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

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

Summary

There were 52 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 regulated by Ret tyrosine kinase 96
Signaling events mediated by Stem cell factor receptor (c-Kit) 89
Endothelins 77
IGF1 pathway 72
FOXM1 transcription factor network 71
Osteopontin-mediated events 69
IL4-mediated signaling events 65
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 65
Plasma membrane estrogen receptor signaling 63
EGFR-dependent Endothelin signaling events 61
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 regulated by Ret tyrosine kinase 96 7910 82 -0.16 0.036 1000 -1000 -0.044 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 89 6950 78 -0.31 0.13 1000 -1000 -0.035 -1000
Endothelins 77 7440 96 -0.18 0.035 1000 -1000 -0.027 -1000
IGF1 pathway 72 4159 57 -0.079 0.052 1000 -1000 -0.028 -1000
FOXM1 transcription factor network 71 3661 51 -0.44 0.034 1000 -1000 -0.055 -1000
Osteopontin-mediated events 69 2630 38 -0.14 0.04 1000 -1000 -0.022 -1000
IL4-mediated signaling events 65 5966 91 -0.53 0.43 1000 -1000 -0.063 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 65 4421 68 -0.35 0.15 1000 -1000 -0.033 -1000
Plasma membrane estrogen receptor signaling 63 5444 86 -0.22 0.21 1000 -1000 -0.041 -1000
EGFR-dependent Endothelin signaling events 61 1293 21 -0.072 0.048 1000 -1000 -0.016 -1000
Syndecan-1-mediated signaling events 57 1957 34 -0.13 0.042 1000 -1000 -0.023 -1000
HIF-1-alpha transcription factor network 57 4339 76 -0.18 0.05 1000 -1000 0 -1000
Signaling events mediated by the Hedgehog family 56 2913 52 -0.096 0.052 1000 -1000 -0.015 -1000
Glucocorticoid receptor regulatory network 56 6458 114 -0.39 0.19 1000 -1000 -0.043 -1000
Thromboxane A2 receptor signaling 49 5146 105 -0.11 0.062 1000 -1000 -0.029 -1000
Wnt signaling 49 344 7 -0.067 0.03 1000 -1000 -0.006 -1000
Fc-epsilon receptor I signaling in mast cells 46 4472 97 -0.098 0.036 1000 -1000 -0.056 -1000
FAS signaling pathway (CD95) 46 2192 47 -0.1 0.049 1000 -1000 -0.034 -1000
TCR signaling in naïve CD8+ T cells 46 4309 93 -0.072 0.048 1000 -1000 -0.036 -1000
Stabilization and expansion of the E-cadherin adherens junction 46 3412 74 -0.095 0.059 1000 -1000 -0.045 -1000
IL12-mediated signaling events 45 3926 87 -0.26 0.043 1000 -1000 -0.038 -1000
IL23-mediated signaling events 44 2643 60 -0.2 0.036 1000 -1000 -0.057 -1000
Nongenotropic Androgen signaling 43 2256 52 -0.12 0.063 1000 -1000 -0.021 -1000
IL27-mediated signaling events 43 2217 51 -0.2 0.099 1000 -1000 -0.062 -1000
IL6-mediated signaling events 43 3234 75 -0.14 0.038 1000 -1000 -0.045 -1000
Noncanonical Wnt signaling pathway 42 1117 26 -0.067 0.036 1000 -1000 -0.041 -1000
E-cadherin signaling in the nascent adherens junction 42 3263 76 -0.082 0.056 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 39 587 15 -0.056 0.033 1000 -1000 -0.025 -1000
LPA receptor mediated events 39 4014 102 -0.077 0.036 1000 -1000 -0.059 -1000
Syndecan-4-mediated signaling events 39 2617 67 -0.061 0.087 1000 -1000 -0.03 -1000
E-cadherin signaling in keratinocytes 39 1705 43 -0.062 0.036 1000 -1000 -0.015 -1000
Ephrin B reverse signaling 36 1731 48 -0.12 0.073 1000 -1000 -0.039 -1000
Arf6 signaling events 35 2213 62 -0.069 0.079 1000 -1000 -0.01 -1000
IL2 signaling events mediated by PI3K 34 2017 58 -0.23 0.036 1000 -1000 -0.027 -1000
E-cadherin signaling events 34 173 5 -0.011 0.028 1000 -1000 0.019 -1000
ErbB4 signaling events 33 2311 69 -0.1 0.059 1000 -1000 -0.025 -1000
TCGA08_p53 33 234 7 -0.028 0.026 1000 -1000 -0.007 -1000
Canonical Wnt signaling pathway 32 1670 51 -0.15 0.09 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 31 93 3 -0.013 0.03 1000 -1000 -0.004 -1000
Syndecan-2-mediated signaling events 31 2158 69 -0.019 0.048 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 30 2322 76 -0.15 0.054 1000 -1000 -0.031 -1000
Integrins in angiogenesis 30 2562 84 -0.12 0.06 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 29 1166 39 -0.074 0.035 1000 -1000 -0.016 -1000
amb2 Integrin signaling 29 2395 82 -0.049 0.047 1000 -1000 -0.018 -1000
Signaling events mediated by PTP1B 28 2195 76 -0.091 0.062 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 28 228 8 -0.011 0.024 1000 -1000 -0.007 -1000
VEGFR1 specific signals 28 1578 56 -0.028 0.036 1000 -1000 -0.026 -1000
Caspase cascade in apoptosis 27 2066 74 -0.066 0.047 1000 -1000 -0.024 -1000
BMP receptor signaling 27 2200 81 -0.11 0.067 1000 -1000 -0.018 -1000
Nectin adhesion pathway 27 1719 63 -0.047 0.054 1000 -1000 -0.03 -1000
Reelin signaling pathway 27 1532 56 -0.068 0.07 1000 -1000 -0.018 -1000
Visual signal transduction: Rods 27 1431 52 -0.064 0.067 1000 -1000 -0.018 -1000
Regulation of nuclear SMAD2/3 signaling 26 3648 136 -0.19 0.067 1000 -1000 -0.032 -1000
BCR signaling pathway 25 2523 99 -0.1 0.065 1000 -1000 -0.031 -1000
Arf6 downstream pathway 24 1039 43 -0.047 0.048 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 24 1058 44 -0.14 0.05 1000 -1000 -0.026 -1000
mTOR signaling pathway 24 1300 53 -0.068 0.045 1000 -1000 -0.031 -1000
IL1-mediated signaling events 24 1544 62 -0.028 0.075 1000 -1000 -0.025 -1000
Aurora B signaling 24 1650 67 -0.062 0.053 1000 -1000 -0.034 -1000
S1P1 pathway 22 804 36 -0.034 0.036 1000 -1000 -0.016 -1000
Regulation of Telomerase 22 2308 102 -0.15 0.063 1000 -1000 -0.017 -1000
Visual signal transduction: Cones 21 816 38 -0.023 0.051 1000 -1000 0 -1000
FOXA2 and FOXA3 transcription factor networks 21 982 46 -0.2 0.043 1000 -1000 -0.037 -1000
Glypican 1 network 21 1046 48 -0.025 0.049 1000 -1000 -0.025 -1000
PLK1 signaling events 21 1826 85 -0.074 0.052 1000 -1000 -0.038 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 21 963 45 -0.041 0.055 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 21 664 31 -0.035 0.045 1000 -1000 -0.036 -1000
Class I PI3K signaling events 21 1534 73 -0.061 0.045 1000 -1000 -0.026 -1000
Presenilin action in Notch and Wnt signaling 20 1261 61 -0.2 0.071 1000 -1000 -0.025 -1000
Ceramide signaling pathway 20 1556 76 -0.069 0.069 1000 -1000 -0.022 -1000
TRAIL signaling pathway 20 985 48 -0.022 0.037 1000 -1000 -0.03 -1000
Insulin Pathway 20 1519 74 -0.063 0.081 1000 -1000 -0.029 -1000
IFN-gamma pathway 19 1307 68 -0.061 0.059 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 19 1909 97 -0.065 0.067 1000 -1000 -0.033 -1000
ceramide signaling pathway 18 929 49 -0.057 0.049 1000 -1000 -0.035 -1000
EPHB forward signaling 18 1545 85 -0.047 0.11 1000 -1000 -0.052 -1000
Ras signaling in the CD4+ TCR pathway 18 308 17 -0.002 0.05 1000 -1000 -0.012 -1000
RXR and RAR heterodimerization with other nuclear receptor 17 898 52 -0.057 0.063 1000 -1000 -0.032 -1000
ErbB2/ErbB3 signaling events 16 1047 65 -0.045 0.048 1000 -1000 -0.057 -1000
p75(NTR)-mediated signaling 16 2045 125 -0.045 0.086 1000 -1000 -0.041 -1000
Atypical NF-kappaB pathway 16 507 31 -0.017 0.036 1000 -1000 -0.009 -1000
Syndecan-3-mediated signaling events 16 578 35 -0.031 0.069 1000 -1000 -0.025 -1000
EPO signaling pathway 15 862 55 -0.11 0.046 1000 -1000 -0.021 -1000
HIF-2-alpha transcription factor network 15 686 43 -0.1 0.11 1000 -1000 -0.041 -1000
LPA4-mediated signaling events 14 173 12 -0.029 0.021 1000 -1000 -0.021 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 806 54 -0.035 0.05 1000 -1000 -0.02 -1000
Hedgehog signaling events mediated by Gli proteins 14 966 65 -0.022 0.076 1000 -1000 -0.027 -1000
Aurora A signaling 14 858 60 -0.007 0.05 1000 -1000 -0.006 -1000
Retinoic acid receptors-mediated signaling 14 848 58 -0.071 0.068 1000 -1000 -0.02 -1000
IL2 signaling events mediated by STAT5 14 310 22 -0.024 0.037 1000 -1000 -0.025 -1000
Neurotrophic factor-mediated Trk receptor signaling 14 1704 120 -0.077 0.09 1000 -1000 -0.044 -1000
Regulation of Androgen receptor activity 14 1036 70 -0.14 0.048 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 13 366 28 -0.009 0.044 1000 -1000 -0.006 -1000
FoxO family signaling 13 886 64 -0.092 0.049 1000 -1000 -0.02 -1000
Signaling mediated by p38-alpha and p38-beta 13 588 44 -0.055 0.056 1000 -1000 -0.013 -1000
Regulation of p38-alpha and p38-beta 13 747 54 -0.018 0.073 1000 -1000 -0.017 -1000
Glypican 2 network 13 54 4 0 0.014 1000 -1000 0 -1000
p38 MAPK signaling pathway 13 588 44 -0.051 0.058 1000 -1000 -0.014 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 12 1073 85 -0.14 0.064 1000 -1000 -0.043 -1000
TCGA08_rtk_signaling 12 313 26 -0.026 0.043 1000 -1000 -0.009 -1000
S1P3 pathway 12 529 42 -0.016 0.044 1000 -1000 -0.014 -1000
Nephrin/Neph1 signaling in the kidney podocyte 11 374 34 -0.039 0.076 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 413 37 -0.024 0.073 1000 -1000 -0.02 -1000
S1P5 pathway 11 194 17 -0.001 0.035 1000 -1000 -0.006 -1000
Signaling events mediated by VEGFR1 and VEGFR2 11 1471 125 -0.025 0.045 1000 -1000 -0.023 -1000
Angiopoietin receptor Tie2-mediated signaling 11 1001 88 -0.063 0.063 1000 -1000 -0.063 -1000
S1P4 pathway 11 289 25 -0.009 0.044 1000 -1000 -0.013 -1000
BARD1 signaling events 10 584 57 -0.048 0.07 1000 -1000 -0.045 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 10 909 83 -0.057 0.069 1000 -1000 -0.013 -1000
Paxillin-dependent events mediated by a4b1 10 379 36 -0.061 0.064 1000 -1000 -0.033 -1000
Effects of Botulinum toxin 10 267 26 -0.062 0.051 1000 -1000 -0.001 -1000
Signaling events mediated by PRL 10 363 34 -0.038 0.051 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 9 688 75 -0.089 0.076 1000 -1000 -0.024 -1000
a4b1 and a4b7 Integrin signaling 9 49 5 0.021 0.042 1000 -1000 0.022 -1000
Signaling events mediated by HDAC Class III 9 392 40 -0.064 0.065 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 9 27 3 -0.026 0.026 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 285 33 -0.015 0.072 1000 -1000 -0.024 -1000
Ephrin A reverse signaling 6 44 7 0 0.042 1000 -1000 0 -1000
JNK signaling in the CD4+ TCR pathway 6 118 17 -0.01 0.08 1000 -1000 -0.019 -1000
Insulin-mediated glucose transport 6 207 32 0 0.042 1000 -1000 -0.015 -1000
Class I PI3K signaling events mediated by Akt 6 432 68 -0.053 0.076 1000 -1000 -0.02 -1000
Arf6 trafficking events 6 429 71 -0.041 0.043 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 5 133 23 0 0.055 1000 -1000 -0.012 -1000
Canonical NF-kappaB pathway 5 200 39 0 0.074 1000 -1000 -0.01 -1000
Alternative NF-kappaB pathway 5 77 13 0 0.082 1000 -1000 0 -1000
Circadian rhythm pathway 4 101 22 -0.01 0.067 1000 -1000 -0.028 -1000
Arf1 pathway 4 237 54 -0.001 0.062 1000 -1000 -0.01 -1000
Aurora C signaling 3 22 7 0 0.054 1000 -1000 -0.01 -1000
Signaling events mediated by HDAC Class I 3 383 104 -0.047 0.081 1000 -1000 -0.026 -1000
Rapid glucocorticoid signaling 2 55 20 -0.001 0.044 1000 -1000 -0.001 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 22 27 0 0.081 1000 -1000 -0.016 -1000
Total 3422 210626 7203 -11 8 131000 -131000 -3.3 -131000
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.13 -10000 0 -0.52 30 30
Crk/p130 Cas/Paxillin -0.13 0.16 -10000 0 -0.33 162 162
JUN -0.13 0.18 0.19 2 -0.4 113 115
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.2 -10000 0 -0.31 228 228
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
FRS2 0.033 0.022 -10000 0 -0.42 1 1
RAP1A/GDP 0.023 0.032 -10000 0 -0.3 5 5
RET51/GFRalpha1/GDNF/DOK1 -0.097 0.21 -10000 0 -0.32 220 220
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Enigma -0.041 0.14 -10000 0 -0.23 171 171
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RAP1A/GTP -0.093 0.18 -10000 0 -0.28 221 221
GRB7 0.024 0.058 -10000 0 -0.42 8 8
RET51/GFRalpha1/GDNF -0.092 0.2 -10000 0 -0.31 217 217
MAPKKK cascade -0.11 0.19 -10000 0 -0.32 203 203
BCAR1 0.03 0.014 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.064 0.17 -10000 0 -0.28 181 181
lamellipodium assembly -0.11 0.16 -10000 0 -0.31 165 165
RET51/GFRalpha1/GDNF/SHC -0.08 0.18 -10000 0 -0.29 195 195
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC -0.028 0.12 -10000 0 -0.23 123 123
RET9/GFRalpha1/GDNF/Shank3 -0.042 0.14 -10000 0 -0.23 174 174
MAPK3 -0.11 0.15 0.24 3 -0.38 90 93
DOK1 0.027 0.061 -10000 0 -0.42 9 9
DOK6 0.005 0.11 -10000 0 -0.42 31 31
PXN 0.036 0.004 -10000 0 -10000 0 0
neurite development -0.11 0.16 0.28 2 -0.37 102 104
DOK5 0.012 0.089 -10000 0 -0.42 20 20
GFRA1 -0.13 0.21 -10000 0 -0.42 177 177
MAPK8 -0.12 0.18 -10000 0 -0.3 218 218
HRAS/GTP -0.11 0.22 -10000 0 -0.35 217 217
tube development -0.03 0.14 0.22 24 -0.22 163 187
MAPK1 -0.12 0.16 0.24 3 -0.38 90 93
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.12 -10000 0 -0.22 157 157
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
SRC 0.033 0.029 -10000 0 -0.42 2 2
PDLIM7 0.035 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.093 0.21 -10000 0 -0.32 220 220
SHC1 0.028 0.025 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.2 -10000 0 -0.31 220 220
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.2 -10000 0 -0.32 213 213
PRKCA 0.032 0.012 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
CREB1 -0.086 0.17 -10000 0 -0.33 147 147
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.039 0.11 -10000 0 -0.23 115 115
RET51/GFRalpha1/GDNF/Grb7 -0.095 0.2 -10000 0 -0.32 211 211
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.095 0.2 -10000 0 -0.42 137 137
DOK4 0.028 0.032 -10000 0 -0.42 2 2
JNK cascade -0.13 0.17 0.19 2 -0.4 113 115
RET9/GFRalpha1/GDNF/FRS2 -0.042 0.14 -10000 0 -0.23 169 169
SHANK3 0.035 0.029 -10000 0 -0.42 2 2
RASA1 0.029 0.05 -10000 0 -0.42 6 6
NCK1 0.034 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.1 -10000 0 -0.22 114 114
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.18 -10000 0 -0.3 205 205
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.19 -10000 0 -0.31 220 220
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.19 -10000 0 -0.34 181 181
PI3K -0.16 0.25 -10000 0 -0.46 167 167
SOS1 0.035 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.028 0.14 -10000 0 -0.22 163 163
GRB10 0.023 0.075 -10000 0 -0.42 14 14
activation of MAPKK activity -0.081 0.15 -10000 0 -0.33 93 93
RET51/GFRalpha1/GDNF/FRS2 -0.095 0.2 -10000 0 -0.31 216 216
GAB1 0.027 0.061 -10000 0 -0.42 9 9
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.2 -10000 0 -0.35 186 186
RET51/GFRalpha1/GDNF/PKC alpha -0.089 0.2 -10000 0 -0.32 200 200
GRB2 0.033 0.011 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GDNF 0.032 0.036 -10000 0 -0.42 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.23 -10000 0 -0.35 226 226
Rac1/GTP -0.12 0.2 0.21 1 -0.37 164 165
RET9/GFRalpha1/GDNF -0.06 0.14 -10000 0 -0.25 172 172
GFRalpha1/GDNF -0.074 0.16 -10000 0 -0.3 172 172
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.12 0.19 0.38 1 -0.41 133 134
CRKL -0.13 0.2 -10000 0 -0.43 138 138
HRAS -0.077 0.17 -10000 0 -0.37 81 81
mol:PIP3 -0.088 0.2 0.28 2 -0.41 101 103
SPRED1 0.02 0.08 -10000 0 -0.42 16 16
SPRED2 0.02 0.082 -10000 0 -0.42 17 17
GAB1 -0.14 0.21 -10000 0 -0.44 138 138
FOXO3 -0.1 0.2 -10000 0 -0.39 128 128
AKT1 -0.11 0.22 -10000 0 -0.43 126 126
BAD -0.1 0.2 -10000 0 -0.4 124 124
megakaryocyte differentiation -0.13 0.21 -10000 0 -0.44 135 135
GSK3B -0.1 0.2 0.34 1 -0.4 121 122
RAF1 -0.056 0.15 0.26 4 -0.31 73 77
SHC1 0.028 0.025 -10000 0 -0.42 1 1
STAT3 -0.12 0.2 -10000 0 -0.43 133 133
STAT1 -0.31 0.48 -10000 0 -0.89 183 183
HRAS/SPRED1 -0.054 0.16 0.26 1 -0.33 78 79
cell proliferation -0.13 0.21 -10000 0 -0.43 136 136
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TEC 0.031 0.045 -10000 0 -0.42 5 5
RPS6KB1 -0.13 0.22 -10000 0 -0.45 135 135
HRAS/SPRED2 -0.053 0.16 0.26 1 -0.32 77 78
LYN/TEC/p62DOK -0.092 0.22 -10000 0 -0.42 123 123
MAPK3 -0.034 0.12 0.25 7 -0.25 30 37
STAP1 -0.13 0.21 -10000 0 -0.44 135 135
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
JAK2 -0.26 0.41 -10000 0 -0.76 177 177
STAT1 (dimer) -0.3 0.46 -10000 0 -0.86 185 185
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.099 0.22 -10000 0 -0.42 126 126
actin filament polymerization -0.13 0.21 -10000 0 -0.43 135 135
LYN 0.03 0.014 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.19 0.3 -10000 0 -0.59 157 157
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
CBL/CRKL/GRB2 -0.1 0.2 -10000 0 -0.4 121 121
PI3K -0.1 0.23 -10000 0 -0.45 123 123
PTEN 0.027 0.061 -10000 0 -0.42 9 9
SCF/KIT/EPO/EPOR -0.3 0.53 -10000 0 -1.2 123 123
MAPK8 -0.13 0.21 -10000 0 -0.44 136 136
STAT3 (dimer) -0.12 0.2 -10000 0 -0.42 133 133
positive regulation of transcription -0.025 0.1 0.23 8 -0.21 27 35
mol:GDP -0.083 0.17 -10000 0 -0.38 86 86
PIK3C2B -0.12 0.2 -10000 0 -0.41 128 128
CBL/CRKL -0.12 0.2 -10000 0 -0.41 132 132
FER -0.13 0.21 -10000 0 -0.44 134 134
SH2B3 -0.13 0.21 -10000 0 -0.44 135 135
PDPK1 -0.07 0.19 0.31 12 -0.38 92 104
SNAI2 -0.14 0.22 -10000 0 -0.46 137 137
positive regulation of cell proliferation -0.22 0.36 -10000 0 -0.7 159 159
KITLG -0.051 0.16 -10000 0 -0.44 72 72
cell motility -0.22 0.36 -10000 0 -0.7 159 159
PTPN6 0.038 0.032 -10000 0 -0.41 2 2
EPOR -0.068 0.18 -10000 0 -0.94 6 6
STAT5A (dimer) -0.19 0.3 -10000 0 -0.6 152 152
SOCS1 0.032 0.023 -10000 0 -0.42 1 1
cell migration 0.13 0.21 0.44 135 -10000 0 135
SOS1 0.035 0.021 -10000 0 -0.42 1 1
EPO 0.012 0.029 -10000 0 -10000 0 0
VAV1 0.019 0.082 -10000 0 -0.42 17 17
GRB10 -0.14 0.21 -10000 0 -0.45 136 136
PTPN11 0.041 0.009 -10000 0 -10000 0 0
SCF/KIT -0.14 0.22 -10000 0 -0.46 135 135
GO:0007205 0.007 0.011 -10000 0 -10000 0 0
MAP2K1 -0.042 0.13 0.24 6 -0.28 33 39
CBL 0.032 0.012 -10000 0 -10000 0 0
KIT -0.27 0.53 -10000 0 -1.3 101 101
MAP2K2 -0.043 0.13 0.27 7 -0.28 36 43
SHC/Grb2/SOS1 -0.08 0.2 -10000 0 -0.42 96 96
STAT5A -0.2 0.32 -10000 0 -0.63 150 150
GRB2 0.033 0.011 -10000 0 -10000 0 0
response to radiation -0.14 0.22 -10000 0 -0.45 138 138
SHC/GRAP2 0.038 0.032 -10000 0 -0.3 2 2
PTPRO -0.14 0.21 -10000 0 -0.45 134 134
SH2B2 -0.13 0.21 -10000 0 -0.44 135 135
DOK1 0.027 0.061 -10000 0 -0.42 9 9
MATK -0.13 0.21 -10000 0 -0.44 135 135
CREBBP -0.008 0.08 -10000 0 -0.12 161 161
BCL2 -0.3 0.56 -10000 0 -1.3 114 114
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.011 0.19 0.27 72 -0.32 100 172
PTK2B 0.028 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.056 0.26 -10000 0 -0.67 51 51
EDN1 -0.01 0.19 0.23 66 -0.43 65 131
EDN3 -0.011 0.12 -10000 0 -0.42 38 38
EDN2 -0.054 0.18 -10000 0 -0.42 93 93
HRAS/GDP -0.065 0.23 0.28 4 -0.46 96 100
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.059 0.2 0.19 2 -0.4 101 103
ADCY4 -0.011 0.17 0.25 10 -0.4 45 55
ADCY5 -0.015 0.16 0.23 5 -0.39 43 48
ADCY6 -0.01 0.16 0.25 8 -0.38 46 54
ADCY7 -0.013 0.16 0.24 8 -0.35 50 58
ADCY1 -0.009 0.16 0.25 8 -0.38 43 51
ADCY2 -0.026 0.17 0.25 6 -0.4 56 62
ADCY3 -0.01 0.16 0.25 10 -0.37 50 60
ADCY8 -0.006 0.14 0.25 5 -0.36 38 43
ADCY9 -0.013 0.16 0.24 9 -0.38 45 54
arachidonic acid secretion -0.089 0.26 0.28 1 -0.5 112 113
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.16 -10000 0 -0.32 105 105
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
ETA receptor/Endothelin-1/G12/GTP 0.03 0.21 0.37 72 -0.3 93 165
ETA receptor/Endothelin-1/Gs/GTP 0.025 0.2 0.35 71 -0.29 96 167
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.016 0.21 0.27 72 -0.44 63 135
EDNRB 0.003 0.097 -10000 0 -0.27 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.008 0.2 0.27 68 -0.5 40 108
CYSLTR1 -0.025 0.23 0.27 72 -0.52 60 132
SLC9A1 -0.004 0.13 0.19 72 -0.3 40 112
mol:GDP -0.081 0.24 0.27 5 -0.47 108 113
SLC9A3 -0.12 0.35 -10000 0 -0.7 110 110
RAF1 -0.094 0.24 -10000 0 -0.49 110 110
JUN -0.098 0.36 -10000 0 -0.96 60 60
JAK2 -0.008 0.19 0.27 73 -0.33 89 162
mol:IP3 -0.074 0.21 0.23 1 -0.43 101 102
ETA receptor/Endothelin-1 0.014 0.25 0.42 72 -0.37 103 175
PLCB1 -0.023 0.14 -10000 0 -0.42 59 59
PLCB2 0.032 0.023 -10000 0 -0.43 1 1
ETA receptor/Endothelin-3 0 0.15 -10000 0 -0.32 72 72
FOS -0.14 0.36 -10000 0 -0.92 79 79
Gai/GDP -0.11 0.32 -10000 0 -0.72 101 101
CRK 0.032 0.023 -10000 0 -0.42 1 1
mol:Ca ++ -0.089 0.27 0.25 9 -0.5 112 121
BCAR1 0.03 0.014 -10000 0 -10000 0 0
PRKCB1 -0.077 0.22 0.26 12 -0.44 103 115
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
GNAL 0.031 0.036 -10000 0 -0.42 3 3
Gs family/GDP -0.064 0.22 0.26 4 -0.44 99 103
ETA receptor/Endothelin-1/Gq/GTP -0.041 0.2 0.2 55 -0.4 85 140
MAPK14 -0.068 0.17 0.23 1 -0.36 94 95
TRPC6 -0.061 0.28 -10000 0 -0.73 49 49
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.18 -10000 0 -0.36 106 106
ETB receptor/Endothelin-2 -0.04 0.15 -10000 0 -0.3 115 115
ETB receptor/Endothelin-3 -0.009 0.11 -10000 0 -0.31 54 54
ETB receptor/Endothelin-1 -0.012 0.17 -10000 0 -0.3 104 104
MAPK3 -0.14 0.34 -10000 0 -0.76 97 97
MAPK1 -0.14 0.34 -10000 0 -0.79 94 94
Rac1/GDP -0.062 0.23 0.28 5 -0.46 95 100
cAMP biosynthetic process -0.004 0.17 0.26 22 -0.39 46 68
MAPK8 -0.072 0.3 -10000 0 -0.67 75 75
SRC 0.033 0.03 -10000 0 -0.42 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.043 0.15 -10000 0 -0.33 85 85
p130Cas/CRK/Src/PYK2 -0.1 0.26 -10000 0 -0.55 100 100
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.062 0.23 0.28 5 -0.46 96 101
COL1A2 -0.074 0.3 0.39 1 -0.56 111 112
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.031 0.18 0.19 8 -0.32 124 132
mol:DAG -0.074 0.21 0.23 1 -0.43 101 102
MAP2K2 -0.11 0.28 0.33 1 -0.59 107 108
MAP2K1 -0.11 0.28 0.3 2 -0.59 106 108
EDNRA 0.016 0.17 0.23 72 -0.37 59 131
positive regulation of muscle contraction -0.012 0.17 0.23 73 -0.32 71 144
Gq family/GDP -0.058 0.22 -10000 0 -0.46 84 84
HRAS/GTP -0.08 0.23 -10000 0 -0.46 101 101
PRKCH -0.075 0.21 0.23 4 -0.43 100 104
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.061 0.21 0.24 22 -0.42 95 117
PRKCB -0.074 0.2 0.22 1 -0.41 102 103
PRKCE -0.076 0.2 0.22 1 -0.42 98 99
PRKCD -0.075 0.2 0.22 1 -0.44 91 92
PRKCG -0.079 0.21 0.22 1 -0.43 97 98
regulation of vascular smooth muscle contraction -0.18 0.42 -10000 0 -1.1 79 79
PRKCQ -0.069 0.2 0.23 7 -0.42 96 103
PLA2G4A -0.099 0.28 0.28 1 -0.54 113 114
GNA14 -0.012 0.13 -10000 0 -0.42 43 43
GNA15 0.026 0.048 -10000 0 -0.42 5 5
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA11 0.029 0.039 -10000 0 -0.42 3 3
Rac1/GTP 0.03 0.21 0.37 72 -0.3 94 166
MMP1 -0.17 0.35 0.24 8 -0.78 120 128
IGF1 pathway

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
NCK2 0.036 0.005 -10000 0 -10000 0 0
PTK2 0.028 0.016 -10000 0 -10000 0 0
CRKL -0.071 0.15 0.17 2 -0.3 136 138
GRB2/SOS1/SHC 0.052 0.036 -10000 0 -0.26 1 1
HRAS 0.032 0.036 -10000 0 -0.42 3 3
IRS1/Crk -0.064 0.16 -10000 0 -0.29 142 142
IGF-1R heterotetramer/IGF1/PTP1B -0.036 0.16 -10000 0 -0.29 132 132
AKT1 -0.077 0.14 0.17 14 -0.29 114 128
BAD -0.075 0.13 0.16 14 -0.28 111 125
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.15 0.17 2 -0.3 130 132
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.06 0.16 -10000 0 -0.3 142 142
RAF1 -0.037 0.14 0.29 4 -0.45 18 22
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.025 0.17 -10000 0 -0.29 129 129
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.063 0.17 0.17 2 -0.3 152 154
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RPS6KB1 -0.071 0.13 0.17 12 -0.3 102 114
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
positive regulation of MAPKKK cascade -0.023 0.14 0.3 11 -0.36 21 32
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
HRAS/GTP -0.04 0.13 -10000 0 -0.26 113 113
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.003 0.13 -10000 0 -0.24 103 103
IGF-1R heterotetramer -0.061 0.18 -10000 0 -0.46 84 84
IGF-1R heterotetramer/IGF1/IRS/Nck -0.043 0.17 -10000 0 -0.28 151 151
Crk/p130 Cas/Paxillin -0.039 0.16 -10000 0 -0.27 142 142
IGF1R -0.061 0.18 -10000 0 -0.46 84 84
IGF1 -0.06 0.18 -10000 0 -0.46 78 78
IRS2/Crk -0.071 0.16 0.17 2 -0.29 150 152
PI3K -0.038 0.17 -10000 0 -0.29 145 145
apoptosis 0.05 0.11 0.31 46 -0.3 4 50
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
PRKCD -0.062 0.18 0.21 1 -0.37 102 103
RAF1/14-3-3 E -0.018 0.13 0.29 4 -0.4 17 21
BAD/14-3-3 -0.053 0.12 0.31 4 -0.33 46 50
PRKCZ -0.075 0.14 0.16 14 -0.27 134 148
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.13 -10000 0 -0.34 44 44
PTPN1 0.03 0.031 -10000 0 -0.42 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.075 0.18 -10000 0 -0.35 130 130
BCAR1 0.03 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.018 0.14 -10000 0 -0.26 122 122
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.035 0.021 -10000 0 -0.42 1 1
IRS1/NCK2 -0.054 0.16 -10000 0 -0.28 151 151
GRB10 0.023 0.075 -10000 0 -0.42 14 14
PTPN11 -0.072 0.15 0.17 2 -0.29 142 144
IRS1 -0.075 0.16 -10000 0 -0.3 151 151
IRS2 -0.079 0.16 0.17 2 -0.31 142 144
IGF-1R heterotetramer/IGF1 -0.072 0.19 -10000 0 -0.37 140 140
GRB2 0.033 0.011 -10000 0 -10000 0 0
PDPK1 -0.075 0.14 0.18 14 -0.29 129 143
YWHAE 0.032 0.012 -10000 0 -10000 0 0
PRKD1 -0.071 0.2 0.21 5 -0.37 125 130
SHC1 0.028 0.025 -10000 0 -0.42 1 1
FOXM1 transcription factor network

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
NFATC3 -0.24 0.52 -9999 0 -1.2 87 87
PLK1 0.017 0.098 -9999 0 -1.1 3 3
BIRC5 -0.087 0.39 -9999 0 -1.4 40 40
HSPA1B -0.25 0.52 -9999 0 -1.1 102 102
MAP2K1 0.005 0.057 -9999 0 -10000 0 0
BRCA2 -0.27 0.54 -9999 0 -1.2 98 98
FOXM1 -0.39 0.86 -9999 0 -1.8 100 100
XRCC1 -0.24 0.52 -9999 0 -1.2 84 84
FOXM1B/p19 -0.3 0.58 -9999 0 -1.3 100 100
Cyclin D1/CDK4 -0.29 0.53 -9999 0 -1 138 138
CDC2 -0.27 0.56 -9999 0 -1.3 88 88
TGFA -0.28 0.5 -9999 0 -1 116 116
SKP2 -0.24 0.52 -9999 0 -1.2 83 83
CCNE1 0.024 0.05 -9999 0 -0.43 5 5
CKS1B -0.22 0.53 -9999 0 -1.2 82 82
RB1 -0.15 0.4 -9999 0 -1 66 66
FOXM1C/SP1 -0.3 0.62 -9999 0 -1.3 107 107
AURKB -0.08 0.31 -9999 0 -0.93 53 53
CENPF -0.23 0.56 -9999 0 -1.2 84 84
CDK4 0.016 0.037 -9999 0 -10000 0 0
MYC -0.23 0.45 -9999 0 -0.97 103 103
CHEK2 0.001 0.066 -9999 0 -0.45 3 3
ONECUT1 -0.28 0.52 -9999 0 -1.1 106 106
CDKN2A 0.014 0.075 -9999 0 -0.42 14 14
LAMA4 -0.25 0.53 -9999 0 -1.2 84 84
FOXM1B/HNF6 -0.35 0.65 -9999 0 -1.4 106 106
FOS -0.33 0.6 -9999 0 -1.2 131 131
SP1 0.034 0.024 -9999 0 -0.42 1 1
CDC25B -0.25 0.52 -9999 0 -1.2 84 84
response to radiation -0.004 0.032 -9999 0 -10000 0 0
CENPB -0.24 0.52 -9999 0 -1.2 84 84
CENPA -0.27 0.55 -9999 0 -1.2 92 92
NEK2 -0.26 0.58 -9999 0 -1.2 108 108
HIST1H2BA -0.25 0.52 -9999 0 -1.2 86 86
CCNA2 0.005 0.11 -9999 0 -0.43 28 28
EP300 0.032 0.03 -9999 0 -0.42 2 2
CCNB1/CDK1 -0.32 0.65 -9999 0 -1.5 86 86
CCNB2 -0.26 0.53 -9999 0 -1.2 86 86
CCNB1 -0.27 0.57 -9999 0 -1.3 86 86
ETV5 -0.25 0.53 -9999 0 -1.1 95 95
ESR1 -0.44 0.65 -9999 0 -1.2 206 206
CCND1 -0.32 0.52 -9999 0 -1 141 141
GSK3A 0.008 0.052 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.022 0.11 -9999 0 -0.33 29 29
CDK2 0.03 0.034 -9999 0 -0.43 2 2
G2/M transition of mitotic cell cycle -0.006 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.57 -9999 0 -1.2 101 101
GAS1 -0.32 0.59 -9999 0 -1.2 121 121
MMP2 -0.28 0.57 -9999 0 -1.2 101 101
RB1/FOXM1C -0.3 0.55 -9999 0 -1.1 139 139
CREBBP 0.033 0.011 -9999 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.037 0.15 0.36 1 -0.27 127 128
NF kappa B1 p50/RelA/I kappa B alpha -0.034 0.17 0.33 1 -0.43 46 47
alphaV/beta3 Integrin/Osteopontin/Src -0.043 0.16 -10000 0 -0.32 124 124
AP1 -0.085 0.23 -10000 0 -0.48 90 90
ILK -0.046 0.14 0.38 1 -0.26 125 126
bone resorption -0.053 0.14 -10000 0 -0.34 48 48
PTK2B 0.028 0.015 -10000 0 -10000 0 0
PYK2/p130Cas -0.027 0.16 -10000 0 -0.26 132 132
ITGAV 0.018 0.082 -10000 0 -0.43 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.04 0.064 -10000 0 -0.3 17 17
alphaV/beta3 Integrin/Osteopontin -0.022 0.16 -10000 0 -0.28 126 126
MAP3K1 -0.059 0.14 0.23 6 -0.27 142 148
JUN -0.001 0.12 -10000 0 -0.42 39 39
MAPK3 -0.059 0.14 0.22 7 -0.27 127 134
MAPK1 -0.064 0.15 0.23 6 -0.28 128 134
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.064 0.13 0.22 8 -0.25 143 151
ITGB3 0.024 0.051 -10000 0 -0.43 5 5
NFKBIA -0.068 0.16 0.35 3 -0.42 59 62
FOS -0.031 0.15 -10000 0 -0.42 66 66
CD44 0.022 0.075 -10000 0 -0.42 14 14
CHUK 0.026 0.067 -10000 0 -0.42 11 11
PLAU -0.14 0.36 -10000 0 -1.1 54 54
NF kappa B1 p50/RelA -0.022 0.19 -10000 0 -0.45 55 55
BCAR1 0.03 0.014 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.031 0.081 -10000 0 -0.32 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.06 0.15 0.22 7 -0.28 146 153
VAV3 -0.099 0.15 0.22 8 -0.27 200 208
MAP3K14 -0.049 0.14 0.27 3 -0.27 127 130
ROCK2 0.033 0.035 -10000 0 -0.42 3 3
SPP1 -0.076 0.19 -10000 0 -0.42 115 115
RAC1 0.035 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.082 0.15 0.19 1 -0.25 186 187
MMP2 -0.1 0.19 -10000 0 -0.45 88 88
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.37 0.64 -10000 0 -1.3 134 134
STAT6 (cleaved dimer) -0.38 0.65 -10000 0 -1.3 142 142
IGHG1 -0.083 0.24 -10000 0 -0.51 34 34
IGHG3 -0.36 0.61 -10000 0 -1.2 143 143
AKT1 -0.12 0.32 -10000 0 -0.83 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.066 0.26 -10000 0 -0.86 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.36 -10000 0 -0.85 56 56
THY1 -0.38 0.66 -10000 0 -1.4 126 126
MYB -0.055 0.18 -10000 0 -0.42 97 97
HMGA1 0.034 0.029 -10000 0 -0.42 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.35 -10000 0 -0.68 81 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.33 -10000 0 -0.89 35 35
SP1 0.023 0.052 -10000 0 -0.27 3 3
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.019 0.056 -10000 0 -0.42 4 4
STAT6 (dimer)/ETS1 -0.37 0.64 -10000 0 -1.3 138 138
SOCS1 -0.2 0.39 -10000 0 -0.77 116 116
SOCS3 -0.12 0.32 -10000 0 -0.99 22 22
FCER2 -0.23 0.46 -10000 0 -0.92 103 103
PARP14 0.03 0.051 -10000 0 -0.42 6 6
CCL17 -0.43 0.71 -10000 0 -1.4 154 154
GRB2 0.033 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.076 0.26 -10000 0 -0.73 27 27
T cell proliferation -0.38 0.67 -10000 0 -1.3 136 136
IL4R/JAK1 -0.37 0.65 -10000 0 -1.3 136 136
EGR2 -0.41 0.7 -10000 0 -1.4 140 140
JAK2 -0.005 0.07 -10000 0 -0.46 2 2
JAK3 0.039 0.014 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
JAK1 0.018 0.048 -10000 0 -0.41 3 3
COL1A2 -0.22 0.54 -10000 0 -1.5 72 72
CCL26 -0.37 0.64 -10000 0 -1.3 124 124
IL4R -0.4 0.71 -10000 0 -1.4 133 133
PTPN6 0.022 0.045 -10000 0 -0.41 2 2
IL13RA2 -0.41 0.68 -10000 0 -1.3 150 150
IL13RA1 -0.009 0.087 -10000 0 -0.46 8 8
IRF4 -0.005 0.16 -10000 0 -1 5 5
ARG1 -0.066 0.26 -10000 0 -0.9 24 24
CBL -0.14 0.32 -10000 0 -0.65 78 78
GTF3A 0.024 0.046 -10000 0 -0.12 15 15
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL13RA1/JAK2 -0.001 0.1 -10000 0 -0.36 8 8
IRF4/BCL6 -0.005 0.16 -10000 0 -0.97 5 5
CD40LG 0.039 0.038 -10000 0 -0.42 3 3
MAPK14 -0.14 0.33 -10000 0 -0.71 62 62
mitosis -0.11 0.31 -10000 0 -0.77 39 39
STAT6 -0.48 0.88 -10000 0 -1.7 141 141
SPI1 0.033 0.051 -10000 0 -0.25 13 13
RPS6KB1 -0.093 0.3 -10000 0 -0.77 34 34
STAT6 (dimer) -0.48 0.88 -10000 0 -1.7 141 141
STAT6 (dimer)/PARP14 -0.42 0.73 -10000 0 -1.4 141 141
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.34 -10000 0 -0.81 55 55
FRAP1 -0.12 0.32 -10000 0 -0.84 39 39
LTA -0.37 0.64 -10000 0 -1.3 120 120
FES 0.03 0.046 -10000 0 -0.42 5 5
T-helper 1 cell differentiation 0.43 0.78 1.5 141 -10000 0 141
CCL11 -0.4 0.66 -10000 0 -1.3 139 139
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.31 -10000 0 -0.89 28 28
IL2RG 0.034 0.042 -10000 0 -0.41 4 4
IL10 -0.33 0.65 -10000 0 -1.3 120 120
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
IL4 -0.063 0.29 -10000 0 -1.3 18 18
IL5 -0.37 0.64 -10000 0 -1.3 125 125
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.51 -10000 0 -0.95 134 134
COL1A1 -0.26 0.59 -10000 0 -1.4 90 90
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.69 -10000 0 -1.4 125 125
IL2R gamma/JAK3 0.054 0.035 -10000 0 -0.29 4 4
TFF3 -0.53 0.76 -10000 0 -1.4 202 202
ALOX15 -0.38 0.65 -10000 0 -1.3 130 130
MYBL1 -0.011 0.13 -10000 0 -0.42 43 43
T-helper 2 cell differentiation -0.28 0.52 -10000 0 -0.99 138 138
SHC1 0.028 0.025 -10000 0 -0.42 1 1
CEBPB 0.029 0.056 -10000 0 -0.3 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.34 -10000 0 -0.79 51 51
mol:PI-3-4-5-P3 -0.12 0.33 -10000 0 -0.83 39 39
PI3K -0.13 0.35 -10000 0 -0.92 38 38
DOK2 0.009 0.086 -10000 0 -0.42 19 19
ETS1 0.015 0.043 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.062 0.25 -10000 0 -0.64 27 27
ITGB3 -0.37 0.65 -10000 0 -1.3 130 130
PIGR -0.46 0.77 -10000 0 -1.4 170 170
IGHE 0.011 0.088 0.21 32 -0.22 10 42
MAPKKK cascade -0.06 0.24 -10000 0 -0.63 27 27
BCL6 0.018 0.085 -10000 0 -0.42 18 18
OPRM1 -0.37 0.64 -10000 0 -1.3 126 126
RETNLB -0.37 0.64 -10000 0 -1.3 132 132
SELP -0.43 0.75 -10000 0 -1.4 153 153
AICDA -0.36 0.62 -10000 0 -1.3 127 127
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 0.034 0.034 -10000 0 -0.26 4 4
NFATC2 -0.052 0.21 -10000 0 -0.52 48 48
NFATC3 -0.018 0.12 -10000 0 -0.26 76 76
CD40LG -0.19 0.38 -10000 0 -0.75 133 133
ITCH 0.013 0.071 -10000 0 -0.22 42 42
CBLB 0.014 0.07 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.33 -10000 0 -0.78 76 76
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.087 -10000 0 -0.26 44 44
T cell anergy -0.016 0.12 0.26 2 -0.36 45 47
TLE4 -0.045 0.17 -10000 0 -0.5 37 37
Jun/NFAT1-c-4/p21SNFT -0.17 0.4 -10000 0 -0.77 129 129
AP-1/NFAT1-c-4 -0.19 0.46 -10000 0 -0.85 133 133
IKZF1 -0.039 0.14 -10000 0 -0.36 48 48
T-helper 2 cell differentiation -0.17 0.3 -10000 0 -0.76 73 73
AP-1/NFAT1 -0.045 0.2 -10000 0 -0.41 80 80
CALM1 0.028 0.058 -10000 0 -0.16 42 42
EGR2 -0.23 0.49 -10000 0 -1.1 90 90
EGR3 -0.29 0.55 -10000 0 -1.1 138 138
NFAT1/FOXP3 -0.018 0.16 -10000 0 -0.4 41 41
EGR1 -0.038 0.16 -10000 0 -0.42 76 76
JUN -0.003 0.12 -10000 0 -0.42 39 39
EGR4 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.046 -10000 0 -0.15 45 45
GBP3 -0.089 0.25 -10000 0 -0.61 79 79
FOSL1 0.035 0.007 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.16 0.4 -10000 0 -0.77 125 125
DGKA -0.04 0.16 -10000 0 -0.44 38 38
CREM 0.034 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.41 -10000 0 -0.79 134 134
CTLA4 -0.027 0.14 -10000 0 -0.37 38 38
NFAT1-c-4 (dimer)/EGR1 -0.2 0.43 -10000 0 -0.83 139 139
NFAT1-c-4 (dimer)/EGR4 -0.17 0.39 -10000 0 -0.77 132 132
FOS -0.034 0.15 -10000 0 -0.42 66 66
IFNG -0.19 0.43 -10000 0 -1.1 73 73
T cell activation -0.1 0.26 -10000 0 -0.67 49 49
MAF 0.015 0.078 -10000 0 -0.42 15 15
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.34 0.66 132 -10000 0 132
TNF -0.2 0.38 -10000 0 -0.75 141 141
FASLG -0.35 0.65 -10000 0 -1.2 158 158
TBX21 -0.044 0.17 -10000 0 -0.43 84 84
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.021 0.061 -10000 0 -0.26 15 15
PTPN1 -0.038 0.15 -10000 0 -0.5 21 21
NFAT1-c-4/ICER1 -0.17 0.4 -10000 0 -0.77 131 131
GATA3 -0.047 0.18 -10000 0 -0.42 91 91
T-helper 1 cell differentiation -0.19 0.41 -10000 0 -1 74 74
IL2RA -0.14 0.33 -10000 0 -0.74 81 81
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.035 0.14 -10000 0 -0.39 37 37
E2F1 0.033 0.054 -10000 0 -0.42 7 7
PPARG 0.012 0.093 -10000 0 -0.42 22 22
SLC3A2 -0.035 0.14 -10000 0 -0.39 37 37
IRF4 0.031 0.031 -10000 0 -0.42 2 2
PTGS2 -0.18 0.36 -10000 0 -0.75 119 119
CSF2 -0.19 0.38 -10000 0 -0.75 135 135
JunB/Fra1/NFAT1-c-4 -0.15 0.39 -10000 0 -0.76 129 129
IL4 -0.18 0.32 -10000 0 -0.81 71 71
IL5 -0.19 0.38 -10000 0 -0.75 133 133
IL2 -0.1 0.27 -10000 0 -0.69 47 47
IL3 -0.013 0.14 -10000 0 -0.85 10 10
RNF128 -0.016 0.16 -10000 0 -0.52 44 44
NFATC1 -0.15 0.34 -10000 0 -0.67 131 131
CDK4 0.1 0.22 0.56 41 -10000 0 41
PTPRK -0.069 0.22 -10000 0 -0.61 60 60
IL8 -0.2 0.39 -10000 0 -0.76 135 135
POU2F1 0.034 0.017 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.007 0.13 -10000 0 -0.22 134 134
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.21 -10000 0 -0.38 141 141
AKT1 -0.22 0.37 -10000 0 -0.74 166 166
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.22 0.38 -10000 0 -0.75 166 166
mol:Ca2+ -0.071 0.15 -10000 0 -0.42 59 59
IGF1R -0.042 0.17 -10000 0 -0.42 84 84
E2/ER alpha (dimer)/Striatin -0.037 0.13 -10000 0 -0.25 135 135
SHC1 0.028 0.025 -10000 0 -0.42 1 1
apoptosis 0.21 0.35 0.7 166 -10000 0 166
RhoA/GTP -0.038 0.11 -10000 0 -0.21 127 127
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.1 0.2 -10000 0 -0.38 151 151
regulation of stress fiber formation 0.038 0.1 0.33 7 -0.26 3 10
E2/ERA-ERB (dimer) -0.037 0.13 -10000 0 -0.25 132 132
KRAS 0.028 0.054 -10000 0 -0.42 7 7
G13/GTP -0.032 0.12 -10000 0 -0.23 123 123
pseudopodium formation -0.038 0.1 0.26 3 -0.33 7 10
E2/ER alpha (dimer)/PELP1 -0.038 0.13 -10000 0 -0.25 131 131
GRB2 0.033 0.011 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.23 -10000 0 -0.45 158 158
E2/ER beta (dimer) 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.075 0.17 -10000 0 -0.34 135 135
mol:NADP -0.14 0.23 -10000 0 -0.45 158 158
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 -0.072 0.15 -10000 0 -0.44 58 58
IGF-1R heterotetramer -0.042 0.17 -10000 0 -0.42 84 84
PLCB1 -0.072 0.16 -10000 0 -0.45 59 59
PLCB2 -0.051 0.15 -10000 0 -0.45 51 51
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
mol:L-citrulline -0.14 0.23 -10000 0 -0.45 158 158
RHOA 0.026 0.061 -10000 0 -0.42 9 9
Gai/GDP -0.099 0.27 -10000 0 -0.62 102 102
JNK cascade 0.026 0.005 -10000 0 -10000 0 0
BCAR1 0.03 0.014 -10000 0 -10000 0 0
ESR2 0.035 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.089 0.2 -10000 0 -0.42 132 132
Gq family/GDP/Gbeta gamma -0.015 0.17 -10000 0 -0.72 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.034 0.13 -10000 0 -0.6 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.089 0.19 0.27 1 -0.38 120 121
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
E2/ER alpha (dimer) -0.062 0.14 -10000 0 -0.3 132 132
STRN 0.031 0.045 -10000 0 -0.42 5 5
GNAL 0.031 0.036 -10000 0 -0.42 3 3
PELP1 0.033 0.011 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
HBEGF -0.11 0.2 0.32 5 -0.5 56 61
cAMP biosynthetic process -0.028 0.1 -10000 0 -0.2 129 129
SRC -0.11 0.2 -10000 0 -0.52 46 46
PI3K 0.036 0.065 -10000 0 -0.3 17 17
GNB1 0.032 0.045 -10000 0 -0.42 5 5
G13/GDP/Gbeta gamma -0.049 0.16 -10000 0 -0.33 112 112
SOS1 0.035 0.021 -10000 0 -0.42 1 1
IGF-1R heterotetramer/IGF1 -0.13 0.19 -10000 0 -0.4 144 144
Gs family/GTP -0.022 0.11 -10000 0 -0.21 129 129
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.054 -10000 0 -0.23 15 15
vasodilation -0.13 0.22 -10000 0 -0.43 158 158
mol:DAG -0.072 0.15 -10000 0 -0.44 58 58
Gs family/GDP/Gbeta gamma -0.064 0.15 -10000 0 -0.32 108 108
MSN -0.042 0.11 0.26 3 -0.35 7 10
Gq family/GTP -0.052 0.15 -10000 0 -0.44 57 57
mol:PI-3-4-5-P3 -0.21 0.36 -10000 0 -0.72 166 166
NRAS 0.029 0.054 -10000 0 -0.42 7 7
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.22 0.43 158 -10000 0 158
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
RhoA/GDP -0.061 0.17 -10000 0 -0.34 124 124
NOS3 -0.14 0.24 -10000 0 -0.47 157 157
GNA11 0.033 0.036 -10000 0 -0.42 3 3
MAPKKK cascade -0.15 0.26 -10000 0 -0.52 156 156
E2/ER alpha (dimer)/PELP1/Src -0.11 0.21 0.28 1 -0.39 151 152
ruffle organization -0.038 0.1 0.26 3 -0.33 7 10
ROCK2 -0.039 0.12 0.28 3 -0.36 8 11
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GNA13 0.029 0.037 -10000 0 -0.42 3 3
MMP9 -0.12 0.2 0.35 7 -0.49 58 65
MMP2 -0.11 0.19 0.27 3 -0.47 59 62
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.015 0.13 -10000 0 -0.42 49 49
EGF/EGFR -0.072 0.18 -10000 0 -0.27 199 199
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.001 0.13 -10000 0 -0.23 104 104
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.002 0.12 -10000 0 -0.42 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.069 0.19 -10000 0 -0.42 110 110
EGF/EGFR dimer/SHC -0.029 0.14 -10000 0 -0.26 120 120
mol:GDP -0.005 0.12 -10000 0 -0.23 104 104
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.038 0.16 -10000 0 -0.42 77 77
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
HRAS/GTP -0.017 0.11 -10000 0 -0.21 106 106
SHC1 0.028 0.025 -10000 0 -0.42 1 1
HRAS/GDP -0.007 0.12 -10000 0 -0.22 106 106
FRAP1 -0.017 0.14 0.36 11 -0.4 5 16
EGF/EGFR dimer -0.061 0.16 -10000 0 -0.3 152 152
SOS1 0.035 0.021 -10000 0 -0.42 1 1
GRB2 0.033 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.029 0.16 -10000 0 -0.33 103 103
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 0.035 0.021 -10000 0 -0.42 1 1
CCL5 -0.014 0.14 -10000 0 -0.42 52 52
SDCBP 0.023 0.058 -10000 0 -0.42 8 8
FGFR/FGF2/Syndecan-1 -0.11 0.23 0.22 6 -0.53 91 97
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.11 0.22 -10000 0 -0.5 91 91
Syndecan-1/Syntenin -0.1 0.22 0.26 1 -0.49 92 93
MAPK3 -0.097 0.2 0.24 1 -0.46 90 91
HGF/MET 0.042 0.055 -10000 0 -0.3 12 12
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
BSG 0.035 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.11 0.22 -10000 0 -0.49 91 91
Syndecan-1/RANTES -0.13 0.24 0.26 1 -0.5 114 115
Syndecan-1/CD147 -0.096 0.23 0.27 1 -0.49 93 94
Syndecan-1/Syntenin/PIP2 -0.1 0.21 0.25 1 -0.47 92 93
LAMA5 0.027 0.05 -10000 0 -0.42 6 6
positive regulation of cell-cell adhesion -0.099 0.2 0.24 1 -0.46 92 93
MMP7 -0.032 0.15 -10000 0 -0.42 68 68
HGF 0.028 0.057 -10000 0 -0.42 8 8
Syndecan-1/CASK -0.12 0.21 -10000 0 -0.5 95 95
Syndecan-1/HGF/MET -0.1 0.23 0.27 1 -0.49 96 97
regulation of cell adhesion -0.1 0.19 0.23 1 -0.45 87 88
HPSE 0.015 0.091 -10000 0 -0.42 21 21
positive regulation of cell migration -0.11 0.23 0.22 6 -0.53 91 97
SDC1 -0.11 0.23 0.28 1 -0.53 91 92
Syndecan-1/Collagen -0.11 0.23 0.22 6 -0.53 91 97
PPIB 0.033 0.03 -10000 0 -0.42 2 2
MET 0.03 0.041 -10000 0 -0.42 4 4
PRKACA 0.036 0.005 -10000 0 -10000 0 0
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
MAPK1 -0.1 0.21 0.24 1 -0.47 92 93
homophilic cell adhesion -0.12 0.22 0.22 6 -0.52 92 98
MMP1 -0.074 0.18 -10000 0 -0.42 107 107
HIF-1-alpha transcription factor network

