004 0.072 -10000 0 -0.39 4 4
ARF6/GDP 0.018 0.03 -10000 0 -0.31 2 2
EXOC7 0.018 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.013 0.079 -10000 0 -0.64 2 2
mol:Phosphatidic acid 0.021 0.041 -10000 0 -0.29 4 4
endocytosis -0.019 0.029 0.28 4 -10000 0 4
SCAMP2 0.015 0.035 -10000 0 -0.43 3 3
ADRB2 0.001 0.096 -10000 0 -0.62 4 4
EXOC3 0.017 0.012 -10000 0 -0.25 1 1
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.027 0.028 -10000 0 -0.27 2 2
KLC1 0.018 0 -10000 0 -10000 0 0
AVPR2 0.03 0.049 -10000 0 -0.45 3 3
RALA 0.018 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.022 0.076 -10000 0 -0.58 2 2
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.016 0.024 -9999 0 -0.25 4 4
CDC42/GTP 0.016 0.067 -9999 0 -0.33 5 5
PLCG1 0.014 0.07 -9999 0 -0.32 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.006 0.075 -9999 0 -0.48 12 12
GNAI3 0.018 0 -9999 0 -10000 0 0
G12/G13 0.021 0.039 -9999 0 -0.37 4 4
cell migration 0.016 0.065 -9999 0 -0.32 5 5
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.014 0.069 -9999 0 -0.32 6 6
MAPK1 0.014 0.07 -9999 0 -0.31 7 7
S1P/S1P5/Gi 0.008 0.072 -9999 0 -0.29 12 12
GNAI1 -0.017 0.12 -9999 0 -0.38 46 46
CDC42/GDP 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.012 0 -9999 0 -10000 0 0
RHOA 0.017 0.056 -9999 0 -0.3 14 14
S1P/S1P4/Gi 0.008 0.072 -9999 0 -0.29 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.088 -9999 0 -0.44 19 19
S1P/S1P4/G12/G13 0.019 0.03 -9999 0 -0.28 4 4
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.011 0.055 -9999 0 -0.36 10 10
CDC42 0.018 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.038 0.06 -9999 0 -0.39 3 3
CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
AKT1 0.011 0.053 -9999 0 -0.37 9 9
AKT2 0.017 0.012 -9999 0 -0.25 1 1
STXBP4 0.008 0.06 -9999 0 -0.32 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.033 0.053 -9999 0 -0.29 2 2
YWHAZ 0.017 0.017 -9999 0 -0.25 2 2
CALM1 0.018 0 -9999 0 -10000 0 0
YWHAQ 0.014 0.039 -9999 0 -0.36 5 5
TBC1D4 0.004 0.086 -9999 0 -0.38 21 21
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.013 0.048 -9999 0 -0.47 5 5
YWHAB 0.015 0.037 -9999 0 -0.39 4 4
SNARE/Synip 0.029 0.042 -9999 0 -0.3 6 6
YWHAG 0.017 0.017 -9999 0 -0.25 2 2
ASIP 0 0 -9999 0 -10000 0 0
PRKCI 0.002 0.085 -9999 0 -0.43 18 18
AS160/CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
RHOQ 0.012 0.053 -9999 0 -0.48 6 6
GYS1 0.031 0.027 -9999 0 -0.26 4 4
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.013 0.048 -9999 0 -0.47 5 5
TC10/GTP/CIP4/Exocyst 0.018 0.045 -9999 0 -0.31 9 9
AS160/14-3-3 0.025 0.066 -9999 0 -0.39 1 1
VAMP2 0.017 0.023 -9999 0 -0.52 1 1
SLC2A4 0.033 0.056 -9999 0 -0.32 2 2
STX4 0.017 0.023 -9999 0 -0.52 1 1
GSK3B 0.026 0.032 -9999 0 -0.31 4 4
SFN -0.015 0.12 -9999 0 -0.45 37 37
LNPEP 0.01 0.06 -9999 0 -0.43 9 9
YWHAE 0.016 0.029 -9999 0 -0.34 3 3
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.033 0.064 -10000 0 -0.29 16 16
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.064 -10000 0 -0.27 14 14
