Thyroid Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/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 38 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
Ephrin A reverse signaling 191
Signaling events mediated by Stem cell factor receptor (c-Kit) 125
Signaling events regulated by Ret tyrosine kinase 109
Reelin signaling pathway 97
Wnt signaling 81
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 81
FOXA2 and FOXA3 transcription factor networks 74
PDGFR-alpha signaling pathway 72
Noncanonical Wnt signaling pathway 71
Signaling events mediated by the Hedgehog family 67
Results
Summary Table

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
Ephrin A reverse signaling 191 1337 7 -0.44 0 1000 -1000 -0.015 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 125 9816 78 -0.74 0.23 1000 -1000 -0.04 -1000
Signaling events regulated by Ret tyrosine kinase 109 8992 82 -0.38 0.026 1000 -1000 -0.059 -1000
Reelin signaling pathway 97 5464 56 -0.47 0.065 1000 -1000 -0.045 -1000
Wnt signaling 81 571 7 -0.35 0.009 1000 -1000 -0.022 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 81 5562 68 -0.71 0.34 1000 -1000 -0.061 -1000
FOXA2 and FOXA3 transcription factor networks 74 3438 46 -0.9 0.03 1000 -1000 -0.061 -1000
PDGFR-alpha signaling pathway 72 3187 44 -0.43 0.043 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 71 1864 26 -0.35 0.026 1000 -1000 -0.045 -1000
Signaling events mediated by the Hedgehog family 67 3496 52 -0.32 0.15 1000 -1000 -0.04 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 64 3466 54 -0.47 0.038 1000 -1000 -0.056 -1000
Nongenotropic Androgen signaling 62 3266 52 -0.27 0.19 1000 -1000 -0.037 -1000
Endothelins 51 4978 96 -0.34 0.027 1000 -1000 -0.051 -1000
Nephrin/Neph1 signaling in the kidney podocyte 48 1661 34 -0.13 0.027 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 47 1464 31 -0.32 0.026 1000 -1000 -0.036 -1000
Glypican 1 network 46 2243 48 -0.31 0.05 1000 -1000 -0.027 -1000
BMP receptor signaling 43 3483 81 -0.46 0.051 1000 -1000 -0.059 -1000
HIF-1-alpha transcription factor network 41 3126 76 -0.5 0.04 1000 -1000 -0.063 -1000
IGF1 pathway 41 2388 57 -0.13 0.055 1000 -1000 -0.051 -1000
IL4-mediated signaling events 38 3466 91 -1.2 0.55 1000 -1000 -0.093 -1000
Glucocorticoid receptor regulatory network 38 4372 114 -0.46 0.26 1000 -1000 -0.057 -1000
Ephrin B reverse signaling 36 1769 48 -0.21 0.11 1000 -1000 -0.035 -1000
TCR signaling in naïve CD8+ T cells 36 3389 93 -0.15 0.047 1000 -1000 -0.055 -1000
Coregulation of Androgen receptor activity 35 2714 76 -0.67 0.074 1000 -1000 -0.03 -1000
EPHB forward signaling 35 2993 85 -0.21 0.1 1000 -1000 -0.07 -1000
IL23-mediated signaling events 35 2133 60 -0.3 0.026 1000 -1000 -0.065 -1000
Arf6 signaling events 33 2055 62 -0.25 0.06 1000 -1000 -0.033 -1000
Signaling mediated by p38-alpha and p38-beta 33 1475 44 -0.23 0.026 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 29 3054 105 -0.16 0.049 1000 -1000 -0.039 -1000
Hedgehog signaling events mediated by Gli proteins 28 1823 65 -0.61 0.063 1000 -1000 -0.04 -1000
IL12-mediated signaling events 23 2027 87 -0.38 0.027 1000 -1000 -0.075 -1000
IL6-mediated signaling events 23 1769 75 -0.16 0.053 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 23 491 21 -0.072 0.037 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 20 1326 65 -0.17 0.036 1000 -1000 -0.049 -1000
Osteopontin-mediated events 20 763 38 -0.16 0.039 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 20 352 17 -0.11 0.032 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 19 1058 54 -0.36 0.063 1000 -1000 -0.049 -1000
Plasma membrane estrogen receptor signaling 19 1717 86 -0.14 0.047 1000 -1000 -0.053 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 17 1513 85 -0.23 0.13 1000 -1000 -0.045 -1000
LPA receptor mediated events 17 1775 102 -0.17 0.034 1000 -1000 -0.06 -1000
Syndecan-1-mediated signaling events 16 547 34 -0.073 0.026 1000 -1000 -0.046 -1000
IFN-gamma pathway 16 1137 68 -0.16 0.036 1000 -1000 -0.053 -1000
FAS signaling pathway (CD95) 16 792 47 -0.26 0.042 1000 -1000 -0.031 -1000
Regulation of Androgen receptor activity 16 1135 70 -0.44 0.034 1000 -1000 -0.043 -1000
Fc-epsilon receptor I signaling in mast cells 15 1531 97 -0.16 0.046 1000 -1000 -0.056 -1000
BCR signaling pathway 15 1572 99 -0.1 0.049 1000 -1000 -0.065 -1000
Syndecan-4-mediated signaling events 15 1023 67 -0.14 0.038 1000 -1000 -0.043 -1000
Integrins in angiogenesis 14 1232 84 -0.13 0.055 1000 -1000 -0.044 -1000
Angiopoietin receptor Tie2-mediated signaling 14 1273 88 -0.25 0.038 1000 -1000 -0.072 -1000
JNK signaling in the CD4+ TCR pathway 13 233 17 -0.075 0.026 1000 -1000 -0.026 -1000
Ceramide signaling pathway 13 1059 76 -0.13 0.073 1000 -1000 -0.045 -1000
Signaling events mediated by PTP1B 12 952 76 -0.2 0.041 1000 -1000 -0.032 -1000
amb2 Integrin signaling 12 1063 82 -0.24 0.038 1000 -1000 -0.034 -1000
ceramide signaling pathway 12 631 49 -0.057 0.038 1000 -1000 -0.044 -1000
IL27-mediated signaling events 12 647 51 -0.13 0.03 1000 -1000 -0.041 -1000
VEGFR1 specific signals 12 709 56 -0.054 0.057 1000 -1000 -0.056 -1000
LPA4-mediated signaling events 11 138 12 -0.064 0.004 1000 -1000 -0.021 -1000
Visual signal transduction: Cones 11 440 38 -0.047 0.05 1000 -1000 -0.013 -1000
p75(NTR)-mediated signaling 11 1469 125 -0.29 0.07 1000 -1000 -0.065 -1000
RXR and RAR heterodimerization with other nuclear receptor 11 612 52 -0.19 0.064 1000 -1000 -0.042 -1000
Regulation of nuclear SMAD2/3 signaling 10 1421 136 -0.25 0.055 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class III 10 401 40 -0.28 0.046 1000 -1000 -0.019 -1000
IL1-mediated signaling events 10 662 62 -0.082 0.06 1000 -1000 -0.049 -1000
Syndecan-3-mediated signaling events 10 376 35 -0.12 0.069 1000 -1000 -0.03 -1000
TCGA08_rtk_signaling 10 270 26 -0.19 0.046 1000 -1000 -0.011 -1000
Neurotrophic factor-mediated Trk receptor signaling 10 1277 120 -0.26 0.073 1000 -1000 -0.052 -1000
Caspase cascade in apoptosis 9 688 74 -0.057 0.043 1000 -1000 -0.042 -1000
ErbB4 signaling events 9 631 69 -0.057 0.037 1000 -1000 -0.045 -1000
Presenilin action in Notch and Wnt signaling 9 584 61 -0.16 0.069 1000 -1000 -0.039 -1000
mTOR signaling pathway 9 497 53 -0.034 0.031 1000 -1000 -0.039 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 442 45 -0.057 0.073 1000 -1000 -0.044 -1000
Rapid glucocorticoid signaling 9 187 20 -0.061 0.034 1000 -1000 -0.009 -1000
Visual signal transduction: Rods 9 491 52 -0.059 0.044 1000 -1000 -0.023 -1000
FOXM1 transcription factor network 9 469 51 -0.24 0.05 1000 -1000 -0.099 -1000
Cellular roles of Anthrax toxin 8 334 39 -0.057 0.026 1000 -1000 -0.024 -1000
IL2 signaling events mediated by PI3K 8 475 58 -0.047 0.049 1000 -1000 -0.042 -1000
Sphingosine 1-phosphate (S1P) pathway 7 216 28 -0.14 0.055 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 7 508 69 -0.14 0.05 1000 -1000 -0.028 -1000
Nectin adhesion pathway 7 503 63 -0.097 0.072 1000 -1000 -0.048 -1000
S1P1 pathway 7 282 36 -0.072 0.026 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 7 425 58 -0.02 0.052 1000 -1000 -0.041 -1000
Stabilization and expansion of the E-cadherin adherens junction 7 544 74 -0.12 0.068 1000 -1000 -0.068 -1000
Insulin Pathway 7 588 74 -0.041 0.064 1000 -1000 -0.054 -1000
BARD1 signaling events 6 352 57 -0.043 0.051 1000 -1000 -0.036 -1000
TCGA08_p53 6 42 7 -0.022 0.025 1000 -1000 -0.008 -1000
Class I PI3K signaling events 6 448 73 -0.2 0.049 1000 -1000 -0.04 -1000
Regulation of Telomerase 6 640 102 -0.2 0.071 1000 -1000 -0.043 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 209 33 -0.13 0.054 1000 -1000 -0.031 -1000
PLK1 signaling events 5 453 85 -0.006 0.057 1000 -1000 -0.031 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 5 470 83 -0.18 0.045 1000 -1000 -0.032 -1000
S1P3 pathway 5 243 42 -0.14 0.046 1000 -1000 -0.049 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 577 125 -0.013 0.067 1000 -1000 -0.05 -1000
IL2 signaling events mediated by STAT5 4 88 22 -0.022 0.032 1000 -1000 -0.034 -1000
Class IB PI3K non-lipid kinase events 4 12 3 -0.016 0.016 1000 -1000 -0.002 -1000
Aurora B signaling 4 270 67 -0.33 0.11 1000 -1000 -0.044 -1000
Canonical NF-kappaB pathway 3 124 39 -0.057 0.059 1000 -1000 -0.033 -1000
a4b1 and a4b7 Integrin signaling 3 16 5 0.005 0.036 1000 -1000 -0.003 -1000
Insulin-mediated glucose transport 3 109 32 -0.075 0.049 1000 -1000 -0.026 -1000
Class I PI3K signaling events mediated by Akt 3 204 68 -0.075 0.049 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class I 3 374 104 -0.057 0.062 1000 -1000 -0.039 -1000
Canonical Wnt signaling pathway 3 174 51 -0.034 0.062 1000 -1000 -0.046 -1000
Effects of Botulinum toxin 3 103 26 -0.071 0.047 1000 -1000 -0.011 -1000
PDGFR-beta signaling pathway 3 339 97 -0.15 0.077 1000 -1000 -0.061 -1000
Signaling events mediated by PRL 3 119 34 -0.09 0.038 1000 -1000 -0.058 -1000
S1P4 pathway 3 76 25 -0.002 0.046 1000 -1000 -0.03 -1000
EPO signaling pathway 2 138 55 -0.019 0.06 1000 -1000 -0.041 -1000
S1P5 pathway 2 45 17 -0.008 0.033 1000 -1000 -0.015 -1000
FoxO family signaling 2 175 64 -0.075 0.1 1000 -1000 -0.044 -1000
Signaling mediated by p38-gamma and p38-delta 2 39 15 0 0.026 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 2 69 31 -0.005 0.038 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 2 20 8 -0.029 0.03 1000 -1000 -0.004 -1000
p38 MAPK signaling pathway 2 125 44 -0.023 0.048 1000 -1000 -0.03 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 37 23 -0.015 0.048 1000 -1000 -0.037 -1000
Circadian rhythm pathway 1 29 22 -0.013 0.045 1000 -1000 -0.029 -1000
Aurora A signaling 1 97 60 -0.024 0.053 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 1 58 37 0 0.063 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 1 70 43 -0.16 0.16 1000 -1000 -0.046 -1000
Paxillin-dependent events mediated by a4b1 1 39 36 -0.053 0.055 1000 -1000 -0.046 -1000
E-cadherin signaling in the nascent adherens junction 1 91 76 -0.049 0.064 1000 -1000 -0.067 -1000
Arf6 trafficking events 1 87 71 -0.046 0.048 1000 -1000 -0.026 -1000
E-cadherin signaling in keratinocytes 1 79 43 -0.027 0.049 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class II 0 62 75 -0.034 0.072 1000 -1000 -0.03 -1000
PLK2 and PLK4 events 0 0 3 0.014 0.026 1000 -1000 -0.019 -1000
Arf6 downstream pathway 0 3 43 -0.053 0.054 1000 -1000 -0.027 -1000
Aurora C signaling 0 1 7 -0.003 0.051 1000 -1000 -0.014 -1000
TRAIL signaling pathway 0 38 48 -0.014 0.073 1000 -1000 -0.037 -1000
Glypican 2 network 0 0 4 -0.014 0.014 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 11 27 0 0.065 1000 -1000 -0.042 -1000
E-cadherin signaling events 0 0 5 0.025 0.049 1000 -1000 -0.004 -1000
Arf1 pathway 0 5 54 -0.001 0.051 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.071 1000 -1000 -0.002 -1000
Total 2566 149062 7203 -23 7.9 131000 -131000 -5.1 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.34 0.27 -9999 0 -0.5 261 261
EFNA5 -0.084 0.26 -9999 0 -0.69 57 57
FYN -0.32 0.24 -9999 0 -0.46 258 258
neuron projection morphogenesis -0.34 0.27 -9999 0 -0.5 261 261
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.34 0.27 -9999 0 -0.5 261 261
EPHA5 -0.44 0.34 -9999 0 -0.69 239 239
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 -0.21 0.2 0.38 1 -0.39 211 212
CRKL -0.22 0.22 -10000 0 -0.41 210 210
HRAS -0.19 0.19 -10000 0 -0.36 178 178
mol:PIP3 -0.2 0.2 -10000 0 -0.39 189 189
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.026 0.005 -10000 0 -10000 0 0
GAB1 -0.23 0.23 -10000 0 -0.43 210 210
FOXO3 -0.19 0.2 0.44 1 -0.37 200 201
AKT1 -0.2 0.22 0.28 1 -0.39 202 203
BAD -0.18 0.2 0.31 1 -0.37 183 184
megakaryocyte differentiation -0.24 0.22 -10000 0 -0.42 216 216
GSK3B -0.18 0.2 0.36 1 -0.37 184 185
RAF1 -0.15 0.16 0.35 1 -0.34 56 57
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.23 0.23 -10000 0 -0.43 208 208
STAT1 -0.58 0.56 -10000 0 -1.1 212 212
HRAS/SPRED1 -0.15 0.16 -10000 0 -0.34 64 64
cell proliferation -0.23 0.23 -10000 0 -0.42 213 213
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
TEC 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 211 211
HRAS/SPRED2 -0.15 0.16 -10000 0 -0.34 66 66
LYN/TEC/p62DOK -0.2 0.24 -10000 0 -0.41 209 209
MAPK3 -0.11 0.13 0.32 5 -0.29 13 18
STAP1 -0.24 0.23 -10000 0 -0.44 210 210
GRAP2 -0.018 0.15 -10000 0 -0.56 24 24
JAK2 -0.48 0.47 -10000 0 -0.88 212 212
STAT1 (dimer) -0.56 0.54 -10000 0 -1 212 212
mol:Gleevec 0.007 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.2 0.23 -10000 0 -0.41 202 202
actin filament polymerization -0.23 0.22 -10000 0 -0.42 208 208
LYN 0.026 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.33 0.32 0.35 1 -0.61 212 213
PIK3R1 0.025 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 204 204
PI3K -0.2 0.23 -10000 0 -0.4 207 207
PTEN 0.025 0.022 -10000 0 -0.38 1 1
SCF/KIT/EPO/EPOR -0.69 0.66 -10000 0 -1.3 212 212
MAPK8 -0.24 0.23 -10000 0 -0.43 213 213
STAT3 (dimer) -0.23 0.22 -10000 0 -0.42 208 208
positive regulation of transcription -0.083 0.12 0.34 7 -0.23 12 19
mol:GDP -0.2 0.2 -10000 0 -0.38 180 180
PIK3C2B -0.22 0.23 -10000 0 -0.43 192 192
CBL/CRKL -0.2 0.21 -10000 0 -0.39 209 209
FER -0.23 0.23 -10000 0 -0.43 212 212
SH2B3 -0.23 0.23 -10000 0 -0.43 212 212
PDPK1 -0.18 0.2 0.29 2 -0.36 186 188
SNAI2 -0.23 0.23 -10000 0 -0.43 212 212
positive regulation of cell proliferation -0.4 0.39 -10000 0 -0.74 212 212
KITLG -0.012 0.071 -10000 0 -0.72 3 3
cell motility -0.4 0.39 -10000 0 -0.74 212 212
PTPN6 0.037 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.18 -10000 0 -1.1 3 3
STAT5A (dimer) -0.33 0.32 -10000 0 -0.61 212 212
SOCS1 0.024 0.013 -10000 0 -10000 0 0
cell migration 0.23 0.23 0.43 209 -10000 0 209
SOS1 0.026 0.005 -10000 0 -10000 0 0
EPO -0.007 0.027 -10000 0 -10000 0 0
VAV1 0.012 0.062 -10000 0 -0.69 2 2
GRB10 -0.23 0.23 -10000 0 -0.43 209 209
PTPN11 0.034 0.011 -10000 0 -10000 0 0
SCF/KIT -0.24 0.24 -10000 0 -0.45 212 212
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.12 0.14 0.34 4 -0.3 18 22
CBL 0.026 0.005 -10000 0 -10000 0 0
KIT -0.74 0.69 -10000 0 -1.3 212 212
MAP2K2 -0.12 0.14 0.37 3 -0.3 18 21
SHC/Grb2/SOS1 -0.19 0.23 -10000 0 -0.41 184 184
STAT5A -0.34 0.33 -10000 0 -0.63 212 212
GRB2 0.025 0.007 -10000 0 -10000 0 0
response to radiation -0.23 0.23 -10000 0 -0.42 212 212
SHC/GRAP2 0.001 0.11 -10000 0 -0.38 24 24
PTPRO -0.24 0.23 -10000 0 -0.43 216 216
SH2B2 -0.23 0.23 -10000 0 -0.43 208 208
DOK1 0.026 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 209 209
CREBBP -0.041 0.076 -10000 0 -10000 0 0
BCL2 -0.2 0.37 -10000 0 -1.5 25 25
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.066 0.1 -10000 0 -0.61 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 191 191
JUN -0.26 0.26 -10000 0 -0.57 122 122
HRAS 0.025 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.27 0.3 -10000 0 -0.5 217 217
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.27 0.3 -10000 0 -0.5 222 222
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.21 0.23 -10000 0 -0.42 204 204
RHOA 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.27 -10000 0 -0.46 213 213
GRB7 0.006 0.047 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.27 0.3 -10000 0 -0.5 218 218
MAPKKK cascade -0.24 0.24 -10000 0 -0.43 213 213
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.26 -10000 0 -0.46 218 218
lamellipodium assembly -0.2 0.18 -10000 0 -0.35 192 192
RET51/GFRalpha1/GDNF/SHC -0.27 0.3 -10000 0 -0.5 215 215
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
RET9/GFRalpha1/GDNF/SHC -0.21 0.22 -10000 0 -0.41 205 205
RET9/GFRalpha1/GDNF/Shank3 -0.22 0.22 -10000 0 -0.41 208 208
MAPK3 -0.25 0.24 -10000 0 -0.44 210 210
DOK1 0.026 0.005 -10000 0 -10000 0 0
DOK6 -0.087 0.26 -10000 0 -0.69 59 59
PXN 0.026 0.006 -10000 0 -10000 0 0
neurite development -0.27 0.26 -10000 0 -0.55 127 127
DOK5 -0.068 0.24 -10000 0 -0.69 49 49
GFRA1 -0.38 0.35 -10000 0 -0.68 213 213
MAPK8 -0.19 0.2 -10000 0 -0.34 221 221
HRAS/GTP -0.26 0.29 -10000 0 -0.48 217 217
tube development -0.2 0.21 -10000 0 -0.4 196 196
MAPK1 -0.24 0.24 0.32 3 -0.43 212 215
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 201 201
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.025 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.31 0.34 -10000 0 -0.55 226 226
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.27 0.3 -10000 0 -0.5 218 218
RET51/GFRalpha1/GDNF/Dok5 -0.32 0.34 -10000 0 -0.56 229 229
PRKCA -0.013 0.16 -10000 0 -0.69 20 20
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
CREB1 -0.2 0.21 -10000 0 -0.38 194 194
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.16 -10000 0 -0.3 192 192
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.3 -10000 0 -0.5 223 223
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.1 0.26 -10000 0 -0.68 62 62
DOK4 0.025 0.006 -10000 0 -10000 0 0
JNK cascade -0.26 0.25 -10000 0 -0.57 117 117
RET9/GFRalpha1/GDNF/FRS2 -0.21 0.23 -10000 0 -0.42 207 207
SHANK3 0.02 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 186 186
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.36 216 216
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.36 221 221
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.41 208 208
PI3K -0.3 0.29 -10000 0 -0.55 196 196
SOS1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.2 0.21 -10000 0 -0.4 196 196
GRB10 0.025 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.33 203 203
RET51/GFRalpha1/GDNF/FRS2 -0.27 0.3 -10000 0 -0.5 221 221
GAB1 0.026 0.004 -10000 0 -10000 0 0
IRS1 -0.041 0.21 -10000 0 -0.69 35 35
IRS2 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.41 207 207
RET51/GFRalpha1/GDNF/PKC alpha -0.29 0.32 -10000 0 -0.53 219 219
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GDNF -0.006 0.023 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.31 0.32 -10000 0 -0.54 228 228
Rac1/GTP -0.23 0.22 -10000 0 -0.43 191 191
RET9/GFRalpha1/GDNF -0.24 0.24 -10000 0 -0.45 212 212
GFRalpha1/GDNF -0.28 0.27 -10000 0 -0.52 212 212
Reelin signaling 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
CDK5R1/CDK5 0.036 0.015 -10000 0 -10000 0 0
VLDLR 0.005 0.12 -10000 0 -0.66 11 11
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
ITGA3 0.024 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.31 0.24 -10000 0 -0.46 262 262
MAPK8IP1/MKK7/MAP3K11/JNK1 0.065 0.045 -10000 0 -0.4 2 2
AKT1 -0.2 0.15 -10000 0 -0.3 253 253
MAP2K7 0.025 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
DAB1 0.007 0.022 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.29 0.23 -10000 0 -0.43 256 256
LRPAP1/LRP8 0.018 0.1 -10000 0 -0.52 13 13
RELN/LRP8/DAB1/Fyn -0.27 0.22 -10000 0 -0.41 256 256
DAB1/alpha3/beta1 Integrin -0.26 0.21 -10000 0 -0.4 248 248
long-term memory -0.27 0.23 -10000 0 -0.42 254 254
DAB1/LIS1 -0.26 0.22 -10000 0 -0.4 251 251
DAB1/CRLK/C3G -0.26 0.21 -10000 0 -0.39 251 251
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
DAB1/NCK2 -0.26 0.23 -10000 0 -0.41 254 254
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.002 0.12 -10000 0 -0.69 11 11
CDK5R1 0.024 0.014 -10000 0 -10000 0 0
RELN -0.47 0.32 -10000 0 -0.69 259 259
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.31 0.24 -10000 0 -0.46 262 262
GRIN2A/RELN/LRP8/DAB1/Fyn -0.28 0.24 -10000 0 -0.43 254 254
MAPK8 0.022 0.052 -10000 0 -0.69 2 2
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.42 262 262
ITGB1 0.026 0.004 -10000 0 -10000 0 0
MAP1B -0.29 0.21 -10000 0 -0.42 256 256
RELN/LRP8 -0.31 0.24 -10000 0 -0.47 260 260
GRIN2B/RELN/LRP8/DAB1/Fyn -0.27 0.23 -10000 0 -0.42 256 256
PI3K 0.036 0.03 -10000 0 -0.52 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.036 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.21 0.48 3 -0.38 189 192
PAFAH1B1 0.025 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.018 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.44 21 21
neuron adhesion -0.22 0.22 0.51 7 -0.59 20 27
LRP8 0.001 0.13 -10000 0 -0.69 13 13
GSK3B -0.19 0.14 -10000 0 -0.43 20 20
RELN/VLDLR/DAB1/Fyn -0.27 0.21 -10000 0 -0.4 261 261
MAP3K11 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.32 256 256
CDK5 0.025 0.006 -10000 0 -10000 0 0
MAPT 0.048 0.16 0.81 13 -0.62 2 15
neuron migration -0.26 0.2 -10000 0 -0.4 245 245
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.44 21 21
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 258 258
Wnt signaling

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
Noncanonical Wnts/FZD -0.25 0.24 -9999 0 -0.41 239 239
FZD6 0.026 0.005 -9999 0 -10000 0 0
WNT6 0.021 0.02 -9999 0 -10000 0 0
WNT4 -0.22 0.34 -9999 0 -0.69 126 126
FZD3 0.026 0.004 -9999 0 -10000 0 0
WNT5A 0.009 0.11 -9999 0 -0.69 9 9
WNT11 -0.35 0.36 -9999 0 -0.68 197 197
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.008 0.099 -10000 0 -0.56 7 7
NFATC2 -0.19 0.31 -10000 0 -0.71 80 80
NFATC3 -0.086 0.14 -10000 0 -0.29 81 81
CD40LG -0.6 0.56 -10000 0 -1.1 197 197
ITCH 0.036 0.018 -10000 0 -10000 0 0
CBLB 0.036 0.018 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.4 0.49 -10000 0 -1.2 89 89
JUNB 0.019 0.06 -10000 0 -0.54 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.02 -10000 0 -0.33 1 1
T cell anergy 0.012 0.076 0.4 5 -0.48 1 6
TLE4 -0.18 0.34 -10000 0 -0.73 85 85
Jun/NFAT1-c-4/p21SNFT -0.53 0.6 -10000 0 -1.1 176 176
AP-1/NFAT1-c-4 -0.68 0.75 -10000 0 -1.3 195 195
IKZF1 -0.14 0.26 -10000 0 -0.6 67 67
T-helper 2 cell differentiation -0.25 0.32 -10000 0 -0.84 64 64
AP-1/NFAT1 -0.3 0.41 -10000 0 -0.75 150 150
CALM1 0.037 0.014 -10000 0 -10000 0 0
EGR2 -0.71 0.79 -10000 0 -1.5 176 176
EGR3 -0.51 0.69 -10000 0 -1.4 108 108
NFAT1/FOXP3 -0.14 0.27 -10000 0 -0.58 80 80
EGR1 -0.12 0.29 -10000 0 -0.69 76 76
JUN -0.14 0.29 -10000 0 -0.68 83 83
EGR4 -0.03 0.17 -10000 0 -0.67 24 24
mol:Ca2+ 0.011 0.01 -10000 0 -10000 0 0
GBP3 -0.13 0.25 -10000 0 -0.63 54 54
FOSL1 0.006 0.048 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.45 0.55 -10000 0 -0.98 176 176
DGKA -0.13 0.23 -10000 0 -0.55 65 65
CREM 0.026 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.47 0.55 -10000 0 -0.99 178 178
CTLA4 -0.16 0.28 0.36 1 -0.68 66 67
NFAT1-c-4 (dimer)/EGR1 -0.54 0.63 -10000 0 -1.1 176 176
NFAT1-c-4 (dimer)/EGR4 -0.5 0.56 -10000 0 -1 180 180
FOS -0.17 0.31 -10000 0 -0.69 100 100
IFNG -0.34 0.49 -10000 0 -1.1 89 89
T cell activation -0.38 0.4 -10000 0 -0.87 125 125
MAF 0.025 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.34 0.41 0.73 172 -10000 0 172
TNF -0.53 0.55 -10000 0 -1 192 192
FASLG -0.68 0.76 -10000 0 -1.4 185 185
TBX21 -0.022 0.16 -10000 0 -0.7 18 18
BATF3 0.016 0.048 -10000 0 -0.69 1 1
PRKCQ 0.014 0.086 -10000 0 -0.64 6 6
PTPN1 -0.13 0.23 -10000 0 -0.56 65 65
NFAT1-c-4/ICER1 -0.46 0.55 -10000 0 -0.99 177 177
GATA3 -0.011 0.16 -10000 0 -0.65 21 21
T-helper 1 cell differentiation -0.32 0.46 -10000 0 -1.1 90 90
IL2RA -0.37 0.45 -10000 0 -1 90 90
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.13 0.23 -10000 0 -0.56 65 65
E2F1 -0.01 0.061 -10000 0 -10000 0 0
PPARG 0.016 0.083 -10000 0 -0.69 5 5
SLC3A2 -0.13 0.23 -10000 0 -0.56 65 65
IRF4 -0.034 0.15 -10000 0 -0.67 18 18
PTGS2 -0.59 0.56 -10000 0 -1.1 193 193
CSF2 -0.58 0.54 -10000 0 -1.1 193 193
JunB/Fra1/NFAT1-c-4 -0.44 0.54 -10000 0 -0.96 175 175
IL4 -0.26 0.34 -10000 0 -0.91 61 61
IL5 -0.57 0.53 -10000 0 -1 192 192
IL2 -0.39 0.41 -10000 0 -0.89 125 125
IL3 -0.067 0.092 -10000 0 -1.1 1 1
RNF128 0.032 0.043 -10000 0 -0.77 1 1
NFATC1 -0.34 0.41 -10000 0 -0.73 172 172
CDK4 0.22 0.25 0.59 62 -10000 0 62
PTPRK -0.13 0.23 -10000 0 -0.56 66 66
IL8 -0.58 0.54 -10000 0 -1 192 192
POU2F1 0.025 0.01 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.5 0.5 -10000 0 -0.98 168 168
PCK1 -0.32 0.45 -10000 0 -1.3 51 51
HNF4A -0.65 0.62 -10000 0 -1.2 189 189
KCNJ11 -0.47 0.49 -10000 0 -1 141 141
AKT1 -0.066 0.14 -10000 0 -0.47 11 11
response to starvation -0.019 0.042 -10000 0 -0.54 1 1
DLK1 -0.48 0.49 -10000 0 -1 147 147
NKX2-1 -0.18 0.19 -10000 0 -0.51 1 1
ACADM -0.5 0.5 -10000 0 -0.99 163 163
TAT -0.19 0.2 -10000 0 -0.57 13 13
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.018 0.074 -10000 0 -0.69 4 4
TTR -0.14 0.23 0.61 4 -0.74 21 25
PKLR -0.49 0.5 -10000 0 -0.93 186 186
APOA1 -0.9 0.85 -10000 0 -1.7 193 193
CPT1C -0.5 0.5 -10000 0 -0.97 176 176
ALAS1 -0.17 0.2 -10000 0 -1.2 1 1
TFRC -0.24 0.27 -10000 0 -0.8 16 16
FOXF1 0.012 0.074 -10000 0 -0.7 4 4
NF1 0.03 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.027 0.007 -10000 0 -10000 0 0
CPT1A -0.5 0.5 -10000 0 -1 154 154
HMGCS1 -0.5 0.5 -10000 0 -0.98 169 169
NR3C1 0.032 0.008 -10000 0 -10000 0 0
CPT1B -0.5 0.49 -10000 0 -0.94 185 185
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0.006 -10000 0 -10000 0 0
GCK -0.63 0.64 -10000 0 -1.2 188 188
CREB1 0.008 0.067 -10000 0 -0.51 1 1
IGFBP1 -0.17 0.18 -10000 0 -10000 0 0
PDX1 -0.19 0.19 -10000 0 -0.61 3 3
UCP2 -0.5 0.5 -10000 0 -0.95 182 182
ALDOB -0.47 0.49 -10000 0 -1 136 136
AFP -0.015 0.084 -10000 0 -0.37 4 4
BDH1 -0.5 0.5 -10000 0 -1 162 162
HADH -0.47 0.49 -10000 0 -0.99 148 148
F2 -0.61 0.6 -10000 0 -1.2 171 171
HNF1A 0.027 0.007 -10000 0 -10000 0 0
G6PC 0 0.068 -10000 0 -10000 0 0
SLC2A2 -0.23 0.24 -10000 0 -0.63 7 7
INS -0.022 0.013 -10000 0 -10000 0 0
FOXA1 -0.015 0.093 -10000 0 -0.32 23 23
FOXA3 -0.011 0.11 -10000 0 -0.32 27 27
FOXA2 -0.53 0.55 -10000 0 -1.1 170 170
ABCC8 -0.73 0.68 -10000 0 -1.3 195 195
ALB -0.059 0.27 -10000 0 -1.1 23 23
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.21 0.33 -10000 0 -0.7 113 113
PDGF/PDGFRA/CRKL -0.14 0.25 -10000 0 -0.51 114 114
positive regulation of JUN kinase activity -0.079 0.21 -10000 0 -0.4 102 102
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.25 -10000 0 -0.53 112 112
AP1 -0.43 0.56 -10000 0 -1.3 106 106
mol:IP3 -0.16 0.25 -10000 0 -0.54 112 112
PLCG1 -0.16 0.25 -10000 0 -0.54 112 112
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.52 113 113
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.25 -10000 0 -0.54 112 112
CAV3 -0.012 0.019 -10000 0 -10000 0 0
CAV1 0.01 0.1 -10000 0 -0.69 8 8
SHC/Grb2/SOS1 -0.078 0.21 -10000 0 -0.41 102 102
PDGF/PDGFRA/Shf -0.14 0.25 -10000 0 -0.52 113 113
FOS -0.42 0.53 -10000 0 -1.2 106 106
JUN -0.15 0.23 -10000 0 -0.59 81 81
oligodendrocyte development -0.14 0.25 -10000 0 -0.52 113 113
GRB2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.25 -10000 0 -0.54 112 112
PDGF/PDGFRA -0.21 0.33 -10000 0 -0.7 113 113
actin cytoskeleton reorganization -0.14 0.25 -10000 0 -0.52 113 113
SRF 0.024 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.23 -10000 0 -0.45 111 111
PDGF/PDGFRA/Crk/C3G -0.1 0.22 -10000 0 -0.44 110 110
JAK1 -0.15 0.24 -10000 0 -0.52 113 113
ELK1/SRF -0.12 0.2 0.32 1 -0.43 103 104
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.026 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.025 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.56 112 112
SOS1 0.026 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.079 0.21 -10000 0 -0.4 102 102
PDGF/PDGFRA/SHB -0.14 0.25 -10000 0 -0.52 113 113
PDGF/PDGFRA/Caveolin-1 -0.15 0.26 -10000 0 -0.53 116 116
ITGAV 0.024 0.037 -10000 0 -0.69 1 1
ELK1 -0.16 0.23 -10000 0 -0.51 109 109
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
PDGF/PDGFRA/Crk -0.14 0.25 -10000 0 -0.51 112 112
JAK-STAT cascade -0.15 0.24 -10000 0 -0.52 113 113
cell proliferation -0.14 0.25 -10000 0 -0.52 113 113
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.062 0.24 -10000 0 -0.69 46 46
GNB1/GNG2 -0.22 0.24 -10000 0 -0.54 96 96
mol:DAG -0.21 0.21 -10000 0 -0.5 92 92
PLCG1 -0.21 0.22 -10000 0 -0.52 92 92
YES1 -0.24 0.23 -10000 0 -0.54 101 101
FZD3 0.026 0.004 -10000 0 -10000 0 0
FZD6 0.026 0.005 -10000 0 -10000 0 0
G protein -0.21 0.22 -10000 0 -0.52 92 92
MAP3K7 -0.18 0.18 0.3 1 -0.43 88 89
mol:Ca2+ -0.2 0.2 -10000 0 -0.48 92 92
mol:IP3 -0.21 0.21 -10000 0 -0.5 92 92
NLK -0.004 0.065 -10000 0 -0.86 2 2
GNB1 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.19 0.19 0.31 1 -0.46 89 90
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.25 0.24 -10000 0 -0.41 239 239
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.24 0.23 -10000 0 -0.56 94 94
GO:0007205 -0.2 0.2 -10000 0 -0.49 92 92
WNT6 0.021 0.02 -10000 0 -10000 0 0
WNT4 -0.22 0.34 -10000 0 -0.69 126 126
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.52 127 127
GNG2 0.026 0.005 -10000 0 -10000 0 0
WNT5A 0.009 0.11 -10000 0 -0.69 9 9
WNT11 -0.35 0.36 -10000 0 -0.68 197 197
CDC42 -0.23 0.22 -10000 0 -0.53 96 96
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.096 0.21 -10000 0 -0.64 21 21
IHH -0.17 0.33 -10000 0 -0.72 100 100
SHH Np/Cholesterol/GAS1 -0.06 0.17 -10000 0 -0.39 72 72
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.059 0.16 0.39 72 -10000 0 72
SMO/beta Arrestin2 -0.086 0.21 -10000 0 -0.43 90 90
SMO -0.1 0.21 -10000 0 -0.45 93 93
AKT1 -0.02 0.1 -10000 0 -0.34 1 1
ARRB2 0.025 0.007 -10000 0 -10000 0 0
BOC 0.013 0.097 -10000 0 -0.69 7 7
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
heart looping -0.1 0.21 -10000 0 -0.44 93 93
STIL -0.075 0.16 -10000 0 -0.47 11 11
DHH N/PTCH2 -0.048 0.2 -10000 0 -0.52 57 57
DHH N/PTCH1 -0.086 0.2 -10000 0 -0.38 105 105
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
DHH 0.02 0.064 -10000 0 -0.69 3 3
PTHLH -0.15 0.31 -10000 0 -1.1 23 23
determination of left/right symmetry -0.1 0.21 -10000 0 -0.44 93 93
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.14 0.31 -10000 0 -1 23 23
IHH N/Hhip -0.32 0.34 -10000 0 -0.61 207 207
DHH N/Hhip -0.19 0.28 -10000 0 -0.52 151 151
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.1 0.21 -10000 0 -0.44 93 93
pancreas development -0.27 0.34 -10000 0 -0.69 151 151
HHAT 0.023 0.038 -10000 0 -0.69 1 1
PI3K 0.036 0.03 -10000 0 -0.52 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.11 0.27 -10000 0 -0.65 76 76
somite specification -0.1 0.21 -10000 0 -0.44 93 93
SHH Np/Cholesterol/PTCH1 -0.078 0.17 -10000 0 -0.35 90 90