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
PKM2 -0.055 0.35 -10000 0 -0.71 77 77
HDAC7 0 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.008 0.35 -10000 0 -0.69 60 60
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
ID2 -0.056 0.36 -10000 0 -0.72 76 76
AP1 -0.033 0.16 -10000 0 -0.35 88 88
ABCG2 -0.057 0.36 -10000 0 -0.73 77 77
HIF1A -0.023 0.16 -10000 0 -0.48 46 46
TFF3 -0.1 0.37 -10000 0 -0.74 88 88
GATA2 0.018 0.054 -10000 0 -0.42 5 5
AKT1 0.012 0.09 -10000 0 -0.24 12 12
response to hypoxia -0.007 0.066 -10000 0 -0.14 32 32
MCL1 -0.058 0.35 -10000 0 -0.72 76 76
NDRG1 -0.065 0.33 -10000 0 -0.74 66 66
SERPINE1 -0.063 0.36 -10000 0 -0.73 79 79
FECH -0.062 0.36 -10000 0 -0.72 79 79
FURIN -0.057 0.35 -10000 0 -0.72 77 77
NCOA2 0.026 0.047 -10000 0 -0.42 5 5
EP300 0.008 0.11 -10000 0 -0.27 34 34
HMOX1 -0.066 0.36 -10000 0 -0.74 76 76
BHLHE40 -0.077 0.34 -10000 0 -0.71 78 78
BHLHE41 -0.077 0.34 -10000 0 -0.71 78 78
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.05 0.17 -10000 0 -0.33 45 45
ENG -0.007 0.13 -10000 0 -0.31 42 42
JUN -0.009 0.12 -10000 0 -0.43 39 39
RORA -0.064 0.36 -10000 0 -0.73 77 77
ABCB1 -0.029 0.24 -10000 0 -0.94 28 28
TFRC -0.072 0.36 -10000 0 -0.73 84 84
CXCR4 -0.067 0.37 -10000 0 -0.74 83 83
TF -0.056 0.35 -10000 0 -0.72 74 74
CITED2 -0.059 0.35 -10000 0 -0.74 71 71
HIF1A/ARNT -0.035 0.43 -10000 0 -0.88 60 60
LDHA 0.01 0.19 -10000 0 -0.85 17 17
ETS1 -0.065 0.35 -10000 0 -0.72 76 76
PGK1 -0.053 0.36 -10000 0 -0.72 76 76
NOS2 -0.077 0.34 -10000 0 -0.71 78 78
ITGB2 -0.064 0.36 -10000 0 -0.74 79 79
ALDOA -0.05 0.35 -10000 0 -0.74 68 68
Cbp/p300/CITED2 -0.057 0.36 -10000 0 -0.8 63 63
FOS -0.038 0.15 -10000 0 -0.42 66 66
HK2 -0.054 0.36 -10000 0 -0.72 76 76
SP1 0.035 0.039 -10000 0 -0.19 7 7
GCK 0.013 0.18 -10000 0 -0.75 10 10
HK1 -0.053 0.35 -10000 0 -0.72 76 76
NPM1 -0.052 0.35 -10000 0 -0.71 76 76
EGLN1 -0.065 0.33 -10000 0 -0.72 71 71
CREB1 0.039 0.027 -10000 0 -0.17 5 5
PGM1 -0.059 0.35 -10000 0 -0.72 77 77
SMAD3 0.027 0.061 -10000 0 -0.42 9 9
EDN1 -0.18 0.48 -10000 0 -1.2 88 88
IGFBP1 -0.053 0.35 -10000 0 -0.72 75 75
VEGFA -0.042 0.27 0.44 1 -0.57 69 70
HIF1A/JAB1 0.003 0.12 -10000 0 -0.34 43 43
CP -0.12 0.38 -10000 0 -0.76 92 92
CXCL12 -0.071 0.38 -10000 0 -0.74 85 85
COPS5 0.027 0.043 -10000 0 -0.42 4 4
SMAD3/SMAD4 0.041 0.063 -10000 0 -0.3 16 16
BNIP3 -0.06 0.36 -10000 0 -0.73 77 77
EGLN3 -0.08 0.38 -10000 0 -0.76 84 84
CA9 -0.06 0.35 -10000 0 -0.72 75 75
TERT -0.056 0.35 -10000 0 -0.72 75 75
ENO1 -0.056 0.35 -10000 0 -0.73 74 74
PFKL -0.056 0.36 -10000 0 -0.73 74 74
NCOA1 0.032 0.045 -10000 0 -0.42 5 5
ADM -0.08 0.38 -10000 0 -0.76 87 87
ARNT 0.015 0.078 -10000 0 -10000 0 0
HNF4A 0.035 0.033 -10000 0 -0.24 5 5
ADFP -0.064 0.37 -10000 0 -0.74 81 81
SLC2A1 -0.03 0.29 -10000 0 -0.58 67 67
LEP -0.072 0.36 -10000 0 -0.74 77 77
HIF1A/ARNT/Cbp/p300 -0.022 0.35 -10000 0 -0.7 63 63
EPO -0.027 0.28 -10000 0 -0.71 39 39
CREBBP 0.017 0.098 -10000 0 -0.25 24 24
HIF1A/ARNT/Cbp/p300/HDAC7 -0.021 0.34 -10000 0 -0.68 63 63
PFKFB3 -0.058 0.35 -10000 0 -0.75 71 71
NT5E -0.059 0.36 -10000 0 -0.73 76 76
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.04 0.19 -10000 0 -0.53 63 63
IHH 0.017 0.088 -10000 0 -0.28 24 24
SHH Np/Cholesterol/GAS1 -0.027 0.11 -10000 0 -0.24 101 101
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.027 0.1 0.23 101 -10000 0 101
SMO/beta Arrestin2 -0.022 0.17 -10000 0 -0.36 81 81
SMO -0.038 0.16 -10000 0 -0.36 88 88
AKT1 -0.015 0.16 -10000 0 -0.54 29 29
ARRB2 0.033 0.011 -10000 0 -10000 0 0
BOC 0.014 0.093 -10000 0 -0.42 22 22
ADRBK1 0.034 0.01 -10000 0 -10000 0 0
heart looping -0.034 0.16 -10000 0 -0.36 88 88
STIL -0.006 0.14 0.2 77 -0.22 112 189
DHH N/PTCH2 0.052 0.011 -10000 0 -10000 0 0
DHH N/PTCH1 -0.001 0.12 -10000 0 -0.29 70 70
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DHH 0.036 0.005 -10000 0 -10000 0 0
PTHLH -0.064 0.25 -10000 0 -0.66 67 67
determination of left/right symmetry -0.034 0.16 -10000 0 -0.36 88 88
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
skeletal system development -0.063 0.25 -10000 0 -0.65 67 67
IHH N/Hhip 0.035 0.065 -10000 0 -0.29 12 12
DHH N/Hhip 0.049 0.029 -10000 0 -0.3 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.034 0.16 -10000 0 -0.36 88 88
pancreas development 0.032 0.036 -10000 0 -0.42 3 3
HHAT -0.017 0.13 -10000 0 -0.42 50 50
PI3K 0.036 0.065 -10000 0 -0.3 17 17
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.16 -10000 0 -0.42 71 71
somite specification -0.034 0.16 -10000 0 -0.36 88 88
SHH Np/Cholesterol/PTCH1 -0.031 0.11 -10000 0 -0.23 103 103
SHH Np/Cholesterol/PTCH2 0.003 0.074 -10000 0 -0.23 44 44
SHH Np/Cholesterol/Megalin -0.055 0.14 -10000 0 -0.27 133 133
SHH -0.016 0.09 -10000 0 -0.3 46 46
catabolic process -0.025 0.12 -10000 0 -0.32 70 70
SMO/Vitamin D3 -0.019 0.15 0.2 44 -0.33 64 108
SHH Np/Cholesterol/Hhip 0.002 0.075 -10000 0 -0.23 45 45
LRP2 -0.096 0.2 -10000 0 -0.42 144 144
receptor-mediated endocytosis -0.071 0.18 -10000 0 -0.34 108 108
SHH Np/Cholesterol/BOC -0.007 0.085 -10000 0 -0.23 63 63
SHH Np/Cholesterol/CDO -0.007 0.083 -10000 0 -0.24 56 56
mesenchymal cell differentiation -0.001 0.074 0.23 45 -10000 0 45
mol:Vitamin D3 -0.007 0.13 0.2 64 -0.23 103 167
IHH N/PTCH2 0.037 0.06 -10000 0 -0.27 10 10
CDON 0.021 0.067 -10000 0 -0.42 11 11
IHH N/PTCH1 -0.005 0.13 -10000 0 -0.33 70 70
Megalin/LRPAP1 -0.049 0.16 -10000 0 -0.3 144 144
PTCH2 0.035 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.007 0.07 -10000 0 -0.23 46 46
PTCH1 -0.025 0.12 -10000 0 -0.32 70 70
HHIP 0.032 0.036 -10000 0 -0.42 3 3
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.054 0.15 0.3 12 -0.83 8 20
SMARCC2 0.036 0.005 -10000 0 -10000 0 0
SMARCC1 0.033 0.03 -10000 0 -0.42 2 2
TBX21 -0.15 0.28 0.36 1 -0.73 87 88
SUMO2 0.029 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.021 0.091 -10000 0 -0.38 23 23
FKBP4 0.03 0.046 -10000 0 -0.42 5 5
FKBP5 -0.003 0.12 -10000 0 -0.42 41 41
GR alpha/HSP90/FKBP51/HSP90 0.061 0.14 0.26 104 -0.25 24 128
PRL -0.035 0.13 0.42 1 -0.79 3 4
cortisol/GR alpha (dimer)/TIF2 0.14 0.24 0.53 110 -0.43 1 111
RELA -0.02 0.11 -10000 0 -0.23 58 58
FGG 0.14 0.23 0.45 137 -0.4 2 139
GR beta/TIF2 0.07 0.14 0.28 100 -0.3 9 109
IFNG -0.26 0.41 -10000 0 -0.87 122 122
apoptosis -0.003 0.17 0.48 5 -0.44 20 25
CREB1 0.038 0.042 -10000 0 -0.37 5 5
histone acetylation -0.025 0.11 0.31 4 -0.3 40 44
BGLAP -0.047 0.14 0.34 1 -0.41 31 32
GR/PKAc 0.11 0.12 0.32 51 -0.27 12 63
NF kappa B1 p50/RelA -0.039 0.19 -10000 0 -0.34 111 111
SMARCD1 0.036 0.004 -10000 0 -10000 0 0
MDM2 0.072 0.1 0.23 112 -10000 0 112
GATA3 -0.039 0.18 -10000 0 -0.41 91 91
AKT1 0.03 0.036 0.19 8 -0.43 2 10
CSF2 -0.05 0.13 -10000 0 -0.86 5 5
GSK3B 0.03 0.02 -10000 0 -10000 0 0
NR1I3 0.029 0.18 0.49 7 -0.59 9 16
CSN2 0.12 0.19 0.39 126 -0.39 4 130
BRG1/BAF155/BAF170/BAF60A 0.083 0.037 -10000 0 -0.23 3 3
NFATC1 0.023 0.09 -10000 0 -0.4 21 21
POU2F1 0.033 0.021 -10000 0 -0.25 1 1
CDKN1A -0.047 0.26 -10000 0 -1.5 14 14
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN 0.012 0.099 -10000 0 -0.42 25 25
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.07 0.14 0.29 59 -0.24 39 98
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.079 0.31 0.46 4 -0.77 79 83
JUN -0.15 0.23 0.37 4 -0.46 142 146
IL4 -0.087 0.19 -10000 0 -0.54 41 41
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.097 0.21 0.21 70 -0.38 146 216
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.086 0.13 0.29 68 -0.23 30 98
cortisol/GR alpha (monomer) 0.19 0.31 0.61 146 -0.44 2 148
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.081 0.16 -10000 0 -0.43 73 73
AP-1/NFAT1-c-4 -0.27 0.37 -10000 0 -0.72 173 173
AFP -0.12 0.19 -10000 0 -0.64 18 18
SUV420H1 0.033 0.022 -10000 0 -0.42 1 1
IRF1 0.095 0.21 0.41 67 -0.71 13 80
TP53 0.014 0.13 -10000 0 -0.46 32 32
PPP5C 0.032 0.041 -10000 0 -0.42 4 4
KRT17 -0.38 0.56 -10000 0 -1.2 147 147
KRT14 -0.26 0.49 -10000 0 -1.3 93 93
TBP 0.04 0.019 -10000 0 -0.28 1 1
CREBBP 0.066 0.096 0.28 80 -10000 0 80
HDAC1 0.03 0.021 -10000 0 -0.42 1 1
HDAC2 0.031 0.023 -10000 0 -0.42 1 1
AP-1 -0.27 0.38 -10000 0 -0.72 173 173
MAPK14 0.033 0.014 -10000 0 -10000 0 0
MAPK10 0.009 0.089 -10000 0 -0.42 20 20
MAPK11 0.028 0.02 -10000 0 -10000 0 0
KRT5 -0.39 0.57 -10000 0 -1.2 148 148
interleukin-1 receptor activity -0.001 0.007 -10000 0 -10000 0 0
NCOA1 0.032 0.048 -10000 0 -0.37 6 6
STAT1 0.021 0.091 -10000 0 -0.38 23 23
CGA -0.071 0.17 -10000 0 -0.56 28 28
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.081 0.16 0.36 93 -0.39 2 95
MAPK3 0.027 0.028 -10000 0 -0.42 1 1
MAPK1 0.03 0.025 -10000 0 -0.42 1 1
ICAM1 -0.16 0.3 -10000 0 -0.74 80 80
NFKB1 -0.021 0.11 -10000 0 -0.23 55 55
MAPK8 -0.11 0.2 0.56 2 -0.38 130 132
MAPK9 0.016 0.085 -10000 0 -0.42 18 18
cortisol/GR alpha (dimer) -0.005 0.18 0.49 5 -0.46 20 25
BAX -0.01 0.1 -10000 0 -10000 0 0
POMC -0.091 0.2 0.62 1 -1.1 6 7
EP300 0.066 0.099 0.28 84 -0.43 2 86
cortisol/GR alpha (dimer)/p53 0.12 0.25 0.53 106 -0.42 1 107
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.11 0.25 81 -10000 0 81
SGK1 0.08 0.14 0.33 94 -0.33 4 98
IL13 -0.22 0.26 -10000 0 -0.63 101 101
IL6 -0.2 0.38 -10000 0 -0.91 91 91
PRKACG 0.034 0.029 -10000 0 -0.42 2 2
IL5 -0.18 0.22 -10000 0 -0.62 47 47
IL2 -0.22 0.33 -10000 0 -0.7 130 130
CDK5 0.034 0.008 -10000 0 -10000 0 0
PRKACB 0.008 0.099 -10000 0 -0.42 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.18 0.34 -10000 0 -0.8 94 94
CDK5R1/CDK5 0.047 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.001 0.18 -10000 0 -0.35 57 57
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.49 139 -0.4 1 140
SMARCA4 0.035 0.021 -10000 0 -0.42 1 1
chromatin remodeling 0.11 0.16 0.33 135 -0.26 1 136
NF kappa B1 p50/RelA/Cbp 0.026 0.18 0.35 40 -0.35 37 77
JUN (dimer) -0.15 0.23 0.37 4 -0.46 142 146
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
VIPR1 -0.1 0.21 -10000 0 -0.56 63 63
NR3C1 0.12 0.21 0.4 140 -0.41 8 148
NR4A1 0.037 0.045 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.037 0.046 -10000 0 -0.35 5 5
MAPKKK cascade -0.003 0.17 0.48 5 -0.44 20 25
cortisol/GR alpha (dimer)/Src-1 0.18 0.26 0.52 149 -0.36 1 150
PBX1 0.02 0.077 -10000 0 -0.4 15 15
POU1F1 0.04 0.025 -10000 0 -0.33 2 2
SELE -0.23 0.42 -10000 0 -0.92 125 125
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.16 0.33 135 -0.26 1 136
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.49 139 -0.4 1 140
mol:cortisol 0.11 0.18 0.35 150 -10000 0 150
MMP1 -0.37 0.54 -10000 0 -1.1 164 164
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.085 -10000 0 -0.42 18 18
GNB1/GNG2 -0.05 0.08 -10000 0 -0.18 127 127
AKT1 -0.013 0.13 0.23 5 -0.23 62 67
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.016 0.063 0.25 5 -0.26 3 8
mol:Ca2+ -0.035 0.17 -10000 0 -0.3 133 133
LYN 0.015 0.057 0.26 4 -0.28 2 6
RhoA/GTP -0.014 0.075 -10000 0 -0.13 113 113
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.055 0.19 0.26 1 -0.35 132 133
GNG2 0.034 0.021 -10000 0 -0.42 1 1
ARRB2 0.033 0.011 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.012 0.14 -10000 0 -0.47 31 31
G beta5/gamma2 -0.053 0.11 -10000 0 -0.24 126 126
PRKCH -0.051 0.2 0.3 3 -0.36 129 132
DNM1 0.033 0.035 -10000 0 -0.42 3 3
TXA2/TP beta/beta Arrestin3 0.028 0.027 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.028 0.054 -10000 0 -0.42 7 7
G12 family/GTP -0.048 0.16 -10000 0 -0.3 118 118
ADRBK1 0.034 0.01 -10000 0 -10000 0 0
ADRBK2 0.024 0.067 -10000 0 -0.42 11 11
RhoA/GTP/ROCK1 0.041 0.04 -10000 0 -0.25 8 8
mol:GDP 0.022 0.14 0.43 31 -0.23 2 33
mol:NADP 0.035 0.007 -10000 0 -10000 0 0
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
PRKG1 0.035 0.006 -10000 0 -10000 0 0
mol:IP3 -0.052 0.21 -10000 0 -0.38 133 133
cell morphogenesis 0.04 0.039 -10000 0 -0.25 8 8
PLCB2 -0.086 0.27 -10000 0 -0.52 132 132
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.058 0.25 4 -0.25 3 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.01 0.075 0.25 5 -0.32 8 13
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PTGIR 0.033 0.029 -10000 0 -0.42 2 2
PRKCB1 -0.055 0.21 -10000 0 -0.4 121 121
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.035 0.007 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.087 0.27 -10000 0 -0.52 131 131
LCK -0.005 0.09 0.25 5 -0.31 12 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.049 0.047 0.23 1 -0.26 1 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.036 0.093 -10000 0 -0.48 12 12
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.044 0.047 0.23 1 -0.25 1 2
MAPK14 -0.032 0.13 0.22 3 -0.24 127 130
TGM2/GTP -0.062 0.23 -10000 0 -0.42 130 130
MAPK11 -0.034 0.13 0.25 3 -0.23 128 131
ARHGEF1 -0.011 0.11 0.2 8 -0.18 112 120
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
JNK cascade -0.054 0.21 -10000 0 -0.38 131 131
RAB11/GDP 0.034 0.021 -10000 0 -0.42 1 1
ICAM1 -0.036 0.16 -10000 0 -0.3 129 129
cAMP biosynthetic process -0.049 0.19 -10000 0 -0.34 132 132
Gq family/GTP/EBP50 -0.021 0.096 -10000 0 -0.23 78 78
actin cytoskeleton reorganization 0.04 0.039 -10000 0 -0.25 8 8
SRC 0.015 0.064 0.25 5 -0.27 2 7
GNB5 0.025 0.067 -10000 0 -0.42 11 11
GNB1 0.032 0.045 -10000 0 -0.42 5 5
EGF/EGFR -0.034 0.11 0.23 6 -0.3 38 44
VCAM1 -0.041 0.17 -10000 0 -0.31 129 129
TP beta/Gq family/GDP/G beta5/gamma2 -0.012 0.14 -10000 0 -0.47 31 31
platelet activation -0.04 0.17 0.27 4 -0.3 131 135
PGI2/IP 0.025 0.021 -10000 0 -0.3 2 2
PRKACA 0.019 0.035 -10000 0 -0.23 9 9
Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.41 30 30
TXA2/TP beta/beta Arrestin2 0.009 0.066 -10000 0 -0.44 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.029 -10000 0 -0.21 8 8
mol:DAG -0.064 0.23 -10000 0 -0.43 129 129
EGFR -0.015 0.13 -10000 0 -0.42 49 49
TXA2/TP alpha -0.074 0.25 -10000 0 -0.47 132 132
Gq family/GTP -0.016 0.077 0.22 2 -0.22 56 58
YES1 0.014 0.068 0.25 5 -0.28 6 11
GNAI2/GTP 0.022 0.052 -10000 0 -0.21 13 13
PGD2/DP 0.02 0.038 -10000 0 -0.3 7 7
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
FYN 0.011 0.067 0.25 4 -0.28 6 10
mol:NO 0.035 0.007 -10000 0 -10000 0 0
GNA15 0.03 0.046 -10000 0 -0.42 5 5
PGK/cGMP 0.046 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.06 -10000 0 -0.41 9 9
TP alpha/TGM2/GDP/G beta/gamma 0.056 0.075 0.28 2 -0.33 5 7
NOS3 0.035 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.04 0.19 0.3 4 -0.35 115 119
PRKCB -0.052 0.19 -10000 0 -0.36 130 130
PRKCE -0.052 0.2 0.29 2 -0.36 127 129
PRKCD -0.059 0.2 -10000 0 -0.39 128 128
PRKCG -0.058 0.21 -10000 0 -0.39 130 130
muscle contraction -0.081 0.25 -10000 0 -0.48 131 131
PRKCZ -0.046 0.18 -10000 0 -0.34 131 131
ARR3 0.036 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.042 0.056 0.28 1 -0.21 11 12
PRKCQ -0.048 0.2 0.29 3 -0.37 125 128
MAPKKK cascade -0.07 0.24 -10000 0 -0.45 131 131
SELE -0.055 0.19 -10000 0 -0.37 129 129
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.067 0.28 2 -0.4 3 5
ROCK1 0.036 0.006 -10000 0 -10000 0 0
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
chemotaxis -0.11 0.31 -10000 0 -0.61 129 129
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
GNA11 0.033 0.036 -10000 0 -0.42 3 3
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.067 0.15 -9999 0 -0.29 136 136
FZD6 -0.028 0.14 -9999 0 -0.42 60 60
WNT6 0.03 0.031 -9999 0 -0.42 2 2
WNT4 -0.019 0.14 -9999 0 -0.42 58 58
FZD3 0.007 0.095 -9999 0 -0.42 23 23
WNT5A -0.025 0.15 -9999 0 -0.42 63 63
WNT11 0.027 0.032 -9999 0 -0.42 2 2
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.029 0.05 -10000 0 -0.42 6 6
LAT2 -0.049 0.14 -10000 0 -0.31 84 84
AP1 -0.06 0.21 -10000 0 -0.48 67 67
mol:PIP3 -0.025 0.19 0.3 20 -0.44 46 66
IKBKB 0.011 0.13 0.21 86 -0.24 42 128
AKT1 0.014 0.18 0.33 74 -0.37 24 98
IKBKG -0.008 0.12 0.18 55 -0.24 44 99
MS4A2 -0.076 0.19 -10000 0 -0.41 120 120
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.04 0.16 0.25 7 -0.39 57 64
mol:Ca2+ -0.013 0.16 0.25 26 -0.33 46 72
LYN 0.032 0.017 -10000 0 -10000 0 0
CBLB -0.047 0.14 -10000 0 -0.31 82 82
SHC1 0.028 0.025 -10000 0 -0.42 1 1
RasGAP/p62DOK 0.035 0.092 -10000 0 -0.24 46 46
positive regulation of cell migration -0.005 0.063 -10000 0 -0.3 23 23
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.004 0.18 0.32 71 -0.31 55 126
PTPN13 -0.07 0.2 -10000 0 -0.62 30 30
PTPN11 0.033 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.004 0.15 0.32 17 -0.33 25 42
SYK 0.006 0.12 -10000 0 -0.42 34 34
GRB2 0.033 0.011 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.056 0.16 -10000 0 -0.38 73 73
LAT -0.045 0.13 -10000 0 -0.31 79 79
PAK2 -0.035 0.17 0.26 7 -0.42 48 55
NFATC2 -0.012 0.066 -10000 0 -0.59 4 4
HRAS -0.036 0.18 0.26 9 -0.45 51 60
GAB2 0.031 0.013 -10000 0 -10000 0 0
PLA2G1B 0.013 0.11 -10000 0 -0.94 5 5
Fc epsilon R1 -0.029 0.16 -10000 0 -0.3 109 109
Antigen/IgE/Fc epsilon R1 -0.024 0.14 -10000 0 -0.27 109 109
mol:GDP -0.051 0.18 0.25 1 -0.48 51 52
JUN -0.001 0.12 -10000 0 -0.42 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
FOS -0.031 0.15 -10000 0 -0.42 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.044 0.14 -10000 0 -0.32 84 84
CHUK -0.011 0.12 0.18 55 -0.25 47 102
KLRG1 -0.038 0.12 -10000 0 -0.38 37 37
VAV1 -0.051 0.14 -10000 0 -0.33 83 83
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.045 0.13 -10000 0 -0.31 80 80
negative regulation of mast cell degranulation -0.041 0.11 -10000 0 -0.36 35 35
BTK -0.057 0.18 -10000 0 -0.52 48 48
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.063 0.18 -10000 0 -0.36 109 109
GAB2/PI3K/SHP2 -0.052 0.1 -10000 0 -0.31 46 46
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.048 0.13 -10000 0 -0.33 65 65
RAF1 0.014 0.11 -10000 0 -1 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.024 0.16 -10000 0 -0.29 116 116
FCER1G 0.032 0.019 -10000 0 -10000 0 0
FCER1A -0.023 0.14 -10000 0 -0.43 56 56
Antigen/IgE/Fc epsilon R1/Fyn -0.016 0.14 -10000 0 -0.26 108 108
MAPK3 0.013 0.11 -10000 0 -0.97 5 5
MAPK1 0.008 0.11 -10000 0 -0.94 5 5
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.041 0.22 -10000 0 -0.66 42 42
DUSP1 0.003 0.11 -10000 0 -0.42 34 34
NF-kappa-B/RelA 0.012 0.084 0.16 31 -0.16 26 57
actin cytoskeleton reorganization -0.044 0.18 -10000 0 -0.65 17 17
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.028 0.18 0.26 1 -0.42 50 51
FER -0.046 0.13 -10000 0 -0.31 82 82
RELA 0.035 0.006 -10000 0 -10000 0 0
ITK -0.032 0.11 -10000 0 -0.39 40 40
SOS1 0.035 0.021 -10000 0 -0.42 1 1
PLCG1 -0.042 0.19 0.27 4 -0.48 50 54
cytokine secretion -0.003 0.051 -10000 0 -0.14 1 1
SPHK1 -0.054 0.14 -10000 0 -0.32 84 84
PTK2 -0.046 0.19 -10000 0 -0.7 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.057 0.17 -10000 0 -0.39 81 81
EDG1 -0.005 0.064 -10000 0 -0.3 23 23
mol:DAG -0.03 0.19 0.29 14 -0.44 51 65
MAP2K2 0.008 0.11 -10000 0 -0.97 5 5
MAP2K1 0.01 0.11 -10000 0 -0.96 5 5
MAP2K7 0.035 0.021 -10000 0 -0.42 1 1
KLRG1/SHP2 -0.024 0.12 0.21 3 -0.36 34 37
MAP2K4 -0.098 0.36 -10000 0 -0.92 76 76
Fc epsilon R1/FcgammaRIIB -0.026 0.17 -10000 0 -0.31 116 116
mol:Choline -0.003 0.18 0.32 71 -0.31 55 126
SHC/Grb2/SOS1 -0.011 0.14 -10000 0 -0.4 30 30
FYN 0.027 0.054 -10000 0 -0.42 7 7
DOK1 0.027 0.061 -10000 0 -0.42 9 9
PXN -0.045 0.18 -10000 0 -0.63 17 17
HCLS1 -0.05 0.14 -10000 0 -0.32 83 83
PRKCB -0.016 0.15 0.21 55 -0.33 47 102
FCGR2B 0.001 0.11 -10000 0 -0.42 30 30
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.042 0.12 -10000 0 -0.37 35 35
LCP2 0.024 0.067 -10000 0 -0.42 11 11
PLA2G4A -0.052 0.14 -10000 0 -0.33 84 84
RASA1 0.029 0.05 -10000 0 -0.42 6 6
mol:Phosphatidic acid -0.003 0.18 0.32 71 -0.31 55 126
IKK complex 0.01 0.11 0.23 47 -0.2 31 78
WIPF1 0 0 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.024 0.082 0.2 80 -0.19 6 86
RFC1 0.021 0.074 0.19 76 -0.19 5 81
PRKDC 0.044 0.1 0.21 120 -0.2 5 125
RIPK1 0.036 0.008 -10000 0 -10000 0 0
CASP7 -0.007 0.14 -10000 0 -0.68 18 18
FASLG/FAS/FADD/FAF1 0.003 0.091 0.2 37 -0.26 28 65
MAP2K4 -0.025 0.17 0.44 2 -0.44 47 49
mol:ceramide -0.013 0.11 -10000 0 -0.35 35 35
GSN 0.019 0.086 0.19 78 -0.22 14 92
FASLG/FAS/FADD/FAF1/Caspase 8 0.006 0.11 0.23 3 -0.31 32 35
FAS 0.003 0.11 -10000 0 -0.42 29 29
BID -0.017 0.053 0.26 12 -0.27 7 19
MAP3K1 -0.009 0.14 0.3 4 -0.47 22 26
MAP3K7 0.033 0.011 -10000 0 -10000 0 0
RB1 0.019 0.071 0.19 67 -0.2 5 72
CFLAR 0.032 0.046 -10000 0 -0.42 5 5
HGF/MET 0.016 0.12 -10000 0 -0.26 77 77
ARHGDIB 0.016 0.09 0.2 70 -0.24 14 84
FADD 0.025 0.021 -10000 0 -10000 0 0
actin filament polymerization -0.018 0.087 0.22 16 -0.19 73 89
NFKB1 0.004 0.1 -10000 0 -0.68 7 7
MAPK8 -0.044 0.21 0.51 2 -0.5 69 71
DFFA 0.023 0.078 0.19 77 -0.19 6 83
DNA fragmentation during apoptosis 0.022 0.08 0.19 80 -0.19 6 86
FAS/FADD/MET 0.034 0.077 -10000 0 -0.26 27 27
CFLAR/RIP1 0.049 0.038 -10000 0 -0.3 5 5
FAIM3 0.015 0.078 -10000 0 -0.42 15 15
FAF1 0.028 0.03 -10000 0 -0.42 1 1
PARP1 0.028 0.098 0.22 87 -0.21 8 95
DFFB 0.022 0.08 0.19 80 -0.19 6 86
CHUK -0.008 0.11 -10000 0 -0.58 10 10
FASLG -0.011 0.12 -10000 0 -0.42 36 36
FAS/FADD 0.02 0.077 -10000 0 -0.3 23 23
HGF 0.028 0.057 -10000 0 -0.42 8 8
LMNA 0.024 0.1 0.34 26 -0.22 6 32
CASP6 0.02 0.081 0.19 76 -0.21 9 85
CASP10 0.03 0.02 -10000 0 -10000 0 0
CASP3 0.032 0.092 0.23 81 -0.22 6 87
PTPN13 -0.03 0.16 -10000 0 -0.42 72 72
CASP8 -0.013 0.057 0.33 13 -10000 0 13
IL6 -0.1 0.41 -10000 0 -1.2 59 59
MET 0.03 0.041 -10000 0 -0.42 4 4
ICAD/CAD 0.018 0.073 0.17 69 -10000 0 69
FASLG/FAS/FADD/FAF1/Caspase 10 -0.014 0.11 -10000 0 -0.36 35 35
activation of caspase activity by cytochrome c -0.017 0.053 0.26 12 -0.27 7 19
PAK2 0.021 0.077 0.19 76 -0.2 2 78
BCL2 -0.056 0.18 -10000 0 -0.42 99 99
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.004 0.17 0.24 38 -0.34 67 105
FYN -0.038 0.2 0.28 5 -0.43 74 79
LAT/GRAP2/SLP76 -0.021 0.17 0.24 6 -0.38 65 71
IKBKB 0.03 0.014 -10000 0 -10000 0 0
AKT1 -0.026 0.15 0.25 14 -0.33 70 84
B2M 0.026 0.062 -10000 0 -0.43 9 9
IKBKG 0 0.055 0.12 20 -0.13 29 49
MAP3K8 0.004 0.11 -10000 0 -0.42 32 32
mol:Ca2+ -0.017 0.021 0.093 2 -0.058 67 69
integrin-mediated signaling pathway 0.03 0.048 -10000 0 -0.25 12 12
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.052 0.2 0.26 2 -0.44 81 83
TRPV6 -0.028 0.22 1.2 9 -0.42 57 66
CD28 0 0.12 -10000 0 -0.42 37 37
SHC1 -0.022 0.2 0.24 45 -0.39 82 127
receptor internalization -0.069 0.2 0.17 1 -0.4 124 125
PRF1 -0.054 0.22 -10000 0 -0.79 28 28
KRAS 0.028 0.054 -10000 0 -0.42 7 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
COT/AKT1 -0.015 0.14 0.25 11 -0.29 64 75
LAT -0.042 0.19 0.24 13 -0.38 94 107
EntrezGene:6955 0 0.002 -10000 0 -0.016 7 7
CD3D 0.016 0.077 -10000 0 -0.43 14 14
CD3E 0.032 0.015 -10000 0 -10000 0 0
CD3G -0.021 0.14 -10000 0 -0.42 54 54
RASGRP2 -0.001 0.043 0.078 1 -0.17 27 28
RASGRP1 -0.043 0.17 0.32 2 -0.36 79 81
HLA-A 0.018 0.086 -10000 0 -0.43 18 18
RASSF5 0.019 0.064 -10000 0 -0.42 10 10
RAP1A/GTP/RAPL 0.03 0.048 -10000 0 -0.25 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.067 0.14 32 -0.12 27 59
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.022 0.071 -10000 0 -0.18 54 54
PRKCA -0.01 0.09 0.17 14 -0.21 47 61
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
mol:IP3 -0.022 0.14 0.21 30 -0.32 60 90
EntrezGene:6957 0 0.003 0.011 2 -0.016 11 13
TCR/CD3/MHC I/CD8 -0.031 0.14 -10000 0 -0.32 77 77
ORAI1 0.007 0.16 0.48 2 -1 9 11
CSK -0.045 0.18 0.26 2 -0.4 83 85
B7 family/CD28 -0.027 0.22 0.29 1 -0.47 75 76
CHUK 0.026 0.067 -10000 0 -0.42 11 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.06 0.21 0.26 1 -0.42 103 104
PTPN6 -0.053 0.19 0.24 4 -0.4 88 92
VAV1 -0.059 0.2 0.26 2 -0.41 99 101
Monovalent TCR/CD3 -0.018 0.11 -10000 0 -0.3 61 61
CBL 0.032 0.012 -10000 0 -10000 0 0
LCK -0.046 0.21 0.28 3 -0.47 75 78
PAG1 -0.031 0.19 0.23 16 -0.4 82 98
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
TCR/CD3/MHC I/CD8/LCK -0.062 0.21 0.28 1 -0.42 104 105
CD80 0.034 0.022 -10000 0 -0.42 1 1
CD86 0.017 0.09 -10000 0 -0.42 20 20
PDK1/CARD11/BCL10/MALT1 -0.013 0.09 -10000 0 -0.22 55 55
HRAS 0.032 0.036 -10000 0 -0.42 3 3
GO:0035030 -0.052 0.17 0.25 1 -0.4 75 76
CD8A 0 0.003 0.01 3 -0.014 11 14
CD8B 0 0.004 0.011 3 -0.013 24 27
PTPRC 0.006 0.095 -10000 0 -0.42 23 23
PDK1/PKC theta -0.028 0.18 0.32 18 -0.38 73 91
CSK/PAG1 -0.025 0.18 0.23 12 -0.41 67 79
SOS1 0.035 0.021 -10000 0 -0.42 1 1
peptide-MHC class I 0.033 0.088 -10000 0 -0.36 23 23
GRAP2/SLP76 -0.034 0.2 0.29 1 -0.41 81 82
STIM1 0.008 0.11 1.3 3 -10000 0 3
RAS family/GTP 0.013 0.085 0.16 12 -0.18 36 48
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.072 0.21 0.17 1 -0.41 123 124
mol:DAG -0.042 0.11 0.12 1 -0.28 67 68
RAP1A/GDP 0.011 0.034 0.076 16 -0.073 14 30
PLCG1 0.034 0.008 -10000 0 -10000 0 0
CD247 0 0.002 -10000 0 -0.016 7 7
cytotoxic T cell degranulation -0.051 0.21 -10000 0 -0.74 29 29
RAP1A/GTP 0 0.018 -10000 0 -0.065 31 31
mol:PI-3-4-5-P3 -0.04 0.17 0.25 2 -0.37 81 83
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.021 0.18 0.23 24 -0.4 60 84
NRAS 0.029 0.054 -10000 0 -0.42 7 7
ZAP70 0.034 0.022 -10000 0 -0.42 1 1
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
LAT/GRAP2/SLP76/VAV1 -0.031 0.17 0.25 2 -0.4 65 67
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
CD8 heterodimer 0.001 0.006 0.02 3 -0.017 20 23
CARD11 0.028 0.054 -10000 0 -0.42 7 7
PRKCB -0.033 0.077 0.11 2 -0.2 67 69
PRKCE -0.012 0.097 0.17 15 -0.23 47 62
PRKCQ -0.045 0.19 0.29 3 -0.42 79 82
LCP2 0.024 0.067 -10000 0 -0.42 11 11
BCL10 0.035 0.008 -10000 0 -10000 0 0
regulation of survival gene product expression -0.019 0.13 0.23 15 -0.28 69 84
IKK complex 0.013 0.061 0.16 33 -0.1 17 50
RAS family/GDP -0.004 0.015 -10000 0 -0.049 19 19
MAP3K14 -0.014 0.1 0.2 14 -0.23 59 73
PDPK1 -0.021 0.14 0.28 18 -0.32 65 83
TCR/CD3/MHC I/CD8/Fyn -0.061 0.2 -10000 0 -0.43 92 92
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.013 0.083 -10000 0 -0.21 68 68
epithelial cell differentiation 0.026 0.094 -10000 0 -0.22 57 57
CYFIP2 -0.006 0.13 -10000 0 -0.42 45 45
ENAH -0.028 0.075 0.3 2 -0.31 8 10
EGFR -0.015 0.13 -10000 0 -0.42 49 49
EPHA2 0.032 0.036 -10000 0 -0.42 3 3
MYO6 -0.036 0.077 0.18 7 -0.22 69 76
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
ABI1/Sra1/Nap1 0.041 0.09 -10000 0 -0.26 40 40
AQP5 -0.095 0.17 -10000 0 -0.45 84 84
CTNND1 0.034 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 -0.032 0.07 0.18 6 -0.21 58 64
regulation of calcium-dependent cell-cell adhesion -0.032 0.069 0.18 5 -0.21 60 65
EGF -0.069 0.19 -10000 0 -0.42 110 110
NCKAP1 0.035 0.021 -10000 0 -0.42 1 1
AQP3 -0.094 0.17 -10000 0 -0.45 84 84
cortical microtubule organization 0.026 0.094 -10000 0 -0.22 57 57
GO:0000145 -0.033 0.065 0.16 1 -0.2 58 59
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.097 -10000 0 -0.22 57 57
MLLT4 0.02 0.078 -10000 0 -0.42 15 15
ARF6/GDP -0.041 0.067 -10000 0 -0.22 54 54
ARF6 0.034 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.072 -10000 0 -0.23 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.026 0.093 -10000 0 -0.35 17 17
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
ZYX -0.034 0.074 0.18 8 -0.21 64 72
ARF6/GTP 0.059 0.077 -10000 0 -0.24 20 20
CDH1 -0.011 0.13 -10000 0 -0.42 45 45
EGFR/EGFR/EGF/EGF -0.057 0.14 -10000 0 -0.22 191 191
RhoA/GDP 0.023 0.099 -10000 0 -0.22 64 64
actin cytoskeleton organization -0.04 0.074 -10000 0 -0.21 66 66
IGF-1R heterotetramer -0.042 0.17 -10000 0 -0.42 84 84
GIT1 0.034 0.022 -10000 0 -0.42 1 1
IGF1R -0.042 0.17 -10000 0 -0.42 84 84
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
DIAPH1 0.002 0.2 -10000 0 -0.59 36 36
Wnt receptor signaling pathway -0.026 0.094 0.22 57 -10000 0 57
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RhoA/GTP -0.043 0.068 -10000 0 -0.22 60 60
CTNNA1 0.035 0.021 -10000 0 -0.42 1 1
VCL -0.041 0.075 -10000 0 -0.22 67 67
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
LPP -0.038 0.071 0.17 8 -0.21 60 68
Ephrin A1/EPHA2 0.01 0.092 -10000 0 -0.22 57 57
SEC6/SEC8 -0.048 0.069 -10000 0 -0.21 75 75
MGAT3 -0.032 0.07 0.18 5 -0.21 60 65
HGF/MET 0.016 0.093 -10000 0 -0.21 66 66
HGF 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.013 0.084 -10000 0 -0.22 68 68
actin cable formation 0.016 0.11 0.26 12 -0.31 8 20
KIAA1543 -0.037 0.07 0.17 7 -0.22 58 65
KIFC3 -0.031 0.068 0.18 6 -0.21 52 58
NCK1 0.034 0.021 -10000 0 -0.42 1 1
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ACTN1 -0.034 0.075 0.18 8 -0.21 65 73
NCK1/GIT1 0.049 0.025 -10000 0 -0.29 2 2
mol:GDP 0.026 0.094 -10000 0 -0.22 57 57
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
STX4 -0.034 0.062 -10000 0 -0.21 57 57
PIP5K1C -0.032 0.071 0.18 6 -0.21 58 64
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.035 0.008 -10000 0 -10000 0 0
ROCK1 -0.009 0.1 0.3 5 -0.32 7 12
adherens junction assembly -0.044 0.12 0.27 1 -0.46 16 17
IGF-1R heterotetramer/IGF1 -0.055 0.15 -10000 0 -0.24 175 175
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
MET 0.03 0.041 -10000 0 -0.42 4 4
PLEKHA7 -0.031 0.07 0.18 8 -0.21 58 66
mol:GTP 0.051 0.071 -10000 0 -0.23 20 20
establishment of epithelial cell apical/basal polarity -0.044 0.072 0.14 13 -0.2 64 77
cortical actin cytoskeleton stabilization -0.013 0.083 -10000 0 -0.21 68 68
regulation of cell-cell adhesion -0.04 0.074 -10000 0 -0.21 66 66
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.013 0.084 -10000 0 -0.22 68 68
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.1 -10000 0 -0.34 16 16
TBX21 -0.26 0.57 -10000 0 -1.4 100 100
B2M 0.024 0.063 -10000 0 -0.42 9 9
TYK2 0.014 0.043 -10000 0 -10000 0 0
IL12RB1 0.013 0.043 -10000 0 -10000 0 0
GADD45B -0.18 0.44 -10000 0 -1.1 84 84
IL12RB2 -0.01 0.1 -10000 0 -0.43 26 26
GADD45G -0.17 0.43 -10000 0 -1 87 87
natural killer cell activation -0.005 0.022 -10000 0 -0.044 85 85
RELB 0.029 0.05 -10000 0 -0.42 6 6
RELA 0.035 0.006 -10000 0 -10000 0 0
IL18 0 0.11 -10000 0 -0.42 32 32
IL2RA 0.004 0.11 -10000 0 -0.42 31 31
IFNG -0.007 0.12 -10000 0 -0.42 38 38
STAT3 (dimer) -0.14 0.37 -10000 0 -0.81 97 97
HLA-DRB5 0.016 0.077 -10000 0 -0.42 14 14
FASLG -0.18 0.5 -10000 0 -1.1 92 92
NF kappa B2 p52/RelB -0.16 0.44 -10000 0 -0.94 100 100
CD4 0.028 0.021 -10000 0 -10000 0 0
SOCS1 0.032 0.023 -10000 0 -0.42 1 1
EntrezGene:6955 -0.003 0.012 -10000 0 -0.03 67 67
CD3D 0.008 0.078 -10000 0 -0.43 14 14
CD3E 0.024 0.026 -10000 0 -10000 0 0
CD3G -0.028 0.14 -10000 0 -0.43 54 54
IL12Rbeta2/JAK2 0.004 0.096 -10000 0 -0.33 26 26
CCL3 -0.17 0.43 -10000 0 -1 85 85
CCL4 -0.18 0.45 -10000 0 -1 86 86
HLA-A 0.017 0.086 -10000 0 -0.42 18 18
IL18/IL18R -0.001 0.16 -10000 0 -0.34 84 84
NOS2 -0.18 0.43 -10000 0 -0.91 106 106
IL12/IL12R/TYK2/JAK2/SPHK2 -0.008 0.11 -10000 0 -0.35 18 18
IL1R1 -0.22 0.5 -10000 0 -1.1 102 102
IL4 0.034 0.052 -10000 0 -0.42 5 5
JAK2 0.011 0.051 -10000 0 -0.46 2 2
EntrezGene:6957 -0.003 0.012 -10000 0 -0.03 65 65
TCR/CD3/MHC I/CD8 -0.073 0.28 -10000 0 -0.77 51 51
RAB7A -0.13 0.34 -10000 0 -0.76 97 97
lysosomal transport -0.12 0.32 -10000 0 -0.72 97 97
FOS -0.24 0.5 -10000 0 -1.1 105 105
STAT4 (dimer) -0.15 0.42 -10000 0 -0.9 97 97
STAT5A (dimer) -0.18 0.44 -10000 0 -0.96 100 100
GZMA -0.17 0.42 -10000 0 -0.92 101 101
GZMB -0.26 0.56 -10000 0 -1.3 99 99
HLX 0 0 -10000 0 -10000 0 0
LCK -0.21 0.5 -10000 0 -1.1 105 105
TCR/CD3/MHC II/CD4 -0.058 0.17 -10000 0 -0.45 62 62
IL2/IL2R 0.043 0.11 -10000 0 -0.29 46 46
MAPK14 -0.18 0.44 -10000 0 -0.99 97 97
CCR5 -0.16 0.4 -10000 0 -0.82 112 112
IL1B -0.021 0.13 -10000 0 -0.44 40 40
STAT6 -0.055 0.2 -10000 0 -0.59 35 35
STAT4 0.01 0.1 -10000 0 -0.42 27 27
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
NFKB1 0.036 0.005 -10000 0 -10000 0 0
NFKB2 0.035 0.021 -10000 0 -0.42 1 1
IL12B 0.01 0.063 -10000 0 -0.42 6 6
CD8A 0 0.008 -10000 0 -0.038 19 19
CD8B -0.001 0.009 -10000 0 -0.044 20 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.1 0.34 16 -10000 0 16
IL2RB 0.011 0.097 -10000 0 -0.42 24 24
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.37 -10000 0 -0.8 97 97
IL2RG 0.031 0.041 -10000 0 -0.42 4 4
IL12 0.015 0.076 -10000 0 -0.33 10 10
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
CD247 -0.002 0.011 -10000 0 -0.028 64 64
IL2 0.032 0.036 -10000 0 -0.42 3 3
SPHK2 0.035 0.007 -10000 0 -10000 0 0
FRAP1 0.035 0.007 -10000 0 -10000 0 0
IL12A 0.006 0.059 -10000 0 -0.42 5 5
IL12/IL12R/TYK2/JAK2 -0.21 0.53 -10000 0 -1.1 101 101
MAP2K3 -0.18 0.46 -10000 0 -1 101 101
RIPK2 0.028 0.015 -10000 0 -10000 0 0
MAP2K6 -0.18 0.45 -10000 0 -1 95 95
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.064 -10000 0 -0.42 9 9
IL18RAP -0.021 0.15 -10000 0 -0.43 58 58
IL12Rbeta1/TYK2 0.027 0.056 -10000 0 -10000 0 0
EOMES -0.048 0.28 -10000 0 -1.2 27 27
STAT1 (dimer) -0.15 0.38 -10000 0 -0.81 103 103
T cell proliferation -0.11 0.3 -10000 0 -0.64 102 102
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.016 0.091 -10000 0 -0.43 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.33 -10000 0 -0.68 104 104
ATF2 -0.16 0.4 -10000 0 -0.89 97 97
IL23-mediated signaling 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
CCL2 -0.16 0.54 -10000 0 -1.3 71 71
IL23A -0.13 0.49 -10000 0 -1.2 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.099 0.48 -10000 0 -1.1 68 68
positive regulation of T cell mediated cytotoxicity -0.14 0.52 -10000 0 -1.2 68 68
ITGA3 -0.13 0.48 -10000 0 -1.1 72 72
IL17F -0.049 0.33 0.47 5 -0.69 70 75
IL12B 0.02 0.075 -10000 0 -0.44 6 6
STAT1 (dimer) -0.14 0.5 -10000 0 -1.2 69 69
CD4 -0.1 0.45 -10000 0 -1.1 54 54
IL23 -0.12 0.47 -10000 0 -1.2 62 62
IL23R -0.001 0.22 -10000 0 -1.3 11 11
IL1B -0.15 0.53 -10000 0 -1.3 71 71
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.077 0.46 -10000 0 -1.1 57 57
TYK2 0.02 0.046 -10000 0 -10000 0 0
STAT4 0.01 0.1 -10000 0 -0.42 27 27
STAT3 0.029 0.032 -10000 0 -0.42 2 2
IL18RAP -0.022 0.15 -10000 0 -0.42 58 58
IL12RB1 0.02 0.046 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL12Rbeta1/TYK2 0.031 0.059 -10000 0 -10000 0 0
IL23R/JAK2 0.012 0.22 -10000 0 -1.2 11 11
positive regulation of chronic inflammatory response -0.14 0.52 -10000 0 -1.2 68 68
natural killer cell activation 0 0.012 0.081 7 -10000 0 7
JAK2 0.023 0.063 -10000 0 -0.46 2 2
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.11 0.45 -10000 0 -1.1 63 63
ALOX12B -0.11 0.45 -10000 0 -1.1 52 52
CXCL1 -0.17 0.55 -10000 0 -1.2 98 98
T cell proliferation -0.14 0.52 -10000 0 -1.2 68 68
NFKBIA 0.034 0.03 -10000 0 -0.42 2 2
IL17A -0.027 0.26 -10000 0 -0.54 60 60
PI3K -0.12 0.49 -10000 0 -1.1 71 71
IFNG -0.006 0.05 0.14 6 -0.13 45 51
STAT3 (dimer) -0.12 0.46 -10000 0 -1.1 70 70
IL18R1 0.015 0.09 -10000 0 -0.42 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.035 0.29 0.51 1 -0.7 39 40
IL18/IL18R -0.009 0.16 -10000 0 -0.34 84 84
macrophage activation -0.006 0.021 -10000 0 -0.044 55 55
TNF -0.13 0.48 -10000 0 -1.2 63 63
STAT3/STAT4 -0.13 0.49 -10000 0 -1.2 69 69
STAT4 (dimer) -0.14 0.52 -10000 0 -1.2 70 70
IL18 -0.001 0.11 -10000 0 -0.42 32 32
IL19 -0.077 0.46 -10000 0 -1.1 57 57
STAT5A (dimer) -0.14 0.49 -10000 0 -1.2 67 67
STAT1 0.02 0.075 -10000 0 -0.42 14 14
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
CXCL9 -0.2 0.58 -10000 0 -1.2 108 108
MPO -0.097 0.45 -10000 0 -1.1 60 60
positive regulation of humoral immune response -0.14 0.52 -10000 0 -1.2 68 68
IL23/IL23R/JAK2/TYK2 -0.15 0.56 -10000 0 -1.3 68 68
IL6 -0.17 0.56 -10000 0 -1.3 88 88
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
IL2 0.029 0.039 -10000 0 -0.42 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.012 0.081 7 -10000 0 7
CD3E -0.11 0.45 -10000 0 -1.1 54 54
keratinocyte proliferation -0.14 0.52 -10000 0 -1.2 68 68
NOS2 -0.11 0.45 -10000 0 -1.1 68 68
Nongenotropic Androgen signaling

