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 65 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) 114
Signaling events regulated by Ret tyrosine kinase 111
FOXM1 transcription factor network 86
Wnt signaling 83
EGFR-dependent Endothelin signaling events 83
IGF1 pathway 83
Endothelins 82
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 79
HIF-1-alpha transcription factor network 77
Plasma membrane estrogen receptor signaling 75
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) 114 8909 78 -0.39 0.17 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 111 9126 82 -0.23 0.018 1000 -1000 -0.06 -1000
FOXM1 transcription factor network 86 4424 51 -0.43 0.024 1000 -1000 -0.12 -1000
Wnt signaling 83 584 7 -0.13 -0.011 1000 -1000 -0.012 -1000
EGFR-dependent Endothelin signaling events 83 1747 21 -0.17 0.024 1000 -1000 -0.049 -1000
IGF1 pathway 83 4786 57 -0.14 0.058 1000 -1000 -0.059 -1000
Endothelins 82 7963 96 -0.24 0.018 1000 -1000 -0.044 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 79 5392 68 -0.43 0.22 1000 -1000 -0.072 -1000
HIF-1-alpha transcription factor network 77 5888 76 -0.26 0.025 1000 -1000 -0.048 -1000
Plasma membrane estrogen receptor signaling 75 6487 86 -0.2 0.19 1000 -1000 -0.056 -1000
Syndecan-1-mediated signaling events 74 2533 34 -0.19 0.018 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 69 558 8 -0.053 0.026 1000 -1000 -0.006 -1000
FAS signaling pathway (CD95) 68 3222 47 -0.16 0.072 1000 -1000 -0.026 -1000
IL6-mediated signaling events 68 5146 75 -0.18 0.043 1000 -1000 -0.035 -1000
Glucocorticoid receptor regulatory network 67 7743 114 -0.55 0.28 1000 -1000 -0.051 -1000
IL4-mediated signaling events 66 6070 91 -0.51 0.39 1000 -1000 -0.12 -1000
TCR signaling in naïve CD8+ T cells 66 6187 93 -0.13 0.071 1000 -1000 -0.046 -1000
IL12-mediated signaling events 62 5422 87 -0.3 0.029 1000 -1000 -0.083 -1000
IL27-mediated signaling events 62 3181 51 -0.27 0.17 1000 -1000 -0.059 -1000
Fc-epsilon receptor I signaling in mast cells 61 6012 97 -0.15 0.038 1000 -1000 -0.054 -1000
Arf6 signaling events 60 3728 62 -0.15 0.034 1000 -1000 -0.011 -1000
Osteopontin-mediated events 59 2244 38 -0.15 0.018 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 59 1552 26 -0.13 0.018 1000 -1000 -0.032 -1000
IL23-mediated signaling events 58 3498 60 -0.28 0.017 1000 -1000 -0.096 -1000
Thromboxane A2 receptor signaling 56 5882 105 -0.14 0.038 1000 -1000 -0.046 -1000
Signaling events mediated by the Hedgehog family 53 2776 52 -0.16 0.056 1000 -1000 -0.012 -1000
Nongenotropic Androgen signaling 53 2764 52 -0.13 0.063 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 50 150 3 -0.049 0.008 1000 -1000 -0.011 -1000
E-cadherin signaling events 50 250 5 -0.049 0.011 1000 -1000 -0.007 -1000
BMP receptor signaling 48 3934 81 -0.23 0.046 1000 -1000 -0.067 -1000
Stabilization and expansion of the E-cadherin adherens junction 48 3583 74 -0.14 0.03 1000 -1000 -0.061 -1000
Syndecan-4-mediated signaling events 48 3250 67 -0.079 0.022 1000 -1000 -0.025 -1000
ErbB4 signaling events 45 3155 69 -0.17 0.099 1000 -1000 -0.056 -1000
Ephrin B reverse signaling 42 2020 48 -0.14 0.02 1000 -1000 -0.043 -1000
LPA receptor mediated events 41 4202 102 -0.13 0.018 1000 -1000 -0.05 -1000
amb2 Integrin signaling 39 3253 82 -0.12 0.023 1000 -1000 -0.05 -1000
TCGA08_p53 39 277 7 -0.037 0.029 1000 -1000 -0.007 -1000
Caspase cascade in apoptosis 38 2874 74 -0.086 0.045 1000 -1000 -0.023 -1000
Syndecan-2-mediated signaling events 38 2639 69 -0.073 0.022 1000 -1000 -0.017 -1000
Integrins in angiogenesis 38 3232 84 -0.19 0.031 1000 -1000 -0.053 -1000
BCR signaling pathway 38 3819 99 -0.16 0.043 1000 -1000 -0.06 -1000
Signaling events mediated by PTP1B 37 2832 76 -0.15 0.054 1000 -1000 -0.05 -1000
IL2 signaling events mediated by PI3K 37 2166 58 -0.23 0.018 1000 -1000 -0.056 -1000
Canonical Wnt signaling pathway 37 1887 51 -0.25 0.098 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 37 1962 52 -0.1 0.026 1000 -1000 -0.05 -1000
Calcium signaling in the CD4+ TCR pathway 36 1140 31 -0.14 0.027 1000 -1000 -0.041 -1000
Ras signaling in the CD4+ TCR pathway 35 601 17 -0.037 0.013 1000 -1000 -0.009 -1000
Coregulation of Androgen receptor activity 34 2593 76 -0.19 0.029 1000 -1000 -0.026 -1000
TRAIL signaling pathway 34 1643 48 -0.049 0.018 1000 -1000 -0.042 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 34 1552 45 -0.13 0.018 1000 -1000 -0.056 -1000
Glypican 2 network 34 138 4 -0.016 0 1000 -1000 -0.002 -1000
Cellular roles of Anthrax toxin 33 1299 39 -0.14 0.018 1000 -1000 -0.015 -1000
Glypican 1 network 33 1623 48 -0.064 0.017 1000 -1000 -0.014 -1000
IL1-mediated signaling events 33 2050 62 -0.083 0.051 1000 -1000 -0.05 -1000
Class IB PI3K non-lipid kinase events 33 99 3 -0.004 -1000 1000 -1000 -0.002 -1000
Signaling mediated by p38-gamma and p38-delta 32 483 15 -0.07 0.014 1000 -1000 -0.01 -1000
Presenilin action in Notch and Wnt signaling 31 1929 61 -0.22 0.036 1000 -1000 -0.043 -1000
Nectin adhesion pathway 31 1970 63 -0.11 0.024 1000 -1000 -0.051 -1000
E-cadherin signaling in the nascent adherens junction 31 2428 76 -0.079 0.024 1000 -1000 -0.057 -1000
Regulation of nuclear SMAD2/3 signaling 30 4123 136 -0.2 0.065 1000 -1000 -0.027 -1000
Syndecan-3-mediated signaling events 30 1068 35 -0.099 0.032 1000 -1000 -0.027 -1000
PDGFR-alpha signaling pathway 29 1283 44 -0.18 0.028 1000 -1000 -0.021 -1000
Regulation of Telomerase 29 3000 102 -0.2 0.044 1000 -1000 -0.07 -1000
Visual signal transduction: Cones 28 1091 38 -0.071 0.025 1000 -1000 -0.008 -1000
Class I PI3K signaling events 27 2040 73 -0.089 0.031 1000 -1000 -0.032 -1000
Ceramide signaling pathway 26 2029 76 -0.14 0.055 1000 -1000 -0.015 -1000
Reelin signaling pathway 26 1494 56 -0.09 0.038 1000 -1000 -0.053 -1000
IL2 signaling events mediated by STAT5 26 584 22 -0.072 0.021 1000 -1000 -0.014 -1000
Insulin Pathway 26 1966 74 -0.16 0.05 1000 -1000 -0.06 -1000
E-cadherin signaling in keratinocytes 26 1148 43 -0.077 0.018 1000 -1000 -0.018 -1000
Aurora B signaling 26 1760 67 -0.096 0.02 1000 -1000 -0.04 -1000
p75(NTR)-mediated signaling 25 3138 125 -0.13 0.036 1000 -1000 -0.059 -1000
IFN-gamma pathway 25 1756 68 -0.087 0.023 1000 -1000 -0.059 -1000
Effects of Botulinum toxin 25 674 26 -0.17 0.019 1000 -1000 -0.019 -1000
TCGA08_rtk_signaling 25 652 26 -0.077 0.039 1000 -1000 -0.007 -1000
FOXA2 and FOXA3 transcription factor networks 24 1145 46 -0.2 0.074 1000 -1000 -0.023 -1000
RXR and RAR heterodimerization with other nuclear receptor 24 1273 52 -0.12 0.037 1000 -1000 -0.046 -1000
Sphingosine 1-phosphate (S1P) pathway 23 662 28 -0.081 0.02 1000 -1000 -0.016 -1000
PLK1 signaling events 22 1934 85 -0.1 0.028 1000 -1000 -0.032 -1000
Regulation of Androgen receptor activity 22 1608 70 -0.18 0.026 1000 -1000 -0.03 -1000
S1P1 pathway 21 770 36 -0.062 0.018 1000 -1000 -0.05 -1000
Atypical NF-kappaB pathway 21 667 31 -0.073 0.028 1000 -1000 -0.009 -1000
Angiopoietin receptor Tie2-mediated signaling 21 1849 88 -0.16 0.053 1000 -1000 -0.086 -1000
Arf6 downstream pathway 20 901 43 -0.022 0.019 1000 -1000 -0.026 -1000
HIF-2-alpha transcription factor network 20 883 43 -0.084 0.085 1000 -1000 -0.054 -1000
Aurora A signaling 19 1182 60 -0.037 0.034 1000 -1000 -0.012 -1000
mTOR signaling pathway 19 1054 53 -0.037 0.035 1000 -1000 -0.042 -1000
ceramide signaling pathway 19 935 49 -0.12 0.036 1000 -1000 -0.019 -1000
VEGFR1 specific signals 19 1069 56 -0.034 0.027 1000 -1000 -0.024 -1000
PDGFR-beta signaling pathway 19 1872 97 -0.081 0.036 1000 -1000 -0.05 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 18 984 54 -0.092 0.031 1000 -1000 -0.058 -1000
ErbB2/ErbB3 signaling events 17 1152 65 -0.06 0.024 1000 -1000 -0.046 -1000
JNK signaling in the CD4+ TCR pathway 17 294 17 -0.036 0.029 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 17 1121 65 -0.051 0.041 1000 -1000 -0.039 -1000
EPHB forward signaling 17 1496 85 -0.038 0.036 1000 -1000 -0.06 -1000
Regulation of p38-alpha and p38-beta 17 947 54 -0.073 0.043 1000 -1000 -0.04 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 17 590 33 -0.074 0.049 1000 -1000 -0.027 -1000
Signaling events mediated by PRL 17 593 34 -0.097 0.026 1000 -1000 -0.011 -1000
p38 MAPK signaling pathway 17 778 44 -0.079 0.034 1000 -1000 -0.053 -1000
BARD1 signaling events 16 944 57 -0.039 0.04 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class III 16 670 40 -0.08 0.034 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 16 934 58 -0.086 0.039 1000 -1000 -0.057 -1000
Signaling events mediated by VEGFR1 and VEGFR2 16 2007 125 -0.061 0.055 1000 -1000 -0.068 -1000
S1P3 pathway 16 689 42 -0.081 0.02 1000 -1000 -0.024 -1000
Neurotrophic factor-mediated Trk receptor signaling 16 1996 120 -0.12 0.053 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 15 1315 85 -0.14 0.038 1000 -1000 -0.05 -1000
Paxillin-independent events mediated by a4b1 and a4b7 15 563 37 -0.024 0.028 1000 -1000 -0.02 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 15 1264 83 -0.12 0.057 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 15 693 44 -0.091 0.024 1000 -1000 -0.023 -1000
EPO signaling pathway 14 798 55 -0.15 0.023 1000 -1000 -0.053 -1000
LPA4-mediated signaling events 13 164 12 -0.029 0.015 1000 -1000 -0.009 -1000
a4b1 and a4b7 Integrin signaling 13 68 5 -0.007 0.018 1000 -1000 -0.005 -1000
Signaling events mediated by HDAC Class II 12 951 75 -0.16 0.039 1000 -1000 -0.028 -1000
Paxillin-dependent events mediated by a4b1 11 421 36 -0.033 0.036 1000 -1000 -0.05 -1000
Aurora C signaling 10 72 7 -0.007 0.015 1000 -1000 -0.027 -1000
Nephrin/Neph1 signaling in the kidney podocyte 9 338 34 -0.01 0.035 1000 -1000 -0.016 -1000
Circadian rhythm pathway 9 198 22 -0.045 0.042 1000 -1000 -0.033 -1000
S1P5 pathway 9 159 17 -0.015 0.018 1000 -1000 -0.015 -1000
FoxO family signaling 9 624 64 -0.12 0.067 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 9 117 13 0 0.034 1000 -1000 -0.005 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 8 184 23 -0.031 0.032 1000 -1000 -0.026 -1000
Canonical NF-kappaB pathway 8 347 39 -0.056 0.06 1000 -1000 -0.053 -1000
Ephrin A reverse signaling 8 59 7 0 0.016 1000 -1000 -0.002 -1000
Class I PI3K signaling events mediated by Akt 6 412 68 -0.038 0.053 1000 -1000 -0.023 -1000
S1P4 pathway 6 168 25 -0.015 0.02 1000 -1000 -0.018 -1000
Insulin-mediated glucose transport 5 172 32 -0.015 0.033 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 5 522 104 -0.033 0.053 1000 -1000 -0.033 -1000
Arf6 trafficking events 5 357 71 -0.021 0.031 1000 -1000 -0.057 -1000
Rapid glucocorticoid signaling 5 118 20 -0.005 0.02 1000 -1000 -0.008 -1000
Arf1 pathway 3 172 54 -0.001 0.036 1000 -1000 -0.014 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 39 27 -0.001 0.04 1000 -1000 -0.038 -1000
Total 4378 259957 7203 -16 -990 131000 -131000 -4.8 -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 -0.38 141 141
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 -0.42 155 155
AKT1 -0.16 0.21 -10000 0 -0.44 163 163
BAD -0.14 0.2 -10000 0 -0.41 158 158
megakaryocyte differentiation -0.17 0.23 -10000 0 -0.47 167 167
GSK3B -0.14 0.2 -10000 0 -0.41 154 154
RAF1 -0.089 0.16 -10000 0 -0.33 92 92
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 -0.9 213 213
HRAS/SPRED1 -0.095 0.17 -10000 0 -0.35 101 101
cell proliferation -0.17 0.22 -10000 0 -0.45 165 165
PIK3CA 0.015 0.029 -10000 0 -0.35 3 3
TEC 0.013 0.052 -10000 0 -0.52 5 5
RPS6KB1 -0.17 0.22 -10000 0 -0.46 170 170
HRAS/SPRED2 -0.096 0.17 -10000 0 -0.36 91 91
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.45 161 161
MAPK3 -0.054 0.12 -10000 0 -0.26 53 53
STAP1 -0.19 0.24 -10000 0 -0.48 176 176
GRAP2 0.011 0.044 -10000 0 -0.28 11 11
JAK2 -0.31 0.4 -10000 0 -0.75 214 214
STAT1 (dimer) -0.36 0.47 -10000 0 -0.88 213 213
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 -0.44 182 182
LYN 0.014 0.031 -10000 0 -0.26 7 7
STAP1/STAT5A (dimer) -0.24 0.31 -10000 0 -0.61 181 181
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
CBL/CRKL/GRB2 -0.13 0.2 -10000 0 -0.41 153 153
PI3K -0.16 0.23 -10000 0 -0.46 168 168
PTEN -0.001 0.1 -10000 0 -0.52 19 19
SCF/KIT/EPO/EPOR -0.39 0.54 -10000 0 -1.2 153 153
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 -10000 0 -0.21 52 52
mol:GDP -0.12 0.2 -10000 0 -0.4 147 147
PIK3C2B -0.17 0.22 -10000 0 -0.47 164 164
CBL/CRKL -0.14 0.21 -10000 0 -0.42 164 164
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 -10000 0 -0.4 150 150
SNAI2 -0.19 0.25 -10000 0 -0.5 176 176
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 -0.8 3 3
STAT5A (dimer) -0.23 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 0.46 171 -10000 0 171
SOS1 0.017 0.023 -10000 0 -0.52 1 1
EPO -0.031 0.1 -10000 0 -0.27 80 80
VAV1 -0.015 0.12 -10000 0 -0.39 42 42
GRB10 -0.18 0.23 -10000 0 -0.48 166 166
PTPN11 0.022 0.024 -10000 0 -0.5 1 1
SCF/KIT -0.18 0.23 -10000 0 -0.47 182 182
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 -0.26 1 1
KIT -0.33 0.53 -10000 0 -1.2 122 122
MAP2K2 -0.064 0.13 -10000 0 -0.29 59 59
SHC/Grb2/SOS1 -0.14 0.22 -10000 0 -0.43 159 159
STAT5A -0.23 0.31 -10000 0 -0.57 213 213
GRB2 0.016 0.024 -10000 0 -0.26 4 4
response to radiation -0.19 0.24 -10000 0 -0.49 176 176
SHC/GRAP2 0.021 0.035 -10000 0 -0.37 2 2
PTPRO -0.18 0.23 -10000 0 -0.48 167 167
SH2B2 -0.18 0.22 -10000 0 -0.45 182 182
DOK1 0.002 0.083 -10000 0 -0.41 19 19
MATK -0.18 0.23 -10000 0 -0.47 171 171
CREBBP 0.004 0.059 -10000 0 -0.54 2 2
BCL2 -0.33 0.55 -10000 0 -1.3 117 117
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 0.17 -9999 0 -0.4 164 164
JUN -0.17 0.21 -9999 0 -0.42 172 172
HRAS 0.012 0.051 -9999 0 -0.41 7 7
RET51/GFRalpha1/GDNF/GRB10 -0.21 0.22 -9999 0 -0.39 276 276
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
FRS2 0.01 0.047 -9999 0 -0.28 13 13
RAP1A/GDP 0.008 0.045 -9999 0 -0.38 7 7
RET51/GFRalpha1/GDNF/DOK1 -0.21 0.22 -9999 0 -0.39 270 270
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 -0.36 246 246
GRB7 -0.017 0.1 -9999 0 -0.29 59 59
RET51/GFRalpha1/GDNF -0.2 0.21 -9999 0 -0.38 264 264
MAPKKK cascade -0.18 0.19 -9999 0 -0.45 146 146
BCAR1 0.017 0.012 -9999 0 -0.26 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 -0.38 265 265
PIK3CA 0.016 0.029 -9999 0 -0.35 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 -0.17 0.18 -9999 0 -0.43 136 136
DOK1 0.002 0.083 -9999 0 -0.41 19 19
DOK6 -0.027 0.14 -9999 0 -0.44 51 51
PXN 0.018 0 -9999 0 -10000 0 0
neurite development -0.16 0.19 -9999 0 -0.41 147 147
DOK5 -0.025 0.13 -9999 0 -0.38 57 57
GFRA1 -0.22 0.24 -9999 0 -0.43 281 281
MAPK8 -0.16 0.2 -9999 0 -0.43 146 146
HRAS/GTP -0.21 0.22 -9999 0 -0.52 146 146
tube development -0.091 0.13 -9999 0 -0.26 193 193
MAPK1 -0.17 0.18 -9999 0 -0.43 136 136
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 -0.26 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.2 0.23 -9999 0 -0.4 250 250
SHC1 0.017 0.023 -9999 0 -0.52 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.2 0.21 -9999 0 -0.38 268 268
RET51/GFRalpha1/GDNF/Dok5 -0.22 0.23 -9999 0 -0.41 275 275
PRKCA 0.014 0.034 -9999 0 -0.26 8 8
HRAS/GDP 0.009 0.037 -9999 0 -0.29 7 7
CREB1 -0.14 0.19 -9999 0 -0.44 122 122
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
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 -0.4 274 274
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 -0.41 172 172
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 0.079 -9999 0 -0.42 16 16
NCK1 0.011 0.046 -9999 0 -0.28 12 12
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.077 0.12 -9999 0 -0.44 4 4
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.16 0.19 -9999 0 -0.43 134 134
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.17 0.21 -9999 0 -0.46 144 144
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.23 -9999 0 -0.54 132 132
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 0.098 -9999 0 -0.43 24 24
activation of MAPKK activity -0.13 0.16 -9999 0 -0.37 123 123
RET51/GFRalpha1/GDNF/FRS2 -0.2 0.21 -9999 0 -0.38 267 267
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 -0.55 137 137
RET51/GFRalpha1/GDNF/PKC alpha -0.2 0.21 -9999 0 -0.39 264 264
GRB2 0.016 0.024 -9999 0 -0.26 4 4
PRKACA 0.018 0 -9999 0 -10000 0 0
GDNF 0.014 0.042 -9999 0 -0.46 4 4
RAC1 0.018 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.23 0.26 -9999 0 -0.44 273 273
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
FOXM1 transcription factor network

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
NFATC3 -0.24 0.56 -9999 0 -1.2 99 99
PLK1 0.024 0.058 -9999 0 -10000 0 0
BIRC5 -0.092 0.39 -9999 0 -1.4 40 40
HSPA1B -0.24 0.56 -9999 0 -1.1 119 119
MAP2K1 0.018 0.046 -9999 0 -0.3 1 1
BRCA2 -0.26 0.59 -9999 0 -1.2 114 114
FOXM1 -0.4 0.93 -9999 0 -1.8 118 118
XRCC1 -0.24 0.56 -9999 0 -1.2 98 98
FOXM1B/p19 -0.42 0.55 -9999 0 -1.2 135 135
Cyclin D1/CDK4 -0.3 0.57 -9999 0 -1.1 152 152
CDC2 -0.26 0.61 -9999 0 -1.2 106 106
TGFA -0.29 0.55 -9999 0 -1 141 141
SKP2 -0.24 0.57 -9999 0 -1.2 97 97
CCNE1 -0.019 0.1 -9999 0 -0.29 64 64
CKS1B -0.24 0.57 -9999 0 -1.2 104 104
RB1 -0.22 0.32 -9999 0 -0.93 67 67
FOXM1C/SP1 -0.3 0.66 -9999 0 -1.3 123 123
AURKB 0.012 0.13 -9999 0 -1.4 3 3
CENPF -0.26 0.6 -9999 0 -1.2 103 103
CDK4 0.013 0.032 -9999 0 -0.26 5 5
MYC -0.22 0.52 -9999 0 -0.97 129 129
CHEK2 0.011 0.073 -9999 0 -0.41 9 9
ONECUT1 -0.28 0.57 -9999 0 -1.1 133 133
CDKN2A -0.057 0.15 -9999 0 -0.33 108 108
LAMA4 -0.24 0.57 -9999 0 -1.2 105 105
FOXM1B/HNF6 -0.37 0.71 -9999 0 -1.4 133 133
FOS -0.34 0.64 -9999 0 -1.2 147 147
SP1 0.016 0.024 -9999 0 -0.52 1 1
CDC25B -0.24 0.57 -9999 0 -1.2 101 101
response to radiation 0 0.039 -9999 0 -10000 0 0
CENPB -0.24 0.56 -9999 0 -1.2 94 94
CENPA -0.26 0.6 -9999 0 -1.2 108 108
NEK2 -0.28 0.62 -9999 0 -1.2 129 129
HIST1H2BA -0.24 0.57 -9999 0 -1.1 103 103
CCNA2 -0.025 0.14 -9999 0 -0.41 53 53
EP300 0.014 0.047 -9999 0 -0.52 4 4
CCNB1/CDK1 -0.31 0.7 -9999 0 -1.5 97 97
CCNB2 -0.25 0.58 -9999 0 -1.2 101 101
CCNB1 -0.27 0.62 -9999 0 -1.3 108 108
ETV5 -0.25 0.58 -9999 0 -1.2 110 110
ESR1 -0.43 0.71 -9999 0 -1.2 214 214
CCND1 -0.31 0.6 -9999 0 -1.1 153 153
GSK3A 0.019 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.013 0.13 -9999 0 -0.35 52 52
CDK2 0.011 0.049 -9999 0 -0.32 10 10
G2/M transition of mitotic cell cycle 0 0.046 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.37 0.53 -9999 0 -1.2 124 124
GAS1 -0.32 0.64 -9999 0 -1.2 148 148
MMP2 -0.27 0.61 -9999 0 -1.2 115 115
RB1/FOXM1C -0.3 0.6 -9999 0 -1.1 144 144
CREBBP 0.016 0.033 -9999 0 -0.52 2 2
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.47 103 103
FZD6 -0.077 0.2 -9999 0 -0.45 108 108
WNT6 -0.011 0.088 -9999 0 -0.27 54 54
WNT4 -0.063 0.18 -9999 0 -0.45 90 90
FZD3 -0.031 0.15 -9999 0 -0.48 52 52
WNT5A -0.084 0.2 -9999 0 -0.43 120 120
WNT11 -0.013 0.09 -9999 0 -0.27 57 57
EGFR-dependent Endothelin 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
HRAS 0.012 0.051 -9999 0 -0.41 7 7
EGFR -0.077 0.17 -9999 0 -0.35 136 136
EGF/EGFR -0.17 0.21 -9999 0 -0.36 243 243
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.084 0.16 -9999 0 -0.29 168 168
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.032 0.15 -9999 0 -0.5 50 50
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 -0.35 173 173
mol:GDP -0.086 0.15 -9999 0 -0.29 168 168
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.097 0.21 -9999 0 -0.44 134 134
GRB2/SOS1 0.024 0.024 -9999 0 -0.37 1 1
HRAS/GTP -0.1 0.12 -9999 0 -0.34 59 59
SHC1 0.017 0.023 -9999 0 -0.52 1 1
HRAS/GDP -0.08 0.14 -9999 0 -0.35 59 59
FRAP1 -0.078 0.14 -9999 0 -0.35 57 57
EGF/EGFR dimer -0.15 0.2 -9999 0 -0.42 172 172
SOS1 0.017 0.023 -9999 0 -0.52 1 1
GRB2 0.016 0.024 -9999 0 -0.26 4 4
ETA receptor/Endothelin-1 -0.09 0.19 -9999 0 -0.41 121 121
IGF1 pathway

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
NCK2 0.015 0.027 -10000 0 -0.26 5 5
PTK2 0.016 0.029 -10000 0 -0.35 3 3
CRKL -0.11 0.19 -10000 0 -0.37 155 155
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 -0.37 155 155
IGF-1R heterotetramer/IGF1/PTP1B -0.11 0.19 -10000 0 -0.37 156 156
AKT1 -0.086 0.18 -10000 0 -0.43 84 84
BAD -0.075 0.17 -10000 0 -0.4 84 84
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.19 -10000 0 -0.36 155 155
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.1 0.19 -10000 0 -0.35 170 170
RAF1 -0.064 0.16 -10000 0 -0.4 70 70
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.089 0.19 -10000 0 -0.35 154 154
YWHAZ 0.017 0.017 -10000 0 -0.26 2 2
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.21 -10000 0 -0.38 170 170
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
RPS6KB1 -0.087 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 -10000 0 -0.34 70 70
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
HRAS/GTP -0.1 0.16 -10000 0 -0.43 72 72
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.061 0.16 -10000 0 -0.35 71 71
IGF-1R heterotetramer -0.11 0.22 -10000 0 -0.51 110 110
IGF-1R heterotetramer/IGF1/IRS/Nck -0.1 0.2 -10000 0 -0.37 156 156
Crk/p130 Cas/Paxillin -0.079 0.18 -10000 0 -0.45 72 72
IGF1R -0.11 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 -0.36 167 167
PI3K -0.1 0.2 -10000 0 -0.35 166 166
apoptosis 0.058 0.15 0.34 84 -10000 0 84
HRAS/GDP 0.009 0.037 -10000 0 -0.29 7 7
PRKCD -0.097 0.21 -10000 0 -0.39 154 154
RAF1/14-3-3 E -0.048 0.14 -10000 0 -0.34 68 68
BAD/14-3-3 -0.061 0.16 -10000 0 -0.36 84 84
PRKCZ -0.091 0.18 -10000 0 -0.32 165 165
Crk/p130 Cas/Paxillin/FAK1 -0.088 0.14 -10000 0 -0.39 67 67
PTPN1 0.002 0.071 -10000 0 -0.29 28 28
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.11 0.22 -10000 0 -0.41 154 154
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.087 0.17 -10000 0 -0.32 164 164
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 -0.37 153 153
GRB10 -0.003 0.098 -10000 0 -0.43 24 24
PTPN11 -0.1 0.19 -10000 0 -0.35 170 170
IRS1 -0.12 0.2 -10000 0 -0.38 170 170
IRS2 -0.13 0.21 -10000 0 -0.38 170 170
IGF-1R heterotetramer/IGF1 -0.14 0.23 -10000 0 -0.46 157 157
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PDPK1 -0.094 0.19 -10000 0 -0.33 165 165
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
PRKD1 -0.12 0.23 -10000 0 -0.42 156 156
SHC1 0.017 0.023 -10000 0 -0.52 1 1
Endothelins

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
AKT1 -0.043 0.26 -10000 0 -0.59 60 60
PTK2B 0.017 0.017 -10000 0 -0.26 2 2
mol:Ca2+ -0.072 0.26 -10000 0 -0.67 56 56
EDN1 -0.063 0.24 0.23 56 -0.48 107 163
EDN3 -0.11 0.18 -10000 0 -0.33 194 194
EDN2 -0.13 0.22 -10000 0 -0.41 187 187
HRAS/GDP -0.11 0.24 -10000 0 -0.46 123 123
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.087 0.22 -10000 0 -0.42 123 123
ADCY4 -0.043 0.22 -10000 0 -0.53 57 57
ADCY5 -0.06 0.22 -10000 0 -0.49 74 74
ADCY6 -0.041 0.21 -10000 0 -0.51 59 59
ADCY7 -0.046 0.22 -10000 0 -0.52 61 61
ADCY1 -0.04 0.21 -10000 0 -0.51 58 58
ADCY2 -0.075 0.24 -10000 0 -0.5 87 87
ADCY3 -0.044 0.21 -10000 0 -0.51 63 63
ADCY8 -0.043 0.21 -10000 0 -0.51 59 59
ADCY9 -0.051 0.22 -10000 0 -0.51 68 68
arachidonic acid secretion -0.12 0.26 -10000 0 -0.5 130 130
ETB receptor/Endothelin-1/Gq/GTP -0.08 0.18 -10000 0 -0.35 118 118
GNAO1 0.016 0.024 -10000 0 -0.26 4 4
HRAS 0.011 0.051 -10000 0 -0.41 7 7
ETA receptor/Endothelin-1/G12/GTP -0.002 0.27 0.36 75 -0.56 57 132
ETA receptor/Endothelin-1/Gs/GTP -0.006 0.26 0.34 74 -0.54 58 132
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.047 0.28 -10000 0 -0.67 58 58
EDNRB -0.031 0.13 -10000 0 -0.39 53 53
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.042 0.26 -10000 0 -0.63 56 56
CYSLTR1 -0.075 0.3 -10000 0 -0.66 81 81
SLC9A1 -0.01 0.15 0.2 20 -0.3 56 76
mol:GDP -0.12 0.26 -10000 0 -0.48 132 132
SLC9A3 -0.13 0.34 -10000 0 -0.67 125 125
RAF1 -0.13 0.25 -10000 0 -0.48 133 133
JUN -0.11 0.36 -10000 0 -0.99 60 60
JAK2 -0.043 0.26 0.28 58 -0.54 72 130
mol:IP3 -0.11 0.22 -10000 0 -0.44 123 123
ETA receptor/Endothelin-1 -0.019 0.33 0.42 79 -0.57 86 165
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 -0.082 0.19 -10000 0 -0.41 100 100
FOS -0.18 0.35 -10000 0 -0.88 89 89
Gai/GDP -0.007 0.14 -10000 0 -0.81 11 11
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 -0.26 1 1
PRKCB1 -0.13 0.24 -10000 0 -0.46 136 136
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
GNAL 0.01 0.052 -10000 0 -0.33 11 11
Gs family/GDP -0.12 0.21 -10000 0 -0.45 119 119
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.23 -10000 0 -0.44 108 108
MAPK14 -0.084 0.17 -10000 0 -0.38 94 94
TRPC6 -0.078 0.28 -10000 0 -0.71 56 56
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.097 0.18 -10000 0 -0.35 132 132
ETB receptor/Endothelin-2 -0.11 0.18 -10000 0 -0.4 137 137
ETB receptor/Endothelin-3 -0.094 0.16 -10000 0 -0.38 95 95
ETB receptor/Endothelin-1 -0.067 0.21 -10000 0 -0.4 120 120
MAPK3 -0.17 0.34 -10000 0 -0.76 106 106
MAPK1 -0.17 0.34 -10000 0 -0.76 105 105
Rac1/GDP -0.1 0.24 -10000 0 -0.46 122 122
cAMP biosynthetic process -0.048 0.22 0.27 1 -0.5 71 72
MAPK8 -0.09 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 -0.036 0.16 -10000 0 -0.39 50 50
p130Cas/CRK/Src/PYK2 -0.1 0.25 -10000 0 -0.52 110 110
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.1 0.24 -10000 0 -0.46 122 122
COL1A2 -0.12 0.38 -10000 0 -0.82 98 98
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.099 0.22 -10000 0 -0.4 152 152
mol:DAG -0.11 0.22 -10000 0 -0.44 123 123
MAP2K2 -0.15 0.28 -10000 0 -0.59 119 119
MAP2K1 -0.15 0.28 -10000 0 -0.6 115 115
EDNRA -0.003 0.21 -10000 0 -0.57 50 50
positive regulation of muscle contraction -0.031 0.23 -10000 0 -0.52 60 60
Gq family/GDP -0.13 0.21 -10000 0 -0.48 106 106
HRAS/GTP -0.12 0.23 -10000 0 -0.44 132 132
PRKCH -0.1 0.22 -10000 0 -0.44 116 116
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCA -0.098 0.22 -10000 0 -0.44 113 113
PRKCB -0.1 0.21 -10000 0 -0.41 130 130
PRKCE -0.099 0.22 -10000 0 -0.44 115 115
PRKCD -0.099 0.22 -10000 0 -0.44 115 115
PRKCG -0.097 0.22 -10000 0 -0.44 111 111
regulation of vascular smooth muscle contraction -0.21 0.41 -10000 0 -1.1 87 87
PRKCQ -0.11 0.23 -10000 0 -0.45 123 123
PLA2G4A -0.14 0.28 -10000 0 -0.55 130 130
GNA14 -0.083 0.18 -10000 0 -0.36 141 141
GNA15 0 0.079 -10000 0 -0.33 25 25
GNA12 0.018 0 -10000 0 -10000 0 0
GNA11 0.012 0.047 -10000 0 -0.52 4 4
Rac1/GTP -0.001 0.27 0.36 75 -0.56 56 131
MMP1 -0.24 0.4 0.33 1 -0.89 132 133
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.016 0.037 -10000 0 -0.36 3 3
NFATC2 -0.11 0.26 -10000 0 -0.63 66 66
NFATC3 -0.055 0.11 -10000 0 -0.26 28 28
CD40LG -0.32 0.43 -10000 0 -0.89 155 155
ITCH 0.006 0.085 -10000 0 -10000 0 0
CBLB 0.004 0.092 -10000 0 -0.6 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.38 -10000 0 -0.89 94 94
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 49 49
T cell anergy -0.033 0.14 -10000 0 -0.39 49 49
TLE4 -0.071 0.23 -10000 0 -0.72 37 37
Jun/NFAT1-c-4/p21SNFT -0.29 0.45 -10000 0 -0.91 146 146
AP-1/NFAT1-c-4 -0.37 0.52 -10000 0 -1 154 154
IKZF1 -0.079 0.23 -10000 0 -0.72 39 39
T-helper 2 cell differentiation -0.22 0.35 -10000 0 -0.82 102 102
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.52 108 108
CALM1 0.002 0.058 -10000 0 -10000 0 0
EGR2 -0.29 0.51 -10000 0 -1.1 117 117
EGR3 -0.37 0.58 -10000 0 -1.3 132 132
NFAT1/FOXP3 -0.064 0.2 -10000 0 -0.54 45 45
EGR1 -0.1 0.2 -10000 0 -0.39 155 155
JUN -0.036 0.15 -10000 0 -0.47 54 54
EGR4 0 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.06 -10000 0 -0.17 49 49
GBP3 -0.14 0.31 -10000 0 -0.75 94 94
FOSL1 0.016 0.024 -10000 0 -0.26 4 4
NFAT1-c-4/MAF/IRF4 -0.27 0.44 -10000 0 -0.85 158 158
DGKA -0.065 0.21 -10000 0 -0.7 32 32
CREM 0.016 0.017 -10000 0 -0.26 2 2
NFAT1-c-4/PPARG -0.3 0.45 -10000 0 -0.89 161 161
CTLA4 -0.051 0.18 -10000 0 -0.53 41 41
NFAT1-c-4 (dimer)/EGR1 -0.33 0.47 -10000 0 -0.94 164 164
NFAT1-c-4 (dimer)/EGR4 -0.28 0.44 -10000 0 -0.88 157 157
FOS -0.11 0.2 -10000 0 -0.37 171 171
IFNG -0.3 0.47 -10000 0 -1.1 98 98
T cell activation -0.17 0.29 -10000 0 -0.77 58 58
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 0.72 151 -10000 0 151
TNF -0.29 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 -0.33 51 51
PTPN1 -0.068 0.2 -10000 0 -0.64 36 36
NFAT1-c-4/ICER1 -0.28 0.44 -10000 0 -0.88 155 155
GATA3 -0.1 0.23 -10000 0 -0.51 124 124
T-helper 1 cell differentiation -0.29 0.44 -10000 0 -1 102 102
IL2RA -0.25 0.36 -10000 0 -0.83 104 104
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.058 0.19 -10000 0 -0.62 30 30
E2F1 0.013 0.071 -10000 0 -0.37 16 16
PPARG -0.035 0.13 -10000 0 -0.33 79 79
SLC3A2 -0.059 0.19 -10000 0 -0.61 32 32
IRF4 -0.01 0.086 -10000 0 -0.27 52 52
PTGS2 -0.33 0.44 -10000 0 -0.9 155 155
CSF2 -0.33 0.43 -10000 0 -0.9 155 155
JunB/Fra1/NFAT1-c-4 -0.25 0.43 -10000 0 -0.83 156 156
IL4 -0.24 0.37 -10000 0 -0.88 98 98
IL5 -0.32 0.43 -10000 0 -0.89 151 151
IL2 -0.18 0.29 -10000 0 -0.79 56 56
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 -0.73 151 151
CDK4 0.14 0.22 0.59 39 -10000 0 39
PTPRK -0.12 0.3 -10000 0 -0.76 79 79
IL8 -0.36 0.44 -10000 0 -0.93 157 157
POU2F1 0.027 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.16 0.47 -9999 0 -0.92 102 102
HDAC7 0.001 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.13 0.39 -9999 0 -0.78 88 88
SMAD4 0.01 0.067 -9999 0 -0.49 9 9
ID2 -0.16 0.48 -9999 0 -0.93 104 104
AP1 -0.1 0.19 -9999 0 -0.43 107 107
ABCG2 -0.16 0.48 -9999 0 -0.94 101 101
HIF1A -0.055 0.19 -9999 0 -0.53 58 58
TFF3 -0.23 0.52 -9999 0 -0.97 131 131
GATA2 -0.013 0.096 -9999 0 -0.33 40 40
AKT1 -0.007 0.1 -9999 0 -0.45 8 8
response to hypoxia -0.02 0.083 -9999 0 -0.18 10 10
MCL1 -0.16 0.47 -9999 0 -0.94 97 97
NDRG1 -0.17 0.48 -9999 0 -0.98 98 98
SERPINE1 -0.17 0.48 -9999 0 -0.94 105 105
FECH -0.16 0.48 -9999 0 -0.92 107 107
FURIN -0.16 0.48 -9999 0 -0.92 106 106
NCOA2 0.009 0.063 -9999 0 -0.4 11 11
EP300 0.008 0.12 -9999 0 -0.38 12 12
HMOX1 -0.17 0.49 -9999 0 -0.95 104 104
BHLHE40 -0.17 0.46 -9999 0 -0.9 108 108
BHLHE41 -0.17 0.46 -9999 0 -0.9 108 108
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.009 0.16 -9999 0 -0.36 49 49
ENG 0.007 0.15 -9999 0 -0.35 43 43
JUN -0.037 0.16 -9999 0 -0.47 57 57
RORA -0.17 0.48 -9999 0 -0.92 112 112
ABCB1 -0.099 0.25 -9999 0 -1 29 29
TFRC -0.18 0.49 -9999 0 -0.94 111 111
CXCR4 -0.18 0.49 -9999 0 -0.95 109 109
TF -0.16 0.47 -9999 0 -0.95 96 96
CITED2 -0.16 0.48 -9999 0 -0.93 103 103
HIF1A/ARNT -0.2 0.54 -9999 0 -1.1 93 93
LDHA -0.043 0.15 -9999 0 -1.2 8 8
ETS1 -0.16 0.48 -9999 0 -0.94 99 99
PGK1 -0.16 0.47 -9999 0 -0.92 102 102
NOS2 -0.17 0.46 -9999 0 -0.9 108 108
ITGB2 -0.17 0.49 -9999 0 -0.94 109 109
ALDOA -0.16 0.47 -9999 0 -0.93 103 103
Cbp/p300/CITED2 -0.16 0.48 -9999 0 -0.98 92 92
FOS -0.11 0.2 -9999 0 -0.38 171 171
HK2 -0.16 0.47 -9999 0 -0.92 104 104
SP1 0.022 0.031 -9999 0 -0.52 1 1
GCK 0.01 0.2 -9999 0 -1 6 6
HK1 -0.16 0.47 -9999 0 -0.92 102 102
NPM1 -0.16 0.47 -9999 0 -0.92 103 103
EGLN1 -0.16 0.48 -9999 0 -0.92 106 106
CREB1 0.025 0.024 -9999 0 -0.52 1 1
PGM1 -0.16 0.48 -9999 0 -0.95 100 100
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 -0.92 102 102
VEGFA -0.087 0.36 -9999 0 -0.7 84 84
HIF1A/JAB1 -0.038 0.14 -9999 0 -0.38 62 62
CP -0.26 0.5 -9999 0 -0.95 134 134
CXCL12 -0.18 0.51 -9999 0 -0.98 110 110
COPS5 0.009 0.056 -9999 0 -0.36 11 11
SMAD3/SMAD4 0.013 0.074 -9999 0 -0.36 18 18
BNIP3 -0.17 0.48 -9999 0 -0.93 104 104
EGLN3 -0.2 0.5 -9999 0 -0.98 110 110
CA9 -0.17 0.48 -9999 0 -0.94 106 106
TERT -0.16 0.47 -9999 0 -0.93 101 101
ENO1 -0.16 0.47 -9999 0 -0.92 105 105
PFKL -0.16 0.47 -9999 0 -0.93 102 102
NCOA1 0.011 0.057 -9999 0 -0.52 6 6
ADM -0.2 0.51 -9999 0 -0.95 122 122
ARNT 0.003 0.076 -9999 0 -10000 0 0
HNF4A 0.02 0.034 -9999 0 -0.52 2 2
ADFP -0.17 0.49 -9999 0 -0.96 105 105
SLC2A1 -0.086 0.36 -9999 0 -0.7 84 84
LEP -0.19 0.48 -9999 0 -0.91 116 116
HIF1A/ARNT/Cbp/p300 -0.14 0.4 -9999 0 -0.8 86 86
EPO -0.094 0.35 -9999 0 -0.71 69 69
CREBBP 0.01 0.12 -9999 0 -0.36 10 10
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.39 -9999 0 -0.79 86 86
PFKFB3 -0.16 0.48 -9999 0 -0.93 105 105
NT5E -0.16 0.48 -9999 0 -0.94 100 100
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.058 0.13 -10000 0 -0.26 153 153
ER alpha/Gai/GDP/Gbeta gamma -0.089 0.19 -10000 0 -0.35 155 155
AKT1 -0.2 0.35 -10000 0 -0.73 153 153
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.2 0.35 -10000 0 -0.74 153 153
mol:Ca2+ -0.11 0.18 -10000 0 -0.39 115 115
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 0.7 153 -10000 0 153
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 0.042 0.12 0.29 41 -10000 0 41
E2/ERA-ERB (dimer) -0.087 0.15 -10000 0 -0.31 149 149
KRAS 0.008 0.069 -10000 0 -0.45 11 11
G13/GTP -0.082 0.14 -10000 0 -0.29 151 151
pseudopodium formation -0.042 0.12 -10000 0 -0.29 41 41
E2/ER alpha (dimer)/PELP1 -0.086 0.15 -10000 0 -0.31 149 149
GRB2 0.016 0.024 -10000 0 -0.26 4 4
GNG2 0.016 0.029 -10000 0 -0.35 3 3
GNAO1 0.016 0.024 -10000 0 -0.26 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 -0.38 151 151
mol:NADP -0.11 0.22 -10000 0 -0.44 152 152
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
mol:IP3 -0.11 0.19 -10000 0 -0.41 115 115
IGF-1R heterotetramer -0.083 0.2 -10000 0 -0.47 110 110
PLCB1 -0.12 0.19 -10000 0 -0.42 114 114
PLCB2 -0.075 0.17 -10000 0 -0.5 60 60
IGF1 -0.1 0.21 -10000 0 -0.42 146 146
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 0.13 -10000 0 -0.75 11 11
JNK cascade 0.013 0.008 -10000 0 -0.17 1 1
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
ESR2 0.017 0.012 -10000 0 -0.26 1 1
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.16 0.24 -10000 0 -0.45 202 202
Gq family/GDP/Gbeta gamma -0.025 0.12 -10000 0 -0.5 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 0.002 0.085 -10000 0 -0.43 18 18
E2/ER alpha (dimer) -0.12 0.17 -10000 0 -0.32 202 202
STRN 0.011 0.056 -10000 0 -0.42 8 8
GNAL 0.01 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 0.017 0.023 -10000 0 -0.52 1 1
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
HBEGF -0.091 0.19 -10000 0 -0.43 63 63
cAMP biosynthetic process -0.082 0.11 -10000 0 -0.25 151 151
SRC -0.078 0.18 -10000 0 -0.33 156 156
PI3K 0.006 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 -0.34 151 151
SOS1 0.017 0.023 -10000 0 -0.52 1 1
IGF-1R heterotetramer/IGF1 -0.16 0.21 -10000 0 -0.44 171 171
Gs family/GTP -0.067 0.13 -10000 0 -0.26 151 151
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 -0.42 153 153
mol:DAG -0.11 0.19 -10000 0 -0.41 115 115
Gs family/GDP/Gbeta gamma -0.1 0.15 -10000 0 -0.32 152 152
MSN -0.046 0.13 -10000 0 -0.32 41 41
Gq family/GTP -0.086 0.18 -10000 0 -0.47 72 72
mol:PI-3-4-5-P3 -0.19 0.34 -10000 0 -0.71 153 153
NRAS 0.006 0.072 -10000 0 -0.4 15 15
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.1 0.22 0.42 153 -10000 0 153
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
RhoA/GDP -0.094 0.18 -10000 0 -0.37 150 150
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 -0.4 154 154
ruffle organization -0.042 0.12 -10000 0 -0.29 41 41
ROCK2 -0.053 0.13 -10000 0 -0.37 29 29
GNA14 -0.081 0.18 -10000 0 -0.35 141 141
GNA15 0.001 0.078 -10000 0 -0.33 25 25
GNA13 0.009 0.059 -10000 0 -0.38 11 11
MMP9 -0.095 0.18 -10000 0 -0.45 47 47
MMP2 -0.088 0.2 -10000 0 -0.46 57 57
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.017 0.023 -9999 0 -0.52 1 1
CCL5 -0.05 0.18 -9999 0 -0.49 70 70
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
FGFR/FGF2/Syndecan-1 -0.17 0.27 -9999 0 -0.58 116 116
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 -0.58 111 111
Syndecan-1/Syntenin -0.16 0.26 -9999 0 -0.59 108 108
MAPK3 -0.13 0.24 -9999 0 -0.56 94 94
HGF/MET 0.006 0.075 -9999 0 -0.38 14 14
TGFB1/TGF beta receptor Type II 0.017 0.023 -9999 0 -0.52 1 1
BSG 0.016 0.024 -9999 0 -0.26 4 4
keratinocyte migration -0.15 0.25 -9999 0 -0.57 111 111
Syndecan-1/RANTES -0.18 0.28 -9999 0 -0.61 122 122
Syndecan-1/CD147 -0.14 0.25 -9999 0 -0.58 102 102
Syndecan-1/Syntenin/PIP2 -0.15 0.25 -9999 0 -0.57 108 108
LAMA5 0.005 0.075 -9999 0 -0.42 15 15
positive regulation of cell-cell adhesion -0.15 0.24 -9999 0 -0.55 108 108
MMP7 -0.094 0.21 -9999 0 -0.44 128 128
HGF 0.008 0.069 -9999 0 -0.45 11 11
Syndecan-1/CASK -0.16 0.26 -9999 0 -0.56 116 116
Syndecan-1/HGF/MET -0.15 0.25 -9999 0 -0.56 110 110
regulation of cell adhesion -0.12 0.23 -9999 0 -0.53 96 96
HPSE -0.017 0.12 -9999 0 -0.4 44 44
positive regulation of cell migration -0.17 0.27 -9999 0 -0.58 116 116
SDC1 -0.17 0.27 -9999 0 -0.59 116 116
Syndecan-1/Collagen -0.17 0.27 -9999 0 -0.58 116 116
PPIB 0.014 0.044 -9999 0 -0.42 5 5
MET -0.001 0.078 -9999 0 -0.3 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 -0.56 96 96
homophilic cell adhesion -0.16 0.26 -9999 0 -0.58 116 116
MMP1 -0.19 0.22 -9999 0 -0.39 268 268
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 45 45
CDKN2C 0.005 0.085 -10000 0 -0.37 23 23
CDKN2A -0.053 0.15 -10000 0 -0.33 107 107
CCND2 0.019 0.084 0.2 74 -0.15 6 80
RB1 -0.022 0.092 0.15 3 -0.22 76 79
CDK4 0.026 0.095 0.23 77 -10000 0 77
CDK6 0.019 0.093 0.24 61 -0.19 7 68
G1/S progression 0.022 0.092 0.22 76 -0.15 3 79
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 0.066 0.099 0.24 117 -10000 0 117
RFC1 0.067 0.099 0.24 121 -10000 0 121
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 -10000 0 -0.68 14 14
FASLG/FAS/FADD/FAF1 -0.013 0.13 0.22 49 -0.3 47 96
MAP2K4 -0.045 0.16 -10000 0 -0.42 45 45
mol:ceramide -0.044 0.14 -10000 0 -0.38 58 58
GSN 0.055 0.11 0.24 122 -0.3 12 134
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 50 50
BID 0.011 0.065 0.29 15 -0.32 8 23
MAP3K1 -0.017 0.13 0.26 2 -0.37 30 32
MAP3K7 0.015 0.021 -10000 0 -0.26 3 3
RB1 0.054 0.11 0.24 114 -0.29 9 123
CFLAR 0.011 0.064 -10000 0 -0.46 9 9
HGF/MET -0.036 0.14 -10000 0 -0.32 91 91
ARHGDIB 0.044 0.12 0.24 109 -0.29 20 129
FADD -0.002 0.068 -10000 0 -0.26 34 34
actin filament polymerization -0.055 0.11 0.3 12 -0.24 122 134
NFKB1 -0.043 0.08 -10000 0 -0.3 14 14
MAPK8 -0.061 0.19 -10000 0 -0.46 72 72
DFFA 0.066 0.098 0.24 116 -10000 0 116
DNA fragmentation during apoptosis 0.066 0.098 0.24 122 -10000 0 122
FAS/FADD/MET -0.014 0.1 -10000 0 -0.32 39 39
CFLAR/RIP1 0.021 0.05 -10000 0 -0.36 8 8
FAIM3 0 0.096 -10000 0 -0.49 19 19
FAF1 0.013 0.025 -10000 0 -0.52 1 1
PARP1 0.064 0.1 0.24 121 -0.28 5 126
DFFB 0.066 0.098 0.24 122 -10000 0 122
CHUK -0.026 0.092 -10000 0 -0.33 15 15
FASLG -0.066 0.17 -10000 0 -0.38 107 107
FAS/FADD -0.019 0.11 -10000 0 -0.38 32 32
HGF 0.008 0.069 -10000 0 -0.45 11 11
LMNA 0.06 0.095 0.22 112 -0.26 7 119
CASP6 0.062 0.1 0.23 122 -0.27 4 126
CASP10 0.012 0.03 -10000 0 -0.26 6 6
CASP3 0.072 0.12 0.28 127 -10000 0 127
PTPN13 -0.071 0.2 -10000 0 -0.49 93 93
CASP8 0.012 0.066 0.37 17 -10000 0 17
IL6 -0.16 0.4 -10000 0 -1.2 60 60
MET -0.001 0.078 -10000 0 -0.3 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 58 58
activation of caspase activity by cytochrome c 0.011 0.065 0.29 15 -0.32 8 23
PAK2 0.067 0.098 0.24 121 -10000 0 121
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.11 0.3 -10000 0 -0.7 64 64
CRP -0.11 0.3 -10000 0 -0.73 52 52
cell cycle arrest -0.14 0.34 -10000 0 -0.73 97 97
TIMP1 -0.11 0.3 -10000 0 -0.74 66 66
IL6ST -0.11 0.22 -10000 0 -0.46 143 143
Rac1/GDP -0.11 0.22 0.28 1 -0.45 115 116
AP1 -0.05 0.16 -10000 0 -0.45 33 33
GAB2 0.011 0.047 -10000 0 -0.26 16 16
TNFSF11 -0.18 0.41 -10000 0 -0.93 97 97
HSP90B1 0.007 0.11 -10000 0 -0.74 7 7
GAB1 0.007 0.074 -10000 0 -0.42 14 14
MAPK14 -0.11 0.22 -10000 0 -0.51 77 77
AKT1 0.038 0.073 -10000 0 -0.57 2 2
FOXO1 0.036 0.085 -10000 0 -0.5 4 4
MAP2K6 -0.12 0.22 0.27 1 -0.43 133 134
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.11 0.25 -10000 0 -0.49 110 110
MITF -0.11 0.22 0.29 1 -0.43 121 122
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 -0.045 0.28 -10000 0 -1.4 23 23
CEBPB 0.013 0.073 -10000 0 -0.34 20 20
GRB2/SOS1/GAB family/SHP2 -0.018 0.1 -10000 0 -0.41 9 9
STAT3 -0.15 0.37 -10000 0 -0.78 97 97
STAT1 -0.042 0.17 -10000 0 -0.95 16 16
CEBPD -0.16 0.39 -10000 0 -0.91 83 83
PIK3CA 0.017 0.029 -10000 0 -0.34 3 3
PI3K 0.009 0.083 -10000 0 -0.37 21 21
JUN -0.034 0.15 -10000 0 -0.46 57 57
PIAS3/MITF -0.097 0.21 0.27 1 -0.44 101 102
MAPK11 -0.11 0.22 -10000 0 -0.51 77 77
STAT3 (dimer)/FOXO1 -0.085 0.29 -10000 0 -0.62 78 78
GRB2/SOS1/GAB family -0.11 0.18 -10000 0 -0.47 72 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.13 0.22 -10000 0 -0.41 149 149
GRB2 0.017 0.024 -10000 0 -0.26 4 4
JAK2 0.01 0.054 -10000 0 -0.32 12 12
LBP -0.1 0.26 -10000 0 -0.59 60 60
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
JAK1 0.013 0.058 -10000 0 -0.53 6 6
MYC -0.15 0.37 -10000 0 -0.85 84 84
FGG -0.11 0.3 -10000 0 -0.71 62 62
macrophage differentiation -0.14 0.34 -10000 0 -0.73 97 97
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.13 0.2 -10000 0 -0.34 215 215
JUNB -0.11 0.29 -10000 0 -0.66 72 72
FOS -0.11 0.2 -10000 0 -0.37 171 171
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.31 1 -0.42 146 147
STAT1/PIAS1 -0.11 0.22 0.32 1 -0.43 127 128
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.067 -10000 0 -0.38 4 4
STAT3 (dimer) -0.15 0.37 -10000 0 -0.77 97 97
PRKCD -0.1 0.27 -10000 0 -0.57 90 90
IL6R 0.002 0.085 -10000 0 -0.38 23 23
SOCS3 -0.1 0.23 -10000 0 -0.69 40 40
gp130 (dimer)/JAK1/JAK1/LMO4 -0.097 0.19 -10000 0 -0.35 171 171
Rac1/GTP -0.11 0.24 -10000 0 -0.46 116 116
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 -0.17 0.38 -10000 0 -0.84 100 100
IRF1 -0.13 0.34 -10000 0 -0.76 79 79
mol:GDP -0.12 0.23 0.29 1 -0.43 139 140
SOS1 0.018 0.024 -10000 0 -0.52 1 1
VAV1 -0.12 0.23 0.29 1 -0.44 139 140
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.12 0.22 -10000 0 -0.48 90 90
PTPN11 0.004 0.058 -10000 0 -1.2 1 1
IL6/IL6RA -0.057 0.14 -10000 0 -0.36 76 76
gp130 (dimer)/TYK2/TYK2/LMO4 -0.096 0.18 -10000 0 -0.34 170 170
gp130 (dimer)/JAK2/JAK2/LMO4 -0.1 0.18 -10000 0 -0.35 175 175
IL6 -0.085 0.18 -10000 0 -0.36 146 146
PIAS3 0.018 0 -10000 0 -10000 0 0
PTPRE 0 0.082 -10000 0 -0.46 15 15
PIAS1 0.017 0.012 -10000 0 -0.26 1 1
RAC1 0.018 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.18 0.27 1 -0.34 167 168
LMO4 -0.074 0.18 -10000 0 -0.38 124 124
STAT3 (dimer)/PIAS3 -0.14 0.34 -10000 0 -0.72 98 98
MCL1 0.043 0.084 -10000 0 -1.2 1 1
Glucocorticoid receptor regulatory network