SHH Np/Cholesterol/PTCH2 -0.042 0.15 -10000 0 -0.39 56 56
SHH Np/Cholesterol/Megalin -0.084 0.18 -10000 0 -0.4 93 93
SHH -0.006 0.031 -10000 0 -0.52 1 1
catabolic process -0.1 0.21 -10000 0 -0.42 113 113
SMO/Vitamin D3 -0.084 0.19 -10000 0 -0.39 88 88
SHH Np/Cholesterol/Hhip -0.15 0.21 -10000 0 -0.41 151 151
LRP2 -0.16 0.31 -10000 0 -0.68 96 96
receptor-mediated endocytosis -0.15 0.21 -10000 0 -0.58 36 36
SHH Np/Cholesterol/BOC 0.012 0.061 -10000 0 -0.38 8 8
SHH Np/Cholesterol/CDO -0.098 0.19 -10000 0 -0.39 107 107
mesenchymal cell differentiation 0.15 0.21 0.4 151 -10000 0 151
mol:Vitamin D3 -0.074 0.17 -10000 0 -0.35 90 90
IHH N/PTCH2 -0.18 0.29 -10000 0 -0.54 141 141
CDON -0.18 0.32 -10000 0 -0.69 107 107
IHH N/PTCH1 -0.1 0.22 -10000 0 -0.42 113 113
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.51 96 96
PTCH2 -0.081 0.25 -10000 0 -0.68 56 56
SHH Np/Cholesterol 0.009 0.025 -10000 0 -0.42 1 1
PTCH1 -0.1 0.21 -10000 0 -0.42 113 113
HHIP -0.27 0.34 -10000 0 -0.69 151 151
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.005 -10000 0 -10000 0 0
VLDLR 0.005 0.12 -10000 0 -0.66 11 11
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.31 0.24 -10000 0 -0.47 260 260
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.29 0.21 -10000 0 -0.43 253 253
IQGAP1/CaM 0.038 0.008 -10000 0 -10000 0 0
DAB1 0.007 0.022 -10000 0 -10000 0 0
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
PLA2G7 -0.084 0.26 -10000 0 -0.69 58 58
CALM1 0.026 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.018 0.1 -10000 0 -0.52 13 13
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.006 -10000 0 -10000 0 0
CDK5R1 0.024 0.014 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.003 -10000 0 -10000 0 0
CDK5R2 0 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.31 0.24 -10000 0 -0.46 262 262
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.22 0.19 0.37 4 -0.35 245 249
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.016 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.25 0.2 -10000 0 -0.39 247 247
RELN -0.47 0.32 -10000 0 -0.69 259 259
PAFAH/LIS1 -0.044 0.17 -10000 0 -0.44 58 58
LIS1/CLIP170 0.029 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.5 10 10
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.16 -10000 0 -0.3 251 251
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.24 0.18 -10000 0 -0.36 246 246
LIS1/IQGAP1 0.029 0.009 -10000 0 -10000 0 0
RHOA 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.015 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.012 -10000 0 -10000 0 0
PAFAH1B2 0.022 0.052 -10000 0 -0.69 2 2
MAP1B/LIS1/Dynein heavy chain 0.029 0.011 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.21 0.18 0.32 1 -0.55 13 14
LRP8 0.001 0.13 -10000 0 -0.69 13 13
NDEL1/Katanin 60 -0.22 0.18 0.29 3 -0.35 246 249
P39/CDK5 -0.26 0.2 -10000 0 -0.39 252 252
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.029 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.2 -10000 0 -0.4 253 253
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.008 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.41 248 248
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 258 258
CDC42 0.016 0.005 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.13 0.22 -10000 0 -0.41 140 140
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.3 141 141
GNAO1 0.009 0.1 -10000 0 -0.69 8 8
HRAS 0.025 0.009 -10000 0 -10000 0 0
SHBG/T-DHT 0.007 0.068 -10000 0 -0.45 8 8
PELP1 0.024 0.007 -10000 0 -10000 0 0
AKT1 0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.21 0.54 5 -0.38 138 143
T-DHT/AR -0.19 0.26 -10000 0 -0.52 145 145
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.006 102 102
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.037 -10000 0 -0.69 1 1
mol:GDP -0.2 0.26 -10000 0 -0.54 142 142
cell proliferation -0.2 0.27 0.49 10 -0.53 109 119
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
FOS -0.27 0.38 0.54 7 -0.85 104 111
mol:Ca2+ -0.025 0.029 -10000 0 -0.067 76 76
MAPK3 -0.16 0.25 0.53 11 -0.55 59 70
MAPK1 -0.17 0.22 0.34 5 -0.42 126 131
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 94 94
cAMP biosynthetic process 0.013 0.076 0.25 7 -0.43 8 15
GNG2 0.026 0.005 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 94 94
HRAS/GTP -0.13 0.21 -10000 0 -0.4 138 138
actin cytoskeleton reorganization 0.037 0.024 -10000 0 -0.37 1 1
SRC 0.025 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 94 94
PI3K 0.033 0.026 -10000 0 -0.45 1 1
apoptosis 0.19 0.26 0.52 115 -0.45 7 122
T-DHT/AR/PELP1 -0.16 0.24 -10000 0 -0.45 144 144
HRAS/GDP -0.19 0.26 -10000 0 -0.51 143 143
CREB1 -0.21 0.28 0.49 6 -0.57 115 121
RAC1-CDC42/GTP 0.047 0.027 -10000 0 -0.38 1 1
AR -0.25 0.35 -10000 0 -0.68 145 145
GNB1 0.026 0.005 -10000 0 -10000 0 0
RAF1 -0.13 0.21 0.55 5 -0.39 138 143
RAC1-CDC42/GDP -0.16 0.26 -10000 0 -0.49 142 142
T-DHT/AR/PELP1/Src -0.13 0.22 -10000 0 -0.42 138 138
MAP2K2 -0.14 0.2 0.5 3 -0.38 136 139
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.3 141 141
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.01 0.1 -10000 0 -0.69 8 8
Gi family/GNB1/GNG2/GDP -0.029 0.093 -10000 0 -0.45 10 10
mol:T-DHT -0.001 0.003 0.002 2 -0.005 58 60
RAC1 0.025 0.006 -10000 0 -10000 0 0
GNRH1 0.007 0.028 -10000 0 -0.52 1 1
Gi family/GTP -0.082 0.11 -10000 0 -0.3 33 33
CDC42 0.026 0.005 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.034 0.096 -10000 0 -0.46 9 9
PTK2B 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.28 0.45 2 -0.66 60 62
EDN1 -0.007 0.11 -10000 0 -0.62 7 7
EDN3 -0.33 0.36 -10000 0 -0.69 184 184
EDN2 0.013 0.078 -10000 0 -0.69 4 4
HRAS/GDP -0.12 0.23 0.48 2 -0.49 72 74
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.08 0.15 -10000 0 -0.34 76 76
ADCY4 -0.074 0.15 0.35 1 -0.42 50 51
ADCY5 -0.13 0.21 0.35 1 -0.47 87 88
ADCY6 -0.072 0.15 0.35 1 -0.42 49 50
ADCY7 -0.072 0.15 0.35 1 -0.43 49 50
ADCY1 -0.075 0.16 0.35 1 -0.44 50 51
ADCY2 -0.11 0.19 -10000 0 -0.46 70 70
ADCY3 -0.073 0.16 0.35 1 -0.43 51 52
ADCY8 -0.097 0.16 0.35 1 -0.45 51 52
ADCY9 -0.072 0.15 0.35 1 -0.43 48 49
arachidonic acid secretion -0.2 0.32 0.39 7 -0.6 121 128
ETB receptor/Endothelin-1/Gq/GTP -0.09 0.18 -10000 0 -0.37 95 95
GNAO1 0.009 0.1 -10000 0 -0.69 8 8
HRAS 0.025 0.009 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.027 0.11 -10000 0 -0.41 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.03 0.18 -10000 0 -0.45 52 52
mol:GTP -0.004 0.009 -10000 0 -10000 0 0
COL3A1 -0.039 0.1 -10000 0 -0.49 9 9
EDNRB 0.017 0.075 -10000 0 -0.69 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.071 0.16 -10000 0 -0.66 19 19
CYSLTR1 -0.037 0.12 -10000 0 -0.62 10 10
SLC9A1 -0.003 0.06 -10000 0 -0.28 10 10
mol:GDP -0.14 0.24 0.47 3 -0.51 77 80
SLC9A3 -0.051 0.2 0.39 1 -0.7 23 24
RAF1 -0.18 0.28 0.44 3 -0.54 114 117
JUN -0.3 0.49 0.48 1 -1.1 97 98
JAK2 -0.034 0.099 -10000 0 -0.5 9 9
mol:IP3 -0.11 0.2 -10000 0 -0.41 101 101
ETA receptor/Endothelin-1 0.014 0.14 -10000 0 -0.52 12 12
PLCB1 0.022 0.038 -10000 0 -0.7 1 1
PLCB2 0.018 0.023 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.25 0.28 -10000 0 -0.54 185 185
FOS -0.29 0.45 0.6 2 -1 103 105
Gai/GDP -0.008 0.13 -10000 0 -0.63 15 15
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.19 -10000 0 -0.45 57 57
BCAR1 0.025 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.4 101 101
GNAQ 0.014 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.061 0.23 -10000 0 -0.67 47 47
Gs family/GDP -0.16 0.26 0.28 1 -0.53 91 92
ETA receptor/Endothelin-1/Gq/GTP -0.096 0.18 -10000 0 -0.37 96 96
MAPK14 -0.075 0.15 -10000 0 -0.34 63 63
TRPC6 -0.17 0.29 0.45 2 -0.7 59 61
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.037 -10000 0 -0.69 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.078 0.16 -10000 0 -0.32 96 96
ETB receptor/Endothelin-2 0.026 0.082 -10000 0 -0.52 8 8
ETB receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.53 186 186
ETB receptor/Endothelin-1 0.012 0.1 -10000 0 -0.56 9 9
MAPK3 -0.26 0.41 0.41 4 -0.86 107 111
MAPK1 -0.31 0.45 0.62 2 -0.96 108 110
Rac1/GDP -0.12 0.22 -10000 0 -0.49 69 69
cAMP biosynthetic process -0.08 0.19 0.5 8 -0.46 52 60
MAPK8 -0.19 0.34 0.51 1 -0.64 102 103
SRC 0.025 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.003 0.071 -10000 0 -0.27 18 18
p130Cas/CRK/Src/PYK2 -0.16 0.28 0.44 7 -0.54 110 117
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.22 -10000 0 -0.48 71 71
COL1A2 -0.009 0.11 -10000 0 -0.64 5 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.015 0.083 -10000 0 -0.55 5 5
mol:DAG -0.11 0.2 -10000 0 -0.41 101 101
MAP2K2 -0.21 0.33 0.38 8 -0.68 107 115
MAP2K1 -0.22 0.34 0.43 3 -0.69 112 115
EDNRA -0.001 0.073 -10000 0 -0.4 4 4
positive regulation of muscle contraction -0.027 0.08 -10000 0 -0.44 5 5
Gq family/GDP -0.16 0.28 0.37 1 -0.56 100 101
HRAS/GTP -0.15 0.24 0.36 4 -0.49 91 95
PRKCH -0.11 0.2 -10000 0 -0.41 92 92
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.13 0.22 -10000 0 -0.45 100 100
PRKCB -0.12 0.2 -10000 0 -0.43 81 81
PRKCE -0.12 0.2 -10000 0 -0.44 79 79
PRKCD -0.11 0.2 -10000 0 -0.44 79 79
PRKCG -0.11 0.2 -10000 0 -0.43 85 85
regulation of vascular smooth muscle contraction -0.34 0.53 0.64 2 -1.2 103 105
PRKCQ -0.12 0.2 -10000 0 -0.44 85 85
PLA2G4A -0.22 0.35 0.42 6 -0.67 121 127
GNA14 -0.15 0.3 -10000 0 -0.66 91 91
GNA15 0.004 0.054 -10000 0 -0.69 1 1
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.012 0.066 -10000 0 -0.69 3 3
Rac1/GTP 0.027 0.11 -10000 0 -0.42 7 7
MMP1 -0.029 0.08 0.64 2 -10000 0 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.095 0.24 0.53 83 -10000 0 83
KIRREL -0.03 0.17 -10000 0 -0.71 21 21
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.095 0.24 -10000 0 -0.53 83 83
PLCG1 0.026 0.005 -10000 0 -10000 0 0
ARRB2 0.025 0.007 -10000 0 -10000 0 0
WASL 0.025 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.05 0.2 -10000 0 -0.43 77 77
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.052 0.15 -10000 0 -0.34 74 74
FYN -0.071 0.18 0.26 17 -0.4 76 93
mol:Ca2+ -0.051 0.19 -10000 0 -0.43 75 75
mol:DAG -0.051 0.2 -10000 0 -0.43 75 75
NPHS2 -0.02 0.037 -10000 0 -10000 0 0
mol:IP3 -0.051 0.2 -10000 0 -0.43 75 75
regulation of endocytosis -0.046 0.18 -10000 0 -0.38 75 75
Nephrin/NEPH1/podocin/Cholesterol -0.062 0.19 -10000 0 -0.43 77 77
establishment of cell polarity -0.095 0.24 -10000 0 -0.53 83 83
Nephrin/NEPH1/podocin/NCK1-2 -0.035 0.19 -10000 0 -0.4 76 76
Nephrin/NEPH1/beta Arrestin2 -0.046 0.18 -10000 0 -0.39 75 75
NPHS1 -0.13 0.26 -10000 0 -0.69 66 66
Nephrin/NEPH1/podocin -0.056 0.18 -10000 0 -0.4 77 77
TJP1 0.026 0.004 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.05 0.2 -10000 0 -0.43 75 75
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.051 0.2 -10000 0 -0.43 74 74
GRB2 0.025 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.075 0.19 0.28 15 -0.41 77 92
cytoskeleton organization -0.079 0.19 -10000 0 -0.45 74 74
Nephrin/NEPH1 -0.067 0.18 -10000 0 -0.39 83 83
Nephrin/NEPH1/ZO-1 -0.064 0.21 -10000 0 -0.45 78 78
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.066 -10000 0 -0.46 6 6
NFATC2 -0.059 0.16 -10000 0 -0.46 46 46
NFATC3 -0.001 0.029 -10000 0 -10000 0 0
CD40LG -0.31 0.36 -10000 0 -0.74 127 127
PTGS2 -0.3 0.36 0.38 1 -0.75 119 120
JUNB 0.019 0.06 -10000 0 -0.54 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.023 -10000 0 -10000 0 0
CaM/Ca2+ 0.007 0.023 -10000 0 -10000 0 0
CALM1 0.017 0.02 -10000 0 -10000 0 0
JUN -0.14 0.29 -10000 0 -0.69 82 82
mol:Ca2+ -0.007 0.02 -10000 0 -0.19 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.006 0.048 -10000 0 -10000 0 0
CREM 0.026 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.16 0.24 -10000 0 -0.46 116 116
FOS -0.17 0.31 -10000 0 -0.69 100 100
IFNG -0.31 0.36 0.38 1 -0.72 139 140
AP-1/NFAT1-c-4 -0.32 0.44 -10000 0 -0.85 126 126
FASLG -0.29 0.34 0.38 1 -0.71 125 126
NFAT1-c-4/ICER1 -0.06 0.16 -10000 0 -0.42 50 50
IL2RA -0.29 0.34 -10000 0 -0.71 122 122
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.3 0.32 0.38 1 -0.69 123 124
JunB/Fra1/NFAT1-c-4 -0.051 0.16 -10000 0 -0.41 50 50
IL4 -0.28 0.32 0.37 1 -0.68 119 120
IL2 0.003 0.064 -10000 0 -1.1 1 1
IL3 -0.009 0.057 -10000 0 -0.87 1 1
FKBP1A 0.026 0.005 -10000 0 -10000 0 0
BATF3 0.016 0.048 -10000 0 -0.69 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.05 0.029 -9999 0 -0.45 1 1
fibroblast growth factor receptor signaling pathway 0.05 0.029 -9999 0 -0.45 1 1
LAMA1 -0.025 0.18 -9999 0 -0.68 27 27
PRNP 0.026 0.005 -9999 0 -10000 0 0
GPC1/SLIT2 -0.036 0.19 -9999 0 -0.52 49 49
SMAD2 0.016 0.03 -9999 0 -0.42 1 1
GPC1/PrPc/Cu2+ 0.034 0.008 -9999 0 -10000 0 0
GPC1/Laminin alpha1 -0.003 0.14 -9999 0 -0.51 27 27
TDGF1 -0.28 0.35 -9999 0 -0.69 158 158
CRIPTO/GPC1 -0.2 0.28 -9999 0 -0.52 158 158
APP/GPC1 0.037 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.18 0.23 -9999 0 -0.45 156 156
FLT1 0.025 0.006 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.032 -9999 0 -0.45 1 1
SERPINC1 0.021 0.013 -9999 0 -10000 0 0
FYN -0.18 0.23 -9999 0 -0.45 156 156
FGR -0.18 0.23 -9999 0 -0.45 156 156
positive regulation of MAPKKK cascade -0.24 0.26 -9999 0 -0.52 159 159
SLIT2 -0.069 0.24 -9999 0 -0.68 50 50
GPC1/NRG -0.017 0.17 -9999 0 -0.52 37 37
NRG1 -0.044 0.21 -9999 0 -0.68 37 37
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.04 -9999 0 -0.45 2 2
LYN -0.18 0.23 -9999 0 -0.45 156 156
mol:Spermine 0.008 0.004 -9999 0 -10000 0 0
cell growth 0.05 0.029 -9999 0 -0.45 1 1
BMP signaling pathway -0.025 0.009 -9999 0 -10000 0 0
SRC -0.18 0.23 -9999 0 -0.45 156 156
TGFBR1 0.02 0.024 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.17 0.3 -9999 0 -0.69 95 95
GPC1 0.025 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.02 0.024 -9999 0 -10000 0 0
VEGFA 0.023 0.052 -9999 0 -0.69 2 2
BLK -0.31 0.31 -9999 0 -0.56 210 210
HCK -0.18 0.23 -9999 0 -0.45 156 156
FGF2 0.026 0.004 -9999 0 -10000 0 0
FGFR1 0.024 0.037 -9999 0 -0.69 1 1
VEGFR1 homodimer 0.025 0.006 -9999 0 -10000 0 0
TGFBR2 0.024 0.037 -9999 0 -0.69 1 1
cell death 0.037 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.035 0.013 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.24 -9999 0 -0.52 95 95
LCK -0.18 0.23 -9999 0 -0.45 156 156
neuron differentiation -0.017 0.17 -9999 0 -0.51 37 37
PrPc/Cu2+ 0.019 0.004 -9999 0 -10000 0 0
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.037 -9999 0 -0.69 1 1
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.19 0.31 -10000 0 -0.51 166 166
SMAD6-7/SMURF1 0.051 0.014 -10000 0 -10000 0 0
NOG -0.027 0.18 -10000 0 -0.69 26 26
SMAD9 -0.19 0.28 -10000 0 -0.55 126 126
SMAD4 0.026 0.004 -10000 0 -10000 0 0
SMAD5 -0.095 0.17 -10000 0 -0.32 126 126
BMP7/USAG1 -0.25 0.28 -10000 0 -0.52 193 193
SMAD5/SKI -0.079 0.18 0.31 3 -0.45 23 26
SMAD1 -0.037 0.093 -10000 0 -10000 0 0
BMP2 0.003 0.13 -10000 0 -0.69 12 12
SMAD1/SMAD1/SMAD4 -0.024 0.085 -10000 0 -10000 0 0
BMPR1A 0.026 0.005 -10000 0 -10000 0 0
BMPR1B -0.22 0.34 -10000 0 -0.69 130 130
BMPR1A-1B/BAMBI -0.12 0.24 -10000 0 -0.46 130 130
AHSG -0.002 0.034 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.015 0.12 -10000 0 -0.46 21 21
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.074 0.17 -10000 0 -0.55 23 23
BMP2-4 (homodimer) 0.005 0.13 -10000 0 -0.52 21 21
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.1 0.23 -10000 0 -0.42 130 130
RGMA 0.002 0.13 -10000 0 -0.69 13 13
SMURF1 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.086 0.16 -10000 0 -0.28 129 129
BMP2-4/USAG1 -0.24 0.26 -10000 0 -0.47 204 204
SMAD6/SMURF1/SMAD5 -0.077 0.17 0.31 1 -0.44 21 22
SOSTDC1 -0.35 0.35 -10000 0 -0.69 193 193
BMP7/BMPR2/BMPR1A-1B -0.1 0.23 -10000 0 -0.41 129 129
SKI 0.026 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.002 -10000 0 -10000 0 0
HFE2 -0.003 0.021 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.14 -10000 0 -0.47 28 28
SMAD5/SMAD5/SMAD4 -0.077 0.18 0.31 3 -0.45 23 26
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.061 0.15 -10000 0 -0.4 27 27
BMP7 (homodimer) 0.026 0.005 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.029 0.025 -10000 0 -10000 0 0
SMAD1/SKI -0.029 0.1 0.33 1 -10000 0 1
SMAD6 0.026 0.003 -10000 0 -10000 0 0
CTDSP2 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.021 0.12 -10000 0 -0.46 21 21
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.68 83 83
BMPR2 (homodimer) 0.026 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.06 -10000 0 -0.45 5 5
BMPR1A-1B (homodimer) -0.16 0.27 -10000 0 -0.52 130 130
CHRDL1 -0.46 0.33 -10000 0 -0.68 256 256
ENDOFIN/SMAD1 -0.031 0.098 -10000 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.015 0.1 -10000 0 -10000 0 0
SMAD6/SMURF1 0.025 0.006 -10000 0 -10000 0 0
BAMBI 0.02 0.044 -10000 0 -0.69 1 1
SMURF2 0.025 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.31 0.25 -10000 0 -0.47 258 258
BMP2-4/GREM1 -0.078 0.24 -10000 0 -0.5 89 89
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.27 -10000 0 -0.54 119 119
SMAD1/SMAD6 -0.029 0.096 -10000 0 -10000 0 0
TAK1/SMAD6 0.037 0.01 -10000 0 -10000 0 0
BMP7 0.026 0.005 -10000 0 -10000 0 0
BMP6 0.027 0.002 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.064 0.14 -10000 0 -0.42 24 24
PPM1A 0.026 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.028 0.098 0.33 1 -0.34 1 2
SMAD7/SMURF1 0.037 0.01 -10000 0 -10000 0 0
CTDSPL 0.026 0.004 -10000 0 -10000 0 0
PPP1CA 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
CTDSP1 0.026 0.005 -10000 0 -10000 0 0
PPP1R15A 0.016 0.082 -10000 0 -0.69 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.18 0.27 -10000 0 -0.41 173 173
CHRD 0.011 0.1 -10000 0 -0.69 8 8
BMPR2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.088 0.16 -10000 0 -0.29 134 134
BMP4 0.006 0.11 -10000 0 -0.66 10 10
FST -0.15 0.31 -10000 0 -0.69 92 92
BMP2-4/NOG -0.013 0.17 -10000 0 -0.46 46 46
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.087 0.22 -10000 0 -0.4 125 125
HIF-1-alpha transcription factor network

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
PKM2 -0.21 0.36 0.63 1 -0.89 32 33
HDAC7 0.027 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.26 0.4 -10000 0 -0.83 83 83
SMAD4 0.027 0.004 -10000 0 -10000 0 0
ID2 -0.21 0.35 0.62 2 -0.86 36 38
AP1 -0.2 0.38 -10000 0 -0.74 117 117
ABCG2 -0.21 0.36 0.6 1 -0.88 36 37
HIF1A -0.025 0.072 -10000 0 -10000 0 0
TFF3 -0.5 0.44 0.62 2 -0.92 143 145
GATA2 0.026 0.011 -10000 0 -10000 0 0
AKT1 -0.06 0.11 -10000 0 -0.26 18 18
response to hypoxia -0.074 0.11 -10000 0 -0.24 62 62
MCL1 -0.2 0.35 0.62 2 -0.88 32 34
NDRG1 -0.21 0.36 0.61 3 -0.87 34 37
SERPINE1 -0.21 0.35 0.6 1 -0.88 35 36
FECH -0.2 0.36 0.62 2 -0.87 34 36
FURIN -0.21 0.36 0.62 2 -0.87 35 37
NCOA2 -0.017 0.17 -10000 0 -0.69 23 23
EP300 -0.11 0.18 -10000 0 -0.35 124 124
HMOX1 -0.22 0.34 0.63 1 -0.87 35 36
BHLHE40 -0.21 0.36 0.62 2 -0.85 40 42
BHLHE41 -0.21 0.35 0.6 1 -0.88 35 36
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.023 0.099 -10000 0 -10000 0 0
ENG 0.008 0.094 0.47 3 -10000 0 3
JUN -0.13 0.3 -10000 0 -0.69 82 82
RORA -0.21 0.36 0.61 3 -0.87 36 39
ABCB1 -0.057 0.17 -10000 0 -1.2 6 6
TFRC -0.21 0.36 0.62 2 -0.88 33 35
CXCR4 -0.21 0.36 0.62 2 -0.86 36 38
TF -0.26 0.42 0.62 2 -0.98 59 61
CITED2 -0.23 0.39 0.61 3 -0.94 47 50
HIF1A/ARNT -0.24 0.39 -10000 0 -0.97 35 35
LDHA -0.038 0.11 -10000 0 -0.67 8 8
ETS1 -0.21 0.35 0.62 2 -0.86 36 38
PGK1 -0.21 0.35 0.6 1 -0.87 35 36
NOS2 -0.21 0.35 0.61 2 -0.86 36 38
ITGB2 -0.21 0.36 0.62 2 -0.87 37 39
ALDOA -0.21 0.35 0.6 1 -0.88 33 34
Cbp/p300/CITED2 -0.32 0.46 -10000 0 -0.98 89 89
FOS -0.16 0.32 -10000 0 -0.69 100 100
HK2 -0.21 0.36 0.62 2 -0.86 39 41
SP1 0.031 0.017 -10000 0 -10000 0 0
GCK -0.42 0.65 -10000 0 -1.4 108 108
HK1 -0.21 0.35 0.62 2 -0.86 36 38
NPM1 -0.21 0.35 0.6 1 -0.87 35 36
EGLN1 -0.2 0.35 0.61 3 -0.87 34 37
CREB1 0.032 0.006 -10000 0 -10000 0 0
PGM1 -0.21 0.35 0.62 2 -0.86 35 37
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.21 0.3 0.49 1 -0.69 67 68
IGFBP1 -0.21 0.35 0.6 1 -0.87 35 36
VEGFA -0.22 0.35 -10000 0 -0.73 74 74
HIF1A/JAB1 0 0.058 -10000 0 -10000 0 0
CP -0.34 0.47 0.62 2 -0.94 107 109
CXCL12 -0.25 0.41 0.62 2 -0.96 56 58
COPS5 0.027 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.04 0.007 -10000 0 -10000 0 0
BNIP3 -0.21 0.35 0.62 2 -0.85 38 40
EGLN3 -0.22 0.36 -10000 0 -0.88 41 41
CA9 -0.21 0.36 0.6 2 -0.86 39 41
TERT -0.21 0.34 0.6 1 -0.85 38 39
ENO1 -0.2 0.35 0.61 3 -0.86 36 39
PFKL -0.21 0.35 0.62 2 -0.87 34 36
NCOA1 0.026 0.005 -10000 0 -10000 0 0
ADM -0.22 0.36 0.62 2 -0.88 35 37
ARNT -0.018 0.07 -10000 0 -0.33 1 1
HNF4A -0.017 0.058 -10000 0 -10000 0 0
ADFP -0.22 0.34 -10000 0 -0.82 44 44
SLC2A1 -0.21 0.35 -10000 0 -0.74 67 67
LEP -0.21 0.35 0.6 1 -0.87 35 36
HIF1A/ARNT/Cbp/p300 -0.27 0.41 -10000 0 -0.85 87 87
EPO -0.14 0.26 -10000 0 -0.82 13 13
CREBBP -0.089 0.17 -10000 0 -0.33 106 106
HIF1A/ARNT/Cbp/p300/HDAC7 -0.25 0.41 -10000 0 -0.84 79 79
PFKFB3 -0.21 0.35 0.62 2 -0.88 34 36
NT5E -0.21 0.36 0.61 3 -0.9 34 37
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.026 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.089 0.18 -10000 0 -0.37 100 100
GRB2/SOS1/SHC 0.047 0.019 -10000 0 -10000 0 0
HRAS 0.025 0.009 -10000 0 -10000 0 0
IRS1/Crk -0.08 0.18 -10000 0 -0.38 97 97
IGF-1R heterotetramer/IGF1/PTP1B -0.056 0.19 -10000 0 -0.44 73 73
AKT1 -0.08 0.16 -10000 0 -0.36 70 70
BAD -0.079 0.15 -10000 0 -0.61 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.086 0.18 -10000 0 -0.38 97 97
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.077 0.19 -10000 0 -0.38 100 100
RAF1 -0.059 0.15 0.38 1 -0.56 9 10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.051 0.19 -10000 0 -0.36 96 96
YWHAZ 0.026 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.084 0.2 -10000 0 -0.4 102 102
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
RPS6KB1 -0.079 0.16 -10000 0 -0.36 69 69
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.05 0.13 0.32 5 -0.48 8 13
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.062 0.16 -10000 0 -0.36 68 68
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.022 0.16 -10000 0 -0.36 68 68
IGF-1R heterotetramer -0.006 0.057 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.066 0.2 -10000 0 -0.38 100 100
Crk/p130 Cas/Paxillin -0.046 0.19 -10000 0 -0.35 96 96
IGF1R -0.006 0.057 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.71 74 74
IRS2/Crk -0.074 0.18 -10000 0 -0.36 97 97
PI3K -0.053 0.2 -10000 0 -0.36 100 100
apoptosis 0.055 0.14 0.51 8 -0.39 1 9
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
PRKCD -0.081 0.19 -10000 0 -0.46 73 73
RAF1/14-3-3 E -0.037 0.14 0.34 2 -0.48 9 11
BAD/14-3-3 -0.058 0.15 0.39 2 -0.55 8 10
PRKCZ -0.079 0.16 0.25 1 -0.36 70 71
Crk/p130 Cas/Paxillin/FAK1 -0.049 0.15 -10000 0 -0.55 8 8
PTPN1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.084 0.2 -10000 0 -0.48 74 74
BCAR1 0.025 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.036 0.18 -10000 0 -0.39 71 71
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.076 0.19 -10000 0 -0.37 100 100
GRB10 0.025 0.006 -10000 0 -10000 0 0
PTPN11 -0.087 0.18 -10000 0 -0.38 100 100
IRS1 -0.095 0.2 -10000 0 -0.4 102 102
IRS2 -0.088 0.18 -10000 0 -0.37 101 101
IGF-1R heterotetramer/IGF1 -0.089 0.23 -10000 0 -0.55 74 74
GRB2 0.025 0.007 -10000 0 -10000 0 0
PDPK1 -0.079 0.17 -10000 0 -0.38 72 72
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.082 0.19 -10000 0 -0.46 73 73
SHC1 0.025 0.007 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.41 -10000 0 -1.2 57 57
STAT6 (cleaved dimer) -0.5 0.42 -10000 0 -1.1 85 85
IGHG1 -0.17 0.13 -10000 0 -0.42 2 2
IGHG3 -0.48 0.39 -10000 0 -1 82 82
AKT1 -0.26 0.28 0.66 1 -0.86 37 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.3 -10000 0 -0.98 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.29 0.29 -10000 0 -0.86 45 45
THY1 -0.5 0.41 -10000 0 -1.2 58 58
MYB 0.01 0.1 -10000 0 -0.65 8 8
HMGA1 0.026 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.33 0.31 -10000 0 -0.86 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.28 -10000 0 -0.92 33 33
SP1 0.03 0.01 -10000 0 -10000 0 0
INPP5D 0.016 0.035 -10000 0 -10000 0 0
SOCS5 0.038 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.49 0.42 -10000 0 -1.1 72 72
SOCS1 -0.34 0.26 -10000 0 -0.74 53 53
SOCS3 -0.32 0.38 0.59 2 -1.2 40 42
FCER2 -0.48 0.41 -10000 0 -1 84 84
PARP14 0.027 0.004 -10000 0 -10000 0 0
CCL17 -0.52 0.43 -10000 0 -1.2 63 63
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.2 -10000 0 -0.67 32 32
T cell proliferation -0.49 0.42 -10000 0 -1.2 61 61
IL4R/JAK1 -0.49 0.42 -10000 0 -1.2 59 59
EGR2 -0.82 0.7 -10000 0 -1.6 170 170
JAK2 -0.03 0.035 -10000 0 -10000 0 0
JAK3 -0.006 0.057 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.003 0.022 -10000 0 -10000 0 0
COL1A2 -0.15 0.16 -10000 0 -1.2 3 3
CCL26 -0.49 0.41 -10000 0 -1.2 58 58
IL4R -0.52 0.44 -10000 0 -1.3 58 58
PTPN6 0.039 0.012 -10000 0 -10000 0 0
IL13RA2 -0.6 0.56 -10000 0 -1.5 86 86
IL13RA1 -0.03 0.034 -10000 0 -10000 0 0
IRF4 -0.24 0.43 -10000 0 -1.2 56 56
ARG1 -0.13 0.14 -10000 0 -1.2 2 2
CBL -0.31 0.29 -10000 0 -0.84 52 52
GTF3A 0.026 0.014 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
IL13RA1/JAK2 -0.036 0.048 -10000 0 -10000 0 0
IRF4/BCL6 -0.23 0.4 -10000 0 -1.1 56 56
CD40LG -0.054 0.22 -10000 0 -0.66 42 42
MAPK14 -0.33 0.34 -10000 0 -0.97 53 53
mitosis -0.25 0.26 0.61 2 -0.8 38 40
STAT6 -0.56 0.5 -10000 0 -1.3 68 68
SPI1 0.022 0.03 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.25 0.7 3 -0.76 34 37
STAT6 (dimer) -0.56 0.5 -10000 0 -1.3 68 68
STAT6 (dimer)/PARP14 -0.52 0.45 -10000 0 -1.2 68 68
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.31 -10000 0 -0.96 41 41
FRAP1 -0.26 0.28 0.61 2 -0.86 38 40
LTA -0.5 0.41 -10000 0 -1.2 59 59
FES 0.026 0.003 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.55 0.47 1.3 71 -10000 0 71
CCL11 -0.48 0.4 -10000 0 -1.1 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.3 -10000 0 -0.95 41 41
IL2RG -0.012 0.14 -10000 0 -0.63 16 16
IL10 -0.5 0.43 -10000 0 -1.2 60 60
IRS1 -0.041 0.21 -10000 0 -0.69 35 35
IRS2 0.025 0.006 -10000 0 -10000 0 0
IL4 -0.11 0.094 -10000 0 -10000 0 0
IL5 -0.5 0.41 -10000 0 -1.2 58 58
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.43 0.37 -10000 0 -0.98 67 67
COL1A1 -0.2 0.24 -10000 0 -1 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.49 0.43 -10000 0 -1.3 50 50
IL2R gamma/JAK3 0 0.12 -10000 0 -0.48 16 16
TFF3 -1.2 0.6 -10000 0 -1.4 299 299
ALOX15 -0.5 0.41 -10000 0 -1.2 58 58
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.42 0.35 -10000 0 -0.96 65 65
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.029 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.27 -10000 0 -0.93 30 30
mol:PI-3-4-5-P3 -0.26 0.28 0.61 2 -0.86 37 39
PI3K -0.27 0.3 0.66 1 -0.95 37 38
DOK2 0.019 0.056 -10000 0 -0.69 2 2
ETS1 0.037 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.19 -10000 0 -0.66 28 28
ITGB3 -0.51 0.44 -10000 0 -1.2 62 62
PIGR -0.52 0.45 -10000 0 -1.3 62 62
IGHE 0.044 0.047 0.26 7 -10000 0 7
MAPKKK cascade -0.19 0.19 0.57 1 -0.64 28 29
BCL6 0.024 0.037 -10000 0 -0.69 1 1
OPRM1 -0.5 0.41 -10000 0 -1.2 59 59
RETNLB -0.5 0.41 -10000 0 -1.2 59 59
SELP -0.5 0.43 -10000 0 -1.2 56 56
AICDA -0.48 0.39 -10000 0 -1.1 58 58
Glucocorticoid receptor regulatory network

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
PCK2 0.084 0.087 0.34 2 -10000 0 2
SMARCC2 0.025 0.018 -10000 0 -10000 0 0
SMARCC1 0.026 0.017 -10000 0 -10000 0 0
TBX21 -0.13 0.25 0.32 1 -0.66 46 47
SUMO2 0.022 0.019 -10000 0 -10000 0 0
STAT1 (dimer) 0.029 0.023 -10000 0 -10000 0 0
FKBP4 0.026 0.005 -10000 0 -10000 0 0
FKBP5 0.021 0.064 -10000 0 -0.69 3 3
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.32 43 -0.44 2 45
PRL -0.066 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.2 0.28 0.52 118 -0.49 9 127
RELA -0.033 0.1 -10000 0 -0.28 23 23
FGG 0.17 0.2 0.47 77 -10000 0 77
GR beta/TIF2 0.087 0.18 0.33 52 -0.46 23 75
IFNG -0.36 0.47 -10000 0 -0.95 112 112
apoptosis -0.014 0.23 0.46 36 -0.55 15 51
CREB1 0.027 0.009 -10000 0 -10000 0 0
histone acetylation -0.081 0.15 -10000 0 -0.43 43 43
BGLAP -0.079 0.13 -10000 0 -0.5 8 8
GR/PKAc 0.12 0.099 0.35 23 -10000 0 23
NF kappa B1 p50/RelA -0.055 0.18 -10000 0 -0.4 56 56
SMARCD1 0.025 0.017 -10000 0 -10000 0 0
MDM2 0.085 0.098 0.24 71 -10000 0 71
GATA3 -0.009 0.16 -10000 0 -0.65 21 21
AKT1 0.02 0.004 -10000 0 -10000 0 0
CSF2 -0.11 0.13 -10000 0 -0.53 14 14
GSK3B 0.023 0.019 -10000 0 -10000 0 0
NR1I3 0.003 0.24 0.5 26 -0.59 10 36
CSN2 0.14 0.16 0.39 72 -10000 0 72
BRG1/BAF155/BAF170/BAF60A 0.062 0.05 -10000 0 -0.3 5 5
NFATC1 0.016 0.09 -10000 0 -0.69 6 6
POU2F1 0.025 0.01 -10000 0 -10000 0 0
CDKN1A 0.024 0.036 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.014 -10000 0 -10000 0 0
SFN -0.075 0.11 -10000 0 -0.69 8 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.12 0.34 43 -0.38 6 49
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.48 21 -0.83 79 100
JUN -0.24 0.27 -10000 0 -0.56 127 127
IL4 -0.1 0.16 -10000 0 -0.61 15 15
CDK5R1 0.024 0.015 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.27 0.32 -10000 0 -0.69 116 116
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.11 0.34 31 -0.4 2 33
cortisol/GR alpha (monomer) 0.26 0.3 0.62 120 -10000 0 120
NCOA2 -0.018 0.17 -10000 0 -0.69 23 23
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.2 0.31 -10000 0 -0.7 101 101
AP-1/NFAT1-c-4 -0.39 0.42 -10000 0 -0.78 170 170
AFP -0.17 0.2 -10000 0 -0.6 31 31
SUV420H1 0.026 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.45 33 -10000 0 33
TP53 0.04 0.012 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
KRT17 -0.3 0.38 -10000 0 -0.79 99 99
KRT14 -0.078 0.12 -10000 0 -0.46 8 8
TBP 0.033 0.006 -10000 0 -10000 0 0
CREBBP 0.029 0.042 -10000 0 -0.26 6 6
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
AP-1 -0.39 0.43 -10000 0 -0.79 170 170
MAPK14 0.025 0.019 -10000 0 -10000 0 0
MAPK10 0.024 0.018 -10000 0 -10000 0 0
MAPK11 0.016 0.019 -10000 0 -10000 0 0
KRT5 -0.41 0.53 -10000 0 -1.1 111 111