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
PTK2 0.007 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.12 -10000 0 -0.24 102 102
regulation of S phase of mitotic cell cycle -0.026 0.11 -10000 0 -0.23 100 100
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
SHBG/T-DHT 0.022 0.008 -10000 0 -10000 0 0
PELP1 0.032 0.011 -10000 0 -10000 0 0
AKT1 0.007 0.019 -10000 0 -0.3 2 2
MAP2K1 -0.056 0.097 0.18 13 -0.32 21 34
T-DHT/AR -0.037 0.13 -10000 0 -0.3 99 99
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 73 73
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
mol:GDP -0.073 0.15 -10000 0 -0.37 99 99
cell proliferation -0.075 0.17 0.29 2 -0.43 76 78
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FOS -0.12 0.28 -10000 0 -0.79 73 73
mol:Ca2+ -0.009 0.024 -10000 0 -0.062 58 58
MAPK3 -0.06 0.14 0.28 3 -0.33 69 72
MAPK1 -0.045 0.13 -10000 0 -0.42 28 28
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 0 0.002 -10000 0 -0.004 71 71
cAMP biosynthetic process 0.003 0.017 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 71 71
HRAS/GTP -0.006 0.12 -10000 0 -0.22 99 99
actin cytoskeleton reorganization 0.039 0.051 -10000 0 -0.21 17 17
SRC 0.033 0.03 -10000 0 -0.42 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 71 71
PI3K 0.033 0.056 -10000 0 -0.25 17 17
apoptosis 0.063 0.17 0.43 77 -10000 0 77
T-DHT/AR/PELP1 -0.015 0.12 -10000 0 -0.25 99 99
HRAS/GDP -0.052 0.16 -10000 0 -0.36 100 100
CREB1 -0.069 0.18 -10000 0 -0.46 77 77
RAC1-CDC42/GTP 0.05 0.056 -10000 0 -0.21 17 17
AR -0.054 0.18 -10000 0 -0.42 99 99
GNB1 0.032 0.045 -10000 0 -0.42 5 5
RAF1 -0.035 0.1 0.22 5 -0.22 93 98
RAC1-CDC42/GDP -0.03 0.16 -10000 0 -0.35 97 97
T-DHT/AR/PELP1/Src 0.001 0.12 -10000 0 -0.23 98 98
MAP2K2 -0.057 0.098 0.18 15 -0.31 24 39
T-DHT/AR/PELP1/Src/PI3K -0.027 0.11 -10000 0 -0.24 100 100
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
SHBG 0.032 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.037 0.13 -10000 0 -0.41 35 35
mol:T-DHT 0 0.001 0.002 2 -0.003 41 43
RAC1 0.035 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.014 -10000 0 -0.3 1 1
Gi family/GTP -0.028 0.084 -10000 0 -0.23 46 46
CDC42 0.035 0.008 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.099 0.24 0.62 65 -0.53 2 67
IL27/IL27R/JAK1 -0.088 0.34 0.89 2 -1.1 36 38
TBX21 -0.096 0.3 0.63 21 -0.59 93 114
IL12B 0.026 0.052 -10000 0 -0.42 6 6
IL12A 0.003 0.031 -10000 0 -0.3 5 5
IL6ST -0.05 0.16 -10000 0 -0.4 87 87
IL27RA/JAK1 -0.063 0.33 0.44 2 -1.2 35 37
IL27 -0.036 0.16 -10000 0 -0.42 73 73
TYK2 0.029 0.029 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.013 0.087 0.2 13 -0.25 54 67
T-helper 2 cell differentiation 0.099 0.24 0.62 65 -0.53 2 67
T cell proliferation during immune response 0.099 0.24 0.62 65 -0.53 2 67
MAPKKK cascade -0.099 0.24 0.53 2 -0.62 65 67
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT2 0.036 0.005 -10000 0 -10000 0 0
STAT1 0.022 0.077 -10000 0 -0.42 14 14
IL12RB1 0.036 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.081 0.29 0.68 19 -0.61 73 92
IL27/IL27R/JAK2/TYK2 -0.1 0.25 0.53 2 -0.64 65 67
positive regulation of T cell mediated cytotoxicity -0.099 0.24 0.53 2 -0.62 65 67
STAT1 (dimer) -0.1 0.39 0.57 30 -0.99 55 85
JAK2 0.024 0.038 -10000 0 -0.43 2 2
JAK1 0.035 0.036 -10000 0 -0.39 3 3
STAT2 (dimer) -0.084 0.24 0.47 2 -0.6 64 66
T cell proliferation -0.11 0.25 0.48 2 -0.62 70 72
IL12/IL12R/TYK2/JAK2 0.001 0.2 -10000 0 -0.92 17 17
IL17A -0.013 0.087 0.2 13 -0.25 54 67
mast cell activation 0.099 0.24 0.62 65 -0.53 2 67
IFNG -0.01 0.05 0.13 6 -0.13 50 56
T cell differentiation -0.005 0.01 0.026 10 -0.025 74 84
STAT3 (dimer) -0.075 0.24 0.47 2 -0.6 63 65
STAT5A (dimer) -0.076 0.24 0.47 2 -0.6 63 65
STAT4 (dimer) -0.094 0.26 0.47 2 -0.61 70 72
STAT4 0.01 0.1 -10000 0 -0.42 27 27
T cell activation -0.002 0.032 0.12 32 -10000 0 32
IL27R/JAK2/TYK2 -0.08 0.32 -10000 0 -1.1 36 36
GATA3 -0.2 0.52 0.82 9 -1.3 91 100
IL18 -0.013 0.074 -10000 0 -0.3 32 32
positive regulation of mast cell cytokine production -0.073 0.23 0.46 2 -0.58 63 65
IL27/EBI3 -0.008 0.13 0.23 5 -0.31 76 81
IL27RA -0.091 0.33 -10000 0 -1.3 35 35
IL6 -0.018 0.14 -10000 0 -0.42 52 52
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
monocyte differentiation 0 0.002 -10000 0 -0.013 1 1
IL2 0.022 0.15 0.46 36 -1.2 3 39
IL1B -0.017 0.082 -10000 0 -0.3 40 40
EBI3 0.026 0.053 0.16 1 -0.43 5 6
TNF 0.002 0.041 -10000 0 -0.3 9 9
IL6-mediated signaling events

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
BCL2L1 -0.075 0.28 -10000 0 -0.73 50 50
CRP -0.044 0.3 0.57 3 -0.75 45 48
cell cycle arrest -0.095 0.34 0.49 1 -0.79 68 69
TIMP1 -0.069 0.3 -10000 0 -0.75 58 58
IL6ST -0.049 0.17 -10000 0 -0.42 88 88
Rac1/GDP -0.05 0.19 0.28 1 -0.42 63 64
AP1 0.013 0.18 -10000 0 -0.52 24 24
GAB2 0.033 0.014 -10000 0 -10000 0 0
TNFSF11 -0.14 0.4 -10000 0 -0.95 85 85
HSP90B1 0 0.12 -10000 0 -0.83 8 8
GAB1 0.028 0.061 -10000 0 -0.42 9 9
MAPK14 -0.045 0.17 -10000 0 -0.52 32 32
AKT1 0.03 0.081 0.28 1 -0.39 7 8
FOXO1 0.037 0.08 -10000 0 -0.37 7 7
MAP2K6 -0.05 0.16 0.24 1 -0.42 55 56
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.061 0.21 0.36 1 -0.47 68 69
MITF -0.054 0.17 0.24 1 -0.4 65 66
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.036 0.005 -10000 0 -10000 0 0
A2M -0.053 0.33 -10000 0 -1.3 32 32
CEBPB 0.027 0.05 -10000 0 -0.42 6 6
GRB2/SOS1/GAB family/SHP2 0.005 0.12 0.3 1 -0.43 18 19
STAT3 -0.11 0.37 0.5 1 -0.87 68 69
STAT1 -0.01 0.17 -10000 0 -0.88 17 17
CEBPD -0.097 0.37 0.59 1 -0.9 69 70
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K 0.038 0.066 -10000 0 -0.3 17 17
JUN -0.001 0.12 -10000 0 -0.42 39 39
PIAS3/MITF -0.045 0.17 -10000 0 -0.4 60 60
MAPK11 -0.044 0.16 -10000 0 -0.52 33 33
STAT3 (dimer)/FOXO1 -0.052 0.28 0.44 3 -0.63 58 61
GRB2/SOS1/GAB family -0.017 0.17 0.3 1 -0.44 35 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.062 0.17 -10000 0 -0.38 78 78
GRB2 0.034 0.011 -10000 0 -10000 0 0
JAK2 0.032 0.03 -10000 0 -0.42 2 2
LBP -0.031 0.23 0.45 1 -0.6 40 41
PIK3R1 0.02 0.08 -10000 0 -0.42 16 16
JAK1 0.031 0.039 -10000 0 -0.42 3 3
MYC -0.067 0.37 0.59 2 -0.89 63 65
FGG -0.076 0.29 -10000 0 -0.74 49 49
macrophage differentiation -0.095 0.34 0.49 1 -0.79 68 69
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.023 0.16 -10000 0 -0.25 132 132
JUNB -0.075 0.28 -10000 0 -0.73 48 48
FOS -0.031 0.15 -10000 0 -0.42 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.06 0.17 0.27 1 -0.4 71 72
STAT1/PIAS1 -0.046 0.19 0.3 2 -0.42 66 68
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.081 -10000 0 -0.36 10 10
STAT3 (dimer) -0.1 0.36 0.49 1 -0.85 68 69
PRKCD -0.072 0.24 0.36 1 -0.56 68 69
IL6R 0.021 0.06 -10000 0 -0.43 8 8
SOCS3 -0.042 0.19 0.43 1 -0.77 17 18
gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.15 -10000 0 -0.26 135 135
Rac1/GTP -0.053 0.2 -10000 0 -0.43 69 69
HCK 0.018 0.087 -10000 0 -0.42 19 19
MAPKKK cascade 0.021 0.14 -10000 0 -0.54 19 19
bone resorption -0.13 0.37 -10000 0 -0.87 85 85
IRF1 -0.09 0.32 -10000 0 -0.81 57 57
mol:GDP -0.056 0.18 -10000 0 -0.42 65 65
SOS1 0.036 0.022 -10000 0 -0.42 1 1
VAV1 -0.057 0.18 -10000 0 -0.42 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.043 0.18 -10000 0 -0.56 32 32
PTPN11 0.016 0.091 -10000 0 -1.1 3 3
IL6/IL6RA 0.004 0.1 -10000 0 -0.3 46 46
gp130 (dimer)/TYK2/TYK2/LMO4 -0.022 0.14 -10000 0 -0.25 133 133
gp130 (dimer)/JAK2/JAK2/LMO4 -0.024 0.15 -10000 0 -0.26 134 134
IL6 -0.021 0.14 -10000 0 -0.42 52 52
PIAS3 0.035 0.006 -10000 0 -10000 0 0
PTPRE 0.02 0.07 -10000 0 -0.41 12 12
PIAS1 0.035 0.007 -10000 0 -10000 0 0
RAC1 0.036 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.053 0.13 0.23 1 -0.27 101 102
LMO4 -0.019 0.14 -10000 0 -0.42 53 53
STAT3 (dimer)/PIAS3 -0.09 0.34 0.46 1 -0.8 64 65
MCL1 0.038 0.094 -10000 0 -0.78 2 2
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.03 0.036 -10000 0 -0.42 3 3
GNB1/GNG2 -0.048 0.17 -10000 0 -0.39 58 58
mol:DAG -0.056 0.15 -10000 0 -0.36 55 55
PLCG1 -0.059 0.15 -10000 0 -0.37 57 57
YES1 -0.066 0.15 -10000 0 -0.41 54 54
FZD3 0.007 0.095 -10000 0 -0.42 23 23
FZD6 -0.028 0.14 -10000 0 -0.42 60 60
G protein -0.035 0.17 0.29 10 -0.38 53 63
MAP3K7 -0.057 0.12 0.24 2 -0.32 50 52
mol:Ca2+ -0.054 0.14 -10000 0 -0.35 55 55
mol:IP3 -0.056 0.15 -10000 0 -0.36 55 55
NLK -0.036 0.25 -10000 0 -0.82 45 45
GNB1 0.032 0.045 -10000 0 -0.42 5 5
CAMK2A -0.056 0.14 0.25 2 -0.34 53 55
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.067 0.15 -10000 0 -0.29 136 136
CSNK1A1 0.036 0.006 -10000 0 -10000 0 0
GNAS -0.064 0.14 -10000 0 -0.39 52 52
GO:0007205 -0.059 0.14 0.26 2 -0.36 54 56
WNT6 0.03 0.031 -10000 0 -0.42 2 2
WNT4 -0.019 0.14 -10000 0 -0.42 58 58
NFAT1/CK1 alpha -0.047 0.16 0.29 2 -0.39 50 52
GNG2 0.034 0.021 -10000 0 -0.42 1 1
WNT5A -0.025 0.15 -10000 0 -0.42 63 63
WNT11 0.027 0.032 -10000 0 -0.42 2 2
CDC42 -0.062 0.15 0.19 2 -0.39 53 55
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.07 0.16 -10000 0 -0.34 129 129
KLHL20 -0.025 0.09 0.21 2 -0.23 24 26
CYFIP2 -0.006 0.13 -10000 0 -0.42 45 45
Rac1/GDP -0.035 0.12 0.27 4 -0.26 65 69
ENAH -0.065 0.16 -10000 0 -0.34 118 118
AP1M1 0.035 0.021 -10000 0 -0.42 1 1
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
CDC42/GTP -0.013 0.083 -10000 0 -0.2 57 57
ABI1/Sra1/Nap1 -0.046 0.054 -10000 0 -0.16 43 43
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.03 0.1 -10000 0 -0.23 58 58
RAPGEF1 -0.073 0.15 0.24 3 -0.36 83 86
CTNND1 0.034 0.022 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.074 0.18 -10000 0 -0.35 146 146
CRK -0.069 0.16 -10000 0 -0.35 116 116
E-cadherin/gamma catenin/alpha catenin 0.018 0.098 -10000 0 -0.26 49 49
alphaE/beta7 Integrin 0.044 0.039 -10000 0 -0.3 5 5
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
NCKAP1 0.035 0.021 -10000 0 -0.42 1 1
Rap1/GTP/I-afadin 0.047 0.064 -10000 0 -0.23 22 22
DLG1 -0.082 0.18 -10000 0 -0.34 150 150
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.031 0.056 -10000 0 -0.15 62 62
MLLT4 0.02 0.078 -10000 0 -0.42 15 15
ARF6/GTP/NME1/Tiam1 0.056 0.045 -10000 0 -0.24 9 9
PI3K -0.036 0.074 -10000 0 -0.19 58 58
ARF6 0.033 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.004 0.1 -10000 0 -0.3 48 48
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin(dimer)/Ca2+ 0.03 0.097 -10000 0 -0.22 57 57
AKT1 -0.024 0.053 0.17 3 -0.17 5 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.036 0.12 0.27 4 -0.27 66 70
actin cytoskeleton organization -0.017 0.068 0.16 3 -0.16 24 27
CDC42/GDP -0.033 0.12 0.27 4 -0.26 64 68
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.077 -10000 0 -0.22 56 56
ITGB7 0.036 0.005 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.033 0.1 -10000 0 -0.23 57 57
E-cadherin/Ca2+/beta catenin/alpha catenin 0.018 0.087 -10000 0 -0.22 56 56
mol:GDP -0.054 0.12 0.27 4 -0.3 67 71
CDC42/GTP/IQGAP1 0.045 0.014 -10000 0 -10000 0 0
JUP 0.028 0.042 -10000 0 -0.42 4 4
p120 catenin/RhoA/GDP -0.031 0.13 0.28 3 -0.27 67 70
RAC1/GTP/IQGAP1 0.046 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.033 -10000 0 -0.3 4 4
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CDC42 0.035 0.008 -10000 0 -10000 0 0
CTNNA1 0.035 0.021 -10000 0 -0.42 1 1
positive regulation of S phase of mitotic cell cycle -0.03 0.077 0.15 1 -0.18 82 83
NME1 0.033 0.01 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.08 0.18 -10000 0 -0.34 142 142
regulation of cell-cell adhesion -0.018 0.069 -10000 0 -0.17 60 60
WASF2 -0.016 0.042 0.12 2 -0.1 20 22
Rap1/GTP -0.015 0.091 0.25 1 -0.21 58 59
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.036 0.1 -10000 0 -0.23 53 53
CCND1 -0.038 0.094 0.17 1 -0.23 82 83
VAV2 -0.068 0.18 -10000 0 -0.41 75 75
RAP1/GDP -0.02 0.1 0.26 1 -0.23 60 61
adherens junction assembly -0.078 0.17 -10000 0 -0.34 144 144
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.035 0.008 -10000 0 -10000 0 0
PIP5K1C 0.033 0.036 -10000 0 -0.42 3 3
regulation of heterotypic cell-cell adhesion 0.028 0.11 -10000 0 -0.22 62 62
E-cadherin/beta catenin -0.024 0.1 -10000 0 -0.29 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.081 0.18 -10000 0 -0.34 144 144
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP -0.076 0.13 -10000 0 -0.35 40 40
E-cadherin/beta catenin/alpha catenin 0.02 0.1 -10000 0 -0.25 56 56
ITGAE 0.028 0.046 -10000 0 -0.42 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.076 0.19 -10000 0 -0.36 146 146
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.036 -10000 0 -0.26 11 11
SNTA1 0.032 0.041 -10000 0 -0.42 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.022 0.05 -10000 0 -0.26 22 22
MAPK12 0.004 0.085 0.21 41 -0.23 34 75
CCND1 -0.056 0.16 -10000 0 -0.42 81 81
p38 gamma/SNTA1 0.026 0.09 0.21 47 -0.22 39 86
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
PKN1 0.033 0.035 -10000 0 -0.42 3 3
G2/M transition checkpoint 0.004 0.084 0.21 41 -0.23 34 75
MAP2K6 0.013 0.096 0.24 46 -0.24 34 80
MAPT -0.054 0.13 0.27 6 -0.28 106 112
MAPK13 0.006 0.052 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.064 -10000 0 -0.29 23 23
LPA receptor mediated 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
GNB1/GNG2 0.031 0.072 -10000 0 -0.21 34 34
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.095 0.27 6 -0.3 9 15
AP1 -0.034 0.12 -10000 0 -0.25 101 101
mol:PIP3 -0.031 0.091 -10000 0 -0.22 88 88
AKT1 -0.005 0.1 0.25 3 -0.31 26 29
PTK2B -0.042 0.1 0.14 1 -0.21 115 116
RHOA -0.015 0.1 -10000 0 -0.32 35 35
PIK3CB 0.031 0.045 -10000 0 -0.42 5 5
mol:Ca2+ -0.01 0.091 0.19 41 -0.2 53 94
MAGI3 0.013 0.099 -10000 0 -0.42 25 25
RELA 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.003 0.054 -10000 0 -0.18 39 39
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
positive regulation of microtubule depolymerization -0.075 0.12 0.18 3 -0.24 129 132
NF kappa B1 p50/RelA -0.02 0.082 -10000 0 -0.24 31 31
endothelial cell migration -0.01 0.12 -10000 0 -0.51 27 27
ADCY4 -0.016 0.089 -10000 0 -0.28 42 42
ADCY5 -0.016 0.086 -10000 0 -0.28 37 37
ADCY6 -0.014 0.083 -10000 0 -0.26 43 43
ADCY7 -0.015 0.089 -10000 0 -0.28 39 39
ADCY1 -0.014 0.084 -10000 0 -0.26 41 41
ADCY2 -0.026 0.1 -10000 0 -0.26 64 64
ADCY3 -0.015 0.085 -10000 0 -0.25 46 46
ADCY8 -0.013 0.075 -10000 0 -0.26 32 32
ADCY9 -0.016 0.081 -10000 0 -0.23 49 49
GSK3B -0.042 0.098 0.16 1 -0.21 108 109
arachidonic acid secretion -0.018 0.09 -10000 0 -0.27 48 48
GNG2 0.034 0.021 -10000 0 -0.42 1 1
TRIP6 0.009 0.071 -10000 0 -0.36 17 17
GNAO1 0.006 0.055 -10000 0 -0.22 27 27
HRAS 0.032 0.036 -10000 0 -0.42 3 3
NFKBIA -0.008 0.091 0.21 14 -0.26 19 33
GAB1 0.027 0.061 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.022 0.2 -10000 0 -0.92 22 22
JUN -0.001 0.12 -10000 0 -0.42 39 39
LPA/LPA2/NHERF2 -0.004 0.077 -10000 0 -0.19 65 65
TIAM1 0 0.23 -10000 0 -1.1 22 22
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 -0.009 0.09 0.18 45 -0.21 50 95
PLCB3 0.01 0.09 0.19 46 -0.23 42 88
FOS -0.031 0.15 -10000 0 -0.42 66 66
positive regulation of mitosis -0.018 0.09 -10000 0 -0.27 48 48
LPA/LPA1-2-3 -0.007 0.05 -10000 0 -0.17 42 42
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.03 0.014 -10000 0 -10000 0 0
stress fiber formation -0.006 0.082 -10000 0 -0.27 25 25
GNAZ -0.001 0.072 -10000 0 -0.21 49 49
EGFR/PI3K-beta/Gab1 -0.023 0.098 -10000 0 -0.22 88 88
positive regulation of dendritic cell cytokine production -0.007 0.05 -10000 0 -0.17 42 42
LPA/LPA2/MAGI-3 0.005 0.065 -10000 0 -0.17 50 50
ARHGEF1 0.027 0.077 0.19 54 -0.21 22 76
GNAI2 0.001 0.069 -10000 0 -0.21 45 45
GNAI3 0.006 0.058 -10000 0 -0.19 38 38
GNAI1 -0.005 0.082 -10000 0 -0.23 54 54
LPA/LPA3 -0.005 0.025 -10000 0 -0.086 42 42
LPA/LPA2 -0.004 0.025 -10000 0 -0.085 42 42
LPA/LPA1 -0.01 0.067 -10000 0 -0.22 42 42
HB-EGF/EGFR -0.026 0.13 -10000 0 -0.28 91 91
HBEGF -0.02 0.099 -10000 0 -0.3 56 56
mol:DAG -0.009 0.09 0.18 45 -0.21 50 95
cAMP biosynthetic process -0.02 0.09 0.2 3 -0.27 41 44
NFKB1 0.036 0.005 -10000 0 -10000 0 0
SRC 0.033 0.029 -10000 0 -0.42 2 2
GNB1 0.032 0.045 -10000 0 -0.42 5 5
LYN 0.005 0.094 0.24 20 -0.25 12 32
GNAQ -0.004 0.02 -10000 0 -0.07 42 42
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.008 0.039 -10000 0 -0.13 42 42
IL8 -0.072 0.18 -10000 0 -0.41 92 92
PTK2 0.011 0.042 -10000 0 -0.16 26 26
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
CASP3 0.003 0.054 -10000 0 -0.18 39 39
EGFR -0.015 0.13 -10000 0 -0.42 49 49
PLCG1 -0.002 0.042 -10000 0 -0.12 47 47
PLD2 0.01 0.053 -10000 0 -0.17 38 38
G12/G13 0.03 0.063 -10000 0 -0.18 35 35
PI3K-beta -0.019 0.1 -10000 0 -0.34 28 28
cell migration 0.008 0.068 -10000 0 -0.26 22 22
SLC9A3R2 -0.004 0.12 -10000 0 -0.42 40 40
PXN -0.007 0.083 -10000 0 -0.27 25 25
HRAS/GTP -0.019 0.092 -10000 0 -0.27 48 48
RAC1 0.035 0.006 -10000 0 -10000 0 0
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
PRKCE 0.03 0.05 -10000 0 -0.42 6 6
PRKCD -0.011 0.088 0.18 41 -0.21 40 81
Gi(beta/gamma) -0.009 0.088 -10000 0 -0.26 41 41
mol:LPA -0.008 0.039 -10000 0 -0.13 42 42
TRIP6/p130 Cas/FAK1/Paxillin 0.009 0.081 -10000 0 -0.26 23 23
MAPKKK cascade -0.018 0.09 -10000 0 -0.27 48 48
contractile ring contraction involved in cytokinesis -0.016 0.1 -10000 0 -0.32 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.014 0.074 -10000 0 -0.2 60 60
GNA15 0.007 0.035 -10000 0 -0.11 28 28
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
MAPT -0.077 0.12 0.18 3 -0.24 130 133
GNA11 0.008 0.03 -10000 0 -0.25 3 3
Rac1/GTP 0.021 0.22 -10000 0 -0.98 22 22
MMP2 -0.01 0.12 -10000 0 -0.52 27 27
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.027 0.18 -10000 0 -0.45 64 64
Syndecan-4/Syndesmos -0.033 0.2 -10000 0 -0.49 61 61
positive regulation of JNK cascade -0.045 0.22 -10000 0 -0.49 72 72
Syndecan-4/ADAM12 -0.051 0.23 -10000 0 -0.53 72 72
CCL5 -0.014 0.14 -10000 0 -0.42 52 52
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DNM2 0.036 0.005 -10000 0 -10000 0 0
ITGA5 0.034 0.029 -10000 0 -0.42 2 2
SDCBP 0.023 0.058 -10000 0 -0.42 8 8
PLG 0.022 0.04 -10000 0 -0.31 3 3
ADAM12 -0.014 0.14 -10000 0 -0.42 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.046 -10000 0 -0.42 5 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.033 0.21 -10000 0 -0.5 66 66
Syndecan-4/CXCL12/CXCR4 -0.048 0.23 -10000 0 -0.53 70 70
Syndecan-4/Laminin alpha3 -0.055 0.22 -10000 0 -0.51 68 68
MDK 0.018 0.085 -10000 0 -0.42 18 18
Syndecan-4/FZD7 -0.049 0.22 -10000 0 -0.51 70 70
Syndecan-4/Midkine -0.039 0.21 -10000 0 -0.5 67 67
FZD7 -0.006 0.13 -10000 0 -0.42 43 43
Syndecan-4/FGFR1/FGF -0.033 0.2 -10000 0 -0.48 56 56
THBS1 0.001 0.12 -10000 0 -0.42 37 37
integrin-mediated signaling pathway -0.04 0.21 -10000 0 -0.48 75 75
positive regulation of MAPKKK cascade -0.045 0.22 -10000 0 -0.49 72 72
Syndecan-4/TACI -0.034 0.21 -10000 0 -0.5 66 66
CXCR4 0.007 0.11 -10000 0 -0.42 30 30
cell adhesion 0.012 0.1 0.2 46 -0.27 41 87
Syndecan-4/Dynamin -0.031 0.21 -10000 0 -0.5 66 66
Syndecan-4/TSP1 -0.045 0.22 -10000 0 -0.5 69 69
Syndecan-4/GIPC -0.031 0.21 -10000 0 -0.49 66 66
Syndecan-4/RANTES -0.053 0.22 -10000 0 -0.52 67 67
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
LAMA1 0.034 0.009 -10000 0 -10000 0 0
LAMA3 -0.019 0.14 -10000 0 -0.42 58 58
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA 0.087 0.26 0.8 57 -10000 0 57
Syndecan-4/alpha-Actinin -0.034 0.22 -10000 0 -0.51 66 66
TFPI 0.034 0.008 -10000 0 -10000 0 0
F2 0.031 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.048 0.037 -10000 0 -0.3 5 5
positive regulation of cell adhesion -0.061 0.2 -10000 0 -0.5 68 68
ACTN1 0.027 0.061 -10000 0 -0.42 9 9
TNC 0.004 0.11 -10000 0 -0.42 31 31
Syndecan-4/CXCL12 -0.049 0.22 -10000 0 -0.51 74 74
FGF6 0.027 0.057 -10000 0 -0.42 8 8
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CXCL12 -0.008 0.13 -10000 0 -0.42 47 47
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.02 0.064 -10000 0 -0.42 10 10
Syndecan-4/PI-4-5-P2 -0.058 0.19 -10000 0 -0.49 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.019 0.13 -10000 0 -0.4 51 51
cell migration -0.015 0.015 -10000 0 -10000 0 0
PRKCD 0.024 0.039 -10000 0 -0.39 2 2
vasculogenesis -0.043 0.21 -10000 0 -0.48 69 69
SDC4 -0.057 0.21 -10000 0 -0.52 66 66
Syndecan-4/Tenascin C -0.043 0.22 -10000 0 -0.51 70 70
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.034 0.2 -10000 0 -0.5 60 60
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
Rac1/GTP 0.012 0.1 0.2 46 -0.28 41 87
cytoskeleton organization -0.031 0.19 -10000 0 -0.48 61 61
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
Syndecan-4/TFPI -0.034 0.21 -10000 0 -0.5 66 66
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.012 0.089 0.22 2 -0.27 23 25
adherens junction organization -0.045 0.13 -10000 0 -0.28 86 86
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.11 0.27 4 -0.27 28 32
FMN1 -0.036 0.12 -10000 0 -0.26 88 88
mol:IP3 -0.016 0.076 -10000 0 -0.23 23 23
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.035 0.13 -10000 0 -0.27 88 88
CTNNB1 0.026 0.067 -10000 0 -0.42 11 11
AKT1 -0.017 0.093 0.19 2 -0.28 21 23
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.062 0.19 -10000 0 -0.43 73 73
CTNND1 0.035 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 -0.032 0.12 0.22 1 -0.25 80 81
VASP -0.039 0.12 -10000 0 -0.27 83 83
ZYX -0.038 0.12 -10000 0 -0.26 86 86
JUB -0.047 0.13 -10000 0 -0.28 88 88
EGFR(dimer) -0.041 0.14 0.23 1 -0.27 105 106
E-cadherin/beta catenin-gamma catenin 0.015 0.099 -10000 0 -0.24 58 58
mol:PI-3-4-5-P3 -0.001 0.11 0.23 2 -0.26 27 29
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K -0.001 0.11 0.23 2 -0.26 27 29
FYN -0.017 0.092 0.22 2 -0.29 25 27
mol:Ca2+ -0.015 0.074 -10000 0 -0.23 23 23
JUP 0.03 0.042 -10000 0 -0.42 4 4
PIK3R1 0.02 0.08 -10000 0 -0.42 16 16
mol:DAG -0.016 0.076 -10000 0 -0.23 23 23
CDH1 -0.011 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.016 0.11 0.26 3 -0.27 33 36
establishment of polarity of embryonic epithelium -0.037 0.12 0.22 1 -0.26 83 84
SRC 0.033 0.029 -10000 0 -0.42 2 2
RAC1 0.035 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
EGFR -0.015 0.13 -10000 0 -0.42 49 49
CASR -0.013 0.078 0.22 2 -0.24 17 19
RhoA/GTP -0.001 0.09 0.21 2 -0.24 19 21
AKT2 -0.016 0.093 0.19 2 -0.28 19 21
actin cable formation -0.037 0.12 0.2 6 -0.26 83 89
apoptosis 0.009 0.099 0.27 26 -0.24 5 31
CTNNA1 0.036 0.022 -10000 0 -0.43 1 1
mol:GDP -0.03 0.1 0.22 2 -0.27 34 36
PIP5K1A -0.034 0.12 -10000 0 -0.26 80 80
PLCG1 -0.016 0.077 -10000 0 -0.24 23 23
Rac1/GTP -0.03 0.14 -10000 0 -0.3 55 55
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.017 0.08 -10000 0 -0.42 16 16
EPHB2 0.033 0.03 -10000 0 -0.42 2 2
EFNB1 0.015 0.029 -10000 0 -0.3 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.073 0.065 -10000 0 -0.23 17 17
Ephrin B2/EPHB1-2 0.044 0.067 -10000 0 -0.24 23 23
neuron projection morphogenesis 0.048 0.056 -10000 0 -0.22 17 17
Ephrin B1/EPHB1-2/Tiam1 0.064 0.064 -10000 0 -0.24 17 17
DNM1 0.034 0.035 -10000 0 -0.42 3 3
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.082 0.21 -10000 0 -0.55 79 79
YES1 -0.11 0.3 -10000 0 -0.8 79 79
Ephrin B1/EPHB1-2/NCK2 0.069 0.051 -10000 0 -0.22 12 12
PI3K -0.049 0.23 -10000 0 -0.56 79 79
mol:GDP 0.062 0.063 -10000 0 -0.24 17 17
ITGA2B 0.034 0.01 -10000 0 -10000 0 0
endothelial cell proliferation 0.02 0.081 -10000 0 -0.26 35 35
FYN -0.11 0.3 -10000 0 -0.8 79 79
MAP3K7 -0.082 0.22 0.23 2 -0.59 76 78
FGR -0.1 0.3 -10000 0 -0.78 79 79
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RGS3 0.036 0.005 -10000 0 -10000 0 0
cell adhesion -0.057 0.21 -10000 0 -0.53 77 77
LYN -0.1 0.3 -10000 0 -0.79 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.1 0.28 -10000 0 -0.74 79 79
Ephrin B1/EPHB1-2 -0.089 0.24 -10000 0 -0.64 78 78
SRC -0.1 0.3 -10000 0 -0.79 79 79
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
EPHB1 0.027 0.05 -10000 0 -0.42 6 6
EPHB4 0.016 0.091 -10000 0 -0.42 21 21
RAC1 0.035 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.021 0.081 -10000 0 -0.26 35 35
alphaIIb/beta3 Integrin 0.046 0.035 -10000 0 -0.3 4 4
BLK -0.12 0.3 -10000 0 -0.8 79 79
HCK -0.11 0.3 -10000 0 -0.79 79 79
regulation of stress fiber formation -0.067 0.05 0.22 12 -10000 0 12
MAPK8 -0.08 0.2 -10000 0 -0.53 79 79
Ephrin B1/EPHB1-2/RGS3 0.069 0.051 -10000 0 -0.22 12 12
endothelial cell migration -0.079 0.19 -10000 0 -0.51 75 75
NCK2 0.036 0.005 -10000 0 -10000 0 0
PTPN13 -0.046 0.2 -10000 0 -0.54 72 72
regulation of focal adhesion formation -0.067 0.05 0.22 12 -10000 0 12
chemotaxis -0.066 0.05 0.22 12 -10000 0 12
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.062 0.061 -10000 0 -0.23 17 17
angiogenesis -0.09 0.23 -10000 0 -0.63 79 79
LCK -0.12 0.3 -10000 0 -0.8 79 79
Arf6 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
CENTA1/KIF3B 0.015 0.032 -10000 0 -0.25 6 6
ARNO/beta Arrestin1-2 0.014 0.069 -10000 0 -0.2 41 41
EGFR -0.015 0.13 -10000 0 -0.42 49 49
EPHA2 0.032 0.036 -10000 0 -0.42 3 3
USP6 0.032 0.012 -10000 0 -10000 0 0
IQSEC1 0.034 0.021 -10000 0 -0.42 1 1
EGFR/EGFR/EGF/EGF -0.061 0.16 -10000 0 -0.3 152 152
ARRB2 0.011 0.043 -10000 0 -0.3 9 9
mol:GTP 0.006 0.02 0.11 5 -0.11 2 7
ARRB1 0.027 0.05 -10000 0 -0.42 6 6
FBXO8 0.035 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.05 -10000 0 -0.42 6 6
EGF -0.069 0.19 -10000 0 -0.42 110 110
somatostatin receptor activity 0 0 0 2 -0.001 67 69
ARAP2 0 0 0 2 0 72 74
mol:GDP -0.029 0.1 -10000 0 -0.26 56 56
mol:PI-3-4-5-P3 0 0 0 3 -0.001 69 72
ITGA2B 0.034 0.01 -10000 0 -10000 0 0
ARF6 0.033 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.072 -10000 0 -0.23 20 20
ADAP1 0 0 0 3 0 42 45
KIF13B 0.022 0.051 -10000 0 -0.42 6 6
HGF/MET 0.042 0.055 -10000 0 -0.3 12 12
PXN 0.036 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.034 0.1 0.17 2 -0.25 63 65
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.035 0.15 -10000 0 -0.26 151 151
ADRB2 0.003 0.11 -10000 0 -0.42 33 33
receptor agonist activity 0 0 0 3 0 51 54
actin filament binding 0 0 0 2 0 77 79
SRC 0.033 0.029 -10000 0 -0.42 2 2
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
GNAQ 0 0 0.001 3 -0.001 52 55
EFA6/PI-4-5-P2 0 0 0.001 4 -0.001 44 48
ARF6/GDP 0.004 0.075 0.2 2 -0.27 14 16
ARF6/GDP/GULP/ACAP1 -0.017 0.13 -10000 0 -0.27 72 72
alphaIIb/beta3 Integrin/paxillin/GIT1 0.079 0.043 -10000 0 -0.23 5 5
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 2 0 71 73
LHCGR/beta Arrestin2 0.018 0.06 -10000 0 -0.38 9 9
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
HGF 0.028 0.057 -10000 0 -0.42 8 8
CYTH3 0 0 0.001 3 -0.001 51 54
CYTH2 -0.001 0.002 -10000 0 -0.004 80 80
NCK1 0.034 0.021 -10000 0 -0.42 1 1
fibronectin binding 0 0 0 3 0 48 51
endosomal lumen acidification 0 0 0 3 0 61 64
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0 0.12 -10000 0 -0.42 39 39
GNAQ/ARNO -0.001 0.003 0.007 4 -0.006 43 47
mol:Phosphatidic acid 0 0 0 2 0 71 73
PIP3-E 0.029 0.037 -10000 0 -0.42 3 3
MET 0.03 0.041 -10000 0 -0.42 4 4
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GIT1 0.034 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 0 0 0.001 3 -0.001 52 55
GNA11 0.033 0.036 -10000 0 -0.42 3 3
LHCGR 0.027 0.061 -10000 0 -0.42 9 9
AGTR1 -0.047 0.16 -10000 0 -0.42 80 80
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0.06 -10000 0 -0.38 9 9
IPCEF1/ARNO -0.024 0.12 -10000 0 -0.2 150 150
alphaIIb/beta3 Integrin 0.046 0.035 -10000 0 -0.3 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.015 0.12 -10000 0 -0.51 8 8
UGCG -0.09 0.27 -10000 0 -0.73 73 73
AKT1/mTOR/p70S6K/Hsp90/TERT -0.062 0.19 0.31 1 -0.37 101 102
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.088 0.26 -10000 0 -0.71 74 74
mol:DAG -0.006 0.029 0.17 12 -10000 0 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.079 0.23 0.34 1 -0.44 115 116
FRAP1 -0.1 0.26 0.36 1 -0.5 115 116
FOXO3 -0.049 0.21 0.32 2 -0.47 61 63
AKT1 -0.054 0.22 0.33 2 -0.51 61 63
GAB2 0.029 0.015 -10000 0 -10000 0 0
SMPD1 -0.005 0.13 -10000 0 -0.68 16 16
SGMS1 -0.004 0.035 0.058 2 -0.077 51 53
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 -0.008 0.048 -10000 0 -0.25 17 17
CALM1 0.035 0.007 -10000 0 -10000 0 0
cell proliferation -0.041 0.19 0.4 1 -0.37 95 96
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.034 0.066 -10000 0 -0.3 17 17
RPS6KB1 -0.043 0.16 -10000 0 -0.87 12 12
mol:sphingomyelin -0.006 0.029 0.17 12 -10000 0 12
natural killer cell activation -0.002 0.004 -10000 0 -0.014 21 21
JAK3 0.035 0.008 -10000 0 -10000 0 0
PIK3R1 0.018 0.08 -10000 0 -0.42 16 16
JAK1 0.032 0.036 -10000 0 -0.42 3 3
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MYC -0.027 0.29 0.42 4 -0.94 36 40
MYB -0.23 0.5 -10000 0 -1.2 104 104
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.021 0.15 -10000 0 -0.37 49 49
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.025 0.16 -10000 0 -0.78 12 12
mol:PI-3-4-5-P3 -0.02 0.15 -10000 0 -0.36 48 48
Rac1/GDP 0.008 0.051 -10000 0 -0.23 17 17
T cell proliferation -0.018 0.14 0.29 3 -0.34 47 50
SHC1 0.026 0.026 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.01 0.028 -10000 0 -0.065 103 103
PRKCZ -0.021 0.15 -10000 0 -0.36 47 47
NF kappa B1 p50/RelA -0.069 0.24 0.36 1 -0.45 104 105
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.013 0.13 -10000 0 -0.42 32 32
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
IL2RA 0.002 0.11 -10000 0 -0.42 31 31
IL2RB 0.011 0.097 -10000 0 -0.42 24 24
TERT 0.032 0.03 -10000 0 -0.42 2 2
E2F1 -0.072 0.2 -10000 0 -0.43 113 113
SOS1 0.032 0.023 -10000 0 -0.43 1 1
RPS6 0.034 0.022 -10000 0 -0.42 1 1
mol:cAMP 0.004 0.013 0.031 100 -10000 0 100
PTPN11 0.032 0.012 -10000 0 -10000 0 0
IL2RG 0.029 0.042 -10000 0 -0.42 4 4
actin cytoskeleton organization -0.018 0.14 0.29 3 -0.34 47 50
GRB2 0.031 0.013 -10000 0 -10000 0 0
IL2 0.031 0.037 -10000 0 -0.42 3 3
PIK3CA 0.032 0.024 -10000 0 -0.42 1 1
Rac1/GTP 0.033 0.064 -10000 0 -0.22 17 17
LCK -0.019 0.14 -10000 0 -0.42 54 54
BCL2 -0.18 0.38 -10000 0 -0.82 118 118
E-cadherin signaling 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
E-cadherin/beta catenin-gamma catenin 0.014 0.1 -9999 0 -0.26 58 58
E-cadherin/beta catenin 0.004 0.11 -9999 0 -0.3 55 55
CTNNB1 0.025 0.067 -9999 0 -0.42 11 11
JUP 0.028 0.042 -9999 0 -0.42 4 4
CDH1 -0.011 0.13 -9999 0 -0.42 45 45
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.06 0.29 -10000 0 -0.92 46 46
epithelial cell differentiation -0.027 0.25 -10000 0 -0.72 48 48
ITCH 0.035 0.039 -10000 0 -0.11 6 6
WWP1 -0.087 0.39 -10000 0 -1.4 42 42
FYN 0.027 0.054 -10000 0 -0.42 7 7
EGFR -0.015 0.13 -10000 0 -0.42 49 49
PRL 0.034 0.022 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.019 0.21 0.34 8 -0.64 43 51
PTPRZ1 0.023 0.061 -10000 0 -0.42 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.028 0.22 -10000 0 -0.71 43 43
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.064 0.25 -10000 0 -0.87 43 43
ADAM17 0.036 0.037 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.079 0.3 -10000 0 -1 45 45
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.062 0.29 -10000 0 -0.9 47 47
NCOR1 0.032 0.012 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.054 0.25 -10000 0 -0.82 43 43
GRIN2B -0.062 0.22 -10000 0 -0.75 43 43
ErbB4/ErbB2/betacellulin -0.069 0.26 -10000 0 -0.72 56 56
STAT1 0.02 0.075 -10000 0 -0.42 14 14
HBEGF 0.029 0.05 -10000 0 -0.42 6 6
PRLR -0.001 0.12 -10000 0 -0.42 40 40
E4ICDs/ETO2 -0.1 0.32 -10000 0 -0.85 61 61
axon guidance -0.068 0.28 -10000 0 -0.91 45 45
NEDD4 0.025 0.076 -10000 0 -0.42 11 11
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.094 -10000 0 -0.3 39 39
CBFA2T3 -0.047 0.16 -10000 0 -0.42 81 81
ErbB4/ErbB2/HBEGF -0.05 0.26 -10000 0 -0.78 49 49
MAPK3 -0.016 0.22 0.35 8 -0.66 43 51
STAT1 (dimer) -0.064 0.29 -10000 0 -0.9 47 47
MAPK1 -0.016 0.22 0.35 8 -0.66 43 51
JAK2 0.032 0.03 -10000 0 -0.42 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.063 0.25 -10000 0 -0.77 50 50
NRG1 0.013 0.021 -10000 0 -10000 0 0
NRG3 0.028 0.054 -10000 0 -0.42 7 7
NRG2 0.025 0.061 -10000 0 -0.42 9 9
NRG4 0.033 0.022 -10000 0 -0.42 1 1
heart development -0.068 0.28 -10000 0 -0.91 45 45
neural crest cell migration -0.062 0.25 -10000 0 -0.75 50 50
ERBB2 0.006 0.058 -10000 0 -0.3 15 15
WWOX/E4ICDs -0.071 0.28 -10000 0 -0.92 46 46
SHC1 0.028 0.025 -10000 0 -0.42 1 1
ErbB4/EGFR/neuregulin 4 -0.065 0.28 -10000 0 -0.84 48 48
apoptosis 0.059 0.28 0.84 49 -10000 0 49
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.062 0.29 -10000 0 -0.91 47 47
ErbB4/ErbB2/epiregulin -0.053 0.26 -10000 0 -0.77 50 50
ErbB4/ErbB4/betacellulin/betacellulin -0.079 0.29 -10000 0 -0.88 50 50
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.031 0.28 -10000 0 -0.73 56 56
MDM2 -0.068 0.29 0.28 14 -0.92 45 59
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.044 0.23 -10000 0 -0.77 43 43
STAT5A -0.041 0.28 0.33 8 -0.87 45 53
ErbB4/EGFR/neuregulin 1 beta -0.07 0.25 -10000 0 -0.79 46 46
DLG4 0.032 0.012 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.029 -10000 0 -0.3 1 1
E4ICDs/TAB2/NCoR1 -0.048 0.28 -10000 0 -0.86 46 46
STAT5A (dimer) -0.019 0.28 -10000 0 -0.81 48 48
MAP3K7IP2 0.032 0.03 -10000 0 -0.42 2 2
STAT5B (dimer) -0.045 0.28 -10000 0 -0.87 46 46
LRIG1 0.006 0.11 -10000 0 -0.42 31 31
EREG 0.025 0.051 -10000 0 -0.42 6 6
BTC -0.009 0.13 -10000 0 -0.42 47 47
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.07 0.28 -10000 0 -0.92 45 45
ERBB4 -0.08 0.3 -10000 0 -1 45 45
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
YAP1 -0.024 0.15 -10000 0 -0.41 48 48
GRB2 0.033 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.048 0.26 -10000 0 -0.76 50 50
glial cell differentiation 0.047 0.27 0.85 46 -10000 0 46
WWOX 0.027 0.016 -10000 0 -10000 0 0
cell proliferation -0.077 0.26 0.34 1 -0.81 47 48
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 -0.002 0.05 -10000 0 -0.3 14 14
TP53 -0.025 0.091 0.26 1 -0.26 58 59
Senescence -0.028 0.093 0.25 1 -0.25 66 67
Apoptosis -0.028 0.093 0.25 1 -0.25 66 67
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.004 0.061 0.26 25 -10000 0 25
MDM4 0.026 0.032 -10000 0 -0.42 2 2
Canonical Wnt signaling pathway

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
HDAC1 0.053 0.052 0.23 21 -0.42 1 22
AES 0.052 0.042 0.21 21 -10000 0 21
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.055 -10000 0 -0.3 12 12
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
DKK2 0.006 0.11 -10000 0 -0.42 31 31
TLE1 0.022 0.12 0.22 21 -0.42 33 54
MACF1 0.035 0.021 -10000 0 -0.42 1 1
CTNNB1 -0.003 0.1 0.28 3 -0.38 10 13
WIF1 0.03 0.014 -10000 0 -10000 0 0
beta catenin/RanBP3 0.073 0.21 0.41 115 -0.36 7 122
KREMEN2 -0.09 0.19 -10000 0 -0.42 129 129
DKK1 -0.027 0.14 -10000 0 -0.42 60 60
beta catenin/beta TrCP1 0.011 0.11 0.29 3 -0.37 10 13
FZD1 0.028 0.057 -10000 0 -0.42 8 8
AXIN2 -0.047 0.4 0.6 52 -1.3 32 84
AXIN1 0.037 0.002 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.044 0.066 -10000 0 -0.59 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.008 0.17 0.33 5 -0.52 28 33
Axin1/APC/GSK3 0.033 0.051 0.32 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.081 0.33 3 -0.36 5 8
HNF1A 0.017 0.045 0.18 22 -10000 0 22
CTBP1 0.05 0.046 0.23 18 -10000 0 18
MYC 0.028 0.47 0.59 112 -1.3 39 151
RANBP3 0.036 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.044 0.15 -10000 0 -0.26 154 154
NKD1 0.027 0.037 -10000 0 -0.42 3 3
TCF4 0.031 0.1 0.23 17 -0.4 22 39
TCF3 0.048 0.052 0.22 18 -0.42 2 20
WNT1/LRP6/FZD1/Axin1 0.076 0.058 -10000 0 -0.23 13 13
Ran/GTP 0.028 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.09 0.26 0.51 109 -0.44 15 124
LEF1 0.038 0.085 0.23 19 -0.4 13 32
DVL1 0.03 0.049 -10000 0 -0.29 2 2
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.045 0.19 -10000 0 -0.54 38 38
DKK1/LRP6/Kremen 2 -0.06 0.16 -10000 0 -0.27 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.053 0.048 0.23 20 -10000 0 20
NLK 0.029 0.026 -10000 0 -0.43 1 1
CCND1 -0.15 0.6 0.58 75 -1.4 87 162
WNT1 0.035 0.021 -10000 0 -0.42 1 1
GSK3A 0.036 0.005 -10000 0 -10000 0 0
GSK3B 0.036 0.005 -10000 0 -10000 0 0
FRAT1 0.029 0.054 -10000 0 -0.42 7 7
PPP2R5D 0.028 0.065 0.24 1 -0.3 13 14
APC -0.012 0.059 0.24 7 -0.22 17 24
WNT1/LRP6/FZD1 0.022 0.051 -10000 0 -0.23 8 8
CREBBP 0.048 0.044 0.22 17 -10000 0 17
PLK2 and PLK4 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
PLK2 -0.005 0.12 -9999 0 -0.42 41 41
PLK4 0.03 0.05 -9999 0 -0.42 6 6
regulation of centriole replication -0.013 0.091 -9999 0 -0.3 46 46
Syndecan-2-mediated signaling events

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.006 0.11 -10000 0 -0.3 52 52
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
Syndecan-2/TACI 0.011 0.064 -10000 0 -0.24 28 28
LAMA1 0.034 0.009 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.019 0.14 -10000 0 -0.25 86 86
HRAS 0.032 0.036 -10000 0 -0.42 3 3
Syndecan-2/CASK -0.005 0.057 -10000 0 -0.24 28 28
ITGA5 0.034 0.029 -10000 0 -0.42 2 2
BAX -0.008 0.052 -10000 0 -10000 0 0
EPB41 0.034 0.021 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion 0.008 0.065 -10000 0 -0.23 33 33
LAMA3 -0.019 0.14 -10000 0 -0.42 58 58
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.095 -10000 0 -0.42 23 23
Syndecan-2/MMP2 0 0.089 -10000 0 -0.29 40 40
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.015 0.1 -10000 0 -0.3 48 48
dendrite morphogenesis 0.012 0.065 -10000 0 -0.24 29 29
Syndecan-2/GM-CSF 0.011 0.066 -10000 0 -0.24 30 30
determination of left/right symmetry -0.005 0.069 -10000 0 -0.29 28 28
Syndecan-2/PKC delta 0.012 0.067 -10000 0 -0.24 30 30
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
MAPK3 0.033 0.09 0.2 82 -0.22 27 109
MAPK1 0.037 0.095 0.2 94 -0.22 29 123
Syndecan-2/RACK1 0.025 0.067 -10000 0 -0.22 31 31
NF1 0.032 0.03 -10000 0 -0.42 2 2
FGFR/FGF/Syndecan-2 -0.005 0.069 -10000 0 -0.29 28 28
ITGA2 -0.01 0.13 -10000 0 -0.42 48 48
MAPK8 -0.005 0.059 -10000 0 -0.24 29 29
Syndecan-2/alpha2/beta1 Integrin 0.043 0.11 -10000 0 -0.24 50 50
Syndecan-2/Kininogen 0.013 0.065 -10000 0 -0.25 28 28
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
SRC 0.037 0.093 0.19 88 -0.22 29 117
Syndecan-2/CASK/Protein 4.1 0.012 0.059 -10000 0 -0.22 29 29
extracellular matrix organization 0.013 0.065 -10000 0 -0.24 28 28
actin cytoskeleton reorganization -0.006 0.1 -10000 0 -0.3 52 52
Syndecan-2/Caveolin-2/Ras 0.016 0.092 -10000 0 -0.27 41 41
Syndecan-2/Laminin alpha3 -0.013 0.1 -10000 0 -0.26 68 68
Syndecan-2/RasGAP 0.034 0.075 -10000 0 -0.21 35 35
alpha5/beta1 Integrin 0.048 0.037 -10000 0 -0.3 5 5
PRKCD 0.033 0.03 -10000 0 -0.42 2 2
Syndecan-2 dimer 0.012 0.066 -10000 0 -0.24 29 29
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.019 0.067 -10000 0 -0.21 33 33
RHOA 0.026 0.061 -10000 0 -0.42 9 9
SDCBP 0.023 0.058 -10000 0 -0.42 8 8
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
RASA1 0.029 0.05 -10000 0 -0.42 6 6
alpha2/beta1 Integrin 0.015 0.1 -10000 0 -0.3 48 48
Syndecan-2/Synbindin 0.011 0.064 -10000 0 -0.24 28 28
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CASP3 0.034 0.093 0.2 88 -0.22 29 117
FN1 -0.01 0.14 -10000 0 -0.42 50 50
Syndecan-2/IL8 -0.007 0.094 -10000 0 -0.27 53 53
SDC2 -0.005 0.069 -10000 0 -0.29 28 28
KNG1 0.035 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.011 0.067 -10000 0 -0.25 30 30
TRAPPC4 0.032 0.012 -10000 0 -10000 0 0
CSF2 0.031 0.036 -10000 0 -0.42 3 3
Syndecan-2/TGFB1 0.013 0.065 -10000 0 -0.25 28 28
Syndecan-2/Syntenin/PI-4-5-P2 0.009 0.065 -10000 0 -0.23 33 33
Syndecan-2/Ezrin 0.009 0.064 -10000 0 -0.22 34 34
PRKACA 0.036 0.095 0.2 93 -0.22 30 123
angiogenesis -0.007 0.094 -10000 0 -0.27 53 53
MMP2 0.005 0.1 -10000 0 -0.42 27 27
IL8 -0.004 0.12 -10000 0 -0.42 37 37
calcineurin-NFAT signaling pathway 0.011 0.064 -10000 0 -0.24 28 28
Coregulation of Androgen receptor activity