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
PCK2 0.017 0.16 0.34 14 -0.84 11 25
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 -0.76 118 118
SUMO2 0.014 0.022 -10000 0 -0.26 3 3
STAT1 (dimer) -0.024 0.14 -10000 0 -0.35 67 67
FKBP4 0.012 0.055 -10000 0 -0.45 7 7
FKBP5 -0.045 0.16 -10000 0 -0.43 75 75
GR alpha/HSP90/FKBP51/HSP90 0.073 0.16 0.3 67 -0.31 28 95
PRL -0.057 0.14 -10000 0 -0.87 3 3
cortisol/GR alpha (dimer)/TIF2 0.24 0.26 0.53 186 -0.4 2 188
RELA -0.053 0.091 -10000 0 -0.26 22 22
FGG 0.2 0.22 0.49 135 -0.39 2 137
GR beta/TIF2 0.11 0.14 0.3 108 -0.31 14 122
IFNG -0.41 0.43 -10000 0 -0.88 182 182
apoptosis -0.005 0.18 0.49 7 -0.5 8 15
CREB1 0.007 0.057 -10000 0 -0.36 5 5
histone acetylation -0.045 0.14 0.28 2 -0.36 51 53
BGLAP -0.074 0.15 -10000 0 -0.6 8 8
GR/PKAc 0.093 0.14 0.3 58 -0.34 12 70
NF kappa B1 p50/RelA -0.093 0.17 -10000 0 -0.38 78 78
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.099 0.1 0.24 121 -10000 0 121
GATA3 -0.093 0.23 -10000 0 -0.5 124 124
AKT1 0.007 0.06 0.21 4 -0.38 9 13
CSF2 -0.074 0.15 -10000 0 -0.66 13 13
GSK3B 0.016 0.008 -10000 0 -10000 0 0
NR1I3 0.008 0.18 0.48 6 -0.91 3 9
CSN2 0.17 0.18 0.41 125 -0.39 5 130
BRG1/BAF155/BAF170/BAF60A 0.041 0.034 -10000 0 -0.27 5 5
NFATC1 -0.004 0.12 -10000 0 -0.42 38 38
POU2F1 0.025 0.012 -10000 0 -0.22 1 1
CDKN1A -0.033 0.27 -10000 0 -1.5 15 15
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 0.3 59 -0.32 29 88
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.086 0.33 0.46 6 -0.8 79 85
JUN -0.22 0.24 -10000 0 -0.53 145 145
IL4 -0.1 0.2 -10000 0 -0.66 29 29
CDK5R1 0.013 0.032 -10000 0 -0.26 7 7
PRKACA 0.018 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.28 0.21 46 -0.5 218 264
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.081 0.15 0.3 64 -0.3 23 87
cortisol/GR alpha (monomer) 0.28 0.32 0.63 190 -0.47 2 192
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 -0.45 171 171
AP-1/NFAT1-c-4 -0.44 0.39 -10000 0 -0.79 246 246
AFP -0.16 0.2 -10000 0 -0.6 42 42
SUV420H1 0.014 0.037 -10000 0 -0.3 7 7
IRF1 0.11 0.25 0.43 63 -0.79 20 83
TP53 -0.014 0.17 -10000 0 -0.54 46 46
PPP5C 0.012 0.052 -10000 0 -0.39 8 8
KRT17 -0.54 0.58 -10000 0 -1.1 211 211
KRT14 -0.32 0.51 -10000 0 -1.3 100 100
TBP 0.028 0.011 -10000 0 -10000 0 0
CREBBP 0.061 0.1 0.26 65 -0.53 2 67
HDAC1 0.011 0.025 -10000 0 -0.53 1 1
HDAC2 0.008 0.054 -10000 0 -0.29 15 15
AP-1 -0.45 0.4 -10000 0 -0.8 248 248
MAPK14 0.015 0.014 -10000 0 -0.26 1 1
MAPK10 -0.027 0.13 -10000 0 -0.36 59 59
MAPK11 0.016 0.008 -10000 0 -10000 0 0
KRT5 -0.55 0.58 -10000 0 -1.1 238 238
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 -0.024 0.14 -10000 0 -0.35 67 67
CGA -0.12 0.2 -10000 0 -0.53 59 59
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.17 0.37 111 -0.35 4 115
MAPK3 0.014 0.027 -10000 0 -0.39 2 2
MAPK1 0.014 0.034 -10000 0 -0.52 2 2
ICAM1 -0.23 0.34 -10000 0 -0.71 127 127
NFKB1 -0.054 0.093 -10000 0 -0.25 34 34
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 0.49 7 -0.53 8 15
BAX 0.002 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 0.55 160 -0.48 4 164
proteasomal ubiquitin-dependent protein catabolic process 0.071 0.081 0.22 67 -10000 0 67
SGK1 0.11 0.13 0.34 101 -0.26 4 105
IL13 -0.31 0.29 -10000 0 -0.7 138 138
IL6 -0.29 0.41 -10000 0 -0.93 117 117
PRKACG 0.016 0.033 -10000 0 -0.52 2 2
IL5 -0.27 0.24 -10000 0 -0.77 34 34
IL2 -0.32 0.33 -10000 0 -0.74 147 147
CDK5 0.015 0.027 -10000 0 -0.4 2 2
PRKACB -0.035 0.14 -10000 0 -0.34 78 78
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
IL8 -0.27 0.37 -10000 0 -0.78 139 139
CDK5R1/CDK5 0.02 0.03 -10000 0 -0.37 1 1
NF kappa B1 p50/RelA/PKAc -0.064 0.15 -10000 0 -0.38 47 47
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.24 0.52 177 -10000 0 177
SMARCA4 0.015 0.031 -10000 0 -0.32 4 4
chromatin remodeling 0.16 0.16 0.36 147 -10000 0 147
NF kappa B1 p50/RelA/Cbp -0.019 0.16 0.32 22 -0.39 25 47
JUN (dimer) -0.22 0.24 -10000 0 -0.52 145 145
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
VIPR1 -0.11 0.23 -10000 0 -0.61 70 70
NR3C1 0.16 0.21 0.42 141 -0.45 11 152
NR4A1 0.01 0.064 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.017 0.056 -10000 0 -0.42 6 6
MAPKKK cascade -0.005 0.18 0.49 7 -0.5 8 15
cortisol/GR alpha (dimer)/Src-1 0.24 0.26 0.54 184 -0.43 3 187
PBX1 0.004 0.1 -10000 0 -0.48 23 23
POU1F1 0.023 0.034 -10000 0 -0.3 5 5
SELE -0.36 0.48 -10000 0 -1 157 157
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.36 147 -10000 0 147
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.24 0.52 177 -10000 0 177
mol:cortisol 0.16 0.19 0.37 191 -10000 0 191
MMP1 -0.44 0.52 -10000 0 -1.3 132 132
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 0.62 -10000 0 -1.3 117 117
STAT6 (cleaved dimer) -0.43 0.56 -10000 0 -1.2 143 143
IGHG1 -0.081 0.25 -10000 0 -0.44 65 65
IGHG3 -0.33 0.59 -10000 0 -1.2 138 138
AKT1 -0.11 0.31 -10000 0 -0.71 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.063 0.24 -10000 0 -0.68 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.34 -10000 0 -0.76 59 59
THY1 -0.34 0.65 -10000 0 -1.3 123 123
MYB -0.098 0.22 -10000 0 -0.49 121 121
HMGA1 0.014 0.039 -10000 0 -0.36 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.35 -10000 0 -0.65 93 93
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.31 -10000 0 -0.78 30 30
SP1 0.021 0.03 -10000 0 -0.53 1 1
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.015 0.055 -10000 0 -0.4 7 7
STAT6 (dimer)/ETS1 -0.33 0.63 -10000 0 -1.2 135 135
SOCS1 -0.18 0.4 -10000 0 -0.78 101 101
SOCS3 -0.11 0.33 -10000 0 -0.92 26 26
FCER2 -0.22 0.46 -10000 0 -0.91 101 101
PARP14 0.006 0.078 -10000 0 -0.43 15 15
CCL17 -0.41 0.71 -10000 0 -1.4 154 154
GRB2 0.016 0.024 -10000 0 -0.26 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.081 0.26 -10000 0 -0.67 22 22
T cell proliferation -0.35 0.65 -10000 0 -1.3 126 126
IL4R/JAK1 -0.34 0.64 -10000 0 -1.3 123 123
EGR2 -0.38 0.69 -10000 0 -1.4 137 137
JAK2 0.001 0.072 -10000 0 -0.35 12 12
JAK3 0.021 0.008 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
JAK1 0.012 0.061 -10000 0 -0.52 6 6
COL1A2 -0.22 0.54 -10000 0 -1.5 70 70
CCL26 -0.33 0.63 -10000 0 -1.3 121 121
IL4R -0.37 0.7 -10000 0 -1.4 120 120
PTPN6 0.02 0.038 -10000 0 -0.42 3 3
IL13RA2 -0.38 0.67 -10000 0 -1.3 142 142
IL13RA1 -0.002 0.089 -10000 0 -0.49 12 12
IRF4 -0.037 0.2 -10000 0 -0.88 8 8
ARG1 -0.063 0.27 -10000 0 -0.98 22 22
CBL -0.13 0.32 -10000 0 -0.61 90 90
GTF3A 0.02 0.032 -10000 0 -0.38 2 2
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
IL13RA1/JAK2 0.004 0.099 -10000 0 -0.36 18 18
IRF4/BCL6 -0.043 0.19 -10000 0 -0.86 7 7
CD40LG 0.012 0.072 -10000 0 -0.32 21 21
MAPK14 -0.13 0.33 -10000 0 -0.65 75 75
mitosis -0.1 0.3 -10000 0 -0.66 42 42
STAT6 -0.43 0.85 -10000 0 -1.6 138 138
SPI1 0.011 0.074 -10000 0 -0.44 12 12
RPS6KB1 -0.097 0.29 -10000 0 -0.66 35 35
STAT6 (dimer) -0.43 0.86 -10000 0 -1.6 138 138
STAT6 (dimer)/PARP14 -0.38 0.7 -10000 0 -1.4 139 139
mast cell activation 0.003 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.11 0.3 -10000 0 -0.69 45 45
FRAP1 -0.11 0.31 -10000 0 -0.7 42 42
LTA -0.33 0.62 -10000 0 -1.3 115 115
FES 0.011 0.054 -10000 0 -0.38 9 9
T-helper 1 cell differentiation 0.39 0.75 1.4 138 -10000 0 138
CCL11 -0.38 0.65 -10000 0 -1.3 141 141
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.099 0.3 -10000 0 -0.7 30 30
IL2RG 0.001 0.081 -10000 0 -0.29 35 35
IL10 -0.33 0.63 -10000 0 -1.3 117 117
IRS1 -0.048 0.17 -10000 0 -0.49 68 68
IRS2 -0.026 0.13 -10000 0 -0.39 57 57
IL4 -0.038 0.22 -10000 0 -1.4 6 6
IL5 -0.33 0.63 -10000 0 -1.4 99 99
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.24 0.5 -10000 0 -0.95 126 126
COL1A1 -0.22 0.56 -10000 0 -1.5 71 71
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.36 0.67 -10000 0 -1.5 103 103
IL2R gamma/JAK3 0.017 0.059 -10000 0 -0.33 5 5
TFF3 -0.51 0.77 -10000 0 -1.4 190 190
ALOX15 -0.34 0.64 -10000 0 -1.3 119 119
MYBL1 -0.067 0.17 -10000 0 -0.37 116 116
T-helper 2 cell differentiation -0.25 0.49 -10000 0 -0.96 124 124
SHC1 0.017 0.023 -10000 0 -0.52 1 1
CEBPB 0.008 0.075 -10000 0 -0.33 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.32 -10000 0 -0.75 40 40
mol:PI-3-4-5-P3 -0.11 0.31 -10000 0 -0.7 42 42
PI3K -0.12 0.33 -10000 0 -0.76 42 42
DOK2 -0.021 0.13 -10000 0 -0.41 48 48
ETS1 0.007 0.067 -10000 0 -0.35 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.071 0.25 -10000 0 -0.62 23 23
ITGB3 -0.34 0.63 -10000 0 -1.3 122 122
PIGR -0.49 0.76 -10000 0 -1.4 181 181
IGHE 0.022 0.086 0.21 44 -0.25 4 48
MAPKKK cascade -0.069 0.24 -10000 0 -0.61 23 23
BCL6 -0.005 0.1 -10000 0 -0.46 24 24
OPRM1 -0.33 0.63 -10000 0 -1.3 116 116
RETNLB -0.33 0.63 -10000 0 -1.3 115 115
SELP -0.46 0.75 -10000 0 -1.5 158 158
AICDA -0.34 0.61 -10000 0 -1.3 126 126
TCR signaling in naïve CD8+ T 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
GRB2/SOS1/SHC -0.058 0.21 -10000 0 -0.46 94 94
FYN -0.085 0.26 -10000 0 -0.55 106 106
LAT/GRAP2/SLP76 -0.099 0.21 -10000 0 -0.48 109 109
IKBKB 0.011 0.047 -10000 0 -0.31 10 10
AKT1 -0.048 0.19 -10000 0 -0.38 109 109
B2M -0.006 0.11 -10000 0 -0.46 26 26
IKBKG 0.002 0.062 -10000 0 -0.13 54 54
MAP3K8 -0.036 0.15 -10000 0 -0.39 69 69
mol:Ca2+ -0.022 0.031 -10000 0 -0.072 106 106
integrin-mediated signaling pathway 0.007 0.067 -10000 0 -0.31 19 19
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.084 0.26 -10000 0 -0.54 112 112
TRPV6 -0.11 0.19 -10000 0 -0.38 160 160
CD28 -0.044 0.16 -10000 0 -0.4 78 78
SHC1 -0.09 0.26 -10000 0 -0.56 103 103
receptor internalization -0.12 0.3 -10000 0 -0.6 121 121
PRF1 -0.081 0.25 -10000 0 -0.72 45 45
KRAS 0.008 0.069 -10000 0 -0.45 11 11
GRB2 0.016 0.024 -10000 0 -0.26 4 4
COT/AKT1 -0.047 0.16 -10000 0 -0.32 103 103
LAT -0.096 0.27 -10000 0 -0.56 112 112
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.028 0.13 -10000 0 -0.35 66 66
CD3E 0.016 0.018 -10000 0 -0.27 2 2
CD3G -0.092 0.2 -10000 0 -0.42 135 135
RASGRP2 -0.002 0.036 -10000 0 -0.14 17 17
RASGRP1 -0.061 0.2 -10000 0 -0.38 121 121
HLA-A -0.013 0.12 -10000 0 -0.44 35 35
RASSF5 -0.002 0.091 -10000 0 -0.38 27 27
RAP1A/GTP/RAPL 0.008 0.067 -10000 0 -0.31 19 19
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 -0.2 88 88
PRKCA -0.044 0.11 -10000 0 -0.24 96 96
GRAP2 0.011 0.044 -10000 0 -0.28 11 11
mol:IP3 -0.052 0.19 0.19 83 -0.37 105 188
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.081 0.22 -10000 0 -0.46 99 99
ORAI1 0.071 0.11 0.3 68 -0.38 1 69
CSK -0.089 0.26 -10000 0 -0.56 103 103
B7 family/CD28 -0.11 0.3 -10000 0 -0.6 118 118
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 -0.64 106 106
PTPN6 -0.094 0.26 -10000 0 -0.57 103 103
VAV1 -0.1 0.28 -10000 0 -0.59 107 107
Monovalent TCR/CD3 -0.095 0.22 -10000 0 -0.4 145 145
CBL 0.017 0.012 -10000 0 -0.26 1 1
LCK -0.098 0.28 -10000 0 -0.59 107 107
PAG1 -0.093 0.26 -10000 0 -0.57 104 104
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
TCR/CD3/MHC I/CD8/LCK -0.12 0.3 -10000 0 -0.61 117 117
CD80 0.009 0.049 -10000 0 -0.28 14 14
CD86 -0.009 0.12 -10000 0 -0.5 27 27
PDK1/CARD11/BCL10/MALT1 -0.055 0.095 -10000 0 -0.24 92 92
HRAS 0.012 0.051 -10000 0 -0.41 7 7
GO:0035030 -0.091 0.24 -10000 0 -0.5 118 118
CD8A 0 0.005 -10000 0 -10000 0 0
CD8B 0.001 0.07 -10000 0 -0.28 29 29
PTPRC -0.041 0.16 -10000 0 -0.42 71 71
PDK1/PKC theta -0.061 0.23 -10000 0 -0.47 109 109
CSK/PAG1 -0.08 0.25 -10000 0 -0.54 98 98
SOS1 0.017 0.023 -10000 0 -0.52 1 1
peptide-MHC class I -0.012 0.13 -10000 0 -0.47 33 33
GRAP2/SLP76 -0.086 0.26 -10000 0 -0.55 107 107
STIM1 0.035 0.059 -10000 0 -0.36 2 2
RAS family/GTP -0.002 0.088 -10000 0 -0.17 68 68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.33 -10000 0 -0.64 121 121
mol:DAG -0.072 0.15 -10000 0 -0.33 108 108
RAP1A/GDP 0.002 0.032 -10000 0 -0.08 20 20
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
CD247 -0.1 0.21 -10000 0 -0.42 151 151
cytotoxic T cell degranulation -0.077 0.24 -10000 0 -0.69 45 45
RAP1A/GTP -0.005 0.015 -10000 0 -0.076 18 18
mol:PI-3-4-5-P3 -0.064 0.22 -10000 0 -0.45 112 112
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.076 0.23 0.21 78 -0.48 107 185
NRAS 0.006 0.072 -10000 0 -0.4 15 15
ZAP70 0.005 0.061 -10000 0 -0.27 24 24
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
LAT/GRAP2/SLP76/VAV1 -0.1 0.21 0.16 1 -0.48 110 111
MALT1 0.011 0.054 -10000 0 -0.38 9 9
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
CD8 heterodimer 0.002 0.049 -10000 0 -0.2 29 29
CARD11 0.002 0.078 -10000 0 -0.34 24 24
PRKCB -0.048 0.1 -10000 0 -0.23 110 110
PRKCE -0.045 0.11 -10000 0 -0.24 98 98
PRKCQ -0.079 0.26 -10000 0 -0.52 113 113
LCP2 -0.005 0.1 -10000 0 -0.41 28 28
BCL10 0.017 0.012 -10000 0 -0.26 1 1
regulation of survival gene product expression -0.037 0.16 -10000 0 -0.32 108 108
IKK complex 0.012 0.059 -10000 0 -0.1 52 52
RAS family/GDP -0.008 0.015 -10000 0 -0.064 20 20
MAP3K14 -0.029 0.13 -10000 0 -0.25 91 91
PDPK1 -0.042 0.18 -10000 0 -0.36 105 105
TCR/CD3/MHC I/CD8/Fyn -0.092 0.26 -10000 0 -0.59 92 92
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.03 0.12 -10000 0 -0.32 38 38
TBX21 -0.3 0.59 -10000 0 -1.3 119 119
B2M -0.006 0.1 -10000 0 -0.45 26 26
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 89 89
IL12RB2 -0.076 0.16 -10000 0 -0.32 141 141
GADD45G -0.18 0.43 -10000 0 -0.98 97 97
natural killer cell activation -0.005 0.024 -10000 0 -10000 0 0
RELB 0.003 0.079 -10000 0 -0.38 19 19
RELA 0.018 0 -10000 0 -10000 0 0
IL18 -0.048 0.17 -10000 0 -0.44 78 78
IL2RA -0.031 0.14 -10000 0 -0.41 61 61
IFNG -0.089 0.17 -10000 0 -0.33 161 161
STAT3 (dimer) -0.14 0.37 -10000 0 -0.76 112 112
HLA-DRB5 -0.004 0.098 -10000 0 -0.51 19 19
FASLG -0.24 0.52 -10000 0 -1.1 110 110
NF kappa B2 p52/RelB -0.24 0.41 -10000 0 -0.87 129 129
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 -0.032 0.13 -10000 0 -0.35 66 66
CD3E 0.013 0.021 -10000 0 -0.28 2 2
CD3G -0.097 0.2 -10000 0 -0.42 135 135
IL12Rbeta2/JAK2 -0.048 0.13 -10000 0 -0.27 102 102
CCL3 -0.2 0.44 -10000 0 -0.97 102 102
CCL4 -0.2 0.46 -10000 0 -1 103 103
HLA-A -0.013 0.12 -10000 0 -0.43 35 35
IL18/IL18R -0.059 0.22 -10000 0 -0.41 117 117
NOS2 -0.19 0.43 -10000 0 -0.86 124 124
IL12/IL12R/TYK2/JAK2/SPHK2 -0.03 0.12 -10000 0 -0.33 37 37
IL1R1 -0.25 0.51 -10000 0 -1.1 118 118
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 -0.65 105 105
RAB7A -0.12 0.34 -10000 0 -0.8 81 81
lysosomal transport -0.12 0.33 -10000 0 -0.75 82 82
FOS -0.29 0.49 -10000 0 -1.1 132 132
STAT4 (dimer) -0.18 0.43 -10000 0 -0.88 119 119
STAT5A (dimer) -0.27 0.42 -10000 0 -0.89 136 136
GZMA -0.2 0.43 -10000 0 -0.87 126 126
GZMB -0.28 0.57 -10000 0 -1.2 119 119
HLX 0.005 0.079 -10000 0 -0.48 13 13
LCK -0.25 0.52 -10000 0 -1 137 137
TCR/CD3/MHC II/CD4 -0.11 0.23 -10000 0 -0.46 122 122
IL2/IL2R -0.015 0.14 -10000 0 -0.34 71 71
MAPK14 -0.18 0.44 -10000 0 -0.94 104 104
CCR5 -0.19 0.46 -10000 0 -1 94 94
IL1B -0.053 0.17 -10000 0 -0.42 81 81
STAT6 -0.067 0.18 -10000 0 -0.38 76 76
STAT4 -0.023 0.13 -10000 0 -0.42 49 49
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 0.078 -10000 0 -0.35 21 21
CD8A -0.001 0.008 -10000 0 -10000 0 0
CD8B 0.001 0.071 -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 0.32 38 -10000 0 38
IL2RB -0.017 0.12 -10000 0 -0.44 40 40
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.38 -10000 0 -0.78 119 119
IL2RG -0.003 0.079 -10000 0 -0.29 35 35
IL12 -0.012 0.09 -10000 0 -0.26 35 35
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
CD247 -0.11 0.21 -10000 0 -0.42 151 151
IL2 0.011 0.051 -10000 0 -0.34 10 10
SPHK2 0.016 0.033 -10000 0 -0.52 2 2
FRAP1 0.018 0 -10000 0 -10000 0 0
IL12A -0.02 0.097 -10000 0 -0.28 56 56
IL12/IL12R/TYK2/JAK2 -0.25 0.54 -10000 0 -1.1 126 126
MAP2K3 -0.18 0.44 -10000 0 -0.94 107 107
RIPK2 0.013 0.041 -10000 0 -0.29 9 9
MAP2K6 -0.19 0.45 -10000 0 -0.95 109 109
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 -0.074 0.19 -10000 0 -0.41 117 117
IL12Rbeta1/TYK2 0.018 0.032 -10000 0 -10000 0 0
EOMES -0.057 0.26 -10000 0 -1.3 20 20
STAT1 (dimer) -0.2 0.39 -10000 0 -0.79 126 126
T cell proliferation -0.12 0.31 -10000 0 -0.64 115 115
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 -0.68 122 122
ATF2 -0.15 0.4 -10000 0 -0.85 102 102
IL27-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
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 0.64 93 -10000 0 93
IL27/IL27R/JAK1 -0.2 0.35 -10000 0 -0.94 69 69
TBX21 -0.22 0.3 -10000 0 -0.62 146 146
IL12B 0.001 0.075 -10000 0 -0.35 21 21
IL12A -0.01 0.066 -10000 0 -0.19 56 56
IL6ST -0.12 0.22 -10000 0 -0.47 143 143
IL27RA/JAK1 -0.11 0.32 -10000 0 -1.2 38 38
IL27 -0.083 0.2 -10000 0 -0.5 99 99
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 0.64 93 -10000 0 93
T cell proliferation during immune response 0.17 0.26 0.64 93 -10000 0 93
MAPKKK cascade -0.17 0.26 -10000 0 -0.64 93 93
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 -0.61 134 134
IL27/IL27R/JAK2/TYK2 -0.17 0.26 -10000 0 -0.65 93 93
positive regulation of T cell mediated cytotoxicity -0.17 0.26 -10000 0 -0.64 93 93
STAT1 (dimer) -0.27 0.39 0.48 7 -0.98 86 93
JAK2 0.004 0.055 -10000 0 -0.34 12 12
JAK1 0.011 0.057 -10000 0 -0.52 6 6
STAT2 (dimer) -0.16 0.25 -10000 0 -0.61 92 92
T cell proliferation -0.2 0.27 -10000 0 -0.62 114 114
IL12/IL12R/TYK2/JAK2 -0.034 0.15 -10000 0 -0.85 9 9
IL17A -0.006 0.11 -10000 0 -1.4 1 1
mast cell activation 0.17 0.26 0.64 93 -10000 0 93
IFNG -0.032 0.047 -10000 0 -0.11 96 96
T cell differentiation -0.01 0.009 0.024 1 -0.022 151 152
STAT3 (dimer) -0.16 0.25 -10000 0 -0.61 93 93
STAT5A (dimer) -0.16 0.26 -10000 0 -0.62 94 94
STAT4 (dimer) -0.17 0.27 -10000 0 -0.61 110 110
STAT4 -0.023 0.13 -10000 0 -0.42 49 49
T cell activation 0.002 0.038 0.11 45 -10000 0 45
IL27R/JAK2/TYK2 -0.16 0.33 -10000 0 -0.98 56 56
GATA3 -0.25 0.55 -10000 0 -1.3 119 119
IL18 -0.036 0.12 -10000 0 -0.31 78 78
positive regulation of mast cell cytokine production -0.15 0.25 -10000 0 -0.6 93 93
IL27/EBI3 -0.061 0.16 -10000 0 -0.39 92 92
IL27RA -0.12 0.34 -10000 0 -1.3 37 37
IL6 -0.079 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 37 -1.2 3 40
IL1B -0.034 0.12 -10000 0 -0.29 81 81
EBI3 0.001 0.071 -10000 0 -0.44 12 12
TNF -0.003 0.067 -10000 0 -0.25 31 31
Fc-epsilon receptor I signaling in mast 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
PPAP2A 0.007 0.074 -9999 0 -0.5 11 11
LAT2 -0.088 0.18 -9999 0 -0.42 86 86
AP1 -0.14 0.22 -9999 0 -0.5 116 116
mol:PIP3 -0.1 0.22 -9999 0 -0.48 95 95
IKBKB -0.044 0.12 -9999 0 -0.26 87 87
AKT1 -0.067 0.16 -9999 0 -0.4 74 74
IKBKG -0.042 0.12 -9999 0 -0.25 90 90
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 -0.35 3 3
MAP3K1 -0.086 0.2 -9999 0 -0.43 99 99
mol:Ca2+ -0.071 0.16 -9999 0 -0.36 95 95
LYN 0.012 0.033 -9999 0 -0.27 7 7
CBLB -0.086 0.18 -9999 0 -0.42 81 81
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 -0.015 0.092 -9999 0 -0.29 48 48
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.088 0.18 -9999 0 -0.38 106 106
PTPN13 -0.12 0.21 -9999 0 -0.55 77 77
PTPN11 0.013 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 75 75
SYK -0.024 0.14 -9999 0 -0.49 42 42
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 -0.43 84 84
PAK2 -0.081 0.2 -9999 0 -0.45 88 88
NFATC2 -0.042 0.082 -9999 0 -0.62 5 5
HRAS -0.096 0.21 -9999 0 -0.48 93 93
GAB2 0.009 0.047 -9999 0 -0.26 16 16
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 94 94
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 32 32
FOS -0.11 0.2 -9999 0 -0.37 171 171
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.097 0.18 -9999 0 -0.36 138 138
CHUK -0.046 0.12 -9999 0 -0.26 93 93
KLRG1 -0.083 0.17 -9999 0 -0.41 75 75
VAV1 -0.1 0.2 -9999 0 -0.45 91 91
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.085 0.18 -9999 0 -0.43 76 76
negative regulation of mast cell degranulation -0.078 0.16 -9999 0 -0.39 75 75
BTK -0.11 0.23 -9999 0 -0.53 89 89
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.13 0.25 -9999 0 -0.5 123 123
GAB2/PI3K/SHP2 -0.1 0.15 -9999 0 -0.43 76 76
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.096 0.2 -9999 0 -0.5 78 78
RAF1 0.029 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.21 -9999 0 -0.36 185 185
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 -0.33 169 169
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 -0.2 17 17
actin cytoskeleton reorganization -0.087 0.18 -9999 0 -0.47 68 68
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 -0.41 83 83
RELA 0.018 0 -9999 0 -10000 0 0
ITK -0.052 0.13 -9999 0 -0.42 47 47
SOS1 0.017 0.023 -9999 0 -0.52 1 1
PLCG1 -0.1 0.22 -9999 0 -0.51 92 92
cytokine secretion -0.029 0.044 -9999 0 -0.19 1 1
SPHK1 -0.11 0.2 -9999 0 -0.43 104 104
PTK2 -0.091 0.19 -9999 0 -0.5 66 66
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.21 -9999 0 -0.51 98 98
EDG1 -0.015 0.092 -9999 0 -0.29 48 48
mol:DAG -0.095 0.22 -9999 0 -0.47 99 99
MAP2K2 0.032 0.031 -9999 0 -10000 0 0
MAP2K1 0.033 0.024 -9999 0 -10000 0 0
MAP2K7 0.017 0.023 -9999 0 -0.52 1 1
KLRG1/SHP2 -0.072 0.15 -9999 0 -0.39 70 70
MAP2K4 -0.011 0.16 -9999 0 -0.91 16 16
Fc epsilon R1/FcgammaRIIB -0.12 0.22 -9999 0 -0.38 185 185
mol:Choline -0.086 0.17 -9999 0 -0.37 106 106
SHC/Grb2/SOS1 -0.066 0.17 -9999 0 -0.42 68 68
FYN 0.009 0.063 -9999 0 -0.4 11 11
DOK1 0.002 0.083 -9999 0 -0.41 19 19
PXN -0.078 0.18 -9999 0 -0.46 65 65
HCLS1 -0.095 0.19 -9999 0 -0.44 90 90
PRKCB -0.069 0.16 -9999 0 -0.35 99 99
FCGR2B -0.032 0.15 -9999 0 -0.5 51 51
IGHE -0.003 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.08 0.16 -9999 0 -0.4 75 75
LCP2 -0.005 0.1 -9999 0 -0.41 28 28
PLA2G4A -0.11 0.21 -9999 0 -0.46 106 106
RASA1 0.004 0.079 -9999 0 -0.42 16 16
mol:Phosphatidic acid -0.086 0.17 -9999 0 -0.37 106 106
IKK complex -0.023 0.098 -9999 0 -0.2 76 76
WIPF1 0.005 0.076 -9999 0 -0.41 16 16
Arf6 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
CENTA1/KIF3B 0 0.058 -10000 0 -0.26 23 23
ARNO/beta Arrestin1-2 -0.013 0.09 -10000 0 -0.24 59 59
EGFR -0.077 0.17 -10000 0 -0.35 136 136
EPHA2 0.008 0.06 -10000 0 -0.33 14 14
USP6 0.011 0.041 -10000 0 -0.26 12 12
IQSEC1 0.016 0.026 -10000 0 -0.39 2 2
EGFR/EGFR/EGF/EGF -0.15 0.2 -10000 0 -0.42 172 172
ARRB2 0.011 0.052 -10000 0 -0.32 12 12
mol:GTP 0.006 0.015 0.066 1 -0.13 2 3
ARRB1 0.004 0.075 -10000 0 -0.38 18 18
FBXO8 0.015 0.04 -10000 0 -0.52 3 3
TSHR 0.008 0.071 -10000 0 -0.5 10 10
EGF -0.14 0.23 -10000 0 -0.42 193 193
somatostatin receptor activity 0 0 -10000 0 -0.001 102 102
ARAP2 0 0 -10000 0 0 117 117
mol:GDP -0.054 0.11 -10000 0 -0.25 91 91
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 103 103
ITGA2B 0.016 0.021 -10000 0 -0.26 3 3
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
ADAP1 0 0 -10000 0 0 90 90
KIF13B -0.002 0.095 -10000 0 -0.43 23 23
HGF/MET 0.006 0.075 -10000 0 -0.38 14 14
PXN 0.018 0 -10000 0 -10000 0 0
ARF6/GTP -0.067 0.11 -10000 0 -0.26 99 99
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.12 0.18 -10000 0 -0.35 172 172
ADRB2 -0.045 0.16 -10000 0 -0.4 80 80
receptor agonist activity 0 0 -10000 0 0 101 101
actin filament binding 0 0 -10000 0 0 101 101
SRC 0.015 0.035 -10000 0 -0.43 3 3
ITGB3 0.002 0.076 -10000 0 -0.32 25 25
GNAQ 0 0 -10000 0 -0.001 96 96
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 96 96
ARF6/GDP -0.003 0.059 -10000 0 -0.3 5 5
ARF6/GDP/GULP/ACAP1 -0.057 0.13 -10000 0 -0.3 92 92
alphaIIb/beta3 Integrin/paxillin/GIT1 0.034 0.048 -10000 0 -0.26 8 8
ACAP1 0 0 -10000 0 0 30 30
ACAP2 0 0 -10000 0 0 115 115
LHCGR/beta Arrestin2 0.009 0.07 -10000 0 -0.44 12 12
EFNA1 0 0.094 -10000 0 -0.49 18 18
HGF 0.008 0.069 -10000 0 -0.45 11 11
CYTH3 0 0 -10000 0 -0.001 102 102
CYTH2 -0.001 0.002 -10000 0 -0.004 107 107
NCK1 0.011 0.046 -10000 0 -0.28 12 12
fibronectin binding 0 0 -10000 0 0 85 85
endosomal lumen acidification 0 0 -10000 0 0 95 95
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.033 0.15 -10000 0 -0.44 59 59
GNAQ/ARNO -0.001 0.003 -10000 0 -0.006 94 94
mol:Phosphatidic acid 0 0 -10000 0 0 115 115
PIP3-E 0.004 0.069 -10000 0 -0.3 23 23
MET -0.001 0.078 -10000 0 -0.3 31 31
GNA14 -0.081 0.18 -10000 0 -0.35 141 141
GNA15 0.001 0.078 -10000 0 -0.33 25 25
GIT1 0.014 0.035 -10000 0 -0.3 6 6
mol:PI-4-5-P2 0 0 -10000 0 -0.001 97 97
GNA11 0.013 0.047 -10000 0 -0.52 4 4
LHCGR 0.003 0.083 -10000 0 -0.46 16 16
AGTR1 -0.15 0.21 -10000 0 -0.36 229 229
desensitization of G-protein coupled receptor protein signaling pathway 0.009 0.07 -10000 0 -0.44 12 12
IPCEF1/ARNO -0.095 0.14 -10000 0 -0.28 178 178
alphaIIb/beta3 Integrin 0.014 0.056 -10000 0 -0.36 7 7
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 -0.063 0.17 -9999 0 -0.43 52 52
NF kappa B1 p50/RelA/I kappa B alpha -0.044 0.18 -9999 0 -0.47 47 47
alphaV/beta3 Integrin/Osteopontin/Src -0.099 0.19 -9999 0 -0.39 134 134
AP1 -0.15 0.26 -9999 0 -0.6 93 93
ILK -0.065 0.16 -9999 0 -0.42 43 43
bone resorption -0.056 0.17 -9999 0 -0.42 50 50
PTK2B 0.017 0.017 -9999 0 -0.26 2 2
PYK2/p130Cas -0.059 0.17 -9999 0 -0.4 54 54
ITGAV -0.002 0.1 -9999 0 -0.49 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.082 -9999 0 -0.37 22 22
alphaV/beta3 Integrin/Osteopontin -0.078 0.18 -9999 0 -0.33 145 145
MAP3K1 -0.091 0.18 -9999 0 -0.32 169 169
JUN -0.034 0.15 -9999 0 -0.46 57 57
MAPK3 -0.064 0.17 -9999 0 -0.46 48 48
MAPK1 -0.064 0.17 -9999 0 -0.46 49 49
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 -0.081 0.17 -9999 0 -0.41 67 67
ITGB3 0.003 0.078 -9999 0 -0.32 25 25
NFKBIA -0.064 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 0.37 -9999 0 -1.2 53 53
NF kappa B1 p50/RelA -0.047 0.19 -9999 0 -0.52 46 46
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
RELA 0.018 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.003 0.1 -9999 0 -0.42 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.086 0.18 -9999 0 -0.32 164 164
VAV3 -0.12 0.2 -9999 0 -0.44 97 97
MAP3K14 -0.07 0.17 -9999 0 -0.31 140 140
ROCK2 0.012 0.053 -9999 0 -0.48 6 6
SPP1 -0.14 0.23 -9999 0 -0.43 188 188
RAC1 0.018 0 -9999 0 -10000 0 0
Rac1/GTP -0.11 0.18 -9999 0 -0.41 89 89
MMP2 -0.13 0.24 -9999 0 -0.55 96 96
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.013 0.048 -9999 0 -0.47 5 5
GNB1/GNG2 -0.11 0.2 -9999 0 -0.42 104 104
mol:DAG -0.094 0.18 -9999 0 -0.47 63 63
PLCG1 -0.097 0.18 -9999 0 -0.49 62 62
YES1 -0.12 0.2 -9999 0 -0.45 105 105
FZD3 -0.031 0.15 -9999 0 -0.48 52 52
FZD6 -0.077 0.2 -9999 0 -0.45 108 108
G protein -0.1 0.19 -9999 0 -0.49 65 65
MAP3K7 -0.069 0.15 -9999 0 -0.39 59 59
mol:Ca2+ -0.091 0.17 -9999 0 -0.45 63 63
mol:IP3 -0.094 0.18 -9999 0 -0.47 63 63
NLK 0.016 0.044 -9999 0 -0.9 1 1
GNB1 0.013 0.052 -9999 0 -0.52 5 5
CAMK2A -0.08 0.16 -9999 0 -0.42 62 62
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.47 103 103
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
GNAS -0.12 0.2 -9999 0 -0.44 105 105
GO:0007205 -0.093 0.18 -9999 0 -0.46 63 63
WNT6 -0.011 0.088 -9999 0 -0.27 54 54
WNT4 -0.063 0.18 -9999 0 -0.45 90 90
NFAT1/CK1 alpha -0.092 0.19 -9999 0 -0.48 66 66
GNG2 0.016 0.029 -9999 0 -0.35 3 3
WNT5A -0.084 0.2 -9999 0 -0.43 120 120
WNT11 -0.013 0.09 -9999 0 -0.27 57 57
CDC42 -0.11 0.2 -9999 0 -0.49 73 73
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 -0.24 0.54 -10000 0 -1.3 83 83
IL23A -0.21 0.49 -10000 0 -1.2 71 71
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.42 -10000 0 -1 90 90
positive regulation of T cell mediated cytotoxicity -0.21 0.51 -10000 0 -1.1 92 92
ITGA3 -0.2 0.48 -10000 0 -1.1 82 82
IL17F -0.1 0.32 -10000 0 -0.68 77 77
IL12B 0.003 0.084 -10000 0 -0.36 21 21
STAT1 (dimer) -0.22 0.49 -10000 0 -1.1 93 93
CD4 -0.18 0.44 -10000 0 -1 74 74
IL23 -0.21 0.47 -10000 0 -1.2 71 71
IL23R -0.013 0.18 -10000 0 -1.4 7 7
IL1B -0.24 0.53 -10000 0 -1.3 83 83
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.18 0.44 -10000 0 -1.1 61 61
TYK2 0.013 0.024 -10000 0 -10000 0 0
STAT4 -0.023 0.13 -10000 0 -0.42 49 49
STAT3 0.015 0.041 -10000 0 -0.52 3 3
IL18RAP -0.078 0.19 -10000 0 -0.41 117 117
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 0.03 -10000 0 -10000 0 0
IL23R/JAK2 -0.014 0.19 -10000 0 -1.3 7 7
positive regulation of chronic inflammatory response -0.21 0.51 -10000 0 -1.1 92 92
natural killer cell activation 0.002 0.012 0.073 8 -10000 0 8
JAK2 0.01 0.065 -10000 0 -0.34 12 12
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
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 -0.2 0.45 -10000 0 -1.1 71 71
ALOX12B -0.18 0.44 -10000 0 -1.1 67 67
CXCL1 -0.27 0.54 -10000 0 -1.1 118 118
T cell proliferation -0.21 0.51 -10000 0 -1.1 92 92
NFKBIA 0.014 0.043 -10000 0 -0.46 4 4
IL17A -0.055 0.26 -10000 0 -0.55 56 56
PI3K -0.19 0.47 -10000 0 -1.1 89 89
IFNG -0.028 0.05 0.12 2 -0.12 63 65
STAT3 (dimer) -0.21 0.42 -10000 0 -0.99 90 90
IL18R1 -0.014 0.11 -10000 0 -0.41 37 37
IL23/IL23R/JAK2/TYK2/SOCS3 -0.083 0.28 -10000 0 -0.63 48 48
IL18/IL18R -0.085 0.2 -10000 0 -0.41 117 117
macrophage activation -0.015 0.017 -10000 0 -0.044 69 69
TNF -0.21 0.49 -10000 0 -1.2 75 75
STAT3/STAT4 -0.24 0.45 -10000 0 -1 97 97
STAT4 (dimer) -0.22 0.5 -10000 0 -1.1 96 96
IL18 -0.052 0.17 -10000 0 -0.44 78 78
IL19 -0.19 0.44 -10000 0 -1.1 75 75
STAT5A (dimer) -0.21 0.49 -10000 0 -1.1 92 92
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
SOCS3 0.005 0.074 -10000 0 -0.38 17 17
CXCL9 -0.28 0.56 -10000 0 -1.2 121 121
MPO -0.18 0.44 -10000 0 -1 72 72
positive regulation of humoral immune response -0.21 0.51 -10000 0 -1.1 92 92
IL23/IL23R/JAK2/TYK2 -0.23 0.54 -10000 0 -1.2 91 91
IL6 -0.27 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 -0.35 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.073 8 -10000 0 8
CD3E -0.18 0.44 -10000 0 -1 71 71
keratinocyte proliferation -0.21 0.51 -10000 0 -1.1 92 92
NOS2 -0.18 0.44 -10000 0 -0.96 93 93
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 -0.014 0.11 -10000 0 -0.38 42 42
GNB1/GNG2 -0.058 0.077 -10000 0 -0.18 139 139
AKT1 -0.024 0.12 -10000 0 -0.22 60 60
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+ -0.049 0.17 -10000 0 -0.29 142 142
LYN 0.029 0.062 -10000 0 -0.29 5 5
RhoA/GTP -0.041 0.056 -10000 0 -0.13 79 79
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.19 -10000 0 -0.35 143 143
GNG2 0.016 0.029 -10000 0 -0.35 3 3
ARRB2 0.018 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.005 0.1 -10000 0 -0.39 22 22
G beta5/gamma2 -0.076 0.1 -10000 0 -0.24 138 138
PRKCH -0.063 0.19 -10000 0 -0.35 140 140
DNM1 0.012 0.052 -10000 0 -0.39 8 8
TXA2/TP beta/beta Arrestin3 0.002 0.02 -10000 0 -0.25 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.002 0.088 -10000 0 -0.35 29 29
G12 family/GTP -0.097 0.13 -10000 0 -0.3 142 142
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 0.36 18 -10000 0 18
mol:NADP 0.017 0.012 -10000 0 -0.26 1 1
RAB11A 0.016 0.029 -10000 0 -0.35 3 3
PRKG1 0.017 0.012 -10000 0 -0.26 1 1
mol:IP3 -0.068 0.2 -10000 0 -0.37 142 142
cell morphogenesis 0.016 0.05 -10000 0 -0.31 12 12
PLCB2 -0.1 0.26 -10000 0 -0.5 142 142
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 -0.38 12 12
RHOA 0.005 0.08 -10000 0 -0.52 12 12
PTGIR 0.016 0.033 -10000 0 -0.52 2 2
PRKCB1 -0.082 0.22 -10000 0 -0.4 144 144
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.012 -10000 0 -0.26 1 1
TXA2/TXA2-R family -0.11 0.27 -10000 0 -0.52 141 141
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 0.062 -10000 0 -0.56 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.034 0.044 -10000 0 -0.36 2 2
MAPK14 -0.034 0.13 -10000 0 -0.23 138 138
TGM2/GTP -0.08 0.23 -10000 0 -0.41 148 148
MAPK11 -0.033 0.14 -10000 0 -0.23 138 138
ARHGEF1 -0.021 0.1 -10000 0 -0.17 138 138
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
JNK cascade -0.07 0.21 -10000 0 -0.38 141 141
RAB11/GDP 0.016 0.028 -10000 0 -0.34 3 3
ICAM1 -0.053 0.17 -10000 0 -0.3 141 141
cAMP biosynthetic process -0.063 0.19 -10000 0 -0.34 142 142
Gq family/GTP/EBP50 -0.039 0.11 -10000 0 -0.25 95 95
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 -0.027 0.11 -10000 0 -0.3 41 41
VCAM1 -0.055 0.17 -10000 0 -0.31 145 145
TP beta/Gq family/GDP/G beta5/gamma2 -0.005 0.1 -10000 0 -0.39 22 22
platelet activation -0.043 0.17 -10000 0 -0.3 141 141
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 -0.006 0.049 -10000 0 -0.54 4 4
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 -0.08 0.22 -10000 0 -0.41 142 142
EGFR -0.077 0.17 -10000 0 -0.35 136 136
TXA2/TP alpha -0.092 0.25 -10000 0 -0.46 140 140
Gq family/GTP -0.039 0.079 -10000 0 -0.24 60 60
YES1 0.026 0.07 -10000 0 -0.34 6 6
GNAI2/GTP -0.015 0.055 -10000 0 -0.33 5 5
PGD2/DP -0.001 0.063 -10000 0 -0.24 29 29
SLC9A3R1 -0.044 0.16 -10000 0 -0.44 71 71
FYN 0.027 0.072 -10000 0 -0.33 10 10
mol:NO 0.017 0.012 -10000 0 -0.26 1 1
GNA15 0.001 0.078 -10000 0 -0.33 25 25
PGK/cGMP 0.023 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.079 -10000 0 -0.51 12 12
TP alpha/TGM2/GDP/G beta/gamma 0.029 0.076 -10000 0 -0.36 6 6
NOS3 0.017 0.012 -10000 0 -0.26 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCA -0.062 0.19 -10000 0 -0.34 140 140
PRKCB -0.065 0.19 -10000 0 -0.35 142 142
PRKCE -0.063 0.19 -10000 0 -0.35 140 140
PRKCD -0.069 0.2 -10000 0 -0.37 141 141
PRKCG -0.07 0.2 -10000 0 -0.37 141 141
muscle contraction -0.097 0.25 -10000 0 -0.48 141 141
PRKCZ -0.061 0.18 -10000 0 -0.34 141 141
ARR3 0.017 0.012 -10000 0 -0.26 1 1
TXA2/TP beta 0.028 0.059 -10000 0 -0.31 2 2
PRKCQ -0.069 0.2 -10000 0 -0.35 146 146
MAPKKK cascade -0.087 0.23 -10000 0 -0.44 142 142
SELE -0.078 0.2 -10000 0 -0.38 145 145
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 -0.081 0.18 -10000 0 -0.35 141 141
chemotaxis -0.13 0.31 -10000 0 -0.6 140 140
GNA12 0.018 0 -10000 0 -10000 0 0
GNA13 0.009 0.059 -10000 0 -0.38 11 11
GNA11 0.014 0.047 -10000 0 -0.52 4 4
Rac1/GTP 0.013 0.002 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.099 0.25 -10000 0 -0.62 80 80
IHH -0.013 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 -0.053 0.17 -10000 0 -0.47 47 47
SMO -0.064 0.18 -10000 0 -0.46 58 58
AKT1 -0.027 0.13 -10000 0 -0.52 21 21
ARRB2 0.018 0 -10000 0 -10000 0 0
BOC -0.018 0.12 -10000 0 -0.38 48 48
ADRBK1 0.018 0 -10000 0 -10000 0 0
heart looping -0.063 0.18 -10000 0 -0.46 58 58
STIL -0.052 0.15 -10000 0 -0.36 56 56
DHH N/PTCH2 0.026 0 -10000 0 -10000 0 0
DHH N/PTCH1 -0.027 0.13 -10000 0 -0.37 23 23
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
DHH 0.018 0 -10000 0 -10000 0 0
PTHLH -0.12 0.31 -10000 0 -0.76 79 79
determination of left/right symmetry -0.063 0.18 -10000 0 -0.46 58 58
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
skeletal system development -0.12 0.3 -10000 0 -0.75 79 79
IHH N/Hhip 0.004 0.069 -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 -0.063 0.18 -10000 0 -0.46 58 58
pancreas development 0.01 0.052 -10000 0 -0.33 11 11
HHAT -0.045 0.17 -10000 0 -0.51 63 63
PI3K 0.006 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 -0.063 0.18 -10000 0 -0.46 58 58
SHH Np/Cholesterol/PTCH1 -0.048 0.14 -10000 0 -0.36 48 48
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 74 74
SMO/Vitamin D3 -0.06 0.16 -10000 0 -0.4 64 64
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 -0.45 97 97
SHH Np/Cholesterol/BOC -0.026 0.12 -10000 0 -0.28 83 83
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 -0.046 0.14 -10000 0 -0.36 48 48
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 74 74
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 -0.042 0.14 -10000 0 -0.33 74 74
HHIP 0.01 0.052 -10000 0 -0.33 11 11
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.015 0.024 -10000 0 -0.26 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 -0.005 165 165
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
mol:GDP -0.088 0.17 -10000 0 -0.41 109 109
cell proliferation -0.066 0.18 -10000 0 -0.41 82 82
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
FOS -0.13 0.29 -10000 0 -0.8 76 76
mol:Ca2+ -0.014 0.022 -10000 0 -0.083 22 22
MAPK3 -0.05 0.14 -10000 0 -0.41 34 34
MAPK1 -0.029 0.092 -10000 0 -0.27 26 26
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
mol:IP3 -0.001 0.002 -10000 0 -0.003 171 171
cAMP biosynthetic process 0.013 0.021 -10000 0 -10000 0 0
GNG2 0.016 0.029 -10000 0 -0.35 3 3
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.003 171 171
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 -0.44 3 3
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.003 171 171
PI3K 0.007 0.07 -10000 0 -0.31 21 21
apoptosis 0.063 0.17 0.41 83 -10000 0 83
T-DHT/AR/PELP1 -0.044 0.13 -10000 0 -0.31 104 104
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 -0.031 0.12 -10000 0 -0.24 120 120
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
SHBG 0.018 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.002 0.11 -10000 0 -0.45 16 16
mol:T-DHT 0 0.001 0.002 1 -0.003 51 52
RAC1 0.018 0 -10000 0 -10000 0 0
GNRH1 0 0.06 -10000 0 -0.24 27 27
Gi family/GTP -0.022 0.094 -10000 0 -0.3 20 20
CDC42 0.018 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.049 0.17 -9999 0 -0.44 78 78
PLK4 0.008 0.065 -9999 0 -0.38 13 13
regulation of centriole replication -0.03 0.13 -9999 0 -0.37 59 59
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 71 71
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.065 0.12 -9999 0 -0.32 61 61
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 -0.021 0.11 -9999 0 -0.62 11 11
SMAD4 0.009 0.067 -9999 0 -0.49 9 9
SMAD5 -0.063 0.14 -9999 0 -0.41 45 45
BMP7/USAG1 -0.19 0.19 -9999 0 -0.39 205 205
SMAD5/SKI -0.052 0.14 -9999 0 -0.4 41 41
SMAD1 0.024 0.061 -9999 0 -0.37 7 7
BMP2 -0.018 0.11 -9999 0 -0.32 57 57
SMAD1/SMAD1/SMAD4 -0.01 0.044 -9999 0 -0.33 3 3
BMPR1A 0.01 0.064 -9999 0 -0.46 9 9
BMPR1B -0.11 0.16 -9999 0 -0.3 218 218
BMPR1A-1B/BAMBI -0.13 0.17 -9999 0 -0.37 156 156
AHSG 0.016 0.024 -9999 0 -0.26 4 4
CER1 0.017 0.012 -9999 0 -0.26 1 1
BMP2-4/CER1 -0.052 0.14 -9999 0 -0.34 84 84
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.054 0.14 -9999 0 -0.39 42 42
BMP2-4 (homodimer) -0.075 0.16 -9999 0 -0.41 83 83
RGMB 0.008 0.073 -9999 0 -0.52 10 10
BMP6/BMPR2/BMPR1A-1B -0.043 0.11 -9999 0 -0.3 52 52
RGMA -0.027 0.12 -9999 0 -0.3 74 74
SMURF1 0.018 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.073 0.14 -9999 0 -0.32 98 98
BMP2-4/USAG1 -0.2 0.2 -9999 0 -0.38 249 249
SMAD6/SMURF1/SMAD5 -0.051 0.14 -9999 0 -0.41 36 36
SOSTDC1 -0.23 0.23 -9999 0 -0.4 314 314
BMP7/BMPR2/BMPR1A-1B -0.062 0.12 -9999 0 -0.3 67 67
SKI 0.017 0.017 -9999 0 -0.26 2 2
BMP6 (homodimer) -0.006 0.089 -9999 0 -0.3 39 39
HFE2 0.004 0.08 -9999 0 -0.45 15 15
ZFYVE16 0.015 0.04 -9999 0 -0.52 3 3
MAP3K7 0.016 0.021 -9999 0 -0.26 3 3
BMP2-4/CHRD -0.059 0.16 -9999 0 -0.37 84 84
SMAD5/SMAD5/SMAD4 -0.056 0.14 -9999 0 -0.41 39 39
MAPK1 0.016 0.033 -9999 0 -0.52 2 2
TAK1/TAB family -0.032 0.13 -9999 0 -0.44 24 24
BMP7 (homodimer) -0.042 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 -0.26 4 4
CTDSP2 0.014 0.044 -9999 0 -0.42 5 5
BMP2-4/FETUA -0.053 0.14 -9999 0 -0.34 84 84
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
GREM1 -0.038 0.16 -9999 0 -0.46 62 62
BMPR2 (homodimer) 0.016 0.033 -9999 0 -0.52 2 2
GADD34/PP1CA 0.029 0.042 -9999 0 -0.3 6 6
BMPR1A-1B (homodimer) -0.069 0.12 -9999 0 -0.2 223 223
CHRDL1 -0.013 0.091 -9999 0 -0.27 56 56
ENDOFIN/SMAD1 0.031 0.065 -9999 0 -0.36 8 8
SMAD6-7/SMURF1/SMAD1 0.046 0.058 -9999 0 -0.37 3 3
SMAD6/SMURF1 0.018 0 -9999 0 -10000 0 0
BAMBI -0.13 0.22 -9999 0 -0.41 185 185
SMURF2 0.009 0.058 -9999 0 -0.34 13 13
BMP2-4/CHRDL1 -0.068 0.16 -9999 0 -0.35 97 97
BMP2-4/GREM1 -0.085 0.17 -9999 0 -0.37 120 120
SMAD7 0.016 0.026 -9999 0 -0.39 2 2
SMAD8A/SMAD8A/SMAD4 -0.015 0.11 -9999 0 -0.52 14 14
SMAD1/SMAD6 0.033 0.059 -9999 0 -0.34 7 7
TAK1/SMAD6 0.025 0.014 -9999 0 -10000 0 0
BMP7 -0.042 0.13 -9999 0 -0.29 101 101
BMP6 -0.006 0.089 -9999 0 -0.3 39 39
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 -0.37 39 39
PPM1A 0.016 0.026 -9999 0 -0.39 2 2
SMAD1/SMURF2 0.029 0.067 -9999 0 -0.35 8 8
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 -0.31 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 -0.35 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.081 0.15 -9999 0 -0.35 89 89
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 -0.075 0.15 -9999 0 -0.33 98 98
BMP4 -0.092 0.19 -9999 0 -0.39 143 143
FST -0.015 0.1 -9999 0 -0.31 52 52
BMP2-4/NOG -0.056 0.15 -9999 0 -0.35 88 88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.049 0.11 -9999 0 -0.3 52 52
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.027 0.13 -10000 0 -0.26 111 111
epithelial cell differentiation -0.007 0.1 -10000 0 -0.26 76 76
CYFIP2 -0.042 0.16 -10000 0 -0.46 65 65
ENAH 0.012 0.097 -10000 0 -0.32 12 12
EGFR -0.077 0.17 -10000 0 -0.35 136 136
EPHA2 0.008 0.06 -10000 0 -0.33 14 14
MYO6 -0.013 0.11 -10000 0 -0.25 92 92
CTNNB1 0.001 0.09 -10000 0 -0.45 19 19
ABI1/Sra1/Nap1 -0.003 0.1 -10000 0 -0.31 52 52
AQP5 -0.086 0.19 -10000 0 -0.45 97 97
CTNND1 0.016 0.029 -10000 0 -0.35 3 3
mol:PI-4-5-P2 -0.005 0.1 -10000 0 -0.24 78 78
regulation of calcium-dependent cell-cell adhesion -0.015 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 -0.089 0.2 -10000 0 -0.47 97 97
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 -0.005 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 -0.007 0.12 -10000 0 -0.45 14 14
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 71 71
EGFR/EGFR/EGF/EGF -0.13 0.14 -10000 0 -0.38 92 92
RhoA/GDP -0.01 0.11 -10000 0 -0.25 85 85
actin cytoskeleton organization -0.008 0.11 -10000 0 -0.38 7 7
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 0.21 -10000 0 -0.42 146 146
DIAPH1 -0.054 0.18 -10000 0 -0.58 52 52
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 -0.008 0.11 -10000 0 -0.4 7 7
EFNA1 0 0.094 -10000 0 -0.49 18 18
LPP -0.004 0.1 -10000 0 -0.4 7 7
Ephrin A1/EPHA2 -0.045 0.094 -10000 0 -0.43 8 8
SEC6/SEC8 -0.045 0.092 -10000 0 -0.41 10 10
MGAT3 -0.015 0.11 -10000 0 -0.25 82 82
HGF/MET -0.044 0.089 -10000 0 -0.34 10 10
HGF 0.008 0.069 -10000 0 -0.45 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.028 0.13 -10000 0 -0.26 111 111
actin cable formation 0.017 0.1 -10000 0 -0.3 15 15
KIAA1543 0.001 0.1 -10000 0 -0.35 9 9
KIFC3 -0.005 0.1 -10000 0 -0.24 77 77
NCK1 0.011 0.046 -10000 0 -0.28 12 12
EXOC3 0.017 0.012 -10000 0 -0.26 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 -0.005 0.1 -10000 0 -0.24 78 78
LIMA1 -0.025 0.15 -10000 0 -0.52 42 42
ABI1 0.016 0.021 -10000 0 -0.26 3 3
ROCK1 0.009 0.1 -10000 0 -0.36 10 10
adherens junction assembly 0.012 0.1 -10000 0 -0.38 10 10
IGF-1R heterotetramer/IGF1 -0.12 0.16 -10000 0 -0.43 73 73
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 -0.001 0.078 -10000 0 -0.3 31 31
PLEKHA7 -0.003 0.099 -10000 0 -0.24 77 77
mol:GTP 0.024 0.071 -10000 0 -0.27 24 24
establishment of epithelial cell apical/basal polarity 0.005 0.11 -10000 0 -0.41 10 10
cortical actin cytoskeleton stabilization -0.027 0.13 -10000 0 -0.26 111 111
regulation of cell-cell adhesion -0.008 0.11 -10000 0 -0.38 7 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.028 0.13 -10000 0 -0.26 111 111
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 -0.04 0.18 -9999 0 -0.51 64 64
Syndecan-4/Syndesmos -0.043 0.2 -9999 0 -0.51 71 71
positive regulation of JNK cascade -0.072 0.22 -9999 0 -0.5 88 88
Syndecan-4/ADAM12 -0.069 0.24 -9999 0 -0.54 93 93
CCL5 -0.05 0.18 -9999 0 -0.49 70 70
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DNM2 0.017 0.012 -9999 0 -0.26 1 1
ITGA5 0.014 0.042 -9999 0 -0.46 4 4
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
PLG 0.016 0.033 -9999 0 -0.51 2 2
ADAM12 -0.049 0.17 -9999 0 -0.47 72 72
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 -0.04 0.2 -9999 0 -0.51 71 71
Syndecan-4/CXCL12/CXCR4 -0.076 0.24 -9999 0 -0.54 88 88
Syndecan-4/Laminin alpha3 -0.079 0.22 -9999 0 -0.54 77 77
MDK -0.016 0.12 -9999 0 -0.37 46 46
Syndecan-4/FZD7 -0.07 0.23 -9999 0 -0.53 84 84
Syndecan-4/Midkine -0.054 0.21 -9999 0 -0.52 76 76
FZD7 -0.05 0.16 -9999 0 -0.4 86 86
Syndecan-4/FGFR1/FGF -0.073 0.21 -9999 0 -0.48 87 87
THBS1 -0.025 0.14 -9999 0 -0.51 43 43
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 -0.5 88 88
Syndecan-4/TACI -0.041 0.2 -9999 0 -0.5 72 72
CXCR4 -0.028 0.14 -9999 0 -0.42 55 55
cell adhesion -0.006 0.1 -9999 0 -0.29 54 54
Syndecan-4/Dynamin -0.039 0.2 -9999 0 -0.5 71 71
Syndecan-4/TSP1 -0.059 0.22 -9999 0 -0.52 81 81
Syndecan-4/GIPC -0.041 0.2 -9999 0 -0.5 71 71
Syndecan-4/RANTES -0.071 0.23 -9999 0 -0.54 78 78
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
LAMA1 0.015 0.027 -9999 0 -0.26 5 5
LAMA3 -0.069 0.18 -9999 0 -0.43 102 102
RAC1 0.018 0 -9999 0 -10000 0 0
PRKCA 0.017 0.05 -9999 0 -0.25 6 6
Syndecan-4/alpha-Actinin -0.045 0.21 -9999 0 -0.52 73 73
TFPI 0.005 0.061 -9999 0 -0.27 24 24
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 -0.071 0.22 -9999 0 -0.52 77 77
ACTN1 0.005 0.079 -9999 0 -0.48 13 13
TNC -0.04 0.15 -9999 0 -0.36 81 81
Syndecan-4/CXCL12 -0.066 0.23 -9999 0 -0.53 82 82
FGF6 0.009 0.067 -9999 0 -0.49 9 9
RHOA 0.005 0.08 -9999 0 -0.52 12 12
CXCL12 -0.041 0.16 -9999 0 -0.46 64 64
TNFRSF13B 0.013 0.036 -9999 0 -0.26 9 9
FGF2 -0.064 0.16 -9999 0 -0.34 121 121
FGFR1 -0.011 0.1 -9999 0 -0.35 42 42
Syndecan-4/PI-4-5-P2 -0.05 0.2 -9999 0 -0.51 71 71
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.045 0.16 -9999 0 -0.45 71 71
cell migration 0.001 0.008 -9999 0 -10000 0 0
PRKCD 0.015 0.041 -9999 0 -0.44 4 4
vasculogenesis -0.056 0.21 -9999 0 -0.5 81 81
SDC4 -0.052 0.22 -9999 0 -0.54 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 -0.046 0.21 -9999 0 -0.51 73 73
MMP9 -0.04 0.17 -9999 0 -0.5 60 60
Rac1/GTP -0.007 0.1 -9999 0 -0.3 54 54
cytoskeleton organization -0.04 0.2 -9999 0 -0.49 71 71
GIPC1 0.014 0.042 -9999 0 -0.46 4 4
Syndecan-4/TFPI -0.045 0.2 -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 0.009 0.063 -10000 0 -0.4 11 11
EGFR -0.077 0.17 -10000 0 -0.35 136 136
PRL 0.015 0.031 -10000 0 -0.32 4 4
neuron projection morphogenesis -0.033 0.22 -10000 0 -0.72 45 45
PTPRZ1 -0.027 0.11 -10000 0 -0.29 78 78
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.048 0.25 -10000 0 -0.82 45 45
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.081 0.28 -10000 0 -0.91 47 47
ADAM17 0.017 0.037 -10000 0 -0.26 4 4
ErbB4/ErbB4 -0.11 0.32 -10000 0 -1 52 52
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.1 0.3 -10000 0 -0.88 57 57
NCOR1 0.016 0.033 -10000 0 -0.52 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.073 0.27 -10000 0 -0.86 48 48
GRIN2B -0.074 0.26 -10000 0 -0.81 48 48
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 0.006 0.069 -10000 0 -0.35 17 17
PRLR -0.03 0.15 -10000 0 -0.49 50 50
E4ICDs/ETO2 -0.17 0.34 -10000 0 -0.8 89 89
axon guidance -0.08 0.28 -10000 0 -0.88 50 50
NEDD4 0.002 0.099 -10000 0 -0.53 16 16
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 -0.092 0.27 -10000 0 -0.81 55 55
MAPK3 -0.04 0.23 -10000 0 -0.75 45 45
STAT1 (dimer) -0.11 0.3 -10000 0 -0.87 59 59
MAPK1 -0.041 0.23 -10000 0 -0.75 45 45
JAK2 0.01 0.054 -10000 0 -0.32 12 12
ErbB4/ErbB2/neuregulin 1 beta -0.091 0.27 -10000 0 -0.83 53 53
NRG1 0.019 0.044 -10000 0 -0.26 5 5
NRG3 0 0.082 -10000 0 -0.34 27 27
NRG2 -0.016 0.1 -10000 0 -0.3 57 57
NRG4 0.009 0.051 -10000 0 -0.27 16 16
heart development -0.08 0.28 -10000 0 -0.88 50 50
neural crest cell migration -0.089 0.27 -10000 0 -0.81 53 53
ERBB2 -0.007 0.088 -10000 0 -0.32 22 22
WWOX/E4ICDs -0.1 0.3 -10000 0 -0.88 55 55
SHC1 0.017 0.023 -10000 0 -0.52 1 1
ErbB4/EGFR/neuregulin 4 -0.13 0.31 -10000 0 -0.79 71 71
apoptosis 0.099 0.28 0.8 60 -10000 0 60
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 -0.76 62 62
ErbB4/ErbB4/betacellulin/betacellulin -0.13 0.31 -10000 0 -0.87 62 62
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.089 0.29 -10000 0 -0.72 74 74
MDM2 -0.097 0.3 -10000 0 -0.89 55 55
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.063 0.25 -10000 0 -0.84 45 45
STAT5A -0.072 0.27 -10000 0 -0.84 50 50
ErbB4/EGFR/neuregulin 1 beta -0.11 0.29 -10000 0 -0.78 63 63
DLG4 0.018 0 -10000 0 -10000 0 0
GRB2/SHC 0.024 0.024 -10000 0 -0.37 1 1
E4ICDs/TAB2/NCoR1 -0.082 0.28 -10000 0 -0.85 54 54
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 -0.052 0.17 -10000 0 -0.42 84 84
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.081 0.28 -10000 0 -0.9 50 50
ERBB4 -0.11 0.32 -10000 0 -1 52 52
STAT5B 0.016 0.026 -10000 0 -0.39 2 2
YAP1 -0.015 0.1 -10000 0 -0.71 6 6
GRB2 0.016 0.024 -10000 0 -0.26 4 4
ErbB4/ErbB2/neuregulin 4 -0.09 0.27 -10000 0 -0.83 53 53
glial cell differentiation 0.081 0.28 0.84 54 -10000 0 54
WWOX -0.003 0.073 -10000 0 -0.26 40 40
cell proliferation -0.1 0.27 -10000 0 -0.72 68 68
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 -0.006 0.1 -10000 0 -0.39 31 31
EPHB2 0.008 0.062 -10000 0 -0.32 16 16
EFNB1 0.017 0.053 -10000 0 -0.39 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.084 -10000 0 -0.33 12 12
Ephrin B2/EPHB1-2 -0.005 0.088 -10000 0 -0.28 32 32
neuron projection morphogenesis -0.024 0.063 -10000 0 -0.29 17 17
Ephrin B1/EPHB1-2/Tiam1 0.013 0.09 -10000 0 -0.3 25 25
DNM1 0.012 0.052 -10000 0 -0.39 8 8
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.084 0.23 -10000 0 -0.59 84 84
YES1 -0.13 0.3 -10000 0 -0.84 81 81
Ephrin B1/EPHB1-2/NCK2 0.018 0.081 -10000 0 -0.3 17 17
PI3K -0.081 0.23 -10000 0 -0.59 87 87
mol:GDP 0.012 0.088 -10000 0 -0.29 25 25
ITGA2B 0.016 0.021 -10000 0 -0.26 3 3
endothelial cell proliferation -0.007 0.096 -10000 0 -0.34 35 35
FYN -0.13 0.3 -10000 0 -0.83 81 81
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 32 32
RGS3 0.017 0.012 -10000 0 -0.26 1 1
cell adhesion -0.069 0.22 -10000 0 -0.56 82 82
LYN -0.12 0.3 -10000 0 -0.82 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 0.076 -10000 0 -0.32 25 25
EPHB1 -0.023 0.11 -10000 0 -0.28 73 73
EPHB4 -0.01 0.11 -10000 0 -0.42 33 33
RAC1 0.018 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.007 0.096 -10000 0 -0.34 35 35
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 81 81
regulation of stress fiber formation -0.017 0.08 0.29 17 -10000 0 17
MAPK8 -0.074 0.22 -10000 0 -0.56 82 82
Ephrin B1/EPHB1-2/RGS3 0.019 0.078 -10000 0 -0.29 15 15
endothelial cell migration -0.088 0.21 -10000 0 -0.52 94 94
NCK2 0.015 0.027 -10000 0 -0.26 5 5
PTPN13 -0.089 0.24 -10000 0 -0.62 85 85
regulation of focal adhesion formation -0.017 0.08 0.29 17 -10000 0 17
chemotaxis -0.018 0.077 0.29 15 -10000 0 15
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
Rac1/GTP 0.014 0.08 -10000 0 -0.3 16 16
angiogenesis -0.11 0.24 -10000 0 -0.68 81 81
LCK -0.14 0.31 -10000 0 -0.84 81 81
LPA receptor mediated events