SUMO1 0.018 0 -10000 0 -10000 0 0
ZFPM1 0.009 0.068 -10000 0 -0.47 10 10
NPC/RanGAP1/SUMO1/Ubc9 0.023 0.013 -10000 0 -0.2 1 1
FKBP3 0.013 0.048 -10000 0 -0.47 5 5
Histones 0.043 0.05 -10000 0 -0.28 2 2
YY1/LSF 0.02 0.056 -10000 0 -0.26 20 20
SMG5 0.016 0.029 -10000 0 -0.34 3 3
RAN 0.017 0.012 -10000 0 -0.25 1 1
I kappa B alpha/HDAC3 0.025 0.056 -10000 0 -0.24 19 19
I kappa B alpha/HDAC1 0.027 0.051 -10000 0 -0.31 6 6
SAP18 0.018 0 -10000 0 -10000 0 0
RELA 0.03 0.051 -10000 0 -10000 0 0
HDAC1/Smad7 0.035 0.022 -10000 0 -0.3 2 2
RANGAP1 0.014 0.037 -10000 0 -0.29 7 7
HDAC3/TR2 0.026 0.053 -10000 0 -0.28 9 9
NuRD/MBD3 Complex 0.045 0.038 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA 0.035 0.049 -10000 0 -0.24 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.007 0.093 -10000 0 -0.31 40 40
GATA1 0.018 0 -10000 0 -10000 0 0
Mad/Max 0.024 0.021 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.053 0.054 -10000 0 -0.48 2 2
RBBP7 0.01 0.051 -10000 0 -0.3 13 13
NPC 0.01 0.008 -10000 0 -10000 0 0
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
MAX 0.018 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
NFKBIA 0.02 0.054 -10000 0 -0.36 5 5
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.041 0.036 -10000 0 -10000 0 0
SIN3 complex 0.042 0.032 -10000 0 -0.27 5 5
SMURF1 0.018 0 -10000 0 -10000 0 0
CHD3 0.015 0.037 -10000 0 -0.39 4 4
SAP30 0.012 0.053 -10000 0 -0.48 6 6
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.016 0.033 -10000 0 -0.52 2 2
YY1/HDAC3 0.032 0.046 -10000 0 -0.29 2 2
YY1/HDAC2 0.022 0.045 -10000 0 -0.25 11 11
YY1/HDAC1 0.027 0.036 -10000 0 -0.23 10 10
NuRD/MBD2 Complex (MeCP1) 0.044 0.038 -10000 0 -0.33 1 1
PPARG 0.006 0.096 -10000 0 -0.3 38 38
HDAC8/hEST1B 0.034 0.027 -10000 0 -0.3 3 3
UBE2I 0.018 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.035 -10000 0 -0.43 3 3
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
HDAC3/SMRT (N-CoR2) 0.03 0.041 -10000 0 -0.32 2 2
MBD3L2 0.007 0.072 -10000 0 -0.45 12 12
ubiquitin-dependent protein catabolic process 0.034 0.022 -10000 0 -0.3 2 2
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
NuRD/MBD3/MBD3L2 Complex 0.049 0.051 -10000 0 -0.32 2 2
HDAC1 0.017 0.023 -10000 0 -0.52 1 1
HDAC3 0.023 0.045 -10000 0 -0.36 2 2
HDAC2 0.009 0.053 -10000 0 -0.29 15 15
YY1 0.021 0.038 -10000 0 -0.27 9 9
HDAC8 0.016 0.033 -10000 0 -0.52 2 2
SMAD7 0.016 0.026 -10000 0 -0.39 2 2
NCOR2 0.018 0 -10000 0 -10000 0 0
MXD1 0.014 0.031 -10000 0 -0.25 7 7
STAT3 0.024 0.044 -10000 0 -0.31 9 9
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.017 0.017 -10000 0 -0.25 2 2
YY1/LSF/HDAC1 0.03 0.054 -10000 0 -0.23 21 21
YY1/SAP30/HDAC1 0.033 0.047 -10000 0 -0.24 14 14
EP300 0.014 0.047 -10000 0 -0.52 4 4
STAT3 (dimer non-phopshorylated) 0.024 0.044 -10000 0 -0.31 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.054 -10000 0 -0.36 5 5
histone deacetylation 0.044 0.038 -10000 0 -0.32 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.035 0.051 -10000 0 -0.32 3 3