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
NRIP1 -0.009 0.14 -9999 0 -0.42 51 51
SVIL 0.022 0.078 -9999 0 -0.42 15 15
ZNF318 0.033 0.006 -9999 0 -10000 0 0
JMJD2C 0.04 0.011 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.036 0.12 -9999 0 -0.25 106 106
CARM1 0.035 0.021 -9999 0 -0.42 1 1
PRDX1 0.033 0.036 -9999 0 -0.42 3 3
PELP1 0.032 0.011 -9999 0 -10000 0 0
CTNNB1 0.026 0.067 -9999 0 -0.42 11 11
AKT1 0.032 0.03 -9999 0 -0.42 2 2
PTK2B 0.028 0.016 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.025 0.046 -9999 0 -0.42 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.037 0.005 -9999 0 -10000 0 0
GSN 0.023 0.078 -9999 0 -0.42 15 15
NCOA2 0.025 0.047 -9999 0 -0.42 5 5
NCOA6 0.037 0.007 -9999 0 -10000 0 0
DNA-PK 0.054 0.036 -9999 0 -0.26 2 2
NCOA4 0.03 0.05 -9999 0 -0.42 6 6
PIAS3 0.036 0.006 -9999 0 -10000 0 0
cell proliferation -0.014 0.097 -9999 0 -0.56 13 13
XRCC5 0.035 0.004 -9999 0 -10000 0 0
UBE3A 0.036 0.029 -9999 0 -0.42 2 2
T-DHT/AR/SNURF -0.051 0.12 -9999 0 -0.25 112 112
FHL2 -0.11 0.31 -9999 0 -0.9 65 65
RANBP9 0.036 0.008 -9999 0 -10000 0 0
JMJD1A 0.01 0.072 -9999 0 -0.15 73 73
CDK6 0.025 0.058 -9999 0 -0.42 8 8
TGFB1I1 0.018 0.085 -9999 0 -0.42 18 18
T-DHT/AR/CyclinD1 -0.073 0.17 -9999 0 -0.33 134 134
XRCC6 0.033 0.009 -9999 0 -10000 0 0
T-DHT/AR -0.062 0.14 -9999 0 -0.22 210 210
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
CTDSP2 0.032 0.029 -9999 0 -0.42 2 2
BRCA1 0.023 0.07 -9999 0 -0.42 12 12
TCF4 0.014 0.093 -9999 0 -0.42 22 22
CDKN2A 0.015 0.075 -9999 0 -0.42 14 14
SRF 0.018 0.061 -9999 0 -0.15 36 36
NKX3-1 -0.047 0.1 -9999 0 -0.24 90 90
KLK3 0.021 0.054 -9999 0 -10000 0 0
TMF1 0.035 0.008 -9999 0 -10000 0 0
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.036 0.008 -9999 0 -10000 0 0
APPL1 0.004 0.02 -9999 0 -0.3 2 2
T-DHT/AR/Caspase 8 -0.038 0.13 -9999 0 -0.25 111 111
AR -0.077 0.18 -9999 0 -0.42 101 101
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.024 0.072 -9999 0 -0.42 13 13
PRKDC 0.029 0.031 -9999 0 -0.42 2 2
PA2G4 0.035 0.005 -9999 0 -10000 0 0
UBE2I 0.032 0.011 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.031 0.11 -9999 0 -0.23 106 106
RPS6KA3 0.034 0.041 -9999 0 -0.42 4 4
T-DHT/AR/ARA70 -0.041 0.13 -9999 0 -0.25 116 116
LATS2 0.024 0.061 -9999 0 -0.42 9 9
T-DHT/AR/PRX1 -0.035 0.12 -9999 0 -0.23 112 112
Cyclin D3/CDK11 p58 0.026 0.005 -9999 0 -10000 0 0
VAV3 -0.038 0.17 -9999 0 -0.42 81 81
KLK2 -0.012 0.087 -9999 0 -0.46 6 6
CASP8 0.036 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.021 0.12 -9999 0 -0.23 97 97
TMPRSS2 -0.15 0.35 -9999 0 -0.87 91 91
CCND1 -0.041 0.16 -9999 0 -0.42 79 79
PIAS1 0.037 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.013 0.03 -9999 0 -0.064 116 116
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.036 -9999 0 -0.42 3 3
T-DHT/AR/CDK6 -0.04 0.13 -9999 0 -0.25 116 116
CMTM2 0.029 0.025 -9999 0 -0.42 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.013 0.03 -9999 0 -0.065 116 116
CCND3 0.035 0.007 -9999 0 -10000 0 0
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.031 0.046 -9999 0 -0.42 5 5
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.025 0.025 -10000 0 -0.3 3 3
alphaV beta3 Integrin 0.031 0.1 -10000 0 -0.26 51 51
PTK2 0.01 0.12 0.36 5 -0.42 18 23
IGF1R -0.042 0.17 -10000 0 -0.42 84 84
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.017 0.085 -10000 0 -0.42 18 18
SRC 0.033 0.029 -10000 0 -0.42 2 2
CDKN1B -0.008 0.12 -10000 0 -0.46 29 29
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.015 0.063 -10000 0 -0.48 5 5
ROCK1 0.036 0.006 -10000 0 -10000 0 0
AKT1 0.002 0.073 0.21 3 -0.42 8 11
PTK2B 0.006 0.059 0.21 9 -0.24 20 29
alphaV/beta3 Integrin/JAM-A 0.058 0.1 -10000 0 -0.23 42 42
CBL 0.032 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.051 0.073 -10000 0 -0.27 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.037 0.19 -10000 0 -0.31 151 151
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.07 -10000 0 -0.22 35 35
alphaV/beta3 Integrin/Syndecan-1 0.029 0.11 -10000 0 -0.27 56 56
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.079 0.21 -10000 0 -0.32 191 191
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin -0.019 0.15 -10000 0 -0.27 124 124
RPS6KB1 -0.12 0.17 0.52 1 -0.44 78 79
TLN1 0.035 0.021 -10000 0 -0.42 1 1
MAPK3 -0.045 0.19 -10000 0 -0.53 55 55
GPR124 0.017 0.073 -10000 0 -0.42 13 13
MAPK1 -0.049 0.2 -10000 0 -0.55 57 57
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
alphaV/beta3 Integrin/Tumstatin 0.053 0.073 -10000 0 -0.28 21 21
cell adhesion 0.024 0.1 -10000 0 -0.27 47 47
ANGPTL3 0.031 0.041 -10000 0 -0.42 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.029 -10000 0 -0.25 4 4
IGF-1R heterotetramer -0.042 0.17 -10000 0 -0.42 84 84
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 0.033 0.036 -10000 0 -0.42 3 3
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
RAC1 0.035 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.035 0.086 -10000 0 -0.3 26 26
apoptosis 0.022 0.077 -10000 0 -0.42 15 15
CD47 0.019 0.085 -10000 0 -0.42 18 18
alphaV/beta3 Integrin/CD47 0.042 0.089 -10000 0 -0.26 37 37
VCL 0.035 0.021 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Del1 -0.009 0.14 -10000 0 -0.28 104 104
CSF1 0.034 0.021 -10000 0 -0.42 1 1
PIK3C2A 0.011 0.08 -10000 0 -0.54 8 8
PI4 Kinase/Pyk2 0.004 0.075 -10000 0 -0.21 50 50
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.051 0.067 -10000 0 -0.25 20 20
FAK1/Vinculin 0.026 0.12 0.35 5 -0.34 18 23
alphaV beta3/Integrin/ppsTEM5 0.035 0.086 -10000 0 -0.3 26 26
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VTN 0.035 0.008 -10000 0 -10000 0 0
BCAR1 0.03 0.014 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
F11R -0.005 0.072 -10000 0 -0.3 28 28
alphaV/beta3 Integrin/Lactadherin 0.044 0.092 -10000 0 -0.31 27 27
alphaV/beta3 Integrin/TGFBR2 0.052 0.071 -10000 0 -0.27 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.06 0.066 -10000 0 -0.23 15 15
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.051 0.063 -10000 0 -0.24 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.01 0.14 -10000 0 -0.42 50 50
alphaV/beta3 Integrin/Pyk2 0.035 0.065 -10000 0 -0.24 20 20
SDC1 -0.003 0.13 -10000 0 -0.42 42 42
VAV3 -0.05 0.087 -10000 0 -0.24 74 74
PTPN11 0.036 0.004 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
FAK1/Paxillin 0.025 0.12 0.35 5 -0.34 18 23
cell migration 0.019 0.11 0.32 6 -0.32 16 22
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
PI3K 0.058 0.11 -10000 0 -0.23 47 47
SPP1 -0.073 0.19 -10000 0 -0.42 115 115
KDR 0.033 0.035 -10000 0 -0.42 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.022 0.077 -10000 0 -0.42 15 15
COL4A3 0.033 0.036 -10000 0 -0.42 3 3
angiogenesis -0.036 0.2 -10000 0 -0.56 52 52
Rac1/GTP -0.012 0.097 -10000 0 -0.22 81 81
EDIL3 -0.056 0.18 -10000 0 -0.42 97 97
cell proliferation 0.052 0.071 -10000 0 -0.27 21 21
Cellular roles of Anthrax toxin

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
ANTXR1 0.006 0.11 -10000 0 -0.42 32 32
ANTXR2 0.022 0.078 -10000 0 -0.42 15 15
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.017 -10000 0 -0.063 40 40
monocyte activation -0.017 0.12 -10000 0 -0.37 56 56
MAP2K2 0.004 0.1 -10000 0 -0.63 12 12
MAP2K1 -0.009 0.015 -10000 0 -0.087 6 6
MAP2K7 -0.009 0.018 -10000 0 -0.11 7 7
MAP2K6 -0.013 0.041 0.13 3 -0.21 17 20
CYAA -0.025 0.066 -10000 0 -0.24 40 40
MAP2K4 -0.008 0.018 -10000 0 -0.12 5 5
IL1B -0.026 0.07 0.16 2 -0.21 54 56
Channel 0.021 0.085 -10000 0 -0.26 40 40
NLRP1 -0.006 0.016 -10000 0 -0.058 40 40
CALM1 0.035 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.074 -10000 0 -0.43 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.017 0.063 40 -10000 0 40
MAPK3 -0.007 0.023 0.13 6 -0.11 6 12
MAPK1 -0.009 0.018 -10000 0 -0.11 7 7
PGR -0.074 0.1 -10000 0 -0.22 169 169
PA/Cellular Receptors 0.021 0.093 -10000 0 -0.28 40 40
apoptosis -0.006 0.017 -10000 0 -0.063 40 40
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.081 -10000 0 -0.24 40 40
macrophage activation 0.001 0.051 0.17 35 -0.2 2 37
TNF 0.026 0.061 -10000 0 -0.42 9 9
VCAM1 -0.018 0.13 -10000 0 -0.37 56 56
platelet activation 0 0.074 -10000 0 -0.43 13 13
MAPKKK cascade 0.001 0.032 0.12 6 -0.074 46 52
IL18 -0.02 0.064 0.14 1 -0.24 34 35
negative regulation of macrophage activation -0.006 0.017 -10000 0 -0.063 40 40
LEF -0.006 0.017 -10000 0 -0.063 40 40
CASP1 -0.008 0.031 -10000 0 -0.085 61 61
mol:cAMP 0 0.075 -10000 0 -0.44 13 13
necrosis -0.006 0.017 -10000 0 -0.063 40 40
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.08 -10000 0 -0.24 40 40
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.018 0.11 -10000 0 -0.3 44 44
alphaM/beta2 Integrin/GPIbA 0.035 0.084 -10000 0 -0.29 22 22
alphaM/beta2 Integrin/proMMP-9 0.01 0.12 -10000 0 -0.29 61 61
PLAUR 0.009 0.11 -10000 0 -0.42 29 29
HMGB1 0.025 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.037 0.087 -10000 0 -0.3 23 23
AGER 0.025 0.037 -10000 0 -0.42 1 1
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
SELPLG 0.025 0.07 -10000 0 -0.42 12 12
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.043 0.12 -10000 0 -0.24 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.013 0.14 -10000 0 -0.42 52 52
CYR61 -0.004 0.12 -10000 0 -0.42 40 40
TLN1 0.035 0.021 -10000 0 -0.42 1 1
Rap1/GTP 0.011 0.13 -10000 0 -0.35 36 36
RHOA 0.026 0.061 -10000 0 -0.42 9 9
P-selectin oligomer -0.039 0.16 -10000 0 -0.42 73 73
MYH2 -0.016 0.14 0.23 1 -0.42 33 34
MST1R -0.005 0.13 -10000 0 -0.42 44 44
leukocyte activation during inflammatory response 0.041 0.079 -10000 0 -0.25 23 23
APOB 0.036 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.005 0.1 -10000 0 -0.42 27 27
JAM3 0.014 0.087 -10000 0 -0.42 19 19
GP1BA 0.03 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.018 0.12 -10000 0 -0.32 45 45
alphaM/beta2 Integrin -0.01 0.13 -10000 0 -0.38 37 37
JAM3 homodimer 0.014 0.087 -10000 0 -0.42 19 19
ICAM2 0.027 0.046 -10000 0 -0.42 5 5
ICAM1 0.018 0.085 -10000 0 -0.42 18 18
phagocytosis triggered by activation of immune response cell surface activating receptor -0.009 0.13 -10000 0 -0.38 37 37
cell adhesion 0.034 0.083 -10000 0 -0.29 22 22
NFKB1 0 0.15 0.39 1 -0.37 51 52
THY1 0.015 0.085 -10000 0 -0.42 18 18
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
Lipoprotein(a) 0.045 0.019 -10000 0 -0.25 1 1
alphaM/beta2 Integrin/LRP/tPA 0.016 0.12 -10000 0 -0.26 61 61
IL6 -0.049 0.23 0.36 2 -0.62 61 63
ITGB2 0.006 0.098 -10000 0 -0.44 21 21
elevation of cytosolic calcium ion concentration 0.015 0.15 -10000 0 -0.35 61 61
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.13 -10000 0 -0.31 48 48
JAM2 0.012 0.099 -10000 0 -0.42 25 25
alphaM/beta2 Integrin/ICAM1 0.04 0.13 -10000 0 -0.27 64 64
alphaM/beta2 Integrin/uPA/Plg 0.026 0.13 -10000 0 -0.28 58 58
RhoA/GTP -0.03 0.14 -10000 0 -0.44 37 37
positive regulation of phagocytosis 0.004 0.14 -10000 0 -0.41 36 36
Ron/MSP 0.02 0.1 -10000 0 -0.3 44 44
alphaM/beta2 Integrin/uPAR/uPA 0.017 0.15 -10000 0 -0.35 61 61
alphaM/beta2 Integrin/uPAR 0.024 0.11 -10000 0 -0.33 39 39
PLAU -0.013 0.14 -10000 0 -0.42 52 52
PLAT -0.021 0.14 -10000 0 -0.42 51 51
actin filament polymerization -0.013 0.14 0.24 3 -0.4 33 36
MST1 0.034 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.047 0.083 -10000 0 -0.25 23 23
TNF -0.015 0.16 0.35 2 -0.42 45 47
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
alphaM/beta2 Integrin/uPA 0.013 0.13 -10000 0 -0.31 56 56
fibrinolysis 0.024 0.12 -10000 0 -0.28 58 58
HCK 0.018 0.087 -10000 0 -0.42 19 19
dendritic cell antigen processing and presentation -0.009 0.13 -10000 0 -0.38 37 37
VTN 0.035 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.019 0.12 -10000 0 -0.29 48 48
LPA 0.033 0.022 -10000 0 -0.42 1 1
LRP1 0.035 0.021 -10000 0 -0.42 1 1
cell migration -0.011 0.13 -10000 0 -0.28 76 76
FN1 -0.01 0.14 -10000 0 -0.42 50 50
alphaM/beta2 Integrin/Thy1 0.024 0.1 -10000 0 -0.29 38 38
MPO 0.032 0.013 -10000 0 -10000 0 0
KNG1 0.035 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.041 0.037 -10000 0 -0.25 7 7
ROCK1 -0.019 0.14 -10000 0 -0.42 37 37
ELA2 0.035 0.008 -10000 0 -10000 0 0
PLG 0.032 0.03 -10000 0 -0.42 2 2
CTGF 0.002 0.11 -10000 0 -0.42 34 34
alphaM/beta2 Integrin/Hck 0.03 0.11 -10000 0 -0.37 28 28
ITGAM 0.022 0.053 -10000 0 -0.43 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.003 0.14 -10000 0 -0.28 77 77
HP 0.027 0.037 -10000 0 -0.42 3 3
leukocyte adhesion 0 0.15 -10000 0 -0.42 36 36
SELP -0.039 0.16 -10000 0 -0.42 73 73
Signaling events mediated by PTP1B

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
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
Jak2/Leptin Receptor -0.035 0.14 -10000 0 -0.4 36 36
PTP1B/AKT1 -0.045 0.14 0.3 2 -0.37 45 47
FYN 0.027 0.054 -10000 0 -0.42 7 7
p210 bcr-abl/PTP1B -0.062 0.14 0.28 3 -0.35 65 68
EGFR -0.024 0.14 -10000 0 -0.43 49 49
EGF/EGFR -0.091 0.18 0.29 2 -0.34 127 129
CSF1 0.034 0.021 -10000 0 -0.42 1 1
AKT1 0.033 0.03 -10000 0 -0.43 2 2
INSR 0.034 0.029 -10000 0 -0.42 2 2
PTP1B/N-cadherin -0.056 0.15 0.3 2 -0.38 59 61
Insulin Receptor/Insulin -0.008 0.13 0.31 2 -0.35 34 36
HCK 0.018 0.087 -10000 0 -0.42 19 19
CRK 0.032 0.023 -10000 0 -0.42 1 1
TYK2 -0.061 0.14 0.3 4 -0.38 46 50
EGF -0.073 0.19 -10000 0 -0.43 110 110
YES1 0.029 0.05 -10000 0 -0.42 6 6
CAV1 -0.071 0.15 0.27 3 -0.37 67 70
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.056 0.16 0.3 2 -0.36 67 69
cell migration 0.062 0.14 0.35 65 -0.28 3 68
STAT3 0.028 0.032 -10000 0 -0.42 2 2
PRLR 0.001 0.12 -10000 0 -0.4 42 42
ITGA2B 0.033 0.01 -10000 0 -10000 0 0
CSF1R 0.035 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.028 0.098 -10000 0 -0.3 41 41
FGR 0.035 0.008 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.045 0.14 0.3 1 -0.34 62 63
Crk/p130 Cas -0.038 0.14 0.3 1 -0.36 46 47
DOK1 -0.054 0.14 0.26 3 -0.39 50 53
JAK2 -0.043 0.14 -10000 0 -0.42 36 36
Jak2/Leptin Receptor/Leptin -0.038 0.14 0.25 1 -0.39 38 39
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
PTPN1 -0.062 0.14 0.28 3 -0.35 66 69
LYN 0.03 0.014 -10000 0 -10000 0 0
CDH2 0.013 0.091 -10000 0 -0.42 21 21
SRC -0.003 0.12 -10000 0 -0.63 14 14
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
CAT1/PTP1B -0.085 0.2 0.32 2 -0.46 78 80
CAPN1 0.025 0.065 -10000 0 -0.43 10 10
CSK 0.034 0.022 -10000 0 -0.42 1 1
PI3K -0.003 0.14 0.28 2 -0.35 38 40
mol:H2O2 -0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.033 0.14 -10000 0 -0.38 33 33
negative regulation of transcription -0.042 0.14 -10000 0 -0.41 37 37
FCGR2A 0.018 0.07 -10000 0 -0.42 12 12
FER 0.032 0.022 -10000 0 -0.43 1 1
alphaIIb/beta3 Integrin 0.044 0.035 -10000 0 -0.31 4 4
BLK 0.022 0.038 -10000 0 -0.42 3 3
Insulin Receptor/Insulin/Shc 0.053 0.04 -10000 0 -0.26 3 3
RHOA 0.025 0.062 -10000 0 -0.43 9 9
LEPR 0.026 0.058 -10000 0 -0.42 8 8
BCAR1 0.03 0.014 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.01 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.068 0.21 0.26 1 -0.48 79 80
PRL 0.036 0.026 -10000 0 -0.26 3 3
SOCS3 0.006 0.19 -10000 0 -1.3 10 10
SPRY2 0.005 0.11 -10000 0 -0.43 29 29
Insulin Receptor/Insulin/IRS1 0.032 0.11 -10000 0 -0.27 55 55
CSF1/CSF1R -0.035 0.15 0.3 2 -0.37 45 47
Ras protein signal transduction 0.055 0.17 0.62 39 -10000 0 39
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
INS 0.034 0.022 -10000 0 -0.43 1 1
LEP 0.001 0.11 -10000 0 -0.42 32 32
STAT5B -0.052 0.14 0.25 2 -0.36 50 52
STAT5A -0.054 0.14 0.25 2 -0.36 56 58
GRB2 0.033 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.05 0.15 0.3 2 -0.36 65 67
CSN2 0.022 0.11 -10000 0 -1.4 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
LAT -0.009 0.12 -10000 0 -0.53 19 19
YBX1 0.037 0.043 -10000 0 -0.38 5 5
LCK -0.017 0.14 -10000 0 -0.42 54 54
SHC1 0.028 0.025 -10000 0 -0.42 1 1
NOX4 -0.023 0.15 -10000 0 -0.43 58 58
TCGA08_retinoblastoma

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
CDKN2B 0.021 0.068 -10000 0 -0.39 12 12
CDKN2C 0.024 0.064 -10000 0 -0.37 12 12
CDKN2A 0.019 0.071 -10000 0 -0.39 14 14
CCND2 0.003 0.047 0.18 27 -0.13 2 29
RB1 -0.011 0.062 0.24 2 -0.21 37 39
CDK4 0.007 0.057 0.22 29 -10000 0 29
CDK6 0.004 0.058 0.21 28 -0.17 6 34
G1/S progression 0.018 0.073 0.21 56 -0.26 3 59
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.003 0.12 -10000 0 -0.31 52 52
VEGFR1 homodimer/NRP1 -0.017 0.11 -10000 0 -0.31 52 52
mol:DAG -0.009 0.11 0.2 8 -0.29 49 57
VEGFR1 homodimer/NRP1/VEGFR 121 -0.015 0.098 -10000 0 -0.28 52 52
CaM/Ca2+ 0.009 0.11 -10000 0 -0.28 47 47
HIF1A -0.006 0.14 -10000 0 -0.41 53 53
GAB1 0.027 0.061 -10000 0 -0.42 9 9
AKT1 -0.016 0.11 0.33 1 -0.43 16 17
PLCG1 -0.009 0.11 0.2 8 -0.29 49 57
NOS3 0 0.11 0.48 1 -0.47 16 17
CBL 0.032 0.012 -10000 0 -10000 0 0
mol:NO 0.002 0.11 0.33 4 -0.46 16 20
FLT1 -0.015 0.12 -10000 0 -0.37 47 47
PGF 0.031 0.041 -10000 0 -0.42 4 4
VEGFR1 homodimer/NRP2/VEGFR121 0.002 0.11 -10000 0 -0.29 52 52
CALM1 0.035 0.007 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
eNOS/Hsp90 -0.004 0.11 0.24 1 -0.44 16 17
endothelial cell proliferation -0.002 0.12 0.3 8 -0.42 17 25
mol:Ca2+ -0.009 0.11 0.2 8 -0.28 49 57
MAPK3 -0.024 0.083 0.35 1 -0.48 10 11
MAPK1 -0.028 0.086 0.19 8 -0.49 9 17
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
PLGF homodimer 0.031 0.041 -10000 0 -0.42 4 4
PRKACA 0.036 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.027 0.054 -10000 0 -0.42 7 7
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.017 0.11 -10000 0 -0.31 52 52
platelet activating factor biosynthetic process -0.005 0.1 0.33 5 -0.45 10 15
PI3K 0.026 0.13 -10000 0 -0.27 67 67
PRKCA -0.027 0.093 0.2 13 -0.29 38 51
PRKCB -0.028 0.095 0.18 15 -0.28 43 58
VEGFR1 homodimer/PLGF homodimer 0.002 0.12 -10000 0 -0.31 55 55
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
mol:IP3 -0.009 0.11 0.2 8 -0.29 49 57
RASA1 -0.013 0.11 -10000 0 -0.3 49 49
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFR1 homodimer -0.015 0.12 -10000 0 -0.37 47 47
VEGFB homodimer 0.034 0.021 -10000 0 -0.42 1 1
NCK1 0.034 0.021 -10000 0 -0.42 1 1
eNOS/Caveolin-1 0.015 0.12 0.36 3 -0.47 17 20
PTPN11 0.036 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.024 0.13 -10000 0 -0.27 67 67
mol:L-citrulline 0.002 0.11 0.33 4 -0.46 16 20
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.016 0.11 -10000 0 -0.27 51 51
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.002 0.11 -10000 0 -0.28 53 53
CD2AP 0.035 0.007 -10000 0 -10000 0 0
PI3K/GAB1 0.032 0.14 -10000 0 -0.32 31 31
PDPK1 -0.007 0.11 0.35 2 -0.44 13 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.003 0.11 -10000 0 -0.28 52 52
mol:NADP 0.002 0.11 0.33 4 -0.46 16 20
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.015 0.1 -10000 0 -0.27 51 51
VEGFR1 homodimer/NRP2 0.003 0.12 -10000 0 -0.32 52 52
Caspase cascade in apoptosis

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
TOP1 -0.005 0.11 0.24 1 -0.46 10 11
ACTA1 -0.016 0.12 0.23 12 -0.3 50 62
NUMA1 -0.014 0.12 0.22 1 -0.42 16 17
SPTAN1 -0.021 0.12 0.24 8 -0.31 47 55
LIMK1 -0.033 0.13 0.24 3 -0.33 49 52
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BIRC2 0.032 0.012 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
CASP10 -0.048 0.091 -10000 0 -0.26 75 75
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.011 0.12 0.26 1 -0.51 11 12
DIABLO 0.036 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.12 0.24 8 -0.3 47 55
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.03 0.05 -10000 0 -0.42 6 6
GSN -0.028 0.12 0.25 6 -0.32 51 57
MADD 0.036 0.005 -10000 0 -10000 0 0
TFAP2A -0.003 0.16 -10000 0 -0.59 31 31
BID -0.022 0.069 -10000 0 -0.17 82 82
MAP3K1 -0.034 0.14 -10000 0 -0.41 53 53
TRADD 0.03 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.03 0.13 0.3 6 -0.33 51 57
CASP9 0.034 0.022 -10000 0 -0.42 1 1
DNA repair -0.022 0.069 0.28 9 -0.19 10 19
neuron apoptosis -0.031 0.2 -10000 0 -0.67 41 41
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.018 0.12 0.25 1 -0.3 48 49
APAF1 0.032 0.041 -10000 0 -0.42 4 4
CASP6 -0.014 0.15 -10000 0 -0.79 15 15
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
ICAD/CAD -0.024 0.11 0.23 5 -0.31 45 50
CASP7 0.031 0.1 0.25 45 -0.34 12 57
KRT18 -0.066 0.22 -10000 0 -0.57 73 73
apoptosis -0.016 0.12 0.28 2 -0.37 23 25
DFFA -0.023 0.12 0.24 4 -0.31 46 50
DFFB -0.023 0.12 0.24 4 -0.31 48 52
PARP1 0.022 0.07 0.19 10 -0.28 9 19
actin filament polymerization 0.033 0.13 0.32 49 -0.29 7 56
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS -0.008 0.057 0.15 3 -0.21 10 13
SATB1 -0.028 0.16 -10000 0 -0.71 16 16
SLK -0.023 0.12 0.25 3 -0.31 46 49
p15 BID/BAX -0.002 0.077 -10000 0 -0.25 14 14
CASP2 -0.016 0.1 0.22 4 -0.35 24 28
JNK cascade 0.034 0.14 0.41 53 -10000 0 53
CASP3 -0.021 0.12 0.26 4 -0.32 50 54
LMNB2 -0.009 0.12 0.25 1 -0.44 19 20
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CASP4 0.023 0.061 -10000 0 -0.42 9 9
Mammalian IAPs/DIABLO 0.034 0.082 -10000 0 -0.23 39 39
negative regulation of DNA binding -0.002 0.16 -10000 0 -0.58 31 31
stress fiber formation -0.022 0.12 0.24 3 -0.3 46 49
GZMB -0.033 0.12 -10000 0 -0.31 75 75
CASP1 -0.008 0.1 -10000 0 -0.36 32 32
LMNB1 -0.06 0.16 0.25 1 -0.39 45 46
APP -0.031 0.2 -10000 0 -0.68 41 41
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM -0.012 0.13 0.29 2 -0.39 23 25
LMNA -0.008 0.099 0.25 1 -0.32 20 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.016 0.11 -10000 0 -0.34 31 31
LRDD 0.035 0.008 -10000 0 -10000 0 0
SREBF1 -0.036 0.13 0.25 3 -0.32 49 52
APAF-1/Caspase 9 0.016 0.11 -10000 0 -0.64 12 12
nuclear fragmentation during apoptosis -0.013 0.12 0.22 1 -0.42 16 17
CFL2 -0.034 0.13 0.29 7 -0.32 49 56
GAS2 -0.031 0.13 0.24 6 -0.32 52 58
positive regulation of apoptosis -0.028 0.12 0.26 1 -0.39 24 25
PRF1 0.027 0.054 -10000 0 -0.42 7 7
BMP receptor signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.045 0.1 -9999 0 -0.24 49 49
SMAD6-7/SMURF1 0.067 0.025 -9999 0 -0.26 1 1
NOG 0.029 0.037 -9999 0 -0.42 3 3
SMAD9 -0.029 0.16 -9999 0 -0.45 55 55
SMAD4 0.029 0.054 -9999 0 -0.42 7 7
SMAD5 -0.026 0.12 -9999 0 -0.34 39 39
BMP7/USAG1 -0.063 0.16 -9999 0 -0.31 139 139
SMAD5/SKI -0.014 0.13 -9999 0 -0.38 29 29
SMAD1 0.012 0.07 -9999 0 -0.32 6 6
BMP2 0.021 0.073 -9999 0 -0.42 13 13
SMAD1/SMAD1/SMAD4 0.033 0.077 -9999 0 -0.32 2 2
BMPR1A 0.031 0.045 -9999 0 -0.42 5 5
BMPR1B -0.004 0.11 -9999 0 -0.42 30 30
BMPR1A-1B/BAMBI -0.02 0.14 -9999 0 -0.26 120 120
AHSG 0.034 0.008 -9999 0 -10000 0 0
CER1 0.034 0.009 -9999 0 -10000 0 0
BMP2-4/CER1 0.016 0.12 -9999 0 -0.26 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.015 0.12 -9999 0 -0.36 30 30
BMP2-4 (homodimer) -0.006 0.13 -9999 0 -0.31 74 74
RGMB 0.028 0.057 -9999 0 -0.42 8 8
BMP6/BMPR2/BMPR1A-1B 0.051 0.091 -9999 0 -0.24 41 41
RGMA 0.019 0.073 -9999 0 -0.42 13 13
SMURF1 0.036 0.006 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.03 0.12 -9999 0 -0.36 32 32
BMP2-4/USAG1 -0.075 0.18 -9999 0 -0.29 189 189
SMAD6/SMURF1/SMAD5 -0.013 0.13 -9999 0 -0.38 28 28
SOSTDC1 -0.11 0.2 -9999 0 -0.42 151 151
BMP7/BMPR2/BMPR1A-1B 0.041 0.095 -9999 0 -0.24 45 45
SKI 0.036 0.002 -9999 0 -10000 0 0
BMP6 (homodimer) 0.027 0.05 -9999 0 -0.42 6 6
HFE2 0.026 0.064 -9999 0 -0.42 10 10
ZFYVE16 0.034 0.022 -9999 0 -0.42 1 1
MAP3K7 0.033 0.011 -9999 0 -10000 0 0
BMP2-4/CHRD 0.014 0.12 -9999 0 -0.28 70 70
SMAD5/SMAD5/SMAD4 -0.017 0.13 -9999 0 -0.38 30 30
MAPK1 0.033 0.022 -9999 0 -0.42 1 1
TAK1/TAB family 0.012 0.13 -9999 0 -0.36 24 24
BMP7 (homodimer) 0.016 0.072 -9999 0 -0.42 13 13
NUP214 0.035 0.021 -9999 0 -0.42 1 1
BMP6/FETUA 0.044 0.041 -9999 0 -0.3 6 6
SMAD1/SKI 0.027 0.08 -9999 0 -0.31 8 8
SMAD6 0.035 0.008 -9999 0 -10000 0 0
CTDSP2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/FETUA 0.017 0.12 -9999 0 -0.26 69 69
MAP3K7IP1 0.034 0.009 -9999 0 -10000 0 0
GREM1 -0.002 0.12 -9999 0 -0.42 40 40
BMPR2 (homodimer) 0.034 0.029 -9999 0 -0.42 2 2
GADD34/PP1CA 0.06 0.039 -9999 0 -0.26 4 4
BMPR1A-1B (homodimer) 0.02 0.087 -9999 0 -0.3 34 34
CHRDL1 0.03 0.037 -9999 0 -0.42 3 3
ENDOFIN/SMAD1 0.026 0.08 -9999 0 -0.31 7 7
SMAD6-7/SMURF1/SMAD1 0.055 0.086 -9999 0 -0.31 5 5
SMAD6/SMURF1 0.036 0.006 -9999 0 -10000 0 0
BAMBI -0.054 0.17 -9999 0 -0.42 93 93
SMURF2 0.028 0.042 -9999 0 -0.42 4 4
BMP2-4/CHRDL1 0.014 0.12 -9999 0 -0.27 75 75
BMP2-4/GREM1 -0.009 0.15 -9999 0 -0.29 101 101
SMAD7 0.034 0.021 -9999 0 -0.42 1 1
SMAD8A/SMAD8A/SMAD4 -0.023 0.17 -9999 0 -0.44 59 59
SMAD1/SMAD6 0.026 0.08 -9999 0 -0.31 8 8
TAK1/SMAD6 0.048 0.017 -9999 0 -10000 0 0
BMP7 0.016 0.073 -9999 0 -0.42 13 13
BMP6 0.027 0.05 -9999 0 -0.42 6 6
MAP3K7IP2 0.032 0.03 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.018 0.11 -9999 0 -0.33 35 35
PPM1A 0.034 0.021 -9999 0 -0.42 1 1
SMAD1/SMURF2 0.022 0.076 -9999 0 -0.31 7 7
SMAD7/SMURF1 0.05 0.02 -9999 0 -0.3 1 1
CTDSPL 0.029 0.054 -9999 0 -0.42 7 7
PPP1CA 0.031 0.03 -9999 0 -0.42 2 2
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
PPP1R15A 0.034 0.021 -9999 0 -0.42 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.034 0.14 -9999 0 -0.41 36 36
CHRD 0.029 0.046 -9999 0 -0.42 5 5
BMPR2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.12 -9999 0 -0.38 31 31
BMP4 -0.028 0.15 -9999 0 -0.42 65 65
FST 0.023 0.064 -9999 0 -0.42 10 10
BMP2-4/NOG 0.012 0.12 -9999 0 -0.26 72 72
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.052 0.097 -9999 0 -0.23 45 45
Nectin adhesion pathway

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
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
alphaV beta3 Integrin 0.036 0.071 -10000 0 -0.31 19 19
PTK2 -0.025 0.14 -10000 0 -0.43 36 36
positive regulation of JNK cascade -0.002 0.13 -10000 0 -0.32 44 44
CDC42/GDP 0.009 0.17 -10000 0 -0.42 44 44
Rac1/GDP 0.01 0.16 -10000 0 -0.41 46 46
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
CDC42/GTP 0 0.16 -10000 0 -0.39 44 44
nectin-3/I-afadin 0.022 0.098 -10000 0 -0.32 35 35
RAPGEF1 -0.016 0.16 -10000 0 -0.44 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.021 0.18 -10000 0 -0.47 61 61
PDGFB-D/PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
TLN1 -0.015 0.074 0.19 4 -0.34 16 20
Rap1/GTP -0.006 0.12 -10000 0 -0.31 58 58
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.064 -10000 0 -0.23 22 22
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.098 -10000 0 -0.32 35 35
PVR 0.031 0.041 -10000 0 -0.42 4 4
Necl-5(dimer) 0.031 0.041 -10000 0 -0.42 4 4
mol:GDP -0.012 0.19 -10000 0 -0.51 47 47
MLLT4 0.02 0.078 -10000 0 -0.42 15 15
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.054 0.12 -10000 0 -0.28 47 47
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.064 -10000 0 -0.3 16 16
positive regulation of lamellipodium assembly 0.005 0.12 -10000 0 -0.32 46 46
PVRL1 0.03 0.024 -10000 0 -0.42 1 1
PVRL3 0.013 0.097 -10000 0 -0.42 24 24
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
CDH1 -0.011 0.13 -10000 0 -0.42 45 45
CLDN1 -0.047 0.17 -10000 0 -0.42 86 86
JAM-A/CLDN1 0.002 0.14 -10000 0 -0.27 87 87
SRC -0.035 0.2 -10000 0 -0.51 64 64
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.064 -10000 0 -0.3 16 16
FARP2 -0.017 0.2 -10000 0 -0.53 44 44
RAC1 0.035 0.006 -10000 0 -10000 0 0
CTNNA1 0.035 0.021 -10000 0 -0.42 1 1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.038 0.097 -10000 0 -0.28 38 38
nectin-1/I-afadin 0.033 0.064 -10000 0 -0.3 16 16
nectin-2/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
RAC1/GTP/IQGAP1/filamentous actin 0.046 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.035 0.093 -10000 0 -0.28 36 36
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.014 -10000 0 -10000 0 0
F11R 0.026 0.038 -10000 0 -0.42 3 3
positive regulation of filopodium formation -0.002 0.13 -10000 0 -0.32 44 44
alphaV/beta3 Integrin/Talin 0.008 0.11 0.27 1 -0.39 19 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.076 -10000 0 -0.3 24 24
PIP5K1C -0.011 0.077 -10000 0 -0.36 16 16
VAV2 -0.006 0.19 -10000 0 -0.5 46 46
RAP1/GDP 0.01 0.16 -10000 0 -0.39 46 46
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.035 0.1 -10000 0 -0.28 42 42
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.098 -10000 0 -0.32 35 35
Rac1/GTP 0.008 0.15 -10000 0 -0.38 46 46
PTPRM -0.006 0.089 -10000 0 -0.27 40 40
E-cadherin/beta catenin/alpha catenin 0.025 0.12 -10000 0 -0.22 78 78
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.008 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.048 0.017 -10000 0 -10000 0 0
VLDLR -0.007 0.12 -10000 0 -0.42 42 42
CRKL 0.031 0.041 -10000 0 -0.42 4 4
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
FYN 0.027 0.054 -10000 0 -0.42 7 7
ITGA3 0.023 0.07 -10000 0 -0.42 12 12
RELN/VLDLR/Fyn 0.027 0.1 -10000 0 -0.27 51 51
MAPK8IP1/MKK7/MAP3K11/JNK1 0.07 0.07 -10000 0 -0.22 15 15
AKT1 -0.017 0.088 -10000 0 -0.23 57 57
MAP2K7 0.035 0.021 -10000 0 -0.42 1 1
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.007 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.039 0.081 -10000 0 -0.23 40 40
LRPAP1/LRP8 0.024 0.089 -10000 0 -0.3 35 35
RELN/LRP8/DAB1/Fyn 0.045 0.09 -10000 0 -0.22 46 46
DAB1/alpha3/beta1 Integrin 0.016 0.12 -10000 0 -0.22 86 86
long-term memory 0.049 0.1 -10000 0 -0.22 55 55
DAB1/LIS1 0.032 0.12 -10000 0 -0.22 80 80
DAB1/CRLK/C3G 0.021 0.11 -10000 0 -0.22 82 82
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DAB1/NCK2 0.039 0.12 -10000 0 -0.22 80 80
ARHGEF2 0.022 0.055 -10000 0 -0.42 7 7
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.033 0.011 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
RELN 0.03 0.046 -10000 0 -0.42 5 5
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RELN/LRP8/Fyn 0.031 0.096 -10000 0 -0.26 46 46
GRIN2A/RELN/LRP8/DAB1/Fyn 0.056 0.094 -10000 0 -0.22 41 41
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1 0.032 0.088 -10000 0 -0.23 46 46
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
MAP1B -0.027 0.12 0.32 5 -0.25 96 101
RELN/LRP8 0.039 0.089 -10000 0 -0.25 40 40
GRIN2B/RELN/LRP8/DAB1/Fyn 0.047 0.11 -10000 0 -0.23 61 61
PI3K 0.036 0.065 -10000 0 -0.3 17 17
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.059 -10000 0 -0.32 12 12
RAP1A -0.042 0.097 0.34 7 -0.43 3 10
PAFAH1B1 0.032 0.023 -10000 0 -0.42 1 1
MAPK8IP1 0.034 0.029 -10000 0 -0.42 2 2
CRLK/C3G 0.047 0.034 -10000 0 -0.3 4 4
GRIN2B 0.018 0.082 -10000 0 -0.42 17 17
NCK2 0.036 0.005 -10000 0 -10000 0 0
neuron differentiation 0.018 0.083 -10000 0 -0.32 9 9
neuron adhesion -0.041 0.11 0.35 7 -0.39 6 13
LRP8 -0.001 0.12 -10000 0 -0.42 35 35
GSK3B -0.015 0.092 0.19 5 -0.41 10 15
RELN/VLDLR/DAB1/Fyn 0.039 0.097 -10000 0 -0.23 51 51
MAP3K11 0.034 0.029 -10000 0 -0.42 2 2
RELN/VLDLR/DAB1/P13K -0.007 0.095 -10000 0 -0.24 60 60
CDK5 0.035 0.007 -10000 0 -10000 0 0
MAPT -0.068 0.18 0.77 6 -0.38 96 102
neuron migration -0.024 0.12 0.3 11 -0.33 19 30
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.082 -10000 0 -0.32 9 9
RELN/VLDLR 0.025 0.12 -10000 0 -0.24 80 80
Visual signal transduction: Rods

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
mol:K + 0.03 0.046 -10000 0 -0.42 5 5
GNAT1/GTP 0.024 0.025 -10000 0 -0.3 3 3
Metarhodopsin II/Arrestin 0.009 0.094 -10000 0 -0.25 57 57
PDE6G/GNAT1/GTP 0.042 0.028 -10000 0 -0.25 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.036 -10000 0 -0.42 3 3
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.015 0.12 -10000 0 -0.22 123 123
mol:Na + 0.025 0.098 -10000 0 -0.24 49 49
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.037 0.11 -10000 0 -0.25 49 49
CNGB1 0.03 0.014 -10000 0 -10000 0 0
RDH5 0.033 0.011 -10000 0 -10000 0 0
SAG -0.024 0.14 -10000 0 -0.42 58 58
mol:Ca2+ -0.034 0.087 0.33 6 -0.39 10 16
Na + (4 Units) 0.016 0.093 -10000 0 -0.24 47 47
RGS9 0.017 0.07 -10000 0 -0.42 12 12
GNB1/GNGT1 0.036 0.062 -10000 0 -0.3 16 16
GNAT1/GDP 0.018 0.11 -10000 0 -0.23 76 76
GUCY2D 0.032 0.012 -10000 0 -10000 0 0
GNGT1 0.017 0.067 -10000 0 -0.42 11 11
GUCY2F 0.027 0.064 -10000 0 -0.42 10 10
GNB5 0.025 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) -0.02 0.1 -10000 0 -0.22 105 105
mol:11-cis-retinal 0.033 0.01 -10000 0 -10000 0 0
mol:cGMP 0.048 0.084 -10000 0 -0.26 29 29
GNB1 0.032 0.045 -10000 0 -0.42 5 5
Rhodopsin 0.051 0.011 -10000 0 -10000 0 0
SLC24A1 0.03 0.046 -10000 0 -0.42 5 5
CNGA1 0.004 0.1 -10000 0 -0.42 28 28
Metarhodopsin II 0.023 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.064 0.077 -10000 0 -0.25 23 23
RGS9BP -0.023 0.15 -10000 0 -0.42 61 61
Metarhodopsin II/Transducin 0.015 0.047 -10000 0 -0.21 20 20
GCAP Family/Ca ++ 0.051 0.068 -10000 0 -0.25 23 23
PDE6A/B -0.027 0.15 -10000 0 -0.3 112 112
mol:Pi 0.006 0.12 -10000 0 -0.27 73 73
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.05 0.058 -10000 0 -0.23 19 19
PDE6B -0.064 0.19 -10000 0 -0.42 111 111
PDE6A 0.033 0.029 -10000 0 -0.42 2 2
PDE6G 0.034 0.01 -10000 0 -10000 0 0
RHO 0.036 0.006 -10000 0 -10000 0 0
PDE6 -0.015 0.15 -10000 0 -0.24 139 139
GUCA1A 0.022 0.075 -10000 0 -0.42 14 14
GC2/GCAP Family 0.067 0.09 -10000 0 -0.28 29 29
GUCA1C 0.026 0.064 -10000 0 -0.42 10 10
GUCA1B 0.034 0.021 -10000 0 -0.42 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.035 0.036 -10000 0 -0.41 2 2
HSPA8 0.018 0.073 -10000 0 -0.42 13 13
SMAD3/SMAD4/ER alpha -0.034 0.18 0.24 1 -0.29 135 136
AKT1 0.03 0.038 -10000 0 -0.42 2 2
GSC -0.19 0.49 -10000 0 -1.3 75 75
NKX2-5 0.028 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.012 0.17 0.39 52 -10000 0 52
SMAD2-3/SMAD4/SP1 0.022 0.18 -10000 0 -0.37 56 56
SMAD4 -0.004 0.097 -10000 0 -0.26 38 38
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.033 0.01 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.062 0.049 -10000 0 -0.23 4 4
SMAD3/SMAD4/VDR 0.059 0.12 -10000 0 -0.25 33 33
MYC -0.001 0.1 -10000 0 -0.41 29 29
CDKN2B -0.1 0.32 -10000 0 -1.3 27 27
AP1 -0.03 0.18 -10000 0 -0.44 65 65
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.099 -10000 0 -0.35 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.007 0.092 -10000 0 -0.29 37 37
SP3 0.028 0.03 -10000 0 -10000 0 0
CREB1 0.035 0.021 -10000 0 -0.42 1 1
FOXH1 0.013 0.059 -10000 0 -0.19 9 9
SMAD3/SMAD4/GR 0.027 0.12 -10000 0 -0.28 43 43
GATA3 -0.044 0.17 -10000 0 -0.41 91 91
SKI/SIN3/HDAC complex/NCoR1 0.015 0.073 -10000 0 -0.31 12 12
MEF2C/TIF2 -0.014 0.13 0.33 1 -0.37 39 40
endothelial cell migration 0.005 0.24 1.1 21 -10000 0 21
MAX 0.035 0.011 -10000 0 -10000 0 0
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
RUNX2 0.031 0.041 -10000 0 -0.42 4 4
RUNX3 -0.01 0.13 -10000 0 -0.42 46 46
RUNX1 0.008 0.11 -10000 0 -0.42 29 29
CTBP1 0.035 0.008 -10000 0 -10000 0 0
NR3C1 0.024 0.072 -10000 0 -0.42 13 13
VDR 0.02 0.082 -10000 0 -0.42 17 17
CDKN1A -0.042 0.24 -10000 0 -1.2 17 17
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.015 0.14 -10000 0 -0.28 82 82
DCP1A 0.034 0.022 -10000 0 -0.42 1 1
SKI 0.036 0.002 -10000 0 -10000 0 0
SERPINE1 -0.006 0.25 -10000 0 -1.1 21 21
SMAD3/SMAD4/ATF2 0.034 0.11 -10000 0 -0.26 33 33
SMAD3/SMAD4/ATF3 0.015 0.12 -10000 0 -0.3 43 43
SAP30 0.03 0.046 -10000 0 -0.42 5 5
Cbp/p300/PIAS3 0.067 0.051 0.22 3 -0.26 1 4
JUN -0.043 0.18 -10000 0 -0.45 63 63
SMAD3/SMAD4/IRF7 0.032 0.12 -10000 0 -0.28 39 39
TFE3 0.033 0.035 -10000 0 -0.16 4 4
COL1A2 -0.076 0.33 -10000 0 -0.87 70 70
mesenchymal cell differentiation -0.03 0.11 0.29 32 -10000 0 32
DLX1 0.033 0.011 -10000 0 -10000 0 0
TCF3 0.033 0.03 -10000 0 -0.42 2 2
FOS -0.038 0.16 -10000 0 -0.45 66 66
SMAD3/SMAD4/Max 0.033 0.11 -10000 0 -0.26 32 32
Cbp/p300/SNIP1 0.06 0.045 -10000 0 -0.26 4 4
ZBTB17 0.035 0.013 -10000 0 -10000 0 0
LAMC1 -0.007 0.11 -10000 0 -0.45 20 20
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.11 -10000 0 -0.27 37 37
IRF7 0.028 0.059 -10000 0 -0.42 8 8
ESR1 -0.082 0.19 -10000 0 -0.41 132 132
HNF4A 0.033 0.03 -10000 0 -0.42 2 2
MEF2C -0.03 0.14 0.34 3 -0.38 45 48
SMAD2-3/SMAD4 0.018 0.13 -10000 0 -0.28 41 41
Cbp/p300/Src-1 0.062 0.049 -10000 0 -0.23 5 5
IGHV3OR16-13 -0.003 0.065 -10000 0 -0.44 8 8
TGIF2/HDAC complex 0.029 0.05 -10000 0 -0.42 6 6
CREBBP 0.034 0.019 -10000 0 -10000 0 0
SKIL 0.028 0.05 -10000 0 -0.42 6 6
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
SNIP1 0.032 0.036 -10000 0 -0.42 3 3
GCN5L2 0.031 0.029 -10000 0 -0.42 1 1
SMAD3/SMAD4/TFE3 0.04 0.12 -10000 0 -0.31 36 36
MSG1/HSC70 0.032 0.062 -10000 0 -0.3 15 15
SMAD2 0.011 0.059 -10000 0 -0.16 10 10
SMAD3 0.01 0.091 -10000 0 -0.32 21 21
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.079 -10000 0 -0.26 21 21
SMAD2/SMAD2/SMAD4 -0.001 0.063 0.26 4 -0.23 15 19
NCOR1 0.032 0.012 -10000 0 -10000 0 0
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
MYOD/E2A 0.032 0.077 -10000 0 -0.3 25 25
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.18 -10000 0 -0.36 51 51
IFNB1 -0.005 0.096 0.36 1 -0.31 27 28
SMAD3/SMAD4/MEF2C -0.003 0.17 -10000 0 -0.43 42 42
CITED1 0.029 0.031 -10000 0 -0.42 2 2
SMAD2-3/SMAD4/ARC105 0.021 0.12 -10000 0 -0.25 41 41
RBL1 0.033 0.022 -10000 0 -0.42 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.004 0.12 -10000 0 -0.44 28 28
RUNX1-3/PEBPB2 0.013 0.12 -10000 0 -0.26 70 70
SMAD7 -0.041 0.21 -10000 0 -0.54 52 52
MYC/MIZ-1 0.016 0.082 0.19 5 -0.3 28 33
SMAD3/SMAD4 0.04 0.13 0.31 42 -0.39 19 61
IL10 -0.034 0.12 -10000 0 -0.28 86 86
PIASy/HDAC complex 0.024 0.043 -10000 0 -0.42 3 3
PIAS3 0.036 0.011 -10000 0 -10000 0 0
CDK2 0.035 0.033 -10000 0 -0.42 2 2
IL5 -0.035 0.13 -10000 0 -0.31 60 60
CDK4 0.038 0.017 -10000 0 -10000 0 0
PIAS4 0.024 0.043 -10000 0 -0.42 3 3
ATF3 0.011 0.084 -10000 0 -0.42 18 18
SMAD3/SMAD4/SP1 0.014 0.17 -10000 0 -0.34 64 64
FOXG1 -0.001 0.003 -10000 0 -10000 0 0
FOXO3 0.006 0.03 -10000 0 -0.2 4 4
FOXO1 0.006 0.029 -10000 0 -0.2 4 4
FOXO4 0.006 0.029 -10000 0 -0.2 4 4
heart looping -0.029 0.14 0.34 3 -0.38 45 48
CEBPB 0.025 0.053 -10000 0 -0.42 6 6
SMAD3/SMAD4/DLX1 0.033 0.11 -10000 0 -0.26 31 31
MYOD1 0.014 0.095 -10000 0 -0.42 23 23
SMAD3/SMAD4/HNF4 0.032 0.11 -10000 0 -0.28 29 29
SMAD3/SMAD4/GATA3 -0.011 0.17 -10000 0 -0.3 106 106
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.05 -10000 0 -0.42 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.017 0.15 -10000 0 -0.27 82 82
SMAD3/SMAD4/SP1-3 0.029 0.18 -10000 0 -0.36 64 64
MED15 0 0 -10000 0 -10000 0 0
SP1 0.009 0.076 -10000 0 -0.2 33 33
SIN3B 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.035 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.032 0.15 -10000 0 -0.26 88 88
ITGB5 -0.045 0.18 -10000 0 -0.5 59 59
TGIF/SIN3/HDAC complex/CtBP 0.018 0.061 -10000 0 -0.29 9 9
SMAD3/SMAD4/AR -0.023 0.18 -10000 0 -0.31 115 115
AR -0.053 0.18 -10000 0 -0.42 99 99
negative regulation of cell growth 0.012 0.099 -10000 0 -0.34 20 20
SMAD3/SMAD4/MYOD 0.018 0.12 -10000 0 -0.26 56 56
E2F5 0.011 0.087 -10000 0 -0.42 19 19
E2F4 0.03 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.045 0.13 -10000 0 -0.25 46 46
SMAD2-3/SMAD4/FOXO1-3a-4 -0.004 0.1 -10000 0 -0.31 38 38
TFDP1 0.032 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.007 0.2 -10000 0 -0.44 65 65
SMAD3/SMAD4/RUNX2 0.031 0.11 -10000 0 -0.29 32 32
TGIF2 0.029 0.05 -10000 0 -0.42 6 6
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.003 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.021 0.16 0.26 4 -0.42 44 48
IKBKB 0.017 0.092 0.33 2 -0.3 4 6
AKT1 0.024 0.11 0.24 46 -0.23 18 64
IKBKG 0.027 0.079 0.24 5 -0.28 6 11
CALM1 -0.01 0.13 0.25 5 -0.4 31 36
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.02 0.18 0.29 5 -0.46 48 53
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.14 0.26 5 -0.38 39 44
DOK1 0.027 0.061 -10000 0 -0.42 9 9
AP-1 -0.018 0.1 0.21 2 -0.25 42 44
LYN 0.03 0.014 -10000 0 -10000 0 0
BLNK 0.013 0.099 -10000 0 -0.42 25 25
SHC1 0.028 0.025 -10000 0 -0.42 1 1
BCR complex 0.025 0.074 -10000 0 -0.3 23 23
CD22 -0.018 0.12 0.26 1 -0.44 30 31
CAMK2G -0.009 0.12 0.24 7 -0.39 27 34
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.004 0.077 -10000 0 -0.25 31 31
GO:0007205 -0.011 0.14 0.26 5 -0.39 39 44
SYK 0.005 0.11 -10000 0 -0.42 34 34
ELK1 -0.012 0.13 0.25 5 -0.4 31 36
NFATC1 0.022 0.13 0.26 25 -0.36 30 55
B-cell antigen/BCR complex 0.025 0.074 -10000 0 -0.3 23 23
PAG1/CSK 0.035 0.051 -10000 0 -0.3 9 9
NFKBIB 0.027 0.05 0.15 7 -0.13 10 17
HRAS 0.003 0.12 0.25 13 -0.36 26 39
NFKBIA 0.028 0.05 0.15 7 -0.12 11 18
NF-kappa-B/RelA/I kappa B beta 0.032 0.045 0.16 7 -10000 0 7
RasGAP/Csk 0.038 0.1 -10000 0 -0.26 35 35
mol:GDP -0.01 0.14 0.26 5 -0.4 34 39
PTEN 0.027 0.061 -10000 0 -0.42 9 9
CD79B 0.007 0.094 -10000 0 -0.42 23 23
NF-kappa-B/RelA/I kappa B alpha 0.032 0.044 0.16 7 -10000 0 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.01 0.18 0.34 2 -0.5 40 42
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 -0.012 0.14 0.27 4 -0.39 39 43
CSK 0.034 0.022 -10000 0 -0.42 1 1
FOS -0.036 0.14 0.24 4 -0.38 44 48
CHUK 0.016 0.1 0.25 4 -0.33 18 22
IBTK 0.032 0.03 -10000 0 -0.42 2 2
CARD11/BCL10/MALT1/TAK1 0.01 0.13 0.27 1 -0.39 27 28
PTPN6 -0.01 0.12 0.25 1 -0.48 23 24
RELA 0.036 0.006 -10000 0 -10000 0 0
BCL2A1 0.023 0.035 0.14 3 -10000 0 3
VAV2 0 0.14 0.26 2 -0.49 27 29
ubiquitin-dependent protein catabolic process 0.03 0.05 0.16 7 -0.12 10 17
BTK -0.012 0.19 -10000 0 -1.1 15 15
CD19 -0.017 0.12 0.26 1 -0.43 31 32
MAP4K1 0.035 0.007 -10000 0 -10000 0 0
CD72 0.009 0.1 -10000 0 -0.42 27 27
PAG1 0.02 0.061 -10000 0 -0.42 9 9
MAPK14 -0.015 0.16 0.27 5 -0.4 47 52
SH3BP5 0.021 0.078 -10000 0 -0.42 15 15
PIK3AP1 -0.02 0.15 0.28 4 -0.45 36 40
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.16 -10000 0 -0.51 35 35
RAF1 0.003 0.12 0.25 10 -0.35 22 32
RasGAP/p62DOK/SHIP 0.026 0.099 -10000 0 -0.26 40 40
CD79A 0.031 0.023 -10000 0 -0.42 1 1
re-entry into mitotic cell cycle -0.018 0.1 0.21 2 -0.25 42 44
RASA1 0.029 0.05 -10000 0 -0.42 6 6
MAPK3 0.012 0.1 0.25 14 -0.31 16 30
MAPK1 0.002 0.1 0.31 4 -0.32 17 21
CD72/SHP1 0.018 0.16 0.31 12 -0.47 29 41
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.016 0.16 0.28 7 -0.4 45 52
actin cytoskeleton organization 0.019 0.14 0.28 17 -0.44 27 44
NF-kappa-B/RelA 0.065 0.087 0.29 6 -0.3 2 8
Calcineurin 0.004 0.13 -10000 0 -0.38 27 27
PI3K -0.025 0.11 -10000 0 -0.39 28 28
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.011 0.15 0.28 5 -0.43 39 44
SOS1 0.035 0.021 -10000 0 -0.42 1 1
Bam32/HPK1 -0.065 0.31 -10000 0 -0.73 80 80
DAPP1 -0.1 0.34 -10000 0 -0.83 80 80
cytokine secretion 0.023 0.13 0.25 26 -0.34 30 56
mol:DAG -0.012 0.14 0.27 4 -0.39 39 43
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
MAP2K1 0.002 0.11 0.25 10 -0.34 19 29
B-cell antigen/BCR complex/FcgammaRIIB 0.02 0.094 -10000 0 -0.29 34 34
mol:PI-3-4-5-P3 0 0.11 0.24 23 -0.3 25 48
ETS1 -0.009 0.11 0.23 7 -0.37 26 33
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.033 0.12 -10000 0 -0.26 55 55
B-cell antigen/BCR complex/LYN -0.013 0.12 0.27 1 -0.45 31 32
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
RAC1 0.008 0.14 0.3 9 -0.46 27 36
B-cell antigen/BCR complex/LYN/SYK -0.002 0.14 -10000 0 -0.5 25 25
CARD11 -0.013 0.14 0.26 7 -0.41 35 42
FCGR2B 0.001 0.11 -10000 0 -0.42 30 30
PPP3CA 0.027 0.061 -10000 0 -0.42 9 9
BCL10 0.034 0.008 -10000 0 -10000 0 0
IKK complex 0.024 0.05 0.16 21 -0.14 1 22
PTPRC 0.007 0.094 -10000 0 -0.42 23 23
PDPK1 0.005 0.085 0.2 34 -0.22 16 50
PPP3CB 0.035 0.021 -10000 0 -0.42 1 1
PPP3CC 0.024 0.043 -10000 0 -0.42 4 4
POU2F2 0.025 0.032 0.13 4 -10000 0 4
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.029 0.23 -10000 0 -0.98 28 28
regulation of axonogenesis -0.001 0.058 0.29 12 -10000 0 12
myoblast fusion -0.006 0.11 0.4 31 -10000 0 31
mol:GTP 0.01 0.066 -10000 0 -0.23 34 34
regulation of calcium-dependent cell-cell adhesion -0.047 0.082 0.24 33 -10000 0 33
ARF1/GTP 0.024 0.056 -10000 0 -0.19 25 25
mol:GM1 0 0.047 -10000 0 -0.18 30 30
mol:Choline -0.001 0.057 -10000 0 -0.22 27 27
lamellipodium assembly -0.007 0.12 -10000 0 -0.45 34 34
MAPK3 0.009 0.085 -10000 0 -0.33 29 29
ARF6/GTP/NME1/Tiam1 0.048 0.082 -10000 0 -0.24 33 33
ARF1 0.027 0.025 -10000 0 -0.42 1 1
ARF6/GDP 0.006 0.11 -10000 0 -0.4 31 31
ARF1/GDP 0.008 0.099 -10000 0 -0.36 29 29
ARF6 0.031 0.056 -10000 0 -0.18 26 26
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
TIAM1 0.025 0.06 -10000 0 -0.42 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.086 -10000 0 -0.34 28 28
actin filament bundle formation -0.016 0.11 0.37 34 -10000 0 34
KALRN 0.001 0.082 -10000 0 -0.31 31 31
RAB11FIP3/RAB11A 0.047 0.043 -10000 0 -0.3 7 7
RhoA/GDP 0.017 0.11 -10000 0 -0.37 34 34
NME1 0.031 0.02 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.11 -10000 0 -0.37 33 33
substrate adhesion-dependent cell spreading 0.01 0.066 -10000 0 -0.23 34 34
cortical actin cytoskeleton organization -0.007 0.13 -10000 0 -0.46 34 34
RAC1 0.035 0.006 -10000 0 -10000 0 0
liver development 0.01 0.066 -10000 0 -0.23 34 34
ARF6/GTP 0.01 0.066 -10000 0 -0.23 34 34
RhoA/GTP 0.025 0.071 -10000 0 -0.21 38 38
mol:GDP -0.009 0.1 -10000 0 -0.4 32 32
ARF6/GTP/RAB11FIP3/RAB11A 0.048 0.067 -10000 0 -0.18 31 31
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PLD1 0.007 0.068 -10000 0 -0.23 32 32
RAB11FIP3 0.031 0.049 -10000 0 -0.42 6 6
tube morphogenesis -0.007 0.12 -10000 0 -0.45 34 34
ruffle organization 0.001 0.058 -10000 0 -0.29 12 12
regulation of epithelial cell migration 0.01 0.066 -10000 0 -0.23 34 34
PLD2 0.012 0.052 -10000 0 -0.2 23 23
PIP5K1A 0.001 0.058 -10000 0 -0.3 12 12
mol:Phosphatidic acid -0.001 0.057 -10000 0 -0.22 27 27
Rac1/GTP -0.007 0.13 -10000 0 -0.46 34 34
PDGFR-alpha signaling pathway