interleukin-1 receptor activity 0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.023 -10000 0 -10000 0 0
CGA -0.096 0.14 -10000 0 -0.45 21 21
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.079 0.12 0.34 28 -10000 0 28
MAPK3 0.023 0.018 -10000 0 -10000 0 0
MAPK1 0.018 0.018 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.61 67 67
NFKB1 -0.031 0.1 -10000 0 -0.26 28 28
MAPK8 -0.13 0.17 -10000 0 -0.41 69 69
MAPK9 0.025 0.016 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.019 0.24 0.48 30 -0.57 15 45
BAX 0.034 0.085 0.85 3 -10000 0 3
POMC -0.46 0.65 -10000 0 -1.4 101 101
EP300 0.023 0.038 -10000 0 -0.26 5 5
cortisol/GR alpha (dimer)/p53 0.23 0.25 0.53 126 -10000 0 126
proteasomal ubiquitin-dependent protein catabolic process 0.081 0.13 0.33 61 -10000 0 61
SGK1 0.012 0.21 0.51 1 -1.4 7 8
IL13 -0.22 0.26 -10000 0 -0.79 36 36
IL6 -0.33 0.52 -10000 0 -1.1 99 99
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.19 0.22 -10000 0 -0.7 29 29
IL2 -0.26 0.28 -10000 0 -0.65 88 88
CDK5 0.026 0.009 -10000 0 -10000 0 0
PRKACB 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.29 -10000 0 -0.71 59 59
CDK5R1/CDK5 0.037 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.011 0.15 -10000 0 -0.39 19 19
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.22 0.23 0.51 116 -10000 0 116
SMARCA4 0.024 0.017 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.37 77 -0.45 1 78
NF kappa B1 p50/RelA/Cbp -0.023 0.16 -10000 0 -0.43 23 23
JUN (dimer) -0.24 0.27 -10000 0 -0.56 127 127
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.22 0.37 -10000 0 -0.93 73 73
NR3C1 0.15 0.19 0.44 84 -10000 0 84
NR4A1 -0.28 0.37 -10000 0 -0.69 160 160
TIF2/SUV420H1 0.004 0.14 -10000 0 -0.52 23 23
MAPKKK cascade -0.014 0.23 0.46 36 -0.55 15 51
cortisol/GR alpha (dimer)/Src-1 0.23 0.25 0.53 119 -10000 0 119
PBX1 0.023 0.038 -10000 0 -0.69 1 1
POU1F1 0.004 0.022 -10000 0 -10000 0 0
SELE -0.27 0.46 -10000 0 -1.1 70 70
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.37 76 -0.45 1 77
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.22 0.23 0.51 116 -10000 0 116
mol:cortisol 0.14 0.19 0.36 119 -10000 0 119
MMP1 -0.093 0.13 -10000 0 -0.85 6 6
Ephrin B reverse signaling

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
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EPHB2 0.019 0.064 -10000 0 -0.69 3 3
EFNB1 -0.01 0.1 -10000 0 -0.49 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.23 -10000 0 -0.41 127 127
Ephrin B2/EPHB1-2 -0.11 0.22 -10000 0 -0.41 125 125
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.39 127 127
Ephrin B1/EPHB1-2/Tiam1 -0.12 0.24 -10000 0 -0.43 128 128
DNM1 -0.006 0.14 -10000 0 -0.63 17 17
cell-cell signaling -0.001 0.004 -10000 0 -10000 0 0
MAP2K4 0.002 0.067 0.41 1 -0.57 3 4
YES1 0.009 0.072 -10000 0 -0.78 3 3
Ephrin B1/EPHB1-2/NCK2 -0.11 0.22 -10000 0 -0.4 128 128
PI3K 0.03 0.068 -10000 0 -0.79 2 2
mol:GDP -0.12 0.23 -10000 0 -0.43 128 128
ITGA2B -0.056 0.23 -10000 0 -0.68 43 43
endothelial cell proliferation 0.032 0.01 -10000 0 -10000 0 0
FYN 0.01 0.072 -10000 0 -0.78 3 3
MAP3K7 -0.005 0.055 -10000 0 -0.6 3 3
FGR 0.008 0.071 -10000 0 -0.77 3 3
TIAM1 -0.049 0.074 -10000 0 -0.69 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.008 -10000 0 -10000 0 0
cell adhesion -0.033 0.16 -10000 0 -0.41 47 47
LYN 0.01 0.073 -10000 0 -0.79 3 3
Ephrin B1/EPHB1-2/Src Family Kinases 0.001 0.068 -10000 0 -0.75 3 3
Ephrin B1/EPHB1-2 -0.005 0.06 -10000 0 -0.64 3 3
SRC 0.008 0.071 -10000 0 -0.77 3 3
ITGB3 0.007 0.11 -10000 0 -0.66 10 10
EPHB1 -0.21 0.34 -10000 0 -0.69 125 125
EPHB4 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.032 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.04 0.2 -10000 0 -0.55 49 49
BLK -0.041 0.11 -10000 0 -0.85 3 3
HCK 0.01 0.071 -10000 0 -0.77 3 3
regulation of stress fiber formation 0.11 0.22 0.4 128 -10000 0 128
MAPK8 0.004 0.086 0.35 5 -0.58 4 9
Ephrin B1/EPHB1-2/RGS3 -0.11 0.22 -10000 0 -0.4 128 128
endothelial cell migration -0.001 0.055 0.41 1 -0.55 2 3
NCK2 0.026 0.005 -10000 0 -10000 0 0
PTPN13 0.03 0.045 -10000 0 -0.81 1 1
regulation of focal adhesion formation 0.11 0.22 0.4 128 -10000 0 128
chemotaxis 0.11 0.22 0.4 128 -10000 0 128
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
Rac1/GTP -0.1 0.22 -10000 0 -0.4 127 127
angiogenesis -0.005 0.059 -10000 0 -0.64 3 3
LCK 0.007 0.077 -10000 0 -0.83 3 3
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.056 0.24 0.29 13 -0.6 52 65
FYN -0.099 0.32 0.6 3 -0.78 56 59
LAT/GRAP2/SLP76 -0.081 0.25 -10000 0 -0.61 60 60
IKBKB 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.057 0.22 0.69 7 -0.47 58 65
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.017 0.054 0.11 2 -0.16 17 19
MAP3K8 0.019 0.074 -10000 0 -0.69 4 4
mol:Ca2+ -0.031 0.044 0.091 5 -0.11 77 82
integrin-mediated signaling pathway 0.033 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.31 0.71 5 -0.73 60 65
TRPV6 -0.11 0.37 0.99 16 -0.7 79 95
CD28 -0.012 0.15 -10000 0 -0.66 17 17
SHC1 -0.099 0.32 0.31 16 -0.78 56 72
receptor internalization -0.12 0.34 -10000 0 -0.8 65 65
PRF1 -0.1 0.33 0.5 1 -0.85 49 50
KRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.042 0.18 0.68 4 -0.37 60 64
LAT -0.11 0.31 0.31 2 -0.77 59 61
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.051 0.21 -10000 0 -0.66 40 40
CD3E -0.029 0.18 -10000 0 -0.65 29 29
CD3G -0.091 0.26 -10000 0 -0.66 62 62
RASGRP2 -0.003 0.031 0.092 3 -0.18 7 10
RASGRP1 -0.047 0.23 0.72 8 -0.46 59 67
HLA-A 0.026 0.013 -10000 0 -10000 0 0
RASSF5 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.033 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.16 0.46 19 -0.13 26 45
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.046 0.084 -10000 0 -0.24 43 43
PRKCA -0.04 0.13 -10000 0 -0.3 54 54
GRAP2 -0.018 0.15 -10000 0 -0.56 24 24
mol:IP3 -0.029 0.21 0.27 57 -0.45 54 111
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.35 -10000 0 -0.85 58 58
ORAI1 0.047 0.21 0.7 2 -0.77 13 15
CSK -0.11 0.32 0.37 1 -0.78 60 61
B7 family/CD28 -0.11 0.34 -10000 0 -0.8 61 61
CHUK 0.026 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.38 -10000 0 -0.92 60 60
PTPN6 -0.11 0.32 -10000 0 -0.79 58 58
VAV1 -0.11 0.31 -10000 0 -0.75 60 60
Monovalent TCR/CD3 -0.12 0.32 -10000 0 -0.65 75 75
CBL 0.026 0.005 -10000 0 -10000 0 0
LCK -0.1 0.33 0.67 2 -0.81 56 58
PAG1 -0.11 0.32 0.37 1 -0.78 60 61
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.13 0.38 -10000 0 -0.92 59 59
CD80 -0.052 0.22 -10000 0 -0.69 40 40
CD86 0.015 0.06 -10000 0 -0.7 2 2
PDK1/CARD11/BCL10/MALT1 -0.039 0.11 -10000 0 -0.28 48 48
HRAS 0.025 0.009 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 0.32 1 -0.63 61 62
CD8A -0.022 0.18 -10000 0 -0.66 26 26
CD8B -0.057 0.22 -10000 0 -0.66 43 43
PTPRC -0.006 0.13 -10000 0 -0.7 13 13
PDK1/PKC theta -0.072 0.27 0.69 10 -0.58 58 68
CSK/PAG1 -0.1 0.3 0.37 1 -0.78 55 56
SOS1 0.026 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.039 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.3 -10000 0 -0.74 60 60
STIM1 0.018 0.17 1.2 2 -0.89 8 10
RAS family/GTP 0.012 0.12 0.32 18 -0.19 29 47
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.38 -10000 0 -0.88 65 65
mol:DAG -0.057 0.16 0.15 7 -0.39 58 65
RAP1A/GDP 0.013 0.098 0.4 10 -10000 0 10
PLCG1 0.026 0.005 -10000 0 -10000 0 0
CD247 -0.007 0.14 -10000 0 -0.7 15 15
cytotoxic T cell degranulation -0.099 0.31 0.5 1 -0.79 51 52
RAP1A/GTP 0 0.011 -10000 0 -0.069 5 5
mol:PI-3-4-5-P3 -0.079 0.26 0.71 6 -0.57 60 66
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.046 0.26 0.29 56 -0.59 56 112
NRAS 0.026 0.005 -10000 0 -10000 0 0
ZAP70 -0.005 0.14 -10000 0 -0.67 15 15
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.08 0.24 -10000 0 -0.58 60 60
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.037 -10000 0 -0.69 1 1
CD8 heterodimer -0.057 0.24 -10000 0 -0.59 56 56
CARD11 -0.02 0.1 -10000 0 -0.69 6 6
PRKCB -0.03 0.12 -10000 0 -0.29 47 47
PRKCE -0.031 0.12 -10000 0 -0.29 51 51
PRKCQ -0.092 0.3 0.73 7 -0.67 60 67
LCP2 0.022 0.023 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.044 0.19 0.67 7 -0.4 58 65
IKK complex 0.019 0.16 0.55 15 -0.12 11 26
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.035 0.12 0.32 1 -0.3 43 44
PDPK1 -0.053 0.22 0.59 10 -0.45 57 67
TCR/CD3/MHC I/CD8/Fyn -0.15 0.41 -10000 0 -0.96 65 65
Coregulation of Androgen receptor activity

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
NRIP1 -0.005 0.051 -10000 0 -10000 0 0
SVIL -0.002 0.047 -10000 0 -10000 0 0
ZNF318 0.074 0.079 0.21 90 -10000 0 90
JMJD2C -0.065 0.066 -10000 0 -0.12 210 210
T-DHT/AR/Ubc9 -0.22 0.24 -10000 0 -0.51 143 143
CARM1 0.022 0.01 -10000 0 -10000 0 0
PRDX1 0.028 0.007 -10000 0 -10000 0 0
PELP1 0.031 0.013 -10000 0 -10000 0 0
CTNNB1 0.003 0.039 -10000 0 -10000 0 0
AKT1 0.037 0.02 -10000 0 -10000 0 0
PTK2B 0.007 0.032 -10000 0 -10000 0 0
MED1 0.036 0.021 -10000 0 -10000 0 0
MAK 0.064 0.12 0.22 42 -0.66 5 47
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.005 0.059 -10000 0 -0.69 1 1
GSN 0 0.044 -10000 0 -10000 0 0
NCOA2 -0.021 0.17 -10000 0 -0.69 23 23
NCOA6 -0.001 0.045 -10000 0 -10000 0 0
DNA-PK 0.073 0.076 -10000 0 -10000 0 0
NCOA4 0.025 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation -0.001 0.14 -10000 0 -0.92 5 5
XRCC5 0.036 0.018 -10000 0 -10000 0 0
UBE3A -0.011 0.063 -10000 0 -0.18 1 1
T-DHT/AR/SNURF -0.24 0.26 -10000 0 -0.54 148 148
FHL2 -0.14 0.34 -10000 0 -1.2 34 34
RANBP9 -0.001 0.045 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 26 26
CDK6 0.024 0.038 -10000 0 -0.69 1 1
TGFB1I1 -0.002 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.23 0.24 -10000 0 -0.51 149 149
XRCC6 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR -0.27 0.27 -10000 0 -0.54 166 166
CTDSP1 0.012 0.023 -10000 0 -10000 0 0
CTDSP2 0.056 0.051 -10000 0 -10000 0 0
BRCA1 -0.002 0.046 -10000 0 -10000 0 0
TCF4 0.046 0.035 -10000 0 -10000 0 0
CDKN2A 0.008 0.079 -10000 0 -10000 0 0
SRF 0.032 0.052 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.72 8 8
KLK3 -0.37 0.64 -10000 0 -1.4 101 101
TMF1 0.019 0.015 -10000 0 -10000 0 0
HNRNPA1 0.042 0.028 -10000 0 -10000 0 0
AOF2 -0.019 0.032 -10000 0 -0.072 101 101
APPL1 0.039 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.21 0.24 -10000 0 -0.51 142 142
AR -0.3 0.34 -10000 0 -0.72 145 145
UBA3 0.012 0.023 -10000 0 -10000 0 0
PATZ1 0.032 0.03 -10000 0 -10000 0 0
PAWR 0.019 0.015 -10000 0 -10000 0 0
PRKDC 0.036 0.017 -10000 0 -10000 0 0
PA2G4 0.046 0.036 -10000 0 -10000 0 0
UBE2I 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.46 147 147
RPS6KA3 -0.002 0.045 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.22 0.24 -10000 0 -0.51 148 148
LATS2 0.04 0.028 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.46 143 143
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.004 0.081 -10000 0 -0.69 4 4
KLK2 -0.67 0.56 -10000 0 -1.2 212 212
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.23 0.26 -10000 0 -0.53 145 145
TMPRSS2 -0.16 0.28 -10000 0 -1.1 26 26
CCND1 0.012 0.03 -10000 0 -10000 0 0
PIAS1 -0.011 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.04 -10000 0 -0.077 142 142
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.028 0.089 -10000 0 -0.19 43 43
T-DHT/AR/CDK6 -0.22 0.24 -10000 0 -0.5 148 148
CMTM2 0.027 0.012 -10000 0 -10000 0 0
SNURF -0.003 0.14 -10000 0 -0.67 15 15
ZMIZ1 -0.023 0.049 -10000 0 -10000 0 0
CCND3 0.028 0.003 -10000 0 -10000 0 0
TGIF1 0.042 0.028 -10000 0 -10000 0 0
FKBP4 -0.001 0.045 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.044 0.18 -10000 0 -0.46 59 59
cell-cell adhesion 0.1 0.16 0.34 114 -10000 0 114
Ephrin B/EPHB2/RasGAP 0.063 0.06 -10000 0 -0.39 5 5
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.047 0.019 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.22 -10000 0 -0.44 124 124
HRAS/GDP -0.072 0.16 -10000 0 -0.36 14 14
Ephrin B/EPHB1/GRB7 -0.082 0.22 -10000 0 -0.41 117 117
Endophilin/SYNJ1 0.022 0.072 0.44 4 -0.36 5 9
KRAS 0.026 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.082 0.22 -10000 0 -0.4 118 118
endothelial cell migration 0.051 0.029 -10000 0 -0.39 1 1
GRB2 0.025 0.007 -10000 0 -10000 0 0
GRB7 0.006 0.047 -10000 0 -10000 0 0
PAK1 0.024 0.079 0.46 5 -0.37 5 10
HRAS 0.025 0.009 -10000 0 -10000 0 0
RRAS 0.021 0.073 0.42 5 -0.37 5 10
DNM1 -0.006 0.14 -10000 0 -0.64 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.11 0.19 -10000 0 -0.38 118 118
lamellipodium assembly -0.1 0.16 -10000 0 -0.34 114 114
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.076 0.16 -10000 0 -0.3 109 109
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.02 0.064 -10000 0 -0.69 3 3
EPHB3 -0.055 0.066 -10000 0 -10000 0 0
EPHB1 -0.21 0.34 -10000 0 -0.69 125 125
EPHB4 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.067 0.13 -10000 0 -0.39 9 9
Ephrin B/EPHB2 0.049 0.056 -10000 0 -0.39 5 5
Ephrin B/EPHB3 0.065 0.048 -10000 0 -0.44 2 2
JNK cascade -0.11 0.19 0.36 1 -0.39 116 117
Ephrin B/EPHB1 -0.092 0.21 -10000 0 -0.4 119 119
RAP1/GDP -0.041 0.14 -10000 0 -0.35 7 7
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EFNB3 0.016 0.058 -10000 0 -0.69 2 2
EFNB1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.11 0.22 -10000 0 -0.42 125 125
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.074 0.19 -10000 0 -0.34 115 115
Rap1/GTP -0.091 0.17 -10000 0 -0.35 107 107
axon guidance -0.044 0.18 -10000 0 -0.46 59 59
MAPK3 -0.075 0.14 -10000 0 -0.45 7 7
MAPK1 -0.073 0.13 -10000 0 -0.45 7 7
Rac1/GDP -0.053 0.14 -10000 0 -0.36 7 7
actin cytoskeleton reorganization -0.073 0.13 -10000 0 -0.35 4 4
CDC42/GDP -0.051 0.14 0.37 1 -0.36 9 10
PI3K 0.056 0.03 -10000 0 -0.4 1 1
EFNA5 -0.084 0.26 -10000 0 -0.69 57 57
Ephrin B2/EPHB4 0.033 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.025 0.042 -10000 0 -0.32 4 4
CDC42 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.091 0.17 -10000 0 -0.34 112 112
PTK2 0.03 0.076 0.59 5 -10000 0 5
MAP4K4 -0.11 0.2 0.36 1 -0.4 116 117
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.026 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.037 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.07 0.14 0.29 4 -0.35 1 5
MAP2K1 -0.074 0.14 -10000 0 -0.4 12 12
WASL 0.025 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.096 0.22 -10000 0 -0.42 116 116
cell migration -0.073 0.18 0.54 4 -0.44 12 16
NRAS 0.026 0.005 -10000 0 -10000 0 0
SYNJ1 0.022 0.073 0.44 4 -0.37 5 9
PXN 0.026 0.006 -10000 0 -10000 0 0
TF -0.036 0.14 0.41 3 -0.38 46 49
HRAS/GTP -0.081 0.19 -10000 0 -0.36 116 116
Ephrin B1/EPHB1-2 -0.11 0.22 -10000 0 -0.41 125 125
cell adhesion mediated by integrin -0.007 0.067 0.39 2 -0.4 5 7
RAC1 0.025 0.006 -10000 0 -10000 0 0
mol:GTP -0.085 0.2 -10000 0 -0.38 117 117
RAC1-CDC42/GTP -0.13 0.16 -10000 0 -0.38 86 86
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.043 0.14 -10000 0 -0.36 4 4
ruffle organization -0.093 0.18 0.62 4 -0.5 1 5
NCK1 0.026 0.004 -10000 0 -10000 0 0
receptor internalization -0.004 0.097 0.41 3 -0.39 16 19
Ephrin B/EPHB2/KALRN 0.063 0.06 -10000 0 -0.39 5 5
ROCK1 -0.019 0.044 -10000 0 -10000 0 0
RAS family/GDP -0.069 0.1 -10000 0 -0.35 3 3
Rac1/GTP -0.1 0.17 -10000 0 -0.35 114 114
Ephrin B/EPHB1/Src/Paxillin -0.08 0.16 -10000 0 -0.31 119 119
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.53 -10000 0 -1.3 57 57
IL23A -0.2 0.54 -10000 0 -1.3 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.53 -10000 0 -1.3 58 58
positive regulation of T cell mediated cytotoxicity -0.22 0.6 -10000 0 -1.5 57 57
ITGA3 -0.17 0.5 -10000 0 -1.2 56 56
IL17F -0.093 0.33 0.69 2 -0.74 54 56
IL12B 0.008 0.073 -10000 0 -0.71 2 2
STAT1 (dimer) -0.2 0.57 -10000 0 -1.4 57 57
CD4 -0.17 0.49 -10000 0 -1.2 54 54
IL23 -0.18 0.52 -10000 0 -1.2 60 60
IL23R 0.003 0.11 -10000 0 -0.97 2 2
IL1B -0.21 0.56 -10000 0 -1.4 57 57
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.16 0.49 -10000 0 -1.2 54 54
TYK2 0.016 0.035 -10000 0 -10000 0 0
STAT4 0.001 0.1 -10000 0 -0.59 9 9
STAT3 0.025 0.007 -10000 0 -10000 0 0
IL18RAP -0.021 0.16 -10000 0 -0.69 21 21
IL12RB1 -0.001 0.074 -10000 0 -0.62 3 3
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
IL12Rbeta1/TYK2 0.02 0.067 -10000 0 -0.48 3 3
IL23R/JAK2 0.011 0.13 -10000 0 -0.87 2 2
positive regulation of chronic inflammatory response -0.22 0.6 -10000 0 -1.5 57 57
natural killer cell activation 0.001 0.009 -10000 0 -0.055 1 1
JAK2 0.017 0.045 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.49 -10000 0 -1.1 61 61
ALOX12B -0.17 0.49 -10000 0 -1.2 54 54
CXCL1 -0.18 0.52 -10000 0 -1.2 58 58
T cell proliferation -0.22 0.6 -10000 0 -1.5 57 57
NFKBIA 0.026 0.006 -10000 0 -10000 0 0
IL17A -0.053 0.26 -10000 0 -0.58 45 45
PI3K -0.18 0.54 -10000 0 -1.3 55 55
IFNG -0.014 0.054 0.16 2 -0.14 48 50
STAT3 (dimer) -0.16 0.5 -10000 0 -1.2 55 55
IL18R1 -0.001 0.09 -10000 0 -0.57 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.096 0.34 -10000 0 -0.82 47 47
IL18/IL18R -0.003 0.16 -10000 0 -0.49 29 29
macrophage activation -0.008 0.021 -10000 0 -0.045 57 57
TNF -0.24 0.6 -10000 0 -1.4 71 71
STAT3/STAT4 -0.19 0.54 -10000 0 -1.3 58 58
STAT4 (dimer) -0.2 0.58 -10000 0 -1.4 58 58
IL18 -0.005 0.1 -10000 0 -0.65 7 7
IL19 -0.16 0.49 -10000 0 -1.2 54 54
STAT5A (dimer) -0.2 0.57 -10000 0 -1.4 57 57
STAT1 0.022 0.022 -10000 0 -10000 0 0
SOCS3 -0.019 0.17 -10000 0 -0.69 23 23
CXCL9 -0.23 0.59 -10000 0 -1.3 71 71
MPO -0.17 0.5 -10000 0 -1.2 56 56
positive regulation of humoral immune response -0.22 0.6 -10000 0 -1.5 57 57
IL23/IL23R/JAK2/TYK2 -0.26 0.73 -10000 0 -1.7 57 57
IL6 -0.3 0.65 -10000 0 -1.3 95 95
STAT5A 0.025 0.007 -10000 0 -10000 0 0
IL2 0.001 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -0.055 1 1
CD3E -0.2 0.54 -10000 0 -1.4 54 54
keratinocyte proliferation -0.22 0.6 -10000 0 -1.5 57 57
NOS2 -0.16 0.49 -10000 0 -1.2 54 54
Arf6 signaling events

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
CENTA1/KIF3B 0.034 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.016 0.14 -10000 0 -0.7 9 9
EGFR 0.016 0.082 -10000 0 -0.69 5 5
EPHA2 0.025 0.011 -10000 0 -10000 0 0
USP6 0.024 0.014 -10000 0 -10000 0 0
IQSEC1 0.026 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.045 0.2 -10000 0 -0.52 55 55
ARRB2 -0.034 0.13 -10000 0 -0.4 42 42
mol:GTP 0.024 0.039 0.18 14 -0.14 1 15
ARRB1 0.024 0.037 -10000 0 -0.69 1 1
FBXO8 0.026 0.004 -10000 0 -10000 0 0
TSHR 0.022 0.052 -10000 0 -0.69 2 2
EGF -0.072 0.24 -10000 0 -0.68 51 51
somatostatin receptor activity 0 0.001 0.003 11 -0.001 103 114
ARAP2 0.024 0.037 -10000 0 -0.69 1 1
mol:GDP -0.1 0.14 0.28 6 -0.3 86 92
mol:PI-3-4-5-P3 0 0 0.002 10 -0.001 52 62
ITGA2B -0.056 0.23 -10000 0 -0.68 43 43
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.024 -10000 0 -10000 0 0
ADAP1 0.025 0.006 -10000 0 -10000 0 0
KIF13B 0.026 0.004 -10000 0 -10000 0 0
HGF/MET -0.073 0.18 -10000 0 -0.54 47 47
PXN 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.17 0.55 8 -0.29 109 117
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.023 0.18 -10000 0 -0.45 55 55
ADRB2 0.008 0.11 -10000 0 -0.69 9 9
receptor agonist activity 0 0 0.001 16 0 108 124
actin filament binding 0 0.001 0.002 11 -0.001 105 116
SRC 0.025 0.008 -10000 0 -10000 0 0
ITGB3 0.007 0.11 -10000 0 -0.66 10 10
GNAQ 0.024 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.006 11 -0.001 47 58
ARF6/GDP -0.006 0.089 0.37 2 -0.41 6 8
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 80 80
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.003 0.17 -10000 0 -0.44 49 49
ACAP1 0.018 0.048 -10000 0 -0.54 2 2
ACAP2 0.026 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.047 0.19 -10000 0 -0.58 42 42
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.065 0.24 -10000 0 -0.69 47 47
CYTH3 0.006 0.028 -10000 0 -0.52 1 1
CYTH2 -0.007 0.15 -10000 0 -0.93 9 9
NCK1 0.026 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0.002 15 0 73 88
endosomal lumen acidification 0 0 0.002 6 -0.001 106 112
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 -0.095 0.27 -10000 0 -0.67 65 65
GNAQ/ARNO 0.007 0.14 -10000 0 -0.85 9 9
mol:Phosphatidic acid 0 0 0.001 11 -10000 0 11
PIP3-E 0 0 0.001 9 0 9 18
MET -0.029 0.066 -10000 0 -10000 0 0
GNA14 -0.14 0.3 -10000 0 -0.66 91 91
GNA15 0.011 0.053 -10000 0 -0.69 1 1
GIT1 0.025 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.004 11 -0.001 84 95
GNA11 0.019 0.064 -10000 0 -0.69 3 3
LHCGR -0.072 0.22 -10000 0 -0.69 42 42
AGTR1 -0.25 0.35 -10000 0 -0.69 145 145
desensitization of G-protein coupled receptor protein signaling pathway -0.047 0.19 -10000 0 -0.57 42 42
IPCEF1/ARNO -0.034 0.17 -10000 0 -0.69 10 10
alphaIIb/beta3 Integrin -0.04 0.2 -10000 0 -0.55 49 49
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.36 -10000 0 -1.2 38 38
MKNK1 0.026 0.005 -10000 0 -10000 0 0
MAPK14 -0.024 0.12 -10000 0 -0.34 33 33
ATF2/c-Jun -0.21 0.36 -10000 0 -0.82 91 91
MAPK11 -0.018 0.1 -10000 0 -0.34 28 28
MITF -0.03 0.13 -10000 0 -0.41 34 34
MAPKAPK5 -0.025 0.12 -10000 0 -0.4 30 30
KRT8 -0.025 0.12 -10000 0 -0.4 30 30
MAPKAPK3 0.026 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.034 0.16 -10000 0 -0.51 31 31
CEBPB -0.027 0.12 -10000 0 -0.4 32 32
SLC9A1 -0.031 0.13 -10000 0 -0.4 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.076 0.18 -10000 0 -0.42 62 62
p38alpha-beta/MNK1 -0.019 0.14 -10000 0 -0.41 30 30
JUN -0.21 0.36 -10000 0 -0.82 91 91
PPARGC1A -0.23 0.25 -10000 0 -0.46 193 193
USF1 -0.031 0.13 -10000 0 -0.4 35 35
RAB5/GDP/GDI1 -0.041 0.1 -10000 0 -0.34 18 18
NOS2 -0.035 0.13 -10000 0 -0.49 9 9
DDIT3 -0.025 0.12 -10000 0 -0.4 30 30
RAB5A 0.026 0.004 -10000 0 -10000 0 0
HSPB1 -0.019 0.099 0.38 2 -0.38 11 13
p38alpha-beta/HBP1 -0.014 0.13 -10000 0 -0.41 26 26
CREB1 -0.055 0.16 -10000 0 -0.45 35 35
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.03 0.11 -10000 0 -0.37 28 28
RPS6KA4 -0.028 0.13 -10000 0 -0.41 32 32
PLA2G4A -0.055 0.17 -10000 0 -0.54 31 31
GDI1 -0.024 0.12 -10000 0 -0.41 29 29
TP53 -0.039 0.14 -10000 0 -0.49 30 30
RPS6KA5 -0.057 0.18 -10000 0 -0.45 53 53
ESR1 -0.061 0.2 -10000 0 -0.55 44 44
HBP1 0.025 0.006 -10000 0 -10000 0 0
MEF2C -0.024 0.12 -10000 0 -0.4 30 30
MEF2A -0.031 0.13 -10000 0 -0.41 35 35
EIF4EBP1 -0.055 0.16 -10000 0 -0.45 36 36
KRT19 -0.058 0.19 -10000 0 -0.53 38 38
ELK4 -0.031 0.13 -10000 0 -0.4 35 35
ATF6 -0.031 0.13 -10000 0 -0.4 35 35
ATF1 -0.052 0.15 -10000 0 -0.45 33 33
p38alpha-beta/MAPKAPK2 -0.02 0.14 -10000 0 -0.41 31 31
p38alpha-beta/MAPKAPK3 -0.019 0.14 -10000 0 -0.41 31 31
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.048 -10000 0 -10000 0 0
GNB1/GNG2 -0.033 0.067 -10000 0 -0.19 52 52
AKT1 0.011 0.14 0.49 14 -0.22 11 25
EGF -0.072 0.24 -10000 0 -0.68 51 51
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.081 0.38 6 -0.4 3 9
mol:Ca2+ -0.017 0.15 0.44 12 -0.31 54 66
LYN 0.013 0.079 0.39 5 -0.4 3 8
RhoA/GTP -0.01 0.054 -10000 0 -0.14 25 25
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.019 0.17 0.48 13 -0.34 53 66
GNG2 0.026 0.005 -10000 0 -10000 0 0
ARRB2 0.025 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.031 0.12 0.27 1 -0.64 6 7
G beta5/gamma2 -0.044 0.091 -10000 0 -0.26 52 52
PRKCH -0.023 0.17 0.5 11 -0.36 53 64
DNM1 -0.006 0.14 -10000 0 -0.64 17 17
TXA2/TP beta/beta Arrestin3 -0.012 0.12 -10000 0 -0.41 26 26
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.003 0.14 -10000 0 -0.69 15 15
G12 family/GTP -0.035 0.12 -10000 0 -0.31 52 52
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.035 0.007 -10000 0 -10000 0 0
mol:GDP 0.049 0.15 0.41 31 -0.36 8 39
mol:NADP 0.025 0.006 -10000 0 -10000 0 0
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.68 98 98
mol:IP3 -0.027 0.18 0.49 11 -0.38 54 65
cell morphogenesis 0.034 0.007 -10000 0 -10000 0 0
PLCB2 -0.052 0.22 0.48 8 -0.52 54 62
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.083 0.18 0.4 4 -0.34 108 112
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.008 0.069 0.32 2 -0.4 3 5
RHOA 0.026 0.004 -10000 0 -10000 0 0
PTGIR 0.017 0.074 -10000 0 -0.69 4 4
PRKCB1 -0.028 0.18 0.46 11 -0.38 54 65
GNAQ 0.024 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.025 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.047 0.23 0.52 12 -0.54 53 65
LCK 0.01 0.091 0.38 6 -0.48 5 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.024 0.081 -10000 0 -0.33 13 13
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.025 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.082 -10000 0 -0.33 13 13
MAPK14 -0.006 0.13 0.4 14 -0.23 50 64
TGM2/GTP -0.048 0.18 0.35 1 -0.43 54 55
MAPK11 -0.009 0.13 0.42 14 -0.23 50 64
ARHGEF1 -0.016 0.073 -10000 0 -0.18 47 47
GNAI2 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.025 0.19 0.48 13 -0.39 53 66
RAB11/GDP 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.016 0.15 0.43 13 -0.29 53 66
cAMP biosynthetic process -0.029 0.17 0.49 11 -0.36 54 65
Gq family/GTP/EBP50 -0.048 0.12 0.24 1 -0.23 92 93
actin cytoskeleton reorganization 0.034 0.007 -10000 0 -10000 0 0
SRC 0.008 0.069 0.32 2 -0.4 3 5
GNB5 0.026 0.003 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.024 0.13 0.49 11 -0.29 12 23
VCAM1 -0.013 0.15 0.42 13 -0.3 53 66
TP beta/Gq family/GDP/G beta5/gamma2 -0.031 0.12 0.27 1 -0.64 6 7
platelet activation -0.006 0.17 0.54 14 -0.3 53 67
PGI2/IP 0.013 0.056 -10000 0 -0.52 4 4
PRKACA 0.002 0.086 -10000 0 -0.38 16 16
Gq family/GDP/G beta5/gamma2 -0.032 0.11 0.28 1 -0.57 7 8
TXA2/TP beta/beta Arrestin2 -0.003 0.12 -10000 0 -0.54 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.001 0.078 -10000 0 -0.36 15 15
mol:DAG -0.033 0.2 0.49 11 -0.43 54 65
EGFR 0.016 0.082 -10000 0 -0.69 5 5
TXA2/TP alpha -0.045 0.22 0.55 11 -0.49 54 65
Gq family/GTP -0.07 0.13 0.22 1 -0.27 106 107
YES1 0.014 0.082 0.4 6 -0.4 3 9
GNAI2/GTP 0.007 0.07 -10000 0 -0.47 3 3
PGD2/DP -0.003 0.11 -10000 0 -0.52 15 15
SLC9A3R1 0.025 0.007 -10000 0 -10000 0 0
FYN 0.015 0.084 0.38 7 -0.4 3 10
mol:NO 0.025 0.006 -10000 0 -10000 0 0
GNA15 0.011 0.053 -10000 0 -0.69 1 1
PGK/cGMP -0.091 0.21 -10000 0 -0.45 97 97
RhoA/GDP 0.026 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.087 -10000 0 -0.34 13 13
NOS3 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.034 0.18 0.49 11 -0.38 56 67
PRKCB -0.025 0.18 0.46 14 -0.37 52 66
PRKCE -0.03 0.16 0.41 9 -0.37 54 63
PRKCD -0.028 0.18 0.48 10 -0.39 53 63
PRKCG -0.028 0.18 0.46 12 -0.39 51 63
muscle contraction -0.039 0.22 0.53 12 -0.49 53 65
PRKCZ -0.018 0.17 0.48 13 -0.34 53 66
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.014 0.08 -10000 0 -0.33 15 15
PRKCQ -0.029 0.17 0.46 11 -0.36 55 66
MAPKKK cascade -0.038 0.21 0.49 13 -0.46 54 67
SELE -0.03 0.18 0.42 13 -0.42 53 66
TP beta/GNAI2/GDP/G beta/gamma 0.038 0.084 -10000 0 -0.51 3 3
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 -0.14 0.3 -10000 0 -0.66 91 91
chemotaxis -0.054 0.26 0.55 12 -0.62 53 65
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.007 -10000 0 -10000 0 0
GNA11 0.019 0.064 -10000 0 -0.69 3 3
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.015 -10000 0 -10000 0 0
forebrain development -0.3 0.28 0.32 2 -0.54 191 193
GNAO1 0.007 0.1 -10000 0 -0.69 8 8
SMO/beta Arrestin2 0.013 0.028 -10000 0 -10000 0 0
SMO 0.015 0.015 -10000 0 -10000 0 0
ARRB2 0.02 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.038 0.064 -10000 0 -0.4 2 2
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.004 -10000 0 -10000 0 0
GNAI2 0.024 0.008 -10000 0 -10000 0 0
SIN3/HDAC complex 0.063 0.034 -10000 0 -0.42 1 1
GNAI1 0.021 0.037 -10000 0 -0.69 1 1
XPO1 0.014 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.22 0.22 -10000 0 -0.5 104 104
SAP30 0.025 0.037 -10000 0 -0.69 1 1
mol:GDP 0.015 0.015 -10000 0 -10000 0 0
MIM/GLI2A -0.034 0.067 -10000 0 -10000 0 0
IFT88 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.008 -10000 0 -10000 0 0
GLI2 0 0.082 0.3 3 -0.35 8 11
GLI3 0.029 0.067 0.26 3 -0.39 3 6
CSNK1D 0.025 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.026 0.005 -10000 0 -10000 0 0
Gi family/GTP -0.015 0.063 -10000 0 -0.3 9 9
SIN3B 0.026 0.007 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.036 0.059 -10000 0 -0.58 1 1
GLI2/Su(fu) 0.005 0.078 -10000 0 -0.58 2 2
FOXA2 -0.61 0.62 -10000 0 -1.2 190 190
neural tube patterning -0.3 0.28 0.32 2 -0.54 191 193
SPOP 0.025 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.033 0.027 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.007 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.034 0.067 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.32 2 -0.54 191 193
SUFU 0.017 0.011 -10000 0 -10000 0 0
LGALS3 -0.023 0.065 -10000 0 -10000 0 0
catabolic process 0.031 0.095 -10000 0 -0.51 4 4
GLI3A/CBP -0.18 0.2 -10000 0 -0.38 186 186
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.31 0.29 0.32 2 -0.55 191 193
RAB23 0.021 0.064 -10000 0 -0.69 3 3
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.033 0.041 -10000 0 -10000 0 0
GNAZ 0.018 0.012 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
CSNK1G1 0.026 0.003 -10000 0 -10000 0 0
PIAS1 0.026 0.003 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GLI2/SPOP 0.008 0.082 -10000 0 -0.38 6 6
STK36 0.014 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.008 0.048 -10000 0 -0.31 1 1
PTCH1 -0.27 0.26 0.4 1 -0.59 109 110
MIM/GLI1 -0.44 0.38 0.34 1 -0.7 216 217
CREBBP -0.18 0.2 -10000 0 -0.38 186 186
Su(fu)/SIN3/HDAC complex 0.036 0.062 -10000 0 -0.66 2 2
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.022 0.13 -10000 0 -0.37 24 24
TBX21 -0.12 0.42 -10000 0 -1.1 46 46
B2M 0.023 0.017 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0.002 0.072 -10000 0 -0.6 3 3
GADD45B -0.1 0.4 -10000 0 -1.1 43 43
IL12RB2 -0.002 0.12 -10000 0 -0.69 11 11
GADD45G -0.088 0.34 -10000 0 -1 30 30
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
IL18 0.001 0.1 -10000 0 -0.66 7 7
IL2RA -0.01 0.14 -10000 0 -0.65 16 16
IFNG -0.067 0.22 -10000 0 -0.69 42 42
STAT3 (dimer) -0.079 0.3 -10000 0 -0.8 42 42
HLA-DRB5 -0.013 0.074 -10000 0 -0.69 2 2
FASLG -0.13 0.45 -10000 0 -1.2 43 43