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
GNB1/GNG2 0.007 0.078 -9999 0 -0.24 45 45
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.086 -9999 0 -0.27 23 23
AP1 -0.091 0.14 -9999 0 -0.3 131 131
mol:PIP3 -0.065 0.11 -9999 0 -0.28 84 84
AKT1 0.008 0.11 -9999 0 -0.37 22 22
PTK2B -0.008 0.063 -9999 0 -0.2 44 44
RHOA -0.006 0.092 -9999 0 -0.42 16 16
PIK3CB 0.012 0.055 -9999 0 -0.44 7 7
mol:Ca2+ -0.024 0.094 -9999 0 -0.26 60 60
MAGI3 -0.014 0.12 -9999 0 -0.46 35 35
RELA 0.018 0 -9999 0 -10000 0 0
apoptosis -0.003 0.065 -9999 0 -0.22 41 41
HRAS/GDP 0.009 0.037 -9999 0 -0.29 7 7
positive regulation of microtubule depolymerization -0.044 0.12 -9999 0 -0.26 117 117
NF kappa B1 p50/RelA -0.039 0.092 -9999 0 -0.27 46 46
endothelial cell migration -0.032 0.17 -9999 0 -0.55 51 51
ADCY4 -0.004 0.11 -9999 0 -0.31 45 45
ADCY5 -0.012 0.11 -9999 0 -0.31 45 45
ADCY6 -0.002 0.1 -9999 0 -0.29 44 44
ADCY7 -0.006 0.11 -9999 0 -0.32 44 44
ADCY1 -0.001 0.1 -9999 0 -0.29 44 44
ADCY2 -0.023 0.12 -9999 0 -0.34 48 48
ADCY3 -0.004 0.1 -9999 0 -0.29 46 46
ADCY8 -0.003 0.1 -9999 0 -0.29 44 44
ADCY9 -0.009 0.11 -9999 0 -0.3 45 45
GSK3B -0.001 0.06 -9999 0 -0.18 42 42
arachidonic acid secretion 0.003 0.1 -9999 0 -0.3 38 38
GNG2 0.016 0.029 -9999 0 -0.34 3 3
TRIP6 0 0.088 -9999 0 -0.4 23 23
GNAO1 -0.003 0.076 -9999 0 -0.25 41 41
HRAS 0.012 0.051 -9999 0 -0.41 7 7
NFKBIA -0.013 0.091 -9999 0 -0.25 41 41
GAB1 0.006 0.074 -9999 0 -0.43 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.008 0.15 -9999 0 -0.89 14 14
JUN -0.034 0.15 -9999 0 -0.46 57 57
LPA/LPA2/NHERF2 -0.023 0.099 -9999 0 -0.3 52 52
TIAM1 -0.023 0.17 -9999 0 -1 14 14
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
mol:IP3 -0.025 0.095 -9999 0 -0.26 60 60
PLCB3 -0.015 0.094 -9999 0 -0.29 49 49
FOS -0.11 0.2 -9999 0 -0.37 171 171
positive regulation of mitosis 0.003 0.1 -9999 0 -0.3 38 38
LPA/LPA1-2-3 -0.013 0.066 -9999 0 -0.21 51 51
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 -0.26 1 1
stress fiber formation 0.002 0.062 -9999 0 -0.19 42 42
GNAZ -0.011 0.092 -9999 0 -0.28 52 52
EGFR/PI3K-beta/Gab1 -0.067 0.11 -9999 0 -0.29 84 84
positive regulation of dendritic cell cytokine production -0.013 0.066 -9999 0 -0.21 51 51
LPA/LPA2/MAGI-3 -0.013 0.08 -9999 0 -0.28 35 35
ARHGEF1 0.01 0.073 -9999 0 -0.22 44 44
GNAI2 -0.008 0.094 -9999 0 -0.29 46 46
GNAI3 -0.002 0.076 -9999 0 -0.25 42 42
GNAI1 -0.021 0.11 -9999 0 -0.31 55 55
LPA/LPA3 -0.01 0.032 -9999 0 -0.1 51 51
LPA/LPA2 -0.01 0.032 -9999 0 -0.1 51 51
LPA/LPA1 -0.017 0.088 -9999 0 -0.28 51 51
HB-EGF/EGFR -0.068 0.15 -9999 0 -0.34 102 102
HBEGF -0.026 0.13 -9999 0 -0.38 63 63
mol:DAG -0.025 0.095 -9999 0 -0.26 60 60
cAMP biosynthetic process -0.005 0.11 -9999 0 -0.3 48 48
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 -0.28 26 26
GNAQ -0.005 0.026 -9999 0 -0.081 51 51
LPAR2 0 0.001 -9999 0 -10000 0 0
LPAR3 0 0.001 -9999 0 -10000 0 0
LPAR1 -0.011 0.051 -9999 0 -0.16 51 51
IL8 -0.13 0.19 -9999 0 -0.4 125 125
PTK2 -0.001 0.065 -9999 0 -0.21 42 42
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
CASP3 -0.003 0.066 -9999 0 -0.22 41 41
EGFR -0.077 0.17 -9999 0 -0.35 136 136
PLCG1 -0.014 0.056 -9999 0 -0.14 66 66
PLD2 -0.003 0.069 -9999 0 -0.22 45 45
G12/G13 0.006 0.079 -9999 0 -0.24 44 44
PI3K-beta -0.039 0.098 -9999 0 -0.36 30 30
cell migration 0.017 0.061 -9999 0 -0.25 16 16
SLC9A3R2 -0.032 0.15 -9999 0 -0.49 52 52
PXN 0.002 0.062 -9999 0 -0.2 42 42
HRAS/GTP 0.002 0.1 -9999 0 -0.3 38 38
RAC1 0.018 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
PRKCE 0.011 0.056 -9999 0 -0.42 8 8
PRKCD -0.019 0.093 -9999 0 -0.26 56 56
Gi(beta/gamma) 0.002 0.1 -9999 0 -0.31 36 36
mol:LPA -0.011 0.051 -9999 0 -0.16 51 51
TRIP6/p130 Cas/FAK1/Paxillin 0.013 0.084 -9999 0 -0.32 16 16
MAPKKK cascade 0.003 0.1 -9999 0 -0.3 38 38
contractile ring contraction involved in cytokinesis -0.006 0.091 -9999 0 -0.42 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.043 0.097 -9999 0 -0.18 141 141
GNA15 -0.003 0.052 -9999 0 -0.29 10 10
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
MAPT -0.046 0.13 -9999 0 -0.27 117 117
GNA11 0.003 0.038 -9999 0 -0.3 4 4
Rac1/GTP 0.007 0.16 -9999 0 -0.94 14 14
MMP2 -0.032 0.18 -9999 0 -0.55 51 51
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.027 0.15 -9999 0 -0.4 60 60
alphaM/beta2 Integrin/GPIbA -0.01 0.11 -9999 0 -0.34 39 39
alphaM/beta2 Integrin/proMMP-9 -0.036 0.15 -9999 0 -0.36 79 79
PLAUR -0.017 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 31 31
AGER 0.01 0.031 -9999 0 -0.4 2 2
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
SELPLG -0.003 0.098 -9999 0 -0.43 24 24
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.013 0.13 -9999 0 -0.44 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
CYR61 -0.04 0.16 -9999 0 -0.42 70 70
TLN1 0.017 0.023 -9999 0 -0.52 1 1
Rap1/GTP -0.037 0.1 -9999 0 -0.42 26 26
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 -0.038 0.16 -9999 0 -0.51 56 56
leukocyte activation during inflammatory response 0.007 0.087 -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 -0.029 0.15 -9999 0 -0.47 51 51
JAM3 -0.005 0.11 -9999 0 -0.5 23 23
GP1BA -0.002 0.07 -9999 0 -0.26 37 37
alphaM/beta2 Integrin/CTGF -0.03 0.14 -9999 0 -0.4 56 56
alphaM/beta2 Integrin -0.008 0.13 -9999 0 -0.46 26 26
JAM3 homodimer -0.005 0.11 -9999 0 -0.5 23 23
ICAM2 0.007 0.068 -9999 0 -0.4 13 13
ICAM1 -0.021 0.13 -9999 0 -0.4 49 49
phagocytosis triggered by activation of immune response cell surface activating receptor -0.008 0.13 -9999 0 -0.45 26 26
cell adhesion -0.011 0.11 -9999 0 -0.34 39 39
NFKB1 -0.033 0.17 -9999 0 -0.53 26 26
THY1 -0.005 0.11 -9999 0 -0.5 23 23
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 -0.048 0.14 -9999 0 -0.32 91 91
IL6 -0.088 0.27 -9999 0 -0.71 72 72
ITGB2 -0.022 0.12 -9999 0 -0.43 40 40
elevation of cytosolic calcium ion concentration -0.043 0.18 -9999 0 -0.42 77 77
alphaM/beta2 Integrin/JAM2/JAM3 -0.02 0.15 -9999 0 -0.38 63 63
JAM2 -0.019 0.13 -9999 0 -0.44 43 43
alphaM/beta2 Integrin/ICAM1 -0.029 0.16 -9999 0 -0.33 91 91
alphaM/beta2 Integrin/uPA/Plg -0.026 0.14 -9999 0 -0.34 73 73
RhoA/GTP -0.008 0.14 -9999 0 -0.44 29 29
positive regulation of phagocytosis -0.008 0.16 -9999 0 -0.5 35 35
Ron/MSP -0.016 0.12 -9999 0 -0.37 54 54
alphaM/beta2 Integrin/uPAR/uPA -0.043 0.18 -9999 0 -0.42 77 77
alphaM/beta2 Integrin/uPAR -0.02 0.14 -9999 0 -0.4 51 51
PLAU -0.05 0.17 -9999 0 -0.43 81 81
PLAT -0.092 0.19 -9999 0 -0.37 148 148
actin filament polymerization -0.002 0.13 -9999 0 -0.42 25 25
MST1 0.016 0.021 -9999 0 -0.26 3 3
alphaM/beta2 Integrin/lipoprotein(a) 0.01 0.089 -9999 0 -0.31 30 30
TNF -0.035 0.19 -9999 0 -0.65 28 28
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
alphaM/beta2 Integrin/uPA -0.04 0.15 -9999 0 -0.38 71 71
fibrinolysis -0.027 0.14 -9999 0 -0.34 73 73
HCK -0.005 0.11 -9999 0 -0.47 25 25
dendritic cell antigen processing and presentation -0.008 0.13 -9999 0 -0.45 26 26
VTN 0.016 0.021 -9999 0 -0.26 3 3
alphaM/beta2 Integrin/CYR61 -0.034 0.14 -9999 0 -0.37 67 67
LPA 0.016 0.026 -9999 0 -0.39 2 2
LRP1 0.017 0.023 -9999 0 -0.52 1 1
cell migration -0.05 0.17 -9999 0 -0.36 104 104
FN1 -0.046 0.17 -9999 0 -0.46 71 71
alphaM/beta2 Integrin/Thy1 -0.013 0.12 -9999 0 -0.37 47 47
MPO 0.008 0.051 -9999 0 -0.26 19 19
KNG1 0.017 0.017 -9999 0 -0.26 2 2
RAP1/GDP 0.017 0.046 -9999 0 -0.31 9 9
ROCK1 0 0.13 -9999 0 -0.47 21 21
ELA2 0.017 0.017 -9999 0 -0.26 2 2
PLG 0.016 0.033 -9999 0 -0.52 2 2
CTGF -0.033 0.15 -9999 0 -0.42 61 61
alphaM/beta2 Integrin/Hck -0.012 0.14 -9999 0 -0.44 40 40
ITGAM 0.002 0.071 -9999 0 -0.48 10 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.073 0.18 -9999 0 -0.35 131 131
HP 0.013 0.05 -9999 0 -0.43 6 6
leukocyte adhesion -0.033 0.18 -9999 0 -0.54 42 42
SELP -0.12 0.22 -9999 0 -0.44 156 156
TCGA08_p53