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
PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
PDGF/PDGFRA/CRKL 0.02 0.088 -10000 0 -0.3 32 32
positive regulation of JUN kinase activity 0.048 0.073 -10000 0 -0.23 22 22
CRKL 0.031 0.041 -10000 0 -0.42 4 4
PDGF/PDGFRA/Caveolin-3 0.022 0.086 -10000 0 -0.3 30 30
AP1 -0.14 0.3 -10000 0 -0.81 78 78
mol:IP3 -0.014 0.08 -10000 0 -0.32 27 27
PLCG1 -0.014 0.08 -10000 0 -0.32 27 27
PDGF/PDGFRA/alphaV Integrin 0.014 0.1 -10000 0 -0.32 42 42
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
mol:Ca2+ -0.014 0.08 -10000 0 -0.32 27 27
CAV3 0.034 0.021 -10000 0 -0.42 1 1
CAV1 0.027 0.054 -10000 0 -0.42 7 7
SHC/Grb2/SOS1 0.05 0.074 -10000 0 -0.23 22 22
PDGF/PDGFRA/Shf 0.022 0.086 -10000 0 -0.3 30 30
FOS -0.14 0.3 0.31 2 -0.8 78 80
JUN -0.053 0.083 -10000 0 -0.34 36 36
oligodendrocyte development 0.014 0.1 -10000 0 -0.32 42 42
GRB2 0.033 0.011 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:DAG -0.014 0.08 -10000 0 -0.32 27 27
PDGF/PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
actin cytoskeleton reorganization 0.02 0.09 -10000 0 -0.3 33 33
SRF 0.018 0.012 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
PI3K 0.034 0.099 -10000 0 -0.28 40 40
PDGF/PDGFRA/Crk/C3G 0.044 0.079 -10000 0 -0.25 30 30
JAK1 -0.01 0.079 -10000 0 -0.31 30 30
ELK1/SRF -0.026 0.071 0.15 24 -0.26 30 54
SHB 0.031 0.046 -10000 0 -0.42 5 5
SHF 0.033 0.022 -10000 0 -0.42 1 1
CSNK2A1 0.04 0.021 -10000 0 -10000 0 0
GO:0007205 -0.023 0.084 -10000 0 -0.35 28 28
SOS1 0.035 0.021 -10000 0 -0.42 1 1
Ras protein signal transduction 0.048 0.073 -10000 0 -0.23 22 22
PDGF/PDGFRA/SHB 0.02 0.09 -10000 0 -0.3 33 33
PDGF/PDGFRA/Caveolin-1 0.017 0.097 -10000 0 -0.33 33 33
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
ELK1 -0.036 0.08 0.24 2 -0.32 30 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PDGF/PDGFRA/Crk 0.019 0.085 -10000 0 -0.3 30 30
JAK-STAT cascade -0.01 0.079 -10000 0 -0.31 30 30
cell proliferation 0.022 0.086 -10000 0 -0.3 30 30
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.032 0.023 -10000 0 -0.42 1 1
MKNK1 0.035 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.024 0.1 0.26 5 -0.26 65 70
FRAP1 -0.008 0.11 -10000 0 -0.5 15 15
AKT1 -0.025 0.096 0.17 27 -0.25 58 85
INSR 0.034 0.029 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.045 0.026 -10000 0 -0.25 3 3
mol:GTP 0.011 0.097 0.26 3 -0.22 43 46
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.051 -10000 0 -0.2 14 14
TSC2 0.032 0.023 -10000 0 -0.42 1 1
RHEB/GDP 0.004 0.081 -10000 0 -0.27 12 12
TSC1 0.036 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.009 0.11 -10000 0 -0.3 65 65
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.068 -10000 0 -0.24 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0 0.092 0.24 4 -0.33 16 20
MAP3K5 -0.015 0.086 0.19 7 -0.26 46 53
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
apoptosis -0.015 0.086 0.19 7 -0.26 46 53
mol:LY294002 0 0 0.001 2 -0.001 62 64
EIF4B -0.002 0.085 0.24 4 -0.3 16 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.012 0.082 0.26 1 -0.28 14 15
eIF4E/eIF4G1/eIF4A1 0.002 0.075 -10000 0 -0.31 14 14
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.12 -10000 0 -0.27 74 74
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.061 0.22 3 -0.22 10 13
FKBP1A 0.035 0.007 -10000 0 -10000 0 0
RHEB/GTP 0.02 0.091 0.27 2 -0.27 12 14
mol:Amino Acids 0 0 0.001 2 -0.001 62 64
FKBP12/Rapamycin 0.026 0.006 -10000 0 -10000 0 0
PDPK1 -0.033 0.094 0.17 23 -0.26 60 83
EIF4E 0.036 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.035 0.22 -10000 0 -0.59 55 55
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.054 -10000 0 -0.38 1 1
TSC1/TSC2 0.013 0.1 0.28 3 -0.24 43 46
tumor necrosis factor receptor activity 0 0 0.001 62 -0.001 2 64
RPS6 0.034 0.022 -10000 0 -0.42 1 1
PPP5C 0.032 0.041 -10000 0 -0.42 4 4
EIF4G1 0.031 0.041 -10000 0 -0.42 4 4
IRS1 -0.031 0.11 -10000 0 -0.32 65 65
INS 0.034 0.021 -10000 0 -0.42 1 1
PTEN 0.027 0.06 -10000 0 -0.42 9 9
PDK2 -0.032 0.1 0.17 27 -0.26 62 89
EIF4EBP1 -0.068 0.32 -10000 0 -1.2 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PPP2R5D -0.007 0.1 -10000 0 -0.44 15 15
peptide biosynthetic process 0.017 0.03 0.19 5 -0.23 5 10
RHEB 0.035 0.007 -10000 0 -10000 0 0
EIF4A1 0.032 0.012 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 18 -0.003 5 23
EEF2 0.017 0.03 0.19 5 -0.23 5 10
eIF4E/4E-BP1 -0.048 0.3 -10000 0 -1.1 38 38
IL1-mediated signaling events

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
UBC13/UEV1A 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.032 0.03 -10000 0 -0.42 2 2
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.11 -10000 0 -0.37 29 29
IRAK/TOLLIP 0.041 0.017 0.18 5 -10000 0 5
IKBKB 0.03 0.014 -10000 0 -10000 0 0
IKBKG 0.036 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.026 0.09 -10000 0 -0.3 35 35
IL1A 0.032 0.041 -10000 0 -0.42 4 4
IL1B -0.023 0.11 -10000 0 -0.34 53 53
IRAK/TRAF6/p62/Atypical PKCs 0.059 0.05 -10000 0 -0.21 12 12
IL1R2 0.004 0.11 -10000 0 -0.42 31 31
IL1R1 -0.005 0.13 -10000 0 -0.42 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.022 0.12 -10000 0 -0.4 29 29
TOLLIP 0.035 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.013 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.06 0.034 -10000 0 -0.26 2 2
IKK complex/ELKS 0.025 0.079 0.27 1 -0.32 10 11
JUN -0.028 0.068 0.19 5 -0.23 23 28
MAP3K7 0.033 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.006 0.15 -10000 0 -0.28 94 94
IL1 alpha/IL1R1/IL1RAP/MYD88 0.052 0.098 -10000 0 -0.23 50 50
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.1 -10000 0 -0.22 53 53
IL1 beta fragment/IL1R1/IL1RAP -0.011 0.14 -10000 0 -0.29 87 87
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 -0.014 0.059 0.21 8 -0.22 17 25
IRAK1 0.018 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.003 0.13 -10000 0 -0.32 73 73
IRAK4 0.033 0.035 -10000 0 -0.42 3 3
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
PI3K 0.036 0.065 -10000 0 -0.3 17 17
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.018 0.13 -10000 0 -0.38 39 39
CHUK 0.026 0.067 -10000 0 -0.42 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.011 0.14 -10000 0 -0.29 87 87
IL1 beta/IL1R2 -0.019 0.13 -10000 0 -0.3 85 85
IRAK/TRAF6/TAK1/TAB1/TAB2 0.075 0.045 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA -0.004 0.13 -10000 0 -0.28 74 74
IRAK3 0.027 0.046 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.001 0.13 -10000 0 -0.27 88 88
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.084 -10000 0 -0.34 9 9
IL1 alpha/IL1R1/IL1RAP 0.038 0.095 -10000 0 -0.26 46 46
RELA 0.035 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
MYD88 0.031 0.041 -10000 0 -0.42 4 4
IRAK/TRAF6/MEKK3 0.053 0.03 0.2 5 -0.22 1 6
IL1RAP 0.033 0.022 -10000 0 -0.42 1 1
UBE2N 0.035 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.11 -10000 0 -0.24 86 86
CASP1 0.002 0.11 -10000 0 -0.42 30 30
IL1RN/IL1R2 0.003 0.12 -10000 0 -0.32 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.003 0.14 -10000 0 -0.28 88 88
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.11 -10000 0 -0.32 45 45
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL1RN 0.001 0.12 -10000 0 -0.42 37 37
TRAF6/TAK1/TAB1/TAB2 0.071 0.043 -10000 0 -0.21 3 3
MAP2K6 -0.01 0.057 0.21 6 -0.22 14 20
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.007 0.034 -10000 0 -0.097 60 60
STMN1 0.005 0.051 -10000 0 -0.34 10 10
Aurora B/RasGAP/Survivin 0.028 0.1 -10000 0 -0.28 43 43
Chromosomal passenger complex/Cul3 protein complex -0.044 0.12 -10000 0 -0.35 40 40
BIRC5 -0.004 0.12 -10000 0 -0.44 38 38
DES -0.062 0.26 -10000 0 -0.68 72 72
Aurora C/Aurora B/INCENP 0.053 0.049 -10000 0 -0.24 10 10
Aurora B/TACC1 0.023 0.064 -10000 0 -0.25 23 23
Aurora B/PP2A 0.045 0.034 -10000 0 -0.31 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.022 -10000 0 -0.18 6 6
mitotic metaphase/anaphase transition 0.001 0.006 0.014 49 -0.01 2 51
NDC80 0.005 0.025 -10000 0 -0.31 3 3
Cul3 protein complex 0.015 0.12 -10000 0 -0.26 76 76
KIF2C -0.056 0.21 -10000 0 -0.66 49 49
PEBP1 -0.001 0.004 0.01 2 -0.014 38 40
KIF20A 0.004 0.12 -10000 0 -0.42 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.04 0.051 -10000 0 -0.31 9 9
SEPT1 0.031 0.023 -10000 0 -0.42 1 1
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.044 0.18 -10000 0 -0.51 60 60
PSMA3 0.035 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 0.009 52 -0.009 7 59
H3F3B 0.014 0.028 -10000 0 -0.29 4 4
AURKB 0.03 0.04 -10000 0 -0.45 3 3
AURKC 0.034 0.021 -10000 0 -0.42 1 1
CDCA8 0.017 0.085 -10000 0 -0.44 16 16
cytokinesis -0.045 0.23 -10000 0 -0.64 50 50
Aurora B/Septin1 -0.026 0.22 -10000 0 -0.61 45 45
AURKA 0 0.004 0.009 52 -0.009 7 59
INCENP 0.025 0.053 -10000 0 -0.44 6 6
KLHL13 -0.034 0.16 -10000 0 -0.42 73 73
BUB1 -0.012 0.14 -10000 0 -0.42 52 52
hSgo1/Aurora B/Survivin 0.025 0.12 -10000 0 -0.34 39 39
EVI5 0.031 0.041 -10000 0 -0.42 4 4
RhoA/GTP -0.021 0.22 -10000 0 -0.58 49 49
SGOL1 0.02 0.08 -10000 0 -0.42 16 16
CENPA -0.039 0.15 -10000 0 -0.39 55 55
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.045 0.034 -10000 0 -0.31 3 3
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.044 0.043 -10000 0 -0.31 6 6
RHOA 0.026 0.061 -10000 0 -0.42 9 9
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.02 0.12 -10000 0 -0.32 57 57
RASA1 0.029 0.05 -10000 0 -0.42 6 6
KLHL9 0.032 0.03 -10000 0 -0.42 2 2
mitotic prometaphase -0.001 0.004 0.01 2 -0.014 38 40
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.034 -10000 0 -0.31 3 3
PPP1CC 0.033 0.035 -10000 0 -0.42 3 3
Centraspindlin -0.03 0.23 -10000 0 -0.61 52 52
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
NSUN2 -0.017 0.11 -10000 0 -0.3 57 57
MYLK 0.006 0.059 -10000 0 -0.3 17 17
KIF23 0.006 0.11 -10000 0 -0.43 30 30
VIM -0.006 0.072 -10000 0 -0.3 27 27
RACGAP1 0.02 0.085 -10000 0 -0.43 17 17
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.022 0.13 -10000 0 -0.46 21 21
Chromosomal passenger complex -0.048 0.18 -10000 0 -0.46 59 59
Chromosomal passenger complex/EVI5 0.04 0.13 -10000 0 -0.33 48 48
TACC1 0.011 0.089 -10000 0 -0.42 20 20
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
CUL3 0.032 0.041 -10000 0 -0.42 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.02 0.071 -10000 0 -0.29 24 24
PDGFRB 0.029 0.058 -10000 0 -0.43 8 8
SPHK1 -0.034 0.2 -10000 0 -0.76 35 35
mol:S1P -0.019 0.19 -10000 0 -0.65 35 35
S1P1/S1P/Gi -0.018 0.16 0.23 1 -0.48 35 36
GNAO1 0.031 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0 0.14 0.29 2 -0.46 26 28
PLCG1 -0.016 0.14 0.26 2 -0.45 31 33
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.058 -10000 0 -0.43 8 8
GNAI2 0.029 0.055 -10000 0 -0.42 7 7
GNAI3 0.036 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.088 -10000 0 -0.42 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.12 -10000 0 -0.52 23 23
S1P1/S1P -0.01 0.17 0.25 1 -0.45 54 55
negative regulation of cAMP metabolic process -0.017 0.15 0.22 1 -0.46 35 36
MAPK3 -0.011 0.16 0.31 8 -0.54 26 34
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
KDR 0.029 0.058 -10000 0 -0.22 21 21
PLCB2 -0.009 0.15 0.24 1 -0.4 54 55
RAC1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.14 -10000 0 -0.38 54 54
receptor internalization -0.009 0.16 0.24 1 -0.42 54 55
PTGS2 -0.011 0.16 -10000 0 -0.74 15 15
Rac1/GTP -0.013 0.14 -10000 0 -0.38 53 53
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFA -0.003 0.033 -10000 0 -0.15 24 24
negative regulation of T cell proliferation -0.017 0.15 0.22 1 -0.46 35 36
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.07 -10000 0 -0.42 12 12
MAPK1 -0.019 0.15 -10000 0 -0.54 27 27
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.18 0.3 1 -0.45 48 49
ABCC1 0.03 0.042 -10000 0 -0.42 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex -0.072 0.23 -10000 0 -0.53 72 72
RAD9A 0.034 0.01 -10000 0 -10000 0 0
AP1 -0.025 0.15 -10000 0 -0.34 88 88
IFNAR2 0.028 0.03 -10000 0 -0.43 1 1
AKT1 -0.034 0.11 -10000 0 -0.19 133 133
ER alpha/Oestrogen -0.063 0.14 -10000 0 -0.3 132 132
NFX1/SIN3/HDAC complex 0.012 0.072 -10000 0 -0.35 12 12
EGF -0.069 0.19 -10000 0 -0.42 110 110
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.039 0.037 -10000 0 -0.3 1 1
TERT/c-Abl -0.061 0.22 -10000 0 -0.5 73 73
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.048 0.044 -10000 0 -0.26 4 4
WT1 -0.025 0.14 -10000 0 -0.42 54 54
WRN 0.027 0.025 -10000 0 -0.42 1 1
SP1 0.026 0.033 -10000 0 -0.43 1 1
SP3 0.035 0.007 -10000 0 -10000 0 0
TERF2IP 0.03 0.014 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.046 0.21 -10000 0 -0.46 72 72
Mad/Max 0.048 0.019 -10000 0 -10000 0 0
TERT -0.075 0.24 -10000 0 -0.56 67 67
CCND1 -0.15 0.44 -10000 0 -1.1 86 86
MAX 0.034 0.009 -10000 0 -10000 0 0
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
TERF2 0.027 0.031 -10000 0 -0.36 2 2
PTGES3 0.035 0.021 -10000 0 -0.42 1 1
SIN3A 0.035 0.007 -10000 0 -10000 0 0
Telomerase/911 0.021 0.069 -10000 0 -0.46 5 5
CDKN1B -0.028 0.14 -10000 0 -0.37 66 66
RAD1 0.033 0.029 -10000 0 -0.42 2 2
XRCC5 0.036 0.005 -10000 0 -10000 0 0
XRCC6 0.034 0.009 -10000 0 -10000 0 0
SAP30 0.03 0.046 -10000 0 -0.42 5 5
TRF2/PARP2 0.043 0.032 -10000 0 -0.28 2 2
UBE3A 0.034 0.029 -10000 0 -0.42 2 2
JUN -0.002 0.12 -10000 0 -0.42 39 39
E6 -0.001 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.027 -10000 0 -0.3 2 2
FOS -0.032 0.15 -10000 0 -0.42 66 66
IFN-gamma/IRF1 0.001 0.12 -10000 0 -0.3 70 70
PARP2 0.036 0.002 -10000 0 -10000 0 0
BLM 0.012 0.097 -10000 0 -0.42 24 24
Telomerase 0.012 0.044 0.18 1 -10000 0 1
IRF1 0.016 0.083 -10000 0 -0.26 34 34
ESR1 -0.089 0.2 -10000 0 -0.42 132 132
KU/TER 0.05 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.035 -10000 0 -0.18 2 2
ubiquitin-dependent protein catabolic process 0.023 0.06 -10000 0 -0.27 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.025 0.056 -10000 0 -0.28 7 7
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.025 0.032 -10000 0 -0.42 1 1
ATM 0.02 0.025 0.19 2 -10000 0 2
SMAD3 0.011 0.044 -10000 0 -0.3 10 10
ABL1 0.036 0.005 -10000 0 -10000 0 0
MXD1 0.035 0.007 -10000 0 -10000 0 0
MRE11A 0.031 0.013 -10000 0 -10000 0 0
HUS1 0.035 0.006 -10000 0 -10000 0 0
RPS6KB1 0.031 0.013 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.058 0.23 -10000 0 -0.54 67 67
NR2F2 -0.01 0.14 -10000 0 -0.42 49 49
MAPK3 0.008 0.032 -10000 0 -0.3 4 4
MAPK1 0.008 0.032 -10000 0 -0.3 4 4
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
NFKB1 0.036 0.005 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.19 2 -10000 0 2
NBN 0.028 0.025 -10000 0 -0.42 1 1
EGFR -0.015 0.13 -10000 0 -0.42 49 49
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.16 -10000 0 -0.31 152 152
MYC -0.002 0.1 -10000 0 -0.42 29 29
IL2 0.024 0.043 -10000 0 -0.42 3 3
KU 0.05 0.015 -10000 0 -10000 0 0
RAD50 0.032 0.041 -10000 0 -0.42 4 4
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
TRF2/BLM 0.026 0.073 -10000 0 -0.28 25 25
FRAP1 0.035 0.007 -10000 0 -10000 0 0
KU/TERT -0.049 0.23 -10000 0 -0.51 66 66
SP1/HDAC2 0.038 0.043 -10000 0 -0.3 2 2
PINX1 0.028 0.015 -10000 0 -10000 0 0
Telomerase/EST1A -0.059 0.2 -10000 0 -0.46 74 74
Smad3/Myc 0.006 0.074 -10000 0 -0.25 35 35
911 complex 0.063 0.032 -10000 0 -0.26 2 2
IFNG -0.014 0.12 -10000 0 -0.34 56 56
Telomerase/PinX1 -0.057 0.2 -10000 0 -0.47 69 69
Telomerase/AKT1/mTOR/p70S6K -0.006 0.1 -10000 0 -0.41 17 17
SIN3B 0.036 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
Telomerase/EST1B -0.059 0.2 -10000 0 -0.46 74 74
response to DNA damage stimulus -0.001 0.033 0.13 1 -0.1 35 36
MRN complex/TRF2/Rap1 0.059 0.061 -10000 0 -0.25 5 5
TRF2/WRN 0.034 0.036 -10000 0 -0.28 3 3
Telomerase/hnRNP C1/C2 -0.059 0.2 -10000 0 -0.46 74 74
E2F1 0.021 0.057 -10000 0 -0.42 7 7
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.036 0.006 -10000 0 -10000 0 0
DKC1 0.036 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.047 0.055 -10000 0 -0.23 16 16
RGS9BP -0.023 0.15 -10000 0 -0.42 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.024 0.061 -10000 0 -0.26 19 19
mol:ADP 0.008 0.019 -10000 0 -0.3 2 2
GNAT2 0.019 0.085 -10000 0 -0.42 18 18
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.026 0.076 -10000 0 -0.27 30 30
GRK7 0.034 0.029 -10000 0 -0.42 2 2
CNGB3 0.022 0.051 -10000 0 -0.42 6 6
Cone Metarhodopsin II/X-Arrestin 0.027 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.04 0.089 0.2 91 -0.24 20 111
Cone PDE6 0.02 0.13 -10000 0 -0.24 84 84
Cone Metarhodopsin II 0.022 0.016 -10000 0 -0.22 2 2
Na + (4 Units) 0.038 0.064 -10000 0 -0.24 20 20
GNAT2/GDP 0.011 0.12 -10000 0 -0.24 85 85
GNB5 0.025 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) 0.005 0.078 0.19 16 -0.25 34 50
Cone Transducin 0.051 0.059 -10000 0 -0.24 16 16
SLC24A2 0.032 0.036 -10000 0 -0.42 3 3
GNB3/GNGT2 0.048 0.023 -10000 0 -0.3 1 1
GNB3 0.034 0.009 -10000 0 -10000 0 0
GNAT2/GTP 0.015 0.06 -10000 0 -0.3 18 18
CNGA3 0.018 0.078 -10000 0 -0.42 15 15
ARR3 0.036 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.025 0.061 -10000 0 -0.26 19 19
mol:Pi 0.006 0.12 -10000 0 -0.27 73 73
Cone CNG Channel 0.034 0.099 -10000 0 -0.25 44 44
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.032 0.036 -10000 0 -0.42 3 3
RGS9 0.017 0.07 -10000 0 -0.42 12 12
PDE6C 0.03 0.05 -10000 0 -0.42 6 6
GNGT2 0.033 0.03 -10000 0 -0.42 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.021 0.075 -10000 0 -0.42 14 14
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.031 0.24 -10000 0 -0.76 23 23
PCK1 0.019 0.17 -10000 0 -0.99 5 5
HNF4A -0.01 0.25 0.56 3 -0.77 21 24
KCNJ11 -0.053 0.34 -10000 0 -0.98 44 44
AKT1 -0.001 0.17 -10000 0 -0.41 22 22
response to starvation 0.004 0.002 -10000 0 -10000 0 0
DLK1 -0.023 0.27 0.63 1 -0.8 22 23
NKX2-1 0.038 0.13 0.36 4 -0.35 6 10
ACADM -0.032 0.26 -10000 0 -0.78 27 27
TAT -0.004 0.15 -10000 0 -0.64 2 2
CEBPB 0.031 0.051 -10000 0 -0.42 6 6
CEBPA 0.03 0.07 -10000 0 -0.42 12 12
TTR -0.03 0.28 0.57 1 -0.73 39 40
PKLR 0.013 0.25 -10000 0 -0.72 21 21
APOA1 -0.028 0.28 -10000 0 -0.88 22 22
CPT1C -0.031 0.27 -10000 0 -0.82 29 29
ALAS1 0.011 0.18 -10000 0 -1.1 4 4
TFRC -0.042 0.36 -10000 0 -1.2 37 37
FOXF1 0.027 0.025 -10000 0 -0.42 1 1
NF1 0.037 0.035 -10000 0 -0.37 3 3
HNF1A (dimer) 0.008 0.02 -10000 0 -0.21 4 4
CPT1A -0.023 0.27 0.56 1 -0.86 24 25
HMGCS1 -0.021 0.24 -10000 0 -0.74 23 23
NR3C1 0.034 0.074 -10000 0 -0.4 14 14
CPT1B -0.024 0.24 -10000 0 -0.75 22 22
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.021 -10000 0 -0.42 1 1
GCK -0.025 0.25 -10000 0 -0.76 24 24
CREB1 0.042 0.029 -10000 0 -0.24 4 4
IGFBP1 0.01 0.14 -10000 0 -1.3 1 1
PDX1 0.006 0.15 -10000 0 -0.37 23 23
UCP2 -0.052 0.31 -10000 0 -0.86 46 46
ALDOB -0.024 0.26 -10000 0 -0.79 23 23
AFP -0.024 0.12 -10000 0 -0.69 4 4
BDH1 -0.034 0.26 -10000 0 -0.77 31 31
HADH -0.024 0.26 -10000 0 -0.63 48 48
F2 -0.01 0.28 -10000 0 -0.86 22 22
HNF1A 0.008 0.02 -10000 0 -0.21 4 4
G6PC 0.04 0.091 -10000 0 -1.3 1 1
SLC2A2 0.003 0.2 -10000 0 -0.82 8 8
INS 0.024 0.024 -10000 0 -0.43 1 1
FOXA1 -0.037 0.18 -10000 0 -0.4 97 97
FOXA3 0.043 0.077 -10000 0 -0.26 8 8
FOXA2 -0.011 0.32 -10000 0 -0.78 35 35
ABCC8 -0.2 0.48 -10000 0 -0.9 151 151
ALB -0.03 0.15 -10000 0 -0.95 7 7
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.019 0.11 -10000 0 -0.27 53 53
fibroblast growth factor receptor signaling pathway 0.018 0.1 -10000 0 -0.27 53 53
LAMA1 0.034 0.009 -10000 0 -10000 0 0
PRNP 0.028 0.057 -10000 0 -0.42 8 8
GPC1/SLIT2 0.013 0.11 -10000 0 -0.31 52 52
SMAD2 0.005 0.064 0.19 6 -0.24 29 35
GPC1/PrPc/Cu2+ 0.03 0.069 -10000 0 -0.26 26 26
GPC1/Laminin alpha1 0.036 0.068 -10000 0 -0.3 19 19
TDGF1 0.034 0.008 -10000 0 -10000 0 0
CRIPTO/GPC1 0.037 0.068 -10000 0 -0.3 19 19
APP/GPC1 0.016 0.1 -10000 0 -0.3 47 47
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.06 -10000 0 -0.26 25 25
FLT1 0.026 0.058 -10000 0 -0.42 8 8
GPC1/TGFB/TGFBR1/TGFBR2 0.049 0.081 -10000 0 -0.26 30 30
SERPINC1 0.028 0.025 -10000 0 -0.42 1 1
FYN 0.005 0.057 -10000 0 -0.26 23 23
FGR 0.009 0.053 -10000 0 -0.26 19 19
positive regulation of MAPKKK cascade -0.025 0.12 -10000 0 -0.34 43 43
SLIT2 0.003 0.12 -10000 0 -0.42 35 35
GPC1/NRG 0.028 0.068 -10000 0 -0.3 19 19
NRG1 0.028 0.015 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.027 0.07 -10000 0 -0.26 26 26
LYN 0.009 0.045 -10000 0 -0.25 14 14
mol:Spermine -0.003 0.058 -10000 0 -0.3 19 19
cell growth 0.018 0.1 -10000 0 -0.27 53 53
BMP signaling pathway -0.018 0.087 0.42 19 -10000 0 19
SRC 0.008 0.055 -10000 0 -0.27 19 19
TGFBR1 0.027 0.061 -10000 0 -0.42 9 9
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.013 0.08 -10000 0 -0.42 16 16
GPC1 0.018 0.087 -10000 0 -0.42 19 19
TGFBR1 (dimer) 0.027 0.06 -10000 0 -0.42 9 9
VEGFA 0 0 -10000 0 -10000 0 0
BLK 0.006 0.046 -10000 0 -0.25 15 15
HCK 0.001 0.068 -10000 0 -0.26 33 33
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.02 0.064 -10000 0 -0.42 10 10
VEGFR1 homodimer 0.026 0.057 -10000 0 -0.42 8 8
TGFBR2 0.033 0.036 -10000 0 -0.42 3 3
cell death 0.016 0.1 -10000 0 -0.3 47 47
ATIII/GPC1 0.03 0.065 -10000 0 -0.3 17 17
PLA2G2A/GPC1 0.022 0.09 -10000 0 -0.3 34 34
LCK -0.019 0.095 -10000 0 -0.26 68 68
neuron differentiation 0.028 0.068 -10000 0 -0.3 19 19
PrPc/Cu2+ 0.021 0.04 -10000 0 -0.3 8 8
APP 0.008 0.11 -10000 0 -0.42 29 29
TGFBR2 (dimer) 0.033 0.036 -10000 0 -0.42 3 3
PLK1 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
regulation of centriole-centriole cohesion -0.001 0.047 0.2 23 -0.12 5 28
BUB1B -0.019 0.097 0.11 2 -0.3 43 45
PLK1 0.003 0.033 0.091 10 -0.09 19 29
PLK1S1 0.002 0.019 0.054 10 -0.049 17 27
KIF2A 0.003 0.03 0.08 10 -0.081 19 29
regulation of mitotic centrosome separation 0.003 0.033 0.09 10 -0.089 19 29
GOLGA2 0.036 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.008 0.019 -10000 0 -0.071 26 26
WEE1 -0.006 0.094 -10000 0 -0.36 25 25
cytokinesis -0.022 0.14 -10000 0 -0.44 40 40
PP2A-alpha B56 -0.036 0.28 -10000 0 -0.7 72 72
AURKA 0.002 0.02 0.06 11 -0.051 10 21
PICH/PLK1 -0.018 0.095 -10000 0 -0.33 35 35
CENPE -0.012 0.068 0.2 3 -0.25 31 34
RhoA/GTP 0.02 0.043 -10000 0 -0.3 9 9
positive regulation of microtubule depolymerization 0.003 0.03 0.08 10 -0.08 19 29
PPP2CA 0.031 0.045 -10000 0 -0.42 5 5
FZR1 0.035 0.006 -10000 0 -10000 0 0
TPX2 -0.008 0.078 -10000 0 -0.27 39 39
PAK1 0.014 0.086 -10000 0 -0.43 18 18
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
CLSPN 0.004 0.057 -10000 0 -0.28 18 18
GORASP1 0.034 0.022 -10000 0 -0.42 1 1
metaphase 0.002 0.006 0.019 46 -10000 0 46
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 0.054 10 -0.049 17 27
G2 phase of mitotic cell cycle -0.001 0.002 0.011 2 -10000 0 2
STAG2 0.036 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.007 0.11 -10000 0 -0.51 20 20
spindle elongation 0.003 0.033 0.09 10 -0.089 19 29
ODF2 0.036 0.005 -10000 0 -10000 0 0
BUB1 -0.074 0.29 -10000 0 -0.75 74 74
TPT1 -0.009 0.063 -10000 0 -0.19 52 52
CDC25C -0.014 0.11 -10000 0 -0.36 42 42
CDC25B 0.028 0.045 -10000 0 -0.44 4 4
SGOL1 0.001 0.047 0.12 5 -0.2 23 28
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CCNB1/CDK1 0.028 0.13 -10000 0 -0.4 35 35
CDC14B 0.005 0.024 -10000 0 -0.3 3 3
CDC20 0.017 0.087 -10000 0 -0.42 19 19
PLK1/PBIP1 -0.005 0.056 0.096 1 -0.22 27 28
mitosis 0 0.003 0.013 10 -10000 0 10
FBXO5 -0.003 0.05 0.13 9 -0.21 9 18
CDC2 0.014 0.097 -10000 0 -0.44 22 22
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.004 0.054 -10000 0 -0.25 20 20
ERCC6L -0.013 0.11 -10000 0 -0.38 35 35
NLP/gamma Tubulin 0.007 0.028 0.072 14 -0.083 10 24
microtubule cytoskeleton organization -0.009 0.063 -10000 0 -0.19 52 52
G2/M transition DNA damage checkpoint 0 0.003 0.011 19 -10000 0 19
PPP1R12A 0.036 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.011 19 -10000 0 19
PLK1/PRC1-2 0.014 0.11 -10000 0 -0.33 42 42
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.048 -10000 0 -0.19 2 2
RAB1A 0.035 0.021 -10000 0 -0.42 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.025 0.069 13 -0.069 13 26
mitotic prometaphase -0.001 0.004 0.018 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.054 -10000 0 -0.35 4 4
microtubule-based process 0.006 0.078 0.12 2 -0.25 36 38
Golgi organization 0.003 0.033 0.09 10 -0.089 19 29
Cohesin/SA2 0.021 0.035 0.11 2 -0.11 1 3
PPP1CB/MYPT1 0.052 0.009 -10000 0 -10000 0 0
KIF20A 0.003 0.12 -10000 0 -0.42 35 35
APC/C/CDC20 0.013 0.064 0.12 1 -0.25 20 21
PPP2R1A 0.035 0.007 -10000 0 -10000 0 0
chromosome segregation -0.005 0.055 0.095 1 -0.21 27 28
PRC1 0.009 0.1 -10000 0 -0.42 27 27
ECT2 0.004 0.072 0.23 25 -0.23 16 41
C13orf34 0.003 0.028 0.074 13 -0.078 15 28
NUDC 0.004 0.054 -10000 0 -0.25 20 20
regulation of attachment of spindle microtubules to kinetochore -0.018 0.096 0.11 2 -0.3 43 45
spindle assembly 0.01 0.035 0.091 19 -0.082 12 31
spindle stabilization 0.002 0.019 0.054 10 -0.049 17 27
APC/C/HCDH1 0.03 0.023 -10000 0 -0.25 3 3
MKLP2/PLK1 0.006 0.078 0.12 2 -0.25 36 38
CCNB1 0.011 0.1 -10000 0 -0.44 25 25
PPP1CB 0.036 0.005 -10000 0 -10000 0 0
BTRC 0.034 0.022 -10000 0 -0.42 1 1
ROCK2 0.007 0.059 -10000 0 -0.32 9 9
TUBG1 0.009 0.04 -10000 0 -0.18 16 16
G2/M transition of mitotic cell cycle -0.022 0.11 -10000 0 -0.39 35 35
MLF1IP -0.009 0.069 -10000 0 -0.3 27 27
INCENP 0.028 0.051 -10000 0 -0.43 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.025 -10000 0 -0.42 1 1
Caspase 8 (4 units) 0.029 0.13 -10000 0 -0.4 23 23
NEF -0.011 0.049 -10000 0 -0.17 45 45
NFKBIA 0.022 0.05 -10000 0 -0.35 3 3
BIRC3 -0.012 0.14 -10000 0 -0.46 40 40
CYCS -0.005 0.12 0.19 4 -0.33 40 44
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CD247 -0.011 0.049 -10000 0 -0.17 45 45
MAP2K7 0.004 0.18 -10000 0 -0.78 15 15
protein ubiquitination -0.015 0.12 0.22 2 -0.37 23 25
CRADD 0.03 0.05 -10000 0 -0.42 6 6
DAXX 0.036 0.006 -10000 0 -10000 0 0
FAS 0.008 0.11 -10000 0 -0.42 29 29
BID -0.006 0.12 -10000 0 -0.3 57 57
NF-kappa-B/RelA/I kappa B alpha 0.042 0.099 -10000 0 -0.26 39 39
TRADD 0.03 0.014 -10000 0 -10000 0 0
MAP3K5 0.012 0.095 -10000 0 -0.42 23 23
CFLAR 0.031 0.045 -10000 0 -0.42 5 5
FADD 0.029 0.014 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.042 0.1 -10000 0 -0.26 39 39
MAPK8 0.003 0.16 0.42 1 -0.69 15 16
APAF1 0.032 0.041 -10000 0 -0.42 4 4
TRAF1 0.035 0.021 -10000 0 -0.42 1 1
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.13 -10000 0 -0.31 54 54
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.014 0.14 -10000 0 -0.42 29 29
CHUK -0.019 0.13 0.22 2 -0.4 24 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.095 -10000 0 -0.24 35 35
TCRz/NEF -0.017 0.083 -10000 0 -0.28 45 45
TNF 0.026 0.061 -10000 0 -0.42 9 9
FASLG -0.022 0.14 -10000 0 -0.52 36 36
NFKB1 0.023 0.041 -10000 0 -0.14 2 2
TNFR1A/BAG4/TNF-alpha 0.048 0.047 -10000 0 -0.25 6 6
CASP6 0.022 0.16 -10000 0 -0.55 21 21
CASP7 -0.041 0.2 0.29 1 -0.47 68 69
RELA 0.023 0.042 -10000 0 -0.14 3 3
CASP2 0.035 0.008 -10000 0 -10000 0 0
CASP3 -0.04 0.19 -10000 0 -0.47 64 64
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
TNFR1A/BAG4 0.039 0.028 -10000 0 -0.3 1 1
CASP8 0.036 0.004 -10000 0 -10000 0 0
CASP9 0.034 0.022 -10000 0 -0.42 1 1
MAP3K14 -0.013 0.13 0.24 2 -0.45 21 23
APAF-1/Caspase 9 -0.014 0.14 0.2 1 -0.34 55 56
BCL2 -0.031 0.16 0.58 1 -0.57 19 20
Calcium signaling in the CD4+ TCR 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
NFATC1 0.008 0.055 -10000 0 -0.25 16 16
NFATC2 0.014 0.035 -10000 0 -0.27 3 3
NFATC3 0.016 0.026 -10000 0 -10000 0 0
CD40LG -0.019 0.18 0.38 3 -0.44 52 55
PTGS2 -0.022 0.17 0.38 3 -0.43 48 51
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.11 1 1
CaM/Ca2+ 0.021 0.025 -10000 0 -0.11 1 1
CALM1 0.033 0.019 -10000 0 -10000 0 0
JUN -0.002 0.12 -10000 0 -0.42 39 39
mol:Ca2+ -0.001 0.009 -10000 0 -0.082 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.01 -10000 0 -10000 0 0
FOSL1 0.035 0.007 -10000 0 -10000 0 0
CREM 0.035 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.12 -10000 0 -0.32 29 29
FOS -0.033 0.15 -10000 0 -0.42 66 66
IFNG -0.035 0.2 0.38 3 -0.5 59 62
AP-1/NFAT1-c-4 0.003 0.22 -10000 0 -0.5 53 53
FASLG -0.031 0.2 0.38 3 -0.51 53 56
NFAT1-c-4/ICER1 0.028 0.08 0.23 2 -0.23 16 18
IL2RA -0.029 0.2 0.38 3 -0.48 60 63
FKBP12/FK506 0.026 0.005 -10000 0 -10000 0 0
CSF2 -0.019 0.18 0.38 3 -0.44 53 56
JunB/Fra1/NFAT1-c-4 0.045 0.092 -10000 0 -0.28 9 9
IL4 -0.019 0.18 0.38 3 -0.43 56 59
IL2 0.009 0.15 -10000 0 -1 10 10
IL3 0.02 0.12 -10000 0 -0.7 12 12
FKBP1A 0.035 0.007 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.034 0.017 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.018 0.059 0.19 12 -0.2 19 31
DAPP1 -0.04 0.16 -10000 0 -0.4 62 62
Src family/SYK family/BLNK-LAT/BTK-ITK -0.061 0.23 -10000 0 -0.57 62 62
mol:DAG -0.017 0.092 0.2 6 -0.23 46 52
HRAS 0.031 0.038 -10000 0 -0.42 3 3
RAP1A 0.03 0.047 -10000 0 -0.42 5 5
ARF5/GDP -0.004 0.11 -10000 0 -0.32 29 29
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
PLCG1 0.034 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.021 -10000 0 -0.42 1 1
mol:GTP -0.018 0.06 0.19 14 -0.21 19 33
ARF1/GTP -0.009 0.052 0.22 8 -0.2 16 24
RHOA 0.026 0.061 -10000 0 -0.42 9 9
YES1 0.029 0.05 -10000 0 -0.42 6 6
RAP1A/GTP -0.017 0.061 0.18 28 -0.21 19 47
ADAP1 -0.018 0.056 0.18 13 -0.2 19 32
ARAP3 -0.018 0.06 0.19 14 -0.21 19 33
INPPL1 0.031 0.036 -10000 0 -0.42 3 3
PREX1 -0.036 0.16 -10000 0 -0.42 75 75
ARHGEF6 0.015 0.093 -10000 0 -0.42 22 22
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
ARF1 0.027 0.025 -10000 0 -0.42 1 1
NRAS 0.028 0.054 -10000 0 -0.41 7 7
FYN 0.027 0.054 -10000 0 -0.42 7 7
ARF6 0.034 0.029 -10000 0 -0.42 2 2
FGR 0.035 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.05 0.15 8 -0.13 19 27
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
ZAP70 0.033 0.022 -10000 0 -0.42 1 1
mol:IP3 -0.016 0.067 0.18 8 -0.18 28 36
LYN 0.03 0.014 -10000 0 -10000 0 0
ARF1/GDP -0.002 0.1 -10000 0 -0.33 24 24
RhoA/GDP 0.012 0.091 0.23 6 -0.26 23 29
PDK1/Src/Hsp90 0.042 0.025 -10000 0 -0.25 2 2
BLNK 0.013 0.099 -10000 0 -0.42 25 25
actin cytoskeleton reorganization -0.021 0.11 0.23 5 -0.37 19 24
SRC 0.033 0.029 -10000 0 -0.42 2 2
PLEKHA2 -0.009 0.022 -10000 0 -0.25 4 4
RAC1 0.035 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.059 -10000 0 -0.4 9 9
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.019 0.059 0.17 28 -0.2 19 47
RhoA/GTP -0.022 0.067 0.17 27 -0.24 23 50
Src family/SYK family/BLNK-LAT -0.027 0.16 -10000 0 -0.44 50 50
BLK 0.022 0.038 -10000 0 -0.42 3 3
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
CYTH1 -0.018 0.056 0.18 13 -0.2 19 32
HCK 0.018 0.087 -10000 0 -0.42 19 19
CYTH3 -0.018 0.056 0.18 13 -0.2 19 32
CYTH2 -0.018 0.056 0.18 13 -0.2 19 32
KRAS 0.027 0.055 -10000 0 -0.42 7 7
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.038 0.21 3 -0.19 3 6
SGK1 0.008 0.039 0.17 7 -0.2 3 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.11 -10000 0 -0.32 33 33
SOS1 0.035 0.021 -10000 0 -0.42 1 1
SYK 0.005 0.11 -10000 0 -0.42 34 34
ARF6/GDP -0.003 0.075 0.22 6 -0.26 12 18
mol:PI-3-4-5-P3 -0.018 0.06 0.21 13 -0.21 19 32
ARAP3/RAP1A/GTP -0.017 0.061 0.18 28 -0.21 19 47
VAV1 0.019 0.082 -10000 0 -0.42 17 17
mol:PI-3-4-P2 0.006 0.023 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.045 0.064 0.22 17 -0.21 19 36
PLEKHA1 -0.011 0.029 -10000 0 -0.25 7 7
Rac1/GDP -0.003 0.11 -10000 0 -0.33 28 28
LAT 0.03 0.031 -10000 0 -0.42 2 2
Rac1/GTP -0.018 0.12 -10000 0 -0.35 36 36
ITK -0.032 0.073 0.19 11 -0.22 46 57
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.24 5 -0.31 50 55
LCK -0.017 0.14 -10000 0 -0.42 54 54
BTK -0.025 0.068 0.19 12 -0.23 29 41
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.041 0.11 -10000 0 -0.46 18 18
HDAC1 0.04 0.028 -10000 0 -0.42 1 1
AES 0.037 0.009 -10000 0 -10000 0 0
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
DTX1 0.033 0.035 -10000 0 -0.42 3 3
LRP6/FZD1 0.041 0.055 -10000 0 -0.3 12 12
TLE1 0.006 0.11 -10000 0 -0.42 33 33
AP1 -0.025 0.11 -10000 0 -0.3 55 55
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
ADAM10 0.033 0.03 -10000 0 -0.42 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.037 0.15 -10000 0 -0.53 16 16
NICD/RBPSUH 0.005 0.097 -10000 0 -0.46 18 18
WIF1 0.03 0.014 -10000 0 -10000 0 0
NOTCH1 0.014 0.099 -10000 0 -0.48 18 18
PSENEN 0.035 0.006 -10000 0 -10000 0 0
KREMEN2 -0.09 0.19 -10000 0 -0.42 129 129
DKK1 -0.027 0.14 -10000 0 -0.42 60 60
beta catenin/beta TrCP1 0.012 0.1 0.28 1 -0.36 15 16
APH1B 0.025 0.067 -10000 0 -0.42 11 11
APH1A 0.031 0.036 -10000 0 -0.42 3 3
AXIN1 0.015 0.053 0.26 1 -0.39 2 3
CtBP/CBP/TCF1/TLE1/AES 0.027 0.089 0.29 3 -0.24 28 31
PSEN1 0.032 0.041 -10000 0 -0.42 4 4
FOS -0.031 0.15 -10000 0 -0.42 66 66
JUN -0.001 0.12 -10000 0 -0.42 39 39
MAP3K7 0.036 0.014 -10000 0 -10000 0 0
CTNNB1 -0.004 0.097 0.28 1 -0.37 15 16
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
DKK2/LRP6/Kremen 2 -0.044 0.15 -10000 0 -0.26 154 154
HNF1A 0.002 0.006 -10000 0 -10000 0 0
CTBP1 0.036 0.01 -10000 0 -10000 0 0
MYC -0.083 0.35 -10000 0 -1.3 35 35
NKD1 0.028 0.038 -10000 0 -0.42 3 3
FZD1 0.028 0.057 -10000 0 -0.42 8 8
NOTCH1 precursor/Deltex homolog 1 0.042 0.11 -10000 0 -0.47 18 18
apoptosis -0.025 0.11 -10000 0 -0.3 55 55
Delta 1/NOTCHprecursor 0.04 0.11 -10000 0 -0.46 18 18
DLL1 0.034 0.01 -10000 0 -10000 0 0
PPARD 0.006 0.11 -10000 0 -0.9 6 6
Gamma Secretase 0.069 0.068 -10000 0 -0.22 13 13
APC -0.001 0.1 0.26 1 -0.44 20 21
DVL1 0.025 0.028 -10000 0 -0.27 1 1
CSNK2A1 0.035 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0.037 0.012 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.061 0.16 -10000 0 -0.27 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.035 0.006 -10000 0 -10000 0 0
NLK 0.029 0.025 -10000 0 -0.24 1 1
CCND1 -0.2 0.5 -10000 0 -1.3 84 84
WNT1 0.035 0.021 -10000 0 -0.42 1 1
Axin1/APC/beta catenin 0.021 0.1 0.34 2 -0.45 9 11
DKK2 0.006 0.11 -10000 0 -0.42 31 31
NOTCH1 precursor/DVL1 0.037 0.1 -10000 0 -0.53 10 10
GSK3B 0.036 0.005 -10000 0 -10000 0 0
FRAT1 0.03 0.054 -10000 0 -0.42 7 7
NOTCH/Deltex homolog 1 0.043 0.11 -10000 0 -0.47 18 18
PPP2R5D 0.012 0.068 0.23 3 -0.32 17 20
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
WNT1/LRP6/FZD1 0.071 0.058 -10000 0 -0.23 13 13
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.026 0.02 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.007 0.054 -10000 0 -0.3 15 15
MAP4K4 -0.024 0.11 0.22 3 -0.33 34 37
BAG4 0.028 0.025 -10000 0 -0.42 1 1
PKC zeta/ceramide -0.008 0.048 0.12 3 -0.22 14 17
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BAX 0.011 0.034 -10000 0 -0.37 2 2
RIPK1 0.035 0.007 -10000 0 -10000 0 0
AKT1 0.002 0.082 0.66 7 -0.39 2 9
BAD -0.011 0.05 0.19 2 -0.23 12 14
SMPD1 0.007 0.065 0.18 3 -0.23 17 20
RB1 -0.015 0.057 0.19 1 -0.23 21 22
FADD/Caspase 8 0.011 0.12 0.28 4 -0.35 18 22
MAP2K4 -0.022 0.064 0.19 2 -0.22 35 37
NSMAF 0.027 0.042 -10000 0 -0.42 4 4
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.054 0.19 8 -0.24 10 18
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:ceramide -0.008 0.052 0.13 10 -0.23 14 24
MADD 0.036 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.005 0.075 -10000 0 -0.31 28 28
ASAH1 0.009 0.088 -10000 0 -0.42 20 20
negative regulation of cell cycle -0.015 0.057 0.18 2 -0.23 21 23
cell proliferation -0.011 0.092 0.24 1 -0.22 29 30
BID -0.013 0.14 -10000 0 -0.62 17 17
MAP3K1 -0.02 0.066 0.21 1 -0.22 37 38
EIF2A -0.014 0.064 0.2 11 -0.22 22 33
TRADD 0.03 0.014 -10000 0 -10000 0 0
CRADD 0.03 0.05 -10000 0 -0.42 6 6
MAPK3 -0.007 0.053 0.2 4 -0.23 10 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.061 0.2 3 -0.26 10 13
Cathepsin D/ceramide 0.006 0.06 -10000 0 -0.22 19 19
FADD 0.007 0.11 0.22 53 -0.33 21 74
KSR1 -0.009 0.051 0.19 3 -0.23 12 15
MAPK8 -0.012 0.06 0.15 1 -0.21 23 24
PRKRA -0.009 0.051 0.19 3 -0.23 13 16
PDGFA 0.021 0.082 -10000 0 -0.42 17 17
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
IGF1 -0.038 0.16 -10000 0 -0.42 78 78
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.052 0.13 10 -0.23 14 24
CTSD 0.029 0.046 -10000 0 -0.42 5 5
regulation of nitric oxide biosynthetic process 0.051 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.011 0.098 0.25 1 -0.24 29 30
PRKCD 0.033 0.03 -10000 0 -0.42 2 2
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.005 0.075 -10000 0 -0.31 28 28
RelA/NF kappa B1 0.051 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.072 -10000 0 -0.42 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.1 -10000 0 -0.36 26 26
TNFR1A/BAG4/TNF-alpha 0.048 0.047 -10000 0 -0.25 6 6
mol:Sphingosine-1-phosphate 0.007 0.054 -10000 0 -0.3 15 15
MAP2K1 -0.01 0.053 0.18 9 -0.23 9 18
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
CYCS 0.031 0.07 0.16 65 -0.21 4 69
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
NFKB1 0.036 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.028 -10000 0 -0.3 1 1
EIF2AK2 -0.017 0.06 0.17 5 -0.22 24 29
TNF-alpha/TNFR1A/FAN 0.051 0.05 -10000 0 -0.25 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.091 -10000 0 -0.38 13 13
MAP2K2 -0.011 0.054 0.2 4 -0.23 10 14
SMPD3 -0.026 0.12 0.19 1 -0.3 74 75
TNF 0.026 0.061 -10000 0 -0.42 9 9
PKC zeta/PAR4 0.018 0.051 -10000 0 -0.3 13 13
mol:PHOSPHOCHOLINE 0.037 0.095 0.21 103 -0.2 4 107
NF kappa B1/RelA/I kappa B alpha 0.069 0.057 -10000 0 -0.22 15 15
AIFM1 0.027 0.066 0.15 67 -0.17 8 75
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.13 -10000 0 -0.42 45 45
positive regulation of NF-kappaB transcription factor activity 0.01 0.097 -10000 0 -0.29 45 45
MAP2K4 -0.009 0.1 -10000 0 -0.36 25 25
IKBKB 0.03 0.014 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.047 -10000 0 -0.42 5 5
SMPD1 -0.006 0.071 -10000 0 -0.21 44 44
IKBKG 0.036 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.028 0.016 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.009 0.099 -10000 0 -0.3 45 45
TRAIL/TRAILR3 0.008 0.097 -10000 0 -0.29 46 46
TRAIL/TRAILR1 0.007 0.1 -10000 0 -0.31 47 47
TRAIL/TRAILR4 0.01 0.097 -10000 0 -0.29 45 45
TRAIL/TRAILR1/DAP3/GTP 0.02 0.08 -10000 0 -0.24 36 36
IKK complex 0.013 0.092 -10000 0 -0.4 14 14
RIPK1 0.035 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.018 -10000 0 -0.3 1 1
MAPK3 -0.01 0.085 -10000 0 -0.3 40 40
MAP3K1 -0.006 0.11 -10000 0 -0.38 26 26
TRAILR4 (trimer) 0.027 0.016 -10000 0 -10000 0 0
TRADD 0.03 0.014 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.047 -10000 0 -0.42 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.002 0.085 -10000 0 -0.29 34 34
CFLAR 0.031 0.045 -10000 0 -0.42 5 5
MAPK1 -0.009 0.083 -10000 0 -0.3 38 38
TRAIL/TRAILR1/FADD/TRADD/RIP 0.035 0.09 -10000 0 -0.23 33 33
mol:ceramide -0.006 0.071 -10000 0 -0.21 44 44
FADD 0.029 0.014 -10000 0 -10000 0 0
MAPK8 -0.022 0.11 -10000 0 -0.35 30 30
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
TRAILR3 (trimer) 0.024 0.026 -10000 0 -0.42 1 1
CHUK 0.026 0.067 -10000 0 -0.42 11 11
TRAIL/TRAILR1/FADD 0.023 0.087 -10000 0 -0.26 34 34
DAP3 0.028 0.025 -10000 0 -0.42 1 1
CASP10 0.014 0.083 0.33 4 -0.29 18 22
JNK cascade 0.01 0.097 -10000 0 -0.29 45 45
TRAIL (trimer) -0.007 0.13 -10000 0 -0.42 45 45
TNFRSF10C 0.024 0.026 -10000 0 -0.42 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.027 0.075 -10000 0 -0.22 27 27
TRAIL/TRAILR2/FADD 0.025 0.083 -10000 0 -0.26 33 33
cell death -0.006 0.071 -10000 0 -0.21 44 44
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.083 -10000 0 -0.28 33 33
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.025 0.043 -10000 0 -0.66 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.037 0.086 -10000 0 -0.22 32 32
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.012 0.11 -10000 0 -0.23 75 75
TC10/GTP 0.029 0.068 -10000 0 -0.21 34 34
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.11 -10000 0 -0.25 55 55
HRAS 0.032 0.036 -10000 0 -0.42 3 3
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
FOXO3 -0.014 0.022 -10000 0 -10000 0 0
AKT1 -0.045 0.13 0.31 7 -0.36 17 24
INSR 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.081 0.06 -10000 0 -0.46 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.023 0.075 -10000 0 -0.42 14 14
SORBS1 0.007 0.11 -10000 0 -0.42 29 29
CRK 0.032 0.023 -10000 0 -0.42 1 1
PTPN1 0.005 0.038 -10000 0 -0.45 2 2
CAV1 -0.008 0.083 0.18 4 -0.23 58 62
CBL/APS/CAP/Crk-II/C3G 0.052 0.075 -10000 0 -0.22 30 30
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.11 -10000 0 -0.25 53 53
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.1 -10000 0 -0.22 66 66
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.08 -10000 0 -0.45 5 5
RPS6KB1 -0.04 0.11 0.28 7 -0.34 16 23
PARD6A 0.021 0.061 -10000 0 -0.42 9 9
CBL 0.032 0.012 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.007 0.11 -10000 0 -0.67 12 12
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.004 0.12 0.28 3 -0.34 18 21
HRAS/GTP -0.001 0.063 -10000 0 -0.21 37 37
Insulin Receptor 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.049 0.1 -10000 0 -0.23 42 42
PRKCI 0.004 0.11 -10000 0 -0.48 22 22
Insulin Receptor/Insulin/GRB14/PDK1 -0.036 0.12 -10000 0 -0.23 134 134
SHC1 0.028 0.025 -10000 0 -0.42 1 1
negative regulation of MAPKKK cascade 0.046 0.11 -10000 0 -0.6 12 12
PI3K 0.04 0.11 -10000 0 -0.23 66 66
NCK2 0.036 0.005 -10000 0 -10000 0 0
RHOQ 0.031 0.045 -10000 0 -0.42 5 5
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.024 0.025 -10000 0 -0.3 3 3
AKT2 -0.046 0.13 0.31 7 -0.37 16 23
PRKCZ -0.008 0.084 -10000 0 -0.42 16 16
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.001 0.069 0.18 1 -0.21 44 45
F2RL2 -0.02 0.14 -10000 0 -0.42 58 58
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
Insulin Receptor/Insulin/Shc 0.054 0.041 -10000 0 -0.22 3 3
TC10/GTP/CIP4/Exocyst 0.042 0.041 -10000 0 -0.25 9 9
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.075 0.06 -10000 0 -0.22 4 4
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
RASA1 0.029 0.05 -10000 0 -0.42 6 6
NCK1 0.034 0.021 -10000 0 -0.42 1 1
CBL/APS/CAP/Crk-II 0.039 0.072 -10000 0 -0.23 30 30
TC10/GDP 0.023 0.032 -10000 0 -0.3 5 5
Insulin Receptor/Insulin/SHC/GRB10 0.063 0.066 -10000 0 -0.23 13 13
INPP5D -0.03 0.07 -10000 0 -0.22 55 55
SOS1 0.035 0.021 -10000 0 -0.42 1 1
SGK1 -0.008 0.01 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.004 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
p62DOK/RasGAP 0.046 0.11 -10000 0 -0.61 12 12
INS 0.037 0.024 -10000 0 -0.42 1 1
mol:PI-3-4-P2 -0.03 0.069 -10000 0 -0.22 55 55
GRB2 0.033 0.011 -10000 0 -10000 0 0
EIF4EBP1 -0.049 0.1 0.26 3 -0.34 17 20
PTPRA 0.038 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TC10/GTP/CIP4 0.042 0.041 -10000 0 -0.25 9 9
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.077 -10000 0 -0.36 6 6
Insulin Receptor/Insulin/IRS1 0.035 0.1 -10000 0 -0.24 55 55
Insulin Receptor/Insulin/IRS3 0.054 0.034 -10000 0 -0.3 3 3
Par3/Par6 0.023 0.11 -10000 0 -0.23 69 69
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 0.045 0.086 -10000 0 -0.22 39 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.041 -10000 0 -0.42 4 4
STAT1 (dimer)/Cbp/p300 0.035 0.1 0.31 2 -0.34 14 16
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.052 0.051 -10000 0 -0.26 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.016 0.093 -10000 0 -0.25 48 48
CaM/Ca2+ 0.047 0.085 -10000 0 -0.21 38 38
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
STAT1 (dimer)/SHP2 0.017 0.095 0.28 3 -0.24 43 46
AKT1 -0.01 0.093 0.28 11 -0.34 5 16
MAP2K1 -0.022 0.081 0.27 3 -0.29 11 14
MAP3K11 0.005 0.079 0.26 5 -0.22 25 30
IFNGR1 0.03 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.005 0.13 -10000 0 -0.42 24 24
Rap1/GTP 0.001 0.067 -10000 0 -0.3 7 7
CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.059 0.093 -10000 0 -0.22 39 39
CEBPB -0.016 0.16 0.33 3 -0.51 30 33
STAT3 0.028 0.031 -10000 0 -0.42 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.054 0.13 -10000 0 -0.84 6 6
STAT1 -0.002 0.09 0.29 3 -0.28 23 26
CALM1 0.035 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.007 0.12 -10000 0 -0.42 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
STAT1 (dimer)/PIAS1 0.017 0.093 0.29 3 -0.32 13 16
CEBPB/PTGES2/Cbp/p300 0.005 0.11 -10000 0 -0.33 31 31
mol:Ca2+ 0.042 0.083 -10000 0 -0.21 39 39
MAPK3 -0.015 0.14 0.4 1 -0.63 13 14
STAT1 (dimer) -0.011 0.13 -10000 0 -0.34 46 46
MAPK1 -0.044 0.2 0.4 1 -0.74 31 32
JAK2 0.028 0.036 -10000 0 -0.42 2 2
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
JAK1 0.029 0.04 -10000 0 -0.41 3 3
CAMK2D 0.022 0.075 -10000 0 -0.42 14 14
DAPK1 -0.007 0.13 0.35 1 -0.51 19 20
SMAD7 -0.001 0.058 0.16 8 -0.16 17 25
CBL/CRKL/C3G 0.034 0.084 0.3 2 -0.29 4 6
PI3K 0.036 0.095 -10000 0 -0.24 24 24
IFNG -0.007 0.12 -10000 0 -0.42 38 38
apoptosis -0.061 0.18 0.31 1 -0.42 86 87
CAMK2G 0.036 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.031 -10000 0 -0.42 2 2
CAMK2A 0.035 0.021 -10000 0 -0.42 1 1
CAMK2B -0.012 0.13 -10000 0 -0.42 47 47
FRAP1 -0.016 0.085 0.28 9 -0.34 4 13
PRKCD -0.011 0.092 0.29 10 -0.36 4 14
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
negative regulation of cell growth -0.016 0.093 -10000 0 -0.25 48 48
PTPN2 0.035 0.008 -10000 0 -10000 0 0
EP300 0.032 0.03 -10000 0 -0.42 2 2
IRF1 -0.006 0.1 0.29 8 -0.42 15 23
STAT1 (dimer)/PIASy 0.013 0.094 0.29 3 -0.32 14 17
SOCS1 0.018 0.13 -10000 0 -1.1 6 6
mol:GDP 0.031 0.079 0.28 2 -0.28 4 6
CASP1 -0.012 0.083 0.16 8 -0.24 42 50
PTGES2 0.036 0.005 -10000 0 -10000 0 0
IRF9 0 0.049 0.12 4 -0.14 22 26
mol:PI-3-4-5-P3 0.021 0.086 -10000 0 -0.22 42 42
RAP1/GDP 0.025 0.08 -10000 0 -0.31 7 7
CBL 0.004 0.073 0.29 2 -0.26 5 7
MAP3K1 -0.005 0.089 0.26 5 -0.23 42 47
PIAS1 0.035 0.007 -10000 0 -10000 0 0
PIAS4 0.032 0.036 -10000 0 -0.42 3 3
antigen processing and presentation of peptide antigen via MHC class II -0.016 0.093 -10000 0 -0.25 48 48
PTPN11 0.008 0.08 0.29 4 -0.21 39 43
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.014 0.15 0.28 2 -0.43 28 30
PDGFB-D/PDGFRB/SLAP 0.031 0.056 -10000 0 -0.3 11 11
PDGFB-D/PDGFRB/APS/CBL 0.037 0.041 -10000 0 -0.25 8 8
AKT1 -0.01 0.14 0.34 21 -0.39 11 32
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.004 0.14 0.28 1 -0.48 22 23
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FGR 0.004 0.11 0.31 4 -0.44 20 24
mol:Ca2+ 0.006 0.13 0.26 2 -0.49 21 23
MYC 0.01 0.24 0.36 10 -0.72 40 50
SHC1 0.028 0.025 -10000 0 -0.42 1 1
HRAS/GDP 0.034 0.064 -10000 0 -0.22 16 16
LRP1/PDGFRB/PDGFB 0.058 0.06 -10000 0 -0.29 12 12
GRB10 0.023 0.075 -10000 0 -0.42 14 14
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GO:0007205 0.005 0.13 0.26 2 -0.5 21 23
PTEN 0.027 0.061 -10000 0 -0.42 9 9
GRB2 0.033 0.011 -10000 0 -10000 0 0
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PDGFB-D/PDGFRB/SHP2 0.047 0.046 -10000 0 -0.3 8 8
PDGFB-D/PDGFRB/GRB10 0.036 0.073 -10000 0 -0.3 22 22
cell cycle arrest 0.031 0.055 -10000 0 -0.3 11 11
HRAS 0.032 0.036 -10000 0 -0.42 3 3
HIF1A -0.025 0.13 0.32 19 -0.35 16 35
GAB1 -0.004 0.14 0.32 1 -0.49 25 26
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.005 0.14 0.3 4 -0.44 24 28
PDGFB-D/PDGFRB 0.052 0.055 -10000 0 -0.27 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.045 0.053 -10000 0 -0.3 11 11
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.15 0.3 1 -0.41 30 31
positive regulation of MAPKKK cascade 0.046 0.046 -10000 0 -0.3 8 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 0.005 0.13 0.26 2 -0.5 21 23
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.034 0.022 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/GRB7 0.036 0.064 -10000 0 -0.3 16 16
SHB 0.031 0.046 -10000 0 -0.42 5 5
BLK -0.065 0.2 0.3 2 -0.43 95 97
PTPN2 0.034 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.045 0.046 -10000 0 -0.3 8 8
BCAR1 0.03 0.014 -10000 0 -10000 0 0
VAV2 -0.007 0.16 0.28 2 -0.47 32 34
CBL 0.032 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.042 0.058 -10000 0 -0.3 13 13
LCK -0.051 0.21 0.3 2 -0.55 66 68
PDGFRB 0.028 0.059 -10000 0 -0.43 8 8
ACP1 0.034 0.035 -10000 0 -0.42 3 3
HCK -0.003 0.14 0.32 4 -0.55 24 28
ABL1 -0.007 0.13 0.25 2 -0.44 26 28
PDGFB-D/PDGFRB/CBL -0.011 0.16 -10000 0 -0.55 28 28
PTPN1 0.03 0.031 -10000 0 -0.42 2 2
SNX15 0.035 0.007 -10000 0 -10000 0 0
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
cell proliferation 0.016 0.22 0.33 16 -0.64 40 56
SLA 0.022 0.047 -10000 0 -0.42 5 5
actin cytoskeleton reorganization 0.039 0.071 0.35 4 -0.22 8 12
SRC 0.013 0.094 0.3 5 -0.56 5 10
PI3K -0.038 0.095 -10000 0 -0.24 78 78
PDGFB-D/PDGFRB/GRB7/SHC 0.042 0.062 -10000 0 -0.26 15 15
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.004 0.14 0.28 1 -0.49 22 23
LYN 0.015 0.079 0.3 4 -0.37 8 12
LRP1 0.035 0.021 -10000 0 -0.42 1 1
SOS1 0.035 0.021 -10000 0 -0.42 1 1
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
STAT5A 0.027 0.037 -10000 0 -0.42 3 3
NCK1-2/p130 Cas 0.067 0.068 -10000 0 -0.22 9 9
SPHK1 0.006 0.11 -10000 0 -0.42 30 30
EDG1 0.013 0.096 -10000 0 -0.42 23 23
mol:DAG 0.005 0.13 0.26 2 -0.5 21 23
PLCG1 0.005 0.14 0.26 2 -0.52 21 23
NHERF/PDGFRB 0.002 0.13 -10000 0 -0.28 80 80
YES1 -0.004 0.14 0.3 4 -0.49 27 31
cell migration 0.001 0.13 -10000 0 -0.28 80 80
SHC/Grb2/SOS1 0.06 0.068 -10000 0 -0.23 9 9
SLC9A3R2 -0.004 0.12 -10000 0 -0.42 40 40
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
NHERF1-2/PDGFRB/PTEN 0.011 0.14 -10000 0 -0.27 86 86
FYN -0.013 0.16 0.29 3 -0.51 34 37
DOK1 0.021 0.071 0.2 24 -0.24 15 39
HRAS/GTP 0.024 0.025 -10000 0 -0.3 3 3
PDGFB 0.029 0.046 -10000 0 -0.42 5 5
RAC1 -0.022 0.2 0.29 1 -0.54 46 47
PRKCD 0.022 0.068 0.22 10 -0.26 10 20
FER 0.024 0.069 0.21 26 -0.24 10 36
MAPKKK cascade 0.043 0.11 0.35 22 -0.23 4 26
RASA1 0.021 0.072 0.22 15 -0.24 14 29
NCK1 0.034 0.021 -10000 0 -0.42 1 1
NCK2 0.036 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.042 0.065 0.34 2 -0.22 16 18
PDGFB-D/PDGFRB/SHB 0.042 0.058 -10000 0 -0.31 13 13
chemotaxis -0.006 0.13 0.24 4 -0.43 26 30
STAT1-3-5/STAT1-3-5 0.049 0.075 -10000 0 -0.22 24 24
Bovine Papilomavirus E5/PDGFRB 0.019 0.042 -10000 0 -0.3 8 8
PTPRJ 0.031 0.046 -10000 0 -0.42 5 5
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.035 0.15 -10000 0 -0.42 38 38
BAG4 0.028 0.025 -10000 0 -0.42 1 1
BAD -0.007 0.049 0.19 2 -0.16 17 19
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BAX -0.003 0.056 0.19 10 -0.16 16 26
EnzymeConsortium:3.1.4.12 -0.006 0.034 0.075 4 -0.093 34 38
IKBKB -0.016 0.14 0.3 2 -0.42 28 30
MAP2K2 -0.008 0.055 0.19 11 -0.2 9 20
MAP2K1 -0.007 0.051 0.19 10 -0.2 4 14
SMPD1 -0.006 0.041 -10000 0 -0.16 14 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.004 0.15 0.32 4 -0.41 28 32
MAP2K4 -0.015 0.057 0.18 1 -0.19 21 22
protein ubiquitination -0.032 0.14 0.25 1 -0.42 33 34
EnzymeConsortium:2.7.1.37 -0.011 0.056 0.2 9 -0.2 7 16
response to UV 0 0.001 0.002 12 -0.002 6 18
RAF1 -0.007 0.052 0.2 8 -0.19 6 14
CRADD 0.03 0.05 -10000 0 -0.42 6 6
mol:ceramide -0.006 0.05 0.11 2 -0.15 27 29
I-kappa-B-alpha/RELA/p50/ubiquitin 0.044 0.023 -10000 0 -0.25 2 2
MADD 0.036 0.005 -10000 0 -10000 0 0
MAP3K1 -0.016 0.06 -10000 0 -0.17 40 40
TRADD 0.03 0.014 -10000 0 -10000 0 0
RELA/p50 0.035 0.006 -10000 0 -10000 0 0
MAPK3 -0.004 0.055 0.2 8 -0.19 4 12
MAPK1 -0.007 0.062 0.2 8 -0.21 10 18
p50/RELA/I-kappa-B-alpha 0.049 0.026 -10000 0 -0.3 2 2
FADD -0.001 0.15 0.28 5 -0.42 28 33
KSR1 -0.007 0.05 0.19 3 -0.17 12 15
MAPK8 -0.019 0.058 0.21 3 -0.21 11 14
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.042 0.14 -10000 0 -0.4 41 41
TNF R/SODD 0.039 0.028 -10000 0 -0.3 1 1
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS 0.015 0.069 0.16 28 -0.16 11 39
IKBKG -0.039 0.14 -10000 0 -0.42 34 34
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.03 0.15 -10000 0 -0.44 36 36
RELA 0.035 0.006 -10000 0 -10000 0 0
RIPK1 0.035 0.008 -10000 0 -10000 0 0
AIFM1 0.012 0.067 0.15 28 -0.16 15 43
TNF/TNF R/SODD 0.048 0.047 -10000 0 -0.25 6 6
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.011 0.12 -10000 0 -0.64 15 15
NSMAF -0.011 0.14 0.27 1 -0.42 29 30
response to hydrogen peroxide 0 0.001 0.002 12 -0.002 6 18
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
EPHB forward signaling