NF kappa B2 p52/RelB -0.096 0.38 -10000 0 -0.97 44 44
CD4 0.01 0.031 -10000 0 -10000 0 0
SOCS1 0.024 0.013 -10000 0 -10000 0 0
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.066 0.21 -10000 0 -0.66 40 40
CD3E -0.043 0.18 -10000 0 -0.64 29 29
CD3G -0.1 0.26 -10000 0 -0.67 62 62
IL12Rbeta2/JAK2 0.012 0.1 -10000 0 -0.53 11 11
CCL3 -0.11 0.41 -10000 0 -1.2 36 36
CCL4 -0.15 0.48 -10000 0 -1.4 44 44
HLA-A 0.022 0.019 -10000 0 -10000 0 0
IL18/IL18R 0.027 0.16 -10000 0 -0.5 28 28
NOS2 -0.083 0.34 -10000 0 -0.97 33 33
IL12/IL12R/TYK2/JAK2/SPHK2 -0.023 0.13 -10000 0 -0.38 26 26
IL1R1 -0.1 0.36 -10000 0 -1.1 35 35
IL4 0 0.033 -10000 0 -10000 0 0
JAK2 0.018 0.03 -10000 0 -10000 0 0
EntrezGene:6957 -0.007 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.2 0.46 -10000 0 -1 73 73
RAB7A -0.058 0.29 -10000 0 -0.75 38 38
lysosomal transport -0.052 0.28 -10000 0 -0.7 38 38
FOS -0.38 0.62 -10000 0 -1.2 122 122
STAT4 (dimer) -0.083 0.35 -10000 0 -0.88 44 44
STAT5A (dimer) -0.13 0.39 -10000 0 -0.95 54 54
GZMA -0.11 0.39 -10000 0 -1.1 37 37
GZMB -0.11 0.38 -10000 0 -1.1 35 35
HLX 0.022 0.021 -10000 0 -10000 0 0
LCK -0.12 0.42 -10000 0 -1.1 45 45
TCR/CD3/MHC II/CD4 -0.14 0.28 -10000 0 -0.7 54 54
IL2/IL2R 0.002 0.17 -10000 0 -0.58 25 25
MAPK14 -0.084 0.36 -10000 0 -0.9 45 45
CCR5 -0.084 0.37 -10000 0 -1.2 27 27
IL1B -0.031 0.19 -10000 0 -0.72 26 26
STAT6 -0.007 0.11 -10000 0 -0.47 5 5
STAT4 0.001 0.1 -10000 0 -0.59 9 9
STAT3 0.025 0.007 -10000 0 -10000 0 0
STAT1 0.022 0.022 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.004 -10000 0 -10000 0 0
IL12B 0.008 0.064 -10000 0 -0.7 2 2
CD8A -0.024 0.18 -10000 0 -0.66 26 26
CD8B -0.06 0.22 -10000 0 -0.66 43 43
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.021 0.13 0.37 24 -10000 0 24
IL2RB 0 0.1 -10000 0 -0.62 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.069 0.32 -10000 0 -0.78 44 44
IL2RG -0.014 0.14 -10000 0 -0.63 16 16
IL12 -0.027 0.17 -10000 0 -0.54 36 36
STAT5A 0.025 0.007 -10000 0 -10000 0 0
CD247 -0.02 0.14 -10000 0 -0.7 15 15
IL2 -0.004 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.048 0.21 -10000 0 -0.69 35 35
IL12/IL12R/TYK2/JAK2 -0.13 0.48 -10000 0 -1.2 45 45
MAP2K3 -0.085 0.36 -10000 0 -0.91 42 42
RIPK2 0.026 0.004 -10000 0 -10000 0 0
MAP2K6 -0.092 0.37 -10000 0 -0.9 47 47
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.008 0.078 -10000 0 -0.69 3 3
IL18RAP -0.015 0.17 -10000 0 -0.7 21 21
IL12Rbeta1/TYK2 0.026 0.063 -10000 0 -0.45 3 3
EOMES -0.11 0.38 -10000 0 -1.3 32 32
STAT1 (dimer) -0.12 0.34 -10000 0 -0.78 61 61
T cell proliferation -0.053 0.26 -10000 0 -0.61 46 46
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.089 -10000 0 -0.55 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.064 0.28 -10000 0 -0.66 49 49
ATF2 -0.081 0.33 -10000 0 -0.81 47 47
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.004 0.2 0.6 5 -0.67 9 14
CRP 0.007 0.21 0.59 8 -0.64 14 22
cell cycle arrest -0.011 0.21 0.54 3 -0.72 16 19
TIMP1 -0.026 0.21 0.66 2 -0.7 16 18
IL6ST -0.04 0.21 -10000 0 -0.69 35 35
Rac1/GDP -0.047 0.2 0.3 1 -0.52 36 37
AP1 -0.12 0.28 -10000 0 -0.61 73 73
GAB2 0.026 0.005 -10000 0 -10000 0 0
TNFSF11 -0.006 0.2 0.62 4 -0.66 12 16
HSP90B1 0.041 0.058 -10000 0 -0.65 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.098 0.25 -10000 0 -0.72 41 41
AKT1 0.041 0.039 -10000 0 -10000 0 0
FOXO1 0.039 0.04 -10000 0 -10000 0 0
MAP2K6 -0.083 0.23 -10000 0 -0.61 42 42
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.033 0.19 0.33 5 -0.5 32 37
MITF -0.069 0.21 -10000 0 -0.55 38 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.007 -10000 0 -10000 0 0
A2M 0.024 0.081 -10000 0 -1.1 2 2
CEBPB 0.032 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.01 0.09 -10000 0 -0.52 4 4
STAT3 -0.022 0.22 0.76 1 -0.77 16 17
STAT1 0.011 0.094 -10000 0 -1 3 3
CEBPD 0 0.19 0.64 2 -0.68 10 12
PIK3CA 0.026 0.037 -10000 0 -0.69 1 1
PI3K 0.039 0.03 -10000 0 -0.52 1 1
JUN -0.13 0.3 -10000 0 -0.69 82 82
PIAS3/MITF -0.055 0.2 -10000 0 -0.55 33 33
MAPK11 -0.1 0.24 -10000 0 -0.72 39 39
STAT3 (dimer)/FOXO1 0.019 0.16 -10000 0 -0.58 9 9
GRB2/SOS1/GAB family -0.03 0.2 -10000 0 -0.51 29 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.072 0.21 -10000 0 -0.37 98 98
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.025 0.007 -10000 0 -10000 0 0
LBP 0.01 0.18 0.62 7 -0.56 9 16
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.025 0.017 -10000 0 -10000 0 0
MYC -0.01 0.24 0.62 3 -0.94 12 15
FGG -0.004 0.2 0.63 4 -0.66 12 16
macrophage differentiation -0.011 0.21 0.54 3 -0.72 16 19
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.069 0.25 -10000 0 -0.46 99 99
JUNB -0.003 0.22 0.6 3 -0.81 12 15
FOS -0.16 0.32 -10000 0 -0.69 100 100
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.067 0.22 -10000 0 -0.43 71 71
STAT1/PIAS1 -0.036 0.2 -10000 0 -0.48 36 36
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.038 -10000 0 -0.29 2 2
STAT3 (dimer) -0.016 0.22 0.75 1 -0.75 16 17
PRKCD -0.02 0.19 0.48 4 -0.57 19 23
IL6R 0.006 0.11 -10000 0 -0.69 9 9
SOCS3 -0.12 0.35 -10000 0 -1.1 37 37
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.15 -10000 0 -0.45 33 33
Rac1/GTP -0.044 0.2 -10000 0 -0.52 35 35
HCK 0.018 0.032 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.091 0.34 1 -0.56 4 5
bone resorption -0.003 0.19 0.61 4 -0.61 13 17
IRF1 0.004 0.2 0.64 6 -0.66 9 15
mol:GDP -0.067 0.2 -10000 0 -0.53 39 39
SOS1 0.026 0.005 -10000 0 -10000 0 0
VAV1 -0.068 0.21 -10000 0 -0.54 39 39
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.091 0.25 -10000 0 -0.69 41 41
PTPN11 0.017 0.05 -10000 0 -0.85 1 1
IL6/IL6RA -0.086 0.24 -10000 0 -0.53 83 83
gp130 (dimer)/TYK2/TYK2/LMO4 0.006 0.14 -10000 0 -0.42 35 35
gp130 (dimer)/JAK2/JAK2/LMO4 0.004 0.14 -10000 0 -0.44 34 34
IL6 -0.13 0.29 -10000 0 -0.69 77 77
PIAS3 0.025 0.007 -10000 0 -10000 0 0
PTPRE -0.026 0.075 -10000 0 -0.69 1 1
PIAS1 0.026 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.073 0.2 -10000 0 -0.37 100 100
LMO4 0.026 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.019 0.21 -10000 0 -0.75 16 16
MCL1 0.053 0.059 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.025 0.009 -9999 0 -10000 0 0
EGFR 0.016 0.082 -9999 0 -0.69 5 5
EGF/EGFR -0.019 0.16 -9999 0 -0.38 58 58
EGF/EGFR dimer/SHC/GRB2/SOS1 0.001 0.16 -9999 0 -0.4 51 51
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.023 0.04 -9999 0 -0.69 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.072 0.24 -9999 0 -0.68 51 51
EGF/EGFR dimer/SHC -0.025 0.18 -9999 0 -0.45 55 55
mol:GDP -0.004 0.16 -9999 0 -0.39 51 51
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.017 0.083 -9999 0 -0.69 5 5
GRB2/SOS1 0.037 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.016 0.14 -9999 0 -0.37 51 51
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.15 -9999 0 -0.37 51 51
FRAP1 -0.056 0.13 -9999 0 -0.38 51 51
EGF/EGFR dimer -0.045 0.2 -9999 0 -0.52 55 55
SOS1 0.026 0.005 -9999 0 -10000 0 0
GRB2 0.025 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.028 0.072 -9999 0 -0.52 6 6
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.002 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.004 0.12 -10000 0 -0.38 18 18
NFATC4 -0.027 0.092 0.29 3 -0.29 16 19
ERBB2IP 0.026 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.021 0.12 -10000 0 -0.36 35 35
JUN -0.004 0.1 0.38 10 -0.4 1 11
HRAS 0.025 0.009 -10000 0 -10000 0 0
DOCK7 -0.032 0.11 -10000 0 -0.35 35 35
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.004 0.14 -10000 0 -0.41 35 35
AKT1 0.006 0.006 -10000 0 -10000 0 0
BAD 0.004 0.005 -10000 0 -10000 0 0
MAPK10 -0.013 0.064 0.25 2 -10000 0 2
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.022 0.13 -10000 0 -0.39 35 35
RAF1 -0.016 0.14 0.43 7 -0.4 18 25
ErbB2/ErbB3/neuregulin 2 -0.031 0.15 -10000 0 -0.43 47 47
STAT3 0.027 0.066 -10000 0 -0.85 2 2
cell migration 0.005 0.11 0.39 16 -0.25 2 18
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.16 0.33 0.52 4 -0.69 90 94
FOS -0.13 0.27 0.49 6 -0.51 119 125
NRAS 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.12 -10000 0 -0.36 35 35
MAPK3 -0.087 0.25 0.49 4 -0.52 66 70
MAPK1 -0.17 0.32 0.54 3 -0.64 96 99
JAK2 -0.032 0.11 -10000 0 -0.35 34 34
NF2 -0.013 0.12 -10000 0 -0.64 13 13
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.019 0.12 -10000 0 -0.36 35 35
NRG1 -0.044 0.21 -10000 0 -0.68 37 37
GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
MAPK8 -0.02 0.11 -10000 0 -0.33 35 35
MAPK9 -0.013 0.064 0.25 2 -10000 0 2
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.013 0.085 -10000 0 -0.64 6 6
SHC1 0.024 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
apoptosis 0.002 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.064 -10000 0 -0.83 2 2
RNF41 -0.004 0.007 -10000 0 -10000 0 0
FRAP1 0.001 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.021 0.08 -10000 0 -0.26 15 15
ErbB2/ErbB2/HSP90 (dimer) 0.009 0.016 -10000 0 -10000 0 0
CHRNA1 -0.081 0.2 0.46 4 -0.41 74 78
myelination -0.012 0.15 0.55 15 -0.29 15 30
PPP3CB -0.029 0.1 -10000 0 -0.33 35 35
KRAS 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.014 0.11 -10000 0 -0.34 18 18
NRG2 -0.057 0.23 -10000 0 -0.69 42 42
mol:GDP -0.019 0.12 -10000 0 -0.36 35 35
SOS1 0.025 0.005 -10000 0 -10000 0 0
MAP2K2 -0.031 0.14 0.43 5 -0.39 19 24
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.003 -10000 0 -10000 0 0
PTPN11 -0.03 0.11 0.25 1 -0.35 35 36
MAP2K1 -0.08 0.23 0.52 3 -0.6 28 31
heart morphogenesis -0.021 0.12 -10000 0 -0.36 35 35
RAS family/GDP 0.008 0.12 -10000 0 -0.37 18 18
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.013 0.13 -10000 0 -0.66 14 14
CHRNE 0.008 0.041 0.2 10 -0.23 1 11
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.006 0.006 -10000 0 -10000 0 0
nervous system development -0.021 0.12 -10000 0 -0.36 35 35
CDC42 0.026 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.001 0.12 -10000 0 -0.41 24 24
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.12 0.35 3 -0.42 10 13
alphaV/beta3 Integrin/Osteopontin/Src 0.016 0.13 -10000 0 -0.51 20 20
AP1 -0.14 0.31 -10000 0 -0.71 69 69
ILK -0.007 0.12 -10000 0 -0.43 23 23
bone resorption -0.002 0.12 -10000 0 -0.38 27 27
PTK2B 0.026 0.004 -10000 0 -10000 0 0
PYK2/p130Cas 0.039 0.12 -10000 0 -0.4 24 24
ITGAV 0.026 0.037 -10000 0 -0.69 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.025 0.082 -10000 0 -0.52 8 8
alphaV/beta3 Integrin/Osteopontin 0.025 0.14 -10000 0 -0.47 25 25
MAP3K1 -0.009 0.12 -10000 0 -0.44 24 24
JUN -0.13 0.3 -10000 0 -0.69 82 82
MAPK3 -0.017 0.11 -10000 0 -0.41 24 24
MAPK1 -0.019 0.11 -10000 0 -0.4 24 24
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.016 0.12 -10000 0 -0.42 25 25
ITGB3 0.009 0.11 -10000 0 -0.66 10 10
NFKBIA -0.017 0.1 -10000 0 -0.4 24 24
FOS -0.16 0.32 -10000 0 -0.69 100 100
CD44 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.026 0.004 -10000 0 -10000 0 0
PLAU -0.032 0.12 0.56 2 -0.6 3 5
NF kappa B1 p50/RelA 0.024 0.11 -10000 0 -0.56 3 3
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.096 -10000 0 -0.53 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.009 0.12 -10000 0 -0.44 24 24
VAV3 -0.016 0.12 0.4 1 -0.42 26 27
MAP3K14 -0.012 0.12 -10000 0 -0.43 24 24
ROCK2 0.011 0.1 -10000 0 -0.69 8 8
SPP1 -0.028 0.16 -10000 0 -0.68 19 19
RAC1 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.12 -10000 0 -0.39 26 26
MMP2 -0.13 0.24 -10000 0 -0.56 70 70
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.11 0.23 -10000 0 -0.54 48 48
MAP3K8 0.015 0.074 -10000 0 -0.7 4 4
FOS -0.078 0.18 0.33 2 -0.45 45 47
PRKCA -0.024 0.16 -10000 0 -0.7 20 20
PTPN7 -0.017 0.11 -10000 0 -0.69 9 9
HRAS 0.024 0.009 -10000 0 -10000 0 0
PRKCB -0.004 0.057 -10000 0 -0.69 1 1
NRAS 0.025 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.032 0.032 -10000 0 -10000 0 0
MAPK3 -0.012 0.11 -10000 0 -0.5 12 12
MAP2K1 -0.025 0.13 -10000 0 -0.49 22 22
ELK1 0.011 0.025 -10000 0 -10000 0 0
BRAF -0.019 0.12 -10000 0 -0.5 21 21
mol:GTP -0.002 0.005 -10000 0 -0.007 103 103
MAPK1 -0.098 0.2 -10000 0 -0.54 44 44
RAF1 -0.018 0.12 -10000 0 -0.48 21 21
KRAS 0.025 0.006 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.09 -10000 0 -0.69 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 186 186
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.007 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
MAP3K12 0.026 0.006 -10000 0 -10000 0 0
FGR 0.024 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.045 0.071 -10000 0 -0.32 7 7
PRKG1 -0.16 0.31 -10000 0 -0.68 98 98
DUSP8 0.018 0.066 -10000 0 -0.69 3 3
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.38 101 101
apoptosis -0.044 0.068 -10000 0 -0.31 7 7
RAL/GTP 0.034 0.009 -10000 0 -10000 0 0
LYN 0.026 0.004 -10000 0 -10000 0 0
DUSP1 -0.087 0.26 -10000 0 -0.69 59 59
PAK1 0.026 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.063 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.037 -10000 0 -0.69 1 1
RAC1 0.025 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 0.025 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.01 -10000 0 -10000 0 0
MAPK11 -0.054 0.16 0.43 16 -0.33 23 39
BLK -0.2 0.32 -10000 0 -0.68 112 112
HCK 0.018 0.032 -10000 0 -10000 0 0
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
DUSP16 0.026 0.005 -10000 0 -10000 0 0
DUSP10 0.022 0.039 -10000 0 -0.69 1 1
TRAF6/MEKK3 0.031 0.025 -10000 0 -0.42 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.013 0.13 0.39 14 -0.34 7 21
positive regulation of innate immune response -0.044 0.17 0.48 16 -0.43 8 24
LCK 0.011 0.079 -10000 0 -0.69 4 4
p38alpha-beta/MKP7 -0.05 0.14 0.32 6 -0.46 5 11
p38alpha-beta/MKP5 -0.039 0.16 0.5 11 -0.48 6 17
PGK/cGMP -0.12 0.24 -10000 0 -0.52 98 98
PAK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.1 0.18 0.27 3 -0.41 55 58
CDC42 0.026 0.005 -10000 0 -10000 0 0
RALB 0.026 0.005 -10000 0 -10000 0 0
RALA 0.025 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.35 -10000 0 -0.67 204 204
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.04 0.1 -10000 0 -0.42 16 16
ER alpha/Gai/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.52 18 18
AKT1 -0.013 0.19 -10000 0 -0.76 22 22
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.2 -10000 0 -0.79 21 21
mol:Ca2+ -0.1 0.19 -10000 0 -0.43 92 92
IGF1R 0.026 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.002 0.14 -10000 0 -0.46 29 29
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.18 0.72 22 -10000 0 22
RhoA/GTP 0.005 0.073 -10000 0 -0.36 13 13
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.006 0.13 -10000 0 -0.54 15 15
regulation of stress fiber formation 0.005 0.076 0.29 18 -0.28 1 19
E2/ERA-ERB (dimer) 0.014 0.11 -10000 0 -0.47 17 17
KRAS 0.026 0.005 -10000 0 -10000 0 0
G13/GTP 0.016 0.086 -10000 0 -0.38 16 16
pseudopodium formation -0.005 0.076 0.28 1 -0.29 18 19
E2/ER alpha (dimer)/PELP1 0.016 0.093 -10000 0 -0.42 16 16
GRB2 0.025 0.007 -10000 0 -10000 0 0
GNG2 0.026 0.005 -10000 0 -10000 0 0
GNAO1 0.009 0.1 -10000 0 -0.69 8 8
HRAS 0.025 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.012 0.16 0.48 7 -0.59 17 24
E2/ER beta (dimer) 0.016 0.04 -10000 0 -0.52 2 2
mol:GDP 0.003 0.11 -10000 0 -0.5 16 16
mol:NADP 0.012 0.16 0.48 7 -0.59 17 24
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 92 92
IGF-1R heterotetramer 0.026 0.003 -10000 0 -10000 0 0
PLCB1 -0.1 0.2 -10000 0 -0.45 92 92
PLCB2 -0.1 0.21 -10000 0 -0.46 92 92
IGF1 -0.12 0.28 -10000 0 -0.69 74 74
mol:L-citrulline 0.012 0.16 0.48 7 -0.59 17 24
RHOA 0.026 0.004 -10000 0 -10000 0 0
Gai/GDP 0.007 0.14 -10000 0 -0.69 12 12
JNK cascade 0.016 0.04 -10000 0 -0.52 2 2
BCAR1 0.025 0.006 -10000 0 -10000 0 0
ESR2 0.022 0.052 -10000 0 -0.69 2 2
GNAQ 0.024 0.008 -10000 0 -10000 0 0
ESR1 -0.016 0.15 -10000 0 -0.67 17 17
Gq family/GDP/Gbeta gamma -0.059 0.18 -10000 0 -0.61 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.017 0.1 -10000 0 -0.58 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.003 0.13 -10000 0 -0.54 15 15
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.011 0.11 -10000 0 -0.51 17 17
STRN 0.001 0.13 -10000 0 -0.69 13 13
GNAL -0.061 0.23 -10000 0 -0.67 47 47
PELP1 0.025 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.034 -10000 0 -0.44 2 2
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.037 -10000 0 -0.69 1 1
HBEGF -0.013 0.14 0.42 3 -0.54 15 18
cAMP biosynthetic process -0.036 0.16 -10000 0 -0.4 57 57
SRC -0.003 0.12 -10000 0 -0.5 16 16
PI3K 0.036 0.03 -10000 0 -0.52 1 1
GNB1 0.026 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.032 0.1 -10000 0 -0.44 16 16
SOS1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.065 0.16 -10000 0 -0.43 37 37
Gs family/GTP -0.03 0.17 -10000 0 -0.41 57 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.015 -10000 0 -10000 0 0
vasodilation 0.013 0.15 0.48 7 -0.55 18 25
mol:DAG -0.1 0.2 -10000 0 -0.44 92 92
Gs family/GDP/Gbeta gamma -0.026 0.14 -10000 0 -0.37 52 52
MSN -0.006 0.08 0.29 1 -0.32 18 19
Gq family/GTP -0.1 0.22 -10000 0 -0.48 93 93
mol:PI-3-4-5-P3 -0.008 0.19 -10000 0 -0.75 21 21
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.013 0.15 0.55 18 -0.48 7 25
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.11 -10000 0 -0.47 16 16
NOS3 0.003 0.15 0.39 2 -0.63 17 19
GNA11 0.019 0.064 -10000 0 -0.69 3 3
MAPKKK cascade -0.006 0.16 0.37 1 -0.53 29 30
E2/ER alpha (dimer)/PELP1/Src 0.001 0.13 -10000 0 -0.57 15 15
ruffle organization -0.005 0.076 0.28 1 -0.29 18 19
ROCK2 0.001 0.097 0.36 5 -0.34 18 23
GNA14 -0.14 0.3 -10000 0 -0.66 91 91
GNA15 0.011 0.053 -10000 0 -0.69 1 1
GNA13 0.025 0.007 -10000 0 -10000 0 0
MMP9 -0.028 0.16 -10000 0 -0.59 19 19
MMP2 -0.001 0.12 -10000 0 -0.49 15 15
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.006 0.052 -10000 0 -10000 0 0
CRKL -0.009 0.089 0.36 1 -0.3 3 4
mol:PIP3 -0.001 0.019 0.35 1 -10000 0 1
AKT1 0.006 0.061 0.37 3 -0.46 2 5
PTK2B 0.026 0.004 -10000 0 -10000 0 0
RAPGEF1 0.006 0.11 0.44 8 -10000 0 8
RANBP10 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
HGF/MET/SHIP2 -0.006 0.18 -10000 0 -0.47 47 47
MAP3K5 0.015 0.13 0.48 11 -0.39 6 17
HGF/MET/CIN85/CBL/ENDOPHILINS 0.009 0.17 -10000 0 -0.43 47 47
AP1 -0.19 0.34 -10000 0 -0.67 116 116
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.23 0.4 -10000 0 -0.81 116 116
STAT3 (dimer) -0.017 0.1 -10000 0 -0.29 45 45
GAB1/CRKL/SHP2/PI3K 0.03 0.096 -10000 0 -10000 0 0
INPP5D 0.016 0.035 -10000 0 -10000 0 0
CBL/CRK 0.019 0.11 0.49 5 -10000 0 5
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.022 -10000 0 -0.38 1 1
ELK1 0.034 0.14 0.45 21 -0.25 2 23
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.066 -10000 0 -0.26 3 3
PAK1 0.008 0.065 0.37 6 -0.4 1 7
HGF/MET/RANBP10 -0.007 0.18 -10000 0 -0.47 47 47
HRAS -0.013 0.13 -10000 0 -0.57 2 2
DOCK1 0.006 0.11 0.44 9 -0.34 1 10
GAB1 -0.006 0.093 0.25 1 -0.32 3 4
CRK -0.002 0.094 0.36 1 -0.31 2 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.034 0.18 -10000 0 -0.52 47 47
JUN -0.13 0.3 -10000 0 -0.69 82 82
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.027 0.082 -10000 0 -0.24 46 46
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.002 0.12 0.57 4 -0.46 1 5
GRB2/SHC 0.007 0.083 -10000 0 -0.22 22 22
FOS -0.16 0.32 -10000 0 -0.69 100 100
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.034 0.14 0.44 21 -0.25 2 23
HGF/MET/MUC20 -0.021 0.17 -10000 0 -0.47 47 47
cell migration 0.007 0.082 -10000 0 -0.22 22 22
GRB2 0.025 0.007 -10000 0 -10000 0 0
CBL 0.026 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.006 0.052 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.013 0.11 -10000 0 -0.3 45 45
MET/MUC20 -0.017 0.043 -10000 0 -10000 0 0
RAP1B 0.016 0.13 0.57 11 -10000 0 11
RAP1A 0.012 0.11 0.44 8 -10000 0 8
HGF/MET/RANBP9 -0.005 0.18 -10000 0 -0.47 47 47
RAF1 -0.01 0.12 -10000 0 -0.46 2 2
STAT3 -0.017 0.1 -10000 0 -0.29 45 45
cell proliferation -0.02 0.15 -10000 0 -0.4 44 44
RPS6KB1 0.002 0.03 -10000 0 -10000 0 0
MAPK3 -0.018 0.11 0.5 12 -10000 0 12
MAPK1 0.13 0.29 0.61 94 -10000 0 94
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.032 0.16 0.6 15 -0.46 5 20
SRC -0.019 0.1 -10000 0 -0.29 45 45
PI3K 0.008 0.088 -10000 0 -0.33 2 2
MET/Glomulin -0.007 0.042 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K1 -0.005 0.12 0.31 1 -0.43 2 3
MET -0.029 0.065 -10000 0 -10000 0 0
MAP4K1 0.009 0.12 0.52 6 -0.46 4 10
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.004 0.12 0.31 1 -0.42 2 3
BAD 0.008 0.065 0.37 6 -0.4 1 7
MAP2K4 0.025 0.15 0.53 17 -0.38 5 22
SHP2/GRB2/SOS1/GAB1 0.023 0.095 -10000 0 -10000 0 0
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.026 0.006 -10000 0 -10000 0 0
SH3KBP1 0.025 0.007 -10000 0 -10000 0 0
HGS -0.026 0.076 -10000 0 -0.23 45 45
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.065 0.24 -10000 0 -0.69 47 47
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
PTPRJ 0.026 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.007 0.097 -10000 0 -0.25 46 46
PDPK1 0 0.049 -10000 0 -0.49 2 2
HGF/MET/SHIP -0.009 0.18 -10000 0 -0.47 47 47
LPA receptor mediated 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
GNB1/GNG2 0.017 0.12 -10000 0 -0.42 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.084 0.41 1 -0.44 1 2
AP1 -0.17 0.31 -10000 0 -0.57 124 124
mol:PIP3 -0.014 0.1 -10000 0 -0.38 24 24
AKT1 0.024 0.094 0.28 8 -0.4 2 10
PTK2B -0.013 0.09 0.23 3 -0.28 25 28
RHOA 0.009 0.04 -10000 0 -10000 0 0
PIK3CB 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.069 0.3 4 -10000 0 4
MAGI3 0.024 0.037 -10000 0 -0.69 1 1
RELA 0.026 0.005 -10000 0 -10000 0 0
apoptosis -0.011 0.1 -10000 0 -0.36 28 28
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.11 0.38 9 -0.4 7 16
NF kappa B1 p50/RelA -0.023 0.1 -10000 0 -0.46 5 5
endothelial cell migration -0.016 0.14 -10000 0 -0.51 25 25
ADCY4 -0.029 0.15 -10000 0 -0.52 27 27
ADCY5 -0.059 0.17 -10000 0 -0.56 31 31
ADCY6 -0.029 0.15 -10000 0 -0.52 27 27
ADCY7 -0.03 0.15 -10000 0 -0.53 27 27
ADCY1 -0.031 0.15 -10000 0 -0.51 28 28
ADCY2 -0.052 0.17 -10000 0 -0.55 31 31
ADCY3 -0.029 0.15 -10000 0 -0.53 26 26
ADCY8 -0.035 0.15 -10000 0 -0.53 28 28
ADCY9 -0.03 0.15 -10000 0 -0.53 27 27
GSK3B -0.012 0.088 0.37 2 -0.38 7 9
arachidonic acid secretion -0.029 0.14 -10000 0 -0.45 34 34
GNG2 0.026 0.005 -10000 0 -10000 0 0
TRIP6 0.023 0.009 -10000 0 -10000 0 0
GNAO1 -0.023 0.14 -10000 0 -0.49 31 31
HRAS 0.025 0.009 -10000 0 -10000 0 0
NFKBIA -0.008 0.097 0.48 5 -0.5 1 6
GAB1 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.02 0.18 -10000 0 -0.79 16 16
JUN -0.13 0.3 -10000 0 -0.69 82 82
LPA/LPA2/NHERF2 0.034 0.015 -10000 0 -10000 0 0
TIAM1 0.006 0.21 -10000 0 -0.94 17 17
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.012 0.066 0.36 2 -10000 0 2
PLCB3 0.024 0.03 -10000 0 -10000 0 0
FOS -0.16 0.32 -10000 0 -0.69 100 100
positive regulation of mitosis -0.029 0.14 -10000 0 -0.45 34 34
LPA/LPA1-2-3 0.017 0.12 -10000 0 -0.41 25 25
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.006 -10000 0 -10000 0 0
stress fiber formation -0.003 0.11 0.35 4 -0.33 23 27
GNAZ -0.017 0.12 -10000 0 -0.45 26 26
EGFR/PI3K-beta/Gab1 -0.003 0.11 -10000 0 -0.39 24 24
positive regulation of dendritic cell cytokine production 0.015 0.12 -10000 0 -0.4 25 25
LPA/LPA2/MAGI-3 0.034 0.029 -10000 0 -0.46 1 1
ARHGEF1 0.001 0.11 0.36 1 -0.4 21 22
GNAI2 -0.015 0.13 -10000 0 -0.46 25 25
GNAI3 -0.014 0.12 -10000 0 -0.46 25 25
GNAI1 -0.014 0.12 -10000 0 -0.42 30 30
LPA/LPA3 0.015 0.022 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.011 -10000 0 -10000 0 0
LPA/LPA1 -0.018 0.14 -10000 0 -0.47 32 32
HB-EGF/EGFR -0.019 0.13 -10000 0 -0.45 30 30
HBEGF -0.032 0.14 -10000 0 -0.5 27 27
mol:DAG -0.012 0.066 0.36 2 -10000 0 2
cAMP biosynthetic process -0.034 0.17 0.41 10 -0.48 35 45
NFKB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN -0.011 0.092 0.4 5 -0.42 2 7
GNAQ 0.016 0.014 -10000 0 -10000 0 0
LPAR2 0.025 0.007 -10000 0 -10000 0 0
LPAR3 0.012 0.032 -10000 0 -10000 0 0
LPAR1 -0.026 0.18 -10000 0 -0.62 31 31
IL8 -0.084 0.17 -10000 0 -0.46 31 31
PTK2 -0.006 0.11 -10000 0 -0.4 23 23
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.011 0.1 -10000 0 -0.36 28 28
EGFR 0.016 0.082 -10000 0 -0.69 5 5
PLCG1 -0.014 0.062 -10000 0 -10000 0 0
PLD2 -0.007 0.1 -10000 0 -0.39 22 22
G12/G13 0.019 0.12 -10000 0 -0.41 24 24
PI3K-beta 0.003 0.087 -10000 0 -0.33 21 21
cell migration 0.019 0.073 -10000 0 -0.25 12 12
SLC9A3R2 0.025 0.007 -10000 0 -10000 0 0
PXN -0.005 0.1 0.25 3 -0.33 23 26
HRAS/GTP -0.03 0.14 -10000 0 -0.46 34 34
RAC1 0.025 0.006 -10000 0 -10000 0 0
MMP9 -0.038 0.19 -10000 0 -0.69 27 27
PRKCE 0.02 0.064 -10000 0 -0.69 3 3
PRKCD -0.011 0.087 0.38 7 -0.42 1 8
Gi(beta/gamma) -0.024 0.14 -10000 0 -0.51 25 25
mol:LPA 0.002 0.014 -10000 0 -0.2 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.013 0.12 -10000 0 -0.39 23 23
MAPKKK cascade -0.029 0.14 -10000 0 -0.45 34 34
contractile ring contraction involved in cytokinesis 0.011 0.045 0.29 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.071 0.16 -10000 0 -0.35 89 89
GNA15 0.015 0.026 -10000 0 -0.37 1 1
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.007 -10000 0 -10000 0 0
MAPT -0.007 0.1 0.36 7 -0.42 7 14
GNA11 0.014 0.033 -10000 0 -0.32 3 3
Rac1/GTP 0.02 0.19 -10000 0 -0.83 16 16
MMP2 -0.016 0.14 -10000 0 -0.52 25 25
Syndecan-1-mediated signaling events

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
TGFB1 0.023 0.017 -10000 0 -10000 0 0
CCL5 -0.018 0.16 -10000 0 -0.69 21 21
SDCBP 0.026 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.034 0.14 0.3 1 -0.44 28 29
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 -0.025 0.14 -10000 0 -0.58 15 15
Syndecan-1/Syntenin -0.023 0.15 0.27 1 -0.59 15 16
MAPK3 -0.023 0.13 -10000 0 -0.53 14 14
HGF/MET -0.073 0.18 -10000 0 -0.54 47 47
TGFB1/TGF beta receptor Type II 0.023 0.017 -10000 0 -10000 0 0
BSG 0.025 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.025 0.14 -10000 0 -0.56 15 15
Syndecan-1/RANTES -0.044 0.19 -10000 0 -0.64 28 28
Syndecan-1/CD147 -0.008 0.14 0.46 1 -0.56 15 16
Syndecan-1/Syntenin/PIP2 -0.024 0.14 0.26 1 -0.57 15 16
LAMA5 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.14 0.25 1 -0.55 15 16
MMP7 -0.071 0.15 -10000 0 -0.68 19 19
HGF -0.065 0.24 -10000 0 -0.69 47 47
Syndecan-1/CASK -0.041 0.14 -10000 0 -0.44 29 29
Syndecan-1/HGF/MET -0.051 0.21 -10000 0 -0.51 51 51
regulation of cell adhesion -0.03 0.12 -10000 0 -0.56 11 11
HPSE 0.006 0.1 -10000 0 -0.65 8 8
positive regulation of cell migration -0.034 0.14 0.3 1 -0.44 28 29
SDC1 -0.034 0.14 -10000 0 -0.44 28 28
Syndecan-1/Collagen -0.034 0.14 0.3 1 -0.44 28 29
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.029 0.065 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
MMP9 -0.038 0.19 -10000 0 -0.69 27 27
MAPK1 -0.026 0.13 -10000 0 -0.56 13 13
homophilic cell adhesion -0.033 0.14 0.44 2 -0.48 21 23
MMP1 -0.04 0.065 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.012 0.14 -10000 0 -0.37 42 42
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.004 0.12 -10000 0 -0.34 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.049 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.007 0.07 -10000 0 -0.24 3 3
CaM/Ca2+ 0.016 0.13 -10000 0 -0.35 42 42
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.12 -10000 0 -0.35 42 42
AKT1 -0.014 0.12 0.38 5 -0.32 40 45
MAP2K1 -0.024 0.11 0.29 2 -0.34 40 42
MAP3K11 -0.02 0.12 0.3 4 -0.35 42 46
IFNGR1 0.02 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.016 0.076 -10000 0 -0.45 2 2
Rap1/GTP -0.019 0.093 -10000 0 -0.3 1 1
CRKL/C3G 0.028 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.019 0.15 -10000 0 -0.39 42 42
CEBPB -0.052 0.19 0.58 6 -0.54 16 22
STAT3 0.025 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.021 0.14 -10000 0 -0.66 3 3
STAT1 -0.018 0.13 0.32 6 -0.35 42 48
CALM1 0.026 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.061 0.22 -10000 0 -0.69 42 42
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
STAT1 (dimer)/PIAS1 -0.003 0.13 0.32 6 -0.33 42 48
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.38 6 6
mol:Ca2+ 0.009 0.14 -10000 0 -0.36 42 42
MAPK3 -0.008 0.12 0.42 1 -0.66 3 4
STAT1 (dimer) 0.016 0.095 -10000 0 -0.34 2 2
MAPK1 -0.16 0.3 0.43 1 -0.67 85 86
JAK2 0.019 0.025 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.025 -10000 0 -10000 0 0
CAMK2D 0.026 0.004 -10000 0 -10000 0 0
DAPK1 -0.038 0.19 0.5 9 -0.6 21 30
SMAD7 0.02 0.077 0.5 6 -10000 0 6
CBL/CRKL/C3G -0.006 0.12 0.29 2 -0.32 38 40
PI3K 0.015 0.13 -10000 0 -0.34 41 41
IFNG -0.061 0.23 -10000 0 -0.69 42 42
apoptosis -0.034 0.16 0.55 6 -0.45 26 32
CAMK2G 0.026 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.007 -10000 0 -10000 0 0
CAMK2A 0.012 0.03 -10000 0 -10000 0 0
CAMK2B 0.018 0.074 -10000 0 -0.69 4 4
FRAP1 -0.021 0.11 0.36 5 -0.3 40 45
PRKCD -0.008 0.13 0.44 10 -0.36 2 12
RAP1B 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.007 0.07 -10000 0 -0.24 3 3
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
IRF1 -0.012 0.085 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.12 0.29 2 -0.34 41 43
SOCS1 0.02 0.1 -10000 0 -0.96 4 4
mol:GDP -0.007 0.11 0.28 2 -0.31 38 40
CASP1 0.017 0.076 0.56 4 -0.33 2 6
PTGES2 0.024 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.057 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 0.002 0.12 -10000 0 -0.33 41 41
RAP1/GDP -0.004 0.1 -10000 0 -0.31 1 1
CBL -0.02 0.12 0.29 5 -0.35 42 47
MAP3K1 -0.021 0.12 0.29 2 -0.35 40 42
PIAS1 0.026 0.003 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.007 0.07 -10000 0 -0.24 3 3
PTPN11 -0.023 0.12 -10000 0 -0.36 42 42
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.009 0.055 0.25 17 -10000 0 17
RFC1 0.01 0.057 0.25 19 -10000 0 19
PRKDC 0.01 0.057 0.24 21 -10000 0 21
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.007 0.1 -10000 0 -0.77 5 5
FASLG/FAS/FADD/FAF1 -0.019 0.094 0.24 1 -0.35 24 25
MAP2K4 -0.041 0.18 0.32 2 -0.46 30 32
mol:ceramide -0.029 0.14 -10000 0 -0.45 26 26
GSN 0.009 0.055 0.25 17 -10000 0 17