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
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 0.029 0.072 0.24 31 -0.18 13 44
MDM4 0.013 0.044 -10000 0 -0.32 8 8
Caspase cascade in apoptosis

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
TOP1 -0.002 0.11 0.22 3 -0.26 49 52
ACTA1 -0.03 0.14 0.24 8 -0.35 59 67
NUMA1 -0.005 0.12 0.2 9 -0.26 53 62
SPTAN1 -0.01 0.13 0.24 11 -0.33 54 65
LIMK1 -0.029 0.15 0.23 9 -0.33 76 85
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BIRC2 0.016 0.021 -10000 0 -0.26 3 3
BAX 0.016 0.021 -10000 0 -0.26 3 3
CASP10 -0.042 0.14 -10000 0 -0.31 99 99
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 52 61
DIABLO 0.018 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.13 0.23 11 -0.33 54 65
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.009 0.067 -10000 0 -0.49 9 9
GSN -0.02 0.14 0.23 9 -0.34 63 72
MADD 0.018 0 -10000 0 -10000 0 0
TFAP2A -0.009 0.14 -10000 0 -0.56 27 27
BID -0.022 0.09 -10000 0 -0.2 94 94
MAP3K1 -0.03 0.13 -10000 0 -0.41 44 44
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 -0.34 65 70
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 -0.025 0.17 -10000 0 -0.64 35 35
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.005 0.13 0.24 4 -0.31 51 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 -0.46 4 4
ICAD/CAD -0.003 0.13 0.25 3 -0.32 49 52
CASP7 0.045 0.12 0.29 68 -0.45 9 77
KRT18 -0.072 0.21 -10000 0 -0.57 77 77
apoptosis -0.005 0.14 0.26 8 -0.31 54 62
DFFA -0.01 0.13 0.24 11 -0.33 54 65
DFFB -0.01 0.13 0.24 11 -0.33 54 65
PARP1 0.02 0.075 0.19 37 -0.3 8 45
actin filament polymerization 0.026 0.15 0.34 60 -0.22 9 69
TNF -0.004 0.094 -10000 0 -0.36 31 31
CYCS -0.012 0.062 -10000 0 -0.16 35 35
SATB1 -0.018 0.13 -10000 0 -0.43 28 28
SLK -0.01 0.13 0.24 11 -0.33 54 65
p15 BID/BAX -0.011 0.082 -10000 0 -0.28 12 12
CASP2 0.01 0.089 -10000 0 -0.38 11 11
JNK cascade 0.029 0.13 0.41 44 -10000 0 44
CASP3 -0.017 0.14 0.25 11 -0.36 54 65
LMNB2 0.017 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 -0.025 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 -0.33 54 65
GZMB -0.058 0.16 -10000 0 -0.38 97 97
CASP1 -0.038 0.16 -10000 0 -0.42 60 60
LMNB1 -0.033 0.12 -10000 0 -0.29 38 38
APP -0.025 0.17 -10000 0 -0.64 35 35
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 0.14 0.22 31 -0.31 55 86
LMNA 0.014 0.076 -10000 0 -0.3 11 11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.095 -10000 0 -0.38 13 13
LRDD 0.018 0 -10000 0 -10000 0 0
SREBF1 -0.036 0.15 0.24 10 -0.36 63 73
APAF-1/Caspase 9 0.015 0.068 -10000 0 -0.39 5 5
nuclear fragmentation during apoptosis -0.005 0.12 0.2 9 -0.26 53 62
CFL2 -0.027 0.15 0.22 9 -0.34 60 69
GAS2 -0.035 0.15 0.24 10 -0.32 78 88
positive regulation of apoptosis -0.003 0.08 -10000 0 -0.26 21 21
PRF1 -0.009 0.093 -10000 0 -0.31 43 43
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.04 0.15 -9999 0 -0.38 74 74
EPHB2 0.007 0.062 -9999 0 -0.32 16 16
Syndecan-2/TACI -0.006 0.091 -9999 0 -0.3 37 37
LAMA1 0.015 0.027 -9999 0 -0.26 5 5
Syndecan-2/alpha2 ITGB1 -0.061 0.17 -9999 0 -0.31 137 137
HRAS 0.012 0.051 -9999 0 -0.41 7 7
Syndecan-2/CASK -0.016 0.088 -9999 0 -0.31 37 37
ITGA5 0.014 0.042 -9999 0 -0.46 4 4
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 -0.01 0.093 -9999 0 -0.28 48 48
LAMA3 -0.069 0.18 -9999 0 -0.43 102 102
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.017 0.12 -9999 0 -0.38 46 46
Syndecan-2/MMP2 -0.03 0.14 -9999 0 -0.38 62 62
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.023 0.12 -9999 0 -0.37 56 56
dendrite morphogenesis -0.009 0.095 -9999 0 -0.3 41 41
Syndecan-2/GM-CSF -0.013 0.099 -9999 0 -0.31 42 42
determination of left/right symmetry -0.016 0.11 -9999 0 -0.37 37 37
Syndecan-2/PKC delta -0.005 0.093 -9999 0 -0.3 40 40
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
MAPK3 -0.004 0.09 -9999 0 -0.27 43 43
MAPK1 -0.005 0.092 -9999 0 -0.28 43 43
Syndecan-2/RACK1 0.004 0.087 -9999 0 -0.26 43 43
NF1 0.015 0.035 -9999 0 -0.43 3 3
FGFR/FGF/Syndecan-2 -0.016 0.11 -9999 0 -0.37 37 37
ITGA2 -0.047 0.17 -9999 0 -0.46 72 72
MAPK8 0.002 0.093 -9999 0 -0.3 40 40
Syndecan-2/alpha2/beta1 Integrin -0.017 0.13 -9999 0 -0.3 82 82
Syndecan-2/Kininogen -0.004 0.09 -9999 0 -0.3 37 37
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
SRC 0.008 0.085 -9999 0 -0.25 44 44
Syndecan-2/CASK/Protein 4.1 -0.003 0.082 -9999 0 -0.27 38 38
extracellular matrix organization -0.004 0.091 -9999 0 -0.3 38 38
actin cytoskeleton reorganization -0.04 0.15 -9999 0 -0.38 74 74
Syndecan-2/Caveolin-2/Ras -0.013 0.12 -9999 0 -0.33 53 53
Syndecan-2/Laminin alpha3 -0.055 0.15 -9999 0 -0.34 98 98
Syndecan-2/RasGAP 0.007 0.093 -9999 0 -0.25 51 51
alpha5/beta1 Integrin 0.022 0.041 -9999 0 -0.37 5 5
PRKCD 0.014 0.042 -9999 0 -0.46 4 4
Syndecan-2 dimer -0.009 0.095 -9999 0 -0.3 41 41
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 0.093 -9999 0 -0.24 52 52
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 0.036 -9999 0 -0.26 9 9
RASA1 0.004 0.079 -9999 0 -0.42 16 16
alpha2/beta1 Integrin -0.023 0.12 -9999 0 -0.37 56 56
Syndecan-2/Synbindin -0.003 0.09 -9999 0 -0.3 37 37
TGFB1 0.017 0.023 -9999 0 -0.52 1 1
CASP3 0.004 0.084 -9999 0 -0.27 40 40
FN1 -0.046 0.17 -9999 0 -0.46 71 71
Syndecan-2/IL8 -0.055 0.14 -9999 0 -0.33 86 86
SDC2 -0.016 0.11 -9999 0 -0.37 37 37
KNG1 0.017 0.017 -9999 0 -0.26 2 2
Syndecan-2/Neurofibromin -0.005 0.092 -9999 0 -0.3 39 39
TRAPPC4 0.018 0 -9999 0 -10000 0 0
CSF2 -0.001 0.075 -9999 0 -0.28 33 33
Syndecan-2/TGFB1 -0.004 0.091 -9999 0 -0.3 38 38
Syndecan-2/Syntenin/PI-4-5-P2 -0.01 0.094 -9999 0 -0.28 48 48
Syndecan-2/Ezrin -0.009 0.091 -9999 0 -0.28 49 49
PRKACA 0.004 0.083 -9999 0 -0.27 39 39
angiogenesis -0.055 0.14 -9999 0 -0.33 86 86
MMP2 -0.029 0.15 -9999 0 -0.47 51 51
IL8 -0.073 0.17 -9999 0 -0.34 135 135
calcineurin-NFAT signaling pathway -0.006 0.091 -9999 0 -0.3 37 37
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.065 -9999 0 -0.37 9 9
alphaV beta3 Integrin -0.035 0.13 -9999 0 -0.33 63 63
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 30 30
VEGFA 0 0.076 -9999 0 -0.29 31 31
ILK 0.002 0.073 -9999 0 -0.75 2 2
ROCK1 0.018 0 -9999 0 -10000 0 0
AKT1 0.007 0.075 -9999 0 -0.49 5 5
PTK2B 0.012 0.092 -9999 0 -0.32 28 28
alphaV/beta3 Integrin/JAM-A -0.015 0.12 -9999 0 -0.28 61 61
CBL 0.017 0.012 -9999 0 -0.26 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.009 0.09 -9999 0 -0.33 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.22 -9999 0 -0.39 170 170
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.02 0.086 -9999 0 -0.38 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 -0.19 0.24 -9999 0 -0.54 131 131
PI4 Kinase 0.025 0.024 -9999 0 -0.37 2 2
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
alphaV/beta3 Integrin/Osteopontin -0.084 0.16 -9999 0 -0.33 144 144
RPS6KB1 -0.15 0.24 -9999 0 -0.49 135 135
TLN1 0.017 0.023 -9999 0 -0.52 1 1
MAPK3 -0.094 0.23 -9999 0 -0.64 61 61
GPR124 0.001 0.092 -9999 0 -0.52 16 16
MAPK1 -0.094 0.23 -9999 0 -0.65 59 59
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
alphaV/beta3 Integrin/Tumstatin 0.011 0.089 -9999 0 -0.34 25 25
cell adhesion -0.01 0.12 -9999 0 -0.31 59 59
ANGPTL3 0.01 0.061 -9999 0 -0.43 9 9
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 0.012 0.055 -9999 0 -0.45 7 7
ITGB3 0.002 0.076 -9999 0 -0.32 25 25
IGF1 -0.1 0.21 -9999 0 -0.42 146 146
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 -0.003 0.1 -9999 0 -0.48 22 22
CD47 -0.005 0.11 -9999 0 -0.47 25 25
alphaV/beta3 Integrin/CD47 -0.001 0.1 -9999 0 -0.32 43 43
VCL 0.016 0.029 -9999 0 -0.35 3 3
alphaV/beta3 Integrin/Del1 -0.066 0.17 -9999 0 -0.36 115 115
CSF1 0.014 0.037 -9999 0 -0.3 7 7
PIK3C2A -0.005 0.1 -9999 0 -0.71 8 8
PI4 Kinase/Pyk2 -0.043 0.093 -9999 0 -0.39 19 19
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.013 0.1 -9999 0 -0.34 30 30
FAK1/Vinculin 0.003 0.11 -9999 0 -0.37 27 27
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 0.021 -9999 0 -0.26 3 3
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
FGF2 -0.064 0.16 -9999 0 -0.34 121 121
F11R -0.037 0.12 -9999 0 -0.37 41 41
alphaV/beta3 Integrin/Lactadherin -0.007 0.12 -9999 0 -0.39 39 39
alphaV/beta3 Integrin/TGFBR2 0.01 0.093 -9999 0 -0.36 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.031 0.063 -9999 0 -0.27 20 20
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
alphaV/beta3 Integrin/Talin 0.013 0.077 -9999 0 -0.3 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.046 0.17 -9999 0 -0.46 71 71
alphaV/beta3 Integrin/Pyk2 0.017 0.094 -9999 0 -0.32 28 28
SDC1 -0.037 0.16 -9999 0 -0.46 61 61
VAV3 -0.024 0.13 -9999 0 -0.27 103 103
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 26 26
cell migration 0.011 0.1 -9999 0 -0.33 26 26
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
PI3K -0.017 0.12 -9999 0 -0.42 21 21
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 -0.003 0.1 -9999 0 -0.48 22 22
COL4A3 0.013 0.047 -9999 0 -0.37 7 7
angiogenesis -0.083 0.22 -9999 0 -0.65 58 58
Rac1/GTP -0.013 0.12 -9999 0 -0.42 11 11
EDIL3 -0.11 0.22 -9999 0 -0.44 151 151
cell proliferation 0.01 0.093 -9999 0 -0.35 27 27
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.061 0.16 -10000 0 -0.4 68 68
IKBKB 0.005 0.077 -10000 0 -0.25 10 10
AKT1 -0.017 0.098 0.21 10 -0.23 38 48
IKBKG 0.008 0.078 -10000 0 -0.24 13 13
CALM1 -0.03 0.13 0.21 11 -0.36 44 55
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
MAP3K1 -0.076 0.19 -10000 0 -0.47 72 72
MAP3K7 0.016 0.021 -10000 0 -0.26 3 3
mol:Ca2+ -0.039 0.13 0.21 11 -0.38 47 58
DOK1 0.002 0.083 -10000 0 -0.41 19 19
AP-1 -0.045 0.1 0.18 1 -0.24 67 68
LYN 0.014 0.031 -10000 0 -0.26 7 7
BLNK -0.013 0.12 -10000 0 -0.51 31 31
SHC1 0.017 0.023 -10000 0 -0.52 1 1
BCR complex -0.033 0.13 -10000 0 -0.35 70 70
CD22 -0.056 0.19 -10000 0 -0.49 62 62
CAMK2G -0.021 0.12 -10000 0 -0.38 31 31
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 -0.45 20 20
GO:0007205 -0.04 0.14 0.21 11 -0.39 47 58
SYK -0.022 0.14 -10000 0 -0.48 42 42
ELK1 -0.032 0.13 0.21 11 -0.36 46 57
NFATC1 -0.041 0.16 -10000 0 -0.38 61 61
B-cell antigen/BCR complex -0.033 0.13 -10000 0 -0.35 70 70
PAG1/CSK 0.008 0.074 -10000 0 -0.37 16 16
NFKBIB 0.014 0.031 0.097 1 -0.11 3 4
HRAS -0.028 0.13 -10000 0 -0.38 34 34
NFKBIA 0.015 0.03 0.097 1 -0.11 2 3
NF-kappa-B/RelA/I kappa B beta 0.02 0.027 0.099 1 -0.16 1 2
RasGAP/Csk -0.026 0.15 -10000 0 -0.31 78 78
mol:GDP -0.038 0.13 0.21 11 -0.36 50 61
PTEN -0.002 0.1 -10000 0 -0.52 19 19
CD79B -0.042 0.15 -10000 0 -0.36 83 83
NF-kappa-B/RelA/I kappa B alpha 0.02 0.027 0.099 1 -0.16 1 2
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PI3K/BCAP/CD19 -0.063 0.18 -10000 0 -0.5 55 55
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
mol:IP3 -0.04 0.14 0.21 11 -0.39 46 57
CSK 0.015 0.031 -10000 0 -0.32 4 4
FOS -0.078 0.15 0.21 8 -0.4 63 71
CHUK 0.001 0.094 -10000 0 -0.31 22 22
IBTK 0.016 0.033 -10000 0 -0.52 2 2
CARD11/BCL10/MALT1/TAK1 -0.022 0.12 -10000 0 -0.41 28 28
PTPN6 -0.047 0.18 -10000 0 -0.52 47 47
RELA 0.018 0 -10000 0 -10000 0 0
BCL2A1 0.013 0.03 -10000 0 -0.094 11 11
VAV2 -0.066 0.19 -10000 0 -0.51 60 60
ubiquitin-dependent protein catabolic process 0.019 0.03 0.1 1 -0.1 3 4
BTK -0.036 0.2 -10000 0 -1.1 18 18
CD19 -0.074 0.2 -10000 0 -0.45 85 85
MAP4K1 0.011 0.041 -10000 0 -0.26 12 12
CD72 -0.031 0.14 -10000 0 -0.38 65 65
PAG1 -0.005 0.097 -10000 0 -0.38 30 30
MAPK14 -0.057 0.17 -10000 0 -0.41 64 64
SH3BP5 -0.005 0.1 -10000 0 -0.44 26 26
PIK3AP1 -0.045 0.16 0.23 11 -0.43 51 62
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.055 0.19 -10000 0 -0.46 63 63
RAF1 -0.019 0.12 -10000 0 -0.38 27 27
RasGAP/p62DOK/SHIP -0.036 0.15 -10000 0 -0.32 80 80
CD79A -0.01 0.085 -10000 0 -0.26 53 53
re-entry into mitotic cell cycle -0.045 0.1 0.18 1 -0.24 67 68
RASA1 0.004 0.079 -10000 0 -0.42 16 16
MAPK3 -0.003 0.1 -10000 0 -0.33 23 23
MAPK1 -0.003 0.1 -10000 0 -0.33 24 24
CD72/SHP1 -0.055 0.19 -10000 0 -0.51 60 60
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MAPK8 -0.059 0.17 -10000 0 -0.41 67 67
actin cytoskeleton organization -0.049 0.17 -10000 0 -0.44 58 58
NF-kappa-B/RelA 0.043 0.054 0.19 1 -0.23 3 4
Calcineurin -0.023 0.12 -10000 0 -0.39 29 29
PI3K -0.087 0.14 -10000 0 -0.4 67 67
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.15 0.24 11 -0.43 45 56
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 0.2 1 -0.36 61 62
mol:DAG -0.04 0.14 0.21 11 -0.39 46 57
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
MAP2K1 -0.011 0.11 -10000 0 -0.35 26 26
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 62 75
ETS1 -0.018 0.12 -10000 0 -0.4 24 24
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 0.054 -10000 0 -0.38 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 -0.51 57 57
CARD11 -0.038 0.14 0.21 11 -0.38 53 64
FCGR2B -0.032 0.15 -10000 0 -0.5 51 51
PPP3CA 0.006 0.073 -10000 0 -0.44 13 13
BCL10 0.017 0.012 -10000 0 -0.26 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 -0.22 37 46
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
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 -0.038 0.12 0.21 1 -0.34 49 50
PTP1B/AKT1 -0.042 0.12 0.29 2 -0.33 42 44
FYN 0.009 0.063 -10000 0 -0.4 11 11
p210 bcr-abl/PTP1B -0.054 0.12 0.32 2 -0.32 61 63
EGFR -0.083 0.18 -10000 0 -0.36 136 136
EGF/EGFR -0.14 0.2 -10000 0 -0.36 192 192
CSF1 0.014 0.037 -10000 0 -0.3 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 -0.064 0.15 0.28 2 -0.35 71 73
Insulin Receptor/Insulin -0.019 0.099 -10000 0 -0.36 19 19
HCK -0.005 0.11 -10000 0 -0.47 25 25
CRK 0.016 0.033 -10000 0 -0.52 2 2
TYK2 -0.044 0.12 0.3 2 -0.32 53 55
EGF -0.15 0.23 -10000 0 -0.43 193 193
YES1 0.007 0.07 -10000 0 -0.43 12 12
CAV1 -0.072 0.14 0.29 2 -0.36 63 65
TXN 0.013 0.017 -10000 0 -0.26 2 2
PTP1B/IRS1/GRB2 -0.066 0.15 -10000 0 -0.36 80 80
cell migration 0.054 0.12 0.32 61 -0.32 2 63
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 0.021 -10000 0 -0.26 3 3
CSF1R 0.017 0.017 -10000 0 -0.26 2 2
Prolactin Receptor/Prolactin -0.002 0.12 -10000 0 -0.36 47 47
FGR 0.017 0.017 -10000 0 -0.26 2 2
PTP1B/p130 Cas -0.043 0.12 0.28 2 -0.32 53 55
Crk/p130 Cas -0.034 0.12 -10000 0 -0.35 34 34
DOK1 -0.038 0.13 0.3 2 -0.38 40 42
JAK2 -0.036 0.12 -10000 0 -0.33 50 50
Jak2/Leptin Receptor/Leptin -0.069 0.13 -10000 0 -0.36 52 52
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
PTPN1 -0.055 0.12 0.32 2 -0.32 61 63
LYN 0.014 0.031 -10000 0 -0.26 7 7
CDH2 -0.029 0.13 -10000 0 -0.35 67 67
SRC -0.004 0.07 -10000 0 -0.68 3 3
ITGB3 0.001 0.076 -10000 0 -0.32 25 25
CAT1/PTP1B -0.084 0.17 0.25 2 -0.44 63 65
CAPN1 0.003 0.078 -10000 0 -0.44 15 15
CSK 0.015 0.031 -10000 0 -0.32 4 4
PI3K -0.035 0.1 -10000 0 -0.34 30 30
mol:H2O2 -0.003 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.062 0.12 -10000 0 -0.38 40 40
negative regulation of transcription -0.036 0.11 -10000 0 -0.32 50 50
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 -0.018 0.1 -10000 0 -0.29 61 61
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 0.091 -10000 0 -0.34 33 33
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
p210 bcr-abl/Grb2 0.016 0.024 -10000 0 -0.26 4 4
mol:NADPH -0.003 0.004 -10000 0 -10000 0 0
TRPV6 -0.059 0.16 -10000 0 -0.43 55 55
PRL 0.018 0.033 -10000 0 -0.32 4 4
SOCS3 -0.005 0.17 -10000 0 -1.3 8 8
SPRY2 -0.034 0.15 -10000 0 -0.43 58 58
Insulin Receptor/Insulin/IRS1 -0.008 0.12 -10000 0 -0.32 62 62
CSF1/CSF1R -0.036 0.12 -10000 0 -0.3 54 54
Ras protein signal transduction 0.029 0.038 -10000 0 -0.2 2 2
IRS1 -0.048 0.17 -10000 0 -0.49 68 68
INS 0.017 0.024 -10000 0 -0.53 1 1
LEP -0.052 0.16 -10000 0 -0.36 99 99
STAT5B -0.042 0.11 0.25 2 -0.28 62 64
STAT5A -0.043 0.11 0.25 2 -0.28 63 65
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PDGFB-D/PDGFRB -0.047 0.13 0.28 2 -0.35 53 55
CSN2 0.019 0.1 -10000 0 -1.4 2 2
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
LAT -0.025 0.12 -10000 0 -0.56 19 19
YBX1 0.007 0.073 -10000 0 -0.33 16 16
LCK -0.073 0.18 -10000 0 -0.4 115 115
SHC1 0.017 0.023 -10000 0 -0.52 1 1
NOX4 -0.057 0.18 -10000 0 -0.49 76 76
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.004 0.13 -10000 0 -0.5 11 11
UGCG -0.11 0.27 -10000 0 -0.77 74 74
AKT1/mTOR/p70S6K/Hsp90/TERT -0.07 0.19 -10000 0 -0.39 100 100
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 -0.96 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.14 0.2 -10000 0 -0.46 107 107
FRAP1 -0.12 0.27 -10000 0 -0.54 107 107
FOXO3 -0.064 0.2 -10000 0 -0.42 77 77
AKT1 -0.073 0.21 -10000 0 -0.44 83 83
GAB2 0.008 0.047 -10000 0 -0.26 16 16
SMPD1 -0.004 0.079 -10000 0 -0.8 4 4
SGMS1 -0.01 0.099 -10000 0 -0.74 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 -0.29 25 25
CALM1 0.018 0 -10000 0 -10000 0 0
cell proliferation -0.088 0.21 -10000 0 -0.47 94 94
EIF3A 0.017 0.012 -10000 0 -0.26 1 1
PI3K 0.006 0.083 -10000 0 -0.36 22 22
RPS6KB1 -0.035 0.1 -10000 0 -0.37 1 1
mol:sphingomyelin -0.014 0.12 -10000 0 -0.96 8 8
natural killer cell activation -0.002 0.004 -10000 0 -0.015 9 9
JAK3 0.018 0.004 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
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 -0.82 50 50
MYB -0.23 0.5 -10000 0 -1.2 107 107
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.043 0.16 -10000 0 -0.42 41 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.015 0.099 -10000 0 -0.41 3 3
mol:PI-3-4-5-P3 -0.042 0.16 -10000 0 -0.41 41 41
Rac1/GDP 0.011 0.064 -10000 0 -0.28 21 21
T cell proliferation -0.038 0.15 -10000 0 -0.38 41 41
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 -0.061 120 120
PRKCZ -0.041 0.15 -10000 0 -0.4 41 41
NF kappa B1 p50/RelA -0.085 0.23 -10000 0 -0.46 103 103
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 -0.033 0.14 -10000 0 -0.41 61 61
IL2RB -0.016 0.12 -10000 0 -0.43 40 40
TERT 0.013 0.042 -10000 0 -0.33 7 7
E2F1 -0.077 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 0.029 120 -10000 0 120
PTPN11 0.015 0.024 -10000 0 -0.52 1 1
IL2RG -0.002 0.079 -10000 0 -0.29 35 35
actin cytoskeleton organization -0.038 0.15 -10000 0 -0.38 41 41
GRB2 0.014 0.024 -10000 0 -0.26 4 4
IL2 0.011 0.051 -10000 0 -0.34 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 -0.072 0.18 -10000 0 -0.4 115 115
BCL2 -0.19 0.39 -10000 0 -0.87 119 119
Canonical Wnt signaling pathway

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.05 0.22 3 -0.53 1 4
AES 0.033 0.037 0.2 3 -10000 0 3
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 -0.025 0.14 -10000 0 -0.43 51 51
TLE1 -0.017 0.16 0.2 2 -0.45 55 57
MACF1 0.016 0.026 -10000 0 -0.39 2 2
CTNNB1 -0.006 0.098 0.28 2 -0.36 13 15
WIF1 -0.025 0.1 -10000 0 -0.26 82 82
beta catenin/RanBP3 0.069 0.19 0.37 124 -0.42 2 126
KREMEN2 -0.19 0.23 -10000 0 -0.41 258 258
DKK1 -0.12 0.19 -10000 0 -0.34 198 198
beta catenin/beta TrCP1 0.005 0.097 0.27 2 -0.37 11 13
FZD1 0.003 0.082 -10000 0 -0.43 17 17
AXIN2 -0.098 0.33 -10000 0 -1.3 31 31
AXIN1 0.017 0.012 -10000 0 -0.26 1 1
RAN 0.018 0.012 -10000 0 -0.26 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 0.27 2 -0.48 24 26
Axin1/APC/GSK3 0.049 0.042 0.25 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.037 0.067 -10000 0 -0.3 2 2
HNF1A 0.031 0.046 0.2 1 -0.25 4 5
CTBP1 0.033 0.041 0.21 2 -0.26 1 3
MYC -0.12 0.36 -10000 0 -1.2 48 48
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 0.007 0.068 -10000 0 -0.4 13 13
TCF4 0.01 0.12 0.2 2 -0.49 24 26
TCF3 0.028 0.062 0.21 2 -0.38 6 8
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 0.49 123 -0.48 9 132
LEF1 -0.007 0.13 0.2 3 -0.32 63 66
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 -0.5 34 34
DKK1/LRP6/Kremen 2 -0.17 0.18 -10000 0 -0.34 248 248
LRP6 0.008 0.065 -10000 0 -0.38 13 13
CSNK1A1 0.035 0.048 0.21 4 -0.45 1 5
NLK 0.008 0.045 -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 0.029 0.039 0.26 8 -10000 0 8
APC 0.026 0.062 -10000 0 -0.24 23 23
WNT1/LRP6/FZD1 0.038 0.06 -10000 0 -0.24 10 10
CREBBP 0.032 0.051 0.21 1 -0.52 2 3
Visual signal transduction: Rods

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
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 -0.046 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 -0.083 0.12 -9999 0 -0.27 142 142
mol:Na + -0.042 0.088 -9999 0 -0.43 13 13
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.055 0.15 -9999 0 -0.34 95 95
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.004 0.11 -9999 0 -0.44 13 13
CNGB1 0.018 0 -9999 0 -10000 0 0
RDH5 -0.003 0.073 -9999 0 -0.26 40 40
SAG -0.099 0.19 -9999 0 -0.36 162 162
mol:Ca2+ -0.001 0.11 -9999 0 -0.39 16 16
Na + (4 Units) -0.04 0.084 -9999 0 -0.38 16 16
RGS9 -0.032 0.13 -9999 0 -0.31 80 80
GNB1/GNGT1 -0.033 0.1 -9999 0 -0.37 18 18
GNAT1/GDP -0.039 0.13 -9999 0 -0.28 98 98
GUCY2D 0.018 0 -9999 0 -10000 0 0
GNGT1 -0.063 0.14 -9999 0 -0.28 143 143
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 -0.26 119 119
mol:11-cis-retinal -0.003 0.073 -9999 0 -0.26 40 40
mol:cGMP 0.026 0.088 -9999 0 -0.3 31 31
GNB1 0.013 0.052 -9999 0 -0.52 5 5
Rhodopsin 0.012 0.05 -9999 0 -10000 0 0
SLC24A1 0.011 0.056 -9999 0 -0.42 8 8
CNGA1 -0.063 0.16 -9999 0 -0.32 125 125
Metarhodopsin II 0.011 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.026 0.076 -9999 0 -0.29 25 25
RGS9BP -0.071 0.18 -9999 0 -0.41 110 110
Metarhodopsin II/Transducin -0.005 0.064 -9999 0 -0.25 22 22
GCAP Family/Ca ++ 0.015 0.075 -9999 0 -0.3 25 25
PDE6A/B -0.067 0.17 -9999 0 -0.37 116 116
mol:Pi -0.055 0.15 -9999 0 -0.33 95 95
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.014 0.084 -9999 0 -0.29 22 22
PDE6B -0.1 0.22 -9999 0 -0.5 123 123
PDE6A 0.011 0.048 -9999 0 -0.31 11 11
PDE6G 0.016 0.024 -9999 0 -0.26 4 4
RHO 0.018 0 -9999 0 -10000 0 0
PDE6 -0.088 0.17 -9999 0 -0.41 62 62
GUCA1A 0.001 0.092 -9999 0 -0.48 18 18
GC2/GCAP Family 0.02 0.093 -9999 0 -0.32 31 31
GUCA1C 0.004 0.081 -9999 0 -0.44 16 16
GUCA1B 0.014 0.035 -9999 0 -0.3 6 6
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 -9999 0 -0.3 26 26
NFATC2 0.012 0.044 -9999 0 -0.3 5 5
NFATC3 0.015 0.031 -9999 0 -10000 0 0
CD40LG -0.099 0.26 -9999 0 -0.55 87 87
PTGS2 -0.11 0.26 -9999 0 -0.57 87 87
JUNB 0.011 0.055 -9999 0 -0.36 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.019 -9999 0 -10000 0 0
CaM/Ca2+ 0.008 0.019 -9999 0 -10000 0 0
CALM1 0.016 0.009 -9999 0 -10000 0 0
JUN -0.035 0.15 -9999 0 -0.46 57 57
mol:Ca2+ -0.004 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.011 -9999 0 -0.15 2 2
FOSL1 0.016 0.024 -9999 0 -0.26 4 4
CREM 0.016 0.017 -9999 0 -0.26 2 2
Jun/NFAT1-c-4/p21SNFT -0.025 0.15 -9999 0 -0.36 49 49
FOS -0.11 0.2 -9999 0 -0.37 171 171
IFNG -0.14 0.3 -9999 0 -0.6 115 115
AP-1/NFAT1-c-4 -0.1 0.31 -9999 0 -0.62 95 95
FASLG -0.13 0.3 -9999 0 -0.62 109 109
NFAT1-c-4/ICER1 0.007 0.095 -9999 0 -0.31 14 14
IL2RA -0.12 0.28 -9999 0 -0.57 106 106
FKBP12/FK506 0.012 0.011 -9999 0 -0.17 2 2
CSF2 -0.1 0.26 -9999 0 -0.55 90 90
JunB/Fra1/NFAT1-c-4 0.015 0.1 -9999 0 -0.32 18 18
IL4 -0.097 0.25 -9999 0 -0.55 86 86
IL2 -0.005 0.1 -9999 0 -1.3 3 3
IL3 0.008 0.021 -9999 0 -10000 0 0
FKBP1A 0.017 0.017 -9999 0 -0.26 2 2
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.027 0 -9999 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 -0.035 0.14 -9999 0 -0.33 75 75
MAP3K8 -0.037 0.15 -9999 0 -0.39 69 69
FOS -0.014 0.092 -9999 0 -0.29 13 13
PRKCA 0.01 0.034 -9999 0 -0.26 8 8
PTPN7 0.006 0.05 -9999 0 -0.28 14 14
HRAS 0.011 0.051 -9999 0 -0.41 7 7
PRKCB -0.003 0.007 -9999 0 -0.013 171 171
NRAS 0.005 0.073 -9999 0 -0.4 15 15
RAS family/GTP 0.013 0.064 -9999 0 -0.28 20 20
MAPK3 0.001 0.057 -9999 0 -0.45 2 2
MAP2K1 -0.005 0.065 -9999 0 -0.23 11 11
ELK1 0.01 0.038 -9999 0 -0.39 4 4
BRAF 0.004 0.06 -9999 0 -0.41 8 8
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 0.029 -9999 0 -10000 0 0
KRAS 0.007 0.069 -9999 0 -0.45 11 11
Coregulation of Androgen receptor activity

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
NRIP1 -0.042 0.16 -9999 0 -0.46 67 67
SVIL -0.004 0.1 -9999 0 -0.44 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 -0.066 0.14 -9999 0 -0.33 103 103
CARM1 0.014 0.039 -9999 0 -0.36 5 5
PRDX1 0.011 0.055 -9999 0 -0.45 7 7
PELP1 0.017 0.001 -9999 0 -10000 0 0
CTNNB1 0.002 0.09 -9999 0 -0.45 19 19
AKT1 0.01 0.054 -9999 0 -0.38 9 9
PTK2B 0.017 0.017 -9999 0 -0.26 2 2
MED1 -0.001 0.068 -9999 0 -0.26 34 34
MAK -0.018 0.096 -9999 0 -0.28 56 56
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.019 0.012 -9999 0 -0.26 1 1
GSN -0.001 0.098 -9999 0 -0.43 24 24
NCOA2 0.009 0.063 -9999 0 -0.4 11 11
NCOA6 0.019 0.012 -9999 0 -0.26 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 -0.044 0.092 -9999 0 -0.84 5 5
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 -0.077 0.14 -9999 0 -0.29 139 139
FHL2 -0.16 0.35 -9999 0 -0.98 73 73
RANBP9 0.019 0.012 -9999 0 -0.26 1 1
JMJD1A -0.002 0.056 -9999 0 -10000 0 0
CDK6 -0.02 0.11 -9999 0 -0.3 63 63
TGFB1I1 -0.003 0.1 -9999 0 -0.49 23 23
T-DHT/AR/CyclinD1 -0.13 0.21 -9999 0 -0.42 154 154
XRCC6 0.016 0.012 -9999 0 -0.26 1 1
T-DHT/AR -0.087 0.17 -9999 0 -0.33 142 142
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 -0.008 0.11 -9999 0 -0.51 24 24
CDKN2A -0.055 0.15 -9999 0 -0.34 108 108
SRF -0.001 0.055 -9999 0 -0.28 4 4
NKX3-1 -0.057 0.11 -9999 0 -0.24 107 107
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 -0.067 0.14 -9999 0 -0.34 103 103
AR -0.11 0.22 -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 0.046 -9999 0 -0.32 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 -0.06 0.13 -9999 0 -0.3 106 106
RPS6KA3 0.011 0.057 -9999 0 -0.34 12 12
T-DHT/AR/ARA70 -0.072 0.15 -9999 0 -0.34 110 110
LATS2 0.004 0.078 -9999 0 -0.48 13 13
T-DHT/AR/PRX1 -0.064 0.14 -9999 0 -0.31 107 107
Cyclin D3/CDK11 p58 0.013 0.008 -9999 0 -0.17 1 1
VAV3 -0.082 0.2 -9999 0 -0.48 107 107
KLK2 -0.013 0.076 -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 -0.3 112 112
TMPRSS2 -0.19 0.38 -9999 0 -0.96 99 99
CCND1 -0.09 0.2 -9999 0 -0.44 125 125
PIAS1 0.019 0.012 -9999 0 -0.26 1 1
mol:T-DHT -0.019 0.037 -9999 0 -0.077 132 132
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.016 0.05 -9999 0 -0.43 6 6
T-DHT/AR/CDK6 -0.086 0.17 -9999 0 -0.38 118 118
CMTM2 0.016 0.023 -9999 0 -0.52 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.003 0.05 -9999 0 -0.32 6 6
CCND3 0.017 0.012 -9999 0 -0.26 1 1
TGIF1 0.006 0.073 -9999 0 -0.52 10 10
FKBP4 0.013 0.055 -9999 0 -0.44 7 7
TRAIL signaling pathway