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.04 0.038 -10000 0 -0.25 7 7
cell-cell adhesion 0.036 0.06 0.23 32 -10000 0 32
Ephrin B/EPHB2/RasGAP 0.069 0.081 -10000 0 -0.24 23 23
ITSN1 0.034 0.029 -10000 0 -0.42 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SHC1 0.028 0.025 -10000 0 -0.42 1 1
Ephrin B1/EPHB3 0.035 0.058 -10000 0 -0.25 19 19
Ephrin B1/EPHB1 0.042 0.036 -10000 0 -0.25 7 7
HRAS/GDP -0.001 0.11 -10000 0 -0.29 35 35
Ephrin B/EPHB1/GRB7 0.063 0.084 -10000 0 -0.22 30 30
Endophilin/SYNJ1 -0.012 0.053 0.18 14 -0.21 20 34
KRAS 0.028 0.054 -10000 0 -0.42 7 7
Ephrin B/EPHB1/Src 0.07 0.079 -10000 0 -0.24 22 22
endothelial cell migration 0.032 0.094 -10000 0 -0.24 48 48
GRB2 0.033 0.011 -10000 0 -10000 0 0
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PAK1 -0.02 0.067 0.29 2 -0.23 1 3
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RRAS -0.015 0.057 0.18 13 -0.22 22 35
DNM1 0.033 0.035 -10000 0 -0.42 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.058 0.18 16 -0.22 19 35
lamellipodium assembly -0.036 0.06 -10000 0 -0.23 32 32
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.069 -10000 0 -0.31 12 12
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
EPHB3 0.018 0.085 -10000 0 -0.42 18 18
EPHB1 0.026 0.05 -10000 0 -0.42 6 6
EPHB4 0.016 0.091 -10000 0 -0.42 21 21
mol:GDP -0.018 0.09 -10000 0 -0.33 25 25
Ephrin B/EPHB2 0.058 0.064 -10000 0 -0.22 19 19
Ephrin B/EPHB3 0.048 0.081 -10000 0 -0.23 32 32
JNK cascade -0.014 0.059 0.33 5 -0.23 16 21
Ephrin B/EPHB1 0.056 0.068 -10000 0 -0.22 22 22
RAP1/GDP -0.005 0.11 -10000 0 -0.3 30 30
EFNB2 0.017 0.08 -10000 0 -0.42 16 16
EFNB3 0.032 0.012 -10000 0 -10000 0 0
EFNB1 0.035 0.021 -10000 0 -0.42 1 1
Ephrin B2/EPHB1-2 0.044 0.067 -10000 0 -0.24 23 23
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CDC42/GTP 0.036 0.091 -10000 0 -0.27 21 21
Rap1/GTP 0.015 0.069 -10000 0 -0.4 5 5
axon guidance 0.039 0.038 -10000 0 -0.25 7 7
MAPK3 0.025 0.072 0.2 20 -0.39 6 26
MAPK1 0.016 0.066 0.24 2 -0.39 6 8
Rac1/GDP -0.017 0.1 -10000 0 -0.3 33 33
actin cytoskeleton reorganization -0.023 0.076 -10000 0 -0.26 20 20
CDC42/GDP -0.016 0.1 -10000 0 -0.29 36 36
PI3K 0.038 0.098 -10000 0 -0.24 48 48
EFNA5 0.03 0.046 -10000 0 -0.42 5 5
Ephrin B2/EPHB4 0.02 0.081 -10000 0 -0.26 35 35
Ephrin B/EPHB2/Intersectin/N-WASP 0.011 0.074 -10000 0 -0.24 29 29
CDC42 0.035 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.067 -10000 0 -0.23 24 24
PTK2 0.11 0.23 0.55 112 -10000 0 112
MAP4K4 -0.015 0.059 0.33 5 -0.24 16 21
SRC 0.033 0.029 -10000 0 -0.42 2 2
KALRN 0.034 0.022 -10000 0 -0.42 1 1
Intersectin/N-WASP 0.045 0.048 -10000 0 -0.3 9 9
neuron projection morphogenesis -0.013 0.084 0.26 2 -0.32 12 14
MAP2K1 0.01 0.063 0.21 1 -0.41 6 7
WASL 0.029 0.054 -10000 0 -0.42 7 7
Ephrin B1/EPHB1-2/NCK1 0.079 0.05 -10000 0 -0.23 10 10
cell migration 0.027 0.093 0.23 8 -0.39 9 17
NRAS 0.029 0.054 -10000 0 -0.42 7 7
SYNJ1 -0.012 0.053 0.18 14 -0.21 20 34
PXN 0.036 0.004 -10000 0 -10000 0 0
TF -0.017 0.05 0.17 14 -0.21 16 30
HRAS/GTP 0.042 0.075 -10000 0 -0.22 28 28
Ephrin B1/EPHB1-2 0.058 0.042 -10000 0 -0.23 9 9
cell adhesion mediated by integrin 0.011 0.059 0.22 16 -0.21 12 28
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:GTP 0.048 0.075 -10000 0 -0.22 28 28
RAC1-CDC42/GTP -0.033 0.061 -10000 0 -0.36 6 6
RASA1 0.029 0.05 -10000 0 -0.42 6 6
RAC1-CDC42/GDP -0.003 0.11 -10000 0 -0.29 33 33
ruffle organization -0.03 0.076 -10000 0 -0.4 5 5
NCK1 0.034 0.021 -10000 0 -0.42 1 1
receptor internalization -0.019 0.051 0.17 13 -0.21 18 31
Ephrin B/EPHB2/KALRN 0.073 0.074 -10000 0 -0.23 19 19
ROCK1 0.018 0.06 0.19 23 -0.23 19 42
RAS family/GDP -0.047 0.07 -10000 0 -0.27 25 25
Rac1/GTP 0 0.076 -10000 0 -0.24 35 35
Ephrin B/EPHB1/Src/Paxillin 0.014 0.075 -10000 0 -0.27 23 23
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.018 0.14 -9999 0 -0.33 46 46
MAP3K8 0.003 0.11 -9999 0 -0.42 32 32
FOS 0.021 0.097 -9999 0 -0.4 8 8
PRKCA 0.025 0.022 -9999 0 -10000 0 0
PTPN7 0.02 0.032 -9999 0 -0.44 1 1
HRAS 0.032 0.036 -9999 0 -0.42 3 3
PRKCB -0.002 0.006 -9999 0 -0.017 73 73
NRAS 0.029 0.054 -9999 0 -0.42 7 7
RAS family/GTP 0.05 0.055 -9999 0 -0.23 15 15
MAPK3 0.028 0.067 -9999 0 -0.44 6 6
MAP2K1 0.009 0.064 -9999 0 -0.23 9 9
ELK1 0.025 0.038 -9999 0 -0.42 2 2
BRAF 0.006 0.047 -9999 0 -0.35 7 7
mol:GTP -0.001 0.002 -9999 0 -0.005 73 73
MAPK1 0.013 0.099 -9999 0 -0.41 18 18
RAF1 0.01 0.023 -9999 0 -0.24 1 1
KRAS 0.028 0.054 -9999 0 -0.42 7 7
RXR and RAR heterodimerization with other nuclear receptor

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.1 0.9 1 -0.78 1 2
VDR 0.02 0.082 -10000 0 -0.42 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.004 0.1 -10000 0 -0.35 14 14
RXRs/LXRs/DNA/Oxysterols 0.013 0.16 -10000 0 -0.42 49 49
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.004 0.092 -10000 0 -0.24 48 48
RXRs/NUR77 0.055 0.08 -10000 0 -0.25 11 11
RXRs/PPAR 0.009 0.076 -10000 0 -0.26 27 27
NCOR2 0.036 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RARs/VDR/DNA/Vit D3 0.053 0.083 -10000 0 -0.23 35 35
RARA 0.03 0.042 -10000 0 -0.42 4 4
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARs/RARs/DNA/9cRA 0.041 0.063 -10000 0 -0.22 23 23
RARG 0.036 0.005 -10000 0 -10000 0 0
RPS6KB1 0.054 0.15 0.54 42 -10000 0 42
RARs/THRs/DNA/SMRT 0.005 0.09 -10000 0 -0.24 47 47
THRA 0.02 0.075 -10000 0 -0.42 14 14
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.083 -10000 0 -0.24 15 15
NR1H4 0.035 0.021 -10000 0 -0.42 1 1
RXRs/LXRs/DNA 0.059 0.11 -10000 0 -0.32 5 5
NR1H2 0.029 0.031 -10000 0 -10000 0 0
NR1H3 0.026 0.052 -10000 0 -0.43 4 4
RXRs/VDR/DNA/Vit D3 0.044 0.084 -10000 0 -0.24 19 19
NR4A1 0.034 0.021 -10000 0 -0.42 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.026 0.063 -10000 0 -0.22 14 14
RXRG 0.017 0.06 -10000 0 -0.43 7 7
RXR alpha/CCPG 0.021 0.029 -10000 0 -0.31 2 2
RXRA 0.028 0.042 -10000 0 -0.44 2 2
RXRB 0.027 0.044 -10000 0 -0.42 2 2
THRB 0.024 0.07 -10000 0 -0.42 12 12
PPARG 0.012 0.093 -10000 0 -0.42 22 22
PPARD 0.036 0.006 -10000 0 -10000 0 0
TNF -0.001 0.19 -10000 0 -0.82 16 16
mol:Oxysterols -0.001 0.017 -10000 0 -10000 0 0
cholesterol transport 0.014 0.16 -10000 0 -0.42 49 49
PPARA 0.032 0.03 -10000 0 -0.42 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.015 0.089 -10000 0 -0.42 20 20
RXRs/NUR77/BCL2 -0.02 0.097 -10000 0 -0.22 84 84
SREBF1 -0.045 0.29 -10000 0 -0.94 45 45
RXRs/RXRs/DNA/9cRA 0.04 0.083 -10000 0 -0.24 15 15
ABCA1 -0.007 0.22 -10000 0 -0.99 16 16
RARs/THRs 0.063 0.1 -10000 0 -0.24 45 45
RXRs/FXR 0.056 0.081 -10000 0 -0.25 12 12
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
ErbB2/ErbB3 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
USP8 -0.009 0.017 -10000 0 -0.26 2 2
RAS family/GTP 0.03 0.11 0.25 1 -0.3 19 20
NFATC4 -0.03 0.068 0.23 1 -0.32 7 8
ERBB2IP 0.034 0.022 -10000 0 -0.42 1 1
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.003 0.087 -10000 0 -0.27 29 29
JUN 0.008 0.074 0.21 1 -10000 0 1
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK7 -0.034 0.077 0.26 1 -0.32 11 12
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.089 -10000 0 -0.27 34 34
AKT1 0.003 0.021 -10000 0 -0.3 2 2
BAD -0.01 0.019 -10000 0 -0.25 3 3
MAPK10 -0.024 0.061 0.2 7 -0.21 14 21
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.002 0.094 -10000 0 -0.29 29 29
RAF1 0.011 0.11 0.28 10 -0.31 19 29
ErbB2/ErbB3/neuregulin 2 0.011 0.093 -10000 0 -0.27 45 45
STAT3 0.005 0.18 -10000 0 -0.88 19 19
cell migration -0.018 0.064 0.23 8 -0.21 10 18
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.043 0.25 -10000 0 -0.65 53 53
FOS -0.045 0.21 0.31 1 -0.44 102 103
NRAS 0.029 0.054 -10000 0 -0.42 7 7
mol:Ca2+ -0.003 0.087 -10000 0 -0.27 29 29
MAPK3 -0.018 0.2 -10000 0 -0.52 45 45
MAPK1 -0.03 0.21 -10000 0 -0.55 48 48
JAK2 -0.032 0.078 0.26 1 -0.33 11 12
NF2 0.01 0.046 -10000 0 -0.68 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.002 0.072 0.18 3 -0.27 25 28
NRG1 0.028 0.015 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
MAPK8 -0.019 0.098 0.22 1 -0.28 30 31
MAPK9 -0.023 0.058 0.2 6 -0.2 10 16
ERBB2 -0.03 0.055 0.6 1 -0.32 13 14
ERBB3 0.006 0.11 -10000 0 -0.42 32 32
SHC1 0.028 0.025 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.005 0.03 0.33 2 -0.21 4 6
STAT3 (dimer) 0.005 0.17 -10000 0 -0.86 19 19
RNF41 -0.013 0.016 -10000 0 -0.24 2 2
FRAP1 -0.009 0.012 -10000 0 -0.26 1 1
RAC1-CDC42/GTP -0.015 0.06 -10000 0 -0.21 27 27
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.04 -10000 0 -0.26 13 13
CHRNA1 -0.004 0.16 0.33 1 -0.44 30 31
myelination -0.023 0.083 0.27 11 -0.32 7 18
PPP3CB -0.034 0.072 0.24 1 -0.29 13 14
KRAS 0.028 0.054 -10000 0 -0.42 7 7
RAC1-CDC42/GDP 0.039 0.096 0.25 1 -0.28 14 15
NRG2 0.025 0.061 -10000 0 -0.42 9 9
mol:GDP 0.002 0.072 0.18 3 -0.27 25 28
SOS1 0.035 0.021 -10000 0 -0.42 1 1
MAP2K2 -0.001 0.11 0.26 8 -0.33 22 30
SRC 0.033 0.029 -10000 0 -0.42 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.035 0.076 0.26 1 -0.32 12 13
MAP2K1 -0.029 0.21 -10000 0 -0.6 33 33
heart morphogenesis -0.003 0.087 -10000 0 -0.27 29 29
RAS family/GDP 0.041 0.11 0.26 1 -0.3 16 17
GRB2 0.033 0.011 -10000 0 -10000 0 0
PRKACA 0.014 0.054 -10000 0 -0.67 3 3
CHRNE 0.009 0.018 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.021 0.3 2 -10000 0 2
nervous system development -0.003 0.087 -10000 0 -0.27 29 29
CDC42 0.035 0.008 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.047 0.04 -10000 0 -0.3 6 6
Necdin/E2F1 0.013 0.11 -10000 0 -0.31 54 54
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.031 0.11 -10000 0 -0.23 70 70
NGF (dimer)/p75(NTR)/BEX1 0.038 0.035 -10000 0 -0.25 6 6
NT-4/5 (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
IKBKB 0.03 0.014 -10000 0 -10000 0 0
AKT1 0.021 0.069 0.19 43 -0.22 20 63
IKBKG 0.036 0 -10000 0 -10000 0 0
BDNF 0.031 0.024 -10000 0 -0.42 1 1
MGDIs/NGR/p75(NTR)/LINGO1 0.034 0.049 -10000 0 -0.25 13 13
FURIN 0.027 0.057 -10000 0 -0.42 8 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.058 0.047 -10000 0 -0.25 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.026 0.054 -10000 0 -0.22 17 17
proBDNF (dimer) 0.031 0.024 -10000 0 -0.42 1 1
NTRK1 0.026 0.032 -10000 0 -0.42 2 2
RTN4R 0.024 0.067 -10000 0 -0.42 11 11
neuron apoptosis -0.008 0.1 0.28 1 -0.44 10 11
IRAK1 0.036 0.004 -10000 0 -10000 0 0
SHC1 0.012 0.022 -10000 0 -0.25 3 3
ARHGDIA 0.033 0.022 -10000 0 -0.42 1 1
RhoA/GTP 0.02 0.043 -10000 0 -0.3 9 9
Gamma Secretase 0.069 0.069 -10000 0 -0.22 13 13
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.04 0.083 -10000 0 -0.24 38 38
MAGEH1 0.006 0.11 -10000 0 -0.42 34 34
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.03 0.097 -10000 0 -0.24 54 54
Mammalian IAPs/DIABLO 0.034 0.082 -10000 0 -0.23 39 39
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
APP 0.008 0.11 -10000 0 -0.42 29 29
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.029 -10000 0 -0.42 2 2
RhoA/GDP/RHOGDI 0.038 0.045 0.18 4 -0.21 12 16
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.01 0.05 0.2 18 -0.21 9 27
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.021 0.031 -10000 0 -0.21 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.03 -10000 0 -0.25 4 4
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
mol:GTP 0.025 0.068 -10000 0 -0.25 28 28
PSENEN 0.035 0.006 -10000 0 -10000 0 0
mol:ceramide 0.016 0.044 0.19 13 -0.23 10 23
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.036 -10000 0 -0.17 15 15
p75(NTR)/beta APP 0.026 0.084 -10000 0 -0.3 30 30
BEX1 0.027 0.037 -10000 0 -0.42 3 3
mol:GDP -0.006 0.019 -10000 0 -0.25 3 3
NGF (dimer) 0.008 0.11 -10000 0 -0.23 76 76
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.049 0.054 -10000 0 -0.23 14 14
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
RAC1/GTP 0.037 0.023 -10000 0 -0.21 3 3
MYD88 0.031 0.041 -10000 0 -0.42 4 4
CHUK 0.026 0.067 -10000 0 -0.42 11 11
NGF (dimer)/p75(NTR)/PKA 0.025 0.069 -10000 0 -0.25 28 28
RHOB -0.011 0.14 -10000 0 -0.42 52 52
RHOA 0.026 0.061 -10000 0 -0.42 9 9
MAGE-G1/E2F1 0.045 0.043 -10000 0 -0.3 7 7
NT3 (dimer) 0.023 0.058 -10000 0 -0.42 8 8
TP53 -0.019 0.066 0.35 1 -0.22 27 28
PRDM4 0.02 0.046 0.19 18 -0.23 9 27
BDNF (dimer) -0.018 0.16 -10000 0 -0.31 110 110
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SORT1 0.03 0.05 -10000 0 -0.42 6 6
activation of caspase activity 0.025 0.11 -10000 0 -0.23 70 70
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.044 -10000 0 -0.23 9 9
RHOC 0.033 0.036 -10000 0 -0.42 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.016 0.079 0.22 1 -0.28 15 16
DIABLO 0.036 0.004 -10000 0 -10000 0 0
SMPD2 0.016 0.045 0.19 13 -0.23 10 23
APH1B 0.025 0.067 -10000 0 -0.42 11 11
APH1A 0.031 0.036 -10000 0 -0.42 3 3
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.041 -10000 0 -0.25 9 9
PSEN1 0.032 0.041 -10000 0 -0.42 4 4
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
NT3 (dimer)/p75(NTR) 0.037 0.053 -10000 0 -0.3 11 11
MAPK8 -0.01 0.066 -10000 0 -0.27 7 7
MAPK9 -0.015 0.078 -10000 0 -0.32 11 11
APAF1 0.032 0.041 -10000 0 -0.42 4 4
NTF3 0.023 0.058 -10000 0 -0.42 8 8
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.012 0.14 -10000 0 -0.42 53 53
RAC1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.018 0.11 -10000 0 -0.22 85 85
p75 CTF/Sortilin/TRAF6/NRIF 0.082 0.047 -10000 0 -0.23 8 8
RhoA-B-C/GTP 0.024 0.068 -10000 0 -0.25 28 28
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.086 0.059 -10000 0 -0.22 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.074 0.052 -10000 0 -0.23 10 10
PRKACB 0.008 0.099 -10000 0 -0.42 25 25
proBDNF (dimer)/p75 ECD 0.048 0.02 -10000 0 -0.3 1 1
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.008 0.12 -10000 0 -0.42 40 40
BIRC2 0.032 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.038 0.08 0.13 2 -0.26 38 40
BAD -0.02 0.079 -10000 0 -0.29 10 10
RIPK2 0.028 0.015 -10000 0 -10000 0 0
NGFR 0.03 0.036 -10000 0 -0.42 3 3
CYCS 0.005 0.064 0.19 13 -0.22 32 45
ADAM17 0.036 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.048 0.04 -10000 0 -0.23 4 4
BCL2L11 -0.019 0.079 -10000 0 -0.29 10 10
BDNF (dimer)/p75(NTR) 0.044 0.034 -10000 0 -0.3 4 4
PI3K 0.046 0.061 -10000 0 -0.23 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.056 0.045 -10000 0 -0.23 9 9
NDNL2 0.035 0.008 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
NGF (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.045 0.074 -10000 0 -0.23 32 32
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.032 0.03 -10000 0 -0.42 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.018 0.046 0.16 2 -0.24 14 16
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
NGFRAP1 -0.025 0.16 -10000 0 -0.42 68 68
CASP3 -0.018 0.077 -10000 0 -0.27 11 11
E2F1 0.029 0.054 -10000 0 -0.42 7 7
CASP9 0.034 0.022 -10000 0 -0.42 1 1
IKK complex 0.042 0.064 -10000 0 -0.31 1 1
NGF (dimer)/TRKA 0.019 0.023 -10000 0 -0.3 2 2
MMP7 -0.032 0.15 -10000 0 -0.42 68 68
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.051 -10000 0 -0.22 11 11
MMP3 -0.045 0.16 -10000 0 -0.42 81 81
APAF-1/Caspase 9 -0.04 0.065 -10000 0 -0.2 54 54
Atypical NF-kappaB 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
BCL3/RelA 0.045 0.048 -10000 0 -0.3 9 9
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
NF kappa B1 p50/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.1 0.2 1 -0.35 19 20
NFKBIA -0.016 0.1 -10000 0 -0.24 75 75
MAPK14 0.036 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.029 0.024 -10000 0 -0.24 2 2
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.025 0.07 -10000 0 -0.42 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.039 -10000 0 -0.25 8 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.017 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
NF kappa B1 p50 dimer 0.023 0.021 0.26 3 -10000 0 3
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
NFKB1 0.014 0.007 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.1 -10000 0 -0.25 52 52
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.003 0.1 -10000 0 -0.35 20 20
SRC 0.033 0.029 -10000 0 -0.42 2 2
PI3K 0.036 0.065 -10000 0 -0.3 17 17
NF kappa B1 p50/RelA -0.003 0.099 -10000 0 -0.25 50 50
IKBKB 0.03 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.029 -10000 0 -0.42 2 2
SYK 0.005 0.11 -10000 0 -0.42 34 34
I kappa B alpha/PIK3R1 -0.008 0.12 -10000 0 -0.24 83 83
cell death 0.003 0.099 -10000 0 -0.33 20 20
NF kappa B1 p105/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
LCK -0.017 0.14 -10000 0 -0.42 54 54
BCL3 0.027 0.061 -10000 0 -0.42 9 9
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.032 -9999 0 -0.42 2 2
Syndecan-3/Src/Cortactin 0.007 0.15 -9999 0 -0.51 24 24
Syndecan-3/Neurocan -0.018 0.12 -9999 0 -0.5 27 27
POMC 0.032 0.036 -9999 0 -0.42 3 3
EGFR -0.015 0.13 -9999 0 -0.42 49 49
Syndecan-3/EGFR -0.011 0.15 -9999 0 -0.53 29 29
AGRP 0.029 0.025 -9999 0 -0.42 1 1
NCSTN 0.028 0.025 -9999 0 -0.42 1 1
PSENEN 0.035 0.006 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.025 0.067 -9999 0 -0.42 11 11
APH1A 0.031 0.036 -9999 0 -0.42 3 3
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.018 0.12 -9999 0 -0.48 24 24
Syndecan-3/IL8 -0.007 0.14 -9999 0 -0.54 28 28
PSEN1 0.032 0.041 -9999 0 -0.42 4 4
Src/Cortactin 0.039 0.038 -9999 0 -0.3 4 4
FYN 0.027 0.054 -9999 0 -0.42 7 7
limb bud formation -0.015 0.12 -9999 0 -0.53 26 26
MC4R 0.034 0.022 -9999 0 -0.42 1 1
SRC 0.033 0.029 -9999 0 -0.42 2 2
PTN -0.029 0.15 -9999 0 -0.42 65 65
FGFR/FGF/Syndecan-3 -0.015 0.12 -9999 0 -0.53 26 26
neuron projection morphogenesis -0.031 0.12 -9999 0 -0.49 24 24
Syndecan-3/AgRP 0.009 0.13 -9999 0 -0.5 27 27
Syndecan-3/AgRP/MC4R 0.024 0.13 -9999 0 -0.5 25 25
Fyn/Cortactin 0.035 0.044 -9999 0 -0.3 6 6
SDC3 -0.016 0.12 -9999 0 -0.54 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.006 0.14 -9999 0 -0.52 29 29
IL8 -0.004 0.12 -9999 0 -0.42 37 37
Syndecan-3/Fyn/Cortactin 0.019 0.13 -9999 0 -0.5 23 23
Syndecan-3/CASK -0.018 0.12 -9999 0 -0.5 27 27
alpha-MSH/MC4R 0.047 0.034 -9999 0 -0.3 4 4
Gamma Secretase 0.069 0.069 -9999 0 -0.22 13 13
EPO signaling pathway

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
BCL2L1 -0.003 0.14 -10000 0 -0.42 2 2
CRKL 0 0.076 0.22 8 -0.23 11 19
mol:DAG 0.019 0.08 0.25 2 -10000 0 2
HRAS 0.023 0.099 0.27 19 -10000 0 19
MAPK8 0.037 0.073 0.2 56 -0.25 2 58
RAP1A 0.001 0.077 0.22 8 -0.23 12 20
GAB1 0 0.076 0.23 4 -0.24 12 16
MAPK14 0.037 0.071 0.2 52 -10000 0 52
EPO 0.023 0.027 -10000 0 -10000 0 0
PLCG1 0.019 0.081 0.25 2 -10000 0 2
EPOR/TRPC2/IP3 Receptors 0.026 0.028 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.052 -10000 0 -0.27 4 4
GAB1/SHC/GRB2/SOS1 0.029 0.075 0.29 1 -0.21 1 2
EPO/EPOR (dimer) 0.037 0.039 -10000 0 -10000 0 0
IRS2 -0.009 0.087 0.27 3 -0.26 28 31
STAT1 -0.003 0.13 0.26 2 -0.33 36 38
STAT5B 0.021 0.081 0.26 1 -0.26 2 3
cell proliferation 0.014 0.079 0.19 76 -0.24 2 78
GAB1/SHIP/PIK3R1/SHP2/SHC 0.009 0.074 -10000 0 -0.27 5 5
TEC 0.001 0.076 0.25 4 -0.22 12 16
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
STAT1 (dimer) -0.001 0.13 0.26 2 -0.32 36 38
JAK2 0.028 0.036 -10000 0 -0.44 2 2
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
EPO/EPOR (dimer)/JAK2 0.036 0.089 0.22 6 -0.17 35 41
EPO/EPOR 0.037 0.039 -10000 0 -10000 0 0
LYN 0.021 0.027 -10000 0 -10000 0 0
TEC/VAV2 0.016 0.081 0.29 2 -0.22 11 13
elevation of cytosolic calcium ion concentration 0.026 0.028 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
EPO/EPOR (dimer)/LYN 0.044 0.053 -10000 0 -10000 0 0
mol:IP3 0.019 0.08 0.25 2 -10000 0 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.005 0.095 0.29 1 -0.23 42 43
SH2B3 -0.003 0.009 -10000 0 -10000 0 0
NFKB1 0.038 0.072 0.2 56 -10000 0 56
EPO/EPOR (dimer)/JAK2/SOCS3 0.023 0.035 -10000 0 -0.21 6 6
PTPN6 -0.002 0.068 0.17 1 -0.19 22 23
TEC/VAV2/GRB2 0.028 0.084 0.3 2 -0.21 8 10
EPOR 0.026 0.028 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.076 0.3 1 -0.22 1 2
SOS1 0.035 0.021 -10000 0 -0.42 1 1
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
CRKL/CBL/C3G 0.021 0.085 0.3 1 -0.24 8 9
VAV2 0.003 0.074 0.2 13 -0.23 8 21
CBL 0 0.071 0.23 4 -0.25 6 10
SHC/Grb2/SOS1 0.015 0.063 -10000 0 -0.2 4 4
STAT5A 0.019 0.082 0.26 1 -0.26 3 4
GRB2 0.033 0.011 -10000 0 -10000 0 0
STAT5 (dimer) 0.018 0.12 0.28 1 -0.31 44 45
LYN/PLCgamma2 0.03 0.043 -10000 0 -0.3 6 6
PTPN11 0.036 0.004 -10000 0 -10000 0 0
BTK -0.003 0.083 0.24 5 -0.24 20 25
BCL2 -0.11 0.33 -10000 0 -0.73 105 105
HIF-2-alpha transcription factor network

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
MMP14 -0.007 0.28 -10000 0 -1 32 32
oxygen homeostasis 0.005 0.01 -10000 0 -10000 0 0
TCEB2 0.033 0.011 -10000 0 -10000 0 0
TCEB1 0.028 0.025 -10000 0 -0.42 1 1
VHL/Elongin B/Elongin C/HIF2A 0.054 0.11 -10000 0 -0.33 11 11
EPO 0.072 0.18 -10000 0 -0.51 17 17
FIH (dimer) 0.037 0.02 -10000 0 -10000 0 0
APEX1 0.035 0.028 -10000 0 -10000 0 0
SERPINE1 0.056 0.2 -10000 0 -0.54 28 28
FLT1 -0.043 0.28 -10000 0 -0.8 48 48
ADORA2A 0.044 0.18 0.34 5 -0.52 26 31
germ cell development 0.064 0.18 -10000 0 -0.52 21 21
SLC11A2 0.065 0.19 -10000 0 -0.55 21 21
BHLHE40 0.053 0.18 0.33 1 -0.49 27 28
HIF1AN 0.038 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.073 0.15 0.33 1 -0.38 20 21
ETS1 0.037 0.033 -10000 0 -0.42 1 1
CITED2 0.016 0.18 -10000 0 -0.86 15 15
KDR -0.015 0.24 -10000 0 -0.82 26 26
PGK1 0.066 0.19 -10000 0 -0.54 20 20
SIRT1 0.036 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.23 -10000 0 -0.59 23 23
EPAS1 0.027 0.12 -10000 0 -0.32 25 25
SP1 0.033 0.039 -10000 0 -0.42 1 1
ABCG2 0.061 0.2 -10000 0 -0.56 23 23
EFNA1 0.032 0.19 -10000 0 -0.52 32 32
FXN 0.052 0.18 0.34 6 -0.52 21 27
POU5F1 0.064 0.19 -10000 0 -0.53 21 21
neuron apoptosis -0.1 0.22 0.57 23 -10000 0 23
EP300 0.032 0.03 -10000 0 -0.42 2 2
EGLN3 -0.012 0.14 -10000 0 -0.42 52 52
EGLN2 0.034 0.045 -10000 0 -0.41 4 4
EGLN1 0.023 0.057 -10000 0 -0.42 7 7
VHL/Elongin B/Elongin C 0.054 0.036 -10000 0 -0.26 1 1
VHL 0.035 0.007 -10000 0 -10000 0 0
ARNT 0.035 0.027 -10000 0 -10000 0 0
SLC2A1 0.046 0.18 0.34 5 -0.5 27 32
TWIST1 0.038 0.21 0.34 5 -0.57 36 41
ELK1 0.039 0.032 -10000 0 -0.42 2 2
HIF2A/ARNT/Cbp/p300 0.071 0.15 0.34 1 -0.37 20 21
VEGFA 0.053 0.18 0.33 1 -0.49 27 28
CREBBP 0.033 0.011 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.015 0.039 -10000 0 -0.25 13 13
ADCY5 -0.013 0.039 -10000 0 -0.25 13 13
ADCY6 -0.012 0.026 -10000 0 -0.25 6 6
ADCY7 -0.009 0.024 -10000 0 -0.25 5 5
ADCY1 -0.011 0.024 -10000 0 -0.25 5 5
ADCY2 -0.029 0.071 -10000 0 -0.26 44 44
ADCY3 -0.014 0.036 -10000 0 -0.25 11 11
ADCY8 -0.008 0.022 -10000 0 -0.25 4 4
PRKCE 0.005 0.033 -10000 0 -0.3 6 6
ADCY9 -0.016 0.045 -10000 0 -0.27 15 15
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.021 0.086 0.2 44 -0.28 7 51
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.035 0.006 -10000 0 -10000 0 0
VLDLR -0.007 0.12 -10000 0 -0.42 42 42
LRPAP1 0.035 0.007 -10000 0 -10000 0 0
NUDC 0.035 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.039 0.089 -10000 0 -0.25 40 40
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
KATNA1 0.033 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.001 0.073 0.19 10 -0.23 40 50
IQGAP1/CaM 0.05 0.015 -10000 0 -10000 0 0
DAB1 0.035 0.007 -10000 0 -10000 0 0
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
PLA2G7 -0.035 0.16 -10000 0 -0.42 74 74
CALM1 0.035 0.007 -10000 0 -10000 0 0
DYNLT1 0.034 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.024 0.089 -10000 0 -0.3 35 35
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.012 -10000 0 -0.25 1 1
CDK5R2 0.036 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.033 0.097 -10000 0 -0.26 46 46
YWHAE 0.032 0.012 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.016 0.07 0.33 1 -0.24 4 5
MAP1B -0.009 0.064 -10000 0 -0.26 30 30
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.008 0.067 0.19 8 -0.21 38 46
RELN 0.03 0.046 -10000 0 -0.42 5 5
PAFAH/LIS1 -0.01 0.1 -10000 0 -0.25 74 74
LIS1/CLIP170 0.011 0.012 -10000 0 -0.25 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.018 0.068 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.009 0.1 -10000 0 -0.26 61 61
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.002 0.062 0.33 1 -0.26 4 5
LIS1/IQGAP1 0.034 0.014 -10000 0 -10000 0 0
RHOA 0.008 0.056 -10000 0 -0.4 9 9
PAFAH1B1 0.014 0.015 -10000 0 -0.3 1 1
PAFAH1B3 0.03 0.054 -10000 0 -0.42 7 7
PAFAH1B2 0.031 0.013 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.015 0.061 -10000 0 -0.26 3 3
NDEL1/Katanin 60/Dynein heavy chain 0.023 0.08 0.37 2 -0.25 4 6
LRP8 -0.001 0.12 -10000 0 -0.42 35 35
NDEL1/Katanin 60 0.009 0.072 0.33 1 -0.25 4 5
P39/CDK5 0.009 0.068 0.19 8 -0.21 40 48
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.019 -10000 0 -0.26 1 1
CDK5 -0.026 0.063 0.18 9 -0.22 40 49
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.011 -10000 0 -0.21 1 1
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.035 0.091 -10000 0 -0.23 46 46
RELN/VLDLR 0.025 0.12 -10000 0 -0.24 80 80
CDC42 0.016 0.007 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
GNB1/GNG2 0.034 0.1 -10000 0 -0.26 53 53
forebrain development -0.005 0.14 -10000 0 -0.56 18 18
GNAO1 0.03 0.014 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.014 0.1 -10000 0 -0.3 48 48
SMO -0.01 0.13 -10000 0 -0.42 48 48
ARRB2 0.033 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.005 0.15 -10000 0 -0.41 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.036 0.005 -10000 0 -10000 0 0
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
SIN3/HDAC complex 0.076 0.045 -10000 0 -0.23 5 5
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
XPO1 0.037 0.005 -10000 0 -10000 0 0
GLI1/Su(fu) -0.02 0.17 -10000 0 -0.56 27 27
SAP30 0.03 0.046 -10000 0 -0.42 5 5
mol:GDP -0.01 0.13 -10000 0 -0.42 48 48
MIM/GLI2A 0.002 0.11 -10000 0 -0.42 31 31
IFT88 0.021 0.075 -10000 0 -0.42 14 14
GNAI3 0.036 0.006 -10000 0 -10000 0 0
GLI2 0.014 0.079 -10000 0 -0.33 15 15
GLI3 -0.008 0.15 0.24 3 -0.42 30 33
CSNK1D 0.034 0.009 -10000 0 -10000 0 0
CSNK1E 0.034 0.009 -10000 0 -10000 0 0
SAP18 0.034 0.01 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.075 -10000 0 -0.42 14 14
GNG2 0.034 0.021 -10000 0 -0.42 1 1
Gi family/GTP -0.017 0.12 -10000 0 -0.3 54 54
SIN3B 0.036 0.005 -10000 0 -10000 0 0
SIN3A 0.035 0.007 -10000 0 -10000 0 0
GLI3/Su(fu) -0.006 0.14 -10000 0 -0.41 37 37
GLI2/Su(fu) 0.004 0.11 -10000 0 -0.4 17 17
FOXA2 -0.022 0.2 -10000 0 -0.69 38 38
neural tube patterning -0.005 0.14 -10000 0 -0.56 18 18
SPOP 0.033 0.022 -10000 0 -0.42 1 1
Su(fu)/PIAS1 0.009 0.091 -10000 0 -0.32 16 16
GNB1 0.032 0.045 -10000 0 -0.42 5 5
CSNK1G2 0.033 0.029 -10000 0 -0.42 2 2
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
MTSS1 0.002 0.11 -10000 0 -0.42 31 31
embryonic limb morphogenesis -0.005 0.14 -10000 0 -0.56 18 18
SUFU -0.001 0.084 -10000 0 -0.35 16 16
LGALS3 -0.009 0.14 -10000 0 -0.42 49 49
catabolic process 0.015 0.15 -10000 0 -0.48 21 21
GLI3A/CBP 0.035 0.042 -10000 0 -0.33 6 6
KIF3A 0.029 0.054 -10000 0 -0.42 7 7
GLI1 -0.006 0.14 -10000 0 -0.58 18 18
RAB23 0.03 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.036 0.006 -10000 0 -10000 0 0
IFT172 0.033 0.035 -10000 0 -0.42 3 3
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
Su(fu)/Galectin3 -0.014 0.12 -10000 0 -0.34 40 40
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
RBBP4 0.035 0.021 -10000 0 -0.42 1 1
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
PIAS1 0.035 0.007 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.082 -10000 0 -0.32 14 14
STK36 0.021 0.082 -10000 0 -0.42 17 17
Gi family/GNB1/GNG2/GDP -0.021 0.12 -10000 0 -0.38 37 37
PTCH1 -0.004 0.13 -10000 0 -0.48 21 21
MIM/GLI1 -0.001 0.14 -10000 0 -0.52 18 18
CREBBP 0.035 0.042 -10000 0 -0.33 6 6
Su(fu)/SIN3/HDAC complex 0.009 0.097 -10000 0 -0.4 18 18
Aurora A signaling