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.12 -10000 0 -0.44 24 24
FAS 0.017 0.02 -10000 0 -10000 0 0
BID -0.018 0.036 0.28 3 -10000 0 3
MAP3K1 -0.017 0.12 0.26 3 -0.57 7 10
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
RB1 0.01 0.056 0.25 18 -10000 0 18
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.007 0.18 -10000 0 -0.47 48 48
ARHGDIB 0.011 0.06 0.24 21 -10000 0 21
FADD 0.017 0.02 -10000 0 -10000 0 0
actin filament polymerization -0.009 0.054 -10000 0 -0.25 17 17
NFKB1 -0.026 0.11 -10000 0 -0.45 5 5
MAPK8 -0.08 0.24 0.4 2 -0.48 86 88
DFFA 0.01 0.057 0.25 19 -10000 0 19
DNA fragmentation during apoptosis 0.01 0.057 0.25 19 -10000 0 19
FAS/FADD/MET 0.042 0.046 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.015 0.069 -10000 0 -0.69 3 3
FAF1 0.016 0.022 -10000 0 -10000 0 0
PARP1 0.013 0.073 0.3 20 -10000 0 20
DFFB 0.01 0.057 0.25 19 -10000 0 19
CHUK -0.024 0.098 -10000 0 -0.53 3 3
FASLG -0.037 0.18 -10000 0 -0.7 24 24
FAS/FADD 0.025 0.029 -10000 0 -10000 0 0
HGF -0.065 0.24 -10000 0 -0.69 47 47
LMNA 0.01 0.064 0.26 19 -10000 0 19
CASP6 0.01 0.057 0.25 19 -10000 0 19
CASP10 0.017 0.02 -10000 0 -10000 0 0
CASP3 0.014 0.071 0.3 22 -10000 0 22
PTPN13 0.024 0.037 -10000 0 -0.69 1 1
CASP8 -0.014 0.039 0.41 3 -10000 0 3
IL6 -0.26 0.56 -10000 0 -1.3 86 86
MET -0.029 0.065 -10000 0 -10000 0 0
ICAD/CAD 0.008 0.051 0.22 19 -10000 0 19
FASLG/FAS/FADD/FAF1/Caspase 10 -0.029 0.14 -10000 0 -0.45 26 26
activation of caspase activity by cytochrome c -0.018 0.036 0.28 3 -10000 0 3
PAK2 0.011 0.059 0.24 22 -10000 0 22
BCL2 -0.015 0.17 -10000 0 -0.68 22 22
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.008 0.013 -10000 0 -10000 0 0
SMARCC1 0.01 0.014 -10000 0 -10000 0 0
REL 0 0.15 -10000 0 -0.69 16 16
HDAC7 -0.065 0.099 -10000 0 -0.47 7 7
JUN -0.13 0.29 -10000 0 -0.69 82 82
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.026 0.004 -10000 0 -10000 0 0
KAT5 0.026 0.005 -10000 0 -10000 0 0
MAPK14 -0.015 0.07 -10000 0 -0.54 6 6
FOXO1 0.024 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.062 0.11 -10000 0 -0.47 9 9
MAP2K6 0.006 0.091 -10000 0 -0.7 6 6
BRM/BAF57 0.017 0.032 -10000 0 -10000 0 0
MAP2K4 0.018 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.014 0.068 -10000 0 -0.51 3 3
NCOA2 -0.024 0.17 -10000 0 -0.7 23 23
CEBPA 0.018 0.074 -10000 0 -0.69 4 4
EHMT2 0.024 0.005 -10000 0 -10000 0 0
cell proliferation -0.076 0.2 0.59 17 -0.45 10 27
NR0B1 -0.008 0.022 -10000 0 -10000 0 0
EGR1 -0.13 0.29 -10000 0 -0.7 76 76
RXRs/9cRA 0.027 0.069 -10000 0 -0.42 2 2
AR/RACK1/Src -0.13 0.13 0.33 2 -0.47 10 12
AR/GR -0.11 0.17 0.27 2 -0.32 139 141
GNB2L1 0.021 0.008 -10000 0 -10000 0 0
PKN1 0.024 0.007 -10000 0 -10000 0 0
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.005 -10000 0 -0.019 11 11
MAPK8 -0.009 0.043 -10000 0 -0.52 2 2
T-DHT/AR/TIF2/CARM1 -0.12 0.16 0.35 2 -0.53 26 28
SRC -0.039 0.064 0.23 1 -0.41 7 8
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.34 0.54 -10000 0 -1.2 101 101
APPBP2 0.023 0.012 -10000 0 -10000 0 0
TRIM24 0.013 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.065 0.11 0.33 5 -0.48 8 13
TMPRSS2 -0.046 0.28 -10000 0 -1.1 23 23
RXRG -0.089 0.067 -10000 0 -0.69 2 2
mol:9cRA -0.002 0.003 -10000 0 -10000 0 0
RXRA 0.023 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.02 0.064 -10000 0 -0.69 3 3
KLK2 -0.44 0.39 0.33 2 -0.77 212 214
AR -0.13 0.17 -10000 0 -0.35 140 140
SENP1 0.025 0.006 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
MDM2 0.034 0.016 -10000 0 -10000 0 0
SRY 0.008 0.014 0.031 101 -10000 0 101
GATA2 0.026 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.012 0.034 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.094 0.12 0.34 3 -0.49 8 11
positive regulation of transcription 0.026 0.008 -10000 0 -10000 0 0
DNAJA1 0.023 0.013 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.008 -10000 0 -10000 0 0
NCOA1 0.017 0.022 -10000 0 -10000 0 0
SPDEF -0.001 0.043 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.079 0.12 0.28 2 -0.41 26 28
T-DHT/AR/Hsp90 -0.066 0.11 0.33 5 -0.45 9 14
GSK3B 0.024 0.007 -10000 0 -10000 0 0
NR2C1 0.027 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.065 0.25 1 -0.42 8 9
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.034 0.017 -10000 0 -10000 0 0
POU2F1 0.031 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.068 0.11 0.32 5 -0.49 8 13
CREBBP 0.025 0.006 -10000 0 -10000 0 0
SMARCE1 0.012 0.022 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.009 -10000 0 -10000 0 0
LAT2 -0.002 0.066 -10000 0 -0.25 6 6
AP1 -0.12 0.26 -10000 0 -0.55 82 82
mol:PIP3 0.028 0.18 0.62 17 -0.36 21 38
IKBKB 0.039 0.18 0.62 21 -0.24 7 28
AKT1 -0.01 0.12 0.32 17 -0.38 5 22
IKBKG 0.045 0.19 0.65 23 -0.26 3 26
MS4A2 -0.014 0.057 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.037 -10000 0 -0.69 1 1
MAP3K1 0.025 0.12 0.51 10 -0.42 3 13
mol:Ca2+ 0.034 0.17 0.57 21 -0.28 21 42
LYN 0.026 0.011 -10000 0 -10000 0 0
CBLB -0.001 0.064 -10000 0 -0.25 5 5
SHC1 0.025 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK -0.025 0.17 -10000 0 -0.42 59 59
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.016 0.035 -10000 0 -10000 0 0
PLD2 -0.013 0.13 0.32 25 -0.38 23 48
PTPN13 0.015 0.14 0.52 4 -0.65 9 13
PTPN11 0.022 0.016 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.032 0.18 0.65 18 -0.36 3 21
SYK 0.024 0.012 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0 0.11 -10000 0 -0.36 22 22
LAT -0.004 0.073 0.2 1 -0.29 9 10
PAK2 0.017 0.1 0.37 5 -0.42 5 10
NFATC2 -0.079 0.21 -10000 0 -0.62 46 46
HRAS 0.011 0.089 -10000 0 -0.46 4 4
GAB2 0.026 0.005 -10000 0 -10000 0 0
PLA2G1B 0.004 0.095 -10000 0 -0.71 5 5
Fc epsilon R1 0.01 0.14 -10000 0 -0.46 25 25
Antigen/IgE/Fc epsilon R1 0.017 0.12 -10000 0 -0.42 25 25
mol:GDP 0.004 0.093 -10000 0 -0.48 6 6
JUN -0.13 0.3 -10000 0 -0.69 82 82
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
FOS -0.16 0.32 -10000 0 -0.69 100 100
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.003 0.07 -10000 0 -0.24 21 21
CHUK 0.039 0.17 0.61 21 -0.26 3 24
KLRG1 -0.008 0.078 -10000 0 -0.26 27 27
VAV1 -0.004 0.073 0.18 2 -0.36 5 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.001 0.063 -10000 0 -0.24 5 5
negative regulation of mast cell degranulation 0.007 0.082 -10000 0 -0.31 8 8
BTK -0.001 0.11 -10000 0 -0.51 10 10
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.017 0.15 -10000 0 -0.47 30 30
GAB2/PI3K/SHP2 -0.028 0.092 -10000 0 -0.37 21 21
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.002 0.075 -10000 0 -0.28 22 22
RAF1 0.013 0.088 -10000 0 -0.9 3 3
Fc epsilon R1/FcgammaRIIB/SHIP 0.028 0.18 -10000 0 -0.51 32 32
FCER1G 0.017 0.032 -10000 0 -10000 0 0
FCER1A -0.035 0.18 -10000 0 -0.69 26 26
Antigen/IgE/Fc epsilon R1/Fyn 0.032 0.12 -10000 0 -0.39 25 25
MAPK3 0.018 0.085 -10000 0 -0.82 3 3
MAPK1 -0.015 0.11 -10000 0 -0.73 5 5
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.004 0.17 -10000 0 -0.61 21 21
DUSP1 -0.087 0.26 -10000 0 -0.69 59 59
NF-kappa-B/RelA 0.014 0.045 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.014 0.13 0.4 4 -0.68 9 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.09 -10000 0 -0.46 3 3
FER -0.003 0.069 -10000 0 -0.33 3 3
RELA 0.026 0.005 -10000 0 -10000 0 0
ITK -0.042 0.15 -10000 0 -0.47 40 40
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG1 0.012 0.11 0.42 6 -0.48 6 12
cytokine secretion 0.004 0.029 -10000 0 -10000 0 0
SPHK1 -0.001 0.067 0.22 3 -0.25 6 9
PTK2 0.013 0.14 0.4 4 -0.72 9 13
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.008 0.11 -10000 0 -0.38 22 22
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.035 0.18 0.74 14 -0.35 21 35
MAP2K2 0.015 0.09 -10000 0 -0.84 3 3
MAP2K1 0.009 0.082 -10000 0 -0.84 3 3
MAP2K7 0.025 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.08 -10000 0 -0.31 11 11
MAP2K4 -0.012 0.2 -10000 0 -0.81 21 21
Fc epsilon R1/FcgammaRIIB 0.016 0.18 -10000 0 -0.54 32 32
mol:Choline -0.013 0.13 0.32 25 -0.38 23 48
SHC/Grb2/SOS1 0.035 0.077 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
DOK1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.019 0.14 0.53 5 -0.64 9 14
HCLS1 -0.002 0.064 -10000 0 -0.26 4 4
PRKCB 0.039 0.19 0.65 21 -0.29 15 36
FCGR2B -0.008 0.15 -10000 0 -0.69 17 17
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.007 0.083 -10000 0 -0.32 8 8
LCP2 0.022 0.024 -10000 0 -10000 0 0
PLA2G4A -0.023 0.12 -10000 0 -0.42 24 24
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.013 0.13 0.32 25 -0.38 23 48
IKK complex 0.046 0.19 0.66 23 -0.22 1 24
WIPF1 0.026 0.005 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.061 0.18 0.43 8 -0.46 23 31
IKBKB 0.013 0.12 0.48 13 -0.31 5 18
AKT1 0.003 0.17 0.56 19 -0.25 10 29
IKBKG 0 0.13 0.43 14 -0.34 11 25
CALM1 -0.017 0.09 0.34 3 -0.47 4 7
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
MAP3K1 -0.006 0.17 0.47 9 -0.56 14 23
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.088 -10000 0 -0.46 5 5
DOK1 0.026 0.005 -10000 0 -10000 0 0
AP-1 -0.056 0.16 0.54 10 -0.26 77 87
LYN 0.026 0.004 -10000 0 -10000 0 0
BLNK 0.026 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.061 0.17 -10000 0 -0.51 43 43
CD22 -0.06 0.18 -10000 0 -0.45 55 55
CAMK2G -0.014 0.087 0.31 4 -0.43 4 8
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
INPP5D 0.016 0.035 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.027 0.12 -10000 0 -0.36 38 38
GO:0007205 -0.021 0.091 -10000 0 -0.47 5 5
SYK 0.024 0.008 -10000 0 -10000 0 0
ELK1 -0.014 0.091 0.34 3 -0.48 4 7
NFATC1 -0.034 0.13 0.38 5 -0.45 14 19
B-cell antigen/BCR complex -0.061 0.17 -10000 0 -0.51 43 43
PAG1/CSK 0.038 0.007 -10000 0 -10000 0 0
NFKBIB 0.02 0.044 0.2 11 -0.13 5 16
HRAS -0.014 0.091 0.29 3 -0.37 4 7
NFKBIA 0.02 0.044 0.2 11 -0.13 5 16
NF-kappa-B/RelA/I kappa B beta 0.024 0.04 0.2 11 -10000 0 11
RasGAP/Csk 0.006 0.18 -10000 0 -0.43 49 49
mol:GDP -0.018 0.089 -10000 0 -0.47 5 5
PTEN 0.025 0.022 -10000 0 -0.38 1 1
CD79B 0.006 0.047 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.041 0.2 11 -10000 0 11
GRB2 0.025 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.026 0.16 0.5 4 -0.49 13 17
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.018 0.085 -10000 0 -0.46 4 4
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.1 0.19 0.46 6 -0.37 101 107
CHUK 0.01 0.1 0.42 12 -0.37 3 15
IBTK 0.026 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.007 0.1 0.32 1 -0.47 5 6
PTPN6 -0.059 0.17 -10000 0 -0.5 30 30
RELA 0.026 0.005 -10000 0 -10000 0 0
BCL2A1 0.015 0.035 0.2 4 -0.11 6 10
VAV2 -0.046 0.15 -10000 0 -0.7 9 9
ubiquitin-dependent protein catabolic process 0.023 0.043 0.2 11 -0.12 5 16
BTK -0.025 0.22 -10000 0 -0.97 19 19
CD19 -0.052 0.15 -10000 0 -0.42 44 44
MAP4K1 0.004 0.095 -10000 0 -0.69 6 6
CD72 0.024 0.014 -10000 0 -10000 0 0
PAG1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.001 0.15 0.42 11 -0.49 12 23
SH3BP5 0.026 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.012 0.092 -10000 0 -0.57 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.04 0.18 -10000 0 -0.44 49 49
RAF1 -0.01 0.092 0.33 6 -0.37 3 9
RasGAP/p62DOK/SHIP 0.008 0.18 -10000 0 -0.42 49 49
CD79A -0.089 0.22 -10000 0 -0.67 44 44
re-entry into mitotic cell cycle -0.055 0.16 0.54 10 -0.26 76 86
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 0 0.099 0.38 12 -0.4 1 13
MAPK1 -0.007 0.085 0.38 6 -0.38 1 7
CD72/SHP1 -0.039 0.17 -10000 0 -0.58 17 17
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.001 0.15 0.47 10 -0.48 14 24
actin cytoskeleton organization -0.033 0.14 0.39 4 -0.56 9 13
NF-kappa-B/RelA 0.049 0.072 0.34 11 -0.2 3 14
Calcineurin 0.012 0.087 -10000 0 -0.42 3 3
PI3K -0.055 0.14 -10000 0 -0.5 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.014 0.097 -10000 0 -0.54 5 5
SOS1 0.026 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.011 0.22 -10000 0 -0.95 14 14
DAPP1 -0.029 0.24 -10000 0 -1.2 12 12
cytokine secretion -0.032 0.12 0.37 5 -0.42 14 19
mol:DAG -0.018 0.085 -10000 0 -0.46 4 4
PLCG2 0.025 0.006 -10000 0 -10000 0 0
MAP2K1 -0.009 0.087 0.34 5 -0.38 2 7
B-cell antigen/BCR complex/FcgammaRIIB -0.048 0.19 -10000 0 -0.48 53 53
mol:PI-3-4-5-P3 -0.047 0.098 -10000 0 -0.36 12 12
ETS1 -0.01 0.086 0.37 4 -0.43 3 7
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.021 0.15 -10000 0 -0.4 40 40
B-cell antigen/BCR complex/LYN -0.035 0.17 -10000 0 -0.44 44 44
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.037 -10000 0 -0.69 1 1
RAC1 -0.038 0.14 0.35 2 -0.61 9 11
B-cell antigen/BCR complex/LYN/SYK -0.03 0.19 -10000 0 -0.48 44 44
CARD11 -0.03 0.11 0.34 3 -0.44 10 13
FCGR2B -0.008 0.15 -10000 0 -0.69 17 17
PPP3CA 0.026 0.005 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.02 0.1 0.44 15 -0.13 4 19
PTPRC -0.006 0.13 -10000 0 -0.69 13 13
PDPK1 -0.028 0.081 0.27 4 -0.26 12 16
PPP3CB 0.026 0.005 -10000 0 -10000 0 0
PPP3CC 0.026 0.004 -10000 0 -10000 0 0
POU2F2 0.02 0.032 0.18 9 -10000 0 9
Syndecan-4-mediated signaling events

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
PTK2 -0.001 0.1 -10000 0 -0.74 5 5
Syndecan-4/Syndesmos -0.021 0.15 -10000 0 -0.56 27 27
positive regulation of JNK cascade -0.044 0.19 -10000 0 -0.56 28 28
Syndecan-4/ADAM12 -0.021 0.16 -10000 0 -0.56 27 27
CCL5 -0.018 0.16 -10000 0 -0.69 21 21
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.025 0.007 -10000 0 -10000 0 0
ITGA5 0.026 0.006 -10000 0 -10000 0 0
SDCBP 0.026 0.004 -10000 0 -10000 0 0
PLG 0.009 0.029 -10000 0 -10000 0 0
ADAM12 -0.008 0.059 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.058 0.031 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.045 0.18 -10000 0 -0.61 26 26
Syndecan-4/CXCL12/CXCR4 -0.046 0.2 -10000 0 -0.6 28 28
Syndecan-4/Laminin alpha3 -0.03 0.17 -10000 0 -0.59 26 26
MDK -0.014 0.061 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.021 0.16 -10000 0 -0.56 27 27
Syndecan-4/Midkine -0.024 0.16 -10000 0 -0.56 26 26
FZD7 0.02 0.06 -10000 0 -0.54 4 4
Syndecan-4/FGFR1/FGF -0.001 0.15 -10000 0 -0.52 26 26
THBS1 0.016 0.036 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.029 0.16 -10000 0 -0.57 27 27
positive regulation of MAPKKK cascade -0.044 0.19 -10000 0 -0.56 28 28
Syndecan-4/TACI -0.1 0.22 -10000 0 -0.64 26 26
CXCR4 0.025 0.015 -10000 0 -10000 0 0
cell adhesion 0.001 0.079 0.2 3 -0.32 20 23
Syndecan-4/Dynamin -0.021 0.15 -10000 0 -0.55 27 27
Syndecan-4/TSP1 -0.019 0.16 -10000 0 -0.56 27 27
Syndecan-4/GIPC -0.021 0.15 -10000 0 -0.55 27 27
Syndecan-4/RANTES -0.041 0.2 -10000 0 -0.7 27 27
ITGB1 0.026 0.004 -10000 0 -10000 0 0
LAMA1 -0.025 0.18 -10000 0 -0.68 27 27
LAMA3 0 0.13 -10000 0 -0.69 12 12
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.003 0.21 0.74 14 -0.64 20 34
Syndecan-4/alpha-Actinin -0.019 0.15 -10000 0 -0.56 26 26
TFPI -0.017 0.17 -10000 0 -0.68 23 23
F2 0.014 0.022 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.038 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.06 0.19 -10000 0 -0.62 25 25
ACTN1 0.026 0.008 -10000 0 -10000 0 0
TNC -0.031 0.087 -10000 0 -0.69 3 3
Syndecan-4/CXCL12 -0.06 0.2 -10000 0 -0.62 28 28
FGF6 -0.016 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CXCL12 -0.055 0.23 -10000 0 -0.69 42 42
TNFRSF13B -0.14 0.29 -10000 0 -0.69 81 81
FGF2 0.026 0.004 -10000 0 -10000 0 0
FGFR1 0.024 0.037 -10000 0 -0.69 1 1
Syndecan-4/PI-4-5-P2 -0.037 0.15 -10000 0 -0.56 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.064 0.071 -10000 0 -0.17 2 2
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.025 0.023 -10000 0 -10000 0 0
vasculogenesis -0.018 0.15 -10000 0 -0.54 27 27
SDC4 -0.037 0.16 -10000 0 -0.59 27 27
Syndecan-4/Tenascin C -0.031 0.17 -10000 0 -0.59 27 27
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.019 0.16 -10000 0 -0.56 27 27
MMP9 -0.037 0.18 -10000 0 -0.69 27 27
Rac1/GTP 0.001 0.081 -10000 0 -0.32 20 20
cytoskeleton organization -0.02 0.15 -10000 0 -0.53 27 27
GIPC1 0.025 0.007 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.041 0.18 -10000 0 -0.58 27 27
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.031 0.065 -10000 0 -0.52 5 5
alphaV beta3 Integrin 0.036 0.088 -10000 0 -0.47 10 10
PTK2 0.006 0.15 0.44 11 -0.49 12 23
IGF1R 0.026 0.003 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.009 0.045 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.04 0.18 -10000 0 -0.55 41 41
VEGFA 0.023 0.052 -10000 0 -0.69 2 2
ILK -0.041 0.18 -10000 0 -0.54 42 42
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.042 0.17 -10000 0 -0.51 41 41
PTK2B 0.011 0.097 0.36 2 -0.45 12 14
alphaV/beta3 Integrin/JAM-A -0.006 0.16 -10000 0 -0.41 45 45
CBL 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.086 -10000 0 -0.45 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.072 0.23 -10000 0 -0.44 100 100
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.008 0.1 -10000 0 -0.25 52 52
alphaV/beta3 Integrin/Syndecan-1 0.037 0.088 -10000 0 -0.5 9 9
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.074 0.23 -10000 0 -0.44 101 101
PI4 Kinase 0.028 0.018 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/Osteopontin 0.016 0.14 -10000 0 -0.46 28 28
RPS6KB1 -0.13 0.19 0.42 2 -0.42 101 103
TLN1 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.052 0.14 -10000 0 -0.66 10 10
GPR124 0.026 0.004 -10000 0 -10000 0 0
MAPK1 -0.063 0.15 -10000 0 -0.59 18 18
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.022 0.13 -10000 0 -0.53 18 18
cell adhesion 0.032 0.082 -10000 0 -0.46 9 9
ANGPTL3 0.006 0.022 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.059 -10000 0 -0.45 5 5
IGF-1R heterotetramer 0.026 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.037 -10000 0 -0.69 1 1
ITGB3 0.007 0.11 -10000 0 -0.66 10 10
IGF1 -0.12 0.28 -10000 0 -0.69 74 74
RAC1 0.025 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.036 0.087 -10000 0 -0.5 9 9
apoptosis 0.024 0.037 -10000 0 -0.69 1 1
CD47 0.026 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.037 0.088 -10000 0 -0.5 9 9
VCL 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.033 0.099 -10000 0 -0.47 13 13
CSF1 0.018 0.074 -10000 0 -0.69 4 4
PIK3C2A -0.041 0.18 -10000 0 -0.54 42 42
PI4 Kinase/Pyk2 -0.023 0.14 -10000 0 -0.37 48 48
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.1 -10000 0 -0.46 13 13
FAK1/Vinculin 0.018 0.13 0.43 10 -0.41 9 19
alphaV beta3/Integrin/ppsTEM5 0.037 0.088 -10000 0 -0.5 9 9
RHOA 0.026 0.004 -10000 0 -10000 0 0
VTN -0.053 0.22 -10000 0 -0.69 40 40
BCAR1 0.025 0.006 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
F11R 0.015 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.04 0.089 -10000 0 -0.5 9 9
alphaV/beta3 Integrin/TGFBR2 0.036 0.089 -10000 0 -0.45 11 11
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.059 -10000 0 -0.42 5 5
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.082 -10000 0 -0.46 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.071 0.06 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.031 0.095 -10000 0 -0.46 12 12
SDC1 0.025 0.013 -10000 0 -10000 0 0
VAV3 0.011 0.07 0.36 1 -0.4 9 10
PTPN11 0.026 0.005 -10000 0 -10000 0 0
IRS1 -0.041 0.21 -10000 0 -0.69 35 35
FAK1/Paxillin 0.012 0.12 0.34 6 -0.4 10 16
cell migration 0.009 0.11 0.34 5 -0.37 9 14
ITGAV 0.024 0.037 -10000 0 -0.69 1 1
PI3K 0.005 0.15 -10000 0 -0.39 45 45
SPP1 -0.031 0.16 -10000 0 -0.69 19 19
KDR 0.02 0.064 -10000 0 -0.69 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.037 -10000 0 -0.69 1 1
COL4A3 0.003 0.13 -10000 0 -0.69 12 12
angiogenesis -0.057 0.16 -10000 0 -0.53 28 28
Rac1/GTP 0.021 0.062 -10000 0 -0.37 9 9
EDIL3 0.012 0.07 -10000 0 -0.69 3 3
cell proliferation 0.035 0.089 -10000 0 -0.45 11 11
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.016 0.2 -10000 0 -0.9 16 16
NCK1/PAK1/Dok-R -0.029 0.089 -10000 0 -0.42 16 16
NCK1/Dok-R -0.005 0.24 -10000 0 -1 17 17
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
mol:beta2-estradiol 0 0.046 0.23 14 -10000 0 14
RELA 0.026 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
F2 -0.01 0.054 0.26 11 -10000 0 11
TNIP2 0.026 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.007 0.22 -10000 0 -0.98 16 16
FN1 -0.071 0.06 -10000 0 -10000 0 0
PLD2 -0.028 0.23 -10000 0 -1.1 16 16
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB14 -0.001 0.14 -10000 0 -0.69 14 14
ELK1 -0.027 0.21 -10000 0 -0.97 16 16
GRB7 0.006 0.047 -10000 0 -10000 0 0
PAK1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.011 0.24 -10000 0 -1.1 16 16
CDKN1A -0.024 0.16 0.54 3 -0.62 16 19
ITGA5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.006 0.23 -10000 0 -1 17 17
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.009 0.18 0.57 8 -0.65 16 24
PLG -0.033 0.23 -10000 0 -1.1 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.015 0.19 -10000 0 -0.85 16 16
GRB2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ANGPT2 -0.1 0.21 -10000 0 -0.82 14 14
BMX -0.035 0.24 -10000 0 -1.1 16 16
ANGPT1 -0.046 0.26 -10000 0 -1.3 14 14
tube development -0.04 0.17 0.53 2 -0.7 16 18
ANGPT4 -0.033 0.2 -10000 0 -0.69 30 30
response to hypoxia -0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.031 0.26 -10000 0 -1.1 16 16
alpha5/beta1 Integrin 0.038 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.039 0.19 -10000 0 -0.8 16 16
mol:L-citrulline 0.009 0.18 0.57 8 -0.65 16 24
AGTR1 -0.25 0.35 -10000 0 -0.69 145 145
MAPK14 -0.026 0.24 -10000 0 -1.1 16 16
Tie2/SHP2 0.001 0.15 -10000 0 -1 5 5
TEK 0.008 0.15 -10000 0 -1.1 5 5
RPS6KB1 -0.01 0.2 0.52 1 -0.86 16 17
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.52 145 145
Tie2/Ang1/GRB2 -0.018 0.24 -10000 0 -1.1 16 16
MAPK3 -0.022 0.21 -10000 0 -0.99 16 16
MAPK1 -0.03 0.21 -10000 0 -1 16 16
Tie2/Ang1/GRB7 -0.017 0.24 -10000 0 -1.1 16 16
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.03 0.23 -10000 0 -1.1 16 16
PI3K -0.022 0.22 -10000 0 -1 16 16
FES -0.028 0.24 -10000 0 -1.1 16 16
Crk/Dok-R -0.006 0.23 -10000 0 -1 17 17
Tie2/Ang1/ABIN2 -0.017 0.24 -10000 0 -1.1 16 16
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.007 0.19 0.54 3 -0.8 16 19
STAT5A 0.025 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.013 0.2 0.53 1 -0.86 16 17
Tie2/Ang2 -0.057 0.22 -10000 0 -0.96 16 16
Tie2/Ang1 -0.028 0.25 -10000 0 -1.2 16 16
FOXO1 -0.004 0.19 0.6 3 -0.8 16 19
ELF1 0.029 0.041 -10000 0 -0.69 1 1
ELF2 -0.025 0.23 -10000 0 -1.1 16 16
mol:Choline -0.025 0.22 -10000 0 -1 16 16
cell migration -0.014 0.056 -10000 0 -0.24 16 16
FYN -0.048 0.19 0.52 1 -0.81 16 17
DOK2 0.019 0.056 -10000 0 -0.69 2 2
negative regulation of cell cycle -0.02 0.15 0.53 3 -0.56 16 19
ETS1 0.024 0.049 -10000 0 -0.24 11 11
PXN 0 0.18 0.56 6 -0.7 16 22
ITGB1 0.026 0.004 -10000 0 -10000 0 0
NOS3 0.002 0.19 0.58 7 -0.75 16 23
RAC1 0.025 0.006 -10000 0 -10000 0 0
TNF -0.059 0.24 -10000 0 -0.69 43 43
MAPKKK cascade -0.025 0.22 -10000 0 -1 16 16
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.02 0.24 -10000 0 -1.1 16 16
NCK1 0.026 0.004 -10000 0 -10000 0 0
vasculogenesis 0.012 0.16 0.54 9 -0.58 16 25
mol:Phosphatidic acid -0.025 0.22 -10000 0 -1 16 16
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.009 0.18 0.57 8 -0.65 16 24
Rac1/GTP -0.009 0.18 -10000 0 -0.8 16 16
MMP2 -0.031 0.23 -10000 0 -1.1 16 16
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.016 0.13 -10000 0 -0.46 21 21
MAP4K1 0.004 0.095 -10000 0 -0.69 6 6
MAP3K8 0.019 0.074 -10000 0 -0.69 4 4
PRKCB 0.007 0.057 -10000 0 -0.69 1 1
DBNL 0.025 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 -0.005 0.096 -10000 0 -0.33 24 24
JUN -0.075 0.2 0.42 2 -0.45 43 45
MAP3K7 -0.005 0.096 -10000 0 -0.33 24 24
GRAP2 -0.018 0.15 -10000 0 -0.56 24 24
CRK 0.025 0.007 -10000 0 -10000 0 0
MAP2K4 -0.007 0.11 0.38 2 -0.34 25 27
LAT 0.018 0.068 -10000 0 -0.61 4 4
LCP2 0.022 0.023 -10000 0 -10000 0 0
MAPK8 0.007 0.11 -10000 0 -0.55 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.003 0.095 -10000 0 -0.35 21 21
LAT/GRAP2/SLP76/HPK1/HIP-55 0.026 0.13 -10000 0 -0.45 20 20
Ceramide 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
SPHK2 0.015 0.005 -10000 0 -10000 0 0
MAP4K4 -0.016 0.11 -10000 0 -0.54 9 9
BAG4 0.024 0.037 -10000 0 -0.69 1 1
PKC zeta/ceramide -0.018 0.097 -10000 0 -0.31 23 23
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 -0.011 0.15 -10000 0 -0.64 19 19
BAX -0.012 0.075 -10000 0 -0.34 15 15
RIPK1 0.027 0.002 -10000 0 -10000 0 0
AKT1 0.028 0.15 0.78 13 -10000 0 13
BAD -0.031 0.088 0.18 1 -0.3 21 22
SMPD1 -0.012 0.092 0.29 6 -0.23 45 51
RB1 -0.031 0.089 -10000 0 -0.38 14 14
FADD/Caspase 8 -0.008 0.11 -10000 0 -0.53 9 9
MAP2K4 -0.017 0.068 0.21 3 -0.33 7 10
NSMAF 0.026 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.022 0.08 -10000 0 -0.4 9 9
EGF -0.072 0.24 -10000 0 -0.68 51 51
mol:ceramide -0.035 0.098 -10000 0 -0.31 26 26
MADD 0.026 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.014 0.028 -10000 0 -0.52 1 1
ASAH1 0.024 0.037 -10000 0 -0.69 1 1
negative regulation of cell cycle -0.031 0.087 -10000 0 -0.38 14 14
cell proliferation -0.054 0.14 -10000 0 -0.33 69 69
BID -0.13 0.28 -10000 0 -0.6 88 88
MAP3K1 -0.026 0.076 -10000 0 -0.37 11 11
EIF2A -0.028 0.077 -10000 0 -0.45 8 8
TRADD 0.025 0.006 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.068 -10000 0 -0.34 7 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.04 0.083 -10000 0 -0.35 10 10
Cathepsin D/ceramide -0.016 0.092 -10000 0 -0.29 23 23
FADD -0.016 0.12 -10000 0 -0.52 10 10
KSR1 -0.024 0.085 0.18 6 -0.38 12 18
MAPK8 -0.014 0.082 -10000 0 -0.38 11 11
PRKRA -0.033 0.091 -10000 0 -0.35 17 17
PDGFA 0.025 0.006 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
IGF1 -0.12 0.28 -10000 0 -0.69 74 74
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.035 0.097 -10000 0 -0.31 26 26
CTSD 0.026 0.005 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.057 0.16 -10000 0 -0.36 69 69
PRKCD 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.014 0.028 -10000 0 -0.52 1 1
RelA/NF kappa B1 0.038 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.54 10 10
TNFR1A/BAG4/TNF-alpha -0.006 0.16 -10000 0 -0.45 43 43
mol:Sphingosine-1-phosphate 0.015 0.005 -10000 0 -10000 0 0
MAP2K1 -0.021 0.075 -10000 0 -0.38 9 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
CYCS -0.007 0.068 0.17 17 -0.25 13 30
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.037 0.03 -10000 0 -0.52 1 1
EIF2AK2 -0.03 0.084 -10000 0 -0.5 8 8
TNF-alpha/TNFR1A/FAN -0.005 0.16 -10000 0 -0.45 42 42
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.07 -10000 0 -0.55 1 1
MAP2K2 -0.014 0.063 -10000 0 -0.36 4 4
SMPD3 -0.019 0.1 -10000 0 -0.35 19 19
TNF -0.057 0.23 -10000 0 -0.69 42 42
PKC zeta/PAR4 0.037 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.015 0.11 0.26 50 -0.28 12 62
NF kappa B1/RelA/I kappa B alpha 0.073 0.022 -10000 0 -10000 0 0
AIFM1 -0.011 0.084 0.17 17 -0.27 19 36
BCL2 -0.015 0.17 -10000 0 -0.68 22 22
Signaling events mediated by PTP1B

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
PDGFRB 0.026 0.006 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0 0.12 0.31 1 -0.37 20 21
PTP1B/AKT1 0.006 0.072 0.31 2 -0.35 3 5
FYN 0.026 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.089 0.35 10 -0.3 6 16
EGFR 0.01 0.084 -10000 0 -0.7 5 5
EGF/EGFR -0.036 0.16 0.23 1 -0.4 54 55
CSF1 0.018 0.074 -10000 0 -0.69 4 4
AKT1 0.026 0.006 -10000 0 -10000 0 0
INSR 0.025 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.12 0.34 6 -0.4 17 23
Insulin Receptor/Insulin 0.016 0.068 -10000 0 -0.32 3 3
HCK 0.018 0.032 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 0.009 0.095 0.35 14 -0.35 3 17
EGF -0.072 0.25 -10000 0 -0.69 51 51
YES1 0.026 0.005 -10000 0 -10000 0 0
CAV1 -0.001 0.12 0.45 11 -0.39 5 16
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.023 0.13 0.32 1 -0.38 36 37
cell migration -0.003 0.089 0.3 6 -0.35 10 16
STAT3 0.025 0.007 -10000 0 -10000 0 0
PRLR -0.012 0.15 -10000 0 -0.69 17 17
ITGA2B -0.057 0.23 -10000 0 -0.69 43 43
CSF1R 0.024 0.016 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.004 0.12 -10000 0 -0.52 17 17
FGR 0.024 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.006 0.073 0.27 3 -0.3 5 8
Crk/p130 Cas 0.011 0.071 -10000 0 -0.34 3 3
DOK1 0.015 0.096 0.42 11 -0.33 3 14
JAK2 -0.006 0.12 0.33 7 -0.38 23 30
Jak2/Leptin Receptor/Leptin -0.021 0.15 -10000 0 -0.52 23 23
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.003 0.09 0.35 10 -0.31 6 16
LYN 0.026 0.004 -10000 0 -10000 0 0
CDH2 -0.067 0.14 -10000 0 -0.65 16 16
SRC 0.025 0.055 0.29 3 -0.42 2 5
ITGB3 0.006 0.11 -10000 0 -0.66 10 10
CAT1/PTP1B -0.061 0.16 0.43 12 -0.36 28 40
CAPN1 0.026 0.005 -10000 0 -10000 0 0
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.022 0.073 -10000 0 -0.49 1 1
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.022 0.15 -10000 0 -0.55 23 23
negative regulation of transcription -0.004 0.12 0.33 7 -0.38 23 30
FCGR2A 0.017 0.046 -10000 0 -0.69 1 1
FER 0.021 0.053 -10000 0 -0.7 2 2
alphaIIb/beta3 Integrin -0.04 0.2 -10000 0 -0.55 49 49
BLK -0.2 0.32 -10000 0 -0.68 112 112
Insulin Receptor/Insulin/Shc 0.041 0.018 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
LEPR 0.017 0.075 -10000 0 -0.61 5 5
BCAR1 0.025 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.006 -10000 0 -10000 0 0
TRPV6 -0.094 0.18 0.42 3 -0.46 31 34
PRL -0.006 0.02 -10000 0 -10000 0 0
SOCS3 -0.074 0.36 -10000 0 -1.3 29 29
SPRY2 0.025 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.15 -10000 0 -0.46 34 34
CSF1/CSF1R 0.01 0.084 0.28 1 -0.4 6 7
Ras protein signal transduction 0.021 0.093 0.41 18 -10000 0 18
IRS1 -0.041 0.21 -10000 0 -0.69 35 35
INS 0.005 0.017 -10000 0 -10000 0 0
LEP 0 0.032 -10000 0 -10000 0 0
STAT5B 0.006 0.095 0.33 10 -0.29 10 20
STAT5A 0.006 0.095 0.33 10 -0.29 10 20
GRB2 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.07 0.28 1 -0.35 3 4
CSN2 0.002 0.065 0.81 1 -10000 0 1
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
LAT 0.019 0.083 0.3 3 -0.46 8 11
YBX1 0.032 0.007 -10000 0 -10000 0 0
LCK 0.011 0.079 -10000 0 -0.69 4 4
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.03 0.066 -10000 0 -10000 0 0