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
TNFSF10 -0.042 0.16 -10000 0 -0.46 66 66
positive regulation of NF-kappaB transcription factor activity -0.018 0.12 -10000 0 -0.37 51 51
MAP2K4 -0.013 0.12 -10000 0 -0.38 29 29
IKBKB 0.011 0.047 -10000 0 -0.31 10 10
TNFRSF10B 0.004 0.083 -10000 0 -0.47 15 15
TNFRSF10A -0.003 0.1 -10000 0 -0.46 23 23
SMPD1 -0.008 0.087 -10000 0 -0.23 57 57
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 -0.41 56 56
TRAIL/TRAILR3 -0.031 0.13 -10000 0 -0.37 53 53
TRAIL/TRAILR1 -0.031 0.14 -10000 0 -0.4 62 62
TRAIL/TRAILR4 -0.018 0.12 -10000 0 -0.37 51 51
TRAIL/TRAILR1/DAP3/GTP -0.012 0.12 -10000 0 -0.3 63 63
IKK complex -0.028 0.084 -10000 0 -0.41 17 17
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 -0.28 2 2
MAPK3 -0.018 0.12 -10000 0 -0.37 51 51
MAP3K1 -0.009 0.12 -10000 0 -0.3 58 58
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) -0.003 0.1 -10000 0 -0.46 23 23
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.11 -10000 0 -0.26 65 65
CFLAR 0.01 0.064 -10000 0 -0.46 9 9
MAPK1 -0.019 0.12 -10000 0 -0.37 52 52
TRAIL/TRAILR1/FADD/TRADD/RIP -0.001 0.12 -10000 0 -0.29 63 63
mol:ceramide -0.008 0.086 -10000 0 -0.23 57 57
FADD 0 0.068 -10000 0 -0.26 34 34
MAPK8 -0.007 0.12 -10000 0 -0.39 24 24
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
TRAILR3 (trimer) -0.004 0.075 -10000 0 -0.26 40 40
CHUK 0.005 0.081 -10000 0 -0.5 13 13
TRAIL/TRAILR1/FADD -0.023 0.13 -10000 0 -0.34 63 63
DAP3 0.016 0.026 -10000 0 -0.39 2 2
CASP10 -0.049 0.12 0.26 1 -0.37 53 54
JNK cascade -0.018 0.12 -10000 0 -0.37 51 51
TRAIL (trimer) -0.041 0.16 -10000 0 -0.46 66 66
TNFRSF10C -0.004 0.075 -10000 0 -0.26 40 40
TRAIL/TRAILR1/DAP3/GTP/FADD -0.01 0.12 -10000 0 -0.29 64 64
TRAIL/TRAILR2/FADD -0.019 0.13 -10000 0 -0.35 57 57
cell death -0.008 0.086 -10000 0 -0.23 57 57
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0.11 -10000 0 -0.27 58 58
TRAILR2 (trimer) 0.004 0.082 -10000 0 -0.47 15 15
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 57 57
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 0.071 -9999 0 -0.29 28 28
Caspase 8 (4 units) -0.033 0.13 -9999 0 -0.42 29 29
NEF -0.015 0.042 -9999 0 -0.18 10 10
NFKBIA -0.004 0.061 -9999 0 -0.52 4 4
BIRC3 -0.065 0.21 -9999 0 -0.55 74 74
CYCS -0.039 0.14 -9999 0 -0.41 35 35
RIPK1 0.017 0.023 -9999 0 -0.52 1 1
CD247 -0.13 0.24 -9999 0 -0.47 151 151
MAP2K7 -0.022 0.13 -9999 0 -0.42 24 24
protein ubiquitination 0.017 0.096 -9999 0 -0.32 17 17
CRADD 0.009 0.067 -9999 0 -0.49 9 9
DAXX 0.017 0.012 -9999 0 -0.26 1 1
FAS -0.023 0.13 -9999 0 -0.42 50 50
BID -0.047 0.14 -9999 0 -0.42 38 38
NF-kappa-B/RelA/I kappa B alpha -0.015 0.12 -9999 0 -0.27 76 76
TRADD 0.016 0.026 -9999 0 -0.39 2 2
MAP3K5 -0.021 0.13 -9999 0 -0.42 46 46
CFLAR 0.01 0.064 -9999 0 -0.46 9 9
FADD 0 0.068 -9999 0 -0.26 34 34
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.12 -9999 0 -0.27 76 76
MAPK8 -0.015 0.12 -9999 0 -0.44 19 19
APAF1 0.012 0.051 -9999 0 -0.41 7 7
TRAF1 0.013 0.041 -9999 0 -0.29 9 9
TRAF2 0.014 0.042 -9999 0 -0.46 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.051 0.14 -9999 0 -0.34 67 67
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.009 0.11 -9999 0 -0.33 23 23
CHUK 0.016 0.1 -9999 0 -0.34 17 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.001 0.11 -9999 0 -0.28 54 54
TCRz/NEF -0.11 0.21 -9999 0 -0.44 132 132
TNF -0.004 0.094 -9999 0 -0.36 31 31
FASLG -0.12 0.26 -9999 0 -0.51 132 132
NFKB1 -0.002 0.046 -9999 0 -0.52 1 1
TNFR1A/BAG4/TNF-alpha 0.012 0.074 -9999 0 -0.31 18 18
CASP6 -0.019 0.13 -9999 0 -0.55 17 17
CASP7 -0.072 0.22 -9999 0 -0.54 79 79
RELA -0.001 0.04 -9999 0 -10000 0 0
CASP2 0.018 0 -9999 0 -10000 0 0
CASP3 -0.065 0.22 -9999 0 -0.54 77 77
TNFRSF1A 0.016 0.033 -9999 0 -0.52 2 2
TNFR1A/BAG4 0.014 0.055 -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 -0.35 17 17
APAF-1/Caspase 9 -0.097 0.15 -9999 0 -0.4 86 86
BCL2 -0.066 0.15 -9999 0 -0.42 40 40
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
Cellular roles of Anthrax toxin

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
ANTXR1 -0.026 0.14 -10000 0 -0.46 48 48
ANTXR2 0.003 0.087 -10000 0 -0.5 15 15
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.021 -10000 0 -0.073 46 46
monocyte activation -0.021 0.12 -10000 0 -0.41 40 40
MAP2K2 0.007 0.06 -10000 0 -0.77 3 3
MAP2K1 0.005 0.021 -10000 0 -0.11 1 1
MAP2K7 0.005 0.024 -10000 0 -0.27 1 1
MAP2K6 -0.01 0.064 -10000 0 -0.21 37 37
CYAA -0.015 0.091 -10000 0 -0.29 46 46
MAP2K4 -0.006 0.056 -10000 0 -0.21 30 30
IL1B -0.03 0.095 -10000 0 -0.28 54 54
Channel -0.01 0.099 -10000 0 -0.31 46 46
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 0.073 46 -10000 0 46
MAPK3 0.004 0.025 -10000 0 -0.19 2 2
MAPK1 0.004 0.027 -10000 0 -0.27 2 2
PGR -0.14 0.12 -10000 0 -0.21 367 367
PA/Cellular Receptors -0.012 0.11 -10000 0 -0.34 46 46
apoptosis -0.007 0.021 -10000 0 -0.073 46 46
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.008 0.094 -10000 0 -0.3 46 46
macrophage activation 0.011 0.028 -10000 0 -0.25 3 3
TNF -0.004 0.094 -10000 0 -0.36 31 31
VCAM1 -0.021 0.12 -10000 0 -0.42 40 40
platelet activation 0.007 0.027 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.034 0.12 18 -10000 0 18
IL18 -0.032 0.11 -10000 0 -0.29 67 67
negative regulation of macrophage activation -0.007 0.021 -10000 0 -0.073 46 46
LEF -0.007 0.021 -10000 0 -0.073 46 46
CASP1 -0.006 0.042 -10000 0 -0.15 25 25
mol:cAMP 0.007 0.027 -10000 0 -10000 0 0
necrosis -0.007 0.021 -10000 0 -0.073 46 46
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.094 -10000 0 -0.3 46 46
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.044 0.14 -10000 0 -0.36 67 67
fibroblast growth factor receptor signaling pathway -0.044 0.14 -10000 0 -0.36 67 67
LAMA1 0.015 0.027 -10000 0 -0.26 5 5
PRNP 0.007 0.07 -10000 0 -0.43 12 12
GPC1/SLIT2 -0.024 0.14 -10000 0 -0.39 59 59
SMAD2 0.011 0.085 -10000 0 -0.28 37 37
GPC1/PrPc/Cu2+ 0.003 0.082 -10000 0 -0.33 29 29
GPC1/Laminin alpha1 0.007 0.082 -10000 0 -0.37 22 22
TDGF1 0.017 0.012 -10000 0 -0.26 1 1
CRIPTO/GPC1 0.009 0.08 -10000 0 -0.37 22 22
APP/GPC1 -0.024 0.13 -10000 0 -0.38 56 56
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.01 0.081 -10000 0 -0.31 30 30
FLT1 0.005 0.077 -10000 0 -0.45 14 14
GPC1/TGFB/TGFBR1/TGFBR2 0.008 0.094 -10000 0 -0.32 36 36
SERPINC1 0.007 0.055 -10000 0 -0.27 19 19
FYN 0.011 0.078 -10000 0 -0.31 28 28
FGR 0.015 0.068 -10000 0 -0.3 22 22
positive regulation of MAPKKK cascade -0.011 0.12 -10000 0 -0.36 41 41
SLIT2 -0.028 0.15 -10000 0 -0.48 49 49
GPC1/NRG 0.003 0.087 -10000 0 -0.38 22 22
NRG1 0.009 0.049 -10000 0 -0.26 17 17
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.003 0.096 -10000 0 -0.32 36 36
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 -0.044 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 0.083 -10000 0 -0.42 18 18
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.057 0.14 -10000 0 -0.3 126 126
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 0.076 -10000 0 -0.29 31 31
BLK -0.004 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 -0.34 121 121
FGFR1 -0.011 0.1 -10000 0 -0.35 42 42
VEGFR1 homodimer 0.005 0.077 -10000 0 -0.44 14 14
TGFBR2 0.012 0.055 -10000 0 -0.45 7 7
cell death -0.024 0.13 -10000 0 -0.38 56 56
ATIII/GPC1 0.002 0.088 -10000 0 -0.38 23 23
PLA2G2A/GPC1 -0.043 0.12 -10000 0 -0.39 41 41
LCK -0.038 0.13 -10000 0 -0.32 81 81
neuron differentiation 0.003 0.087 -10000 0 -0.38 22 22
PrPc/Cu2+ 0.006 0.05 -10000 0 -0.31 12 12
APP -0.028 0.14 -10000 0 -0.42 55 55
TGFBR2 (dimer) 0.012 0.055 -10000 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 41 41
IRAK/TOLLIP 0.029 0.02 -9999 0 -0.24 1 1
IKBKB 0.011 0.047 -9999 0 -0.31 10 10
IKBKG 0.018 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.026 0.12 -9999 0 -0.36 47 47
IL1A 0.006 0.064 -9999 0 -0.32 18 18
IL1B -0.067 0.18 -9999 0 -0.43 86 86
IRAK/TRAF6/p62/Atypical PKCs 0.031 0.054 -9999 0 -0.23 19 19
IL1R2 -0.046 0.15 -9999 0 -0.36 89 89
IL1R1 -0.046 0.16 -9999 0 -0.41 80 80
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.018 0.12 -9999 0 -0.38 25 25
TOLLIP 0.017 0.012 -9999 0 -0.26 1 1
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0.012 -9999 0 -0.26 1 1
TAK1/TAB1/TAB2 0.033 0.034 -9999 0 -0.34 4 4
IKK complex/ELKS 0.051 0.075 -9999 0 -0.36 7 7
JUN 0.014 0.093 -9999 0 -0.44 4 4
MAP3K7 0.016 0.021 -9999 0 -0.26 3 3
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.059 0.18 -9999 0 -0.35 119 119
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.003 0.1 -9999 0 -0.28 57 57
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
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 -0.36 119 119
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 0.019 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.061 0.17 -9999 0 -0.41 87 87
IRAK4 0.014 0.044 -9999 0 -0.42 5 5
PRKCI 0.001 0.088 -9999 0 -0.44 19 19
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
PI3K 0.006 0.082 -9999 0 -0.37 21 21
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.032 0.13 -9999 0 -0.36 48 48
CHUK 0.005 0.081 -9999 0 -0.5 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.069 0.18 -9999 0 -0.36 119 119
IL1 beta/IL1R2 -0.083 0.18 -9999 0 -0.37 127 127
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.034 -9999 0 -0.33 1 1
NF kappa B1 p50/RelA -0.082 0.14 -9999 0 -0.44 55 55
IRAK3 -0.018 0.1 -9999 0 -0.28 64 64
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.056 0.17 -9999 0 -0.34 109 109
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.089 -9999 0 -0.38 4 4
IL1 alpha/IL1R1/IL1RAP -0.014 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 0.022 -9999 0 -0.25 1 1
IL1RAP 0.011 0.044 -9999 0 -0.28 11 11
UBE2N 0.017 0.017 -9999 0 -0.26 2 2
IRAK/TRAF6 -0.07 0.12 -9999 0 -0.39 50 50
CASP1 -0.051 0.17 -9999 0 -0.42 83 83
IL1RN/IL1R2 -0.061 0.16 -9999 0 -0.39 83 83
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.057 0.17 -9999 0 -0.35 110 110
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 -0.35 3 3
IL1RN -0.043 0.16 -9999 0 -0.41 76 76
TRAF6/TAK1/TAB1/TAB2 0.04 0.031 -9999 0 -0.26 5 5
MAP2K6 0.028 0.063 -9999 0 -0.4 2 2
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.004 0.089 0.33 33 -10000 0 33
PI3K Class IB/PDE3B -0.004 0.089 -10000 0 -0.33 33 33
PDE3B -0.004 0.089 -10000 0 -0.33 33 33
Signaling mediated by p38-gamma and p38-delta

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
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 0.091 -9999 0 -0.28 45 45
CCND1 -0.07 0.17 -9999 0 -0.42 91 91
p38 gamma/SNTA1 0.003 0.092 -9999 0 -0.28 34 34
MAP2K3 0.014 0.037 -9999 0 -0.3 7 7
PKN1 0.013 0.045 -9999 0 -0.39 6 6
G2/M transition checkpoint -0.003 0.09 -9999 0 -0.27 45 45
MAP2K6 -0.005 0.09 -9999 0 -0.3 42 42
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 0.004 0.071 -9999 0 -0.33 22 22
Presenilin action in Notch and Wnt 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
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 0.05 -10000 0 -0.35 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 -0.051 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 -0.48 5 5
NICD/RBPSUH 0.027 0.076 -10000 0 -0.63 6 6
WIF1 -0.025 0.1 -10000 0 -0.26 82 82
NOTCH1 -0.003 0.077 -10000 0 -0.67 6 6
PSENEN 0.017 0.012 -10000 0 -0.26 1 1
KREMEN2 -0.19 0.23 -10000 0 -0.41 258 258
DKK1 -0.12 0.19 -10000 0 -0.34 198 198
beta catenin/beta TrCP1 0.004 0.085 0.24 4 -0.35 17 21
APH1B 0 0.096 -10000 0 -0.51 18 18
APH1A 0.003 0.068 -10000 0 -0.29 25 25
AXIN1 0.006 0.04 0.24 8 -0.25 1 9
CtBP/CBP/TCF1/TLE1/AES 0.036 0.1 0.29 5 -10000 0 5
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 0.016 0.029 -10000 0 -0.25 6 6
CTBP1 0.018 0.018 -10000 0 -0.26 2 2
MYC -0.086 0.34 -10000 0 -1.4 34 34
NKD1 0.008 0.068 -10000 0 -0.4 13 13
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 -0.051 0.13 -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 -0.26 1 1
PPARD 0.004 0.045 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.071 -10000 0 -0.26 13 13
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 0.18 -10000 0 -0.34 248 248
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 0.075 0.28 4 -0.35 6 10
DKK2 -0.025 0.14 -10000 0 -0.43 51 51
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 0.014 0.039 0.27 7 -10000 0 7
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
WNT1/LRP6/FZD1 0.008 0.08 -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
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 0.095 -9999 0 -0.4 23 23
PTK2 -0.002 0.15 -9999 0 -0.46 43 43
positive regulation of JNK cascade -0.028 0.086 -9999 0 -0.31 44 44
CDC42/GDP 0.021 0.14 -9999 0 -0.42 42 42
Rac1/GDP 0.023 0.13 -9999 0 -0.41 42 42
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
CDC42/GTP -0.033 0.11 -9999 0 -0.38 44 44
nectin-3/I-afadin -0.017 0.12 -9999 0 -0.41 42 42
RAPGEF1 0.009 0.15 -9999 0 -0.47 42 42
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.001 0.17 -9999 0 -0.54 42 42
PDGFB-D/PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
TLN1 0.004 0.098 -9999 0 -0.41 19 19
Rap1/GTP -0.031 0.094 -9999 0 -0.33 43 43
IQGAP1 0.018 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.014 0.074 -9999 0 -0.28 29 29
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.017 0.12 -9999 0 -0.41 42 42
PVR 0.009 0.055 -9999 0 -0.32 13 13
Necl-5(dimer) 0.009 0.055 -9999 0 -0.32 13 13
mol:GDP 0.011 0.16 -9999 0 -0.51 42 42
MLLT4 -0.006 0.11 -9999 0 -0.46 26 26
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
PI3K 0.001 0.13 -9999 0 -0.32 60 60
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 0.089 -9999 0 -0.32 42 42
PVRL1 0.014 0.035 -9999 0 -0.3 6 6
PVRL3 -0.02 0.13 -9999 0 -0.4 47 47
PVRL2 0.002 0.089 -9999 0 -0.52 15 15
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
CDH1 -0.049 0.17 -9999 0 -0.48 71 71
CLDN1 -0.11 0.21 -9999 0 -0.4 165 165
JAM-A/CLDN1 -0.066 0.16 -9999 0 -0.32 128 128
SRC -0.011 0.18 -9999 0 -0.61 42 42
ITGB3 0.002 0.076 -9999 0 -0.32 25 25
nectin-1(dimer)/I-afadin/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
FARP2 0.005 0.16 -9999 0 -0.51 44 44
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 -0.003 0.11 -9999 0 -0.34 44 44
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 44 44
alphaV/beta3 Integrin/Talin 0.006 0.13 -9999 0 -0.47 21 21
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 -0.003 0.1 -9999 0 -0.42 20 20
VAV2 0.006 0.16 -9999 0 -0.52 42 42
RAP1/GDP 0.018 0.13 -9999 0 -0.38 43 43
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.01 0.12 -9999 0 -0.35 54 54
nectin-3(dimer)/I-afadin/I-afadin -0.017 0.12 -9999 0 -0.41 42 42
Rac1/GTP -0.033 0.11 -9999 0 -0.39 42 42
PTPRM -0.01 0.11 -9999 0 -0.3 47 47
E-cadherin/beta catenin/alpha catenin -0.012 0.13 -9999 0 -0.46 11 11
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.018 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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 -0.037 0.17 -9999 0 -0.45 74 74
KLHL20 -0.015 0.1 -9999 0 -0.24 28 28
CYFIP2 -0.042 0.16 -9999 0 -0.46 65 65
Rac1/GDP 0.006 0.11 -9999 0 -0.31 16 16
ENAH -0.036 0.18 -9999 0 -0.45 76 76
AP1M1 0.017 0.023 -9999 0 -0.52 1 1
RAP1B 0.012 0.044 -9999 0 -0.32 8 8
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
CDC42/GTP -0.033 0.07 -9999 0 -0.3 10 10
ABI1/Sra1/Nap1 -0.042 0.054 -9999 0 -0.17 40 40
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.006 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 -0.35 3 3
regulation of calcium-dependent cell-cell adhesion -0.039 0.17 -9999 0 -0.46 74 74
CRK -0.025 0.16 -9999 0 -0.41 74 74
E-cadherin/gamma catenin/alpha catenin -0.011 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 0.074 -9999 0 -0.28 29 29
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 -0.029 0.055 -9999 0 -0.23 12 12
MLLT4 -0.006 0.11 -9999 0 -0.46 26 26
ARF6/GTP/NME1/Tiam1 0.023 0.053 -9999 0 -0.3 10 10
PI3K -0.036 0.07 -9999 0 -0.3 12 12
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 32 32
CDH1 -0.049 0.17 -9999 0 -0.48 71 71
RhoA/GDP 0.002 0.12 -9999 0 -0.38 15 15
actin cytoskeleton organization -0.009 0.075 -9999 0 -0.18 28 28
CDC42/GDP 0.007 0.11 -9999 0 -0.31 16 16
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.008 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 74 74
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 -0.38 15 15
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 -0.028 0.095 -9999 0 -0.2 100 100
NME1 0.012 0.039 -9999 0 -0.26 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 0.062 -9999 0 -0.26 10 10
WASF2 -0.021 0.031 -9999 0 -0.13 4 4
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 -0.036 0.12 -9999 0 -0.25 100 100
VAV2 -0.023 0.16 -9999 0 -0.4 74 74
RAP1/GDP 0.004 0.11 -9999 0 -0.36 9 9
adherens junction assembly -0.032 0.17 -9999 0 -0.43 75 75
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0.021 -9999 0 -0.26 3 3
PIP5K1C 0.014 0.042 -9999 0 -0.46 4 4
regulation of heterotypic cell-cell adhesion 0.006 0.11 -9999 0 -0.37 5 5
E-cadherin/beta catenin -0.045 0.11 -9999 0 -0.34 66 66
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 -0.35 3 3
Rac1/GTP -0.079 0.12 -9999 0 -0.38 36 36
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
Regulation of nuclear SMAD2/3 signaling

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
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 5 -0.37 156 161
AKT1 0.01 0.056 -10000 0 -0.37 9 9
GSC -0.2 0.49 -10000 0 -1.4 76 76
NKX2-5 -0.018 0.094 -10000 0 -0.26 67 67
muscle cell differentiation 0.065 0.16 0.47 45 -10000 0 45
SMAD2-3/SMAD4/SP1 -0.004 0.18 -10000 0 -0.43 53 53
SMAD4 -0.015 0.1 -10000 0 -0.38 21 21
CBFB 0.015 0.037 -10000 0 -0.39 4 4
SAP18 0.017 0.001 -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 -0.39 21 21
MYC -0.024 0.14 -10000 0 -0.44 48 48
CDKN2B -0.044 0.29 -10000 0 -1.4 23 23
AP1 -0.068 0.22 -10000 0 -0.59 63 63
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 0.006 0.12 -10000 0 -0.35 30 30
SP3 0.014 0.02 -10000 0 -10000 0 0
CREB1 0.017 0.023 -10000 0 -0.52 1 1
FOXH1 0 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.005 0.13 -10000 0 -0.36 45 45
GATA3 -0.098 0.22 -10000 0 -0.5 124 124
SKI/SIN3/HDAC complex/NCoR1 0.042 0.037 -10000 0 -10000 0 0
MEF2C/TIF2 -0.026 0.17 -10000 0 -0.52 37 37
endothelial cell migration 0.015 0.23 1.3 15 -10000 0 15
MAX 0.018 0.009 -10000 0 -10000 0 0
RBBP7 0.009 0.051 -10000 0 -0.3 13 13
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
RUNX2 0.013 0.05 -10000 0 -0.43 6 6
RUNX3 -0.063 0.18 -10000 0 -0.4 102 102
RUNX1 -0.028 0.14 -10000 0 -0.42 56 56
CTBP1 0.017 0.017 -10000 0 -0.26 2 2
NR3C1 -0.003 0.1 -10000 0 -0.51 21 21
VDR -0.003 0.1 -10000 0 -0.51 21 21
CDKN1A -0.027 0.26 -10000 0 -1.2 19 19
KAT2B 0.001 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.014 0.13 -10000 0 -0.31 58 58
DCP1A 0.017 0.023 -10000 0 -0.52 1 1
SKI 0.016 0.017 -10000 0 -0.26 2 2
SERPINE1 -0.017 0.23 -10000 0 -1.3 15 15
SMAD3/SMAD4/ATF2 0.007 0.1 -10000 0 -0.33 28 28
SMAD3/SMAD4/ATF3 -0.017 0.14 -10000 0 -0.35 55 55
SAP30 0.012 0.053 -10000 0 -0.48 6 6
Cbp/p300/PIAS3 0.047 0.053 -10000 0 -0.28 6 6
JUN -0.07 0.22 -10000 0 -0.58 63 63
SMAD3/SMAD4/IRF7 0.003 0.13 -10000 0 -0.4 29 29
TFE3 0.018 0.026 -10000 0 -10000 0 0
COL1A2 -0.099 0.36 -10000 0 -1 70 70
mesenchymal cell differentiation -0.004 0.11 0.36 30 -10000 0 30
DLX1 -0.009 0.082 -10000 0 -0.26 52 52
TCF3 0.012 0.05 -10000 0 -0.35 9 9
FOS -0.11 0.2 -10000 0 -0.38 171 171
SMAD3/SMAD4/Max 0.008 0.1 -10000 0 -0.33 28 28
Cbp/p300/SNIP1 0.035 0.046 -10000 0 -0.3 9 9
ZBTB17 0.019 0.012 -10000 0 -10000 0 0
LAMC1 0.005 0.14 -10000 0 -0.53 28 28
TGIF2/HDAC complex/SMAD3/SMAD4 0 0.12 -10000 0 -0.35 35 35
IRF7 0.008 0.076 -10000 0 -0.49 11 11
ESR1 -0.15 0.23 -10000 0 -0.45 188 188
HNF4A 0.016 0.033 -10000 0 -0.52 2 2
MEF2C -0.033 0.17 -10000 0 -0.55 38 38
SMAD2-3/SMAD4 -0.007 0.12 -10000 0 -0.35 37 37
Cbp/p300/Src-1 0.036 0.054 -10000 0 -0.28 12 12
IGHV3OR16-13 -0.017 0.039 -10000 0 -0.52 1 1
TGIF2/HDAC complex 0.007 0.071 -10000 0 -0.42 13 13
CREBBP 0.019 0.034 -10000 0 -0.51 2 2
SKIL 0.005 0.071 -10000 0 -0.34 19 19
HDAC1 0.016 0.023 -10000 0 -0.52 1 1
HDAC2 0.008 0.054 -10000 0 -0.29 15 15
SNIP1 0.014 0.04 -10000 0 -0.52 3 3
GCN5L2 0.018 0.044 -10000 0 -0.46 4 4
SMAD3/SMAD4/TFE3 0.015 0.12 -10000 0 -0.37 31 31
MSG1/HSC70 -0.02 0.098 -10000 0 -0.41 16 16
SMAD2 -0.002 0.05 -10000 0 -0.51 1 1
SMAD3 -0.003 0.1 -10000 0 -0.5 15 15
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.097 -10000 0 -0.32 19 19
SMAD2/SMAD2/SMAD4 -0.006 0.054 -10000 0 -0.3 10 10
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 -0.002 0.099 -10000 0 -0.37 32 32
SMAD2-3/SMAD4/SP1/MIZ-1 0.009 0.17 -10000 0 -0.43 44 44
IFNB1 0.006 0.13 -10000 0 -0.45 25 25
SMAD3/SMAD4/MEF2C -0.026 0.2 -10000 0 -0.56 44 44
CITED1 -0.029 0.11 -10000 0 -0.26 88 88
SMAD2-3/SMAD4/ARC105 0.01 0.11 -10000 0 -0.33 27 27
RBL1 0.01 0.049 -10000 0 -0.28 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.002 0.15 -10000 0 -0.47 33 33
RUNX1-3/PEBPB2 -0.043 0.14 -10000 0 -0.34 86 86
SMAD7 -0.041 0.22 -10000 0 -0.64 38 38
MYC/MIZ-1 -0.003 0.1 -10000 0 -0.37 34 34
SMAD3/SMAD4 0.046 0.14 0.29 46 -0.4 15 61
IL10 -0.046 0.18 -10000 0 -0.44 55 55
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 -0.046 0.18 -10000 0 -0.46 45 45
CDK4 0.019 0.03 -10000 0 -0.26 5 5
PIAS4 0.009 0.051 -10000 0 -0.44 6 6
ATF3 -0.021 0.13 -10000 0 -0.41 48 48
SMAD3/SMAD4/SP1 -0.008 0.17 -10000 0 -0.44 52 52
FOXG1 -0.007 0.083 -10000 0 -0.28 44 44
FOXO3 0.015 0.061 -10000 0 -0.4 8 8
FOXO1 0.008 0.079 -10000 0 -0.37 19 19
FOXO4 0.019 0.047 -10000 0 -0.37 5 5
heart looping -0.033 0.17 -10000 0 -0.54 38 38
CEBPB 0.004 0.073 -10000 0 -0.34 20 20
SMAD3/SMAD4/DLX1 -0.009 0.12 -10000 0 -0.37 26 26
MYOD1 -0.016 0.13 -10000 0 -0.46 37 37
SMAD3/SMAD4/HNF4 0.006 0.11 -10000 0 -0.34 28 28
SMAD3/SMAD4/GATA3 -0.061 0.2 -10000 0 -0.41 99 99
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.071 -10000 0 -0.34 19 19
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.037 0.17 -10000 0 -0.38 71 71
SMAD3/SMAD4/SP1-3 0.001 0.18 -10000 0 -0.49 45 45
MED15 0.018 0 -10000 0 -10000 0 0
SP1 -0.001 0.068 -10000 0 -0.4 3 3
SIN3B 0.017 0.012 -10000 0 -0.26 1 1
SIN3A 0.017 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.019 0.15 -10000 0 -0.38 46 46
ITGB5 -0.03 0.23 -10000 0 -0.65 55 55
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 -0.015 0.13 -10000 0 -0.32 58 58
E2F5 -0.014 0.12 -10000 0 -0.39 41 41
E2F4 0.017 0.017 -10000 0 -0.26 2 2
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.11 -10000 0 -0.32 18 18
SMAD2-3/SMAD4/FOXO1-3a-4 0.007 0.12 -10000 0 -0.35 40 40
TFDP1 0.011 0.043 -10000 0 -0.26 13 13
SMAD3/SMAD4/AP1 -0.063 0.23 -10000 0 -0.59 63 63
SMAD3/SMAD4/RUNX2 0.004 0.11 -10000 0 -0.36 30 30
TGIF2 0.007 0.071 -10000 0 -0.42 13 13
TGIF1 0.008 0.073 -10000 0 -0.52 10 10
ATF2 0.018 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.003 0.069 -9999 0 -0.29 26 26
Syndecan-3/Src/Cortactin -0.046 0.16 -9999 0 -0.52 34 34
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 -0.077 0.17 -9999 0 -0.35 136 136
Syndecan-3/EGFR -0.048 0.16 -9999 0 -0.39 66 66
AGRP 0.016 0.029 -9999 0 -0.35 3 3
NCSTN 0.017 0.023 -9999 0 -0.52 1 1
PSENEN 0.017 0.012 -9999 0 -0.26 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0.096 -9999 0 -0.51 18 18
APH1A 0.003 0.068 -9999 0 -0.29 25 25
NCAN 0.007 0.054 -9999 0 -0.26 21 21
long-term memory -0.003 0.13 -9999 0 -0.55 25 25
Syndecan-3/IL8 -0.046 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 0.009 0.063 -9999 0 -0.4 11 11
limb bud formation -0.032 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 -0.38 157 157
FGFR/FGF/Syndecan-3 -0.032 0.12 -9999 0 -0.6 24 24
neuron projection morphogenesis -0.045 0.16 -9999 0 -0.5 36 36
Syndecan-3/AgRP -0.003 0.13 -9999 0 -0.56 25 25
Syndecan-3/AgRP/MC4R 0.005 0.13 -9999 0 -0.56 24 24
Fyn/Cortactin 0.01 0.067 -9999 0 -0.38 9 9
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 -0.045 0.15 -9999 0 -0.41 58 58
IL8 -0.073 0.17 -9999 0 -0.34 135 135
Syndecan-3/Fyn/Cortactin -0.003 0.13 -9999 0 -0.56 25 25
Syndecan-3/CASK -0.031 0.12 -9999 0 -0.58 24 24
alpha-MSH/MC4R 0.012 0.057 -9999 0 -0.37 5 5
Gamma Secretase 0.032 0.07 -9999 0 -0.36 1 1
PDGFR-alpha 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
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 -0.005 0.097 -9999 0 -0.37 33 33
AP1 -0.18 0.34 -9999 0 -0.91 83 83
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 -0.018 0.12 -9999 0 -0.4 48 48
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 -0.35 3 3
CAV1 0 0.081 -9999 0 -0.32 28 28
SHC/Grb2/SOS1 0.02 0.077 -9999 0 -0.26 34 34
PDGF/PDGFRA/Shf -0.009 0.1 -9999 0 -0.37 34 34
FOS -0.17 0.34 -9999 0 -0.89 83 83
JUN -0.051 0.11 -9999 0 -0.41 43 43
oligodendrocyte development -0.018 0.12 -9999 0 -0.39 48 48
GRB2 0.016 0.024 -9999 0 -0.26 4 4
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
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 0.009 0.05 -9999 0 -0.28 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 -0.015 0.12 -9999 0 -0.4 36 36
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
ELK1 -0.018 0.1 -9999 0 -0.36 36 36
PIK3CA 0.016 0.029 -9999 0 -0.35 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 34 34
Regulation of Telomerase

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
Telomerase catalytic core complex -0.1 0.22 -10000 0 -0.56 71 71
RAD9A 0.018 0 -10000 0 -10000 0 0
AP1 -0.1 0.18 -10000 0 -0.42 107 107
IFNAR2 0.013 0.037 -10000 0 -0.31 6 6
AKT1 -0.053 0.12 -10000 0 -0.26 70 70
ER alpha/Oestrogen -0.12 0.17 -10000 0 -0.33 202 202
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 -0.35 3 3
SMG6 0.017 0.023 -10000 0 -0.52 1 1
SP3/HDAC2 0.018 0.041 -10000 0 -0.25 6 6
TERT/c-Abl -0.089 0.21 -10000 0 -0.54 62 62
SAP18 0.017 0.001 -10000 0 -10000 0 0
MRN complex 0.029 0.047 -10000 0 -0.3 10 10
WT1 -0.1 0.19 -10000 0 -0.35 170 170
WRN 0.012 0.05 -10000 0 -0.35 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 -0.53 42 42
Mad/Max 0.021 0.024 -10000 0 -10000 0 0
TERT -0.1 0.23 -10000 0 -0.6 62 62
CCND1 -0.2 0.43 -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 -0.073 0.19 -10000 0 -0.44 84 84
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 -0.26 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 -0.077 0.16 -10000 0 -0.37 103 103
PARP2 0.017 0.012 -10000 0 -0.26 1 1
BLM -0.021 0.13 -10000 0 -0.41 48 48
Telomerase 0.025 0.06 -10000 0 -0.36 3 3
IRF1 -0.018 0.12 -10000 0 -0.38 41 41
ESR1 -0.16 0.24 -10000 0 -0.45 202 202
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 -0.46 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.052 -10000 0 -0.47 1 1
HDAC1 0.016 0.023 -10000 0 -0.52 1 1
HDAC2 0.008 0.056 -10000 0 -0.3 15 15
ATM 0.001 0.017 0.21 3 -10000 0 3
SMAD3 0.015 0.06 -10000 0 -0.36 11 11
ABL1 0.018 0 -10000 0 -10000 0 0
MXD1 0.013 0.032 -10000 0 -0.26 7 7
MRE11A 0.018 0 -10000 0 -10000 0 0
HUS1 0.016 0.021 -10000 0 -0.26 3 3
RPS6KB1 0.008 0.05 -10000 0 -0.26 18 18
TERT/NF kappa B1/14-3-3 -0.091 0.22 -10000 0 -0.56 70 70
NR2F2 -0.05 0.17 -10000 0 -0.45 78 78
MAPK3 0.019 0.042 -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 -0.078 0.17 -10000 0 -0.35 136 136
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.15 0.2 -10000 0 -0.42 172 172
MYC -0.027 0.14 -10000 0 -0.43 51 51
IL2 0.01 0.052 -10000 0 -0.34 10 10
KU 0.026 0.008 -10000 0 -10000 0 0
RAD50 0.01 0.066 -10000 0 -0.52 8 8
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 -0.56 52 52
SP1/HDAC2 0.019 0.048 -10000 0 -0.34 5 5
PINX1 0.016 0.021 -10000 0 -0.26 3 3
Telomerase/EST1A -0.099 0.17 -10000 0 -0.53 42 42
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 -0.093 0.18 -10000 0 -0.33 161 161
Telomerase/PinX1 -0.099 0.17 -10000 0 -0.53 42 42
Telomerase/AKT1/mTOR/p70S6K -0.008 0.092 -10000 0 -0.47 5 5
SIN3B 0.017 0.012 -10000 0 -0.26 1 1
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
Telomerase/EST1B -0.1 0.18 -10000 0 -0.53 45 45
response to DNA damage stimulus 0.004 0.005 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.044 0.049 -10000 0 -0.26 12 12
TRF2/WRN 0.02 0.043 -10000 0 -0.35 6 6
Telomerase/hnRNP C1/C2 -0.099 0.17 -10000 0 -0.53 42 42
E2F1 0.005 0.071 -10000 0 -0.38 16 16
ZNFX1 0.007 0.071 -10000 0 -0.42 13 13
PIF1 0.015 0.027 -10000 0 -0.26 5 5
NCL 0.018 0 -10000 0 -10000 0 0
DKC1 0.016 0.021 -10000 0 -0.26 3 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.019 0.061 -9999 0 -0.27 21 21
RGS9BP -0.071 0.18 -9999 0 -0.41 110 110
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 -0.31 3 3
GNAT2 -0.004 0.1 -9999 0 -0.49 23 23
RGS9-1/Gbeta5/R9AP -0.055 0.15 -9999 0 -0.34 95 95
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 0.087 -9999 0 -0.3 39 39
Cone Metarhodopsin II/X-Arrestin 0.013 0.008 -9999 0 -0.17 1 1
mol:Ca2+ -0.01 0.084 -9999 0 -0.3 27 27
Cone PDE6 -0.042 0.14 -9999 0 -0.29 104 104
Cone Metarhodopsin II 0.01 0.019 -9999 0 -0.29 2 2
Na + (4 Units) -0.005 0.086 -9999 0 -0.29 27 27
GNAT2/GDP -0.048 0.14 -9999 0 -0.29 111 111
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 -0.42 5 5
GNB3/GNGT2 0.025 0.026 -9999 0 -0.37 2 2
GNB3 0.017 0.012 -9999 0 -0.26 1 1
GNAT2/GTP -0.003 0.076 -9999 0 -0.35 23 23
CNGA3 -0.028 0.12 -9999 0 -0.32 72 72
ARR3 0.017 0.012 -9999 0 -0.26 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.016 0.09 -9999 0 -0.33 24 24
mol:Pi -0.055 0.15 -9999 0 -0.33 95 95
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 -0.42 5 5
RGS9 -0.032 0.13 -9999 0 -0.31 80 80
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 0.094 -9999 0 -0.45 21 21
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.018 0.072 0.24 15 -0.23 29 44
DAPP1 -0.037 0.14 -10000 0 -0.42 42 42
Src family/SYK family/BLNK-LAT/BTK-ITK -0.049 0.22 -10000 0 -0.54 61 61
mol:DAG 0.001 0.1 0.2 8 -0.23 43 51
HRAS 0.012 0.051 -10000 0 -0.41 7 7
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
ARF5/GDP -0.016 0.11 -10000 0 -0.28 39 39
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 0.069 0.22 15 -0.25 26 41
ARF1/GTP -0.006 0.067 0.22 15 -0.24 26 41
RHOA 0.005 0.08 -10000 0 -0.52 12 12
YES1 0.007 0.07 -10000 0 -0.43 12 12
RAP1A/GTP 0.014 0.07 0.22 15 -0.25 26 41
ADAP1 -0.006 0.066 0.21 15 -0.24 26 41
ARAP3 -0.006 0.068 0.22 15 -0.24 26 41
INPPL1 0.012 0.055 -10000 0 -0.45 7 7
PREX1 -0.089 0.2 -10000 0 -0.44 124 124
ARHGEF6 -0.019 0.13 -10000 0 -0.42 45 45
ARHGEF7 0.016 0.021 -10000 0 -0.26 3 3
ARF1 0.017 0.023 -10000 0 -0.52 1 1
NRAS 0.006 0.073 -10000 0 -0.4 15 15
FYN 0.009 0.063 -10000 0 -0.4 11 11
ARF6 0.016 0.033 -10000 0 -0.52 2 2
FGR 0.017 0.017 -10000 0 -0.26 2 2
mol:Ca2+ 0.006 0.054 -10000 0 -0.15 1 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
ZAP70 0.005 0.061 -10000 0 -0.27 24 24
mol:IP3 0.004 0.073 -10000 0 -0.18 25 25
LYN 0.014 0.031 -10000 0 -0.26 7 7
ARF1/GDP -0.015 0.1 -10000 0 -0.3 34 34
RhoA/GDP 0.002 0.1 0.23 6 -0.34 26 32
PDK1/Src/Hsp90 0.031 0.039 -10000 0 -0.3 6 6
BLNK -0.013 0.12 -10000 0 -0.51 31 31
actin cytoskeleton reorganization -0.007 0.12 0.23 6 -0.41 24 30
SRC 0.015 0.035 -10000 0 -0.43 3 3
PLEKHA2 0.014 0.041 -10000 0 -0.31 7 7
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 0.07 0.24 14 -0.24 21 35
RhoA/GTP 0.015 0.083 0.22 14 -0.27 31 45
Src family/SYK family/BLNK-LAT -0.03 0.17 -10000 0 -0.46 46 46
BLK -0.018 0.1 -10000 0 -0.29 61 61
PDPK1 0.016 0.026 -10000 0 -0.39 2 2
CYTH1 -0.006 0.066 0.21 15 -0.24 26 41
HCK -0.005 0.11 -10000 0 -0.47 25 25
CYTH3 -0.006 0.066 0.21 15 -0.24 26 41
CYTH2 -0.006 0.066 0.21 15 -0.24 26 41
KRAS 0.008 0.069 -10000 0 -0.45 11 11
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.025 0.052 -10000 0 -0.22 5 5
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 -0.3 41 41
SOS1 0.017 0.023 -10000 0 -0.52 1 1
SYK -0.022 0.14 -10000 0 -0.48 42 42
ARF6/GDP 0.005 0.085 0.24 6 -0.3 20 26
mol:PI-3-4-5-P3 -0.004 0.075 0.25 19 -0.25 26 45
ARAP3/RAP1A/GTP 0.014 0.071 0.22 15 -0.25 26 41
VAV1 -0.015 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 0.021 0.07 -10000 0 -0.25 26 26
PLEKHA1 0.012 0.052 -10000 0 -0.32 12 12
Rac1/GDP -0.014 0.1 -10000 0 -0.32 28 28
LAT 0.002 0.069 -10000 0 -0.28 29 29
Rac1/GTP -0.03 0.14 -10000 0 -0.4 42 42
ITK -0.008 0.1 0.22 14 -0.24 62 76
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.008 0.13 0.22 8 -0.32 47 55
LCK -0.073 0.18 -10000 0 -0.4 115 115
BTK 0.006 0.092 0.22 14 -0.27 38 52
Ceramide signaling 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
SPHK2 0.01 0.072 -10000 0 -0.37 17 17
MAP4K4 -0.002 0.11 -10000 0 -0.36 20 20
BAG4 0.002 0.071 -10000 0 -0.29 28 28
PKC zeta/ceramide -0.025 0.04 0.13 8 -0.12 1 9
NFKBIA 0.014 0.042 -10000 0 -0.46 4 4
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
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 -0.35 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 0.094 0.15 6 -0.28 56 62
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 4 -0.18 1 5
EGF -0.14 0.23 -10000 0 -0.42 193 193
mol:ceramide -0.027 0.044 0.14 11 -0.12 1 12
MADD 0.018 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.027 0.13 -10000 0 -0.38 54 54
ASAH1 -0.037 0.15 -10000 0 -0.42 65 65
negative regulation of cell cycle -0.028 0.069 0.15 8 -0.31 20 28
cell proliferation -0.036 0.097 -10000 0 -0.23 84 84
BID -0.013 0.12 -10000 0 -0.52 19 19
MAP3K1 -0.042 0.085 0.15 7 -0.24 56 63
EIF2A -0.013 0.06 -10000 0 -0.25 17 17
TRADD 0.016 0.026 -10000 0 -0.39 2 2
CRADD 0.009 0.067 -10000 0 -0.49 9 9
MAPK3 0.001 0.039 -10000 0 -0.19 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.04 -10000 0 -0.19 1 1
Cathepsin D/ceramide -0.022 0.056 0.14 8 -0.23 12 20
FADD -0.006 0.11 -10000 0 -0.37 21 21
KSR1 -0.018 0.042 0.15 8 -0.2 1 9
MAPK8 -0.031 0.069 0.14 6 -0.19 54 60
PRKRA -0.018 0.041 0.14 11 -0.12 2 13
PDGFA -0.001 0.094 -10000 0 -0.44 22 22
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
IGF1 -0.1 0.21 -10000 0 -0.42 146 146
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.027 0.044 0.14 11 -0.12 1 12
CTSD 0.003 0.074 -10000 0 -0.33 23 23
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 -0.036 0.11 -10000 0 -0.25 84 84
PRKCD 0.014 0.042 -10000 0 -0.46 4 4
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.027 0.13 -10000 0 -0.38 54 54
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 -0.006 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 0.072 -10000 0 -0.37 17 17
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 0.066 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 0.055 -10000 0 -0.37 5 5
EIF2AK2 -0.019 0.062 0.15 8 -0.26 18 26
TNF-alpha/TNFR1A/FAN 0.016 0.074 -10000 0 -0.31 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.062 -10000 0 -0.26 7 7
MAP2K2 -0.004 0.043 -10000 0 -0.27 3 3
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 0.21 133 -10000 0 133
NF kappa B1/RelA/I kappa B alpha 0.03 0.055 -10000 0 -0.25 18 18
AIFM1 0.027 0.066 0.16 76 -10000 0 76
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.023 0.029 -9999 0 -0.37 1 1
VLDLR -0.059 0.17 -9999 0 -0.4 98 98
CRKL 0.014 0.047 -9999 0 -0.52 4 4
LRPAP1 0.016 0.026 -9999 0 -0.39 2 2
FYN 0.009 0.063 -9999 0 -0.4 11 11
ITGA3 -0.003 0.096 -9999 0 -0.42 25 25
RELN/VLDLR/Fyn -0.021 0.12 -9999 0 -0.32 61 61
MAPK8IP1/MKK7/MAP3K11/JNK1 0.038 0.061 -9999 0 -0.26 18 18
AKT1 -0.01 0.11 -9999 0 -0.43 14 14
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 41 41
LRPAP1/LRP8 -0.027 0.11 -9999 0 -0.37 36 36
RELN/LRP8/DAB1/Fyn -0.005 0.093 -9999 0 -0.26 47 47
DAB1/alpha3/beta1 Integrin -0.066 0.1 -9999 0 -0.36 24 24
long-term memory -0.002 0.1 -9999 0 -0.37 5 5
DAB1/LIS1 -0.027 0.12 -9999 0 -0.38 14 14
DAB1/CRLK/C3G -0.058 0.096 -9999 0 -0.37 15 15
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
DAB1/NCK2 -0.028 0.12 -9999 0 -0.36 15 15
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 -0.26 1 1
CDK5R1 0.014 0.031 -9999 0 -0.26 7 7
RELN 0.009 0.059 -9999 0 -0.38 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
RELN/LRP8/Fyn -0.019 0.11 -9999 0 -0.31 47 47
GRIN2A/RELN/LRP8/DAB1/Fyn 0.004 0.095 -9999 0 -0.25 46 46
MAPK8 0.015 0.04 -9999 0 -0.52 3 3
RELN/VLDLR/DAB1 -0.013 0.1 -9999 0 -0.28 57 57
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
MAP1B -0.056 0.14 -9999 0 -0.29 109 109
RELN/LRP8 -0.014 0.1 -9999 0 -0.31 42 42
GRIN2B/RELN/LRP8/DAB1/Fyn -0.009 0.11 -9999 0 -0.26 64 64
PI3K 0.006 0.082 -9999 0 -0.37 21 21
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.01 0.077 -9999 0 -0.39 16 16
RAP1A -0.019 0.12 -9999 0 -0.36 16 16
PAFAH1B1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8IP1 0.011 0.048 -9999 0 -0.31 11 11
CRLK/C3G 0.023 0.034 -9999 0 -0.37 4 4
GRIN2B -0.007 0.11 -9999 0 -0.43 29 29
NCK2 0.015 0.027 -9999 0 -0.26 5 5
neuron differentiation 0.012 0.077 -9999 0 -0.3 4 4
neuron adhesion -0.015 0.12 -9999 0 -0.44 8 8
LRP8 -0.057 0.16 -9999 0 -0.34 109 109
GSK3B -0.003 0.1 -9999 0 -0.42 13 13
RELN/VLDLR/DAB1/Fyn -0.007 0.1 -9999 0 -0.27 61 61
MAP3K11 0.015 0.035 -9999 0 -0.43 3 3
RELN/VLDLR/DAB1/P13K -0.015 0.11 -9999 0 -0.26 72 72
CDK5 0.016 0.026 -9999 0 -0.39 2 2
MAPT -0.09 0.2 -9999 0 -0.48 107 107
neuron migration -0.011 0.12 -9999 0 -0.36 22 22
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.012 0.078 -9999 0 -0.31 4 4
RELN/VLDLR -0.043 0.13 -9999 0 -0.28 111 111
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 0.047 -9999 0 -0.26 16 16
ELF1 -0.013 0.12 -9999 0 -0.37 45 45
CCNA2 -0.024 0.13 -9999 0 -0.4 53 53
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
JAK3 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.11 -9999 0 -0.42 32 32
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 -0.45 25 25
SHC1 0.018 0.023 -9999 0 -0.52 1 1
SP1 0.016 0.069 -9999 0 -0.36 15 15
IL2RA -0.036 0.21 -9999 0 -0.68 44 44
IL2RB -0.016 0.12 -9999 0 -0.44 40 40
SOS1 0.017 0.023 -9999 0 -0.52 1 1
IL2RG -0.002 0.079 -9999 0 -0.29 35 35
G1/S transition of mitotic cell cycle -0.024 0.2 -9999 0 -0.56 47 47
PTPN11 0.018 0.023 -9999 0 -0.52 1 1
CCND2 0.011 0.14 -9999 0 -0.77 15 15
LCK -0.072 0.18 -9999 0 -0.4 115 115
GRB2 0.016 0.024 -9999 0 -0.26 4 4
IL2 0.012 0.051 -9999 0 -0.34 10 10
CDK6 -0.02 0.11 -9999 0 -0.3 63 63
CCND3 0.021 0.13 -9999 0 -0.46 13 13
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.048 0.1 -9999 0 -0.26 86 86
TC10/GTP -0.021 0.061 -9999 0 -0.48 1 1
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 -0.37 247 247
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 0.035 0.08 -9999 0 -0.49 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 -0.003 0.098 -9999 0 -0.43 24 24
SORBS1 -0.032 0.14 -9999 0 -0.39 64 64
CRK 0.016 0.033 -9999 0 -0.52 2 2
PTPN1 0.023 0.076 -9999 0 -0.48 4 4
CAV1 -0.011 0.11 -9999 0 -0.27 68 68
CBL/APS/CAP/Crk-II/C3G 0.015 0.077 -9999 0 -0.25 34 34
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 -0.041 0.095 -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 0.006 0.074 -9999 0 -0.43 14 14
CBL 0.017 0.012 -9999 0 -0.26 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 32 32
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.082 0.11 -9999 0 -0.33 51 51
HRAS/GTP -0.028 0.073 -9999 0 -0.41 4 4
Insulin Receptor 0.015 0.038 -9999 0 -0.38 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.014 0.1 -9999 0 -0.26 62 62
PRKCI -0.032 0.1 -9999 0 -0.52 20 20
Insulin Receptor/Insulin/GRB14/PDK1 -0.099 0.12 -9999 0 -0.37 48 48
SHC1 0.017 0.023 -9999 0 -0.52 1 1
negative regulation of MAPKKK cascade 0.009 0.12 -9999 0 -0.67 12 12
PI3K -0.005 0.11 -9999 0 -0.26 80 80
NCK2 0.015 0.027 -9999 0 -0.26 5 5
RHOQ 0.014 0.042 -9999 0 -0.46 4 4
mol:H2O2 -0.002 0.008 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.037 -9999 0 -0.29 7 7
AKT2 -0.066 0.13 -9999 0 -0.36 42 42
PRKCZ -0.026 0.066 -9999 0 -0.53 7 7
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.002 0.093 -9999 0 -0.25 63 63
F2RL2 -0.072 0.19 -9999 0 -0.44 103 103
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 0.019 0.04 -9999 0 -0.31 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.05 0.036 -9999 0 -0.38 2 2
RAPGEF1 0.018 0 -9999 0 -10000 0 0
RASA1 0.004 0.079 -9999 0 -0.42 16 16
NCK1 0.011 0.046 -9999 0 -0.28 12 12
CBL/APS/CAP/Crk-II 0.005 0.082 -9999 0 -0.28 34 34
TC10/GDP 0.011 0.03 -9999 0 -0.33 4 4
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 -0.68 12 12
INS 0.017 0.025 -9999 0 -0.52 1 1
mol:PI-3-4-P2 -0.013 0.095 -9999 0 -0.27 62 62
GRB2 0.016 0.024 -9999 0 -0.26 4 4
EIF4EBP1 -0.068 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 -0.35 3 3
TC10/GTP/CIP4 0.019 0.04 -9999 0 -0.31 7 7
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 -0.36 3 3
Par3/Par6 -0.017 0.12 -9999 0 -0.27 84 84
E-cadherin signaling in keratinocytes