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
Aurora A/GADD45A 0.032 0.055 -10000 0 -0.24 15 15
BIRC5 -0.002 0.12 -10000 0 -0.42 38 38
NFKBIA 0.018 0.051 0.25 15 -0.25 2 17
CPEB1 0.03 0.046 -10000 0 -0.42 5 5
AKT1 0.014 0.041 0.25 7 -0.25 2 9
NDEL1 0.032 0.012 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.047 -10000 0 -0.23 12 12
NDEL1/TACC3 0.042 0.049 -10000 0 -0.21 4 4
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GSK3B 0.039 0.016 -10000 0 -10000 0 0
PAK1/Aurora A 0.028 0.06 -10000 0 -0.24 18 18
MDM2 0.034 0.009 -10000 0 -10000 0 0
JUB 0.003 0.12 -10000 0 -0.42 35 35
TPX2 -0.007 0.083 -10000 0 -0.3 37 37
TP53 -0.004 0.093 -10000 0 -0.23 67 67
DLG7 -0.006 0.06 0.25 5 -0.18 39 44
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.045 0.052 -10000 0 -0.23 4 4
G2/M transition of mitotic cell cycle 0.028 0.047 -10000 0 -0.22 12 12
AURKA 0.024 0.035 -10000 0 -10000 0 0
AURKB 0.001 0.06 -10000 0 -0.18 43 43
CDC25B 0.014 0.048 -10000 0 -0.29 5 5
G2/M transition checkpoint 0.018 0.069 -10000 0 -0.22 35 35
mRNA polyadenylation 0.033 0.035 -10000 0 -0.2 5 5
Aurora A/CPEB 0.033 0.035 -10000 0 -0.2 5 5
Aurora A/TACC1/TRAP/chTOG 0.05 0.078 -10000 0 -0.23 23 23
BRCA1 0.022 0.07 -10000 0 -0.42 12 12
centrosome duplication 0.028 0.06 -10000 0 -0.24 18 18
regulation of centrosome cycle 0.041 0.048 -10000 0 -0.21 4 4
spindle assembly 0.048 0.076 -10000 0 -0.23 23 23
TDRD7 0.027 0.064 -10000 0 -0.42 10 10
Aurora A/RasGAP/Survivin 0.034 0.08 -10000 0 -0.21 27 27
CENPA -0.005 0.084 -10000 0 -0.27 43 43
Aurora A/PP2A 0.042 0.029 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.044 0.17 5 -0.24 1 6
negative regulation of DNA binding -0.006 0.097 -10000 0 -0.24 68 68
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.046 0.024 -10000 0 -0.3 1 1
RASA1 0.029 0.05 -10000 0 -0.42 6 6
Ajuba/Aurora A 0.019 0.069 -10000 0 -0.22 35 35
mitotic prometaphase 0.004 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.035 -10000 0 -10000 0 0
TACC1 0.011 0.089 -10000 0 -0.42 20 20
TACC3 0.017 0.087 -10000 0 -0.42 19 19
Aurora A/Antizyme1 0.037 0.025 -10000 0 -10000 0 0
Aurora A/RasGAP 0.038 0.042 -10000 0 -0.25 6 6
OAZ1 0.035 0.006 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.039 0.016 -10000 0 -10000 0 0
GIT1 0.034 0.022 -10000 0 -0.42 1 1
GIT1/beta-PIX/PAK1 0.044 0.068 -10000 0 -0.27 18 18
Importin alpha/Importin beta/TPX2 -0.007 0.082 -10000 0 -0.3 37 37
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.008 0.052 -10000 0 -0.16 37 37
PAK1 0.015 0.085 -10000 0 -0.42 18 18
CKAP5 0.036 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
HDAC3 0.036 0.006 -10000 0 -10000 0 0
VDR 0.02 0.082 -10000 0 -0.42 17 17
Cbp/p300/PCAF 0.041 0.026 -10000 0 -0.24 2 2
EP300 0.032 0.03 -10000 0 -0.42 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.014 0.057 0.19 1 -0.28 5 6
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
AKT1 0.028 0.092 0.21 55 -0.23 15 70
RAR alpha/9cRA/Cyclin H 0.045 0.1 0.26 1 -0.31 9 10
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.018 0.065 -10000 0 -0.21 21 21
CDC2 0.01 0.094 -10000 0 -0.42 22 22
response to UV -0.002 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.031 0.06 -10000 0 -0.25 11 11
NCOR2 0.036 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RXRs/RARs/NRIP1/9cRA -0.003 0.19 0.31 1 -0.53 52 53
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
NCOA3 0.032 0.03 -10000 0 -0.42 2 2
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARG 0.031 0.018 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.047 0.01 -10000 0 -10000 0 0
MAPK3 0.027 0.029 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
MAPK8 0.027 0.041 -10000 0 -0.42 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.027 0.13 -10000 0 -0.34 36 36
RARA 0.011 0.044 -10000 0 -0.23 10 10
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.055 -10000 0 -0.2 15 15
PRKCA 0.024 0.032 -10000 0 -0.091 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.008 0.2 -10000 0 -0.57 52 52
RXRG 0.011 0.045 -10000 0 -0.3 6 6
RXRA 0.017 0.09 -10000 0 -0.23 22 22
RXRB 0.017 0.037 -10000 0 -0.28 2 2
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RBP1 -0.028 0.15 -10000 0 -0.42 67 67
CRBP1/9-cic-RA -0.018 0.11 -10000 0 -0.3 67 67
RARB 0.011 0.09 -10000 0 -0.42 20 20
PRKCG 0.029 0.032 -10000 0 -10000 0 0
MNAT1 0.035 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs 0.004 0.14 0.42 1 -0.37 35 36
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.03 0.11 0.27 1 -0.34 14 15
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.074 0.23 1 -0.26 9 10
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.008 0.2 -10000 0 -0.58 52 52
positive regulation of DNA binding 0.033 0.095 -10000 0 -0.3 9 9
NRIP1 -0.071 0.38 -10000 0 -1.2 51 51
RXRs/RARs 0.011 0.16 -10000 0 -0.41 52 52
RXRs/RXRs/DNA/9cRA -0.008 0.11 -10000 0 -0.32 35 35
PRKACA 0.036 0.005 -10000 0 -10000 0 0
CDK7 0.034 0.008 -10000 0 -10000 0 0
TFIIH 0.068 0.024 -10000 0 -0.24 1 1
RAR alpha/9cRA 0.066 0.066 -10000 0 -0.22 4 4
CCNH 0.034 0.022 -10000 0 -0.42 1 1
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.065 0.028 -10000 0 -0.2 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.013 -9999 0 -10000 0 0
ELF1 0.014 0.096 -9999 0 -0.34 33 33
CCNA2 0.009 0.1 -9999 0 -0.42 28 28
PIK3CA 0.034 0.022 -9999 0 -0.42 1 1
JAK3 0.036 0.005 -9999 0 -10000 0 0
PIK3R1 0.02 0.08 -9999 0 -0.42 16 16
JAK1 0.033 0.036 -9999 0 -0.42 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.022 0.14 -9999 0 -0.4 24 24
SHC1 0.028 0.025 -9999 0 -0.42 1 1
SP1 0.032 0.073 -9999 0 -0.37 15 15
IL2RA -0.024 0.17 -9999 0 -0.61 36 36
IL2RB 0.012 0.097 -9999 0 -0.42 24 24
SOS1 0.035 0.021 -9999 0 -0.42 1 1
IL2RG 0.031 0.041 -9999 0 -0.42 4 4
G1/S transition of mitotic cell cycle -0.02 0.19 -9999 0 -0.54 44 44
PTPN11 0.037 0.004 -9999 0 -10000 0 0
CCND2 0.005 0.11 -9999 0 -0.68 13 13
LCK -0.017 0.14 -9999 0 -0.42 54 54
GRB2 0.034 0.011 -9999 0 -10000 0 0
IL2 0.033 0.036 -9999 0 -0.42 3 3
CDK6 0.025 0.058 -9999 0 -0.42 8 8
CCND3 0.025 0.13 -9999 0 -0.48 2 2
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.041 -10000 0 -0.42 4 4
RAS family/GTP/Tiam1 0.011 0.068 -10000 0 -0.28 19 19
NT3 (dimer)/TRKC 0.039 0.046 -10000 0 -0.3 8 8
NT3 (dimer)/TRKB 0.046 0.071 -10000 0 -0.26 22 22
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.05 -10000 0 -0.21 17 17
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
BDNF 0.031 0.024 -10000 0 -0.42 1 1
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DYNLT1 0.034 0.01 -10000 0 -10000 0 0
NTRK1 0.026 0.032 -10000 0 -0.42 2 2
NTRK2 0.02 0.078 -10000 0 -0.42 15 15
NTRK3 0.031 0.013 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.033 0.055 -10000 0 -0.25 17 17
neuron apoptosis 0.002 0.14 0.32 51 -0.28 2 53
SHC 2-3/Grb2 -0.003 0.15 0.32 1 -0.34 51 52
SHC1 0.028 0.025 -10000 0 -0.42 1 1
SHC2 -0.036 0.18 0.24 1 -0.44 75 76
SHC3 0.018 0.11 0.25 3 -0.44 17 20
STAT3 (dimer) -0.016 0.13 -10000 0 -0.34 69 69
NT3 (dimer)/TRKA 0.042 0.055 -10000 0 -0.25 11 11
RIN/GDP 0.068 0.084 0.24 26 -0.26 6 32
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
KRAS 0.028 0.054 -10000 0 -0.42 7 7
DNAJA3 0.007 0.057 0.21 18 -0.28 4 22
RIN/GTP 0.025 0.021 -10000 0 -0.3 2 2
CCND1 -0.077 0.24 -10000 0 -0.69 67 67
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
PTPN11 0.036 0.004 -10000 0 -10000 0 0
RICS 0.023 0.061 -10000 0 -0.42 9 9
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.036 -10000 0 -0.26 1 1
GRB2 0.033 0.011 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.033 0.033 -10000 0 -0.25 4 4
TRKA/NEDD4-2 0.021 0.08 -10000 0 -0.3 27 27
ELMO1 0.035 0.006 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.041 0.039 -10000 0 -0.25 8 8
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK1 0.028 0.057 -10000 0 -0.42 8 8
GAB2 0.031 0.013 -10000 0 -10000 0 0
RIT2 0.033 0.029 -10000 0 -0.42 2 2
RIT1 0.027 0.032 -10000 0 -0.42 2 2
FRS2 0.033 0.022 -10000 0 -0.42 1 1
DNM1 0.033 0.035 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.043 0.068 0.23 21 -0.25 5 26
mol:GDP 0.071 0.11 0.29 26 -0.38 7 33
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.026 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.041 0.071 0.25 7 -0.24 6 13
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
BDNF (dimer)/TRKB 0.052 0.064 -10000 0 -0.25 19 19
KIDINS220/CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
SHC/RasGAP 0.037 0.044 -10000 0 -0.3 6 6
FRS2 family/SHP2 0.067 0.025 -10000 0 -0.26 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.054 -10000 0 -0.23 6 6
RIT1/GTP 0.02 0.023 -10000 0 -0.3 2 2
NT3 (dimer) 0.023 0.058 -10000 0 -0.42 8 8
RAP1/GDP 0.048 0.067 0.18 17 -0.23 6 23
KIDINS220/CRKL 0.031 0.041 -10000 0 -0.42 4 4
BDNF (dimer) 0.031 0.024 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.02 0.068 -10000 0 -0.25 27 27
Schwann cell development -0.007 0.013 -10000 0 -10000 0 0
EHD4 0.031 0.041 -10000 0 -0.42 4 4
FRS2 family/GRB2/SOS1 0.077 0.041 -10000 0 -0.44 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.025 0.06 -10000 0 -0.32 2 2
RAP1B 0.033 0.03 -10000 0 -0.42 2 2
RAP1A 0.031 0.045 -10000 0 -0.42 5 5
CDC42/GTP 0.043 0.07 -10000 0 -0.22 26 26
ABL1 0.036 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
Rap1/GTP 0.023 0.092 -10000 0 -0.38 11 11
STAT3 -0.016 0.13 -10000 0 -0.34 69 69
axon guidance 0.026 0.061 -10000 0 -0.21 26 26
MAPK3 0.05 0.077 0.19 101 -0.23 5 106
MAPK1 0.051 0.077 0.19 103 -0.23 5 108
CDC42/GDP 0.069 0.085 0.24 30 -0.26 6 36
NTF3 0.023 0.058 -10000 0 -0.42 8 8
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.035 0.031 -10000 0 -0.25 3 3
PI3K 0.036 0.065 -10000 0 -0.3 17 17
FRS3 0.035 0.007 -10000 0 -10000 0 0
FAIM 0.035 0.021 -10000 0 -0.42 1 1
GAB1 0.027 0.061 -10000 0 -0.42 9 9
RASGRF1 0.008 0.062 0.22 19 -0.23 8 27
SOS1 0.035 0.021 -10000 0 -0.42 1 1
MCF2L 0.013 0.037 -10000 0 -0.25 9 9
RGS19 0.031 0.031 -10000 0 -0.42 2 2
CDC42 0.035 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.068 0.098 0.32 3 -0.37 8 11
Rac1/GDP 0.068 0.086 0.24 28 -0.27 5 33
NGF (dimer)/TRKA/GRIT 0.026 0.047 -10000 0 -0.25 11 11
neuron projection morphogenesis -0.005 0.2 0.44 2 -0.84 18 20
NGF (dimer)/TRKA/NEDD4-2 0.02 0.068 -10000 0 -0.25 27 27
MAP2K1 0.035 0.1 0.2 129 -0.22 6 135
NGFR 0.03 0.036 -10000 0 -0.42 3 3
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.038 -10000 0 -0.26 7 7
RAS family/GTP/PI3K 0.012 0.065 -10000 0 -0.24 27 27
FRS2 family/SHP2/GRB2/SOS1 0.09 0.047 -10000 0 -0.42 1 1
NRAS 0.029 0.054 -10000 0 -0.42 7 7
GRB2/SOS1 0.048 0.023 -10000 0 -0.3 1 1
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.005 0.061 -10000 0 -0.42 6 6
RASA1 0.029 0.05 -10000 0 -0.42 6 6
TRKA/c-Abl 0.04 0.031 -10000 0 -0.3 2 2
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
BDNF (dimer)/TRKB/GIPC 0.068 0.065 -10000 0 -0.23 18 18
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.047 -10000 0 -0.22 10 10
MATK 0.031 0.03 -10000 0 -0.42 2 2
NEDD4L 0.007 0.11 -10000 0 -0.42 31 31
RAS family/GDP -0.012 0.036 -10000 0 -0.18 10 10
NGF (dimer)/TRKA 0.011 0.058 0.23 17 -0.27 5 22
Rac1/GTP 0 0.052 -10000 0 -0.22 13 13
FRS2 family/SHP2/CRK family 0.082 0.055 -10000 0 -0.22 6 6
Regulation of Androgen receptor activity

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
HDAC1 0.016 0.015 -10000 0 -0.3 1 1
SMARCC1 0.003 0.12 -10000 0 -1.1 5 5
REL 0.024 0.07 -10000 0 -0.42 12 12
HDAC7 -0.036 0.1 0.21 2 -0.32 35 37
JUN -0.001 0.12 -10000 0 -0.42 39 39
EP300 0.032 0.03 -10000 0 -0.42 2 2
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 0 0.058 -10000 0 -0.31 15 15
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.007 0.13 -10000 0 -0.33 35 35
MAP2K6 0.011 0.08 -10000 0 -0.43 15 15
BRM/BAF57 0.048 0.024 -10000 0 -0.3 1 1
MAP2K4 0.023 0.031 -10000 0 -0.42 1 1
SMARCA2 0.034 0.022 -10000 0 -0.42 1 1
PDE9A -0.001 0.12 -10000 0 -0.99 5 5
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
CEBPA 0.024 0.07 -10000 0 -0.42 12 12
EHMT2 0.036 0.005 -10000 0 -10000 0 0
cell proliferation 0.027 0.13 0.32 15 -0.35 13 28
NR0B1 0.03 0.036 -10000 0 -0.42 3 3
EGR1 -0.037 0.16 -10000 0 -0.42 76 76
RXRs/9cRA 0.048 0.051 -10000 0 -0.23 11 11
AR/RACK1/Src 0.003 0.1 0.28 5 -0.27 22 27
AR/GR -0.026 0.12 0.23 2 -0.23 98 100
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
PKN1 0.033 0.035 -10000 0 -0.42 3 3
RCHY1 0.022 0.075 -10000 0 -0.42 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.033 -10000 0 -0.31 3 3
T-DHT/AR/TIF2/CARM1 0.01 0.092 0.36 1 -0.3 11 12
SRC -0.01 0.074 0.19 37 -0.24 18 55
NR3C1 0.024 0.072 -10000 0 -0.42 13 13
KLK3 -0.016 0.093 -10000 0 -10000 0 0
APPBP2 0.025 0.024 -10000 0 -10000 0 0
TRIM24 0.036 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.07 0.15 1 -0.27 23 24
TMPRSS2 -0.14 0.38 -10000 0 -0.95 87 87
RXRG 0.022 0.055 -10000 0 -0.42 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.029 -10000 0 -0.42 2 2
RXRB 0.034 0.029 -10000 0 -0.42 2 2
CARM1 0.035 0.021 -10000 0 -0.42 1 1
NR2C2 0.035 0.008 -10000 0 -10000 0 0
KLK2 0.011 0.075 0.31 3 -0.3 2 5
AR -0.032 0.11 0.19 1 -0.24 92 93
SENP1 0.036 0.006 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
SRY 0.024 0.07 -10000 0 -0.42 12 12
GATA2 0.029 0.046 -10000 0 -0.42 5 5
MYST2 0.032 0.03 -10000 0 -0.42 2 2
HOXB13 0.024 0.018 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.001 0.1 0.29 5 -0.28 22 27
positive regulation of transcription 0.029 0.046 -10000 0 -0.42 5 5
DNAJA1 0.024 0.042 -10000 0 -0.42 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.052 -10000 0 -0.3 13 13
NCOA1 0.036 0.054 -10000 0 -0.33 9 9
SPDEF -0.044 0.18 -10000 0 -0.42 90 90
T-DHT/AR/TIF2 0.014 0.078 0.24 8 -0.3 6 14
T-DHT/AR/Hsp90 -0.032 0.07 0.15 1 -0.27 23 24
GSK3B 0.036 0.005 -10000 0 -10000 0 0
NR2C1 0.03 0.05 -10000 0 -0.42 6 6
mol:T-DHT -0.008 0.072 0.21 30 -0.26 14 44
SIRT1 0.036 0.006 -10000 0 -10000 0 0
ZMIZ2 -0.001 0 -10000 0 -10000 0 0
POU2F1 0.017 0.055 -10000 0 -0.18 2 2
T-DHT/AR/DAX-1 -0.007 0.098 0.27 3 -0.29 22 25
CREBBP 0.033 0.011 -10000 0 -10000 0 0
SMARCE1 0.034 0.01 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.035 0.007 -10000 0 -10000 0 0
SPHK1 0.005 0.11 -10000 0 -0.42 30 30
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
mol:S1P 0.002 0.065 -10000 0 -0.27 25 25
GNAO1 0.03 0.014 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.003 0.074 -10000 0 -0.3 29 29
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.041 0.07 -10000 0 -0.22 23 23
GNAI3 0.035 0.006 -10000 0 -10000 0 0
G12/G13 0.044 0.033 -10000 0 -0.3 3 3
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.013 0.095 -10000 0 -0.42 23 23
S1P1/S1P 0.024 0.088 0.18 3 -0.25 37 40
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
S1P/S1P5/G12 0.029 0.066 -10000 0 -0.22 24 24
S1P/S1P3/Gq -0.001 0.095 -10000 0 -0.26 48 48
S1P/S1P4/Gi 0.002 0.094 -10000 0 -0.32 25 25
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
GNA11 0.033 0.036 -10000 0 -0.42 3 3
ABCC1 0.029 0.042 -10000 0 -0.42 4 4
FoxO family signaling

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
G6PC 0.041 0.096 -10000 0 -1.3 1 1
PLK1 0.01 0.2 -10000 0 -0.75 14 14
CDKN1B 0.042 0.17 -10000 0 -0.45 31 31
FOXO3 -0.005 0.22 -10000 0 -0.48 60 60
KAT2B 0.001 0.019 -10000 0 -0.043 62 62
FOXO1/SIRT1 0.044 0.054 -10000 0 -0.28 3 3
CAT -0.008 0.23 -10000 0 -0.91 16 16
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
AKT1 0.029 0.046 -10000 0 -0.41 2 2
FOXO1 0.026 0.053 0.24 1 -0.28 4 5
MAPK10 0.008 0.06 0.2 9 -0.21 24 33
mol:GTP 0 0.002 -10000 0 -10000 0 0
FOXO4 0.017 0.097 0.28 1 -0.32 19 20
response to oxidative stress 0.004 0.02 -10000 0 -0.053 22 22
FOXO3A/SIRT1 0.021 0.19 -10000 0 -0.45 52 52
XPO1 0.036 0.005 -10000 0 -10000 0 0
EP300 0.034 0.031 -10000 0 -0.42 2 2
BCL2L11 0.029 0.086 -10000 0 -1.2 2 2
FOXO1/SKP2 0.042 0.049 -10000 0 -0.3 2 2
mol:GDP 0.004 0.02 -10000 0 -0.053 22 22
RAN 0.036 0.005 -10000 0 -10000 0 0
GADD45A 0.012 0.22 -10000 0 -0.83 24 24
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
FOXO1/14-3-3 family 0.038 0.12 -10000 0 -0.42 15 15
MST1 0.028 0.036 -10000 0 -10000 0 0
CSNK1D 0.034 0.009 -10000 0 -10000 0 0
CSNK1E 0.034 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.13 -10000 0 -0.4 27 27
YWHAB 0.035 0.008 -10000 0 -10000 0 0
MAPK8 0.018 0.044 0.2 10 -0.21 7 17
MAPK9 0.01 0.058 0.2 8 -0.22 22 30
YWHAG 0.036 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
SIRT1 0.036 0.02 -10000 0 -10000 0 0
SOD2 0.031 0.16 -10000 0 -0.64 12 12
RBL2 -0.076 0.31 -10000 0 -0.73 76 76
RAL/GDP 0.046 0.037 -10000 0 -0.24 4 4
CHUK 0.019 0.074 -10000 0 -0.42 11 11
Ran/GTP 0.026 0.01 -10000 0 -10000 0 0
CSNK1G2 0.033 0.029 -10000 0 -0.42 2 2
RAL/GTP 0.046 0.038 -10000 0 -0.22 4 4
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
FASLG -0.092 0.4 -10000 0 -1.4 45 45
SKP2 0.034 0.009 -10000 0 -10000 0 0
USP7 0.033 0.012 -10000 0 -10000 0 0
IKBKB 0.023 0.035 -10000 0 -10000 0 0
CCNB1 -0.051 0.33 -10000 0 -1.1 37 37
FOXO1-3a-4/beta catenin 0.039 0.16 0.42 1 -0.4 29 30
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -10000 0 -0.3 2 2
CSNK1A1 0.036 0.006 -10000 0 -10000 0 0
SGK1 0.001 0.019 -10000 0 -0.043 62 62
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.049 0.013 -10000 0 -10000 0 0
ZFAND5 0.018 0.084 0.26 1 -0.26 19 20
SFN 0.012 0.099 -10000 0 -0.42 25 25
CDK2 0.036 0.03 -10000 0 -0.31 3 3
FOXO3A/14-3-3 0.016 0.12 -10000 0 -0.38 24 24
CREBBP 0.035 0.013 -10000 0 -0.099 1 1
FBXO32 0.023 0.3 0.44 2 -1.1 22 24
BCL6 -0.007 0.27 -10000 0 -1.1 22 22
RALB 0.033 0.041 -10000 0 -0.42 4 4
RALA 0.036 0.007 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.097 -10000 0 -1 4 4
MKNK1 0.035 0.006 -10000 0 -10000 0 0
MAPK14 0.031 0.049 -10000 0 -0.3 4 4
ATF2/c-Jun -0.022 0.16 -10000 0 -0.54 40 40
MAPK11 0.03 0.048 -10000 0 -0.3 4 4
MITF 0.02 0.053 -10000 0 -0.33 8 8
MAPKAPK5 0.023 0.043 -10000 0 -0.33 4 4
KRT8 0.011 0.073 -10000 0 -0.28 25 25
MAPKAPK3 0.035 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.043 -10000 0 -0.42 4 4
p38alpha-beta/CK2 0.041 0.065 -10000 0 -0.43 4 4
CEBPB 0.019 0.054 -10000 0 -0.32 9 9
SLC9A1 0.023 0.043 -10000 0 -0.33 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.07 0.23 1 -0.31 8 9
p38alpha-beta/MNK1 0.056 0.06 -10000 0 -0.36 3 3
JUN -0.025 0.16 -10000 0 -0.54 40 40
PPARGC1A 0.016 0.068 -10000 0 -0.34 13 13
USF1 0.013 0.057 -10000 0 -0.29 13 13
RAB5/GDP/GDI1 0.024 0.053 -10000 0 -0.23 5 5
NOS2 0.016 0.042 -10000 0 -0.34 4 4
DDIT3 0.023 0.045 -10000 0 -0.32 5 5
RAB5A 0.036 0.006 -10000 0 -10000 0 0
HSPB1 -0.012 0.084 0.28 2 -0.26 48 50
p38alpha-beta/HBP1 0.053 0.068 -10000 0 -0.31 7 7
CREB1 0.015 0.061 -10000 0 -0.3 9 9
RAB5/GDP 0.026 0.004 -10000 0 -10000 0 0
EIF4E 0.016 0.045 0.24 2 -0.32 3 5
RPS6KA4 0.022 0.048 -10000 0 -0.36 5 5
PLA2G4A 0.001 0.064 -10000 0 -0.28 20 20
GDI1 0.023 0.045 -10000 0 -0.32 5 5
TP53 0 0.061 -10000 0 -0.33 9 9
RPS6KA5 0.009 0.075 -10000 0 -0.28 27 27
ESR1 -0.055 0.14 -10000 0 -0.28 132 132
HBP1 0.033 0.036 -10000 0 -0.42 3 3
MEF2C 0.01 0.08 -10000 0 -0.32 24 24
MEF2A 0.022 0.045 -10000 0 -0.32 5 5
EIF4EBP1 0.01 0.066 -10000 0 -0.3 14 14
KRT19 -0.002 0.09 -10000 0 -0.28 43 43
ELK4 0.018 0.041 -10000 0 -0.31 4 4
ATF6 0.018 0.044 -10000 0 -0.32 5 5
ATF1 0.016 0.062 -10000 0 -0.3 9 9
p38alpha-beta/MAPKAPK2 0.042 0.069 -10000 0 -0.35 6 6
p38alpha-beta/MAPKAPK3 0.054 0.063 -10000 0 -0.35 4 4
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 0.041 0.019 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.018 0.078 -10000 0 -0.42 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.024 -10000 0 -0.42 1 1
RAC1-CDC42/GTP/PAK family 0.002 0.065 -10000 0 -0.21 39 39
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.013 -10000 0 -10000 0 0
FYN 0.027 0.054 -10000 0 -0.42 7 7
MAP3K12 0.036 0.004 -10000 0 -10000 0 0
FGR 0.035 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.005 0.14 0.23 1 -0.34 51 52
PRKG1 0.035 0.006 -10000 0 -10000 0 0
DUSP8 0.02 0.08 -10000 0 -0.42 16 16
PGK/cGMP/p38 alpha -0.009 0.14 0.21 1 -0.33 53 54
apoptosis -0.005 0.14 0.22 1 -0.32 51 52
RAL/GTP 0.045 0.028 -10000 0 -0.25 4 4
LYN 0.03 0.014 -10000 0 -10000 0 0
DUSP1 0.003 0.11 -10000 0 -0.42 34 34
PAK1 0.015 0.085 -10000 0 -0.42 18 18
SRC 0.033 0.029 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 0.073 0.041 -10000 0 -0.23 1 1
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.035 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.046 0.013 -10000 0 -10000 0 0
MAPK11 -0.014 0.14 0.24 3 -0.38 41 44
BLK 0.022 0.038 -10000 0 -0.42 3 3
HCK 0.018 0.087 -10000 0 -0.42 19 19
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
DUSP16 0.03 0.046 -10000 0 -0.42 5 5
DUSP10 0.013 0.082 -10000 0 -0.42 17 17
TRAF6/MEKK3 0.039 0.021 -10000 0 -0.23 1 1
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
MAPK14 -0.018 0.14 0.21 5 -0.34 59 64
positive regulation of innate immune response -0.018 0.17 0.26 5 -0.42 50 55
LCK -0.017 0.14 -10000 0 -0.42 54 54
p38alpha-beta/MKP7 -0.007 0.17 0.28 3 -0.4 50 53
p38alpha-beta/MKP5 -0.013 0.16 0.29 2 -0.4 47 49
PGK/cGMP 0.026 0.004 -10000 0 -10000 0 0
PAK2 0.036 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.018 0.17 0.27 5 -0.41 53 58
CDC42 0.035 0.008 -10000 0 -10000 0 0
RALB 0.032 0.041 -10000 0 -0.42 4 4
RALA 0.035 0.007 -10000 0 -10000 0 0
PAK3 0.016 0.085 -10000 0 -0.42 18 18
Glypican 2 network

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
MDK 0.018 0.085 -9999 0 -0.42 18 18
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.014 0.06 -9999 0 -0.3 18 18
neuron projection morphogenesis 0.014 0.06 -9999 0 -0.3 18 18
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.058 -10000 0 -0.2 27 27
TRAF2/ASK1 0.029 0.066 -10000 0 -0.25 25 25
ATM 0.031 0.013 -10000 0 -10000 0 0
MAP2K3 -0.051 0.16 0.28 2 -0.39 68 70
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.042 0.14 0.29 1 -0.35 54 55
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.027 0.064 -10000 0 -0.42 10 10
TXN 0.009 0.002 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GADD45B 0.025 0.067 -10000 0 -0.42 11 11
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
MAP3K6 0.034 0.022 -10000 0 -0.42 1 1
MAP3K7 0.033 0.011 -10000 0 -10000 0 0
MAP3K4 0.034 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.075 -10000 0 -0.3 24 24
TAK1/TAB family 0.014 0.037 -10000 0 -0.26 6 6
RAC1/OSM/MEKK3 0.058 0.027 -10000 0 -10000 0 0
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 -0.019 0.14 -10000 0 -0.32 49 49
TRAF6 0.016 0.024 -10000 0 -0.28 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.012 0.13 -10000 0 -0.42 47 47
CCM2 0.035 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.015 0.086 -10000 0 -0.25 47 47
MAPK11 0.033 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.018 0.1 -10000 0 -0.23 68 68
OSM/MEKK3 0.045 0.02 -10000 0 -10000 0 0
TAOK1 0.012 0.033 -10000 0 -0.29 6 6
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.016 0.015 -10000 0 -0.29 1 1
MAP3K7IP1 0.034 0.009 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0.032 0.03 -10000 0 -0.42 2 2
MAP3K5 0.012 0.095 -10000 0 -0.42 23 23
MAP3K10 0.023 0.075 -10000 0 -0.42 14 14
MAP3K3 0.031 0.013 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.06 -10000 0 -0.24 23 23
GADD45/MTK1/MTK1 0.054 0.082 -10000 0 -0.23 33 33
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.046 0.034 -10000 0 -0.3 4 4
CRKL 0.006 0.1 0.3 2 -0.46 15 17
mol:PIP3 0.011 0.054 0.39 9 -10000 0 9
AKT1 0.022 0.078 0.37 6 -10000 0 6
PTK2B 0.028 0.015 -10000 0 -10000 0 0
RAPGEF1 0.004 0.097 0.32 1 -0.45 14 15
RANBP10 0.03 0.014 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
HGF/MET/SHIP2 0.054 0.059 -10000 0 -0.26 15 15
MAP3K5 0 0.11 0.29 1 -0.44 15 16
HGF/MET/CIN85/CBL/ENDOPHILINS 0.064 0.073 -10000 0 -0.25 20 20
AP1 -0.022 0.13 -10000 0 -0.3 88 88
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
apoptosis -0.14 0.34 -10000 0 -0.77 109 109
STAT3 (dimer) 0.01 0.07 -10000 0 -0.31 7 7
GAB1/CRKL/SHP2/PI3K 0.042 0.12 0.34 1 -0.43 15 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.024 0.097 -10000 0 -0.44 13 13
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.034 0.008 -10000 0 -10000 0 0
PTEN 0.027 0.061 -10000 0 -0.42 9 9
ELK1 -0.001 0.072 0.27 19 -10000 0 19
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.015 0.046 -10000 0 -0.21 5 5
PAK1 0.028 0.099 0.39 11 -10000 0 11
HGF/MET/RANBP10 0.05 0.055 -10000 0 -0.25 12 12
HRAS 0.014 0.1 -10000 0 -0.47 15 15
DOCK1 0.003 0.1 0.31 2 -0.45 14 16
GAB1 0.008 0.1 -10000 0 -0.48 15 15
CRK 0.005 0.098 -10000 0 -0.45 15 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.1 -10000 0 -0.42 22 22
JUN -0.001 0.12 -10000 0 -0.42 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.042 -10000 0 -0.2 17 17
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
cell morphogenesis 0.007 0.1 0.28 11 -0.34 9 20
GRB2/SHC 0.034 0.052 -10000 0 -0.21 7 7
FOS -0.031 0.15 -10000 0 -0.42 66 66
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.001 0.072 0.26 19 -10000 0 19
HGF/MET/MUC20 0.039 0.047 -10000 0 -0.25 12 12
cell migration 0.034 0.051 -10000 0 -0.21 7 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
CBL 0.032 0.012 -10000 0 -10000 0 0
MET/RANBP10 0.039 0.037 -10000 0 -0.29 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.054 -10000 0 -0.23 15 15
MET/MUC20 0.022 0.029 -10000 0 -0.3 4 4
RAP1B 0.008 0.099 0.29 5 -0.43 13 18
RAP1A 0.001 0.097 0.31 1 -0.43 16 17
HGF/MET/RANBP9 0.059 0.053 -10000 0 -0.26 12 12
RAF1 0.017 0.1 -10000 0 -0.45 14 14
STAT3 0.009 0.069 -10000 0 -0.31 7 7
cell proliferation 0.042 0.1 0.27 18 -0.32 10 28
RPS6KB1 0.01 0.048 -10000 0 -0.29 10 10
MAPK3 -0.017 0.082 0.62 6 -10000 0 6
MAPK1 0.007 0.15 0.65 26 -10000 0 26
RANBP9 0.035 0.007 -10000 0 -10000 0 0
MAPK8 0.01 0.11 0.29 1 -0.43 14 15
SRC 0.009 0.063 -10000 0 -0.26 6 6
PI3K 0.033 0.074 -10000 0 -0.22 28 28
MET/Glomulin 0.021 0.037 -10000 0 -0.24 5 5
SOS1 0.035 0.021 -10000 0 -0.42 1 1
MAP2K1 0.015 0.096 -10000 0 -0.43 14 14
MET 0.03 0.041 -10000 0 -0.42 4 4
MAP4K1 0.008 0.11 0.31 1 -0.46 15 16
PTK2 0.028 0.016 -10000 0 -10000 0 0
MAP2K2 0.014 0.098 -10000 0 -0.42 15 15
BAD 0.017 0.074 0.38 4 -10000 0 4
MAP2K4 -0.001 0.1 0.28 1 -0.42 13 14
SHP2/GRB2/SOS1/GAB1 0.044 0.098 -10000 0 -0.39 15 15
INPPL1 0.031 0.036 -10000 0 -0.42 3 3
PXN 0.036 0.004 -10000 0 -10000 0 0
SH3KBP1 0.027 0.064 -10000 0 -0.42 10 10
HGS 0 0.04 -10000 0 -0.18 20 20
PLCgamma1/PKC 0.025 0.006 -10000 0 -10000 0 0
HGF 0.028 0.057 -10000 0 -0.42 8 8
RASA1 0.029 0.05 -10000 0 -0.42 6 6
NCK1 0.034 0.021 -10000 0 -0.42 1 1
PTPRJ 0.031 0.046 -10000 0 -0.42 5 5
NCK/PLCgamma1 0.047 0.056 -10000 0 -0.18 21 21
PDPK1 0.027 0.08 0.33 10 -10000 0 10
HGF/MET/SHIP 0.039 0.047 -10000 0 -0.25 12 12
TCGA08_rtk_signaling