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.011 0.098 -10000 0 -0.55 6 6
alphaM/beta2 Integrin/GPIbA 0.004 0.11 -10000 0 -0.49 11 11
alphaM/beta2 Integrin/proMMP-9 -0.019 0.16 -10000 0 -0.52 28 28
PLAUR -0.018 0.062 -10000 0 -10000 0 0
HMGB1 0.005 0.038 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.014 0.086 -10000 0 -0.61 3 3
AGER -0.056 0.21 -10000 0 -0.71 32 32
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.017 0.034 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.051 0.21 -10000 0 -0.48 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.038 0.19 -10000 0 -0.69 27 27
CYR61 -0.19 0.33 -10000 0 -0.69 112 112
TLN1 0.025 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.09 -10000 0 -0.38 6 6
RHOA 0.026 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.012 0.091 -10000 0 -0.69 6 6
MYH2 -0.033 0.11 -10000 0 -0.42 9 9
MST1R 0.019 0.066 -10000 0 -0.69 3 3
leukocyte activation during inflammatory response 0.016 0.08 -10000 0 -0.54 3 3
APOB 0.009 0.033 -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 0.018 0.068 -10000 0 -0.61 4 4
JAM3 0.026 0.005 -10000 0 -10000 0 0
GP1BA 0.006 0.1 -10000 0 -0.62 9 9
alphaM/beta2 Integrin/CTGF -0.052 0.19 -10000 0 -0.48 55 55
alphaM/beta2 Integrin -0.024 0.093 -10000 0 -0.33 14 14
JAM3 homodimer 0.026 0.005 -10000 0 -10000 0 0
ICAM2 0.025 0.007 -10000 0 -10000 0 0
ICAM1 -0.022 0.063 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.025 0.095 -10000 0 -0.33 15 15
cell adhesion 0.003 0.11 -10000 0 -0.49 11 11
NFKB1 -0.14 0.28 0.38 1 -0.5 119 120
THY1 0.025 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.027 0.019 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.028 0.095 -10000 0 -0.5 6 6
IL6 -0.24 0.41 -10000 0 -0.96 83 83
ITGB2 -0.008 0.061 -10000 0 -0.72 1 1
elevation of cytosolic calcium ion concentration 0.025 0.1 -10000 0 -0.71 2 2
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.097 -10000 0 -0.53 6 6
JAM2 0.018 0.074 -10000 0 -0.69 4 4
alphaM/beta2 Integrin/ICAM1 0.038 0.11 -10000 0 -0.6 5 5
alphaM/beta2 Integrin/uPA/Plg 0.02 0.098 -10000 0 -0.57 3 3
RhoA/GTP -0.029 0.11 -10000 0 -0.34 26 26
positive regulation of phagocytosis -0.007 0.097 -10000 0 -0.6 3 3
Ron/MSP 0.032 0.059 -10000 0 -0.52 4 4
alphaM/beta2 Integrin/uPAR/uPA 0.028 0.11 -10000 0 -0.72 2 2
alphaM/beta2 Integrin/uPAR 0.014 0.094 -10000 0 -0.76 2 2
PLAU -0.033 0.066 -10000 0 -10000 0 0
PLAT 0.02 0.055 -10000 0 -0.69 2 2
actin filament polymerization -0.031 0.1 -10000 0 -0.4 9 9
MST1 0.024 0.037 -10000 0 -0.69 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.021 0.083 -10000 0 -0.55 3 3
TNF -0.18 0.36 0.38 1 -0.93 57 58
RAP1B 0.026 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.013 0.099 -10000 0 -0.61 3 3
fibrinolysis 0.018 0.096 -10000 0 -0.56 3 3
HCK 0.018 0.032 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.025 0.095 -10000 0 -0.33 15 15
VTN -0.053 0.22 -10000 0 -0.69 40 40
alphaM/beta2 Integrin/CYR61 -0.13 0.24 -10000 0 -0.48 112 112
LPA -0.006 0.024 -10000 0 -10000 0 0
LRP1 0.024 0.037 -10000 0 -0.69 1 1
cell migration -0.029 0.16 -10000 0 -0.5 28 28
FN1 -0.071 0.06 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.015 0.087 -10000 0 -0.61 3 3
MPO 0.013 0.074 -10000 0 -0.69 4 4
KNG1 -0.003 0.033 -10000 0 -10000 0 0
RAP1/GDP 0.034 0.009 -10000 0 -10000 0 0
ROCK1 -0.027 0.11 -10000 0 -0.42 9 9
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.012 0.016 -10000 0 -10000 0 0
CTGF -0.078 0.25 -10000 0 -0.67 56 56
alphaM/beta2 Integrin/Hck 0.012 0.09 -10000 0 -0.61 3 3
ITGAM -0.008 0.072 -10000 0 -0.57 3 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.021 0.11 -10000 0 -0.56 8 8
HP -0.016 0.096 -10000 0 -0.69 5 5
leukocyte adhesion -0.042 0.18 -10000 0 -0.53 21 21
SELP 0.012 0.091 -10000 0 -0.69 6 6
ceramide 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
MAP4K4 -0.017 0.12 -10000 0 -0.48 12 12
BAG4 0.024 0.037 -10000 0 -0.69 1 1
BAD 0.007 0.072 0.37 8 -10000 0 8
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 -0.011 0.15 -10000 0 -0.64 19 19
BAX 0.01 0.072 0.28 15 -10000 0 15
EnzymeConsortium:3.1.4.12 0.002 0.042 0.16 10 -0.11 12 22
IKBKB -0.015 0.12 0.33 1 -0.47 11 12
MAP2K2 0.016 0.099 0.34 20 -0.31 1 21
MAP2K1 0.011 0.088 0.32 17 -0.31 1 18
SMPD1 0.005 0.049 0.22 8 -0.14 5 13
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.011 0.12 -10000 0 -0.49 11 11
MAP2K4 0.017 0.1 0.38 20 -10000 0 20
protein ubiquitination -0.011 0.13 0.44 4 -0.48 11 15
EnzymeConsortium:2.7.1.37 0.017 0.11 0.39 21 -0.32 1 22
response to UV 0 0.002 0.007 22 -0.002 2 24
RAF1 0.012 0.091 0.31 19 -0.33 1 20
CRADD 0.026 0.005 -10000 0 -10000 0 0
mol:ceramide 0.004 0.062 0.26 9 -0.16 12 21
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.008 -10000 0 -10000 0 0
MADD 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.082 0.34 14 -10000 0 14
TRADD 0.025 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.092 0.34 17 -0.3 1 18
MAPK1 -0.005 0.097 0.34 15 -0.27 3 18
p50/RELA/I-kappa-B-alpha 0.038 0.009 -10000 0 -10000 0 0
FADD -0.016 0.12 -10000 0 -0.48 12 12
KSR1 0.011 0.085 0.28 20 -0.34 1 21
MAPK8 0.016 0.11 0.39 19 -0.35 2 21
TRAF2 0.024 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 12 -10000 0 12
CHUK -0.015 0.12 0.33 1 -0.46 11 12
TNF R/SODD 0.037 0.03 -10000 0 -0.52 1 1
TNF -0.057 0.23 -10000 0 -0.69 42 42
CYCS 0.017 0.084 0.26 21 -10000 0 21
IKBKG -0.014 0.12 0.37 1 -0.46 11 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.016 0.13 -10000 0 -0.51 12 12
RELA 0.026 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.015 0.083 0.27 18 -0.17 2 20
TNF/TNF R/SODD -0.006 0.16 -10000 0 -0.45 43 43
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 12 -10000 0 12
CASP8 0.011 0.12 -10000 0 -0.73 8 8
NSMAF -0.017 0.12 -10000 0 -0.48 12 12
response to hydrogen peroxide 0 0.002 0.007 22 -0.002 2 24
BCL2 -0.015 0.17 -10000 0 -0.68 22 22
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.03 0.12 0.45 9 -10000 0 9
IL27/IL27R/JAK1 0.006 0.16 -10000 0 -0.54 5 5
TBX21 -0.054 0.17 0.38 3 -0.57 21 24
IL12B 0.008 0.057 -10000 0 -0.69 2 2
IL12A -0.044 0.15 -10000 0 -0.52 35 35
IL6ST -0.046 0.21 -10000 0 -0.7 35 35
IL27RA/JAK1 0.019 0.051 0.54 1 -10000 0 1
IL27 0.01 0.026 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.057 0.14 -10000 0 -0.5 3 3
T-helper 2 cell differentiation 0.03 0.12 0.45 9 -10000 0 9
T cell proliferation during immune response 0.03 0.12 0.45 9 -10000 0 9
MAPKKK cascade -0.03 0.12 -10000 0 -0.45 9 9
STAT3 0.025 0.007 -10000 0 -10000 0 0
STAT2 0.026 0.006 -10000 0 -10000 0 0
STAT1 0.022 0.022 -10000 0 -10000 0 0
IL12RB1 0.006 0.068 -10000 0 -0.59 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.043 0.18 0.51 9 -0.55 14 23
IL27/IL27R/JAK2/TYK2 -0.03 0.12 -10000 0 -0.46 9 9
positive regulation of T cell mediated cytotoxicity -0.03 0.12 -10000 0 -0.45 9 9
STAT1 (dimer) -0.003 0.2 0.52 8 -0.66 7 15
JAK2 0.02 0.019 -10000 0 -10000 0 0
JAK1 0.026 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.02 0.12 -10000 0 -0.44 9 9
T cell proliferation -0.11 0.2 -10000 0 -0.43 79 79
IL12/IL12R/TYK2/JAK2 -0.059 0.22 -10000 0 -0.78 22 22
IL17A -0.058 0.14 -10000 0 -0.5 3 3
mast cell activation 0.03 0.12 0.45 9 -10000 0 9
IFNG -0.013 0.049 0.096 2 -0.13 48 50
T cell differentiation -0.004 0.008 0.013 1 -0.022 42 43
STAT3 (dimer) -0.02 0.12 -10000 0 -0.44 9 9
STAT5A (dimer) -0.02 0.12 -10000 0 -0.45 8 8
STAT4 (dimer) -0.025 0.14 0.33 1 -0.44 14 15
STAT4 0.001 0.1 -10000 0 -0.59 9 9
T cell activation -0.008 0.004 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.01 0.14 -10000 0 -0.5 5 5
GATA3 -0.071 0.32 -10000 0 -1.4 21 21
IL18 -0.01 0.071 -10000 0 -0.49 7 7
positive regulation of mast cell cytokine production -0.02 0.12 -10000 0 -0.43 9 9
IL27/EBI3 -0.007 0.061 -10000 0 -0.28 1 1
IL27RA 0.001 0.024 -10000 0 -10000 0 0
IL6 -0.13 0.29 -10000 0 -0.69 77 77
STAT5A 0.025 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.012 0.023 -10000 0 -10000 0 0
IL1B -0.031 0.14 -10000 0 -0.52 26 26
EBI3 -0.044 0.067 -10000 0 -0.39 1 1
TNF -0.054 0.17 -10000 0 -0.52 42 42
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.015 0.005 -10000 0 -10000 0 0
mol:DAG -0.027 0.13 -10000 0 -0.41 40 40
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.034 -10000 0 -0.41 2 2
CaM/Ca2+ -0.011 0.13 -10000 0 -0.39 40 40
HIF1A 0.032 0.006 -10000 0 -10000 0 0
GAB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.024 0.13 -10000 0 -0.53 3 3
PLCG1 -0.027 0.13 -10000 0 -0.41 40 40
NOS3 -0.02 0.12 -10000 0 -0.4 2 2
CBL 0.026 0.005 -10000 0 -10000 0 0
mol:NO -0.014 0.13 0.46 3 -0.39 2 5
FLT1 0.021 0.006 -10000 0 -10000 0 0
PGF -0.052 0.22 -10000 0 -0.68 41 41
VEGFR1 homodimer/NRP2/VEGFR121 0.046 0.038 -10000 0 -0.41 2 2
CALM1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
eNOS/Hsp90 -0.001 0.12 -10000 0 -10000 0 0
endothelial cell proliferation -0.047 0.16 0.36 2 -0.45 39 41
mol:Ca2+ -0.026 0.13 -10000 0 -0.41 40 40
MAPK3 -0.05 0.15 0.35 2 -0.39 53 55
MAPK1 -0.052 0.14 0.35 1 -0.47 14 15
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.052 0.22 -10000 0 -0.68 41 41
PRKACA 0.025 0.007 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.01 0.1 -10000 0 -0.69 8 8
VEGFA homodimer 0.023 0.052 -10000 0 -0.69 2 2
VEGFR1 homodimer/VEGFA homodimer 0.031 0.037 -10000 0 -0.45 2 2
platelet activating factor biosynthetic process -0.054 0.14 -10000 0 -0.69 4 4
PI3K 0.011 0.14 -10000 0 -0.39 40 40
PRKCA -0.051 0.15 -10000 0 -0.41 55 55
PRKCB -0.038 0.12 -10000 0 -0.38 41 41
VEGFR1 homodimer/PLGF homodimer -0.018 0.15 -10000 0 -0.45 40 40
VEGFA 0.023 0.052 -10000 0 -0.69 2 2
VEGFB 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.027 0.13 -10000 0 -0.41 40 40
RASA1 0.02 0.014 -10000 0 -10000 0 0
NRP2 0.013 0.04 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.007 0.14 0.45 3 -0.57 2 5
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.009 0.14 -10000 0 -0.39 40 40
mol:L-citrulline -0.014 0.13 0.46 3 -0.39 2 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.057 0.039 -10000 0 -0.39 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.037 -10000 0 -0.41 2 2
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.021 0.14 -10000 0 -0.37 40 40
PDPK1 -0.02 0.13 0.34 3 -0.73 1 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.037 -10000 0 -0.41 2 2
mol:NADP -0.014 0.13 0.46 3 -0.39 2 5
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.055 0.038 -10000 0 -0.39 2 2
VEGFR1 homodimer/NRP2 0.035 0.015 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.002 0.041 -10000 0 -0.45 3 3
ADCY5 -0.064 0.16 -10000 0 -0.45 56 56
ADCY6 0.002 0.041 -10000 0 -0.45 3 3
ADCY7 0.001 0.041 -10000 0 -0.45 3 3
ADCY1 -0.002 0.059 -10000 0 -0.46 6 6
ADCY2 -0.042 0.14 -10000 0 -0.46 36 36
ADCY3 0.002 0.041 -10000 0 -0.45 3 3
ADCY8 -0.042 0.048 -10000 0 -0.5 3 3
PRKCE 0.004 0.047 -10000 0 -0.52 3 3
ADCY9 0.001 0.041 -10000 0 -0.45 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.035 0.1 0.38 6 -0.35 13 19
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.029 0.075 -9999 0 -0.39 11 11
RGS9BP -0.022 0.18 -9999 0 -0.68 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.043 0.21 -9999 0 -0.67 36 36
mol:Na + 0.023 0.026 -9999 0 -10000 0 0
mol:ADP -0.047 0.15 -9999 0 -0.52 35 35
GNAT2 0.016 0.02 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.031 0.19 -9999 0 -0.46 58 58
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.01 -9999 0 -10000 0 0
GRK7 0.005 0.022 -9999 0 -10000 0 0
CNGB3 -0.007 0.018 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.025 -9999 0 -10000 0 0
Cone PDE6 -0.012 0.18 -9999 0 -0.42 57 57
Cone Metarhodopsin II -0.013 0.13 -9999 0 -0.41 36 36
Na + (4 Units) 0.034 0.028 -9999 0 -10000 0 0
GNAT2/GDP -0.016 0.17 -9999 0 -0.41 55 55
GNB5 0.026 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) -0.002 0.025 -9999 0 -10000 0 0
Cone Transducin 0.032 0.079 -9999 0 -0.42 11 11
SLC24A2 -0.006 0.028 -9999 0 -10000 0 0
GNB3/GNGT2 0.02 0.095 -9999 0 -0.52 11 11
GNB3 0.005 0.12 -9999 0 -0.69 11 11
GNAT2/GTP 0.017 0.008 -9999 0 -10000 0 0
CNGA3 0.01 0.043 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.027 -9999 0 -10000 0 0
mol:Pi -0.031 0.19 -9999 0 -0.46 58 58
Cone CNG Channel 0.05 0.02 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.006 0.027 -9999 0 -10000 0 0
RGS9 -0.045 0.21 -9999 0 -0.69 36 36
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.024 0.012 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.005 0.02 -9999 0 -10000 0 0
p75(NTR)-mediated 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
Sortilin/TRAF6 0.036 0.031 -10000 0 -0.52 1 1
Necdin/E2F1 0.003 0.065 -10000 0 -0.57 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.051 0.1 -10000 0 -0.42 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.19 0.26 -10000 0 -0.46 173 173
NT-4/5 (dimer)/p75(NTR) -0.011 0.14 -10000 0 -0.54 22 22
IKBKB 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.002 0.1 0.36 1 -0.42 16 17
IKBKG 0.024 0.008 -10000 0 -10000 0 0
BDNF 0.005 0.12 -10000 0 -0.69 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.1 -10000 0 -0.46 14 14
FURIN 0.026 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.022 0.12 -10000 0 -0.43 24 24
LINGO1 0.021 0.027 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.024 -10000 0 -0.36 1 1
proBDNF (dimer) 0.005 0.12 -10000 0 -0.69 10 10
NTRK1 0.011 0.027 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.021 0.14 0.49 9 -0.51 2 11
IRAK1 0.024 0.008 -10000 0 -10000 0 0
SHC1 -0.011 0.1 -10000 0 -0.47 15 15
ARHGDIA 0.025 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.042 0.1 -10000 0 -0.44 15 15
MAGEH1 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.043 0.11 -10000 0 -0.44 16 16
Mammalian IAPs/DIABLO 0.043 0.096 -10000 0 -0.4 15 15
proNGF (dimer) 0.02 0.064 -10000 0 -0.69 3 3
MAGED1 0.025 0.007 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.006 0.11 -10000 0 -0.66 9 9
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.007 0.094 -10000 0 -0.42 15 15
NGF 0.02 0.064 -10000 0 -0.69 3 3
cell cycle arrest 0.054 0.14 0.46 13 -0.4 15 28
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.013 0.076 -10000 0 -0.33 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.019 0.13 -10000 0 -0.47 23 23
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.031 0.11 -10000 0 -0.48 15 15
PSENEN 0.025 0.006 -10000 0 -10000 0 0
mol:ceramide -0.001 0.1 -10000 0 -0.44 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.016 0.063 -10000 0 -0.4 3 3
p75(NTR)/beta APP 0.002 0.11 -10000 0 -0.52 14 14
BEX1 -0.29 0.35 -10000 0 -0.69 162 162
mol:GDP -0.021 0.099 -10000 0 -0.46 16 16
NGF (dimer) 0.041 0.12 -10000 0 -0.42 20 20
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.033 0.097 -10000 0 -0.43 14 14
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.027 0.094 -10000 0 -0.42 15 15
MYD88 0.026 0.004 -10000 0 -10000 0 0
CHUK 0.026 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.031 0.11 -10000 0 -0.48 15 15
RHOB 0.024 0.037 -10000 0 -0.69 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.05 -10000 0 -10000 0 0
NT3 (dimer) -0.019 0.16 -10000 0 -0.69 20 20
TP53 -0.008 0.1 0.31 1 -0.38 21 22
PRDM4 -0.004 0.099 -10000 0 -0.44 15 15
BDNF (dimer) 0.033 0.14 -10000 0 -0.45 27 27
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.045 0.1 -10000 0 -0.42 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.043 0.11 -10000 0 -0.44 16 16
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
MAPK10 0.01 0.12 0.4 11 -0.4 12 23
DIABLO 0.026 0.006 -10000 0 -10000 0 0
SMPD2 -0.001 0.1 -10000 0 -0.44 15 15
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.031 0.11 -10000 0 -0.48 15 15
PSEN1 0.026 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.031 0.16 -10000 0 -0.53 33 33
MAPK8 0.008 0.12 0.4 11 -0.42 13 24
MAPK9 0.004 0.11 0.36 7 -0.4 12 19
APAF1 0.026 0.005 -10000 0 -10000 0 0
NTF3 -0.019 0.16 -10000 0 -0.69 20 20
NTF4 0.006 0.11 -10000 0 -0.66 9 9
NDN 0.022 0.052 -10000 0 -0.69 2 2
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.1 -10000 0 -0.42 15 15
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.049 -10000 0 -0.8 1 1
RhoA-B-C/GTP 0.03 0.11 -10000 0 -0.48 15 15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.044 0.12 -10000 0 -0.4 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.035 0.12 -10000 0 -0.42 22 22
PRKACB 0.026 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.02 0.095 -10000 0 -0.52 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.011 0.15 -10000 0 -0.64 19 19
BIRC2 0.026 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.07 0.15 0.54 9 -0.41 15 24
BAD 0.026 0.16 0.49 21 -0.4 14 35
RIPK2 0.026 0.004 -10000 0 -10000 0 0
NGFR -0.019 0.14 -10000 0 -0.69 14 14
CYCS 0.004 0.11 0.36 9 -0.42 15 24
ADAM17 0.024 0.037 -10000 0 -0.69 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.042 0.11 -10000 0 -0.44 16 16
BCL2L11 0.026 0.16 0.48 21 -0.4 14 35
BDNF (dimer)/p75(NTR) -0.013 0.14 -10000 0 -0.51 24 24
PI3K 0.043 0.11 -10000 0 -0.44 16 16
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.045 0.1 -10000 0 -0.44 15 15
NDNL2 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.026 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.002 0.12 -10000 0 -0.54 16 16
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.042 0.1 -10000 0 -0.44 15 15
TRAF6 0.024 0.037 -10000 0 -0.69 1 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
PLG -0.012 0.016 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.011 0.11 -10000 0 -0.42 23 23
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.025 0.007 -10000 0 -10000 0 0
CASP3 0.029 0.15 0.47 22 -0.37 13 35
E2F1 -0.015 0.062 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.046 0.08 -10000 0 -0.48 3 3
NGF (dimer)/TRKA 0.027 0.054 -10000 0 -0.53 3 3
MMP7 -0.071 0.15 -10000 0 -0.68 19 19
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.051 0.1 -10000 0 -0.42 16 16
MMP3 -0.016 0.043 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.017 0.1 -10000 0 -0.56 6 6
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.034 0.12 0.87 5 -10000 0 5
VDR 0.025 0.009 -10000 0 -10000 0 0
FAM120B 0.026 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.001 0.1 -10000 0 -0.38 5 5
RXRs/LXRs/DNA/Oxysterols -0.007 0.15 -10000 0 -0.41 40 40
MED1 0.025 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.021 0.06 -10000 0 -0.29 13 13
RXRs/NUR77 -0.094 0.24 -10000 0 -0.46 103 103
RXRs/PPAR -0.014 0.081 -10000 0 -0.41 7 7
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.047 0.074 -10000 0 -0.38 10 10
RARA 0.025 0.007 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.009 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.028 0.072 -10000 0 -0.38 10 10
RARG 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.046 0.12 0.55 19 -10000 0 19
RARs/THRs/DNA/SMRT 0.021 0.06 -10000 0 -0.29 13 13
THRA 0.025 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.044 0.095 -10000 0 -0.39 3 3
NR1H4 -0.005 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.064 0.11 -10000 0 -0.47 2 2
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.022 0.026 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.054 0.077 -10000 0 -0.47 1 1
NR4A1 -0.19 0.33 -10000 0 -0.69 114 114
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.007 0.051 -10000 0 -0.32 1 1
RXRG -0.09 0.068 -10000 0 -0.54 3 3
RXR alpha/CCPG 0.031 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.025 -10000 0 -10000 0 0
RXRB 0.022 0.026 -10000 0 -10000 0 0
THRB 0.019 0.074 -10000 0 -0.69 4 4
PPARG 0.016 0.083 -10000 0 -0.69 5 5
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.095 0.37 -10000 0 -1.1 43 43
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.006 0.15 -10000 0 -0.41 40 40
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.007 0.12 -10000 0 -0.69 10 10
RXRs/NUR77/BCL2 -0.1 0.17 -10000 0 -0.34 117 117
SREBF1 -0.008 0.13 -10000 0 -0.6 2 2
RXRs/RXRs/DNA/9cRA 0.044 0.095 -10000 0 -0.39 3 3
ABCA1 -0.008 0.14 -10000 0 -0.6 2 2
RARs/THRs 0.057 0.089 -10000 0 -0.4 13 13
RXRs/FXR 0.055 0.082 -10000 0 -0.49 1 1
BCL2 -0.015 0.17 -10000 0 -0.68 22 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.026 0.38 1 -10000 0 1
HSPA8 0.023 0.022 -10000 0 -0.38 1 1
SMAD3/SMAD4/ER alpha -0.004 0.13 -10000 0 -0.49 16 16
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.19 0.51 -10000 0 -1.4 55 55
NKX2-5 0.017 0.014 -10000 0 -10000 0 0
muscle cell differentiation -0.009 0.081 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.036 0.095 -10000 0 -10000 0 0
SMAD4 -0.009 0.072 -10000 0 -0.26 1 1
CBFB 0.025 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.055 0.062 -10000 0 -0.46 2 2
SMAD3/SMAD4/VDR 0.047 0.075 -10000 0 -10000 0 0
MYC 0.013 0.098 -10000 0 -0.69 7 7
CDKN2B -0.014 0.1 -10000 0 -0.49 1 1
AP1 -0.21 0.42 -10000 0 -0.79 117 117
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.025 0.059 -10000 0 -0.68 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.008 0.04 -10000 0 -10000 0 0
SP3 0.028 0.005 -10000 0 -10000 0 0
CREB1 0.026 0.005 -10000 0 -10000 0 0
FOXH1 0.006 0.05 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.018 0.079 -10000 0 -10000 0 0
GATA3 -0.013 0.16 -10000 0 -0.64 21 21
SKI/SIN3/HDAC complex/NCoR1 0.023 0.063 -10000 0 -0.76 2 2
MEF2C/TIF2 -0.025 0.13 -10000 0 -0.39 21 21
endothelial cell migration -0.023 0.087 1.3 1 -10000 0 1
MAX 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.024 0.007 -10000 0 -10000 0 0
RBBP4 0.025 0.005 -10000 0 -10000 0 0
RUNX2 -0.015 0.078 -10000 0 -0.69 2 2
RUNX3 0.012 0.078 -10000 0 -0.69 4 4
RUNX1 -0.037 0.067 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.025 0.009 -10000 0 -10000 0 0
CDKN1A 0.019 0.045 -10000 0 -10000 0 0
KAT2B 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.011 0.12 -10000 0 -0.29 23 23
DCP1A 0.026 0.004 -10000 0 -10000 0 0
SKI 0.025 0.005 -10000 0 -10000 0 0
SERPINE1 0.023 0.088 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 0.01 0.11 -10000 0 -0.5 8 8
SMAD3/SMAD4/ATF3 -0.088 0.24 -10000 0 -0.53 84 84
SAP30 0.024 0.037 -10000 0 -0.7 1 1
Cbp/p300/PIAS3 0.047 0.043 -10000 0 -10000 0 0
JUN -0.21 0.42 0.3 1 -0.78 116 117
SMAD3/SMAD4/IRF7 0.023 0.08 -10000 0 -10000 0 0
TFE3 0.029 0.01 -10000 0 -10000 0 0
COL1A2 0.026 0.068 -10000 0 -1.1 1 1
mesenchymal cell differentiation -0.016 0.099 0.41 3 -10000 0 3
DLX1 -0.02 0.17 -10000 0 -0.67 25 25
TCF3 0.025 0.007 -10000 0 -10000 0 0
FOS -0.18 0.34 -10000 0 -0.75 100 100
SMAD3/SMAD4/Max 0.017 0.08 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.042 0.029 -10000 0 -10000 0 0
ZBTB17 0.026 0.006 -10000 0 -10000 0 0
LAMC1 0.01 0.062 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.02 0.08 -10000 0 -10000 0 0
IRF7 0.027 0.007 -10000 0 -10000 0 0
ESR1 -0.017 0.15 -10000 0 -0.68 17 17
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.015 0.091 0.32 2 -10000 0 2
SMAD2-3/SMAD4 0.009 0.096 -10000 0 -0.31 1 1
Cbp/p300/Src-1 0.046 0.034 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.035 -10000 0 -0.33 2 2
TGIF2/HDAC complex 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.029 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.004 -10000 0 -10000 0 0
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.025 0.006 -10000 0 -10000 0 0
GCN5L2 0.005 0.014 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.027 0.081 -10000 0 -10000 0 0
MSG1/HSC70 -0.05 0.058 -10000 0 -0.4 4 4
SMAD2 0.011 0.048 -10000 0 -10000 0 0
SMAD3 0.004 0.061 -10000 0 -0.22 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.012 0.06 -10000 0 -0.31 6 6
SMAD2/SMAD2/SMAD4 0.001 0.034 0.23 2 -10000 0 2
NCOR1 0.024 0.007 -10000 0 -10000 0 0
NCOA2 -0.018 0.17 -10000 0 -0.69 23 23
NCOA1 0.026 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.043 0.095 -10000 0 -10000 0 0
IFNB1 -0.002 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.002 0.11 -10000 0 -0.36 1 1
CITED1 -0.084 0.071 -10000 0 -0.59 3 3
SMAD2-3/SMAD4/ARC105 0.011 0.087 -10000 0 -10000 0 0
RBL1 0.012 0.097 -10000 0 -0.69 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.014 0.033 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.05 0.061 -10000 0 -0.47 3 3
SMAD7 -0.095 0.26 -10000 0 -0.54 77 77
MYC/MIZ-1 0.027 0.077 -10000 0 -0.52 7 7
SMAD3/SMAD4 0.023 0.11 0.29 26 -0.53 1 27
IL10 -0.034 0.15 -10000 0 -0.52 26 26
PIASy/HDAC complex 0.017 0.02 -10000 0 -10000 0 0
PIAS3 0.026 0.008 -10000 0 -10000 0 0
CDK2 0.029 0.011 -10000 0 -10000 0 0
IL5 -0.027 0.11 -10000 0 -0.41 19 19
CDK4 0.03 0.012 -10000 0 -10000 0 0
PIAS4 0.017 0.02 -10000 0 -10000 0 0
ATF3 -0.14 0.3 -10000 0 -0.69 85 85
SMAD3/SMAD4/SP1 0.03 0.083 -10000 0 -10000 0 0
FOXG1 0 0.077 -10000 0 -0.69 4 4
FOXO3 0.016 0.005 -10000 0 -10000 0 0
FOXO1 0.015 0.006 -10000 0 -10000 0 0
FOXO4 0.015 0.006 -10000 0 -10000 0 0
heart looping -0.015 0.09 0.32 2 -10000 0 2
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.013 0.15 -10000 0 -0.49 25 25
MYOD1 -0.014 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.015 0.082 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 -0.005 0.14 -10000 0 -0.43 27 27
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.033 0.11 -10000 0 -0.44 3 3
SMAD3/SMAD4/SP1-3 0.05 0.081 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.031 0.012 -10000 0 -10000 0 0
SIN3B 0.024 0.007 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.027 0.11 -10000 0 -0.34 1 1
ITGB5 0.015 0.065 0.36 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.028 0.044 -10000 0 -0.67 1 1
SMAD3/SMAD4/AR -0.17 0.26 -10000 0 -0.5 141 141
AR -0.25 0.34 -10000 0 -0.68 145 145
negative regulation of cell growth -0.026 0.12 -10000 0 -0.35 8 8
SMAD3/SMAD4/MYOD 0.014 0.081 -10000 0 -0.26 1 1
E2F5 0.026 0.004 -10000 0 -10000 0 0
E2F4 0.025 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.027 0.097 -10000 0 -0.3 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.014 0.035 -10000 0 -10000 0 0
TFDP1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.2 0.44 -10000 0 -0.8 117 117
SMAD3/SMAD4/RUNX2 0.017 0.1 -10000 0 -0.41 3 3
TGIF2 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.026 0.005 -10000 0 -10000 0 0
ATF2 0.011 0.1 -10000 0 -0.69 8 8
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.012 -9999 0 -10000 0 0
HDAC4 0.026 0.005 -9999 0 -10000 0 0
induction of apoptosis 0 0 -9999 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.006 -9999 0 -10000 0 0
CDKN1A -0.007 0.009 -9999 0 -10000 0 0
KAT2B 0.026 0.004 -9999 0 -10000 0 0
BAX 0.025 0.007 -9999 0 -10000 0 0
FOXO3 -0.004 0.004 -9999 0 -10000 0 0
FOXO1 0.025 0.007 -9999 0 -10000 0 0
FOXO4 0.013 0.009 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
XRCC6 0.02 0.012 -9999 0 -10000 0 0
TAT 0.011 0.021 -9999 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -10000 0 0
MYOD1 -0.009 0.01 -9999 0 -10000 0 0
PPARGC1A -0.28 0.35 -9999 0 -0.69 161 161
FHL2 -0.033 0.2 -9999 0 -0.69 31 31
response to nutrient levels 0 0 -9999 0 -10000 0 0
KU70/SIRT1 0.027 0.017 -9999 0 -10000 0 0
HIST2H4A 0.013 0.006 -9999 0 -10000 0 0
SIRT1/FOXO3a 0.038 0.047 -9999 0 -10000 0 0
SIRT1 0.023 0.005 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.017 -9999 0 -10000 0 0
SIRT1/Histone H1b -0.006 0.07 -9999 0 -0.31 8 8
apoptosis -0.037 0.023 -9999 0 -10000 0 0
SIRT1/PGC1A -0.18 0.24 -9999 0 -0.45 161 161
p53/SIRT1 0.028 0.012 -9999 0 -10000 0 0
SIRT1/FOXO4 -0.002 0.059 -9999 0 -0.28 2 2
FOXO1/FHL2/SIRT1 0.006 0.13 -9999 0 -0.42 31 31
HIST1H1E 0.006 0.051 -9999 0 -0.35 7 7
SIRT1/p300 0.027 0.017 -9999 0 -10000 0 0
muscle cell differentiation -0.029 0.022 -9999 0 -10000 0 0
TP53 0.022 0.006 -9999 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.024 -9999 0 -10000 0 0
CREBBP 0.025 0.006 -9999 0 -10000 0 0
MEF2D 0.025 0.007 -9999 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.011 -9999 0 -10000 0 0
ACSS2 0.013 0.003 -9999 0 -10000 0 0
SIRT1/PCAF/MYOD 0.03 0.022 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.033 0.009 -9999 0 -10000 0 0
PRKCZ 0.026 0.005 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.026 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.014 0.06 -9999 0 -0.32 1 1
IRAK/TOLLIP 0.028 0.011 -9999 0 -10000 0 0
IKBKB 0.026 0.004 -9999 0 -10000 0 0
IKBKG 0.024 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.065 0.22 -9999 0 -0.55 61 61
IL1A -0.034 0.19 -9999 0 -0.68 30 30
IL1B -0.026 0.14 -9999 0 -0.53 27 27
IRAK/TRAF6/p62/Atypical PKCs 0.06 0.034 -9999 0 -0.38 1 1
IL1R2 -0.051 0.21 -9999 0 -0.67 36 36
IL1R1 0.026 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.05 -9999 0 -0.28 1 1
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.019 0.064 -9999 0 -0.69 3 3
MAP3K3 0.025 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.029 0.059 -9999 0 -10000 0 0
JUN -0.082 0.16 -9999 0 -0.37 81 81
MAP3K7 0.026 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.04 0.12 -9999 0 -0.4 25 25
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.13 -9999 0 -0.42 29 29
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.045 0.13 -9999 0 -0.4 29 29
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.13 -9999 0 -0.44 26 26
NFKB1 0.026 0.004 -9999 0 -10000 0 0
MAPK8 -0.008 0.064 -9999 0 -0.4 8 8
IRAK1 0.014 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.011 0.084 -9999 0 -0.49 8 8
IRAK4 0.026 0.005 -9999 0 -10000 0 0
PRKCI 0.026 0.004 -9999 0 -10000 0 0
TRAF6 0.024 0.037 -9999 0 -0.69 1 1
PI3K 0.036 0.03 -9999 0 -0.52 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.065 -9999 0 -0.36 1 1
CHUK 0.026 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.13 -9999 0 -0.44 26 26
IL1 beta/IL1R2 -0.045 0.2 -9999 0 -0.5 56 56
IRAK/TRAF6/TAK1/TAB1/TAB2 0.034 0.025 -9999 0 -0.38 1 1
NF kappa B1 p50/RelA 0.027 0.11 -9999 0 -0.38 25 25
IRAK3 0.024 0.037 -9999 0 -0.69 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.037 0.13 -9999 0 -0.41 27 27
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.088 -9999 0 -0.3 29 29
IL1 alpha/IL1R1/IL1RAP 0.018 0.14 -9999 0 -0.46 29 29
RELA 0.026 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.026 0.004 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.04 0.029 -9999 0 -0.4 1 1