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
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 -0.018 0.11 -10000 0 -0.34 20 20
FMN1 -0.008 0.1 -10000 0 -0.24 78 78
mol:IP3 0.006 0.081 -10000 0 -0.25 23 23
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 0.093 -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 -0.35 3 3
mol:PI-4-5-P2 0 0.1 -10000 0 -0.33 10 10
VASP -0.007 0.11 -10000 0 -0.36 14 14
ZYX -0.006 0.11 -10000 0 -0.36 13 13
JUB -0.023 0.13 -10000 0 -0.39 21 21
EGFR(dimer) -0.042 0.13 -10000 0 -0.36 31 31
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 -0.35 3 3
PI3K 0.004 0.093 -10000 0 -0.26 28 28
FYN 0.016 0.084 -10000 0 -0.3 14 14
mol:Ca2+ 0.006 0.08 -10000 0 -0.24 23 23
JUP 0.012 0.056 -10000 0 -0.42 8 8
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
mol:DAG 0.006 0.081 -10000 0 -0.25 23 23
CDH1 -0.049 0.17 -10000 0 -0.48 71 71
RhoA/GDP -0.024 0.12 -10000 0 -0.35 27 27
establishment of polarity of embryonic epithelium -0.007 0.11 -10000 0 -0.36 14 14
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 -0.077 0.17 -10000 0 -0.35 136 136
CASR 0.013 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 -0.32 7 7
actin cable formation -0.007 0.11 -10000 0 -0.36 14 14
apoptosis -0.006 0.089 0.26 26 -10000 0 26
CTNNA1 0.017 0.024 -10000 0 -0.52 1 1
mol:GDP -0.029 0.12 -10000 0 -0.36 21 21
PIP5K1A -0.001 0.1 -10000 0 -0.34 10 10
PLCG1 0.006 0.082 -10000 0 -0.25 23 23
Rac1/GTP -0.033 0.12 -10000 0 -0.33 30 30
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.01 0.079 -9999 0 -0.26 31 31
STMN1 0.001 0.089 -9999 0 -0.38 22 22
Aurora B/RasGAP/Survivin -0.012 0.12 -9999 0 -0.34 53 53
Chromosomal passenger complex/Cul3 protein complex -0.054 0.14 -9999 0 -0.34 67 67
BIRC5 -0.039 0.16 -9999 0 -0.43 67 67
DES -0.027 0.13 -9999 0 -0.68 16 16
Aurora C/Aurora B/INCENP 0.014 0.064 -9999 0 -0.29 15 15
Aurora B/TACC1 -0.004 0.086 -9999 0 -0.32 30 30
Aurora B/PP2A 0.019 0.043 -9999 0 -0.39 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.011 0.034 -9999 0 -0.21 9 9
mitotic metaphase/anaphase transition 0 0.005 -9999 0 -10000 0 0
NDC80 -0.015 0.12 -9999 0 -0.4 40 40
Cul3 protein complex -0.049 0.14 -9999 0 -0.33 93 93
KIF2C -0.062 0.24 -9999 0 -0.66 59 59
PEBP1 0.013 0.047 -9999 0 -0.53 4 4
KIF20A -0.027 0.14 -9999 0 -0.47 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 0.053 -9999 0 -0.27 17 17
SMC2 0.003 0.079 -9999 0 -0.38 20 20
SMC4 0.014 0.041 -9999 0 -0.35 6 6
NSUN2/NPM1/Nucleolin 0.015 0.082 -9999 0 -0.87 3 3
PSMA3 0.017 0.012 -9999 0 -0.26 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 0.054 -9999 0 -0.27 18 18
CDCA8 -0.018 0.12 -9999 0 -0.41 44 44
cytokinesis -0.05 0.26 -9999 0 -0.74 50 50
Aurora B/Septin1 -0.037 0.24 -9999 0 -0.71 45 45
AURKA -0.012 0.11 -9999 0 -0.42 36 36
INCENP -0.001 0.086 -9999 0 -0.38 23 23
KLHL13 -0.096 0.2 -9999 0 -0.39 147 147
BUB1 -0.051 0.17 -9999 0 -0.44 79 79
hSgo1/Aurora B/Survivin -0.016 0.14 -9999 0 -0.39 52 52
EVI5 0.013 0.047 -9999 0 -0.52 4 4
RhoA/GTP -0.047 0.25 -9999 0 -0.69 54 54
SGOL1 -0.01 0.11 -9999 0 -0.38 37 37
CENPA -0.042 0.22 -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 0.011 0.041 -9999 0 -0.26 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 -0.007 0.11 -9999 0 -0.46 28 28
NPM1 0.012 0.052 -9999 0 -0.6 3 3
RASA1 0.004 0.079 -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 -0.054 0.28 -9999 0 -0.71 60 60
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
NSUN2 0.012 0.054 -9999 0 -0.6 3 3
MYLK 0.003 0.068 -9999 0 -0.33 19 19
KIF23 -0.025 0.14 -9999 0 -0.45 48 48
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 0.012 0.052 -9999 0 -0.6 3 3
Chromosomal passenger complex -0.047 0.22 -9999 0 -0.59 56 56
Chromosomal passenger complex/EVI5 -0.014 0.15 -9999 0 -0.37 62 62
TACC1 -0.02 0.13 -9999 0 -0.41 47 47
PPP2R5D 0.016 0.021 -9999 0 -0.26 3 3
CUL3 0.01 0.061 -9999 0 -0.43 9 9
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
p75(NTR)-mediated 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
Sortilin/TRAF6 0.019 0.05 -10000 0 -0.37 8 8
Necdin/E2F1 -0.026 0.13 -10000 0 -0.38 61 61
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 0.076 -10000 0 -0.29 12 12
NT-4/5 (dimer)/p75(NTR) 0.004 0.046 -10000 0 -0.2 23 23
IKBKB 0.011 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 0.092 -10000 0 -0.26 64 64
MGDIs/NGR/p75(NTR)/LINGO1 -0.004 0.087 -10000 0 -0.31 22 22
FURIN 0.003 0.077 -10000 0 -0.36 20 20
proBDNF (dimer)/p75(NTR)/Sortilin 0.003 0.076 -10000 0 -0.33 11 11
LINGO1 -0.02 0.097 -10000 0 -0.26 70 70
Sortilin/TRAF6/NRIF -0.018 0.057 -10000 0 -0.34 5 5
proBDNF (dimer) -0.016 0.092 -10000 0 -0.26 64 64
NTRK1 0.01 0.054 -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 -0.41 11 11
IRAK1 0.015 0.029 -10000 0 -0.26 6 6
SHC1 0.013 0.041 -10000 0 -0.31 4 4
ARHGDIA 0.016 0.029 -10000 0 -0.35 3 3
RhoA/GTP 0.004 0.058 -10000 0 -0.38 12 12
Gamma Secretase 0.032 0.07 -10000 0 -0.36 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.002 0.094 -10000 0 -0.3 42 42
MAGEH1 -0.018 0.13 -10000 0 -0.52 35 35
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.012 0.11 -10000 0 -0.3 64 64
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 -0.028 0.14 -10000 0 -0.42 55 55
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 0.058 -10000 0 -0.27 16 16
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.006 0.055 0.15 3 -0.26 10 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.026 0.041 -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 -0.015 0.089 -10000 0 -0.31 30 30
PSENEN 0.017 0.012 -10000 0 -0.26 1 1
mol:ceramide 0.014 0.056 -10000 0 -0.29 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.05 -10000 0 -0.26 1 1
p75(NTR)/beta APP -0.016 0.11 -10000 0 -0.37 38 38
BEX1 -0.04 0.12 -10000 0 -0.26 108 108
mol:GDP 0.002 0.038 -10000 0 -0.32 3 3
NGF (dimer) -0.038 0.13 -10000 0 -0.29 99 99
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.008 0.082 -10000 0 -0.28 23 23
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
RAC1/GTP 0.014 0.033 -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 -0.015 0.089 -10000 0 -0.31 30 30
RHOB -0.04 0.17 -10000 0 -0.52 57 57
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 0.1 -10000 0 -0.28 67 67
TP53 -0.001 0.098 -10000 0 -0.28 38 38
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 -0.35 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 0.096 -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 0.096 -10000 0 -0.51 18 18
APH1A 0.003 0.068 -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 0.089 -10000 0 -0.41 12 12
MAPK8 0.014 0.08 -10000 0 -0.29 8 8
MAPK9 0.005 0.097 -10000 0 -0.31 20 20
APAF1 0.012 0.051 -10000 0 -0.41 7 7
NTF3 -0.021 0.1 -10000 0 -0.28 67 67
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.044 0.17 -10000 0 -0.49 64 64
RAC1/GDP 0.013 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.028 0.11 -10000 0 -0.25 95 95
p75 CTF/Sortilin/TRAF6/NRIF 0.036 0.048 -10000 0 -0.27 10 10
RhoA-B-C/GTP -0.015 0.088 -10000 0 -0.31 30 30
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 -0.035 0.14 -10000 0 -0.34 78 78
proBDNF (dimer)/p75 ECD 0.002 0.065 -10000 0 -0.35 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BIRC2 0.016 0.021 -10000 0 -0.26 3 3
neuron projection morphogenesis -0.032 0.11 0.2 2 -0.34 35 37
BAD 0.008 0.091 -10000 0 -0.3 16 16
RIPK2 0.013 0.041 -10000 0 -0.29 9 9
NGFR 0.004 0.066 -10000 0 -0.29 23 23
CYCS 0.009 0.074 -10000 0 -0.25 34 34
ADAM17 0.016 0.024 -10000 0 -0.26 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 -0.3 15 15
BDNF (dimer)/p75(NTR) -0.006 0.076 -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 0.051 -10000 0 -0.28 10 10
NDNL2 0.018 0 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
PRKCI 0.001 0.088 -10000 0 -0.44 19 19
NGF (dimer)/p75(NTR) 0.004 0.046 -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 -0.28 18 18
SQSTM1 0.012 0.053 -10000 0 -0.48 6 6
NGFRAP1 -0.056 0.18 -10000 0 -0.51 73 73
CASP3 0.01 0.087 -10000 0 -0.28 14 14
E2F1 0.006 0.071 -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 0.038 -10000 0 -0.22 12 12
MMP7 -0.094 0.21 -10000 0 -0.44 128 128
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.028 0.054 -10000 0 -0.25 13 13
MMP3 -0.13 0.22 -10000 0 -0.43 173 173
APAF-1/Caspase 9 -0.046 0.077 -10000 0 -0.31 10 10
IFN-gamma pathway

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.013 0.11 -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 -0.012 0.15 -10000 0 -0.47 27 27
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.014 0.063 -10000 0 -0.35 11 11
antigen processing and presentation of peptide antigen via MHC class I -0.056 0.1 -10000 0 -0.31 54 54
CaM/Ca2+ -0.008 0.098 -10000 0 -0.32 16 16
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
STAT1 (dimer)/SHP2 -0.028 0.13 -10000 0 -0.37 35 35
AKT1 -0.012 0.11 -10000 0 -0.36 19 19
MAP2K1 -0.025 0.12 -10000 0 -0.35 33 33
MAP3K11 -0.012 0.099 -10000 0 -0.33 18 18
IFNGR1 0.01 0.04 -10000 0 -0.31 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.029 0.14 -10000 0 -0.39 44 44
Rap1/GTP -0.031 0.07 -10000 0 -0.41 7 7
CRKL/C3G 0.023 0.034 -10000 0 -0.37 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.01 0.11 -10000 0 -0.31 23 23
CEBPB -0.011 0.16 -10000 0 -0.45 33 33
STAT3 0.015 0.04 -10000 0 -0.52 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0 0.11 -10000 0 -0.67 4 4
STAT1 -0.03 0.13 -10000 0 -0.36 37 37
CALM1 0.018 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.087 0.17 -10000 0 -0.33 161 161
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
STAT1 (dimer)/PIAS1 -0.02 0.12 -10000 0 -0.4 25 25
CEBPB/PTGES2/Cbp/p300 -0.044 0.11 -10000 0 -0.4 28 28
mol:Ca2+ -0.015 0.1 -10000 0 -0.26 57 57
MAPK3 -0.017 0.14 -10000 0 -0.44 21 21
STAT1 (dimer) -0.071 0.15 -10000 0 -0.44 54 54
MAPK1 -0.018 0.14 -10000 0 -0.51 15 15
JAK2 0.006 0.057 -10000 0 -0.34 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
JAK1 0.008 0.059 -10000 0 -0.54 6 6
CAMK2D -0.004 0.098 -10000 0 -0.4 28 28
DAPK1 -0.001 0.14 -10000 0 -0.47 24 24
SMAD7 0.004 0.073 -10000 0 -0.19 17 17
CBL/CRKL/C3G 0.005 0.096 -10000 0 -0.36 10 10
PI3K -0.022 0.11 -10000 0 -0.36 21 21
IFNG -0.087 0.17 -10000 0 -0.33 161 161
apoptosis -0.008 0.12 0.27 2 -0.35 28 30
CAMK2G 0.017 0.017 -10000 0 -0.26 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 -0.079 0.18 -10000 0 -0.37 133 133
FRAP1 -0.005 0.1 -10000 0 -0.35 15 15
PRKCD -0.011 0.11 -10000 0 -0.36 19 19
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
negative regulation of cell growth -0.056 0.1 -10000 0 -0.31 54 54
PTPN2 0.016 0.024 -10000 0 -0.26 4 4
EP300 0.014 0.047 -10000 0 -0.52 4 4
IRF1 -0.009 0.16 -10000 0 -0.48 36 36
STAT1 (dimer)/PIASy -0.025 0.13 -10000 0 -0.42 25 25
SOCS1 0.009 0.064 -10000 0 -1.4 1 1
mol:GDP 0.003 0.092 -10000 0 -0.34 10 10
CASP1 -0.017 0.12 -10000 0 -0.28 67 67
PTGES2 0.017 0.012 -10000 0 -0.26 1 1
IRF9 0.016 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 -0.032 0.072 -10000 0 -0.43 7 7
CBL -0.011 0.098 -10000 0 -0.33 16 16
MAP3K1 -0.034 0.13 -10000 0 -0.34 43 43
PIAS1 0.017 0.012 -10000 0 -0.26 1 1
PIAS4 0.012 0.05 -10000 0 -0.43 6 6
antigen processing and presentation of peptide antigen via MHC class II -0.056 0.1 -10000 0 -0.31 54 54
PTPN11 -0.02 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 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
STX1A 0.009 0.028 -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 -0.26 2 2
ACh/CHRNA1 0.008 0.046 -9999 0 -0.3 9 9
RAB3GAP2/RIMS1/UNC13B 0.019 0.055 -9999 0 -0.33 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 -0.004 0.074 -9999 0 -0.26 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 -0.26 2 2
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.008 0.046 -9999 0 -0.29 9 9
UNC13B 0.011 0.048 -9999 0 -0.31 11 11
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 -0.22 264 264
SNAP25 -0.008 0.056 -9999 0 -0.29 15 15
VAMP2 0.007 0.011 -9999 0 -0.26 1 1
SYT1 -0.17 0.21 -9999 0 -0.36 264 264
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 -0.26 2 2
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.017 0.13 -10000 0 -0.49 37 37
HRAS 0.012 0.051 -10000 0 -0.41 7 7
EGFR -0.077 0.17 -10000 0 -0.35 136 136
AKT 0.015 0.077 -10000 0 -0.32 15 15
FOXO3 0.011 0.054 -10000 0 -0.38 9 9
AKT1 0.011 0.054 -10000 0 -0.38 9 9
FOXO1 0.001 0.089 -10000 0 -0.46 18 18
AKT3 -0.006 0.082 -10000 0 -0.28 42 42
FOXO4 0.017 0.023 -10000 0 -0.52 1 1
MET -0.001 0.078 -10000 0 -0.3 31 31
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
PIK3CB 0.012 0.055 -10000 0 -0.45 7 7
NRAS 0.006 0.072 -10000 0 -0.4 15 15
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 0.096 0.21 1 -0.26 50 51
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 0.098 0.18 4 -0.24 62 66
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
KRAS 0.008 0.069 -10000 0 -0.45 11 11
FOXO 0.039 0.037 -10000 0 -0.18 2 2
AKT2 0.017 0.012 -10000 0 -0.26 1 1
PTEN -0.002 0.1 -10000 0 -0.52 19 19
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.018 0.27 -9999 0 -0.76 29 29
PCK1 0.018 0.2 -9999 0 -0.95 6 6
HNF4A 0.032 0.27 -9999 0 -0.84 14 14
KCNJ11 -0.016 0.38 -9999 0 -1 49 49
AKT1 0.01 0.17 -9999 0 -0.44 27 27
response to starvation 0.006 0.003 -9999 0 -10000 0 0
DLK1 0.018 0.3 -9999 0 -0.78 29 29
NKX2-1 0.074 0.14 -9999 0 -0.49 1 1
ACADM 0.01 0.29 -9999 0 -0.77 36 36
TAT 0.017 0.18 -9999 0 -0.57 5 5
CEBPB 0.01 0.072 -9999 0 -0.33 20 20
CEBPA 0.011 0.085 -9999 0 -0.5 14 14
TTR -0.041 0.28 -9999 0 -0.76 39 39
PKLR 0.022 0.26 -9999 0 -0.73 26 26
APOA1 0.031 0.3 -9999 0 -0.91 15 15
CPT1C -0.001 0.3 -9999 0 -0.83 37 37
ALAS1 0.038 0.19 -9999 0 -1.6 2 2
TFRC -0.045 0.39 -9999 0 -1.1 46 46
FOXF1 -0.003 0.066 -9999 0 -0.32 20 20
NF1 0.023 0.039 -9999 0 -0.46 3 3
HNF1A (dimer) 0.03 0.048 -9999 0 -0.23 10 10
CPT1A 0.005 0.3 -9999 0 -0.84 34 34
HMGCS1 0.017 0.27 -9999 0 -0.74 27 27
NR3C1 0.005 0.11 -9999 0 -0.5 21 21
CPT1B 0.021 0.26 -9999 0 -0.74 26 26
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.02 0.04 -9999 0 -0.3 4 4
GCK 0.016 0.27 -9999 0 -0.73 31 31
CREB1 0.02 0.036 -9999 0 -0.36 2 2
IGFBP1 0.026 0.16 -9999 0 -0.73 4 4
PDX1 0.034 0.26 -9999 0 -1.1 15 15
UCP2 -0.026 0.35 -9999 0 -0.89 53 53
ALDOB 0.023 0.29 -9999 0 -0.78 28 28
AFP -0.049 0.15 -9999 0 -0.45 20 20
BDH1 0.01 0.28 -9999 0 -0.74 36 36
HADH 0.02 0.3 -9999 0 -0.8 30 30
F2 0.031 0.3 -9999 0 -0.92 14 14
HNF1A 0.03 0.048 -9999 0 -0.23 10 10
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 -0.5 106 106
FOXA3 -0.015 0.13 -9999 0 -0.38 30 30
FOXA2 0.031 0.35 -9999 0 -0.86 32 32
ABCC8 -0.2 0.52 -9999 0 -0.9 170 170
ALB -0.055 0.17 -9999 0 -0.67 16 16
RXR and RAR heterodimerization with other nuclear receptor

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
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 0.18 -9999 0 -0.44 67 67
MED1 0 0.068 -9999 0 -0.26 34 34
mol:9cRA -0.001 0.021 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.005 0.11 -9999 0 -0.28 64 64
RXRs/NUR77 0.03 0.077 -9999 0 -0.28 20 20
RXRs/PPAR 0.009 0.09 -9999 0 -0.31 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 0.003 0.097 -9999 0 -0.27 50 50
RARA 0.007 0.07 -9999 0 -0.43 12 12
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 0.004 0.08 -9999 0 -0.27 32 32
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 -0.002 0.11 -9999 0 -0.27 59 59
THRA -0.011 0.11 -9999 0 -0.39 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 0.085 -9999 0 -0.29 19 19
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 0.009 0.071 -9999 0 -0.44 11 11
RXRs/VDR/DNA/Vit D3 0.02 0.089 -9999 0 -0.26 38 38
NR4A1 0.009 0.05 -9999 0 -0.28 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.064 -9999 0 -0.26 9 9
RXRG 0.003 0.087 -9999 0 -0.47 16 16
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 -0.035 0.13 -9999 0 -0.34 79 79
PPARD 0.017 0.017 -9999 0 -0.26 2 2
TNF -0.01 0.23 -9999 0 -0.82 27 27
mol:Oxysterols 0 0.018 -9999 0 -10000 0 0
cholesterol transport 0 0.18 -9999 0 -0.44 67 67
PPARA 0.013 0.041 -9999 0 -0.29 9 9
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.025 0.13 -9999 0 -0.36 60 60
RXRs/NUR77/BCL2 -0.041 0.12 -9999 0 -0.3 40 40
SREBF1 -0.051 0.33 -9999 0 -1 51 51
RXRs/RXRs/DNA/9cRA 0.022 0.085 -9999 0 -0.29 19 19
ABCA1 -0.008 0.24 -9999 0 -0.82 28 28
RARs/THRs -0.001 0.12 -9999 0 -0.29 61 61
RXRs/FXR 0.033 0.075 -9999 0 -0.28 21 21
BCL2 -0.12 0.22 -9999 0 -0.47 145 145
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.016 0.033 -9999 0 -0.52 2 2
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 0.088 -9999 0 -0.3 36 36
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
mol:Sphinganine-1-P -0.008 0.1 -9999 0 -0.38 34 34
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.014 0.076 -9999 0 -0.23 40 40
GNAI3 0.017 0.023 -9999 0 -0.52 1 1
G12/G13 0.02 0.043 -9999 0 -0.37 5 5
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.13 -9999 0 -0.41 48 48
S1P1/S1P -0.014 0.11 -9999 0 -0.29 60 60
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
S1P/S1P5/G12 0.007 0.07 -9999 0 -0.23 36 36
S1P/S1P3/Gq -0.027 0.11 -9999 0 -0.28 67 67
S1P/S1P4/Gi 0.007 0.09 -9999 0 -0.39 13 13
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.085 -9999 0 -0.43 18 18
GNA14 -0.081 0.18 -9999 0 -0.35 141 141
GNA15 0.001 0.078 -9999 0 -0.33 25 25
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
GNA11 0.014 0.047 -9999 0 -0.52 4 4
ABCC1 0.012 0.051 -9999 0 -0.41 7 7
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.001 0.051 0.24 19 -10000 0 19
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 -0.054 41 41
KIF2A 0.005 0.054 -10000 0 -0.28 10 10
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 0.095 -10000 0 -0.31 41 41
WEE1 -0.003 0.093 -10000 0 -0.32 31 31
cytokinesis -0.026 0.16 -10000 0 -0.51 45 45
PP2A-alpha B56 -0.058 0.27 -10000 0 -0.76 61 61
AURKA -0.002 0.064 -10000 0 -0.28 23 23
PICH/PLK1 -0.024 0.18 -10000 0 -0.46 57 57
CENPE -0.011 0.097 -10000 0 -0.32 39 39
RhoA/GTP 0.004 0.058 -10000 0 -0.38 12 12
positive regulation of microtubule depolymerization 0.005 0.054 -10000 0 -0.28 10 10
PPP2CA 0.011 0.062 -10000 0 -0.52 7 7
FZR1 0.018 0 -10000 0 -10000 0 0
TPX2 -0.013 0.084 -10000 0 -0.29 41 41
PAK1 -0.023 0.13 -10000 0 -0.38 53 53
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 -0.35 11 11
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 -0.054 41 41
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 -0.86 59 59
TPT1 0.009 0.019 -10000 0 -10000 0 0
CDC25C -0.017 0.11 -10000 0 -0.44 34 34
CDC25B 0.003 0.07 -10000 0 -0.31 23 23
SGOL1 -0.001 0.051 -10000 0 -0.24 19 19
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 -0.38 51 51
PLK1/PBIP1 -0.011 0.083 -10000 0 -0.27 40 40
mitosis 0.002 0.007 0.035 21 -10000 0 21
FBXO5 0.003 0.054 -10000 0 -0.25 11 11
CDC2 -0.012 0.12 -10000 0 -0.45 34 34
NDC80 -0.03 0.14 -10000 0 -0.42 58 58
metaphase plate congression 0.009 0.023 -10000 0 -10000 0 0
ERCC6L -0.027 0.19 -10000 0 -0.56 47 47
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 0.011 5 -10000 0 5
PPP1R12A 0.015 0.031 -10000 0 -0.32 4 4
interphase 0 0.002 0.011 5 -10000 0 5
PLK1/PRC1-2 -0.018 0.14 -10000 0 -0.42 49 49
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 21 21
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.057 -10000 0 -0.32 6 6
microtubule-based process -0.011 0.1 -10000 0 -0.34 40 40
Golgi organization 0.002 0.041 -10000 0 -0.12 46 46
Cohesin/SA2 0.01 0.036 -10000 0 -0.13 15 15
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 -0.32 30 30
PPP2R1A 0.017 0.012 -10000 0 -0.26 1 1
chromosome segregation -0.011 0.082 -10000 0 -0.27 40 40
PRC1 -0.02 0.13 -10000 0 -0.43 44 44
ECT2 -0.001 0.07 -10000 0 -0.28 22 22
C13orf34 0.006 0.037 -10000 0 -0.13 17 17
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 0.032 -10000 0 -0.094 27 27
spindle stabilization 0.002 0.019 -10000 0 -0.053 41 41
APC/C/HCDH1 0.02 0.025 -10000 0 -0.32 3 3
MKLP2/PLK1 -0.011 0.1 -10000 0 -0.34 40 40
CCNB1 -0.016 0.13 -10000 0 -0.5 35 35
PPP1CB 0.016 0.021 -10000 0 -0.26 3 3
BTRC 0.009 0.054 -10000 0 -0.29 15 15
ROCK2 0.007 0.057 -10000 0 -0.34 8 8
TUBG1 0.008 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.046 0.14 -10000 0 -0.48 41 41
MLF1IP -0.018 0.1 -10000 0 -0.32 49 49
INCENP 0 0.085 -10000 0 -0.38 23 23
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 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 -0.026 0.13 -9999 0 -0.4 29 29
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 0.001 0.084 -9999 0 -0.38 20 20
FOXO1 0.002 0.089 -9999 0 -0.46 18 18
T-DHT/AR -0.019 0.15 -9999 0 -0.42 29 29
MAP2K6 -0.013 0.11 -9999 0 -0.4 37 37
BRM/BAF57 0.026 0.023 -9999 0 -0.37 1 1
MAP2K4 -0.007 0.1 -9999 0 -0.39 30 30
SMARCA2 0.017 0.023 -9999 0 -0.52 1 1
PDE9A -0.024 0.15 -9999 0 -0.86 8 8
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 0.14 -9999 0 -0.37 20 20
NR0B1 -0.01 0.087 -9999 0 -0.27 50 50
EGR1 -0.1 0.2 -9999 0 -0.39 155 155
RXRs/9cRA 0.024 0.059 -9999 0 -0.28 19 19
AR/RACK1/Src 0.003 0.1 -9999 0 -0.34 20 20
AR/GR -0.039 0.13 -9999 0 -0.29 76 76
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 0.079 -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 -0.31 21 21
NR3C1 -0.003 0.1 -9999 0 -0.51 21 21
KLK3 -0.038 0.11 -9999 0 -0.48 5 5
APPBP2 0.009 0.043 -9999 0 -0.26 13 13
TRIM24 0.017 0.024 -9999 0 -0.26 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 97 97
RXRG 0.003 0.086 -9999 0 -0.47 16 16
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 0.021 -9999 0 -0.26 3 3
KLK2 0.021 0.095 -9999 0 -0.4 4 4
AR -0.04 0.13 -9999 0 -0.27 114 114
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 -0.44 18 18
GATA2 -0.008 0.094 -9999 0 -0.32 40 40
MYST2 0.011 0.047 -9999 0 -0.31 10 10
HOXB13 -0.075 0.13 -9999 0 -0.26 182 182
T-DHT/AR/RACK1/Src -0.002 0.11 -9999 0 -0.35 20 20
positive regulation of transcription -0.008 0.093 -9999 0 -0.32 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 0.01 0.08 -9999 0 -0.32 8 8
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 -0.35 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 25 25
CREBBP 0.016 0.033 -9999 0 -0.52 2 2
SMARCE1 0.017 0.021 -9999 0 -0.26 3 3
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 -0.001 0.11 -9999 0 -0.36 32 32
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 -0.003 0.15 -9999 0 -0.57 20 20
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
PDGFB-D/PDGFRB/PLCgamma1 0.007 0.14 -9999 0 -0.52 20 20
PLCG1 0.003 0.14 -9999 0 -0.52 20 20
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 0.017 0.024 -9999 0 -0.53 1 1
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.015 0.16 -9999 0 -0.64 28 28
S1P1/S1P -0.029 0.19 -9999 0 -0.52 57 57
negative regulation of cAMP metabolic process -0.002 0.15 -9999 0 -0.55 20 20
MAPK3 0.001 0.16 -9999 0 -0.58 20 20
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 0.005 0.077 -9999 0 -0.65 5 5
PLCB2 -0.017 0.17 -9999 0 -0.45 57 57
RAC1 0.018 0 -9999 0 -10000 0 0
RhoA/GTP -0.062 0.14 -9999 0 -0.42 60 60
receptor internalization -0.026 0.18 -9999 0 -0.48 57 57
PTGS2 -0.002 0.18 -9999 0 -0.79 12 12
Rac1/GTP -0.058 0.14 -9999 0 -0.42 57 57
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VEGFA -0.007 0.086 -9999 0 -0.3 31 31
negative regulation of T cell proliferation -0.002 0.15 -9999 0 -0.55 20 20
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.003 0.085 -9999 0 -0.44 18 18
MAPK1 0 0.16 -9999 0 -0.58 20 20
S1P1/S1P/PDGFB-D/PDGFRB -0.019 0.2 -9999 0 -0.59 40 40
ABCC1 0.012 0.051 -9999 0 -0.41 7 7
Atypical NF-kappaB pathway

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
BCL3/RelA 0.02 0.049 -9999 0 -0.37 8 8
FBXW11 0.015 0.035 -9999 0 -0.43 3 3
NF kappa B1 p50/c-Rel 0.018 0.063 -9999 0 -0.31 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.11 -9999 0 -0.44 17 17
NFKBIA -0.023 0.12 -9999 0 -0.25 86 86
MAPK14 0.017 0.012 -9999 0 -0.26 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 0.052 -9999 0 -0.3 11 11
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 -0.35 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 32 32
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 -0.013 0.1 -9999 0 -0.23 84 84
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.006 0.11 -9999 0 -0.44 16 16
SRC 0.015 0.035 -9999 0 -0.43 3 3
PI3K 0.006 0.082 -9999 0 -0.37 21 21
NF kappa B1 p50/RelA -0.013 0.1 -9999 0 -0.23 84 84
IKBKB 0.011 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 -0.022 0.14 -9999 0 -0.48 42 42
I kappa B alpha/PIK3R1 -0.026 0.12 -9999 0 -0.37 38 38
cell death 0.006 0.1 -9999 0 -0.42 16 16
NF kappa B1 p105/c-Rel 0.018 0.063 -9999 0 -0.31 15 15
LCK -0.073 0.18 -9999 0 -0.4 115 115
BCL3 0.009 0.067 -9999 0 -0.49 9 9
Angiopoietin receptor Tie2-mediated signaling

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.042 0.17 -10000 0 -0.9 12 12
NCK1/PAK1/Dok-R -0.032 0.083 -10000 0 -0.46 11 11
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 0.053 0.15 -10000 0 -0.9 11 11
FN1 -0.046 0.17 -10000 0 -0.46 71 71
PLD2 0.038 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 -0.37 247 247
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 -0.38 53 53
Tie2/Ang1/alpha5/beta1 Integrin 0.023 0.19 -10000 0 -1 11 11
CDKN1A 0.022 0.2 -10000 0 -0.76 27 27
ITGA5 0.014 0.042 -10000 0 -0.46 4 4
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 0.051 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 0.049 0.16 -10000 0 -0.87 11 11
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
ANGPT2 -0.018 0.16 -10000 0 -0.64 15 15
BMX 0.012 0.19 -10000 0 -1.2 11 11
ANGPT1 0.021 0.085 -10000 0 -1.2 1 1
tube development 0.027 0.17 -10000 0 -0.74 16 16
ANGPT4 0.016 0.035 -10000 0 -0.43 3 3
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 -0.34 121 121
STAT5A (dimer) 0.027 0.2 -10000 0 -0.78 25 25
mol:L-citrulline 0.051 0.14 -10000 0 -0.66 12 12
AGTR1 -0.15 0.21 -10000 0 -0.36 229 229
MAPK14 0.035 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.027 0.16 -10000 0 -1.1 10 10
TEK 0.025 0.18 -10000 0 -1.2 10 10
RPS6KB1 0.041 0.16 -10000 0 -0.88 11 11
Angiotensin II/AT1 -0.099 0.15 -10000 0 -0.25 229 229
Tie2/Ang1/GRB2 0.041 0.16 -10000 0 -1 11 11
MAPK3 0.043 0.15 -10000 0 -0.92 11 11
MAPK1 0.043 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 0.039 0.16 -10000 0 -1 11 11
PI3K 0.036 0.19 -10000 0 -1.1 11 11
FES 0.032 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 0.044 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 0.044 0.16 -10000 0 -0.88 11 11
Tie2/Ang2 0.017 0.21 -10000 0 -1 15 15
Tie2/Ang1 0.035 0.17 -10000 0 -1.1 11 11
FOXO1 0.044 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 18 18
FYN 0.024 0.19 -10000 0 -0.85 16 16
DOK2 -0.021 0.13 -10000 0 -0.41 48 48
negative regulation of cell cycle 0.026 0.18 -10000 0 -0.67 27 27
ETS1 0.012 0.072 -10000 0 -0.3 23 23
PXN 0.051 0.14 -10000 0 -0.72 11 11
ITGB1 0.015 0.037 -10000 0 -0.39 4 4
NOS3 0.05 0.15 -10000 0 -0.75 12 12
RAC1 0.018 0 -10000 0 -10000 0 0
TNF 0.004 0.098 -10000 0 -0.43 19 19
MAPKKK cascade 0.038 0.16 -10000 0 -0.96 11 11
RASA1 0.004 0.079 -10000 0 -0.42 16 16
Tie2/Ang1/Shc 0.042 0.16 -10000 0 -1 11 11
NCK1 0.011 0.046 -10000 0 -0.28 12 12
vasculogenesis 0.052 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 0.051 0.14 -10000 0 -0.66 12 12
Rac1/GTP -0.011 0.14 -10000 0 -0.82 11 11
MMP2 0.017 0.19 -10000 0 -1.1 11 11
Arf6 downstream 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
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 0.25 39 -10000 0 39
ARF1/GTP 0.012 0.05 -10000 0 -0.28 4 4
mol:GM1 0 0.047 -10000 0 -0.25 4 4
mol:Choline 0.008 0.074 -10000 0 -0.34 15 15
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 0.018 0.083 -10000 0 -0.25 39 39
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 -0.35 3 3
TIAM1 0.006 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 0.002 0.11 0.35 41 -10000 0 41
KALRN -0.022 0.078 -10000 0 -0.3 34 34
RAB11FIP3/RAB11A 0.019 0.05 -10000 0 -0.37 8 8
RhoA/GDP -0.002 0.11 -10000 0 -0.36 41 41
NME1 0.012 0.04 -10000 0 -0.26 11 11
Rac1/GDP 0.004 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 0.073 -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 0.077 -10000 0 -0.38 12 12
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 -0.35 7 7
PIP5K1A 0.012 0.065 -10000 0 -0.35 8 8
mol:Phosphatidic acid 0.008 0.074 -10000 0 -0.34 15 15
Rac1/GTP -0.002 0.11 -10000 0 -0.43 32 32
HIF-2-alpha transcription factor network