nuclear export -0.033 0.027 0.3 3 -10000 0 3
PRKACA 0.018 0 -10000 0 -10000 0 0
GATAD2B 0.017 0.023 -10000 0 -0.52 1 1
GATAD2A 0.014 0.037 -10000 0 -0.29 7 7
GATA2/HDAC3 0.017 0.069 -10000 0 -0.32 12 12
GATA1/HDAC1 0.026 0.017 -10000 0 -0.37 1 1
GATA1/HDAC3 0.03 0.041 -10000 0 -0.32 2 2
CHD4 0.017 0.023 -10000 0 -0.52 1 1
TNF-alpha/TNFR1A 0.009 0.071 -10000 0 -0.37 14 14
SIN3/HDAC complex/Mad/Max 0.046 0.033 -10000 0 -0.22 1 1
NuRD Complex 0.052 0.044 -10000 0 -0.32 2 2
positive regulation of chromatin silencing 0.04 0.049 -10000 0 -0.27 2 2
SIN3B 0.017 0.012 -10000 0 -0.25 1 1
MTA2 0.014 0.044 -10000 0 -0.41 5 5
SIN3A 0.018 0 -10000 0 -10000 0 0
XPO1 0.018 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.036 0.018 -10000 0 -0.24 1 1
HDAC complex 0.035 0.045 -10000 0 -0.26 7 7
GATA1/Fog1 0.02 0.049 -10000 0 -0.37 8 8
FKBP25/HDAC1/HDAC2 0.027 0.047 -10000 0 -0.3 8 8
TNF -0.004 0.094 -10000 0 -0.36 31 31
negative regulation of cell growth 0.046 0.033 -10000 0 -0.22 1 1
NuRD/MBD2/PRMT5 Complex 0.044 0.038 -10000 0 -0.33 1 1
Ran/GTP/Exportin 1 0.039 0.013 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.031 0.065 -10000 0 -0.29 16 16
SIN3/HDAC complex/NCoR1 0.043 0.035 -10000 0 -10000 0 0
TFCP2 0.006 0.077 -10000 0 -0.52 11 11
NR2C1 0.011 0.062 -10000 0 -0.52 7 7
MBD3 0.018 0 -10000 0 -10000 0 0
MBD2 0.017 0.017 -10000 0 -0.25 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.024 0.045 -10000 0 -0.29 8 8
MAPK9 -0.005 0.07 -10000 0 -0.33 23 23
adrenocorticotropin secretion 0.005 0.042 -10000 0 -0.2 18 18
GNB1/GNG2 0.02 0.037 -10000 0 -0.31 6 6
GNB1 0.013 0.052 -10000 0 -0.52 5 5
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0.005 -10000 0 -10000 0 0
Gs family/GTP 0.008 0.028 -10000 0 -0.17 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.007 0.048 11 -10000 0 11
GNAL 0.011 0.052 -10000 0 -0.33 11 11
GNG2 0.016 0.029 -10000 0 -0.34 3 3
CRH 0.007 0.06 -10000 0 -0.3 18 18
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.026 -10000 0 -0.33 3 3
MAPK11 0.01 0 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.023 0.017 -10000 0 -0.2 2 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0.019 -10000 0 -0.27 1 1
AP2 0.021 0.04 -10000 0 -0.36 5 5
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.019 0.041 -10000 0 -0.31 8 8
CLTB 0.015 0.035 -10000 0 -0.43 3 3
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0.02 -10000 0 -0.24 3 3
CD4 0.018 0 -10000 0 -10000 0 0
CLTA 0.018 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.012 0.011 -10000 0 -0.17 2 2
mol:PI-4-5-P2 0.012 0.025 0.15 8 -0.18 4 12
ARF1/GTP -0.001 0.015 -10000 0 -0.29 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.028 0.014 -10000 0 -0.2 1 1
mol:Choline 0.011 0.025 0.15 8 -0.19 4 12
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.016 0.024 -10000 0 -0.53 1 1
DDEF1 0.012 0.025 0.15 8 -0.19 4 12
ARF1/GDP 0.009 0.012 -10000 0 -0.11 2 2
AP2M1 0.013 0.049 -10000 0 -0.43 6 6