IL1RAP -0.013 0.061 -9999 0 -10000 0 0
UBE2N 0.026 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 0.006 0.11 -9999 0 -0.4 9 9
CASP1 0.021 0.054 -9999 0 -0.69 2 2
IL1RN/IL1R2 -0.046 0.18 -9999 0 -0.53 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.029 0.13 -9999 0 -0.42 26 26
TMEM189-UBE2V1 -0.003 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.075 -9999 0 -0.37 2 2
PIK3CA 0.024 0.037 -9999 0 -0.69 1 1
IL1RN -0.008 0.11 -9999 0 -0.65 8 8
TRAF6/TAK1/TAB1/TAB2 0.045 0.026 -9999 0 -0.39 1 1
MAP2K6 0.008 0.057 -9999 0 -0.37 7 7
Syndecan-3-mediated signaling events

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
CTTN 0.026 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.02 0.12 -9999 0 -0.35 30 30
Syndecan-3/Neurocan -0.003 0.11 -9999 0 -0.37 27 27
POMC -0.12 0.29 -9999 0 -0.68 78 78
EGFR 0.016 0.082 -9999 0 -0.69 5 5
Syndecan-3/EGFR 0.023 0.052 -9999 0 -0.36 6 6
AGRP 0.004 0.03 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.025 0.006 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.026 0.003 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.037 0.2 -9999 0 -0.68 31 31
long-term memory 0.048 0.031 -9999 0 -0.28 1 1
Syndecan-3/IL8 0.03 0.07 -9999 0 -0.37 9 9
PSEN1 0.026 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.038 0.01 -9999 0 -10000 0 0
FYN 0.026 0.004 -9999 0 -10000 0 0
limb bud formation 0.014 0.006 -9999 0 -10000 0 0
MC4R 0.001 0.026 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.044 0.21 -9999 0 -0.69 36 36
FGFR/FGF/Syndecan-3 0.014 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.034 0.14 -9999 0 -0.35 54 54
Syndecan-3/AgRP 0.029 0.026 -9999 0 -0.32 1 1
Syndecan-3/AgRP/MC4R 0.044 0.031 -9999 0 -0.3 1 1
Fyn/Cortactin 0.038 0.008 -9999 0 -10000 0 0
SDC3 0.014 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.029 0.069 -9999 0 -0.36 9 9
IL8 -0.021 0.11 -9999 0 -0.69 8 8
Syndecan-3/Fyn/Cortactin 0.049 0.031 -9999 0 -0.29 1 1
Syndecan-3/CASK 0.01 0.026 -9999 0 -0.31 1 1
alpha-MSH/MC4R -0.083 0.22 -9999 0 -0.52 78 78
Gamma Secretase 0.069 0.028 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.19 0.33 -10000 0 -0.69 114 114
HRAS 0.025 0.009 -10000 0 -10000 0 0
EGFR 0.016 0.082 -10000 0 -0.69 5 5
AKT 0.013 0.09 0.35 8 -0.24 1 9
FOXO3 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.025 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.007 -10000 0 -10000 0 0
FOXO4 0.025 0.007 -10000 0 -10000 0 0
MET -0.029 0.065 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
PIK3CB 0.026 0.004 -10000 0 -10000 0 0
NRAS 0.026 0.005 -10000 0 -10000 0 0
PIK3CG 0.007 0.11 -10000 0 -0.69 9 9
PIK3R3 0.026 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.007 -10000 0 -10000 0 0
NF1 0.025 0.007 -10000 0 -10000 0 0
RAS -0.034 0.093 -10000 0 -0.18 100 100
ERBB2 0.025 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.036 0.059 0.33 5 -10000 0 5
PI3K -0.017 0.1 0.42 6 -0.24 13 19
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.026 0.005 -10000 0 -10000 0 0
FOXO 0.046 0.06 0.31 7 -10000 0 7
AKT2 0.025 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.022 -10000 0 -0.38 1 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.001 0.068 -10000 0 -0.28 6 6
NT3 (dimer)/TRKC -0.024 0.15 -10000 0 -0.51 31 31
NT3 (dimer)/TRKB 0.002 0.15 -10000 0 -0.46 36 36
SHC/Grb2/SOS1/GAB1/PI3K 0.029 0.021 -10000 0 -0.29 1 1
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
BDNF 0.005 0.12 -10000 0 -0.69 10 10
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
NTRK1 0.011 0.027 -10000 0 -10000 0 0
NTRK2 0.02 0.057 -10000 0 -0.59 3 3
NTRK3 -0.013 0.13 -10000 0 -0.69 11 11
NT-4/5 (dimer)/TRKB 0.014 0.13 -10000 0 -0.46 24 24
neuron apoptosis -0.006 0.11 0.4 13 -10000 0 13
SHC 2-3/Grb2 0.006 0.12 -10000 0 -0.43 13 13
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0 0.1 -10000 0 -0.52 8 8
SHC3 -0.008 0.12 -10000 0 -0.43 22 22
STAT3 (dimer) 0.029 0.014 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.004 0.15 -10000 0 -0.46 32 32
RIN/GDP -0.005 0.081 0.34 5 -0.27 3 8
GIPC1 0.025 0.007 -10000 0 -10000 0 0
KRAS 0.026 0.005 -10000 0 -10000 0 0
DNAJA3 -0.007 0.078 -10000 0 -0.39 14 14
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.019 0.016 -10000 0 -10000 0 0
MAGED1 0.025 0.007 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.006 0.11 -10000 0 -0.66 9 9
SHC/GRB2/SOS1 0.047 0.019 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.035 0.073 -10000 0 -0.46 7 7
TRKA/NEDD4-2 0.032 0.02 -10000 0 -10000 0 0
ELMO1 -0.26 0.35 -10000 0 -0.69 148 148
RhoG/GTP/ELMO1/DOCK1 -0.16 0.24 -10000 0 -0.46 148 148
NGF 0.02 0.064 -10000 0 -0.69 3 3
HRAS 0.025 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.037 -10000 0 -0.69 1 1
GAB2 0.026 0.005 -10000 0 -10000 0 0
RIT2 -0.01 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
DNM1 -0.006 0.14 -10000 0 -0.64 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.14 0.2 -10000 0 -0.36 153 153
mol:GDP -0.012 0.12 0.45 7 -0.38 5 12
NGF (dimer) 0.02 0.064 -10000 0 -0.69 3 3
RhoG/GDP -0.2 0.26 -10000 0 -0.52 148 148
RIT1/GDP -0.003 0.087 0.4 6 -0.26 3 9
TIAM1 -0.049 0.074 -10000 0 -0.69 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.033 0.097 -10000 0 -0.5 11 11
KIDINS220/CRKL/C3G 0.028 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.035 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.059 0.024 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.019 0.16 -10000 0 -0.69 20 20
RAP1/GDP -0.007 0.058 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.005 0.12 -10000 0 -0.69 10 10
ubiquitin-dependent protein catabolic process 0.043 0.048 -10000 0 -0.45 3 3
Schwann cell development -0.031 0.03 -10000 0 -10000 0 0
EHD4 0.026 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.017 0.039 -10000 0 -10000 0 0
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.13 -10000 0 -0.38 37 37
ABL1 0.024 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.01 0.1 -10000 0 -0.51 6 6
STAT3 0.029 0.014 -10000 0 -10000 0 0
axon guidance -0.019 0.12 -10000 0 -0.37 37 37
MAPK3 0.013 0.073 -10000 0 -0.42 7 7
MAPK1 0.008 0.069 -10000 0 -0.42 7 7
CDC42/GDP -0.001 0.089 0.4 6 -0.26 3 9
NTF3 -0.019 0.16 -10000 0 -0.69 20 20
NTF4 0.006 0.11 -10000 0 -0.66 9 9
NGF (dimer)/TRKA/FAIM 0.044 0.048 -10000 0 -0.46 3 3
PI3K 0.036 0.03 -10000 0 -0.52 1 1
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.026 0.004 -10000 0 -10000 0 0
GAB1 0.026 0.004 -10000 0 -10000 0 0
RASGRF1 -0.04 0.09 -10000 0 -0.4 18 18
SOS1 0.026 0.005 -10000 0 -10000 0 0
MCF2L -0.031 0.12 -10000 0 -0.44 30 30
RGS19 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.063 -10000 0 -0.38 1 1
Rac1/GDP -0.006 0.068 -10000 0 -0.26 2 2
NGF (dimer)/TRKA/GRIT 0.028 0.045 -10000 0 -0.46 3 3
neuron projection morphogenesis 0.02 0.095 -10000 0 -0.69 2 2
NGF (dimer)/TRKA/NEDD4-2 0.044 0.049 -10000 0 -0.46 3 3
MAP2K1 0.037 0.059 0.36 4 -10000 0 4
NGFR -0.019 0.14 -10000 0 -0.69 14 14
NGF (dimer)/TRKA/GIPC/GAIP 0.01 0.085 -10000 0 -0.36 16 16
RAS family/GTP/PI3K 0.026 0.02 -10000 0 -0.32 1 1
FRS2 family/SHP2/GRB2/SOS1 0.073 0.023 -10000 0 -10000 0 0
NRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.078 -10000 0 -0.52 5 5
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.02 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.045 0.091 -10000 0 -0.47 10 10
NGF (dimer)/TRKA/p62/Atypical PKCs 0.065 0.05 -10000 0 -0.4 3 3
MATK 0.015 0.077 -10000 0 -0.63 5 5
NEDD4L 0.026 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.043 -10000 0 -0.2 1 1
NGF (dimer)/TRKA -0.001 0.085 -10000 0 -0.4 15 15
Rac1/GTP -0.11 0.13 -10000 0 -0.29 69 69
FRS2 family/SHP2/CRK family 0.057 0.036 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.022 0.081 0.34 4 -0.38 8 12
ACTA1 0.012 0.094 0.35 5 -0.44 8 13
NUMA1 0.018 0.088 0.3 4 -0.42 9 13
SPTAN1 0.008 0.092 0.39 4 -0.46 7 11
LIMK1 0.015 0.1 0.5 6 -0.46 7 13
BIRC3 -0.011 0.15 -10000 0 -0.64 19 19
BIRC2 0.026 0.005 -10000 0 -10000 0 0
BAX 0.025 0.007 -10000 0 -10000 0 0
CASP10 -0.01 0.081 -10000 0 -0.5 9 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
PTK2 0.014 0.099 0.32 4 -0.42 12 16
DIABLO 0.026 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes 0.008 0.091 0.39 4 -0.45 7 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
GSN 0.007 0.093 0.39 4 -0.44 8 12
MADD 0.026 0.005 -10000 0 -10000 0 0
TFAP2A -0.04 0.22 -10000 0 -0.61 45 45
BID -0.012 0.059 -10000 0 -0.31 9 9
MAP3K1 0.017 0.041 0.27 3 -10000 0 3
TRADD 0.025 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.011 0.1 0.5 6 -0.46 7 13
CASP9 0.026 0.006 -10000 0 -10000 0 0
DNA repair -0.016 0.059 0.43 2 -0.21 14 16
neuron apoptosis 0.007 0.11 -10000 0 -0.55 12 12
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.018 0.096 0.34 4 -0.45 9 13
APAF1 0.026 0.005 -10000 0 -10000 0 0
CASP6 0.021 0.085 0.36 2 -0.63 2 4
TRAF2 0.024 0.008 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.11 0.41 12 -0.44 7 19
CASP7 0.006 0.098 0.33 15 -0.53 4 19
KRT18 0.02 0.044 -10000 0 -0.44 2 2
apoptosis 0.018 0.092 0.48 4 -0.41 6 10
DFFA 0.01 0.096 0.36 6 -0.46 7 13
DFFB 0.01 0.096 0.36 6 -0.46 7 13
PARP1 0.016 0.059 0.21 14 -0.43 2 16
actin filament polymerization -0.02 0.12 0.43 7 -0.54 10 17
TNF -0.057 0.23 -10000 0 -0.69 42 42
CYCS 0 0.05 0.24 4 -0.22 6 10
SATB1 0.021 0.085 0.51 2 -0.58 2 4
SLK 0.007 0.093 0.46 3 -0.46 7 10
p15 BID/BAX -0.009 0.069 -10000 0 -0.28 9 9
CASP2 -0.016 0.1 0.21 2 -0.39 12 14
JNK cascade -0.018 0.041 -10000 0 -0.27 3 3
CASP3 0.006 0.095 0.42 3 -0.46 8 11
LMNB2 0.007 0.12 0.36 9 -0.45 8 17
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CASP4 0.026 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.043 0.096 -10000 0 -0.4 15 15
negative regulation of DNA binding -0.039 0.21 -10000 0 -0.6 45 45
stress fiber formation 0.007 0.093 0.46 3 -0.45 7 10
GZMB -0.006 0.094 -10000 0 -0.57 9 9
CASP1 0.013 0.03 -10000 0 -0.4 2 2
LMNB1 0.02 0.092 0.33 11 -0.36 1 12
APP 0.007 0.11 -10000 0 -0.56 12 12
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.008 0.002 -10000 0 -10000 0 0
VIM 0.018 0.087 0.45 3 -0.39 7 10
LMNA 0.016 0.1 0.35 11 -0.42 3 14
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.014 0.11 -10000 0 -0.42 10 10
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.015 0.1 0.51 5 -0.46 7 12
APAF-1/Caspase 9 0.013 0.06 -10000 0 -0.54 3 3
nuclear fragmentation during apoptosis 0.018 0.087 0.3 4 -0.41 9 13
CFL2 0.02 0.12 0.54 10 -0.44 7 17
GAS2 0.004 0.097 0.39 3 -0.43 10 13
positive regulation of apoptosis 0.016 0.1 0.37 9 -0.38 5 14
PRF1 0.017 0.075 -10000 0 -0.69 4 4
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.084 -10000 0 -0.33 1 1
epithelial cell differentiation -0.003 0.098 -10000 0 -0.42 6 6
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.011 0.066 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
EGFR 0.016 0.082 -10000 0 -0.69 5 5
PRL -0.013 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis -0.023 0.12 0.34 3 -0.5 5 8
PTPRZ1 -0.001 0.11 -10000 0 -0.69 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.005 0.14 -10000 0 -0.39 30 30
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.044 0.14 -10000 0 -0.44 36 36
ADAM17 0.033 0.042 -10000 0 -0.69 1 1
ErbB4/ErbB4 -0.016 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.033 0.14 -10000 0 -0.46 25 25
NCOR1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.032 0.14 -10000 0 -0.41 36 36
GRIN2B -0.042 0.13 -10000 0 -0.4 36 36
ErbB4/ErbB2/betacellulin 0.003 0.097 -10000 0 -0.53 7 7
STAT1 0.022 0.022 -10000 0 -10000 0 0
HBEGF 0.02 0.028 -10000 0 -10000 0 0
PRLR -0.013 0.15 -10000 0 -0.69 17 17
E4ICDs/ETO2 -0.002 0.08 -10000 0 -0.33 1 1
axon guidance -0.008 0.069 -10000 0 -10000 0 0
NEDD4 0.037 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.002 0.12 -10000 0 -0.52 17 17
CBFA2T3 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.01 0.069 -10000 0 -0.48 1 1
MAPK3 -0.021 0.12 -10000 0 -0.52 5 5
STAT1 (dimer) -0.002 0.085 -10000 0 -0.31 1 1
MAPK1 -0.022 0.12 -10000 0 -0.51 5 5
JAK2 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.036 0.13 -10000 0 -0.41 33 33
NRG1 -0.033 0.17 -10000 0 -0.54 36 36
NRG3 -0.024 0.18 -10000 0 -0.66 27 27
NRG2 -0.057 0.23 -10000 0 -0.69 42 42
NRG4 0.021 0.02 -10000 0 -10000 0 0
heart development -0.008 0.069 -10000 0 -10000 0 0
neural crest cell migration -0.036 0.13 -10000 0 -0.41 33 33
ERBB2 0.019 0.03 -10000 0 -0.51 1 1
WWOX/E4ICDs -0.003 0.082 -10000 0 -0.33 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.005 0.098 -10000 0 -0.46 5 5
apoptosis 0.024 0.13 0.41 27 -10000 0 27
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.053 0.16 -10000 0 -0.45 43 43
ErbB4/ErbB2/epiregulin 0.013 0.083 -10000 0 -0.48 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.11 -10000 0 -0.52 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.007 0.12 -10000 0 -0.39 17 17
MDM2 -0.013 0.077 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.028 0.14 -10000 0 -0.42 35 35
STAT5A -0.004 0.066 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.035 0.15 -10000 0 -0.42 40 40
DLG4 0.025 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.034 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.003 0.074 -10000 0 -0.29 1 1
STAT5A (dimer) 0.006 0.11 -10000 0 -0.45 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.004 0.069 -10000 0 -10000 0 0
LRIG1 0.021 0.064 -10000 0 -0.69 3 3
EREG -0.043 0.063 -10000 0 -10000 0 0
BTC 0.013 0.097 -10000 0 -0.69 7 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.008 0.069 -10000 0 -10000 0 0
ERBB4 -0.016 0.086 -10000 0 -10000 0 0
STAT5B 0.025 0.007 -10000 0 -10000 0 0
YAP1 0.006 0.057 -10000 0 -0.44 5 5
GRB2 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.009 0.069 -10000 0 -0.44 1 1
glial cell differentiation 0.003 0.074 0.29 1 -10000 0 1
WWOX 0.025 0.007 -10000 0 -10000 0 0
cell proliferation -0.026 0.14 0.4 1 -0.52 10 11
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) 0.015 0.11 -10000 0 -0.67 4 4
HDAC1 0.023 0.007 -10000 0 -10000 0 0
AES 0.024 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.022 0.052 -10000 0 -0.69 2 2
LRP6/FZD1 0.037 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.053 -10000 0 -0.69 2 2
AP1 -0.14 0.25 -10000 0 -0.49 111 111
NCSTN 0.025 0.007 -10000 0 -10000 0 0
ADAM10 0.019 0.074 -10000 0 -0.69 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.071 -10000 0 -0.53 3 3
NICD/RBPSUH 0.014 0.11 -10000 0 -0.65 4 4
WIF1 -0.014 0.041 -10000 0 -10000 0 0
NOTCH1 0.004 0.11 -10000 0 -0.45 17 17
PSENEN 0.025 0.006 -10000 0 -10000 0 0
KREMEN2 0.015 0.035 -10000 0 -10000 0 0
DKK1 0.003 0.069 -10000 0 -0.69 2 2
beta catenin/beta TrCP1 0.045 0.048 0.28 3 -10000 0 3
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.004 0.081 0.24 2 -0.38 10 12
CtBP/CBP/TCF1/TLE1/AES 0.019 0.029 -10000 0 -0.3 2 2
PSEN1 0.026 0.005 -10000 0 -10000 0 0
FOS -0.16 0.32 -10000 0 -0.69 100 100
JUN -0.13 0.3 -10000 0 -0.69 82 82
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.039 0.065 0.3 12 -10000 0 12
MAPK3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.032 0.1 -10000 0 -0.45 15 15
HNF1A 0.025 0.006 -10000 0 -10000 0 0
CTBP1 0.025 0.005 -10000 0 -10000 0 0
MYC -0.012 0.23 -10000 0 -1.2 13 13
NKD1 0.003 0.12 -10000 0 -0.69 11 11
FZD1 0.025 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.012 0.12 -10000 0 -0.65 6 6
apoptosis -0.14 0.25 -10000 0 -0.49 111 111
Delta 1/NOTCHprecursor 0.014 0.11 -10000 0 -0.64 4 4
DLL1 0.026 0.008 -10000 0 -10000 0 0
PPARD 0.026 0.043 -10000 0 -0.72 1 1
Gamma Secretase 0.069 0.028 -10000 0 -10000 0 0
APC 0.005 0.053 0.28 1 -0.3 1 2
DVL1 0.023 0.008 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 0.048 -10000 0 -0.48 2 2
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
NLK 0.013 0.006 -10000 0 -10000 0 0
CCND1 0.014 0.12 -10000 0 -0.87 6 6
WNT1 0.017 0.02 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.049 0.092 0.4 13 -0.33 1 14
DKK2 -0.008 0.15 -10000 0 -0.69 16 16
NOTCH1 precursor/DVL1 0.019 0.1 -10000 0 -0.55 5 5
GSK3B 0.026 0.004 -10000 0 -10000 0 0
FRAT1 0.025 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.013 0.12 -10000 0 -0.66 6 6
PPP2R5D 0.029 0.059 0.34 11 -0.44 1 12
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.064 0.02 -10000 0 -10000 0 0
RBPJ 0.026 0.008 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 -10000 0 0
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.022 0.1 -10000 0 -0.33 34 34
FRAP1 0.012 0.042 0.39 2 -10000 0 2
AKT1 -0.02 0.084 -10000 0 -0.29 31 31
INSR 0.025 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0.009 0.079 -10000 0 -0.46 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.031 -10000 0 -10000 0 0
TSC2 0.025 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.004 0.066 -10000 0 -0.42 1 1
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.015 0.12 -10000 0 -0.38 35 35
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.038 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.023 0.095 0.38 15 -0.3 2 17
MAP3K5 0.005 0.032 0.18 1 -0.22 6 7
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.005 0.033 0.17 2 -0.22 6 8
mol:LY294002 0 0.001 0.001 1 -0.003 47 48
EIF4B 0.028 0.11 0.45 18 -0.28 1 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.064 0.36 4 -10000 0 4
eIF4E/eIF4G1/eIF4A1 0.017 0.019 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.12 -10000 0 -0.36 35 35
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.041 0.25 2 -0.24 1 3
FKBP1A 0.026 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.017 0.071 -10000 0 -0.42 1 1
mol:Amino Acids 0 0.001 0.001 1 -0.003 47 48
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.024 0.095 -10000 0 -0.32 33 33
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.075 0.3 1 -0.51 6 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.012 0.086 0.28 1 -0.5 1 2
tumor necrosis factor receptor activity 0 0.001 0.003 47 -0.001 1 48
RPS6 0.025 0.007 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
EIF4G1 0.026 0.004 -10000 0 -10000 0 0
IRS1 -0.034 0.12 -10000 0 -0.37 42 42
INS -0.017 0.003 -10000 0 -10000 0 0
PTEN 0.024 0.022 -10000 0 -0.38 1 1
PDK2 -0.022 0.092 0.22 2 -0.31 32 34
EIF4EBP1 0.015 0.1 -10000 0 -0.95 4 4
PIK3CA 0.025 0.037 -10000 0 -0.69 1 1
PPP2R5D 0.022 0.073 0.38 11 -10000 0 11
peptide biosynthetic process 0.013 0.018 -10000 0 -10000 0 0
RHEB 0.025 0.006 -10000 0 -10000 0 0
EIF4A1 0.025 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.008 15 -0.004 1 16
EEF2 0.013 0.018 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.029 0.095 -10000 0 -0.88 4 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.024 0.037 -10000 0 -0.69 1 1
Caspase 8 (4 units) 0.023 0.089 -10000 0 -0.43 4 4
NEF -0.01 0.052 -10000 0 -0.22 19 19
NFKBIA 0.02 0.032 -10000 0 -10000 0 0
BIRC3 -0.006 0.15 -10000 0 -0.66 18 18
CYCS -0.007 0.091 0.22 1 -0.38 6 7
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CD247 -0.02 0.16 -10000 0 -0.76 15 15
MAP2K7 -0.001 0.17 0.36 1 -0.68 16 17
protein ubiquitination 0.005 0.097 0.33 5 -0.42 2 7
CRADD 0.026 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.026 0.005 -10000 0 -10000 0 0
BID -0.008 0.097 0.23 1 -0.32 23 24
NF-kappa-B/RelA/I kappa B alpha 0.04 0.08 -10000 0 -0.33 15 15
TRADD 0.025 0.006 -10000 0 -10000 0 0
MAP3K5 0.024 0.037 -10000 0 -0.69 1 1
CFLAR 0.026 0.005 -10000 0 -10000 0 0
FADD 0.026 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.081 -10000 0 -0.33 15 15
MAPK8 0 0.16 0.34 2 -0.62 16 18
APAF1 0.026 0.005 -10000 0 -10000 0 0
TRAF1 0.024 0.008 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.001 0.097 -10000 0 -0.32 24 24
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.1 -10000 0 -0.38 12 12
CHUK 0.001 0.097 0.27 3 -0.46 2 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.032 -10000 0 -0.4 1 1
TCRz/NEF -0.025 0.16 -10000 0 -0.48 34 34
TNF -0.057 0.23 -10000 0 -0.69 42 42
FASLG -0.052 0.23 -10000 0 -0.75 33 33
NFKB1 0.02 0.033 -10000 0 -0.18 2 2
TNFR1A/BAG4/TNF-alpha -0.006 0.16 -10000 0 -0.45 43 43
CASP6 0.037 0.093 -10000 0 -0.63 4 4
CASP7 0.01 0.16 0.38 3 -0.59 19 22
RELA 0.02 0.033 -10000 0 -10000 0 0
CASP2 0.025 0.006 -10000 0 -10000 0 0
CASP3 0.009 0.15 0.35 1 -0.58 19 20
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.037 0.03 -10000 0 -0.52 1 1
CASP8 0.026 0.005 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
MAP3K14 -0.001 0.1 -10000 0 -0.44 4 4
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.49 17 17
BCL2 -0.018 0.16 0.42 2 -0.59 15 17
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.008 0.14 -10000 0 -0.39 44 44
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.019 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.009 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
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 0.008 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.036 0.14 -10000 0 -0.4 47 47
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 0.012 0.033 0.098 47 -10000 0 47
GNAL -0.061 0.23 -10000 0 -0.67 47 47
GNG2 0.026 0.005 -10000 0 -10000 0 0
CRH 0 0.035 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.03 -10000 0 -0.4 2 2
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.006 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.008 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.023 0.041 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.003 0.021 -10000 0 -10000 0 0
GRK1 -0.043 0.21 -10000 0 -0.67 36 36
CNG Channel 0.038 0.057 -10000 0 -0.39 5 5
mol:Na + 0.027 0.078 -10000 0 -0.41 9 9
mol:ADP -0.043 0.21 -10000 0 -0.67 36 36
RGS9-1/Gbeta5/R9AP -0.031 0.19 -10000 0 -0.46 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.037 0.082 -10000 0 -0.42 9 9
CNGB1 0.016 0.028 -10000 0 -10000 0 0
RDH5 -0.059 0.064 -10000 0 -10000 0 0
SAG -0.009 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.12 0.49 12 -0.4 9 21
Na + (4 Units) 0.02 0.073 -10000 0 -0.39 9 9
RGS9 -0.045 0.21 -10000 0 -0.69 36 36
GNB1/GNGT1 0.029 0.011 -10000 0 -10000 0 0
GNAT1/GDP -0.018 0.17 -10000 0 -0.41 57 57
GUCY2D 0.011 0.087 -10000 0 -0.64 6 6
GNGT1 -0.015 0.01 -10000 0 -10000 0 0
GUCY2F -0.013 0.011 -10000 0 -10000 0 0
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.036 -10000 0 -0.39 1 1
mol:11-cis-retinal -0.059 0.064 -10000 0 -10000 0 0
mol:cGMP 0.029 0.065 -10000 0 -0.41 6 6
GNB1 0.026 0.005 -10000 0 -10000 0 0
Rhodopsin -0.034 0.051 -10000 0 -10000 0 0
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 0.015 0.083 -10000 0 -0.69 5 5
Metarhodopsin II -0.012 0.13 -10000 0 -0.41 36 36
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.044 0.072 -10000 0 -0.42 8 8
RGS9BP -0.022 0.18 -10000 0 -0.68 25 25
Metarhodopsin II/Transducin 0.012 0.005 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.037 0.042 -10000 0 -0.43 3 3
PDE6A/B 0.031 0.025 -10000 0 -10000 0 0
mol:Pi -0.031 0.19 -10000 0 -0.46 58 58
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 0.012 -10000 0 -10000 0 0
PDE6B 0.026 0.005 -10000 0 -10000 0 0
PDE6A 0.012 0.033 -10000 0 -10000 0 0
PDE6G 0.012 0.062 -10000 0 -0.69 2 2
RHO 0.006 0.023 -10000 0 -10000 0 0
PDE6 -0.002 0.17 -10000 0 -0.4 57 57
GUCA1A 0.005 0.024 -10000 0 -10000 0 0
GC2/GCAP Family 0.044 0.042 -10000 0 -0.37 3 3
GUCA1C -0.017 0.003 -10000 0 -10000 0 0
GUCA1B 0.021 0.064 -10000 0 -0.69 3 3
FOXM1 transcription factor network

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
NFATC3 -0.019 0.32 0.78 2 -0.99 7 9
PLK1 0.028 0.091 -10000 0 -0.76 4 4
BIRC5 0.024 0.1 -10000 0 -0.95 3 3
HSPA1B -0.025 0.31 -10000 0 -0.99 7 7
MAP2K1 0.023 0.045 -10000 0 -10000 0 0
BRCA2 -0.03 0.33 0.78 1 -1.1 10 11
FOXM1 -0.05 0.34 -10000 0 -1.2 8 8
XRCC1 -0.019 0.31 -10000 0 -0.97 7 7
FOXM1B/p19 -0.048 0.33 -10000 0 -0.94 15 15
Cyclin D1/CDK4 -0.004 0.29 -10000 0 -0.89 6 6
CDC2 -0.029 0.32 -10000 0 -0.92 12 12
TGFA -0.016 0.29 -10000 0 -0.89 6 6
SKP2 -0.018 0.32 0.78 2 -0.99 8 10
CCNE1 0.026 0.011 -10000 0 -10000 0 0
CKS1B -0.014 0.32 0.78 1 -0.99 7 8
RB1 0.025 0.18 -10000 0 -0.6 5 5
FOXM1C/SP1 -0.032 0.33 -10000 0 -1.1 8 8
AURKB 0.008 0.14 -10000 0 -0.89 7 7
CENPF -0.015 0.32 0.78 1 -0.99 7 8
CDK4 0.026 0.019 -10000 0 -10000 0 0
MYC -0.03 0.31 -10000 0 -0.92 13 13
CHEK2 0.019 0.04 -10000 0 -10000 0 0
ONECUT1 -0.015 0.3 -10000 0 -0.94 7 7
CDKN2A -0.03 0.065 -10000 0 -10000 0 0
LAMA4 -0.026 0.31 -10000 0 -0.99 7 7
FOXM1B/HNF6 -0.022 0.32 -10000 0 -1.1 7 7
FOS -0.24 0.6 0.78 2 -1.2 102 104
SP1 0.026 0.008 -10000 0 -10000 0 0
CDC25B -0.019 0.31 0.78 1 -0.98 7 8
response to radiation 0.006 0.026 -10000 0 -10000 0 0
CENPB -0.019 0.31 0.78 1 -0.98 7 8
CENPA -0.034 0.32 -10000 0 -1 10 10
NEK2 -0.015 0.32 0.78 1 -0.99 7 8
HIST1H2BA -0.031 0.31 -10000 0 -1 7 7
CCNA2 0.024 0.023 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.036 0.33 -10000 0 -1.1 7 7
CCNB2 -0.027 0.31 -10000 0 -1 6 6
CCNB1 -0.027 0.32 -10000 0 -1 7 7
ETV5 -0.025 0.31 -10000 0 -0.99 7 7
ESR1 -0.061 0.38 -10000 0 -1.1 20 20
CCND1 -0.01 0.29 -10000 0 -0.9 7 7
GSK3A 0.02 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.05 0.043 -10000 0 -10000 0 0
CDK2 0.027 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.008 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.039 0.31 -10000 0 -1.1 7 7
GAS1 -0.18 0.56 0.78 1 -1.2 78 79
MMP2 -0.024 0.33 0.78 2 -1.2 8 10
RB1/FOXM1C -0.01 0.29 -10000 0 -0.93 6 6
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.012 0.095 -10000 0 -0.61 8 8
ANTXR2 0.024 0.037 -10000 0 -0.69 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.081 9 9
monocyte activation -0.035 0.15 -10000 0 -0.44 46 46
MAP2K2 -0.01 0.12 -10000 0 -0.54 17 17
MAP2K1 -0.002 0.012 -10000 0 -10000 0 0
MAP2K7 -0.002 0.011 -10000 0 -10000 0 0
MAP2K6 -0.008 0.052 -10000 0 -0.41 6 6
CYAA -0.009 0.054 -10000 0 -0.39 7 7
MAP2K4 -0.002 0.011 -10000 0 -10000 0 0
IL1B -0.025 0.099 0.18 1 -0.36 28 29
Channel 0.023 0.063 -10000 0 -0.37 9 9
NLRP1 -0.004 0.031 -10000 0 -0.4 2 2
CALM1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.01 0.031 -10000 0 -0.52 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.081 9 -10000 0 9
MAPK3 -0.002 0.011 -10000 0 -10000 0 0
MAPK1 -0.002 0.011 -10000 0 -10000 0 0
PGR -0.014 0.06 -10000 0 -0.37 9 9
PA/Cellular Receptors 0.024 0.069 -10000 0 -0.4 9 9
apoptosis -0.002 0.013 -10000 0 -0.081 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.06 -10000 0 -0.35 9 9
macrophage activation -0.002 0.01 -10000 0 -10000 0 0
TNF -0.057 0.23 -10000 0 -0.69 42 42
VCAM1 -0.035 0.16 -10000 0 -0.44 46 46
platelet activation 0.01 0.031 -10000 0 -0.52 1 1
MAPKKK cascade -0.003 0.028 0.18 1 -0.14 7 8
IL18 -0.008 0.057 -10000 0 -0.32 9 9
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.081 9 9
LEF -0.002 0.013 -10000 0 -0.082 9 9
CASP1 0 0.019 -10000 0 -0.098 11 11
mol:cAMP 0.01 0.032 -10000 0 -0.53 1 1
necrosis -0.002 0.013 -10000 0 -0.081 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.06 -10000 0 -0.35 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.78 3 3
UGCG -0.047 0.2 -10000 0 -0.61 39 39
AKT1/mTOR/p70S6K/Hsp90/TERT 0.02 0.13 0.42 5 -0.4 12 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.047 0.2 -10000 0 -0.6 40 40
mol:DAG -0.012 0.13 -10000 0 -0.78 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.15 -10000 0 -0.43 28 28
FRAP1 -0.005 0.18 0.43 2 -0.5 30 32
FOXO3 0.004 0.16 0.43 2 -0.61 13 15
AKT1 0 0.16 -10000 0 -0.68 13 13
GAB2 0.026 0.005 -10000 0 -10000 0 0
SMPD1 0.01 0.085 -10000 0 -0.74 4 4
SGMS1 0.001 0.11 -10000 0 -0.62 10 10
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 0.025 -10000 0 -0.46 1 1
CALM1 0.026 0.005 -10000 0 -10000 0 0
cell proliferation -0.02 0.17 0.33 5 -0.53 23 28
EIF3A 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.031 -10000 0 -0.53 1 1
RPS6KB1 0.016 0.067 -10000 0 -0.7 2 2
mol:sphingomyelin -0.012 0.13 -10000 0 -0.78 10 10
natural killer cell activation 0 0.004 -10000 0 -0.027 3 3
JAK3 -0.005 0.056 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC 0.003 0.19 0.48 5 -0.9 11 16
MYB 0.004 0.19 -10000 0 -1.3 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.001 0.14 -10000 0 -0.61 13 13
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.067 -10000 0 -0.63 2 2
mol:PI-3-4-5-P3 0 0.14 -10000 0 -0.58 13 13
Rac1/GDP 0.024 0.026 -10000 0 -0.42 1 1
T cell proliferation -0.001 0.13 -10000 0 -0.54 13 13
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.066 8 8
PRKCZ -0.002 0.14 -10000 0 -0.57 13 13
NF kappa B1 p50/RelA 0.018 0.16 -10000 0 -0.51 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.002 0.11 -10000 0 -0.61 8 8
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
IL2RA -0.01 0.14 -10000 0 -0.65 16 16
IL2RB 0.002 0.1 -10000 0 -0.62 9 9
TERT -0.006 0.021 -10000 0 -10000 0 0
E2F1 0.025 0.07 -10000 0 -0.43 8 8
SOS1 0.026 0.006 -10000 0 -10000 0 0
RPS6 0.025 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 8 -10000 0 8
PTPN11 0.026 0.006 -10000 0 -10000 0 0
IL2RG -0.012 0.14 -10000 0 -0.63 16 16
actin cytoskeleton organization -0.001 0.13 -10000 0 -0.54 13 13
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL2 0.018 0.013 -10000 0 -10000 0 0
PIK3CA 0.026 0.038 -10000 0 -0.7 1 1
Rac1/GTP 0.049 0.032 -10000 0 -0.4 1 1
LCK 0.013 0.079 -10000 0 -0.69 4 4
BCL2 -0.025 0.25 0.48 4 -0.81 29 33
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.023 0.019 -9999 0 -10000 0 0
GNAI2 0.026 0.004 -9999 0 -10000 0 0
mol:S1P 0.016 0.006 -9999 0 -10000 0 0
GNAO1 0.009 0.1 -9999 0 -0.69 8 8
mol:Sphinganine-1-P 0.013 0.012 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.055 0.025 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
G12/G13 0.037 0.011 -9999 0 -10000 0 0
S1PR3 0.024 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.01 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.014 -9999 0 -10000 0 0
S1PR5 0.024 0.014 -9999 0 -10000 0 0
S1PR4 0.023 0.017 -9999 0 -10000 0 0
GNAI1 0.023 0.037 -9999 0 -0.69 1 1
S1P/S1P5/G12 0.043 0.02 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.058 0.16 -9999 0 -0.3 103 103
S1P/S1P4/Gi 0.004 0.074 -9999 0 -0.34 9 9