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
MMP14 -0.049 0.26 -10000 0 -1.2 26 26
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 0.036 0.13 -10000 0 -0.37 22 22
EPO 0.053 0.23 -10000 0 -0.55 30 30
FIH (dimer) 0.024 0.027 -10000 0 -0.52 1 1
APEX1 0.025 0.019 -10000 0 -0.26 1 1
SERPINE1 0.054 0.25 -10000 0 -0.66 34 34
FLT1 -0.019 0.18 -10000 0 -1.1 13 13
ADORA2A 0.042 0.24 -10000 0 -0.63 35 35
germ cell development 0.068 0.22 -10000 0 -0.59 29 29
SLC11A2 0.066 0.23 -10000 0 -0.62 30 30
BHLHE40 0.059 0.23 -10000 0 -0.6 31 31
HIF1AN 0.024 0.027 -10000 0 -0.52 1 1
HIF2A/ARNT/SIRT1 0.041 0.17 -10000 0 -0.42 30 30
ETS1 0.019 0.072 -10000 0 -0.3 23 23
CITED2 -0.013 0.15 -10000 0 -1.1 9 9
KDR -0.008 0.15 -10000 0 -1.1 8 8
PGK1 0.068 0.23 -10000 0 -0.6 29 29
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 0.085 0.27 -10000 0 -0.71 30 30
EPAS1 0.02 0.15 -10000 0 -0.37 35 35
SP1 0.023 0.027 -10000 0 -0.52 1 1
ABCG2 0.06 0.24 -10000 0 -0.65 33 33
EFNA1 0.058 0.24 -10000 0 -0.6 38 38
FXN 0.059 0.22 -10000 0 -0.63 25 25
POU5F1 0.068 0.23 -10000 0 -0.61 29 29
neuron apoptosis -0.084 0.26 0.68 30 -10000 0 30
EP300 0.014 0.047 -10000 0 -0.52 4 4
EGLN3 -0.066 0.19 -10000 0 -0.4 116 116
EGLN2 0.018 0.055 -10000 0 -0.36 9 9
EGLN1 0.009 0.083 -10000 0 -0.36 23 23
VHL/Elongin B/Elongin C 0.032 0.028 -10000 0 -0.3 1 1
VHL 0.014 0.031 -10000 0 -0.26 7 7
ARNT 0.025 0.014 -10000 0 -10000 0 0
SLC2A1 0.053 0.23 -10000 0 -0.61 33 33
TWIST1 0.038 0.27 -10000 0 -0.66 45 45
ELK1 0.022 0.038 -10000 0 -0.39 4 4
HIF2A/ARNT/Cbp/p300 0.054 0.17 -10000 0 -0.44 26 26
VEGFA 0.06 0.24 -10000 0 -0.61 31 31
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
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 23 23
BIRC5 -0.037 0.15 -9999 0 -0.42 67 67
NFKBIA 0.024 0.054 -9999 0 -0.33 3 3
CPEB1 0.004 0.068 -9999 0 -0.31 22 22
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 -0.012 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 0.01 0.044 -9999 0 -0.26 14 14
JUB -0.027 0.15 -9999 0 -0.49 47 47
TPX2 -0.01 0.11 -9999 0 -0.37 41 41
TP53 0.004 0.089 -9999 0 -0.29 37 37
DLG7 -0.006 0.11 -9999 0 -0.35 43 43
AURKAIP1 0.016 0.029 -9999 0 -0.35 3 3
ARHGEF7 0.016 0.021 -9999 0 -0.26 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 -0.21 21 21
AURKB -0.007 0.078 -9999 0 -0.22 47 47
CDC25B 0.011 0.069 -9999 0 -0.37 5 5
G2/M transition checkpoint -0.002 0.088 -9999 0 -0.27 42 42
mRNA polyadenylation 0.016 0.053 -9999 0 -0.26 5 5
Aurora A/CPEB 0.016 0.053 -9999 0 -0.26 5 5
Aurora A/TACC1/TRAP/chTOG 0.017 0.092 -9999 0 -0.27 33 33
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 0.016 0.09 -9999 0 -0.27 33 33
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 47 47
Aurora A/PP2A 0.025 0.047 -9999 0 -0.21 1 1
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 0.029 -9999 0 -0.37 1 1
RASA1 0.004 0.079 -9999 0 -0.42 16 16
Ajuba/Aurora A -0.002 0.089 -9999 0 -0.27 42 42
mitotic prometaphase -0.001 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.058 -9999 0 -0.21 21 21
TACC1 -0.02 0.13 -9999 0 -0.41 47 47
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 -0.26 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 -0.01 0.11 -9999 0 -0.37 41 41
PPP2R5D 0.016 0.021 -9999 0 -0.26 3 3
Aurora A/TPX2 0.006 0.1 -9999 0 -0.4 26 26
PAK1 -0.022 0.13 -9999 0 -0.38 53 53
CKAP5 0.017 0.017 -9999 0 -0.26 2 2
mTOR signaling 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
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 71 79
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 -0.24 28 28
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 15 15
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 -0.2 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.017 0.012 -10000 0 -0.26 1 1
RPS6KB1 0.011 0.065 0.19 8 -0.26 5 13
MAP3K5 -0.013 0.088 -10000 0 -0.36 29 29
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
apoptosis -0.013 0.088 -10000 0 -0.36 29 29
mol:LY294002 0 0.001 0.001 1 -0.001 57 58
EIF4B 0.016 0.062 0.18 8 -0.24 7 15
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 0.033 0.054 0.18 8 -0.3 2 10
FKBP1A 0.017 0.017 -10000 0 -0.26 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 0.012 -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 -0.01 0.14 -10000 0 -0.59 29 29
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 -0.019 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 -0.35 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 6 21
EEF2 0.025 0.031 -10000 0 -0.28 5 5
eIF4E/4E-BP1 -0.001 0.14 -10000 0 -1 10 10
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.008 0.13 -10000 0 -0.51 12 12
BAG4 0.002 0.071 -10000 0 -0.29 28 28
BAD 0.011 0.045 -10000 0 -0.18 9 9
NFKBIA 0.014 0.042 -10000 0 -0.46 4 4
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BAX 0.011 0.045 -10000 0 -0.19 7 7
EnzymeConsortium:3.1.4.12 0.001 0.031 -10000 0 -0.087 22 22
IKBKB -0.003 0.12 -10000 0 -0.44 16 16
MAP2K2 0.022 0.047 -10000 0 -0.24 6 6
MAP2K1 0.023 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 -0.003 0.12 -10000 0 -0.42 19 19
MAP2K4 -0.011 0.09 -10000 0 -0.24 56 56
protein ubiquitination -0.002 0.12 -10000 0 -0.44 15 15
EnzymeConsortium:2.7.1.37 0.02 0.052 -10000 0 -0.26 4 4
response to UV 0 0 -10000 0 -0.002 4 4
RAF1 0.018 0.044 -10000 0 -0.22 4 4
CRADD 0.009 0.067 -10000 0 -0.49 9 9
mol:ceramide 0.005 0.046 -10000 0 -0.16 14 14
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 0.084 -10000 0 -0.24 46 46
TRADD 0.016 0.026 -10000 0 -0.39 2 2
RELA/p50 0.018 0 -10000 0 -10000 0 0
MAPK3 0.026 0.044 -10000 0 -0.22 3 3
MAPK1 0.026 0.044 -10000 0 -0.21 4 4
p50/RELA/I-kappa-B-alpha 0.024 0.031 -10000 0 -0.37 3 3
FADD -0.012 0.13 -10000 0 -0.44 19 19
KSR1 0.012 0.045 -10000 0 -0.19 8 8
MAPK8 -0.004 0.087 -10000 0 -0.22 56 56
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK -0.006 0.13 -10000 0 -0.44 19 19
TNF R/SODD 0.014 0.055 -10000 0 -0.37 5 5
TNF -0.004 0.094 -10000 0 -0.36 31 31
CYCS 0.036 0.056 0.14 64 -0.17 5 69
IKBKG 0 0.12 -10000 0 -0.47 12 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.012 0.13 -10000 0 -0.39 25 25
RELA 0.018 0 -10000 0 -10000 0 0
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
AIFM1 0.036 0.056 0.14 63 -0.17 5 68
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 0.033 -10000 0 -10000 0 0
NSMAF -0.008 0.13 -10000 0 -0.46 15 15
response to hydrogen peroxide 0 0 -10000 0 -0.002 4 4
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.14 -9999 0 -0.38 55 55
VEGFR1 homodimer/NRP1 -0.02 0.14 -9999 0 -0.38 55 55
mol:DAG -0.003 0.13 -9999 0 -0.61 13 13
VEGFR1 homodimer/NRP1/VEGFR 121 -0.016 0.14 -9999 0 -0.35 58 58
CaM/Ca2+ 0.007 0.13 -9999 0 -0.63 11 11
HIF1A -0.034 0.17 -9999 0 -0.47 66 66
GAB1 0.006 0.074 -9999 0 -0.43 14 14
AKT1 0.001 0.14 -9999 0 -0.54 18 18
PLCG1 -0.003 0.13 -9999 0 -0.62 13 13
NOS3 0.019 0.12 -9999 0 -0.58 11 11
CBL 0.017 0.012 -9999 0 -0.26 1 1
mol:NO 0.02 0.12 -9999 0 -0.53 12 12
FLT1 -0.019 0.16 -9999 0 -0.45 55 55
PGF 0.012 0.051 -9999 0 -0.41 7 7
VEGFR1 homodimer/NRP2/VEGFR121 -0.009 0.14 -9999 0 -0.65 14 14
CALM1 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
eNOS/Hsp90 0.027 0.12 -9999 0 -0.54 11 11
endothelial cell proliferation 0.002 0.13 -9999 0 -0.6 13 13
mol:Ca2+ -0.003 0.13 -9999 0 -0.61 13 13
MAPK3 0.008 0.12 -9999 0 -0.57 12 12
MAPK1 0.008 0.12 -9999 0 -0.58 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
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 0.081 -9999 0 -0.32 28 28
VEGFA homodimer 0 0.076 -9999 0 -0.29 31 31
VEGFR1 homodimer/VEGFA homodimer -0.018 0.15 -9999 0 -0.38 58 58
platelet activating factor biosynthetic process 0.013 0.12 -9999 0 -0.55 12 12
PI3K -0.003 0.14 -9999 0 -0.59 16 16
PRKCA 0.002 0.12 -9999 0 -0.62 11 11
PRKCB -0.004 0.12 -9999 0 -0.57 13 13
VEGFR1 homodimer/PLGF homodimer -0.011 0.14 -9999 0 -0.38 58 58
VEGFA 0 0.076 -9999 0 -0.29 31 31
VEGFB 0.017 0.023 -9999 0 -0.52 1 1
mol:IP3 -0.003 0.13 -9999 0 -0.61 13 13
RASA1 -0.007 0.14 -9999 0 -0.63 14 14
NRP2 0.01 0.052 -9999 0 -0.33 11 11
VEGFR1 homodimer -0.019 0.16 -9999 0 -0.44 55 55
VEGFB homodimer 0.017 0.023 -9999 0 -0.52 1 1
NCK1 0.011 0.046 -9999 0 -0.28 12 12
eNOS/Caveolin-1 0.021 0.13 -9999 0 -0.58 12 12
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
mol:PI-3-4-5-P3 -0.004 0.14 -9999 0 -0.58 16 16
mol:L-citrulline 0.02 0.12 -9999 0 -0.53 12 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.005 0.13 -9999 0 -0.62 12 12
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.14 -9999 0 -0.65 13 13
CD2AP 0.016 0.029 -9999 0 -0.35 3 3
PI3K/GAB1 0 0.14 -9999 0 -0.56 16 16
PDPK1 -0.002 0.13 -9999 0 -0.56 15 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.14 -9999 0 -0.63 13 13
mol:NADP 0.02 0.12 -9999 0 -0.53 12 12
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
ubiquitin-dependent protein catabolic process 0.004 0.13 -9999 0 -0.62 12 12
VEGFR1 homodimer/NRP2 -0.012 0.15 -9999 0 -0.38 56 56
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 0.15 -9999 0 -0.46 30 30
PDGFB-D/PDGFRB/SLAP 0.01 0.074 -9999 0 -0.37 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 -0.5 21 21
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
FGR -0.008 0.065 -9999 0 -0.39 10 10
mol:Ca2+ 0.003 0.11 -9999 0 -0.62 11 11
MYC -0.029 0.22 -9999 0 -0.74 42 42
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 0.098 -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 -0.26 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 -0.34 52 52
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 -0.018 0.15 -9999 0 -0.46 34 34
positive regulation of MAPKKK cascade 0.019 0.052 -9999 0 -0.37 9 9
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
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 0.086 -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 -0.26 1 1
VAV2 -0.011 0.14 -9999 0 -0.59 17 17
CBL 0.017 0.012 -9999 0 -0.26 1 1
PDGFB-D/PDGFRB/DEP1 0.015 0.063 -9999 0 -0.37 13 13
LCK -0.081 0.2 -9999 0 -0.56 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 -0.03 0.14 -9999 0 -0.55 28 28
ABL1 -0.005 0.11 -9999 0 -0.5 16 16
PDGFB-D/PDGFRB/CBL -0.01 0.14 -9999 0 -0.66 15 15
PTPN1 0.001 0.071 -9999 0 -0.29 28 28
SNX15 0.017 0.012 -9999 0 -0.26 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 -0.64 43 43
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 -0.01 0.084 -9999 0 -0.46 12 12
PI3K -0.065 0.12 -9999 0 -0.44 31 31
PDGFB-D/PDGFRB/GRB7/SHC 0.009 0.075 -9999 0 -0.31 17 17
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.007 0.14 -9999 0 -0.53 21 21
LYN -0.008 0.066 -9999 0 -0.4 10 10
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 0.063 -9999 0 -0.32 7 7
SPHK1 -0.027 0.14 -9999 0 -0.42 54 54
EDG1 -0.021 0.13 -9999 0 -0.41 48 48
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 90 90
YES1 -0.016 0.096 -9999 0 -0.47 18 18
cell migration -0.038 0.15 -9999 0 -0.35 90 90
SHC/Grb2/SOS1 0.036 0.06 -9999 0 -0.35 4 4
SLC9A3R2 -0.032 0.15 -9999 0 -0.49 52 52
SLC9A3R1 -0.044 0.16 -9999 0 -0.44 71 71
NHERF1-2/PDGFRB/PTEN -0.033 0.16 -9999 0 -0.32 102 102
FYN -0.016 0.13 -9999 0 -0.78 11 11
DOK1 0.013 0.074 -9999 0 -0.3 23 23
HRAS/GTP 0.009 0.037 -9999 0 -0.29 7 7
PDGFB 0.008 0.064 -9999 0 -0.39 12 12
RAC1 -0.012 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 -0.007 0.051 -9999 0 -0.34 4 4
RASA1 0.013 0.072 -9999 0 -0.29 22 22
NCK1 0.011 0.046 -9999 0 -0.28 12 12
NCK2 0.015 0.027 -9999 0 -0.26 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 -0.48 16 16
STAT1-3-5/STAT1-3-5 -0.022 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 -0.45 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 -0.059 0.17 -9999 0 -0.4 98 98
LRPAP1 0.016 0.026 -9999 0 -0.39 2 2
NUDC 0.018 0 -9999 0 -10000 0 0
RELN/LRP8 -0.014 0.1 -9999 0 -0.31 42 42
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 0.092 -9999 0 -0.28 42 42
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 36 36
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 -0.26 7 7
LIS1/Poliovirus Protein 3A 0.018 0.02 -9999 0 -0.31 2 2
CDK5R2 0.017 0.017 -9999 0 -0.26 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.016 0.11 -9999 0 -0.31 57 57
YWHAE 0.016 0.029 -9999 0 -0.35 3 3
NDEL1/14-3-3 E 0.025 0.079 -9999 0 -0.29 4 4
MAP1B -0.014 0.073 -9999 0 -0.29 32 32
RAC1 0.024 0.01 -9999 0 -10000 0 0
p35/CDK5 0.007 0.085 -9999 0 -0.31 4 4
RELN 0.009 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 0.003 0.095 -9999 0 -0.45 3 3
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 -0.26 1 1
MAP1B/LIS1/Dynein heavy chain 0.014 0.054 -9999 0 -0.31 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.031 0.078 -9999 0 -0.27 3 3
LRP8 -0.057 0.16 -9999 0 -0.34 109 109
NDEL1/Katanin 60 0.024 0.079 -9999 0 -0.29 3 3
P39/CDK5 0.009 0.084 -9999 0 -0.23 42 42
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 42 42
PPP2R5D 0.016 0.021 -9999 0 -0.26 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 0.004 0.1 -9999 0 -0.25 57 57
RELN/VLDLR -0.043 0.13 -9999 0 -0.28 111 111
CDC42 0.024 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.015 0.035 -10000 0 -0.32 4 4
RAS family/GTP 0.002 0.098 -10000 0 -0.31 25 25
NFATC4 0.008 0.079 0.2 1 -0.32 11 12
ERBB2IP 0.016 0.033 -10000 0 -0.52 2 2
HSP90 (dimer) 0.013 0.045 -10000 0 -0.39 6 6
mammary gland morphogenesis -0.009 0.094 0.23 1 -0.31 22 23
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 0.22 1 -0.39 10 11
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.012 0.1 0.24 1 -0.3 47 48
AKT1 0.008 0.038 -10000 0 -0.26 9 9
BAD 0.016 0.035 -10000 0 -0.31 5 5
MAPK10 0.002 0.069 -10000 0 -0.22 19 19
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.009 0.1 0.25 1 -0.34 22 23
RAF1 0.007 0.1 -10000 0 -0.33 19 19
ErbB2/ErbB3/neuregulin 2 -0.037 0.12 0.24 1 -0.34 56 57
STAT3 0.016 0.095 -10000 0 -0.95 5 5
cell migration 0.009 0.07 0.18 1 -0.21 16 17
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.045 0.24 -10000 0 -0.62 54 54
FOS -0.06 0.22 -10000 0 -0.45 105 105
NRAS 0.006 0.073 -10000 0 -0.4 15 15
mol:Ca2+ -0.009 0.094 0.23 1 -0.31 22 23
MAPK3 -0.021 0.19 -10000 0 -0.47 51 51
MAPK1 -0.021 0.19 -10000 0 -0.47 53 53
JAK2 -0.003 0.096 0.22 1 -0.38 14 15
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 38 38
NRG1 0.008 0.049 -10000 0 -0.26 17 17
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
MAPK8 0 0.089 0.22 1 -0.26 39 40
MAPK9 0.008 0.067 -10000 0 -0.22 17 17
ERBB2 -0.03 0.085 0.38 1 -0.34 20 21
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 0.021 0.031 -10000 0 -0.28 4 4
FRAP1 0.016 0.032 -10000 0 -0.31 4 4
RAC1-CDC42/GTP -0.022 0.054 -10000 0 -0.27 10 10
ErbB2/ErbB2/HSP90 (dimer) -0.014 0.076 0.26 1 -0.32 18 19
CHRNA1 -0.008 0.16 -10000 0 -0.43 36 36
myelination 0.014 0.079 0.21 1 -0.32 11 12
PPP3CB 0 0.086 0.21 1 -0.37 9 10
KRAS 0.008 0.069 -10000 0 -0.45 11 11
RAC1-CDC42/GDP 0.021 0.074 -10000 0 -0.29 10 10
NRG2 -0.016 0.1 -10000 0 -0.3 57 57
mol:GDP 0.001 0.082 -10000 0 -0.27 38 38
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MAP2K2 0.007 0.11 -10000 0 -0.35 20 20
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 0.22 1 -0.4 9 10
MAP2K1 -0.024 0.17 -10000 0 -0.45 33 33
heart morphogenesis -0.009 0.094 0.23 1 -0.31 22 23
RAS family/GDP 0.013 0.097 -10000 0 -0.32 20 20
GRB2 0.015 0.024 -10000 0 -0.26 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 -0.009 0.094 0.23 1 -0.31 22 23
CDC42 0.018 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.019 0.091 -9999 0 -0.3 34 34
MAP4K1 0.011 0.041 -9999 0 -0.26 12 12
MAP3K8 -0.036 0.15 -9999 0 -0.39 69 69
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 0.005 0.1 -9999 0 -0.35 12 12
JUN -0.008 0.092 -9999 0 -0.33 20 20
MAP3K7 0.029 0.067 -9999 0 -0.28 6 6
GRAP2 0.011 0.044 -9999 0 -0.28 11 11
CRK 0.016 0.033 -9999 0 -0.52 2 2
MAP2K4 0.005 0.096 -9999 0 -0.35 16 16
LAT 0.002 0.069 -9999 0 -0.28 29 29
LCP2 -0.005 0.1 -9999 0 -0.41 28 28
MAPK8 0.011 0.052 -9999 0 -0.58 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0.07 -9999 0 -0.3 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.025 0.089 -9999 0 -0.28 37 37
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.023 -9999 0 -0.52 1 1
HDAC2 0.009 0.054 -9999 0 -0.29 15 15
GNB1/GNG2 -0.007 0.11 -9999 0 -0.31 53 53
forebrain development 0.007 0.13 -9999 0 -0.53 17 17
GNAO1 0.017 0.024 -9999 0 -0.26 4 4
SMO/beta Arrestin2 -0.017 0.12 -9999 0 -0.37 47 47
SMO -0.046 0.16 -9999 0 -0.41 80 80
ARRB2 0.019 0.001 -9999 0 -10000 0 0
GLI3/SPOP 0.01 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 -0.014 0.12 -9999 0 -0.38 44 44
XPO1 0.021 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) -0.003 0.16 -9999 0 -0.56 25 25
SAP30 0.012 0.053 -9999 0 -0.48 6 6
mol:GDP -0.045 0.16 -9999 0 -0.41 80 80
MIM/GLI2A -0.023 0.14 -9999 0 -0.4 61 61
IFT88 -0.001 0.097 -9999 0 -0.48 20 20
GNAI3 0.018 0.023 -9999 0 -0.52 1 1
GLI2 0.036 0.054 -9999 0 -0.41 1 1
GLI3 0.003 0.14 -9999 0 -0.39 28 28
CSNK1D 0.018 0 -9999 0 -10000 0 0
CSNK1E 0.017 0.012 -9999 0 -0.26 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 -0.35 3 3
Gi family/GTP -0.007 0.11 -9999 0 -0.39 23 23
SIN3B 0.017 0.012 -9999 0 -0.26 1 1
SIN3A 0.017 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.009 0.14 -9999 0 -0.46 30 30
GLI2/Su(fu) 0.027 0.099 -9999 0 -0.45 6 6
FOXA2 -0.051 0.18 -9999 0 -0.73 34 34
neural tube patterning 0.007 0.13 -9999 0 -0.53 17 17
SPOP 0.013 0.042 -9999 0 -0.33 7 7
Su(fu)/PIAS1 0.005 0.092 -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 0.007 0.13 -9999 0 -0.53 17 17
SUFU -0.005 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 -0.41 14 14
GLI3A/CBP 0.007 0.069 -9999 0 -0.37 9 9
KIF3A 0.005 0.081 -9999 0 -0.5 13 13
GLI1 0.007 0.13 -9999 0 -0.54 17 17
RAB23 0.009 0.061 -9999 0 -0.37 12 12
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
IFT172 0.013 0.05 -9999 0 -0.43 6 6
RBBP7 0.01 0.051 -9999 0 -0.3 13 13
Su(fu)/Galectin3 -0.027 0.14 -9999 0 -0.34 71 71
GNAZ 0.003 0.085 -9999 0 -0.43 18 18
RBBP4 0.016 0.026 -9999 0 -0.39 2 2
CSNK1G1 0.017 0.012 -9999 0 -0.26 1 1
PIAS1 0.017 0.012 -9999 0 -0.26 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 0.001 0.11 -9999 0 -0.4 20 20
PTCH1 0.016 0.12 -9999 0 -0.6 8 8
MIM/GLI1 0.002 0.16 -9999 0 -0.5 24 24
CREBBP 0.007 0.069 -9999 0 -0.37 9 9
Su(fu)/SIN3/HDAC complex 0.036 0.047 -9999 0 -0.26 1 1
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.011 0.056 -10000 0 -0.31 12 12
cell-cell adhesion 0.036 0.083 0.37 18 -10000 0 18
Ephrin B/EPHB2/RasGAP 0.024 0.086 -10000 0 -0.28 30 30
ITSN1 0.015 0.035 -10000 0 -0.43 3 3
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
SHC1 0.017 0.023 -10000 0 -0.52 1 1
Ephrin B1/EPHB3 0.005 0.072 -10000 0 -0.32 21 21
Ephrin B1/EPHB1 -0.004 0.071 -10000 0 -0.31 13 13
HRAS/GDP -0.033 0.079 -10000 0 -0.31 26 26
Ephrin B/EPHB1/GRB7 -0.002 0.096 -10000 0 -0.27 32 32
Endophilin/SYNJ1 0.019 0.063 -10000 0 -0.23 23 23
KRAS 0.008 0.069 -10000 0 -0.45 11 11
Ephrin B/EPHB1/Src 0.014 0.088 -10000 0 -0.28 24 24
endothelial cell migration -0.003 0.1 -10000 0 -0.28 55 55
GRB2 0.016 0.024 -10000 0 -0.26 4 4
GRB7 -0.017 0.1 -10000 0 -0.29 59 59
PAK1 0.003 0.092 -10000 0 -0.35 8 8
HRAS 0.012 0.051 -10000 0 -0.41 7 7
RRAS 0.016 0.074 -10000 0 -0.25 30 30
DNM1 0.012 0.052 -10000 0 -0.39 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.006 0.078 -10000 0 -0.26 25 25
lamellipodium assembly -0.036 0.083 -10000 0 -0.37 18 18
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.076 -10000 0 -0.47 5 5
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
EPHB2 0.007 0.062 -10000 0 -0.32 16 16
EPHB3 -0.005 0.1 -10000 0 -0.45 26 26
EPHB1 -0.023 0.11 -10000 0 -0.28 73 73
EPHB4 -0.01 0.11 -10000 0 -0.42 33 33
mol:GDP 0.003 0.098 -10000 0 -0.33 23 23
Ephrin B/EPHB2 0.02 0.069 -10000 0 -0.25 24 24
Ephrin B/EPHB3 0.013 0.085 -10000 0 -0.27 36 36
JNK cascade 0.007 0.081 -10000 0 -0.28 21 21
Ephrin B/EPHB1 0.005 0.083 -10000 0 -0.26 31 31
RAP1/GDP 0.014 0.097 -10000 0 -0.33 15 15
EFNB2 -0.006 0.1 -10000 0 -0.39 31 31
EFNB3 0.018 0 -10000 0 -10000 0 0
EFNB1 0.01 0.051 -10000 0 -0.3 13 13
Ephrin B2/EPHB1-2 -0.006 0.088 -10000 0 -0.28 32 32
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
CDC42/GTP -0.03 0.075 -10000 0 -0.39 11 11
Rap1/GTP -0.031 0.079 -10000 0 -0.4 14 14
axon guidance 0.011 0.056 -10000 0 -0.3 12 12
MAPK3 0.028 0.069 -10000 0 -0.42 5 5
MAPK1 0.027 0.07 -10000 0 -0.39 6 6
Rac1/GDP 0.013 0.093 -10000 0 -0.31 21 21
actin cytoskeleton reorganization -0.034 0.073 -10000 0 -0.31 18 18
CDC42/GDP 0.013 0.093 -10000 0 -0.31 21 21
PI3K 0 0.1 -10000 0 -0.28 55 55
EFNA5 0.006 0.069 -10000 0 -0.35 17 17
Ephrin B2/EPHB4 -0.007 0.096 -10000 0 -0.34 35 35
Ephrin B/EPHB2/Intersectin/N-WASP 0.021 0.068 -10000 0 -0.3 3 3
CDC42 0.018 0 -10000 0 -10000 0 0
RAS family/GTP -0.034 0.076 -10000 0 -0.34 17 17
PTK2 0.007 0.034 -10000 0 -0.34 3 3
MAP4K4 0.007 0.082 -10000 0 -0.28 21 21
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 0.011 0.11 -10000 0 -0.34 21 21
MAP2K1 0.022 0.072 -10000 0 -0.44 5 5
WASL 0.01 0.066 -10000 0 -0.52 8 8
Ephrin B1/EPHB1-2/NCK1 0.011 0.082 -10000 0 -0.27 26 26
cell migration 0.027 0.076 -10000 0 -0.45 5 5
NRAS 0.006 0.072 -10000 0 -0.4 15 15
SYNJ1 0.02 0.064 -10000 0 -0.24 23 23
PXN 0.018 0 -10000 0 -10000 0 0
TF 0.02 0.065 -10000 0 -0.32 1 1
HRAS/GTP 0.004 0.092 -10000 0 -0.38 12 12
Ephrin B1/EPHB1-2 0.003 0.075 -10000 0 -0.27 22 22
cell adhesion mediated by integrin 0.012 0.061 0.26 20 -10000 0 20
RAC1 0.018 0 -10000 0 -10000 0 0
mol:GTP 0.008 0.097 -10000 0 -0.41 11 11
RAC1-CDC42/GTP -0.034 0.08 -10000 0 -0.35 18 18
RASA1 0.004 0.079 -10000 0 -0.42 16 16
RAC1-CDC42/GDP 0.02 0.09 -10000 0 -0.34 9 9
ruffle organization 0.01 0.1 -10000 0 -0.38 17 17
NCK1 0.011 0.046 -10000 0 -0.28 12 12
receptor internalization 0.022 0.067 -10000 0 -0.33 2 2
Ephrin B/EPHB2/KALRN 0.025 0.077 -10000 0 -0.27 22 22
ROCK1 0.012 0.064 -10000 0 -0.28 21 21
RAS family/GDP -0.034 0.075 -10000 0 -0.32 18 18
Rac1/GTP -0.038 0.088 -10000 0 -0.39 18 18
Ephrin B/EPHB1/Src/Paxillin 0.014 0.076 -10000 0 -0.27 24 24
Regulation of p38-alpha and p38-beta

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
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 -0.012 0.11 -9999 0 -0.4 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.005 0.099 -9999 0 -0.39 30 30
RAC1-CDC42/GTP/PAK family -0.001 0.071 -9999 0 -0.22 40 40
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 -0.26 1 1
FYN 0.009 0.063 -9999 0 -0.4 11 11
MAP3K12 0.018 0 -9999 0 -10000 0 0
FGR 0.017 0.017 -9999 0 -0.26 2 2
p38 alpha/TAB1 0.011 0.093 -9999 0 -0.28 28 28
PRKG1 0.017 0.012 -9999 0 -0.26 1 1
DUSP8 -0.005 0.11 -9999 0 -0.47 25 25
PGK/cGMP/p38 alpha -0.028 0.07 -9999 0 -0.27 28 28
apoptosis 0.01 0.089 -9999 0 -0.27 28 28
RAL/GTP 0.022 0.029 -9999 0 -0.31 4 4
LYN 0.014 0.031 -9999 0 -0.26 7 7
DUSP1 -0.038 0.15 -9999 0 -0.41 69 69
PAK1 -0.022 0.13 -9999 0 -0.38 53 53
SRC 0.015 0.035 -9999 0 -0.43 3 3
RAC1/OSM/MEKK3/MKK3 0.043 0.022 -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 0.003 0.11 -9999 0 -0.32 33 33
BLK -0.018 0.1 -9999 0 -0.29 61 61
HCK -0.005 0.11 -9999 0 -0.47 25 25
MAP2K3 0.014 0.037 -9999 0 -0.3 7 7
DUSP16 0.005 0.078 -9999 0 -0.43 15 15
DUSP10 -0.017 0.12 -9999 0 -0.4 44 44
TRAF6/MEKK3 0.022 0.015 -9999 0 -0.28 1 1
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.004 0.099 -9999 0 -0.3 32 32
positive regulation of innate immune response 0.003 0.12 -9999 0 -0.37 30 30
LCK -0.073 0.18 -9999 0 -0.4 115 115
p38alpha-beta/MKP7 0.006 0.13 -9999 0 -0.36 34 34
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 -0.012 0.14 -9999 0 -0.36 43 43
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
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.015 0.029 -9999 0 -0.26 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 0.026 -9999 0 -0.24 1 1
FIH (dimer) 0.017 0.023 -9999 0 -0.52 1 1
CDKN2A -0.054 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 18 18
CUL2 0.017 0.017 -9999 0 -0.26 2 2
OS9 0.014 0.041 -9999 0 -0.35 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 -0.32 20 20
PHD1-3/OS9 -0.021 0.12 -9999 0 -0.28 80 80
HIF1A/RACK1/Elongin B/Elongin C 0.012 0.083 -9999 0 -0.34 5 5
VHL 0.014 0.031 -9999 0 -0.26 7 7
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
HIF1A/JAB1 -0.004 0.087 -9999 0 -0.3 20 20
EGLN3 -0.074 0.18 -9999 0 -0.4 116 116
EGLN2 0.011 0.054 -9999 0 -0.38 9 9
EGLN1 0.001 0.082 -9999 0 -0.36 23 23
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 0.021 -9999 0 -0.26 3 3
RBX1 0.018 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.032 0.11 -9999 0 -0.33 33 33
Signaling events mediated by PRL

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
CCNE1 -0.018 0.1 -10000 0 -0.28 64 64
mol:Halofuginone 0.004 0.012 -10000 0 -10000 0 0
ITGA1 0.001 0.093 -10000 0 -0.51 17 17
CDKN1A -0.017 0.12 -10000 0 -0.46 24 24
PRL-3/alpha Tubulin 0.023 0.026 -10000 0 -0.37 1 1
mol:Ca2+ -0.078 0.14 0.38 1 -0.38 65 66
AGT -0.097 0.19 -10000 0 -0.37 159 159
CCNA2 -0.042 0.13 -10000 0 -0.42 20 20
TUBA1B 0.018 0 -10000 0 -10000 0 0
EGR1 -0.06 0.15 -10000 0 -0.37 81 81
CDK2/Cyclin E1 -0.016 0.12 -10000 0 -0.44 27 27
MAPK3 0.022 0.032 -10000 0 -0.37 2 2
PRL-2 /Rab GGTase beta 0.017 0.056 -10000 0 -0.37 9 9
MAPK1 0.021 0.036 -10000 0 -0.37 3 3
PTP4A1 -0.031 0.12 -10000 0 -0.6 5 5
PTP4A3 0.014 0.037 -10000 0 -0.3 7 7
PTP4A2 0.005 0.075 -10000 0 -0.42 15 15
ITGB1 0.02 0.037 -10000 0 -0.37 3 3
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 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.022 0.12 -10000 0 -0.52 6 6
RABGGTA 0.018 0 -10000 0 -10000 0 0
BCAR1 0.002 0.023 0.38 1 -10000 0 1
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 -0.55 5 5
PRL-3/alpha1 Integrin 0.011 0.075 -10000 0 -0.39 16 16
ROCK1 0.002 0.075 -10000 0 -0.36 6 6
RABGGTB 0.017 0.017 -10000 0 -0.26 2 2
CDK2 0.011 0.047 -10000 0 -0.31 10 10
mitosis -0.03 0.12 -10000 0 -0.59 5 5
ATF5 0.013 0.041 -10000 0 -0.29 9 9
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.002 0.073 -9999 0 -0.26 33 33
TRAF2/ASK1 -0.002 0.084 -9999 0 -0.31 32 32
ATM 0.017 0.012 -9999 0 -0.26 1 1
MAP2K3 -0.012 0.12 -9999 0 -0.37 39 39
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.016 0.12 -9999 0 -0.32 45 45
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 -0.46 16 16
TXN 0.01 0.008 -9999 0 -10000 0 0
CALM1 0.018 0 -9999 0 -10000 0 0
GADD45A -0.012 0.11 -9999 0 -0.39 38 38
GADD45B -0.002 0.097 -9999 0 -0.44 23 23
MAP3K1 -0.031 0.14 -9999 0 -0.43 58 58
MAP3K6 0.015 0.035 -9999 0 -0.43 3 3
MAP3K7 0.016 0.021 -9999 0 -0.26 3 3
MAP3K4 0.018 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.003 0.098 -9999 0 -0.37 32 32
TAK1/TAB family 0.01 0.039 -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 -0.46 4 4
RAC1/OSM/MEKK3/MKK3 -0.03 0.079 -9999 0 -0.33 18 18
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 -0.079 0.18 -9999 0 -0.37 133 133
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 86 86
OSM/MEKK3 0.026 0.008 -9999 0 -10000 0 0
TAOK1 0.013 0.041 -9999 0 -0.32 6 6
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 -0.26 1 1
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
MAP3K5 -0.021 0.13 -9999 0 -0.42 46 46
MAP3K10 -0.001 0.097 -9999 0 -0.48 20 20
MAP3K3 0.017 0.012 -9999 0 -0.26 1 1
TRX/ASK1 -0.003 0.078 -9999 0 -0.31 29 29
GADD45/MTK1/MTK1 0.009 0.097 -9999 0 -0.29 42 42
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.021 0.042 -10000 0 -0.37 5 5
ATM 0.017 0.012 -10000 0 -0.26 1 1
UBE2D3 0.018 0 -10000 0 -10000 0 0
PRKDC 0.012 0.046 -10000 0 -0.32 9 9
ATR 0.017 0.012 -10000 0 -0.26 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 -0.26 1 1
M/R/N Complex 0.029 0.047 -10000 0 -0.3 10 10
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 -0.37 6 6
FANCF 0.012 0.057 -10000 0 -0.52 6 6
BRCA1 0 0.094 -10000 0 -0.48 19 19
CCNE1 -0.018 0.1 -10000 0 -0.28 64 64
CDK2/Cyclin E1 -0.002 0.081 -10000 0 -0.38 11 11
FANCG 0.016 0.024 -10000 0 -0.26 4 4
BRCA1/BACH1/BARD1 0.01 0.076 -10000 0 -0.37 20 20
FANCE 0.006 0.062 -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 0.13 -10000 0 -0.31 80 80
DNA repair 0.013 0.12 -10000 0 -0.39 22 22
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 -0.26 7 7
mRNA polyadenylation -0.021 0.042 0.37 5 -10000 0 5
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.058 -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 0.059 -10000 0 -0.38 11 11
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 -0.004 0.12 -10000 0 -0.28 73 73
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 0.074 -10000 0 -0.34 6 6
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 -0.26 2 2
G1/S transition of mitotic cell cycle -0.008 0.11 0.3 51 -10000 0 51
BRCA1/BARD1 0.019 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 0.011 0.047 -10000 0 -0.31 10 10
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.039 0.16 -10000 0 -0.47 62 62
RAD50 0.01 0.066 -10000 0 -0.52 8 8
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
Signaling events mediated by HDAC Class III