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.017 0.013 -10000 0 -0.28 1 1
Rac/GTP 0.014 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.028 0.02 -10000 0 -0.26 2 2
ARFIP2 0.008 0.063 -10000 0 -0.47 9 9
COPA 0.018 0 -10000 0 -10000 0 0
RAC1 0.018 0 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.026 0.017 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.01 0.014 -10000 0 -0.32 1 1
GGA3 0.016 0.026 -10000 0 -0.39 2 2
ARF1/GTP/Membrin 0.017 0.015 -10000 0 -0.27 1 1
AP2A1 0.016 0.024 -10000 0 -0.25 4 4
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.028 0.021 -10000 0 -0.23 3 3
ARF1/GDP/Membrin 0.019 0.015 -10000 0 -0.26 1 1
Arfaptin 2/Rac/GDP 0.018 0.041 -10000 0 -0.31 8 8
CYTH2 0.001 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.021 0.022 -10000 0 -0.32 2 2
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 0 -10000 0 -10000 0 0
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 0.036 0.036 -10000 0 -0.45 2 2
PLD2 0.011 0.026 0.15 8 -0.19 4 12
ARF-GAP1/v-SNARE 0.012 0.011 -10000 0 -0.17 2 2
PIP5K1A 0.012 0.025 0.15 8 -0.18 4 12
ARF1/GTP/Membrin/GBF1/p115 0.018 0.016 -10000 0 -0.26 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.025 0.15 8 -0.19 4 12
KDEL Receptor/Ligand/ARF-GAP1 0.012 0.011 -10000 0 -0.17 2 2
GOSR2 0.015 0.014 -10000 0 -10000 0 0
USO1 0.015 0.013 -10000 0 -10000 0 0
GBF1 0.014 0.023 -10000 0 -0.41 1 1
ARF1/GTP/Arfaptin 2 0.018 0.044 -10000 0 -0.31 9 9
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.032 0.035 -10000 0 -0.3 5 5
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.017 0.023 -9999 0 -0.52 1 1
Ran/GTP/Exportin 1/HDAC4 -0.001 0.012 -9999 0 -0.25 1 1
MDM2/SUMO1 0.033 0.024 -9999 0 -10000 0 0
HDAC4 0.017 0.023 -9999 0 -0.52 1 1
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -0.2 1 1
SUMO1 0.018 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.018 0.015 -9999 0 -0.24 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0.013 -9999 0 -0.18 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.017 0.012 -9999 0 -0.25 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.017 0.017 -9999 0 -0.25 2 2
SUMO1/HDAC4 0.036 0.019 -9999 0 -0.31 1 1
SUMO1/HDAC1 0.036 0.018 -9999 0 -0.24 1 1
RANGAP1 0.014 0.037 -9999 0 -0.29 7 7
MDM2/SUMO1/SUMO1 0.04 0.031 -9999 0 -0.27 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0.013 -9999 0 -0.2 1 1
Ran/GTP 0.031 0.013 -9999 0 -0.18 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.011 0.044 -9999 0 -0.25 14 14
UBE2I 0.018 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.013 -9999 0 -10000 0 0
NPC 0.01 0.008 -9999 0 -10000 0 0
PIAS2 0.015 0.035 -9999 0 -0.43 3 3
PIAS1 0.017 0.012 -9999 0 -0.25 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
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/BRCA/1269422/2.GDAC_MergeDataFiles.Finished/BRCA.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

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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