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
PDGFRA 0.009 0.11 -10000 0 -0.42 29 29
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.015 0.13 -10000 0 -0.42 49 49
AKT 0.027 0.084 0.24 4 -0.28 11 15
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.033 0.03 -10000 0 -0.42 2 2
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.025 0.032 -10000 0 -0.42 2 2
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.03 0.041 -10000 0 -0.42 4 4
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PIK3CB 0.031 0.045 -10000 0 -0.42 5 5
NRAS 0.029 0.054 -10000 0 -0.42 7 7
PIK3CG 0.023 0.072 -10000 0 -0.42 13 13
PIK3R3 0.025 0.067 -10000 0 -0.42 11 11
PIK3R2 0.036 0.004 -10000 0 -10000 0 0
NF1 0.032 0.03 -10000 0 -0.42 2 2
RAS -0.002 0.079 0.17 3 -0.2 51 54
ERBB2 0.017 0.078 -10000 0 -0.42 15 15
proliferation/survival/translation -0.026 0.058 0.22 10 -0.18 6 16
PI3K 0.004 0.084 0.19 7 -0.23 35 42
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
KRAS 0.028 0.054 -10000 0 -0.42 7 7
FOXO 0.043 0.04 0.18 11 -10000 0 11
AKT2 0.036 0.005 -10000 0 -10000 0 0
PTEN 0.027 0.061 -10000 0 -0.42 9 9
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
mol:S1P 0.001 0.002 -10000 0 -0.025 3 3
S1P1/S1P/Gi -0.016 0.11 -10000 0 -0.3 43 43
GNAO1 0.031 0.015 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.039 0.028 -10000 0 -0.23 3 3
AKT1 0.003 0.12 -10000 0 -0.46 29 29
AKT3 -0.004 0.12 -10000 0 -0.69 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
GNAI2 0.029 0.054 -10000 0 -0.42 7 7
GNAI3 0.036 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.087 -10000 0 -0.42 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.002 -10000 0 -0.03 3 3
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.013 0.095 -10000 0 -0.42 23 23
mol:Ca2+ 0.006 0.083 -10000 0 -0.32 20 20
MAPK3 -0.002 0.074 -10000 0 -0.32 14 14
MAPK1 0 0.076 -10000 0 -0.33 15 15
JAK2 -0.014 0.1 0.22 1 -0.35 27 28
CXCR4 -0.013 0.1 -10000 0 -0.35 26 26
FLT1 0.027 0.058 -10000 0 -0.42 8 8
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
SRC -0.004 0.081 -10000 0 -0.33 17 17
S1P/S1P3/Gi 0.006 0.083 -10000 0 -0.32 20 20
RAC1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.005 0.096 -10000 0 -0.31 20 20
VEGFA 0.002 0.003 -10000 0 -0.04 3 3
S1P/S1P2/Gi 0.004 0.08 -10000 0 -0.24 40 40
VEGFR1 homodimer/VEGFA homodimer 0.024 0.042 -10000 0 -0.25 10 10
RHOA 0.026 0.061 -10000 0 -0.42 9 9
S1P/S1P3/Gq -0.006 0.079 -10000 0 -0.23 49 49
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.07 -10000 0 -0.42 12 12
G12/G13 0.044 0.033 -10000 0 -0.3 3 3
GNA14 -0.009 0.13 -10000 0 -0.42 43 43
GNA15 0.03 0.046 -10000 0 -0.42 5 5
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
GNA11 0.033 0.036 -10000 0 -0.42 3 3
Rac1/GTP 0.008 0.092 -10000 0 -0.32 17 17
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.039 0.051 0.3 7 -10000 0 7
KIRREL 0.025 0.057 -10000 0 -0.43 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.04 0.051 -10000 0 -0.31 7 7
PLCG1 0.034 0.008 -10000 0 -10000 0 0
ARRB2 0.033 0.011 -10000 0 -10000 0 0
WASL 0.029 0.054 -10000 0 -0.42 7 7
Nephrin/NEPH1/podocin/CD2AP 0.065 0.059 -10000 0 -0.24 7 7
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.022 0.045 -10000 0 -0.21 13 13
FYN 0.057 0.1 0.28 66 -0.21 13 79
mol:Ca2+ 0.059 0.057 -10000 0 -0.23 7 7
mol:DAG 0.06 0.058 -10000 0 -0.24 7 7
NPHS2 0.03 0.03 -10000 0 -0.43 1 1
mol:IP3 0.06 0.058 -10000 0 -0.24 7 7
regulation of endocytosis 0.046 0.057 -10000 0 -0.2 13 13
Nephrin/NEPH1/podocin/Cholesterol 0.049 0.049 -10000 0 -0.23 7 7
establishment of cell polarity 0.039 0.051 -10000 0 -0.3 7 7
Nephrin/NEPH1/podocin/NCK1-2 0.076 0.065 -10000 0 -0.22 8 8
Nephrin/NEPH1/beta Arrestin2 0.051 0.06 -10000 0 -0.2 13 13
NPHS1 0.041 0.03 -10000 0 -0.38 1 1
Nephrin/NEPH1/podocin 0.048 0.057 0.2 11 -0.21 13 24
TJP1 0.032 0.036 -10000 0 -0.42 3 3
NCK1 0.034 0.021 -10000 0 -0.42 1 1
NCK2 0.036 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.061 0.059 -10000 0 -0.24 7 7
CD2AP 0.035 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.061 0.059 -10000 0 -0.24 7 7
GRB2 0.033 0.011 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.057 0.1 0.28 68 -0.22 11 79
cytoskeleton organization 0.023 0.069 0.23 31 -0.25 7 38
Nephrin/NEPH1 0.035 0.037 -10000 0 -0.21 7 7
Nephrin/NEPH1/ZO-1 0.051 0.056 -10000 0 -0.25 10 10
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.015 0.063 -10000 0 -0.33 14 14
CRKL 0.031 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DOCK1 0.028 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
alpha4/beta7 Integrin/MAdCAM1 0.069 0.075 -10000 0 -0.25 22 22
EPO 0.03 0.014 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.042 0.061 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.039 0.069 -10000 0 -0.33 16 16
EPO/EPOR (dimer) 0.048 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.084 -10000 0 -0.4 9 9
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.036 0.065 -10000 0 -0.3 17 17
ARF6 0.034 0.029 -10000 0 -0.42 2 2
JAK2 0.024 0.049 -10000 0 -0.25 14 14
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
MADCAM1 0.034 0.008 -10000 0 -10000 0 0
cell adhesion 0.066 0.074 -10000 0 -0.25 22 22
CRKL/CBL 0.043 0.037 -10000 0 -0.3 4 4
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
SRC 0.001 0.087 -10000 0 -0.27 39 39
ITGB7 0.036 0.005 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.1 -10000 0 -0.3 37 37
p130Cas/Crk/Dock1 0.018 0.088 -10000 0 -0.24 39 39
VCAM1 0.009 0.1 -10000 0 -0.42 28 28
RHOA 0.026 0.061 -10000 0 -0.42 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.073 0.068 -10000 0 -0.26 17 17
BCAR1 -0.024 0.075 0.18 16 -0.25 35 51
EPOR 0.036 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.012 -10000 0 -10000 0 0
GIT1 0.034 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.013 0.086 -10000 0 -0.41 9 9
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.001 0.09 0.25 29 -10000 0 29
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
S1P/S1P5/G12 0.024 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.092 -10000 0 -0.26 29 29
negative regulation of cAMP metabolic process 0 0.076 -10000 0 -0.24 40 40
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNA12 0.035 0.007 -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 0.077 -10000 0 -0.24 40 40
RhoA/GDP 0.02 0.043 -10000 0 -0.3 9 9
RHOA 0.026 0.061 -10000 0 -0.42 9 9
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.036 0.071 -10000 0 -0.31 19 19
AKT1 0.011 0.12 0.32 1 -0.39 21 22
PTK2B 0 0.089 0.36 1 -0.48 8 9
VEGFR2 homodimer/Frs2 0.029 0.078 -10000 0 -0.38 13 13
CAV1 0.027 0.054 -10000 0 -0.42 7 7
CALM1 0.035 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.027 0.082 -10000 0 -0.5 7 7
endothelial cell proliferation 0.034 0.12 0.32 11 -0.44 8 19
mol:Ca2+ 0.005 0.097 -10000 0 -0.46 10 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.045 0.085 -10000 0 -0.46 8 8
RP11-342D11.1 -0.01 0.096 -10000 0 -0.31 33 33
CDH5 0.027 0.037 -10000 0 -0.42 3 3
VEGFA homodimer 0.037 0.087 -10000 0 -0.23 44 44
SHC1 0.028 0.025 -10000 0 -0.42 1 1
SHC2 -0.025 0.15 -10000 0 -0.42 66 66
HRAS/GDP 0.02 0.09 -10000 0 -0.43 8 8
SH2D2A -0.001 0.11 -10000 0 -0.42 30 30
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.035 0.11 -10000 0 -0.51 8 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.005 0.1 -10000 0 -0.47 10 10
VEGFR1 homodimer 0.026 0.057 -10000 0 -0.42 8 8
SHC/GRB2/SOS1 0.043 0.1 -10000 0 -0.44 9 9
GRB10 -0.003 0.12 -10000 0 -0.5 20 20
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.011 -10000 0 -10000 0 0
PAK1 0.015 0.085 -10000 0 -0.42 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.042 0.1 -10000 0 -0.44 11 11
HRAS 0.032 0.036 -10000 0 -0.42 3 3
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.1 -10000 0 -0.34 25 25
HIF1A -0.007 0.13 -10000 0 -0.42 46 46
FRS2 0.033 0.022 -10000 0 -0.42 1 1
oxygen and reactive oxygen species metabolic process 0.043 0.084 -10000 0 -0.45 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.035 0.006 -10000 0 -10000 0 0
Nck/Pak 0.032 0.068 -10000 0 -0.3 19 19
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.095 -10000 0 -0.38 17 17
mol:GDP 0.031 0.096 -10000 0 -0.43 9 9
mol:NADP 0.019 0.1 -10000 0 -0.44 9 9
eNOS/Hsp90 0.017 0.097 -10000 0 -0.41 9 9
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
mol:IP3 0.004 0.098 -10000 0 -0.47 10 10
HIF1A/ARNT 0.02 0.1 -10000 0 -0.3 44 44
SHB 0.031 0.046 -10000 0 -0.42 5 5
VEGFA -0.001 0.015 -10000 0 -10000 0 0
VEGFC 0.022 0.075 -10000 0 -0.42 14 14
FAK1/Vinculin 0.015 0.12 0.34 2 -0.45 13 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.034 0.1 -10000 0 -0.48 9 9
PTPN6 0.032 0.03 -10000 0 -0.42 2 2
EPAS1 0.028 0.077 -10000 0 -0.4 14 14
mol:L-citrulline 0.019 0.1 -10000 0 -0.44 9 9
ITGAV 0.022 0.078 -10000 0 -0.42 15 15
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.042 0.081 -10000 0 -0.45 7 7
VEGFR2 homodimer/VEGFA homodimer 0.023 0.11 -10000 0 -0.33 34 34
VEGFR2/3 heterodimer 0.03 0.078 -10000 0 -0.39 12 12
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
MAPK11 -0.014 0.11 0.26 1 -0.44 16 17
VEGFR2 homodimer 0.012 0.084 -10000 0 -0.44 13 13
FLT1 0.026 0.058 -10000 0 -0.42 8 8
NEDD4 0.021 0.071 -10000 0 -0.42 11 11
MAPK3 0.003 0.095 0.27 7 -0.38 10 17
MAPK1 -0.002 0.095 0.25 6 -0.41 10 16
VEGFA145/NRP2 0.023 0.023 -10000 0 -0.32 1 1
VEGFR1/2 heterodimer 0.024 0.089 -10000 0 -0.37 18 18
KDR 0.012 0.084 -10000 0 -0.44 13 13
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.11 -10000 0 -0.31 32 32
SRC 0.033 0.029 -10000 0 -0.42 2 2
platelet activating factor biosynthetic process 0.003 0.099 0.27 6 -0.41 10 16
PI3K 0.005 0.13 -10000 0 -0.49 15 15
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.027 0.083 -10000 0 -0.48 8 8
FES 0.001 0.11 -10000 0 -0.51 10 10
GAB1 0.016 0.12 -10000 0 -0.42 22 22
VEGFR2 homodimer/VEGFA homodimer/Src 0.027 0.081 -10000 0 -0.46 8 8
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
SOS1 0.035 0.021 -10000 0 -0.42 1 1
ARNT 0.035 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.031 0.11 -10000 0 -0.44 10 10
VEGFR2 homodimer/VEGFA homodimer/Yes 0.023 0.088 -10000 0 -0.42 11 11
PI3K/GAB1 0.02 0.14 0.28 1 -0.43 20 21
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.042 0.098 -10000 0 -0.41 8 8
PRKACA 0.036 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.099 -10000 0 -0.38 18 18
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.004 0.1 -10000 0 -0.49 10 10
actin cytoskeleton reorganization 0.004 0.1 -10000 0 -0.47 10 10
PTK2 -0.006 0.1 -10000 0 -0.51 12 12
EDG1 -0.006 0.14 -10000 0 -0.52 27 27
mol:DAG 0.004 0.098 -10000 0 -0.47 10 10
CaM/Ca2+ 0.021 0.096 -10000 0 -0.45 9 9
MAP2K3 -0.011 0.098 -10000 0 -0.45 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.016 0.13 -10000 0 -0.51 20 20
PLCG1 0.004 0.099 -10000 0 -0.47 10 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.088 -10000 0 -0.42 9 9
IQGAP1 0.035 0.008 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.083 -10000 0 -0.45 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.027 0.082 -10000 0 -0.48 8 8
cell migration 0.017 0.1 0.3 3 -0.47 9 12
mol:PI-3-4-5-P3 0.006 0.12 -10000 0 -0.45 15 15
FYN 0.027 0.054 -10000 0 -0.42 7 7
VEGFB/NRP1 0.009 0.1 -10000 0 -0.47 10 10
mol:NO 0.019 0.1 -10000 0 -0.44 9 9
PXN 0.036 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.082 -10000 0 -0.43 8 8
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.005 0.13 -10000 0 -0.51 20 20
VHL 0.035 0.007 -10000 0 -10000 0 0
ITGB3 0.029 0.046 -10000 0 -0.42 5 5
NOS3 0.018 0.11 -10000 0 -0.5 9 9
VEGFR2 homodimer/VEGFA homodimer/Sck -0.005 0.12 -10000 0 -0.36 24 24
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.006 0.084 -10000 0 -0.47 7 7
PRKCB -0.009 0.089 -10000 0 -0.44 10 10
VCL 0.035 0.021 -10000 0 -0.42 1 1
VEGFA165/NRP1 -0.007 0.095 -10000 0 -0.3 34 34
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.092 -10000 0 -0.38 15 15
VEGFA165/NRP2 0.023 0.023 -10000 0 -0.32 1 1
MAPKKK cascade 0.032 0.12 0.34 3 -0.44 16 19
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFC homodimer 0.022 0.075 -10000 0 -0.42 14 14
NCK1 0.034 0.021 -10000 0 -0.42 1 1
ROCK1 0.036 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.015 0.12 0.34 2 -0.46 13 15
MAP3K13 0.001 0.11 -10000 0 -0.47 12 12
PDPK1 -0.002 0.1 0.26 2 -0.39 15 17
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.024 0.17 -10000 0 -0.86 11 11
NCK1/PAK1/Dok-R -0.028 0.076 -10000 0 -0.42 11 11
NCK1/Dok-R 0.031 0.15 -10000 0 -0.86 9 9
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
mol:beta2-estradiol -0.007 0.015 0.31 1 -10000 0 1
RELA 0.035 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
Rac/GDP 0.026 0.004 -10000 0 -10000 0 0
F2 0.011 0.025 -10000 0 -10000 0 0
TNIP2 0.033 0.03 -10000 0 -0.42 2 2
NF kappa B/RelA 0.063 0.14 -10000 0 -0.79 9 9
FN1 -0.01 0.14 -10000 0 -0.42 50 50
PLD2 0.021 0.13 -10000 0 -0.85 9 9
PTPN11 0.036 0.004 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
ELK1 0.024 0.13 -10000 0 -0.81 9 9
GRB7 0.024 0.058 -10000 0 -0.42 8 8
PAK1 0.015 0.085 -10000 0 -0.42 18 18
Tie2/Ang1/alpha5/beta1 Integrin 0.04 0.17 -10000 0 -0.88 9 9
CDKN1A 0.001 0.19 -10000 0 -0.74 25 25
ITGA5 0.034 0.029 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.028 0.15 -10000 0 -0.86 9 9
CRK 0.032 0.023 -10000 0 -0.42 1 1
mol:NO 0.027 0.13 -10000 0 -0.63 10 10
PLG 0.019 0.13 -10000 0 -0.85 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.017 0.15 -10000 0 -0.82 10 10
GRB2 0.033 0.011 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
ANGPT2 -0.055 0.21 -10000 0 -0.83 18 18
BMX 0.009 0.15 -10000 0 -0.94 10 10
ANGPT1 0.015 0.035 -10000 0 -10000 0 0
tube development -0.003 0.17 -10000 0 -0.73 14 14
ANGPT4 0.035 0.022 -10000 0 -0.42 1 1
response to hypoxia 0 0.01 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.009 0.16 -10000 0 -0.88 9 9
alpha5/beta1 Integrin 0.048 0.037 -10000 0 -0.3 5 5
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
STAT5A (dimer) -0.001 0.2 -10000 0 -0.8 20 20
mol:L-citrulline 0.027 0.13 -10000 0 -0.63 10 10
AGTR1 -0.046 0.16 -10000 0 -0.42 80 80
MAPK14 0.019 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.011 0.17 -10000 0 -0.85 12 12
TEK 0.005 0.17 -10000 0 -0.96 11 11
RPS6KB1 0.036 0.16 -10000 0 -0.82 11 11
Angiotensin II/AT1 -0.03 0.12 -10000 0 -0.29 80 80
Tie2/Ang1/GRB2 0.034 0.14 -10000 0 -0.85 9 9
MAPK3 0.026 0.13 -10000 0 -0.78 9 9
MAPK1 0.016 0.12 -10000 0 -0.8 9 9
Tie2/Ang1/GRB7 0.03 0.14 -10000 0 -0.85 9 9
NFKB1 0.036 0.005 -10000 0 -10000 0 0
MAPK8 0.02 0.13 -10000 0 -0.85 9 9
PI3K 0.021 0.18 -10000 0 -0.99 11 11
FES 0.014 0.19 -10000 0 -1 13 13
Crk/Dok-R 0.03 0.15 -10000 0 -0.86 9 9
Tie2/Ang1/ABIN2 0.035 0.14 -10000 0 -0.86 9 9
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.026 0.15 -10000 0 -0.76 11 11
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.055 0.17 -10000 0 -0.81 10 10
Tie2/Ang2 -0.012 0.21 -10000 0 -1 14 14
Tie2/Ang1 0.026 0.14 -10000 0 -0.9 9 9
FOXO1 0.026 0.16 -10000 0 -0.77 11 11
ELF1 0.034 0.053 -10000 0 -0.41 6 6
ELF2 0.027 0.13 -10000 0 -0.88 8 8
mol:Choline 0.02 0.12 -10000 0 -0.82 9 9
cell migration -0.013 0.052 -10000 0 -0.22 14 14
FYN -0.007 0.19 -10000 0 -0.85 14 14
DOK2 0.009 0.086 -10000 0 -0.42 19 19
negative regulation of cell cycle 0.005 0.18 -10000 0 -0.66 25 25
ETS1 0.035 0.028 -10000 0 -0.43 1 1
PXN 0.055 0.15 -10000 0 -0.67 10 10
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
NOS3 0.024 0.14 -10000 0 -0.72 10 10
RAC1 0.035 0.006 -10000 0 -10000 0 0
TNF 0.033 0.065 -10000 0 -0.41 10 10
MAPKKK cascade 0.02 0.12 -10000 0 -0.82 9 9
RASA1 0.029 0.05 -10000 0 -0.42 6 6
Tie2/Ang1/Shc 0.028 0.14 -10000 0 -0.9 8 8
NCK1 0.034 0.021 -10000 0 -0.42 1 1
vasculogenesis 0.028 0.12 -10000 0 -0.56 10 10
mol:Phosphatidic acid 0.02 0.12 -10000 0 -0.82 9 9
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.027 0.13 -10000 0 -0.63 10 10
Rac1/GTP 0.034 0.16 -10000 0 -0.76 12 12
MMP2 0.011 0.14 -10000 0 -0.97 8 8
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.003 0.087 -10000 0 -0.28 19 19
PLCG1 -0.009 0.074 -10000 0 -0.29 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.028 0.054 -10000 0 -0.42 7 7
GNAI3 0.035 0.006 -10000 0 -10000 0 0
G12/G13 0.044 0.033 -10000 0 -0.3 3 3
cell migration 0.002 0.085 -10000 0 -0.27 19 19
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.006 0.07 -10000 0 -0.29 15 15
MAPK1 -0.005 0.07 -10000 0 -0.29 18 18
S1P/S1P5/Gi 0 0.077 -10000 0 -0.24 40 40
GNAI1 0.017 0.087 -10000 0 -0.42 19 19
CDC42/GDP 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.07 0.19 63 -0.24 11 74
S1P/S1P4/Gi 0 0.077 -10000 0 -0.24 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.07 -10000 0 -0.42 12 12
S1P/S1P4/G12/G13 0.038 0.027 -10000 0 -0.23 3 3
GNA12 0.035 0.007 -10000 0 -10000 0 0
GNA13 0.029 0.037 -10000 0 -0.42 3 3
CDC42 0.035 0.008 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.045 0.036 -10000 0 -0.3 4 4
ATM 0.031 0.013 -10000 0 -10000 0 0
UBE2D3 0.036 0.006 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
ATR 0.036 0.006 -10000 0 -10000 0 0
UBE2L3 0.034 0.008 -10000 0 -10000 0 0
FANCD2 0.023 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.06 0.073 -10000 0 -0.23 20 20
XRCC5 0.036 0.005 -10000 0 -10000 0 0
XRCC6 0.034 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.048 0.044 -10000 0 -0.26 4 4
MRE11A 0.031 0.013 -10000 0 -10000 0 0
DNA-PK 0.056 0.037 -10000 0 -0.26 2 2
FA complex/FANCD2/Ubiquitin 0.003 0.093 -10000 0 -0.4 11 11
FANCF 0.032 0.041 -10000 0 -0.42 4 4
BRCA1 0.022 0.07 -10000 0 -0.42 12 12
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
CDK2/Cyclin E1 0.044 0.045 -10000 0 -0.34 6 6
FANCG 0.035 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.037 0.062 -10000 0 -0.3 15 15
FANCE 0.032 0.036 -10000 0 -0.42 3 3
FANCC 0.035 0.021 -10000 0 -0.42 1 1
NBN 0.028 0.025 -10000 0 -0.42 1 1
FANCA 0.016 0.064 -10000 0 -0.42 10 10
DNA repair -0.015 0.11 0.28 4 -0.35 16 20
BRCA1/BARD1/ubiquitin 0.037 0.062 -10000 0 -0.3 15 15
BARD1/DNA-PK 0.07 0.05 -10000 0 -0.23 5 5
FANCL 0.036 0.006 -10000 0 -10000 0 0
mRNA polyadenylation -0.045 0.035 0.3 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.08 -10000 0 -0.22 39 39
BRCA1/BACH1/BARD1/TopBP1 0.055 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/P53 0.05 0.091 -10000 0 -0.25 35 35
BARD1/CSTF1/BRCA1 0.049 0.06 -10000 0 -0.26 14 14
BRCA1/BACH1 0.021 0.07 -10000 0 -0.42 12 12
BARD1 0.033 0.035 -10000 0 -0.42 3 3
PCNA 0.03 0.046 -10000 0 -0.42 5 5
BRCA1/BARD1/UbcH5C 0.054 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/UbcH7 0.052 0.059 -10000 0 -0.26 14 14
BRCA1/BARD1/RAD51/PCNA 0.038 0.11 -10000 0 -0.24 59 59
BARD1/DNA-PK/P53 0.059 0.085 -10000 0 -0.22 29 29
BRCA1/BARD1/Ubiquitin 0.037 0.062 -10000 0 -0.3 15 15
BRCA1/BARD1/CTIP 0.034 0.061 -10000 0 -0.23 21 21
FA complex 0.02 0.056 -10000 0 -0.4 2 2
BARD1/EWS 0.047 0.031 -10000 0 -0.3 3 3
RBBP8 0.008 0.042 -10000 0 -0.3 9 9
TP53 0.008 0.1 -10000 0 -0.42 26 26
TOPBP1 0.036 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.048 0.089 0.24 35 -10000 0 35
BRCA1/BARD1 0.066 0.077 -10000 0 -0.23 20 20
CSTF1 0.032 0.023 -10000 0 -0.42 1 1
BARD1/EWS-Fli1 0.025 0.025 -10000 0 -0.3 3 3
CDK2 0.034 0.029 -10000 0 -0.42 2 2
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.006 0.13 -10000 0 -0.42 44 44
RAD50 0.032 0.041 -10000 0 -0.42 4 4
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.037 0.062 -10000 0 -0.3 15 15
EWSR1 0.034 0.009 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.036 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.09 0.3 2 -0.39 7 9
NFATC2 0.018 0.049 0.16 1 -0.19 7 8
NFATC3 0.013 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.019 0.09 0.21 4 -0.36 10 14
Exportin 1/Ran/NUP214 0.069 0.023 -10000 0 -0.26 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.043 0.087 -10000 0 -0.41 5 5
BCL2/BAX -0.018 0.14 -10000 0 -0.3 95 95
CaM/Ca2+/Calcineurin A alpha-beta B1 0.027 0.006 -10000 0 -10000 0 0
CaM/Ca2+ 0.027 0.006 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
BAD 0.034 0.021 -10000 0 -0.42 1 1
CABIN1/MEF2D 0.03 0.082 -10000 0 -0.38 6 6
Calcineurin A alpha-beta B1/BCL2 -0.057 0.18 -10000 0 -0.42 99 99
FKBP8 0.036 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.03 0.081 0.38 6 -10000 0 6
KPNB1 0.03 0.046 -10000 0 -0.42 5 5
KPNA2 0.025 0.058 -10000 0 -0.42 8 8
XPO1 0.036 0.005 -10000 0 -10000 0 0
SFN 0.012 0.099 -10000 0 -0.42 25 25
MAP3K8 0.004 0.11 -10000 0 -0.42 32 32
NFAT4/CK1 alpha 0.017 0.056 -10000 0 -0.21 23 23
MEF2D/NFAT1/Cbp/p300 0.056 0.065 -10000 0 -0.22 3 3
CABIN1 0.019 0.089 0.21 4 -0.37 9 13
CALM1 0.035 0.007 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
CAMK4 0.032 0.036 -10000 0 -0.42 3 3
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.091 -10000 0 -0.3 36 36
YWHAB 0.035 0.008 -10000 0 -10000 0 0
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
MAPK9 0.019 0.085 -10000 0 -0.42 18 18
YWHAG 0.036 0.005 -10000 0 -10000 0 0
FKBP1A 0.035 0.007 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.031 0.09 0.32 1 -0.35 7 8
PRKCH 0.03 0.046 -10000 0 -0.42 5 5
CABIN1/Cbp/p300 0.046 0.029 -10000 0 -0.29 2 2
CASP3 0.035 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0.003 0.049 -10000 0 -0.29 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.06 -10000 0 -0.24 4 4
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.03 0.05 -10000 0 -0.42 6 6
JNK2/NFAT4 -0.002 0.08 -10000 0 -0.16 102 102
BAD/BCL-XL 0.051 0.019 -10000 0 -0.3 1 1
PRKCD 0.033 0.03 -10000 0 -0.42 2 2
NUP214 0.035 0.021 -10000 0 -0.42 1 1
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.012 -10000 0 -10000 0 0
PRKCG 0.036 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.054 -10000 0 -0.42 7 7
FKBP38/BCL2 -0.019 0.14 -10000 0 -0.3 97 97
EP300 0.033 0.03 -10000 0 -0.42 2 2
PRKCB1 0.003 0.11 -10000 0 -0.42 30 30
CSNK2A1 0.035 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.037 0.094 0.31 2 -0.37 7 9
CaM/Ca2+/FKBP38 0.047 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.045 0.026 -10000 0 -0.25 3 3
NFATc/ERK1 0.033 0.091 0.31 2 -0.39 6 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.05 0.097 -10000 0 -0.39 7 7
NR4A1 0.062 0.078 0.23 12 -0.43 1 13
GSK3B 0.036 0.005 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.021 0.036 -10000 0 -0.21 1 1
RCH1/ KPNB1 0.038 0.056 -10000 0 -0.3 12 12
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
PRKACA 0.036 0.005 -10000 0 -10000 0 0
AKAP5 0 0.12 -10000 0 -0.42 37 37
MEF2D 0.029 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.092 0.33 1 -0.37 7 8
CREBBP 0.033 0.011 -10000 0 -10000 0 0
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.035 0.013 -10000 0 -10000 0 0
DOCK1 0.028 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.042 0.061 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.058 0.065 -10000 0 -0.28 16 16
alpha4/beta7 Integrin/Paxillin 0.049 0.051 -10000 0 -0.23 15 15
lamellipodium assembly -0.013 0.13 -10000 0 -0.43 32 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.036 0.065 -10000 0 -0.3 17 17
ARF6 0.034 0.029 -10000 0 -0.42 2 2
TLN1 0.035 0.021 -10000 0 -0.42 1 1
PXN 0.017 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.08 -10000 0 -0.42 16 16
ARF6/GTP 0.059 0.064 -10000 0 -0.23 19 19
cell adhesion 0.062 0.063 -10000 0 -0.24 17 17
CRKL/CBL 0.043 0.037 -10000 0 -0.3 4 4
alpha4/beta1 Integrin/Paxillin 0.046 0.059 -10000 0 -0.26 16 16
ITGB1 0.032 0.036 -10000 0 -0.42 3 3
ITGB7 0.036 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.031 -10000 0 -0.41 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.094 -10000 0 -0.26 37 37
p130Cas/Crk/Dock1 0.05 0.052 -10000 0 -0.25 9 9
VCAM1 0.009 0.1 -10000 0 -0.42 28 28
alpha4/beta1 Integrin/Paxillin/Talin 0.064 0.064 -10000 0 -0.25 17 17
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.064 -10000 0 -0.24 17 17
BCAR1 0.03 0.014 -10000 0 -10000 0 0
mol:GDP -0.061 0.063 0.24 17 -10000 0 17
CBL 0.032 0.012 -10000 0 -10000 0 0
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GIT1 0.034 0.022 -10000 0 -0.42 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.064 0.064 -10000 0 -0.25 17 17
Rac1/GTP -0.017 0.14 -10000 0 -0.48 32 32
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.046 0.027 -10000 0 -0.29 2 2
STXBP1 0.036 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.016 0.044 -10000 0 -0.21 9 9
RAB3GAP2/RIMS1/UNC13B 0.051 0.04 -10000 0 -0.25 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.032 0.012 -10000 0 -10000 0 0
mol:ACh -0.005 0.029 0.088 4 -0.11 18 22
RAB3GAP2 0.028 0.025 -10000 0 -0.42 1 1
STX1A/SNAP25/VAMP2 0.034 0.057 -10000 0 -0.18 3 3
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.016 0.044 -10000 0 -0.21 9 9
UNC13B 0.033 0.03 -10000 0 -0.42 2 2
CHRNA1 0.031 0.05 -10000 0 -0.42 6 6
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.042 0.11 -10000 0 -0.27 96 96
SNAP25 -0.001 0.043 -10000 0 -0.26 14 14
VAMP2 0.005 0.011 -10000 0 -0.23 1 1
SYT1 -0.062 0.17 -10000 0 -0.42 96 96
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.032 0.007 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.034 0.057 -10000 0 -0.18 3 3
Signaling events mediated by PRL

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
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
mol:Halofuginone 0.004 0.009 -10000 0 -0.19 1 1
ITGA1 0.022 0.075 -10000 0 -0.42 14 14
CDKN1A -0.005 0.12 -10000 0 -0.45 27 27
PRL-3/alpha Tubulin 0.02 0.018 -10000 0 -0.3 1 1
mol:Ca2+ -0.036 0.081 0.34 1 -0.31 38 39
AGT -0.022 0.14 -10000 0 -0.42 52 52
CCNA2 -0.038 0.097 -10000 0 -0.52 3 3
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.028 0.11 -10000 0 -0.29 77 77
CDK2/Cyclin E1 0.021 0.13 -10000 0 -0.39 31 31
MAPK3 0.012 0.016 -10000 0 -0.3 1 1
PRL-2 /Rab GGTase beta 0.047 0.04 -10000 0 -0.3 6 6
MAPK1 0.012 0.016 -10000 0 -0.3 1 1
PTP4A1 -0.028 0.085 -10000 0 -0.48 3 3
PTP4A3 0.027 0.025 -10000 0 -0.42 1 1
PTP4A2 0.03 0.05 -10000 0 -0.42 6 6
ITGB1 0.011 0.025 -10000 0 -0.3 3 3
SRC 0.033 0.029 -10000 0 -0.42 2 2
RAC1 0.013 0.059 -10000 0 -0.44 5 5
Rab GGTase beta/Rab GGTase alpha 0.051 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.001 0.098 0.37 1 -0.46 3 4
RABGGTA 0.035 0.007 -10000 0 -10000 0 0
BCAR1 -0.017 0.021 0.34 1 -10000 0 1
RHOC 0.01 0.071 -10000 0 -0.41 10 10
RHOA 0.001 0.092 -10000 0 -0.38 22 22
cell motility 0.012 0.087 0.35 1 -0.35 13 14
PRL-1/alpha Tubulin -0.028 0.079 -10000 0 -0.45 3 3
PRL-3/alpha1 Integrin 0.032 0.06 -10000 0 -0.32 12 12
ROCK1 0.017 0.082 0.35 1 -0.35 12 13
RABGGTB 0.035 0.007 -10000 0 -10000 0 0
CDK2 0.034 0.029 -10000 0 -0.42 2 2
mitosis -0.028 0.084 -10000 0 -0.48 3 3
ATF5 0.034 0.022 -10000 0 -0.42 1 1
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 0.075 0.048 -10000 0 -0.23 6 6
HDAC3 0.036 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.009 -10000 0 -0.19 1 1
GATA1/HDAC4 0.052 0.019 -10000 0 -0.3 1 1
GATA1/HDAC5 0.049 0.021 -10000 0 -0.3 1 1
GATA2/HDAC5 0.044 0.041 -10000 0 -0.3 6 6
HDAC5/BCL6/BCoR 0.048 0.075 -10000 0 -0.26 26 26
HDAC9 0.033 0.022 -10000 0 -0.42 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.04 0.048 -10000 0 -0.25 13 13
HDAC4/ANKRA2 0.04 0.059 -10000 0 -0.3 14 14
HDAC5/YWHAB 0.047 0.023 -10000 0 -0.3 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
GATA2 0.029 0.046 -10000 0 -0.42 5 5
HDAC4/RFXANK 0.051 0.02 -10000 0 -0.3 1 1
BCOR 0.028 0.06 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.032 0.03 -10000 0 -0.42 2 2
HDAC5 0.033 0.022 -10000 0 -0.42 1 1
GNB1/GNG2 0.048 0.039 -10000 0 -0.3 6 6
Histones 0.009 0.069 -10000 0 -0.22 30 30
ADRBK1 0.034 0.01 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
XPO1 0.036 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.058 -10000 0 -0.3 13 13
HDAC4/Ubc9 0.046 0.024 -10000 0 -0.3 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.024 -10000 0 -0.3 1 1
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.036 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.022 -10000 0 -0.3 1 1
CAMK4 0.032 0.036 -10000 0 -0.42 3 3
Tubulin/HDAC6 0.037 0.055 -10000 0 -0.25 17 17
SUMO1 0.036 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.035 0.008 -10000 0 -10000 0 0
GATA1 0.036 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.012 -10000 0 -10000 0 0
NR3C1 0.024 0.072 -10000 0 -0.42 13 13
SUMO1/HDAC4 0.052 0.042 -10000 0 -0.19 1 1
SRF 0.035 0.007 -10000 0 -10000 0 0
HDAC4/YWHAB 0.049 0.021 -10000 0 -0.3 1 1
Tubulin 0.015 0.058 -10000 0 -0.3 17 17
HDAC4/14-3-3 E 0.047 0.023 -10000 0 -0.29 1 1
GNB1 0.032 0.045 -10000 0 -0.42 5 5
RANGAP1 0.033 0.022 -10000 0 -0.42 1 1
BCL6/BCoR 0.032 0.08 -10000 0 -0.3 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.069 0.023 -10000 0 -0.26 1 1
HDAC4/SRF 0.064 0.036 -10000 0 -0.26 4 4
HDAC4/ER alpha -0.046 0.15 -10000 0 -0.3 133 133
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.009 0.068 -10000 0 -0.22 30 30
cell motility 0.036 0.055 -10000 0 -0.25 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
HDAC7/HDAC3 0.026 0.004 -10000 0 -10000 0 0
BCL6 0.018 0.085 -10000 0 -0.42 18 18
HDAC4/CaMK II delta B 0.034 0.021 -10000 0 -0.42 1 1
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 -0.089 0.2 -10000 0 -0.42 132 132
HDAC6/HDAC11 0.035 0.077 -10000 0 -0.3 25 25
Ran/GTP/Exportin 1 0.054 0.041 -10000 0 -0.16 1 1
NPC 0.021 0.003 -10000 0 -10000 0 0
MEF2C 0.015 0.091 -10000 0 -0.42 21 21
RAN 0.036 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.076 0.073 -10000 0 -0.22 19 19
GNG2 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.036 0.005 -10000 0 -10000 0 0
TUBB2A 0.019 0.082 -10000 0 -0.42 17 17
HDAC11 0.013 0.099 -10000 0 -0.42 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
ANKRA2 0.023 0.072 -10000 0 -0.42 13 13
RFXANK 0.036 0.005 -10000 0 -10000 0 0
nuclear import -0.037 0.028 0.26 2 -10000 0 2
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.032 0.036 -9999 0 -0.42 3 3
ITGB7 0.036 0.005 -9999 0 -10000 0 0
ITGA4 0.021 0.078 -9999 0 -0.42 15 15
alpha4/beta7 Integrin 0.042 0.061 -9999 0 -0.3 15 15
alpha4/beta1 Integrin 0.039 0.069 -9999 0 -0.33 16 16
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.03 -10000 0 -0.42 2 2
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.017 -10000 0 -0.13 4 4
CDKN1A -0.018 0.097 0.4 1 -0.56 14 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
FOXO3 -0.006 0.023 0.35 2 -10000 0 2
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.01 0.023 -10000 0 -0.33 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.034 0.009 -10000 0 -10000 0 0
TAT 0.027 0.016 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.005 0.064 -10000 0 -0.3 23 23
PPARGC1A 0.024 0.064 -10000 0 -0.42 10 10
FHL2 -0.022 0.15 -10000 0 -0.42 61 61
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.048 0.019 -10000 0 -10000 0 0
HIST2H4A -0.005 0.017 0.13 4 -10000 0 4
SIRT1/FOXO3a 0.029 0.038 0.26 4 -0.2 2 6
SIRT1 0.035 0.019 0.21 4 -10000 0 4
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.054 0.037 -10000 0 -0.26 1 1
SIRT1/Histone H1b 0.021 0.077 0.18 2 -0.22 33 35
apoptosis -0.064 0.025 -10000 0 -10000 0 0
SIRT1/PGC1A 0.038 0.045 0.16 4 -0.25 10 14
p53/SIRT1 0.026 0.077 0.4 4 -0.3 21 25
SIRT1/FOXO4 0.031 0.045 0.16 3 -0.2 6 9
FOXO1/FHL2/SIRT1 0.011 0.087 -10000 0 -0.22 59 59
HIST1H1E 0 0.066 -10000 0 -0.25 31 31
SIRT1/p300 0.047 0.028 -10000 0 -0.27 2 2
muscle cell differentiation -0.009 0.06 0.25 23 -0.16 6 29
TP53 0.01 0.095 0.21 4 -0.42 22 26
KU70/SIRT1/BAX 0.065 0.025 -10000 0 -10000 0 0
CREBBP 0.033 0.011 -10000 0 -10000 0 0
MEF2D 0.029 0.015 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.041 0.024 -10000 0 -10000 0 0
ACSS2 0.015 0.02 0.36 1 -10000 0 1
SIRT1/PCAF/MYOD 0.01 0.061 0.2 3 -0.25 23 26
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.026 0.061 0.42 9 -10000 0 9
PI3K Class IB/PDE3B 0.026 0.061 -10000 0 -0.42 9 9
PDE3B 0.026 0.061 -10000 0 -0.42 9 9
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.035 0.007 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.033 0.011 -9999 0 -10000 0 0
TCEB1 0.028 0.025 -9999 0 -0.42 1 1
HIF1A/p53 0.007 0.098 -9999 0 -0.27 25 25
HIF1A 0 0.082 -9999 0 -0.28 17 17
COPS5 0.026 0.042 -9999 0 -0.42 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2 0.072 0.053 -9999 0 -0.22 1 1
FIH (dimer) 0.036 0.005 -9999 0 -10000 0 0
CDKN2A 0.015 0.075 -9999 0 -0.42 14 14
ARNT/IPAS 0.051 0.013 -9999 0 -10000 0 0
HIF1AN 0.036 0.005 -9999 0 -10000 0 0
GNB2L1 0.034 0.035 -9999 0 -0.42 3 3
HIF1A/ARNT 0.019 0.088 -9999 0 -0.27 17 17
CUL2 0.035 0.007 -9999 0 -10000 0 0
OS9 0.034 0.029 -9999 0 -0.42 2 2
RACK1/Elongin B/Elongin C 0.054 0.038 -9999 0 -0.26 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.004 0.077 -9999 0 -0.27 17 17
PHD1-3/OS9 0.033 0.1 -9999 0 -0.24 49 49
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.084 -9999 0 -0.3 4 4
VHL 0.035 0.007 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.014 0.081 -9999 0 -0.27 14 14
EGLN3 -0.015 0.14 -9999 0 -0.42 52 52
EGLN2 0.032 0.041 -9999 0 -0.42 4 4
EGLN1 0.021 0.055 -9999 0 -0.42 7 7
TP53 0.008 0.1 -9999 0 -0.42 26 26
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.038 0.062 -9999 0 -0.44 5 5
ARNT 0.035 0.006 -9999 0 -10000 0 0
ARD1A 0.036 0.003 -9999 0 -10000 0 0
RBX1 0.034 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF 0.004 0.093 -9999 0 -0.29 21 21
Ephrin A reverse signaling

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
MAPKKK cascade 0.041 0.037 -10000 0 -0.25 7 7
EFNA5 0.03 0.046 -10000 0 -0.42 5 5
FYN 0.011 0.043 0.19 2 -0.23 14 16
neuron projection morphogenesis 0.041 0.037 -10000 0 -0.25 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.042 0.037 -10000 0 -0.25 7 7
EPHA5 0.034 0.029 -10000 0 -0.42 2 2
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.068 0.058 -10000 0 -0.26 9 9
MAP4K1 0.035 0.007 -10000 0 -10000 0 0
MAP3K8 0.004 0.11 -10000 0 -0.42 32 32
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.034 0.029 -10000 0 -0.42 2 2
CRKL 0.031 0.041 -10000 0 -0.42 4 4
MAP3K1 0.004 0.07 -10000 0 -0.32 4 4
JUN -0.01 0.1 -10000 0 -0.53 10 10
MAP3K7 0.013 0.059 0.21 3 -0.33 4 7
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
CRK 0.032 0.023 -10000 0 -0.42 1 1
MAP2K4 -0.003 0.081 0.21 1 -0.36 11 12
LAT 0.03 0.031 -10000 0 -0.42 2 2
LCP2 0.024 0.067 -10000 0 -0.42 11 11
MAPK8 0.008 0.084 -10000 0 -0.58 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.067 -10000 0 -0.33 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 0.08 0.062 -10000 0 -0.24 9 9
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.028 0.1 0.25 1 -0.27 25 26
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.03 -10000 0 -0.42 2 2
AKT2 0.036 0.005 -10000 0 -10000 0 0
STXBP4 0.03 0.037 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.008 0.099 0.22 2 -0.26 35 37
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
TBC1D4 0.009 0.042 -10000 0 -0.3 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
YWHAB 0.035 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.032 -10000 0 -0.25 4 4
YWHAG 0.036 0.005 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.025 0.064 -10000 0 -0.42 10 10
AS160/CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.031 0.045 -10000 0 -0.42 5 5
GYS1 0.018 0.04 0.25 12 -0.24 2 14
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
TC10/GTP/CIP4/Exocyst 0.042 0.041 -10000 0 -0.25 9 9
AS160/14-3-3 0.018 0.076 -10000 0 -0.28 12 12
VAMP2 0.031 0.023 -10000 0 -0.42 1 1
SLC2A4 0.006 0.11 0.23 2 -0.28 35 37
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.026 0.021 -10000 0 -0.28 2 2
SFN 0.012 0.099 -10000 0 -0.42 25 25
LNPEP 0.033 0.03 -10000 0 -0.42 2 2
YWHAE 0.032 0.012 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.017 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.042 0.031 -10000 0 -0.23 1 1
CDKN1B 0.01 0.077 0.26 2 -0.37 8 10
CDKN1A 0.012 0.071 -10000 0 -0.35 9 9
FRAP1 0.035 0.007 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
FOXO3 0.012 0.056 -10000 0 -0.29 15 15
AKT1 0.012 0.059 -10000 0 -0.3 15 15
BAD 0.034 0.021 -10000 0 -0.42 1 1
AKT3 0.012 0.025 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.012 0.056 -10000 0 -0.29 15 15
AKT1/ASK1 0.035 0.085 -10000 0 -0.31 10 10
BAD/YWHAZ 0.051 0.037 -10000 0 -0.26 1 1
RICTOR 0.035 0.007 -10000 0 -10000 0 0
RAF1 0.036 0.006 -10000 0 -10000 0 0
JNK cascade -0.034 0.082 0.3 10 -10000 0 10
TSC1 0.014 0.061 -10000 0 -0.34 7 7
YWHAZ 0.027 0.016 -10000 0 -10000 0 0
AKT1/RAF1 0.053 0.08 0.28 2 -0.29 14 16
EP300 0.032 0.03 -10000 0 -0.42 2 2
mol:GDP 0.012 0.058 -10000 0 -0.3 15 15
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.008 0.061 0.26 1 -0.36 7 8
YWHAQ 0.034 0.029 -10000 0 -0.42 2 2
TBC1D4 0.005 0.034 0.24 2 -0.24 8 10
MAP3K5 0.012 0.095 -10000 0 -0.42 23 23
MAPKAP1 0.035 0.021 -10000 0 -0.42 1 1
negative regulation of cell cycle -0.034 0.072 0.25 6 -0.2 1 7
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
AKT1S1 0.018 0.074 0.27 1 -0.33 10 11
CASP9 0.016 0.055 -10000 0 -0.36 4 4
YWHAB 0.035 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.043 0.095 0.29 5 -0.4 6 11
GBL 0.032 0.023 -10000 0 -0.42 1 1
PDK1/Src/Hsp90 0.042 0.025 -10000 0 -0.25 2 2
YWHAE 0.032 0.012 -10000 0 -10000 0 0
SRC 0.033 0.029 -10000 0 -0.42 2 2
AKT2/p21CIP1 0.015 0.066 0.25 1 -0.33 7 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.035 0.073 -10000 0 -0.4 6 6
CHUK 0.01 0.069 -10000 0 -0.34 8 8
BAD/BCL-XL 0.056 0.079 0.28 2 -0.38 4 6
mTORC2 0.076 0.041 -10000 0 -0.23 2 2
AKT2 0.016 0.015 -10000 0 -0.28 1 1
FOXO1-3a-4/14-3-3 family 0.044 0.091 0.24 13 -0.32 5 18
PDPK1 0.032 0.023 -10000 0 -0.42 1 1
MDM2 0.017 0.068 0.26 2 -0.33 8 10
MAPKKK cascade -0.053 0.079 0.29 14 -0.28 2 16
MDM2/Cbp/p300 0.055 0.082 0.28 7 -0.41 4 11
TSC1/TSC2 0.017 0.082 0.3 19 -0.43 4 23
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.079 0.27 7 -0.39 4 11
glucose import -0.001 0.03 0.21 2 -0.22 8 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.032 0.078 0.26 1 -0.44 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.001 0.031 0.21 2 -0.22 8 10
GSK3A 0.015 0.064 0.26 1 -0.33 8 9
FOXO1 0.012 0.056 -10000 0 -0.29 15 15
GSK3B 0.014 0.063 -10000 0 -0.33 8 8
SFN 0.012 0.099 -10000 0 -0.42 25 25
G1/S transition of mitotic cell cycle 0.019 0.071 0.26 3 -0.38 4 7
p27Kip1/14-3-3 family 0.021 0.054 -10000 0 -0.34 3 3
PRKACA 0.036 0.005 -10000 0 -10000 0 0
KPNA1 0.036 0.005 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.036 0.005 -10000 0 -10000 0 0
RHEB 0.035 0.007 -10000 0 -10000 0 0
CREBBP 0.033 0.011 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.03 0.024 -10000 0 -0.42 1 1
CLTC 0.025 0.063 0.26 2 -0.42 6 8
calcium ion-dependent exocytosis 0.017 0.038 -10000 0 -0.22 5 5
Dynamin 2/GTP 0.031 0.02 -10000 0 -0.23 2 2
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
CD59 0.017 0.05 -10000 0 -0.36 5 5
CPE -0.007 0.079 -10000 0 -0.26 43 43
CTNNB1 0.025 0.067 -10000 0 -0.42 11 11
membrane fusion 0.013 0.033 -10000 0 -0.23 4 4
CTNND1 0 0.056 0.2 33 -0.22 3 36
DNM2 0.036 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.02 0.047 0.18 3 -0.26 5 8
TSHR 0.013 0.034 -10000 0 -0.25 8 8
INS 0.008 0.096 -10000 0 -0.46 19 19
BIN1 0.035 0.021 -10000 0 -0.42 1 1
mol:Choline 0.013 0.033 -10000 0 -0.23 4 4
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.018 -10000 0 -0.25 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.034 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0.031 0.02 -10000 0 -0.23 2 2
JUP 0.02 0.053 -10000 0 -0.37 5 5
ASAP2/amphiphysin II 0.043 0.023 -10000 0 -0.23 3 3
ARF6/GTP 0.025 0.021 -10000 0 -0.3 2 2
CDH1 -0.002 0.069 -10000 0 -0.38 6 6
clathrin-independent pinocytosis 0.025 0.021 -10000 0 -0.3 2 2
MAPK8IP3 0.024 0.061 -10000 0 -0.42 9 9
positive regulation of endocytosis 0.025 0.021 -10000 0 -0.3 2 2
EXOC2 0.029 0.05 -10000 0 -0.42 6 6
substrate adhesion-dependent cell spreading 0.018 0.075 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.033 0.023 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.031 0.086 0.4 5 -10000 0 5
positive regulation of phagocytosis 0.016 0.021 -10000 0 -0.25 3 3
ARF6/GTP/JIP3 0.036 0.046 -10000 0 -0.25 11 11
ACAP1 0.013 0.031 -10000 0 -0.18 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.045 -10000 0 -0.35 5 5
clathrin heavy chain/ACAP1 0.024 0.063 0.27 4 -0.31 7 11
JIP4/KLC1 0.04 0.025 -10000 0 -0.23 3 3
EXOC1 0.036 0.005 -10000 0 -10000 0 0
exocyst 0.018 0.075 -10000 0 -0.33 4 4
RALA/GTP 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.042 0.027 -10000 0 -0.25 3 3
receptor recycling 0.025 0.021 -10000 0 -0.3 2 2
CTNNA1 0 0.057 0.2 34 -0.22 3 37
NME1 0.015 0.018 -10000 0 -0.25 2 2
clathrin coat assembly 0.028 0.069 0.26 3 -0.39 7 10
IL2RA 0.009 0.067 -10000 0 -0.3 9 9
VAMP3 0.016 0.021 -10000 0 -0.25 3 3
GLUT4/clathrin heavy chain/ACAP1 0.031 0.06 -10000 0 -0.32 5 5
EXOC6 0.011 0.1 -10000 0 -0.42 27 27
PLD1 0.011 0.041 -10000 0 -0.24 11 11
PLD2 0.015 0.021 -10000 0 -0.24 2 2
EXOC5 0.035 0.021 -10000 0 -0.42 1 1
PIP5K1C 0.016 0.042 0.19 2 -0.27 5 7
SDC1 0.004 0.068 -10000 0 -0.39 6 6
ARF6/GDP 0.029 0.02 -10000 0 -0.25 2 2
EXOC7 0.033 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.089 -10000 0 -0.41 5 5
mol:Phosphatidic acid 0.013 0.033 -10000 0 -0.23 4 4
endocytosis -0.041 0.023 0.22 3 -10000 0 3
SCAMP2 0.033 0.029 -10000 0 -0.42 2 2
ADRB2 0.012 0.087 0.25 3 -0.41 9 12
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.039 0.029 0.18 9 -0.23 2 11
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.023 0.068 0.25 3 -0.38 7 10
RALA 0.035 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.086 -10000 0 -0.39 5 5
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
SMAD2 0 0.058 0.21 2 -0.22 12 14
SMAD3 0.019 0.058 0.28 1 -0.25 5 6
SMAD3/SMAD4 0.03 0.09 -10000 0 -0.38 17 17
SMAD4/Ubc9/PIASy 0.055 0.052 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 0.051 0.079 -10000 0 -0.28 3 3
PPM1A 0.034 0.021 -10000 0 -0.42 1 1
CALM1 0.035 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.013 0.066 -10000 0 -0.23 13 13
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
TRAP-1/SMAD4 0.046 0.043 -10000 0 -0.3 7 7
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
NUP214 0.035 0.021 -10000 0 -0.42 1 1
CTDSP1 0.034 0.029 -10000 0 -0.42 2 2
CTDSP2 0.034 0.029 -10000 0 -0.42 2 2
CTDSPL 0.029 0.054 -10000 0 -0.42 7 7
KPNB1 0.03 0.046 -10000 0 -0.42 5 5
TGFBRAP1 0.036 0.004 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
NUP153 0.035 0.008 -10000 0 -10000 0 0
KPNA2 0.025 0.058 -10000 0 -0.42 8 8
PIAS4 0.033 0.036 -10000 0 -0.42 3 3
Canonical NF-kappaB pathway

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
FBXW11 0.035 0.03 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.1 0.26 11 -0.28 8 19
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.011 -10000 0 -10000 0 0
NFKBIA 0.011 0.036 0.21 4 -0.37 3 7
BIRC2 0.032 0.012 -10000 0 -10000 0 0
IKBKB 0.03 0.014 -10000 0 -10000 0 0
RIPK2 0.028 0.015 -10000 0 -10000 0 0
IKBKG 0.011 0.099 -10000 0 -0.34 20 20
IKK complex/A20 0.033 0.12 -10000 0 -0.33 18 18
NEMO/A20/RIP2 0.028 0.015 -10000 0 -10000 0 0
XPO1 0.036 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.022 0.11 -10000 0 -0.31 24 24
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.047 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.1 -10000 0 -0.32 20 20
BCL10/MALT1/TRAF6 0.063 0.041 -10000 0 -0.31 4 4
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.037 0.011 -10000 0 -10000 0 0
RELA 0.037 0.011 -10000 0 -10000 0 0
MALT1 0.031 0.041 -10000 0 -0.42 4 4
cIAP1/UbcH5C 0.046 0.019 -10000 0 -10000 0 0
ATM 0.031 0.013 -10000 0 -10000 0 0
TNF/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
TRAF6 0.035 0.021 -10000 0 -0.42 1 1
PRKCA 0.032 0.012 -10000 0 -10000 0 0
CHUK 0.026 0.067 -10000 0 -0.42 11 11
UBE2D3 0.036 0.006 -10000 0 -10000 0 0
TNF 0.026 0.061 -10000 0 -0.42 9 9
NF kappa B1 p50/RelA 0.074 0.037 -10000 0 -0.24 4 4
BCL10 0.035 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.036 0.21 4 -0.37 3 7
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.03 -10000 0 -0.42 2 2
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
IKK complex 0.023 0.12 -10000 0 -0.34 20 20
CYLD 0.029 0.024 -10000 0 -0.42 1 1
IKK complex/PKC alpha 0.029 0.11 -10000 0 -0.32 17 17
Alternative NF-kappaB 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
IKK alpha homodimer 0.041 0.057 -9999 0 -0.3 13 13
FBXW11 0.033 0.029 -9999 0 -0.42 2 2
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.029 -9999 0 -0.42 2 2
CHUK 0.026 0.067 -9999 0 -0.42 11 11
NF kappa B2 p100/RelB 0.082 0.075 -9999 0 -0.24 20 20
NFKB1 0.036 0.005 -9999 0 -10000 0 0
MAP3K14 0.032 0.03 -9999 0 -0.42 2 2
NF kappa B1 p50/RelB 0.047 0.04 -9999 0 -0.3 6 6
RELB 0.029 0.05 -9999 0 -0.42 6 6
NFKB2 0.035 0.021 -9999 0 -0.42 1 1
NF kappa B2 p52/RelB 0.042 0.036 -9999 0 -0.25 7 7
regulation of B cell activation 0.042 0.036 -9999 0 -0.25 7 7
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.034 0.088 -10000 0 -1.2 1 1
CLOCK 0.037 0.021 -10000 0 -0.42 1 1
TIMELESS/CRY2 0.042 0.061 -10000 0 -1.2 1 1
DEC1/BMAL1 0.043 0.061 -10000 0 -0.32 13 13
ATR 0.036 0.006 -10000 0 -10000 0 0
NR1D1 0.022 0.024 -10000 0 -10000 0 0
ARNTL 0.029 0.061 -10000 0 -0.42 9 9
TIMELESS 0.022 0.059 -10000 0 -1.3 1 1
NPAS2 0.027 0.064 -10000 0 -0.42 10 10
CRY2 0.036 0.005 -10000 0 -10000 0 0
mol:CO -0.01 0.007 0.14 1 -10000 0 1
CHEK1 -0.001 0.11 -10000 0 -0.42 32 32
mol:HEME 0.01 0.007 -10000 0 -0.14 1 1
PER1 0.032 0.012 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.067 0.07 -10000 0 -0.26 19 19
BMAL1/CLOCK 0.027 0.076 -10000 0 -0.49 3 3
S phase of mitotic cell cycle 0.034 0.088 -10000 0 -1.2 1 1
TIMELESS/CHEK1/ATR 0.035 0.09 -10000 0 -1.3 1 1
mol:NADPH 0.01 0.007 -10000 0 -0.14 1 1
PER1/TIMELESS 0.039 0.06 -10000 0 -1.2 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.031 0.045 -10000 0 -0.42 5 5
Arf1 pathway

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
coatomer protein complex 0.015 0.039 0.15 29 -0.18 1 30
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.043 0.15 9 -0.17 5 14
AP2 0.047 0.031 -10000 0 -0.3 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.042 0.035 -10000 0 -0.24 7 7
CLTB 0.034 0.021 -10000 0 -0.42 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.017 0.02 -10000 0 -0.22 2 2
CD4 0.034 0.009 -10000 0 -10000 0 0
CLTA 0.036 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.008 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.033 0.17 5 -0.16 1 6
ARF1/GTP 0.016 0.017 -10000 0 -0.17 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.044 0.17 36 -0.19 1 37
mol:Choline 0.019 0.033 0.18 5 -0.16 1 6
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.026 -10000 0 -0.43 1 1
DDEF1 0.014 0.029 0.16 3 -0.17 1 4
ARF1/GDP 0.001 0.021 -10000 0 -0.088 22 22
AP2M1 0.032 0.036 -10000 0 -0.42 3 3
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.013 -10000 0 -0.23 1 1
Rac/GTP 0.028 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.028 -10000 0 -0.21 1 1
ARFIP2 0.021 0.053 -10000 0 -0.39 7 7
COPA 0.029 0.015 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.016 0.028 -10000 0 -0.18 3 3
ARF1/GTP/ARHGAP10 0.018 0.016 -10000 0 -0.25 1 1
GGA3 0.032 0.023 -10000 0 -0.42 1 1
ARF1/GTP/Membrin 0.016 0.048 -10000 0 -0.24 15 15
AP2A1 0.035 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.03 -10000 0 -0.22 4 4
ARF1/GDP/Membrin 0.015 0.055 -10000 0 -0.26 16 16
Arfaptin 2/Rac/GDP 0.04 0.037 -10000 0 -0.24 7 7
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.034 0.026 -10000 0 -0.26 1 1
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.026 0.004 -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 0.025 0.039 -10000 0 -0.4 2 2
PLD2 0.019 0.033 0.18 5 -0.17 1 6
ARF-GAP1/v-SNARE 0.008 0.003 -10000 0 -10000 0 0
PIP5K1A 0.019 0.033 0.17 5 -0.16 1 6
ARF1/GTP/Membrin/GBF1/p115 0.014 0.025 -10000 0 -0.22 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.033 0.18 5 -0.16 1 6
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.018 0.038 -10000 0 -0.32 5 5
USO1 0.009 0.017 0.091 5 -0.077 1 6
GBF1 0.019 0.036 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.035 0.032 -10000 0 -0.25 3 3
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.036 -10000 0 -0.26 3 3
Aurora C signaling

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
INCENP 0.029 0.05 -9999 0 -0.42 6 6
Aurora C/Aurora B/INCENP 0.054 0.047 -9999 0 -0.23 10 10
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.013 0.03 -9999 0 -0.4 2 2
AURKB 0.029 0.037 -9999 0 -0.42 3 3
AURKC 0.034 0.021 -9999 0 -0.42 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.071 0.071 -10000 0 -0.28 9 9
Ran/GTP/Exportin 1/HDAC1 -0.012 0.009 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.042 0.077 -10000 0 -0.3 11 11
SUMO1 0.036 0.005 -10000 0 -10000 0 0
ZFPM1 0.023 0.055 -10000 0 -0.42 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
FKBP3 0.033 0.035 -10000 0 -0.42 3 3
Histones 0.071 0.063 -10000 0 -0.3 2 2
YY1/LSF 0.029 0.061 -10000 0 -0.22 15 15
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.027 0.039 -10000 0 -0.24 9 9
I kappa B alpha/HDAC1 0.04 0.056 -10000 0 -0.28 7 7
SAP18 0.034 0.01 -10000 0 -10000 0 0
RELA 0.022 0.052 0.28 1 -0.32 2 3
HDAC1/Smad7 0.067 0.028 -10000 0 -0.25 2 2
RANGAP1 0.033 0.022 -10000 0 -0.42 1 1
HDAC3/TR2 0.039 0.056 -10000 0 -0.25 8 8
NuRD/MBD3 Complex 0.032 0.067 -10000 0 -0.32 8 8
NF kappa B1 p50/RelA 0.037 0.073 0.25 1 -0.28 7 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.046 -10000 0 -0.42 5 5
GATA1 0.036 0 -10000 0 -10000 0 0
Mad/Max 0.052 0.011 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.018 0.092 -10000 0 -0.4 11 11
RBBP7 0.034 0.029 -10000 0 -0.42 2 2
NPC 0.021 0.003 -10000 0 -10000 0 0
RBBP4 0.035 0.021 -10000 0 -0.42 1 1
MAX 0.035 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.029 -10000 0 -0.42 2 2
NFKBIA 0.022 0.042 -10000 0 -0.37 4 4
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.057 -10000 0 -0.34 4 4
SIN3 complex 0.077 0.045 -10000 0 -0.23 5 5
SMURF1 0.036 0.006 -10000 0 -10000 0 0
CHD3 0.031 0.023 -10000 0 -0.42 1 1
SAP30 0.03 0.046 -10000 0 -0.42 5 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.012 -10000 0 -10000 0 0
YY1/HDAC3 0.028 0.049 -10000 0 -0.26 4 4
YY1/HDAC2 0.033 0.046 -10000 0 -0.22 6 6
YY1/HDAC1 0.035 0.047 -10000 0 -0.23 5 5
NuRD/MBD2 Complex (MeCP1) 0.032 0.066 -10000 0 -0.32 7 7
PPARG 0.01 0.093 0.3 1 -0.35 24 25
HDAC8/hEST1B 0.047 0.02 -10000 0 -0.25 2 2
UBE2I 0.032 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.029 -10000 0 -0.42 2 2
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
HDAC3/SMRT (N-CoR2) 0.042 0.05 -10000 0 -0.29 3 3
MBD3L2 0.028 0.057 -10000 0 -0.42 8 8
ubiquitin-dependent protein catabolic process 0.067 0.027 -10000 0 -0.25 2 2
CREBBP 0.033 0.011 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.079 -10000 0 -0.32 10 10
HDAC1 0.035 0.021 -10000 0 -0.42 1 1
HDAC3 0.025 0.029 -10000 0 -0.33 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
YY1 0.016 0.018 -10000 0 -0.24 2 2
HDAC8 0.035 0.029 -10000 0 -0.42 2 2
SMAD7 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.036 0.005 -10000 0 -10000 0 0
MXD1 0.036 0.005 -10000 0 -10000 0 0
STAT3 0.019 0.023 -10000 0 -0.28 2 2
NFKB1 0.036 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.047 0.063 -10000 0 -0.21 15 15
YY1/SAP30/HDAC1 0.048 0.058 -10000 0 -0.23 10 10
EP300 0.032 0.03 -10000 0 -0.42 2 2
STAT3 (dimer non-phopshorylated) 0.019 0.023 -10000 0 -0.28 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.042 -10000 0 -0.36 4 4
histone deacetylation 0.032 0.065 -10000 0 -0.31 7 7
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.056 -10000 0 -0.35 4 4
nuclear export -0.047 0.02 0.25 2 -10000 0 2
PRKACA 0.036 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.025 -10000 0 -0.42 1 1
GATAD2A 0.036 0.006 -10000 0 -10000 0 0
GATA2/HDAC3 0.04 0.05 -10000 0 -0.26 5 5
GATA1/HDAC1 0.052 0.018 -10000 0 -0.3 1 1
GATA1/HDAC3 0.043 0.05 -10000 0 -0.29 3 3
CHD4 0.033 0.022 -10000 0 -0.42 1 1
TNF-alpha/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
SIN3/HDAC complex/Mad/Max 0.025 0.058 -10000 0 -0.3 6 6
NuRD Complex 0.037 0.076 -10000 0 -0.31 10 10
positive regulation of chromatin silencing 0.067 0.062 -10000 0 -0.3 2 2
SIN3B 0.036 0.005 -10000 0 -10000 0 0
MTA2 0.033 0.029 -10000 0 -0.42 2 2
SIN3A 0.035 0.007 -10000 0 -10000 0 0
XPO1 0.036 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.053 0.043 -10000 0 -0.22 2 2
HDAC complex 0.081 0.042 -10000 0 -0.23 5 5
GATA1/Fog1 0.038 0.046 -10000 0 -0.3 7 7
FKBP25/HDAC1/HDAC2 0.061 0.04 -10000 0 -0.26 5 5
TNF 0.026 0.061 -10000 0 -0.42 9 9
negative regulation of cell growth 0.025 0.058 -10000 0 -0.3 6 6
NuRD/MBD2/PRMT5 Complex 0.032 0.066 -10000 0 -0.32 7 7
Ran/GTP/Exportin 1 0.054 0.041 -10000 0 -0.16 1 1
NF kappa B/RelA/I kappa B alpha 0.021 0.066 -10000 0 -0.31 11 11
SIN3/HDAC complex/NCoR1 0.017 0.06 -10000 0 -0.29 8 8
TFCP2 0.027 0.064 -10000 0 -0.42 10 10
NR2C1 0.03 0.05 -10000 0 -0.42 6 6
MBD3 0.035 0.008 -10000 0 -10000 0 0
MBD2 0.035 0.007 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.056 0.04 -10000 0 -0.24 7 7
MAPK9 -0.001 0.056 -10000 0 -0.29 18 18
adrenocorticotropin secretion 0.005 0.024 -10000 0 -0.3 3 3
GNB1/GNG2 0.044 0.034 -10000 0 -0.25 6 6
GNB1 0.032 0.045 -10000 0 -0.42 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 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.02 0.02 -10000 0 -0.22 3 3
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 0.002 0.005 0.062 3 -10000 0 3
GNAL 0.031 0.036 -10000 0 -0.42 3 3
GNG2 0.034 0.021 -10000 0 -0.42 1 1
CRH 0.026 0.038 -10000 0 -0.42 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.023 -10000 0 -0.29 3 3
MAPK11 0.009 0.003 -10000 0 -10000 0 0
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 0.035 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -0.18 1 1
MDM2/SUMO1 0.05 0.042 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC1 0.006 0.015 -10000 0 -0.21 1 1
SUMO1 0.036 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0.018 -10000 0 -0.2 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.021 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.052 0.042 -10000 0 -0.19 1 1
SUMO1/HDAC1 0.053 0.043 -10000 0 -0.22 2 2
RANGAP1 0.033 0.022 -10000 0 -0.42 1 1
MDM2/SUMO1/SUMO1 0.081 0.036 -10000 0 -0.23 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
Ran/GTP 0.036 0.038 -10000 0 -0.16 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.009 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.038 0.2 4 -0.16 1 5
NPC 0.021 0.003 -10000 0 -10000 0 0
PIAS2 0.033 0.03 -10000 0 -0.42 2 2
PIAS1 0.035 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 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/1444279/2.GDAC_MergeDataFiles.Finished/BRCA.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/BRCA/1456391/1.GetReducedSegments.Finished/BRCA.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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