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
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 0.026 0.24 3 -10000 0 3
CDKN1A -0.016 0.12 -10000 0 -0.71 15 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.016 0.021 -10000 0 -0.26 3 3
FOXO3 0.001 0.043 0.41 4 -0.25 4 8
FOXO1 0.001 0.089 -10000 0 -0.46 18 18
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 -0.26 1 1
TAT -0.007 0.079 -10000 0 -0.26 48 48
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.012 0.091 -10000 0 -0.33 37 37
PPARGC1A -0.012 0.1 -10000 0 -0.31 48 48
FHL2 -0.08 0.19 -10000 0 -0.41 120 120
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 0.026 -10000 0 -0.24 3 3
SIRT1/FOXO3a 0.005 0.041 0.32 4 -0.2 5 9
SIRT1 0.015 0.039 0.2 9 -0.35 3 12
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 37 37
apoptosis -0.033 0.028 0.3 1 -10000 0 1
SIRT1/PGC1A 0.005 0.064 -10000 0 -0.31 11 11
p53/SIRT1 -0.017 0.11 0.4 9 -0.37 32 41
SIRT1/FOXO4 0.026 0.037 -10000 0 -0.24 7 7
FOXO1/FHL2/SIRT1 -0.031 0.12 -10000 0 -0.3 81 81
HIST1H1E -0.005 0.08 -10000 0 -0.27 39 39
SIRT1/p300 0.021 0.043 -10000 0 -0.36 5 5
muscle cell differentiation 0.002 0.081 0.31 30 -10000 0 30
TP53 -0.023 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 -0.31 30 30
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 0.02 0.062 -10000 0 -0.32 4 4
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.017 0.012 -10000 0 -0.26 1 1
AKT1 0.029 0.093 0.22 53 -0.24 21 74
RAR alpha/9cRA/Cyclin H -0.024 0.063 -10000 0 -0.4 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.014 0.071 -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 0.014 0.052 -10000 0 -0.36 6 6
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 0.012 0.052 -10000 0 -0.39 8 8
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 -0.46 10 10
RARA 0.017 0.052 -10000 0 -0.26 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.013 0.068 -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 0.065 -10000 0 -0.32 13 13
RXRA 0.011 0.08 -10000 0 -0.33 5 5
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 -0.054 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 -0.26 1 1
RAR alpha/RXRs 0.02 0.15 -10000 0 -0.42 19 19
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.022 0.11 -10000 0 -0.37 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.068 -10000 0 -0.29 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.026 0.21 -10000 0 -0.6 54 54
positive regulation of DNA binding -0.023 0.06 -10000 0 -0.38 5 5
NRIP1 -0.086 0.38 -10000 0 -1.2 53 53
RXRs/RARs -0.012 0.15 -10000 0 -0.42 55 55
RXRs/RXRs/DNA/9cRA 0.003 0.12 -10000 0 -0.41 8 8
PRKACA 0.018 0 -10000 0 -10000 0 0
CDK7 0.017 0.012 -10000 0 -0.26 1 1
TFIIH 0.033 0.031 -10000 0 -0.3 4 4
RAR alpha/9cRA 0.039 0.044 -10000 0 -0.26 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 -0.003 0.022 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0 0.095 -9999 0 -0.4 23 23
AKT1 0.03 0.15 -9999 0 -0.5 22 22
PTK2B 0.015 0.13 -9999 0 -0.59 14 14
VEGFR2 homodimer/Frs2 0.021 0.095 -9999 0 -0.48 14 14
CAV1 0 0.081 -9999 0 -0.32 28 28
CALM1 0.018 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.02 0.11 -9999 0 -0.57 10 10
endothelial cell proliferation 0.046 0.13 -9999 0 -0.46 18 18
mol:Ca2+ 0.014 0.14 -9999 0 -0.57 17 17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.033 0.1 -9999 0 -0.55 9 9
RP11-342D11.1 0.004 0.14 -9999 0 -0.58 16 16
CDH5 0.013 0.052 -9999 0 -0.52 5 5
VEGFA homodimer 0.003 0.1 -9999 0 -0.27 52 52
SHC1 0.017 0.023 -9999 0 -0.52 1 1
SHC2 -0.061 0.19 -9999 0 -0.51 78 78
HRAS/GDP -0.036 0.099 -9999 0 -0.51 15 15
SH2D2A -0.038 0.15 -9999 0 -0.38 75 75
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.044 0.12 -9999 0 -0.46 16 16
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.007 0.13 -9999 0 -0.53 14 14
VEGFR1 homodimer 0.005 0.077 -9999 0 -0.44 14 14
SHC/GRB2/SOS1 0.025 0.13 -9999 0 -0.56 15 15
GRB10 0.004 0.17 -9999 0 -0.6 29 29
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
GRB2 0.016 0.024 -9999 0 -0.26 4 4
PAK1 -0.022 0.13 -9999 0 -0.38 53 53
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.029 0.12 -9999 0 -0.53 14 14
HRAS 0.012 0.051 -9999 0 -0.41 7 7
VEGF/Rho/ROCK1/Integrin Complex 0.017 0.12 -9999 0 -0.54 15 15
HIF1A -0.037 0.16 -9999 0 -0.46 61 61
FRS2 0.01 0.047 -9999 0 -0.28 13 13
oxygen and reactive oxygen species metabolic process 0.032 0.1 -9999 0 -0.55 9 9
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 0.019 0.12 -9999 0 -0.62 10 10
mol:GDP -0.038 0.1 -9999 0 -0.53 16 16
mol:NADP 0.042 0.11 -9999 0 -0.4 16 16
eNOS/Hsp90 0.046 0.11 -9999 0 -0.41 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
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 -0.29 31 31
VEGFC 0 0.092 -9999 0 -0.47 19 19
FAK1/Vinculin 0.035 0.13 -9999 0 -0.63 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 -0.61 15 15
PTPN6 0.015 0.035 -9999 0 -0.43 3 3
EPAS1 0.013 0.082 -9999 0 -0.42 16 16
mol:L-citrulline 0.042 0.11 -9999 0 -0.4 16 16
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.029 0.1 -9999 0 -0.53 10 10
VEGFR2 homodimer/VEGFA homodimer 0.012 0.15 -9999 0 -0.64 16 16
VEGFR2/3 heterodimer 0.025 0.092 -9999 0 -0.49 13 13
VEGFB 0.017 0.023 -9999 0 -0.52 1 1
MAPK11 0.014 0.14 -9999 0 -0.57 18 18
VEGFR2 homodimer 0.02 0.1 -9999 0 -0.57 13 13
FLT1 0.005 0.077 -9999 0 -0.45 14 14
NEDD4 -0.001 0.096 -9999 0 -0.53 16 16
MAPK3 0.016 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 0.018 0.11 -9999 0 -0.44 22 22
KDR 0.02 0.1 -9999 0 -0.57 13 13
VEGFA165/NRP1/VEGFR2 homodimer 0.016 0.15 -9999 0 -0.57 18 18
SRC 0.015 0.035 -9999 0 -0.43 3 3
platelet activating factor biosynthetic process 0.017 0.13 -9999 0 -0.54 17 17
PI3K 0.021 0.16 -9999 0 -0.57 23 23
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.02 0.11 -9999 0 -0.59 9 9
FES 0.011 0.15 -9999 0 -0.62 16 16
GAB1 0.02 0.15 -9999 0 -0.57 18 18
VEGFR2 homodimer/VEGFA homodimer/Src 0.022 0.11 -9999 0 -0.59 9 9
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 -0.44 15 15
VEGFR2 homodimer/VEGFA homodimer/Yes 0.018 0.11 -9999 0 -0.55 12 12
PI3K/GAB1 0.028 0.16 -9999 0 -0.48 26 26
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.014 0.12 -9999 0 -0.45 17 17
PRKACA 0.018 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.025 0.11 -9999 0 -0.52 15 15
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
CDC42 0.014 0.14 -9999 0 -0.6 16 16
actin cytoskeleton reorganization -0.007 0.13 -9999 0 -0.52 14 14
PTK2 0.026 0.14 -9999 0 -0.65 13 13
EDG1 -0.005 0.19 -9999 0 -0.65 32 32
mol:DAG 0.014 0.14 -9999 0 -0.58 17 17
CaM/Ca2+ 0.02 0.13 -9999 0 -0.53 17 17
MAP2K3 0.014 0.14 -9999 0 -0.55 19 19
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.01 0.18 -9999 0 -0.61 29 29
PLCG1 0.013 0.14 -9999 0 -0.59 17 17
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.11 -9999 0 -0.48 14 14
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 -0.58 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.022 0.11 -9999 0 -0.59 9 9
cell migration 0.055 0.12 -9999 0 -0.66 8 8
mol:PI-3-4-5-P3 0.022 0.15 -9999 0 -0.52 23 23
FYN 0.009 0.063 -9999 0 -0.4 11 11
VEGFB/NRP1 0.013 0.14 -9999 0 -0.56 16 16
mol:NO 0.042 0.11 -9999 0 -0.4 16 16
PXN 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.036 0.099 -9999 0 -0.51 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.008 0.17 -9999 0 -0.61 29 29
VHL 0.014 0.031 -9999 0 -0.26 7 7
ITGB3 0.002 0.076 -9999 0 -0.32 25 25
NOS3 0.041 0.12 -9999 0 -0.45 16 16
VEGFR2 homodimer/VEGFA homodimer/Sck -0.021 0.15 -9999 0 -0.48 23 23
RAC1 0.018 0 -9999 0 -10000 0 0
PRKCA 0.018 0.14 -9999 0 -0.51 19 19
PRKCB 0.012 0.13 -9999 0 -0.54 17 17
VCL 0.016 0.029 -9999 0 -0.35 3 3
VEGFA165/NRP1 0.008 0.14 -9999 0 -0.59 16 16
VEGFR1/2 heterodimer/VEGFA homodimer 0.017 0.12 -9999 0 -0.57 13 13
VEGFA165/NRP2 0.009 0.065 -9999 0 -0.37 8 8
MAPKKK cascade 0.03 0.15 -9999 0 -0.5 29 29
NRP2 0.01 0.052 -9999 0 -0.33 11 11
VEGFC homodimer 0 0.092 -9999 0 -0.46 19 19
NCK1 0.011 0.046 -9999 0 -0.28 12 12
ROCK1 0.018 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.035 0.13 -9999 0 -0.64 11 11
MAP3K13 0.009 0.15 -9999 0 -0.58 19 19
PDPK1 0.027 0.14 -9999 0 -0.46 23 23
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
mol:S1P 0 0.005 -9999 0 -0.015 42 42
S1P1/S1P/Gi 0 0.1 -9999 0 -0.43 15 15
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
S1P/S1P3/G12/G13 0.02 0.034 -9999 0 -0.28 5 5
AKT1 0.013 0.097 -9999 0 -0.58 12 12
AKT3 0.007 0.13 -9999 0 -1.2 3 3
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 0.017 0.024 -9999 0 -0.52 1 1
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.005 -9999 0 -0.017 42 42
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.13 -9999 0 -0.41 48 48
mol:Ca2+ 0.011 0.082 -9999 0 -0.4 7 7
MAPK3 0.017 0.078 -9999 0 -0.4 6 6
MAPK1 0.016 0.079 -9999 0 -0.4 6 6
JAK2 0.007 0.094 -9999 0 -0.35 17 17
CXCR4 -0.005 0.11 -9999 0 -0.42 17 17
FLT1 0.007 0.077 -9999 0 -0.44 14 14
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.016 0.081 -9999 0 -0.39 8 8
S1P/S1P3/Gi 0.011 0.082 -9999 0 -0.4 7 7
RAC1 0.018 0 -9999 0 -10000 0 0
RhoA/GTP 0.012 0.087 -9999 0 -0.41 8 8
VEGFA 0.001 0.077 -9999 0 -0.29 31 31
S1P/S1P2/Gi 0.01 0.078 -9999 0 -0.31 13 13
VEGFR1 homodimer/VEGFA homodimer 0.011 0.081 -9999 0 -0.34 18 18
RHOA 0.005 0.08 -9999 0 -0.52 12 12
S1P/S1P3/Gq -0.028 0.095 -9999 0 -0.27 59 59
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.003 0.085 -9999 0 -0.43 18 18
G12/G13 0.02 0.043 -9999 0 -0.37 5 5
GNA14 -0.081 0.18 -9999 0 -0.35 141 141
GNA15 0.001 0.078 -9999 0 -0.33 25 25
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
GNA11 0.014 0.047 -9999 0 -0.52 4 4
Rac1/GTP 0.018 0.075 -9999 0 -0.38 6 6
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.014 0.047 -10000 0 -0.52 4 4
RAS family/GTP/Tiam1 0.003 0.08 -10000 0 -0.28 28 28
NT3 (dimer)/TRKC -0.018 0.093 -10000 0 -0.35 16 16
NT3 (dimer)/TRKB -0.015 0.1 -10000 0 -0.32 36 36
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 0.092 -10000 0 -0.26 64 64
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
DYNLT1 0.018 0 -10000 0 -10000 0 0
NTRK1 0.01 0.054 -10000 0 -0.32 12 12
NTRK2 -0.017 0.11 -10000 0 -0.34 52 52
NTRK3 -0.009 0.082 -10000 0 -0.26 52 52
NT-4/5 (dimer)/TRKB -0.004 0.079 -10000 0 -0.31 23 23
neuron apoptosis 0.036 0.15 0.34 80 -10000 0 80
SHC 2-3/Grb2 -0.04 0.16 -10000 0 -0.37 80 80
SHC1 0.017 0.023 -10000 0 -0.52 1 1
SHC2 -0.062 0.2 -10000 0 -0.5 79 79
SHC3 -0.007 0.11 -10000 0 -0.46 18 18
STAT3 (dimer) -0.045 0.14 -10000 0 -0.34 89 89
NT3 (dimer)/TRKA 0.001 0.083 -10000 0 -0.34 16 16
RIN/GDP 0.048 0.049 -10000 0 -0.31 1 1
GIPC1 0.014 0.042 -10000 0 -0.46 4 4
KRAS 0.008 0.069 -10000 0 -0.45 11 11
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 -0.46 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 -0.26 4 4
NGF (dimer)/TRKA/MATK 0.008 0.055 -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 -0.26 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 0.047 -10000 0 -0.26 16 16
RIT2 0.015 0.035 -10000 0 -0.43 3 3
RIT1 0.016 0.033 -10000 0 -0.52 2 2
FRS2 0.01 0.047 -10000 0 -0.28 13 13
DNM1 0.012 0.052 -10000 0 -0.39 8 8
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 20 -0.25 6 26
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 32 32
BDNF (dimer)/TRKB -0.008 0.091 -10000 0 -0.32 24 24
KIDINS220/CRKL/C3G 0.023 0.034 -10000 0 -0.37 4 4
SHC/RasGAP 0.016 0.06 -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 -0.27 11 11
RIT1/GTP 0.012 0.024 -10000 0 -0.38 2 2
NT3 (dimer) -0.021 0.1 -10000 0 -0.28 67 67
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 0.092 -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 -0.28 1 1
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
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 0.024 -10000 0 -0.37 1 1
Rap1/GTP 0.029 0.074 -10000 0 -0.45 5 5
STAT3 -0.045 0.14 -10000 0 -0.34 89 89
axon guidance -0.042 0.074 -10000 0 -0.34 14 14
MAPK3 0.013 0.051 -10000 0 -0.27 8 8
MAPK1 0.013 0.052 -10000 0 -0.27 9 9
CDC42/GDP 0.048 0.048 -10000 0 -0.31 1 1
NTF3 -0.021 0.1 -10000 0 -0.28 67 67
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.018 0.036 -10000 0 -0.31 4 4
PI3K 0.006 0.082 -10000 0 -0.37 21 21
FRS3 0.017 0.012 -10000 0 -0.26 1 1
FAIM 0.016 0.029 -10000 0 -0.35 3 3
GAB1 0.006 0.074 -10000 0 -0.43 14 14
RASGRF1 0.006 0.076 0.23 19 -0.27 11 30
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MCF2L -0.008 0.082 -10000 0 -0.3 20 20
RGS19 0.014 0.039 -10000 0 -0.36 5 5
CDC42 0.018 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.072 -10000 0 -0.4 5 5
Rac1/GDP 0.048 0.048 -10000 0 -0.31 1 1
NGF (dimer)/TRKA/GRIT 0.011 0.06 -10000 0 -0.31 15 15
neuron projection morphogenesis -0.013 0.13 -10000 0 -0.53 10 10
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 0.066 -10000 0 -0.29 23 23
NGF (dimer)/TRKA/GIPC/GAIP 0.027 0.053 -10000 0 -0.31 10 10
RAS family/GTP/PI3K 0.011 0.077 -10000 0 -0.25 39 39
FRS2 family/SHP2/GRB2/SOS1 0.047 0.038 -10000 0 -0.38 2 2
NRAS 0.006 0.072 -10000 0 -0.4 15 15
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
PRKCI 0.001 0.088 -10000 0 -0.44 19 19
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 0.051 -10000 0 -0.47 4 4
RASA1 0.004 0.079 -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 0.006 0.082 -10000 0 -0.28 22 22
NGF (dimer)/TRKA/p62/Atypical PKCs 0.016 0.061 -10000 0 -0.26 21 21
MATK -0.003 0.076 -10000 0 -0.27 38 38
NEDD4L -0.025 0.14 -10000 0 -0.46 48 48
RAS family/GDP -0.01 0.032 -10000 0 -0.28 1 1
NGF (dimer)/TRKA 0.009 0.071 0.24 21 -0.28 6 27
Rac1/GTP -0.02 0.052 -10000 0 -0.23 17 17
FRS2 family/SHP2/CRK family 0.045 0.043 -10000 0 -0.26 8 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.056 -10000 0 -0.37 5 5
CRKL 0.02 0.086 -10000 0 -0.44 12 12
mol:PIP3 -0.004 0.091 0.47 19 -10000 0 19
AKT1 0.007 0.068 0.34 18 -0.28 4 22
PTK2B 0.017 0.017 -10000 0 -0.26 2 2
RAPGEF1 0.026 0.082 -10000 0 -0.42 11 11
RANBP10 0.018 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
HGF/MET/SHIP2 0.015 0.072 -10000 0 -0.31 19 19
MAP3K5 0.018 0.1 -10000 0 -0.4 15 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.021 0.079 -10000 0 -0.29 24 24
AP1 -0.088 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 0.059 -10000 0 -0.29 2 2
GAB1/CRKL/SHP2/PI3K 0.029 0.098 -10000 0 -0.4 15 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.03 0.082 -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 0.037 0.25 3 -0.18 7 10
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.022 0.045 -10000 0 -0.23 7 7
PAK1 -0.005 0.089 0.32 17 -0.27 28 45
HGF/MET/RANBP10 0.019 0.065 -10000 0 -0.31 14 14
HRAS 0.024 0.081 -10000 0 -0.53 7 7
DOCK1 0.021 0.094 -10000 0 -0.47 11 11
GAB1 0.015 0.087 -10000 0 -0.42 15 15
CRK 0.021 0.085 -10000 0 -0.45 11 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.087 -10000 0 -0.49 13 13
JUN -0.034 0.15 -10000 0 -0.46 57 57
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.005 0.052 -10000 0 -0.24 18 18
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
cell morphogenesis 0.038 0.089 -10000 0 -0.36 9 9
GRB2/SHC 0.024 0.05 -10000 0 -0.23 12 12
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 0.037 0.25 3 -0.18 7 10
HGF/MET/MUC20 0.007 0.064 -10000 0 -0.32 14 14
cell migration 0.023 0.049 -10000 0 -0.23 12 12
GRB2 0.016 0.024 -10000 0 -0.26 4 4
CBL 0.017 0.012 -10000 0 -0.26 1 1
MET/RANBP10 0.013 0.055 -10000 0 -0.37 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.025 0.06 -10000 0 -0.23 24 24
MET/MUC20 0 0.054 -10000 0 -0.2 31 31
RAP1B 0.03 0.081 -10000 0 -0.39 12 12
RAP1A 0.029 0.088 -10000 0 -0.44 12 12
HGF/MET/RANBP9 0.019 0.065 -10000 0 -0.31 14 14
RAF1 0.03 0.077 -10000 0 -0.49 7 7
STAT3 0.029 0.06 -10000 0 -0.29 2 2
cell proliferation 0.036 0.072 -10000 0 -0.32 14 14
RPS6KB1 0.009 0.024 -10000 0 -0.15 1 1
MAPK3 -0.011 0.041 0.66 1 -10000 0 1
MAPK1 -0.009 0.055 0.76 2 -10000 0 2
RANBP9 0.017 0.012 -10000 0 -0.26 1 1
MAPK8 0.025 0.093 -10000 0 -0.38 10 10
SRC 0.029 0.059 -10000 0 -0.26 4 4
PI3K 0.011 0.078 -10000 0 -0.26 30 30
MET/Glomulin 0.004 0.049 -10000 0 -0.18 32 32
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MAP2K1 0.036 0.073 -10000 0 -0.48 6 6
MET -0.001 0.078 -10000 0 -0.3 31 31
MAP4K1 0.029 0.082 -10000 0 -0.44 10 10
PTK2 0.016 0.029 -10000 0 -0.35 3 3
MAP2K2 0.035 0.076 -10000 0 -0.5 6 6
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 0.068 -10000 0 -0.38 13 13
INPPL1 0.012 0.055 -10000 0 -0.45 7 7
PXN 0.018 0 -10000 0 -10000 0 0
SH3KBP1 0.001 0.083 -10000 0 -0.38 22 22
HGS 0.012 0.049 -10000 0 -0.22 19 19
PLCgamma1/PKC 0.012 0.019 -10000 0 -0.28 2 2
HGF 0.008 0.069 -10000 0 -0.45 11 11
RASA1 0.004 0.079 -10000 0 -0.42 16 16
NCK1 0.011 0.046 -10000 0 -0.28 12 12
PTPRJ 0.012 0.055 -10000 0 -0.45 7 7
NCK/PLCgamma1 0.024 0.056 -10000 0 -0.24 13 13
PDPK1 0.003 0.071 0.38 18 -10000 0 18
HGF/MET/SHIP 0.007 0.064 -10000 0 -0.32 14 14
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 0.078 -9999 0 -0.38 17 17
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 -0.024 0.099 -9999 0 -0.26 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 0.007 0.083 -9999 0 -0.41 16 16
EPO/EPOR (dimer) -0.003 0.069 -9999 0 -0.32 1 1
lamellipodium assembly 0.022 0.069 -9999 0 -0.35 6 6
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
PI3K 0.006 0.082 -9999 0 -0.37 21 21
ARF6 0.016 0.033 -9999 0 -0.52 2 2
JAK2 0.007 0.076 -9999 0 -0.31 18 18
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
MADCAM1 0.014 0.034 -9999 0 -0.26 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 0.015 0.037 -9999 0 -0.39 4 4
SRC 0 0.1 -9999 0 -0.3 47 47
ITGB7 0.018 0 -9999 0 -10000 0 0
RAC1 0.018 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.004 0.11 -9999 0 -0.34 45 45
p130Cas/Crk/Dock1 0.019 0.099 -9999 0 -0.45 7 7
VCAM1 -0.021 0.13 -9999 0 -0.42 47 47
RHOA 0.005 0.08 -9999 0 -0.52 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.028 0.069 -9999 0 -0.3 17 17
BCAR1 0.007 0.097 -9999 0 -0.29 41 41
EPOR 0.017 0.017 -9999 0 -0.26 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.017 0.012 -9999 0 -0.26 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 -0.35 3 3
Calcineurin A alpha-beta B1/CABIN1 0.004 0.092 -10000 0 -0.36 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 0.023 0.085 -10000 0 -0.39 8 8
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 0.021 -10000 0 -0.26 3 3
MAPK14 0.018 0.012 -10000 0 -0.26 1 1
BAD 0.017 0.023 -10000 0 -0.52 1 1
CABIN1/MEF2D 0.013 0.088 -10000 0 -0.38 10 10
Calcineurin A alpha-beta B1/BCL2 -0.12 0.22 -10000 0 -0.47 145 145
FKBP8 0.017 0.012 -10000 0 -0.26 1 1
activation-induced cell death of T cells -0.013 0.087 0.37 10 -10000 0 10
KPNB1 0.013 0.052 -10000 0 -0.52 5 5
KPNA2 -0.002 0.088 -10000 0 -0.35 28 28
XPO1 0.018 0 -10000 0 -10000 0 0
SFN -0.015 0.12 -10000 0 -0.45 37 37
MAP3K8 -0.035 0.15 -10000 0 -0.39 69 69
NFAT4/CK1 alpha 0.01 0.075 -10000 0 -0.24 38 38
MEF2D/NFAT1/Cbp/p300 0.057 0.059 -10000 0 -0.38 2 2
CABIN1 0.004 0.092 -10000 0 -0.37 13 13
CALM1 0.018 0.001 -10000 0 -10000 0 0
RAN 0.017 0.012 -10000 0 -0.26 1 1
MAP3K1 -0.031 0.14 -10000 0 -0.43 58 58
CAMK4 0.011 0.047 -10000 0 -0.31 10 10
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 -0.011 0.11 -10000 0 -0.37 40 40
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
MAPK8 0.015 0.04 -10000 0 -0.52 3 3
MAPK9 -0.006 0.11 -10000 0 -0.51 24 24
YWHAG 0.017 0.017 -10000 0 -0.26 2 2
FKBP1A 0.017 0.017 -10000 0 -0.26 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 0.036 -10000 0 -0.26 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 0.011 0.056 -10000 0 -0.42 8 8
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 -0.46 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 0.034 -10000 0 -0.26 8 8
PRKCG 0.018 0 -10000 0 -10000 0 0
PRKCQ -0.014 0.1 -10000 0 -0.32 51 51
FKBP38/BCL2 -0.071 0.16 -10000 0 -0.37 115 115
EP300 0.014 0.047 -10000 0 -0.52 4 4
PRKCB1 -0.051 0.16 -10000 0 -0.39 88 88
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 0.022 0.028 -10000 0 -0.31 2 2
NFATc/ERK1 0.041 0.073 -10000 0 -0.49 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.02 0.087 -10000 0 -0.38 10 10
NR4A1 0.052 0.066 -10000 0 -0.52 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 -0.035 0.15 -10000 0 -0.42 63 63
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 -0.26 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 -0.12 0.22 -10000 0 -0.47 145 145
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.003 0.14 -9999 0 -1 5 5
MKNK1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.005 0.055 -9999 0 -0.29 6 6
ATF2/c-Jun -0.028 0.19 -9999 0 -0.64 44 44
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 -0.005 0.1 -9999 0 -0.34 32 32
MAPKAPK3 0.017 0.017 -9999 0 -0.26 2 2
MAPKAPK2 0.014 0.047 -9999 0 -0.52 4 4
p38alpha-beta/CK2 0.008 0.074 -9999 0 -0.39 6 6
CEBPB 0.011 0.073 -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 0.08 -9999 0 -0.31 6 6
p38alpha-beta/MNK1 0.022 0.059 -9999 0 -0.32 5 5
JUN -0.028 0.19 -9999 0 -0.63 44 44
PPARGC1A 0.002 0.089 -9999 0 -0.35 15 15
USF1 0.005 0.085 -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 0.067 -9999 0 -0.37 6 6
RAB5A 0.018 0 -9999 0 -10000 0 0
HSPB1 -0.013 0.12 -9999 0 -0.33 54 54
p38alpha-beta/HBP1 0.02 0.066 -9999 0 -0.34 8 8
CREB1 0.013 0.076 -9999 0 -0.34 6 6
RAB5/GDP 0.013 0 -9999 0 -10000 0 0
EIF4E 0.024 0.049 -9999 0 -0.27 5 5
RPS6KA4 0.017 0.061 -9999 0 -0.32 6 6
PLA2G4A -0.007 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 -0.35 33 33
ESR1 -0.091 0.17 -9999 0 -0.34 154 154
HBP1 0.015 0.04 -9999 0 -0.52 3 3
MEF2C -0.001 0.1 -9999 0 -0.34 31 31
MEF2A 0.017 0.062 -9999 0 -0.33 6 6
EIF4EBP1 0.008 0.081 -9999 0 -0.34 8 8
KRT19 -0.014 0.12 -9999 0 -0.34 53 53
ELK4 0.015 0.066 -9999 0 -0.31 9 9
ATF6 0.017 0.061 -9999 0 -0.32 6 6
ATF1 0.013 0.077 -9999 0 -0.34 6 6
p38alpha-beta/MAPKAPK2 0.02 0.07 -9999 0 -0.37 8 8
p38alpha-beta/MAPKAPK3 0.022 0.06 -9999 0 -0.32 5 5
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.03 0.17 -10000 0 -0.46 10 10
CRKL 0.006 0.075 -10000 0 -0.3 8 8
mol:DAG 0.006 0.083 -10000 0 -0.28 3 3
HRAS 0.023 0.075 -10000 0 -0.41 2 2
MAPK8 0.009 0.059 -10000 0 -0.28 4 4
RAP1A 0.004 0.079 -10000 0 -0.33 10 10
GAB1 0.002 0.081 -10000 0 -0.28 13 13
MAPK14 0.011 0.054 -10000 0 -0.25 1 1
EPO -0.025 0.099 -10000 0 -0.26 80 80
PLCG1 0.005 0.084 -10000 0 -0.29 3 3
EPOR/TRPC2/IP3 Receptors 0.014 0.02 -10000 0 -0.27 2 2
RAPGEF1 0.018 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0 0.073 -10000 0 -0.33 9 9
GAB1/SHC/GRB2/SOS1 0.019 0.074 -10000 0 -0.43 2 2
EPO/EPOR (dimer) -0.005 0.071 -10000 0 -0.19 30 30
IRS2 -0.014 0.1 -10000 0 -0.3 34 34
STAT1 -0.027 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 0.067 -10000 0 -0.31 12 12
TEC 0.005 0.075 -10000 0 -0.27 10 10
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 0.055 -10000 0 -0.33 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
EPO/EPOR (dimer)/JAK2 0.015 0.083 -10000 0 -0.29 6 6
EPO/EPOR -0.005 0.071 -10000 0 -0.19 30 30
LYN 0.012 0.033 -10000 0 -0.27 7 7
TEC/VAV2 0.014 0.076 -10000 0 -0.3 6 6
elevation of cytosolic calcium ion concentration 0.014 0.02 -10000 0 -0.27 2 2
SHC1 0.017 0.023 -10000 0 -0.52 1 1
EPO/EPOR (dimer)/LYN 0.009 0.066 -10000 0 -0.29 1 1
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 38 38
SH2B3 0.015 0.024 -10000 0 -0.52 1 1
NFKB1 0.01 0.056 -10000 0 -0.28 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.051 0.26 1 -0.22 13 14
PTPN6 0 0.073 -10000 0 -0.29 6 6
TEC/VAV2/GRB2 0.021 0.075 -10000 0 -0.29 5 5
EPOR 0.014 0.02 -10000 0 -0.27 2 2
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 -0.29 5 5
CBL 0.007 0.07 -10000 0 -0.31 4 4
SHC/Grb2/SOS1 -0.021 0.044 -10000 0 -0.33 2 2
STAT5A -0.005 0.11 -10000 0 -0.36 5 5
GRB2 0.016 0.024 -10000 0 -0.26 4 4
STAT5 (dimer) -0.013 0.15 -10000 0 -0.36 36 36
LYN/PLCgamma2 -0.002 0.081 -10000 0 -0.36 15 15
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 -0.86 115 115
LPA4-mediated signaling events

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
ADCY4 0.012 0.051 -9999 0 -0.31 12 12
ADCY5 -0.01 0.074 -9999 0 -0.32 14 14
ADCY6 0.015 0.04 -9999 0 -0.31 7 7
ADCY7 0.008 0.058 -9999 0 -0.32 13 13
ADCY1 0.015 0.036 -9999 0 -0.31 5 5
ADCY2 -0.029 0.11 -9999 0 -0.32 50 50
ADCY3 0.011 0.052 -9999 0 -0.31 12 12
ADCY8 0.012 0.044 -9999 0 -0.31 6 6
PRKCE 0.008 0.04 -9999 0 -0.3 8 8
ADCY9 0.002 0.075 -9999 0 -0.32 24 24
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.001 0.069 -9999 0 -0.29 13 13
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
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 0.007 0.083 -9999 0 -0.41 16 16
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 0.046 -10000 0 -0.28 12 12
Glucocorticoid receptor/Hsp90/HDAC6 0.02 0.071 -10000 0 -0.3 23 23
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 0.014 -10000 0 -0.2 1 1
GATA2 -0.008 0.094 -10000 0 -0.32 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 0.047 -10000 0 -0.31 10 10
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 -0.35 3 3
NR3C1 -0.003 0.1 -10000 0 -0.51 21 21
SUMO1/HDAC4 0.036 0.02 -10000 0 -0.31 1 1
SRF 0.016 0.024 -10000 0 -0.26 4 4
HDAC4/YWHAB 0.023 0.032 -10000 0 -0.37 3 3
Tubulin 0.01 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 -0.3 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 0.031 0.035 -10000 0 -0.3 3 3
HDAC4/ER alpha -0.1 0.18 -10000 0 -0.37 150 150
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 -0.46 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 -0.45 202 202
HDAC6/HDAC11 0.004 0.089 -10000 0 -0.37 28 28
Ran/GTP/Exportin 1 0.039 0.014 -10000 0 -10000 0 0
NPC 0.01 0.008 -10000 0 -10000 0 0
MEF2C -0.013 0.12 -10000 0 -0.45 35 35
RAN 0.017 0.012 -10000 0 -0.26 1 1
HDAC4/MEF2C 0.035 0.067 -10000 0 -0.24 27 27
GNG2 0.016 0.029 -10000 0 -0.35 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 -0.26 2 2
ANKRA2 0 0.095 -10000 0 -0.52 17 17
RFXANK 0.017 0.012 -10000 0 -0.26 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 0.072 -10000 0 -0.34 16 16
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 -0.35 3 3
PI3K 0.006 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 32 32
ARF6/GTP 0.031 0.06 -10000 0 -0.47 2 2
cell adhesion 0.034 0.063 -10000 0 -0.27 17 17
CRKL/CBL 0.023 0.035 -10000 0 -0.37 4 4
alpha4/beta1 Integrin/Paxillin 0.026 0.066 -10000 0 -0.3 16 16
ITGB1 0.015 0.037 -10000 0 -0.39 4 4
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 0.016 0.1 -10000 0 -0.29 39 39
p130Cas/Crk/Dock1 0.027 0.054 -10000 0 -0.3 13 13
VCAM1 -0.021 0.13 -10000 0 -0.42 47 47
alpha4/beta1 Integrin/Paxillin/Talin 0.036 0.064 -10000 0 -0.28 17 17
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.065 -10000 0 -0.28 17 17
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
mol:GDP -0.033 0.064 0.27 17 -10000 0 17
CBL 0.017 0.012 -10000 0 -0.26 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 0.036 0.064 -10000 0 -0.28 17 17
Rac1/GTP -0.019 0.087 -10000 0 -0.38 22 22
Aurora C signaling

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
INCENP 0.001 0.084 -9999 0 -0.37 23 23
Aurora C/Aurora B/INCENP 0.015 0.063 -9999 0 -0.28 15 15
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 0.054 -9999 0 -0.27 18 18
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.01 0.068 0.39 10 -10000 0 10
KIRREL 0.009 0.071 -10000 0 -0.53 9 9
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.01 0.068 -10000 0 -0.39 10 10
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 0.029 0.058 -10000 0 -0.28 13 13
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.025 0.06 -10000 0 -0.25 13 13
FYN 0.015 0.057 -10000 0 -0.25 18 18
mol:Ca2+ 0.028 0.059 -10000 0 -0.3 12 12
mol:DAG 0.028 0.059 -10000 0 -0.3 12 12
NPHS2 0.015 0.036 -10000 0 -0.43 3 3
mol:IP3 0.028 0.059 -10000 0 -0.3 12 12
regulation of endocytosis 0.028 0.056 -10000 0 -0.26 12 12
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.054 -10000 0 -0.28 12 12
establishment of cell polarity 0.01 0.068 -10000 0 -0.39 10 10
Nephrin/NEPH1/podocin/NCK1-2 0.035 0.059 -10000 0 -0.25 13 13
Nephrin/NEPH1/beta Arrestin2 0.03 0.057 -10000 0 -0.26 12 12
NPHS1 0.004 0.062 -10000 0 -0.27 25 25
Nephrin/NEPH1/podocin 0.021 0.059 -10000 0 -0.25 18 18
TJP1 0.013 0.052 -10000 0 -0.52 5 5
NCK1 0.011 0.046 -10000 0 -0.28 12 12
NCK2 0.015 0.027 -10000 0 -0.26 5 5
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.029 0.06 -10000 0 -0.3 12 12
CD2AP 0.016 0.029 -10000 0 -0.35 3 3
Nephrin/NEPH1/podocin/GRB2 0.029 0.056 -10000 0 -0.27 12 12
GRB2 0.016 0.024 -10000 0 -0.26 4 4
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.067 -10000 0 -0.27 23 23
cytoskeleton organization 0.03 0.062 -10000 0 -0.28 13 13
Nephrin/NEPH1 0.011 0.048 -10000 0 -0.28 10 10
Nephrin/NEPH1/ZO-1 0.019 0.064 -10000 0 -0.31 15 15
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 -0.26 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 -0.003 0.093 -10000 0 -0.32 37 37
CRY2 0.017 0.012 -10000 0 -0.26 1 1
mol:CO -0.014 0.012 0.14 1 -10000 0 1
CHEK1 -0.045 0.15 -10000 0 -0.38 83 83
mol:HEME 0.014 0.012 -10000 0 -0.14 1 1
PER1 0.014 0.037 -10000 0 -0.3 7 7
BMAL/CLOCK/NPAS2 0.03 0.082 -10000 0 -0.32 21 21
BMAL1/CLOCK 0.042 0.077 -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 0.018 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 0.08 0.3 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 -0.26 4 4
RhoA/GTP 0.01 0.082 -10000 0 -0.31 16 16
negative regulation of cAMP metabolic process 0.008 0.075 -10000 0 -0.31 12 12
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
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 0.075 -10000 0 -0.32 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 -0.015 0.12 -10000 0 -0.38 44 44
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 0.081 -9999 0 -1.3 1 1
PLK1 0.029 0.18 -9999 0 -0.68 9 9
CDKN1B 0.062 0.18 -9999 0 -0.48 31 31
FOXO3 0.021 0.19 -9999 0 -0.58 20 20
KAT2B 0.003 0.021 -9999 0 -0.051 16 16
FOXO1/SIRT1 0.036 0.066 -9999 0 -0.37 5 5
CAT 0.023 0.2 -9999 0 -0.92 10 10
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
AKT1 0.019 0.057 -9999 0 -0.36 9 9
FOXO1 0.036 0.067 -9999 0 -0.39 4 4
MAPK10 0.014 0.074 -9999 0 -0.25 28 28
mol:GTP 0.001 0.003 -9999 0 -10000 0 0
FOXO4 0.06 0.1 -9999 0 -0.4 5 5
response to oxidative stress 0.008 0.022 -9999 0 -0.05 21 21
FOXO3A/SIRT1 0.034 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 -0.05 21 21
RAN 0.018 0.012 -9999 0 -0.26 1 1
GADD45A 0.037 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 0.031 -9999 0 -0.3 3 3
CSNK1D 0.018 0 -9999 0 -10000 0 0
CSNK1E 0.017 0.012 -9999 0 -0.26 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 -0.26 2 2
YWHAE 0.016 0.029 -9999 0 -0.35 3 3
YWHAZ 0.017 0.017 -9999 0 -0.26 2 2
SIRT1 0.018 0.035 -9999 0 -0.35 3 3
SOD2 0.065 0.17 -9999 0 -0.67 8 8
RBL2 0.045 0.16 -9999 0 -0.77 7 7
RAL/GDP 0.031 0.034 -9999 0 -0.31 4 4
CHUK 0.008 0.083 -9999 0 -0.5 13 13
Ran/GTP 0.016 0.009 -9999 0 -0.17 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 -0.26 1 1
FASLG -0.12 0.41 -9999 0 -1.4 49 49
SKP2 0.007 0.053 -9999 0 -0.26 20 20
USP7 0.018 0.013 -9999 0 -0.27 1 1
IKBKB 0.015 0.051 -9999 0 -0.31 10 10
CCNB1 -0.021 0.32 -9999 0 -1.1 38 38
FOXO1-3a-4/beta catenin 0.067 0.17 -9999 0 -0.41 22 22
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.07 -9999 0 -0.42 5 5
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
SGK1 0.003 0.021 -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 0.066 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 -0.31 10 10
FOXO3A/14-3-3 0.043 0.08 -9999 0 -0.38 5 5
CREBBP 0.019 0.033 -9999 0 -0.52 2 2
FBXO32 -0.01 0.3 -9999 0 -1.2 25 25
BCL6 0.015 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 0.079 -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 0.032 0.071 -10000 0 -0.34 10 10
SMAD4/Ubc9/PIASy 0.027 0.052 -10000 0 -0.3 12 12
SMAD2/SMAD2/SMAD4 0.03 0.062 -10000 0 -10000 0 0
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 -0.27 8 9
MAP3K1 -0.031 0.14 -10000 0 -0.43 58 58
TRAP-1/SMAD4 0.02 0.05 -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 -0.42 5 5
CTDSPL 0.011 0.062 -10000 0 -0.52 7 7
KPNB1 0.013 0.052 -10000 0 -0.52 5 5
TGFBRAP1 0.017 0.012 -10000 0 -0.26 1 1
UBE2I 0.018 0 -10000 0 -10000 0 0
NUP153 0.016 0.024 -10000 0 -0.26 4 4
KPNA2 -0.002 0.088 -10000 0 -0.35 28 28
PIAS4 0.013 0.05 -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 -0.32 7 7
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 0.021 -9999 0 -0.26 3 3
IKBKB 0.011 0.047 -9999 0 -0.31 10 10
RIPK2 0.013 0.041 -9999 0 -0.29 9 9
IKBKG 0.016 0.091 -9999 0 -0.51 5 5
IKK complex/A20 0.026 0.1 -9999 0 -0.44 9 9
NEMO/A20/RIP2 0.012 0.041 -9999 0 -0.29 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 -0.26 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 -0.47 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 0.054 -9999 0 -0.38 9 9
cIAP1/UbcH5C 0.025 0.014 -9999 0 -10000 0 0
ATM 0.017 0.012 -9999 0 -0.26 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 0.034 -9999 0 -0.26 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 -0.26 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 -0.43 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 -0.42 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 0.069 -9999 0 -0.35 17 17
FYN 0.016 0.054 -9999 0 -0.28 14 14
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 0.026 0.071 -10000 0 -0.44 6 6
FRAP1 0.018 0 -10000 0 -10000 0 0
PRKDC 0.012 0.046 -10000 0 -0.32 9 9
FOXO3 0.033 0.062 -10000 0 -0.46 6 6
AKT1 0.03 0.054 -10000 0 -0.43 6 6
BAD 0.017 0.023 -10000 0 -0.52 1 1
AKT3 0.008 0.044 -10000 0 -0.32 4 4
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 -0.26 1 1
JNK cascade -0.017 0.078 0.35 10 -10000 0 10
TSC1 0.036 0.051 -10000 0 -0.4 6 6
YWHAZ 0.017 0.017 -10000 0 -0.26 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 0.064 -10000 0 -0.3 19 19
MAP3K5 -0.021 0.13 -10000 0 -0.42 46 46
MAPKAP1 0.016 0.026 -10000 0 -0.39 2 2
negative regulation of cell cycle -0.034 0.049 0.26 2 -10000 0 2
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 -0.35 3 3
SRC 0.015 0.035 -10000 0 -0.43 3 3
AKT2/p21CIP1 0.03 0.067 -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 0.053 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 -0.3 3 3
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 0.028 0.067 -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 -0.26 2 2
RHEB 0.016 0.026 -10000 0 -0.39 2 2
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
CDC42/GTP 0.017 0.069 -9999 0 -0.39 5 5
PLCG1 0.014 0.072 -9999 0 -0.38 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.006 0.075 -9999 0 -0.48 12 12
GNAI3 0.017 0.023 -9999 0 -0.52 1 1
G12/G13 0.02 0.043 -9999 0 -0.37 5 5
cell migration 0.016 0.068 -9999 0 -0.38 5 5
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.014 0.072 -9999 0 -0.38 6 6
MAPK1 0.014 0.073 -9999 0 -0.36 7 7
S1P/S1P5/Gi 0.008 0.075 -9999 0 -0.32 12 12
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
CDC42/GDP 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.012 0 -9999 0 -10000 0 0
RHOA 0.016 0.057 -9999 0 -0.3 15 15
S1P/S1P4/Gi 0.008 0.075 -9999 0 -0.32 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.085 -9999 0 -0.43 18 18
S1P/S1P4/G12/G13 0.018 0.033 -9999 0 -0.28 5 5
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
CDC42 0.018 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.038 0.061 -9999 0 -0.39 3 3
CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
AKT1 0.011 0.054 -9999 0 -0.38 9 9
AKT2 0.017 0.012 -9999 0 -0.26 1 1
STXBP4 0.008 0.061 -9999 0 -0.33 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.033 0.054 -9999 0 -0.29 2 2
YWHAZ 0.017 0.017 -9999 0 -0.26 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 -0.26 2 2
ASIP 0 0 -9999 0 -10000 0 0
PRKCI 0.001 0.088 -9999 0 -0.44 19 19
AS160/CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
RHOQ 0.014 0.042 -9999 0 -0.46 4 4
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 0.019 0.04 -9999 0 -0.31 7 7
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 0.057 -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 0.061 -9999 0 -0.43 9 9
YWHAE 0.016 0.029 -9999 0 -0.35 3 3
Signaling events mediated by HDAC Class I

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
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 0.014 -10000 0 -0.2 1 1
FKBP3 0.013 0.048 -10000 0 -0.47 5 5
Histones 0.043 0.051 -10000 0 -0.28 2 2
YY1/LSF 0.021 0.055 -10000 0 -0.26 19 19
SMG5 0.016 0.029 -10000 0 -0.35 3 3
RAN 0.017 0.012 -10000 0 -0.26 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 -0.3 7 7
HDAC3/TR2 0.026 0.053 -10000 0 -0.28 9 9
NuRD/MBD3 Complex 0.045 0.038 -10000 0 -0.27 2 2
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 -0.008 0.094 -10000 0 -0.32 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 0.033 0.045 -10000 0 -0.29 2 2
YY1/HDAC2 0.023 0.044 -10000 0 -0.25 10 10
YY1/HDAC1 0.027 0.034 -10000 0 -0.23 9 9
NuRD/MBD2 Complex (MeCP1) 0.044 0.038 -10000 0 -0.27 2 2
PPARG 0.007 0.095 -10000 0 -0.3 37 37
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 -0.46 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 0.052 -10000 0 -0.33 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 0.054 -10000 0 -0.29 15 15
YY1 0.021 0.036 -10000 0 -0.27 8 8
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 -0.26 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 -0.26 2 2
YY1/LSF/HDAC1 0.03 0.053 -10000 0 -0.26 12 12
YY1/SAP30/HDAC1 0.033 0.046 -10000 0 -0.3 6 6
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 -0.27 2 2
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 -0.3 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 -10000 0 0
NuRD Complex 0.052 0.044 -10000 0 -0.33 2 2
positive regulation of chromatin silencing 0.04 0.049 -10000 0 -0.27 2 2
SIN3B 0.017 0.012 -10000 0 -0.26 1 1
MTA2 0.014 0.044 -10000 0 -0.42 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 0.046 -10000 0 -0.26 7 7
GATA1/Fog1 0.02 0.05 -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 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.044 0.038 -10000 0 -0.27 2 2
Ran/GTP/Exportin 1 0.039 0.014 -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 -0.26 2 2
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.005 0.061 -10000 0 -0.27 24 24
CLTC 0.024 0.05 -10000 0 -0.49 3 3
calcium ion-dependent exocytosis 0.022 0.039 -10000 0 -0.28 4 4
Dynamin 2/GTP 0.025 0.028 -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 0.04 -10000 0 -0.39 2 2
CTNND1 0.029 0.029 -10000 0 -0.25 3 3
DNM2 0.017 0.012 -10000 0 -0.26 1 1
mol:PI-4-5-P2 0.028 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 0.041 -10000 0 -0.35 6 6
mol:Choline 0.021 0.04 -10000 0 -0.39 2 2
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 0.028 -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 0.086 -10000 0 -0.31 35 35
substrate adhesion-dependent cell spreading 0.022 0.078 -10000 0 -0.44 2 2
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 0.034 -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 0.022 0.079 -10000 0 -0.45 2 2
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 0.024 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 -0.013 0.12 -10000 0 -0.5 31 31
PLD1 0.016 0.049 -10000 0 -0.3 10 10
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 0.005 0.071 -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 0.08 -10000 0 -0.64 2 2
mol:Phosphatidic acid 0.021 0.04 -10000 0 -0.39 2 2
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 -0.26 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 -0.019 0.06 -10000 0 -0.58 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 -0.32 24 24
adrenocorticotropin secretion 0.005 0.042 -10000 0 -0.21 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 0.01 0.052 -10000 0 -0.33 11 11
GNG2 0.016 0.029 -10000 0 -0.35 3 3
CRH 0.007 0.061 -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 0.022 0.018 -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 0.041 -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 0.014 -10000 0 -0.17 3 3
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 0.015 -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 0.008 0.013 -10000 0 -0.12 3 3
AP2M1 0.013 0.05 -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 0.021 -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 -0.26 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 -0.3 5 5
PLD2 0.011 0.026 0.15 8 -0.19 4 12
ARF-GAP1/v-SNARE 0.012 0.014 -10000 0 -0.17 3 3
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 0.014 -10000 0 -0.17 3 3
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 0.013 -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 0.016 -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 -0.26 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.017 0.017 -9999 0 -0.26 2 2
SUMO1/HDAC4 0.036 0.02 -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 -0.3 7 7
MDM2/SUMO1/SUMO1 0.04 0.032 -9999 0 -0.27 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0.014 -9999 0 -0.2 1 1
Ran/GTP 0.031 0.014 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.01 0.044 -9999 0 -0.26 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 -0.26 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/1668779/2.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.

Download Results

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

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