GNAQ 0.024 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.14 0.3 -9999 0 -0.66 91 91
GNA15 0.011 0.053 -9999 0 -0.69 1 1
GNA12 0.025 0.006 -9999 0 -10000 0 0
GNA13 0.025 0.007 -9999 0 -10000 0 0
GNA11 0.019 0.064 -9999 0 -0.69 3 3
ABCC1 0.025 0.006 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.045 0.05 0.17 1 -0.34 5 6
EPHB2 0.02 0.064 -10000 0 -0.69 3 3
Syndecan-2/TACI -0.078 0.2 -10000 0 -0.45 83 83
LAMA1 -0.025 0.18 -10000 0 -0.68 27 27
Syndecan-2/alpha2 ITGB1 0.05 0.09 -10000 0 -0.39 13 13
HRAS 0.025 0.009 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.039 -10000 0 -0.3 5 5
ITGA5 0.026 0.006 -10000 0 -10000 0 0
BAX 0.007 0.042 -10000 0 -0.4 4 4
EPB41 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.036 -10000 0 -0.27 5 5
LAMA3 0 0.13 -10000 0 -0.69 12 12
EZR 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.037 -10000 0 -0.69 1 1
Syndecan-2/MMP2 0.022 0.056 -10000 0 -0.41 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.006 0.052 -10000 0 -10000 0 0
dendrite morphogenesis 0.021 0.059 -10000 0 -0.36 8 8
Syndecan-2/GM-CSF 0.043 0.045 -10000 0 -0.34 4 4
determination of left/right symmetry 0.01 0.045 -10000 0 -0.36 5 5
Syndecan-2/PKC delta 0.026 0.041 -10000 0 -0.31 5 5
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.026 0.041 -10000 0 -0.43 2 2
MAPK1 -0.021 0.04 -10000 0 -0.43 2 2
Syndecan-2/RACK1 0.037 0.037 -10000 0 -0.39 2 2
NF1 0.025 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.045 -10000 0 -0.36 5 5
ITGA2 -0.029 0.066 -10000 0 -10000 0 0
MAPK8 0.01 0.05 -10000 0 -0.44 4 4
Syndecan-2/alpha2/beta1 Integrin 0.033 0.13 -10000 0 -0.42 25 25
Syndecan-2/Kininogen 0.023 0.042 -10000 0 -0.31 5 5
ITGB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.02 0.037 -10000 0 -0.37 2 2
Syndecan-2/CASK/Protein 4.1 0.023 0.037 -10000 0 -0.28 5 5
extracellular matrix organization 0.026 0.037 -10000 0 -0.36 3 3
actin cytoskeleton reorganization 0.044 0.05 0.17 1 -0.34 5 6
Syndecan-2/Caveolin-2/Ras 0.039 0.042 -10000 0 -0.41 3 3
Syndecan-2/Laminin alpha3 0.011 0.093 -10000 0 -0.43 15 15
Syndecan-2/RasGAP 0.049 0.038 -10000 0 -0.37 2 2
alpha5/beta1 Integrin 0.038 0.009 -10000 0 -10000 0 0
PRKCD 0.026 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.059 -10000 0 -0.36 8 8
GO:0007205 0.003 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.039 0.037 -10000 0 -0.36 2 2
RHOA 0.026 0.004 -10000 0 -10000 0 0
SDCBP 0.026 0.004 -10000 0 -10000 0 0
TNFRSF13B -0.14 0.29 -10000 0 -0.69 81 81
RASA1 0.026 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.006 0.052 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.039 -10000 0 -0.33 4 4
TGFB1 0.023 0.017 -10000 0 -10000 0 0
CASP3 0.016 0.039 -10000 0 -0.41 2 2
FN1 -0.071 0.06 -10000 0 -10000 0 0
Syndecan-2/IL8 0.022 0.082 -10000 0 -0.39 13 13
SDC2 0.01 0.045 -10000 0 -0.36 5 5
KNG1 -0.003 0.033 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.037 -10000 0 -0.36 3 3
TRAPPC4 0.026 0.005 -10000 0 -10000 0 0
CSF2 -0.068 0.058 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.026 0.037 -10000 0 -0.36 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.037 -10000 0 -0.27 5 5
Syndecan-2/Ezrin 0.041 0.038 -10000 0 -0.3 4 4
PRKACA 0.016 0.033 -10000 0 -0.41 2 2
angiogenesis 0.022 0.082 -10000 0 -0.39 13 13
MMP2 0.018 0.068 -10000 0 -0.61 4 4
IL8 -0.021 0.11 -10000 0 -0.69 8 8
calcineurin-NFAT signaling pathway -0.078 0.2 -10000 0 -0.45 83 83
Nectin adhesion pathway

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
PDGFRB 0.026 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.022 0.097 -10000 0 -0.54 10 10
PTK2 0.012 0.13 -10000 0 -0.57 16 16
positive regulation of JNK cascade 0.018 0.088 -10000 0 -0.34 16 16
CDC42/GDP 0.035 0.13 0.4 2 -0.46 18 20
Rac1/GDP 0.031 0.12 -10000 0 -0.47 16 16
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.027 0.11 -10000 0 -0.42 16 16
nectin-3/I-afadin 0.014 0.12 -10000 0 -0.51 17 17
RAPGEF1 0.014 0.12 0.35 1 -0.52 15 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0.14 -10000 0 -0.58 17 17
PDGFB-D/PDGFRB 0.026 0.006 -10000 0 -10000 0 0
TLN1 -0.003 0.06 -10000 0 -0.8 1 1
Rap1/GTP 0.017 0.084 -10000 0 -0.36 14 14
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.014 0.12 -10000 0 -0.51 17 17
PVR 0.025 0.006 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.02 0.16 0.44 2 -0.58 20 22
MLLT4 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
PI3K 0.056 0.098 -10000 0 -0.42 14 14
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.017 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.013 0.1 -10000 0 -0.38 16 16
PVRL1 0.023 0.02 -10000 0 -10000 0 0
PVRL3 -0.006 0.15 -10000 0 -0.69 17 17
PVRL2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.025 0.006 -10000 0 -10000 0 0
CLDN1 -0.097 0.1 -10000 0 -0.63 10 10
JAM-A/CLDN1 0.049 0.12 -10000 0 -0.41 22 22
SRC 0.011 0.15 -10000 0 -0.65 17 17
ITGB3 0.007 0.11 -10000 0 -0.66 10 10
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.017 -10000 0 -10000 0 0
FARP2 0.022 0.15 -10000 0 -0.56 19 19
RAC1 0.025 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.028 0.1 -10000 0 -0.44 17 17
nectin-1/I-afadin 0.036 0.017 -10000 0 -10000 0 0
nectin-2/I-afadin 0.037 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.03 0.1 -10000 0 -0.45 16 16
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.008 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.018 0.088 -10000 0 -0.34 16 16
alphaV/beta3 Integrin/Talin 0.021 0.11 -10000 0 -0.56 9 9
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.037 0.01 -10000 0 -10000 0 0
PIP5K1C -0.001 0.064 -10000 0 -0.27 16 16
VAV2 0.004 0.18 0.36 1 -0.63 20 21
RAP1/GDP 0.035 0.11 0.27 1 -0.43 16 17
ITGAV 0.024 0.037 -10000 0 -0.69 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.028 0.1 -10000 0 -0.44 17 17
nectin-3(dimer)/I-afadin/I-afadin 0.014 0.12 -10000 0 -0.51 17 17
Rac1/GTP 0.019 0.12 -10000 0 -0.46 16 16
PTPRM 0.003 0.071 -10000 0 -0.29 16 16
E-cadherin/beta catenin/alpha catenin 0.072 0.026 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.028 0.066 -10000 0 -0.52 5 5
PDGFRB 0.025 0.006 -10000 0 -10000 0 0
SPHK1 0.01 0.035 -10000 0 -0.49 1 1
mol:S1P 0.008 0.036 -10000 0 -0.39 1 1
S1P1/S1P/Gi -0.011 0.13 -10000 0 -0.41 30 30
GNAO1 0.006 0.11 -10000 0 -0.7 8 8
PDGFB-D/PDGFRB/PLCgamma1 -0.01 0.12 -10000 0 -0.48 11 11
PLCG1 -0.012 0.12 -10000 0 -0.39 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.006 -10000 0 -10000 0 0
GNAI2 0.023 0.014 -10000 0 -10000 0 0
GNAI3 0.023 0.014 -10000 0 -10000 0 0
GNAI1 0.021 0.039 -10000 0 -0.69 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.001 0.053 -10000 0 -0.45 5 5
S1P1/S1P 0.001 0.055 -10000 0 -0.32 4 4
negative regulation of cAMP metabolic process -0.01 0.13 -10000 0 -0.4 30 30
MAPK3 -0.026 0.17 -10000 0 -0.57 31 31
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.019 0.064 -10000 0 -0.69 3 3
PLCB2 0.01 0.069 0.43 3 -0.31 3 6
RAC1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.049 -10000 0 -0.29 3 3
receptor internalization 0.001 0.053 -10000 0 -0.3 4 4
PTGS2 -0.072 0.32 0.63 3 -1 38 41
Rac1/GTP 0.009 0.048 -10000 0 -0.29 3 3
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.052 -10000 0 -0.69 2 2
negative regulation of T cell proliferation -0.01 0.13 -10000 0 -0.4 30 30
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.016 -10000 0 -10000 0 0
MAPK1 -0.029 0.18 -10000 0 -0.6 31 31
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.068 -10000 0 -0.34 3 3
ABCC1 0.025 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.025 0.009 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.039 0.025 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.001 0.068 -10000 0 -0.32 5 5
KAT2B 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.011 0.078 0.24 9 -0.35 10 19
RAR alpha/9cRA/Cyclin H 0.026 0.099 -10000 0 -0.35 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.012 0.067 0.24 1 -0.35 6 7
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.012 0.072 -10000 0 -0.39 4 4
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.009 0.14 -10000 0 -0.54 20 20
NCOA2 -0.018 0.17 -10000 0 -0.69 23 23
NCOA3 0.026 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.009 -10000 0 -10000 0 0
RARG 0.026 0.006 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.011 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.023 0.052 -10000 0 -0.69 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.003 0.13 -10000 0 -0.52 20 20
RARA 0.003 0.07 -10000 0 -0.28 21 21
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.007 0.11 0.24 1 -0.45 14 15
PRKCA -0.011 0.16 -10000 0 -0.69 20 20
RXRs/RARs/NRIP1/9cRA/HDAC1 0.004 0.15 0.41 3 -0.53 22 25
RXRG -0.02 0.095 -10000 0 -0.39 22 22
RXRA 0.003 0.075 -10000 0 -0.29 21 21
RXRB 0 0.092 -10000 0 -0.38 20 20
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RBP1 0.015 0.083 -10000 0 -0.69 5 5
CRBP1/9-cic-RA 0.011 0.063 -10000 0 -0.52 5 5
RARB 0.009 0.12 -10000 0 -0.69 10 10
PRKCG 0.021 0.014 -10000 0 -10000 0 0
MNAT1 0.026 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.013 0.14 -10000 0 -0.57 21 21
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.006 0.13 -10000 0 -0.48 21 21
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.085 0.3 2 -0.4 7 9
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.15 0.4 3 -0.52 22 25
positive regulation of DNA binding 0.016 0.09 -10000 0 -0.34 19 19
NRIP1 0.005 0.14 0.49 1 -0.72 4 5
RXRs/RARs -0.003 0.14 -10000 0 -0.53 22 22
RXRs/RXRs/DNA/9cRA -0.016 0.13 -10000 0 -0.54 20 20
PRKACA 0.025 0.007 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.052 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.044 0.064 -10000 0 -10000 0 0
CCNH 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.017 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.027 0.008 -10000 0 -10000 0 0
epithelial cell differentiation 0.053 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.021 0.085 0.48 9 -10000 0 9
EGFR 0.016 0.082 -10000 0 -0.69 5 5
EPHA2 0.025 0.011 -10000 0 -10000 0 0
MYO6 0.032 0.074 0.44 10 -10000 0 10
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.051 0.013 -10000 0 -10000 0 0
AQP5 0.001 0.11 -10000 0 -0.55 14 14
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.054 0.41 6 -10000 0 6
regulation of calcium-dependent cell-cell adhesion -0.006 0.061 0.39 6 -10000 0 6
EGF -0.072 0.24 -10000 0 -0.68 51 51
NCKAP1 0.026 0.005 -10000 0 -10000 0 0
AQP3 -0.047 0.18 -10000 0 -0.55 39 39
cortical microtubule organization 0.053 0.016 -10000 0 -10000 0 0
GO:0000145 0.012 0.054 0.4 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.059 0.017 -10000 0 -10000 0 0
MLLT4 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.013 0.018 -10000 0 -10000 0 0
PVRL2 0.025 0.006 -10000 0 -10000 0 0
ZYX 0.018 0.02 -10000 0 -10000 0 0
ARF6/GTP 0.065 0.027 -10000 0 -10000 0 0
CDH1 0.025 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.012 0.15 -10000 0 -0.37 54 54
RhoA/GDP 0.055 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.02 0.059 0.41 7 -10000 0 7
IGF-1R heterotetramer 0.026 0.003 -10000 0 -10000 0 0
GIT1 0.025 0.007 -10000 0 -10000 0 0
IGF1R 0.026 0.003 -10000 0 -10000 0 0
IGF1 -0.12 0.28 -10000 0 -0.69 74 74
DIAPH1 0.048 0.05 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.053 0.016 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL 0.021 0.059 0.42 7 -10000 0 7
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.013 0.041 0.35 2 -0.37 1 3
Ephrin A1/EPHA2 0.046 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.005 -10000 0 -10000 0 0
MGAT3 -0.007 0.062 0.39 6 -10000 0 6
HGF/MET 0 0.14 -10000 0 -0.39 43 43
HGF -0.065 0.24 -10000 0 -0.69 47 47
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.027 0.008 -10000 0 -10000 0 0
actin cable formation 0.068 0.14 0.55 22 -0.33 1 23
KIAA1543 0.012 0.055 0.37 6 -0.36 1 7
KIFC3 0.019 0.024 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
EXOC3 0.025 0.007 -10000 0 -10000 0 0
ACTN1 0.023 0.04 0.35 3 -10000 0 3
NCK1/GIT1 0.037 0.01 -10000 0 -10000 0 0
mol:GDP 0.053 0.016 -10000 0 -10000 0 0
EXOC4 0.025 0.006 -10000 0 -10000 0 0
STX4 0.019 0.024 -10000 0 -10000 0 0
PIP5K1C 0.024 0.054 0.41 6 -10000 0 6
LIMA1 0.026 0.006 -10000 0 -10000 0 0
ABI1 0.026 0.004 -10000 0 -10000 0 0
ROCK1 0.044 0.11 0.44 19 -10000 0 19
adherens junction assembly 0.027 0.094 0.48 11 -10000 0 11
IGF-1R heterotetramer/IGF1 -0.032 0.16 -10000 0 -0.37 69 69
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.01 -10000 0 -10000 0 0
MET -0.029 0.065 -10000 0 -10000 0 0
PLEKHA7 0.024 0.055 0.38 6 -0.38 1 7
mol:GTP 0.058 0.023 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.027 0.065 0.5 5 -10000 0 5
cortical actin cytoskeleton stabilization 0.027 0.008 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.02 0.059 0.41 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.027 0.008 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.008 0.12 -10000 0 -0.37 35 35
TC10/GTP 0.041 0.036 -10000 0 -0.37 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.013 0.14 -10000 0 -0.43 34 34
HRAS 0.025 0.009 -10000 0 -10000 0 0
APS homodimer 0.025 0.009 -10000 0 -10000 0 0
GRB14 -0.001 0.14 -10000 0 -0.69 14 14
FOXO3 0.002 0.11 -10000 0 -0.66 10 10
AKT1 -0.024 0.13 0.37 4 -0.65 1 5
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.051 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.006 -10000 0 -10000 0 0
SORBS1 0.022 0.052 -10000 0 -0.69 2 2
CRK 0.025 0.007 -10000 0 -10000 0 0
PTPN1 0.015 0.024 -10000 0 -10000 0 0
CAV1 -0.029 0.13 -10000 0 -0.4 40 40
CBL/APS/CAP/Crk-II/C3G 0.064 0.045 -10000 0 -0.4 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.014 0.14 -10000 0 -0.43 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.007 0.13 -10000 0 -0.38 35 35
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.001 0.095 -10000 0 -0.47 3 3
RPS6KB1 -0.038 0.11 0.31 2 -0.58 1 3
PARD6A 0.025 0.006 -10000 0 -10000 0 0
CBL 0.026 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.028 -10000 0 -0.5 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.006 0.12 -10000 0 -0.58 1 1
HRAS/GTP -0.018 0.098 -10000 0 -0.35 25 25
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.024 0.13 -10000 0 -0.4 28 28
PRKCI 0.014 0.069 -10000 0 -0.51 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.019 0.13 -10000 0 -0.37 44 44
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.044 0.045 -10000 0 -0.35 3 3
PI3K 0.016 0.13 -10000 0 -0.39 35 35
NCK2 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
AKT2 -0.025 0.13 0.38 5 -0.65 1 6
PRKCZ 0.015 0.064 -10000 0 -0.51 2 2
SH2B2 0.025 0.009 -10000 0 -10000 0 0
SHC/SHIP -0.009 0.12 0.3 1 -0.38 29 30
F2RL2 -0.014 0.069 -10000 0 -0.69 1 1
TRIP10 0.025 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.04 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.033 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.063 0.029 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.058 0.042 -10000 0 -0.42 2 2
TC10/GDP 0.019 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.054 0.024 -10000 0 -10000 0 0
INPP5D -0.025 0.12 0.31 1 -0.4 34 35
SOS1 0.026 0.005 -10000 0 -10000 0 0
SGK1 -0.012 0.14 -10000 0 -0.83 11 11
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
IRS1 -0.041 0.21 -10000 0 -0.69 35 35
p62DOK/RasGAP 0.044 0.045 -10000 0 -0.35 3 3
INS 0.019 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.025 0.12 0.3 1 -0.4 34 35
GRB2 0.025 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.038 0.12 0.36 3 -0.47 2 5
PTPRA 0.028 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
TC10/GTP/CIP4 0.033 0.01 -10000 0 -10000 0 0
PDPK1 0.023 0.038 -10000 0 -0.69 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.002 0.091 -10000 0 -0.3 28 28
Insulin Receptor/Insulin/IRS1 -0.001 0.14 -10000 0 -0.42 35 35
Insulin Receptor/Insulin/IRS3 0.032 0.012 -10000 0 -10000 0 0
Par3/Par6 0.061 0.029 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.015 0.11 -10000 0 -0.49 16 16
ATM 0.024 0.037 -10000 0 -0.69 1 1
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
PRKDC 0.026 0.004 -10000 0 -10000 0 0
ATR 0.026 0.004 -10000 0 -10000 0 0
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.022 0.022 -10000 0 -0.39 1 1
protein ubiquitination 0.045 0.092 -10000 0 -0.39 14 14
XRCC5 0.026 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.051 0.013 -10000 0 -10000 0 0
MRE11A 0.026 0.005 -10000 0 -10000 0 0
DNA-PK 0.04 0.024 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.004 0.12 -10000 0 -0.51 19 19
FANCF 0.026 0.005 -10000 0 -10000 0 0
BRCA1 0.025 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.007 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.036 0.011 -10000 0 -10000 0 0
FANCG 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.015 0.11 -10000 0 -0.48 16 16
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.024 0.008 -10000 0 -10000 0 0
NBN 0.026 0.004 -10000 0 -10000 0 0
FANCA 0.018 0.029 -10000 0 -10000 0 0
DNA repair 0.016 0.09 0.4 2 -0.49 4 6
BRCA1/BARD1/ubiquitin 0.015 0.11 -10000 0 -0.48 16 16
BARD1/DNA-PK 0.032 0.094 -10000 0 -0.41 14 14
FANCL 0.026 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.015 0.11 0.49 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.069 -10000 0 -0.3 14 14
BRCA1/BACH1/BARD1/TopBP1 0.031 0.096 -10000 0 -0.44 14 14
BRCA1/BARD1/P53 0.045 0.093 -10000 0 -0.42 13 13
BARD1/CSTF1/BRCA1 0.031 0.096 -10000 0 -0.44 14 14
BRCA1/BACH1 0.025 0.007 -10000 0 -10000 0 0
BARD1 -0.003 0.14 -10000 0 -0.65 16 16
PCNA 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.03 0.096 -10000 0 -0.44 14 14
BRCA1/BARD1/UbcH7 0.02 0.095 -10000 0 -0.44 14 14
BRCA1/BARD1/RAD51/PCNA 0.045 0.093 -10000 0 -0.42 13 13
BARD1/DNA-PK/P53 0.039 0.093 -10000 0 -0.39 14 14
BRCA1/BARD1/Ubiquitin 0.015 0.11 -10000 0 -0.48 16 16
BRCA1/BARD1/CTIP 0.024 0.091 -10000 0 -0.42 14 14
FA complex 0.027 0.03 -10000 0 -0.25 1 1
BARD1/EWS 0.007 0.11 -10000 0 -0.48 16 16
RBBP8 0.014 0.028 -10000 0 -0.52 1 1
TP53 0.025 0.007 -10000 0 -10000 0 0
TOPBP1 0.026 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.043 0.091 0.42 13 -10000 0 13
BRCA1/BARD1 0.051 0.095 -10000 0 -0.4 14 14
CSTF1 0.026 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.003 0.1 -10000 0 -0.49 16 16
CDK2 0.026 0.006 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.014 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.015 0.11 -10000 0 -0.48 16 16
EWSR1 0.02 0.012 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.022 0.037 -9999 0 -10000 0 0
TP53 -0.007 0.035 -9999 0 -0.18 14 14
Senescence -0.007 0.035 -9999 0 -0.18 14 14
Apoptosis -0.007 0.035 -9999 0 -0.18 14 14
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.008 0.017 -9999 0 -10000 0 0
MDM4 0.025 0.007 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.025 0.05 0.29 9 -0.4 1 10
DAPP1 -0.038 0.13 0.31 4 -0.48 9 13
Src family/SYK family/BLNK-LAT/BTK-ITK -0.057 0.17 0.32 1 -0.54 15 16
mol:DAG -0.018 0.097 0.38 7 -0.27 7 14
HRAS 0.027 0.011 -10000 0 -10000 0 0
RAP1A 0.027 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.063 0.21 1 -0.36 3 4
PLCG2 0.025 0.006 -10000 0 -10000 0 0
PLCG1 0.026 0.005 -10000 0 -10000 0 0
ARF5 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.051 0.3 9 -10000 0 9
ARF1/GTP 0.002 0.016 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
YES1 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.017 0.016 -10000 0 -10000 0 0
ADAP1 -0.001 0.048 0.28 9 -10000 0 9
ARAP3 0 0.051 0.3 9 -10000 0 9
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PREX1 0.026 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.007 -10000 0 -10000 0 0
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.007 -10000 0 -10000 0 0
NRAS 0.027 0.008 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
FGR 0.024 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.07 0.34 8 -10000 0 8
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.049 0.074 -10000 0 -0.69 1 1
ZAP70 -0.005 0.14 -10000 0 -0.67 15 15
mol:IP3 -0.015 0.066 0.23 7 -0.21 3 10
LYN 0.026 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.035 0.074 0.31 7 -0.37 4 11
RhoA/GDP 0.036 0.043 0.34 2 -10000 0 2
PDK1/Src/Hsp90 0.049 0.03 -10000 0 -0.45 1 1
BLNK 0.026 0.005 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.033 0.08 0.45 7 -10000 0 7
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.003 0.017 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PTEN 0.022 0.024 -10000 0 -0.36 1 1
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.024 0.041 0.29 8 -10000 0 8
RhoA/GTP 0.023 0.042 0.3 7 -10000 0 7
Src family/SYK family/BLNK-LAT -0.051 0.15 -10000 0 -0.46 19 19
BLK -0.2 0.32 -10000 0 -0.68 112 112
PDPK1 0.023 0.038 -10000 0 -0.69 1 1
CYTH1 0.001 0.057 0.31 10 -10000 0 10
HCK 0.018 0.032 -10000 0 -10000 0 0
CYTH3 -0.002 0.052 0.28 9 -0.41 1 10
CYTH2 0.003 0.064 0.32 13 -10000 0 13
KRAS 0.027 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.089 -10000 0 -0.57 7 7
SGK1 0.018 0.098 -10000 0 -0.62 7 7
INPP5D 0.016 0.035 -10000 0 -10000 0 0
mol:GDP 0.029 0.083 0.31 11 -0.33 6 17
SOS1 0.026 0.005 -10000 0 -10000 0 0
SYK 0.024 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.028 0.052 0.29 8 -10000 0 8
mol:PI-3-4-5-P3 -0.008 0.016 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.017 0.016 -10000 0 -10000 0 0
VAV1 0.012 0.062 -10000 0 -0.69 2 2
mol:PI-3-4-P2 0.009 0.022 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.042 0.03 0.33 1 -10000 0 1
PLEKHA1 0.003 0.017 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.062 -10000 0 -0.36 3 3
LAT 0.018 0.068 -10000 0 -0.61 4 4
Rac1/GTP 0.021 0.062 0.27 2 -0.52 2 4
ITK -0.04 0.12 0.28 9 -0.38 35 44
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.032 0.11 0.38 5 -0.36 9 14
LCK 0.011 0.079 -10000 0 -0.69 4 4
BTK -0.005 0.062 0.3 11 -0.38 2 13
Regulation of Telomerase

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
Telomerase catalytic core complex 0 0.1 0.52 5 -10000 0 5
RAD9A 0.026 0.005 -10000 0 -10000 0 0
AP1 -0.2 0.38 -10000 0 -0.74 117 117
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.054 -10000 0 -0.25 15 15
ER alpha/Oestrogen -0.01 0.11 -10000 0 -0.51 17 17
NFX1/SIN3/HDAC complex 0.031 0.023 -10000 0 -10000 0 0
EGF -0.072 0.24 -10000 0 -0.68 51 51
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.025 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.002 0.087 0.51 2 -10000 0 2
SAP18 0.026 0.006 -10000 0 -10000 0 0
MRN complex 0.051 0.013 -10000 0 -10000 0 0
WT1 0.005 0.044 -10000 0 -10000 0 0
WRN 0.026 0.004 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
SP3 0.026 0.005 -10000 0 -10000 0 0
TERF2IP 0.025 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.007 0.081 -10000 0 -10000 0 0
Mad/Max 0.039 0.009 -10000 0 -10000 0 0
TERT 0 0.11 0.52 5 -10000 0 5
CCND1 0.003 0.11 0.58 5 -10000 0 5
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
TERF2 0.022 0.009 -10000 0 -10000 0 0
PTGES3 0.026 0.006 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
Telomerase/911 0.022 0.06 -10000 0 -10000 0 0
CDKN1B -0.028 0.14 -10000 0 -0.44 39 39
RAD1 0.025 0.006 -10000 0 -10000 0 0
XRCC5 0.026 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.024 0.037 -10000 0 -0.69 1 1
TRF2/PARP2 0.036 0.011 -10000 0 -10000 0 0
UBE3A 0.027 0.004 -10000 0 -10000 0 0
JUN -0.13 0.3 -10000 0 -0.69 82 82
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.16 0.32 -10000 0 -0.69 100 100
IFN-gamma/IRF1 -0.015 0.17 -10000 0 -0.5 42 42
PARP2 0.026 0.005 -10000 0 -10000 0 0
BLM 0.026 0.008 -10000 0 -10000 0 0
Telomerase 0.011 0.1 -10000 0 -0.46 10 10
IRF1 0.029 0.009 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.67 17 17
KU/TER 0.029 0.018 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.028 -10000 0 -0.47 1 1
ubiquitin-dependent protein catabolic process 0.036 0.041 -10000 0 -0.41 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.036 0.042 -10000 0 -0.42 2 2
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
ATM 0.009 0.027 -10000 0 -0.49 1 1
SMAD3 0.014 0.01 -10000 0 -10000 0 0
ABL1 0.024 0.008 -10000 0 -10000 0 0
MXD1 0.026 0.005 -10000 0 -10000 0 0
MRE11A 0.026 0.005 -10000 0 -10000 0 0
HUS1 0.025 0.006 -10000 0 -10000 0 0
RPS6KB1 0.025 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.015 0.078 -10000 0 -10000 0 0
NR2F2 0.025 0.003 -10000 0 -10000 0 0
MAPK3 -0.002 0.013 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.023 0.017 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
HNRNPC 0.026 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.027 -10000 0 -0.49 1 1
NBN 0.026 0.004 -10000 0 -10000 0 0
EGFR 0.016 0.082 -10000 0 -0.69 5 5
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.044 0.2 -10000 0 -0.52 55 55
MYC 0.013 0.097 -10000 0 -0.69 7 7
IL2 0.019 0.009 -10000 0 -10000 0 0
KU 0.029 0.018 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
TGFB1 0.023 0.017 -10000 0 -10000 0 0
TRF2/BLM 0.036 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.004 0.088 0.52 2 -10000 0 2
SP1/HDAC2 0.04 0.01 -10000 0 -10000 0 0
PINX1 0.026 0.004 -10000 0 -10000 0 0
Telomerase/EST1A 0.007 0.079 -10000 0 -10000 0 0
Smad3/Myc 0.02 0.063 -10000 0 -0.42 7 7
911 complex 0.051 0.014 -10000 0 -10000 0 0
IFNG -0.057 0.22 -10000 0 -0.68 42 42
Telomerase/PinX1 0.007 0.081 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.012 0.064 0.34 1 -0.43 2 3
SIN3B 0.025 0.007 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.004 0.078 -10000 0 -10000 0 0
response to DNA damage stimulus 0.004 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.071 0.021 -10000 0 -10000 0 0
TRF2/WRN 0.036 0.01 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.007 0.081 -10000 0 -10000 0 0
E2F1 -0.014 0.062 -10000 0 -10000 0 0
ZNFX1 0.026 0.005 -10000 0 -10000 0 0
PIF1 0.017 0.075 -10000 0 -0.69 4 4
NCL 0.026 0.005 -10000 0 -10000 0 0
DKC1 0.024 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.13 0.29 -10000 0 -0.68 80 80
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.007 -10000 0 -10000 0 0
TCEB1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.041 0.35 1 -10000 0 1
HIF1A 0.008 0.026 -10000 0 -0.25 2 2
COPS5 0.026 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.054 0.049 -10000 0 -0.39 2 2
FIH (dimer) 0.026 0.004 -10000 0 -10000 0 0
CDKN2A -0.028 0.065 -10000 0 -10000 0 0
ARNT/IPAS -0.081 0.22 -10000 0 -0.5 80 80
HIF1AN 0.026 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.031 0.053 0.3 7 -10000 0 7
CUL2 0.026 0.004 -10000 0 -10000 0 0
OS9 0.026 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.051 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.03 0.039 0.28 1 -10000 0 1
PHD1-3/OS9 0.049 0.074 -10000 0 -0.42 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.052 0.04 -10000 0 -10000 0 0
VHL 0.022 0.052 -10000 0 -0.69 2 2
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.054 0.33 6 -10000 0 6
EGLN3 0.004 0.11 -10000 0 -0.69 8 8
EGLN2 0.025 0.006 -10000 0 -10000 0 0
EGLN1 0.025 0.007 -10000 0 -10000 0 0
TP53 0.025 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.024 0.075 -10000 0 -0.51 6 6
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.041 0.056 0.31 6 -10000 0 6
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.006 0.018 0.12 1 -0.12 4 5
BUB1B 0.015 0.037 0.22 8 -0.15 1 9
PLK1 0.013 0.033 0.16 12 -0.1 1 13
PLK1S1 0.016 0.029 0.18 9 -10000 0 9
KIF2A 0.02 0.069 0.33 16 -10000 0 16
regulation of mitotic centrosome separation 0.013 0.033 0.16 12 -0.1 1 13
GOLGA2 0.024 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.04 0.032 -10000 0 -10000 0 0
WEE1 0.022 0.048 0.28 6 -0.24 4 10
cytokinesis 0.017 0.057 0.29 7 -0.3 1 8
PP2A-alpha B56 0.057 0.068 -10000 0 -0.48 3 3
AURKA 0.015 0.025 0.16 8 -10000 0 8
PICH/PLK1 0.018 0.014 -10000 0 -10000 0 0
CENPE 0.013 0.052 0.26 11 -0.4 1 12
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.02 0.069 0.33 16 -10000 0 16
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.007 -10000 0 -10000 0 0
TPX2 0.016 0.03 0.19 9 -10000 0 9
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.034 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.014 0.027 0.15 3 -0.25 2 5
GORASP1 0.026 0.004 -10000 0 -10000 0 0
metaphase 0.002 0.006 0.023 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.021 0.1 12 -0.051 1 13
G2 phase of mitotic cell cycle 0 0.004 0.019 10 -10000 0 10
STAG2 0.025 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.022 0.037 -10000 0 -0.47 2 2
spindle elongation 0.013 0.033 0.16 12 -0.1 1 13
ODF2 0.024 0.008 -10000 0 -10000 0 0
BUB1 0.032 0.073 -10000 0 -0.49 7 7
TPT1 0.006 0.044 0.16 5 -0.18 16 21
CDC25C 0.02 0.027 0.2 5 -10000 0 5
CDC25B 0.026 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.018 0.12 4 -0.12 1 5
RHOA 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.041 0.013 -10000 0 -10000 0 0
CDC14B 0.003 0.044 -10000 0 -0.4 4 4
CDC20 0.024 0.016 -10000 0 -10000 0 0
PLK1/PBIP1 0.011 0.022 0.14 5 -10000 0 5
mitosis -0.001 0.003 0.019 5 -10000 0 5
FBXO5 0.014 0.037 0.24 7 -10000 0 7
CDC2 0.001 0.001 0.01 1 -10000 0 1
NDC80 0.002 0.052 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.029 0.17 2 -0.23 3 5
ERCC6L 0.024 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.012 0.03 0.13 15 -10000 0 15
microtubule cytoskeleton organization 0.006 0.044 0.16 5 -0.18 16 21
G2/M transition DNA damage checkpoint 0 0.004 0.02 11 -10000 0 11
PPP1R12A 0.026 0.006 -10000 0 -10000 0 0
interphase 0 0.004 0.02 11 -10000 0 11
PLK1/PRC1-2 0.04 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.021 -10000 0 -10000 0 0
RAB1A 0.026 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.03 0.14 13 -10000 0 13
mitotic prometaphase 0 0.004 0.026 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.026 -10000 0 -10000 0 0
microtubule-based process 0.026 0.025 -10000 0 -10000 0 0
Golgi organization 0.013 0.033 0.16 12 -0.1 1 13
Cohesin/SA2 0.02 0.016 0.17 1 -10000 0 1
PPP1CB/MYPT1 0.038 0.009 -10000 0 -10000 0 0
KIF20A 0 0.053 -10000 0 -10000 0 0
APC/C/CDC20 0.026 0.025 0.2 3 -10000 0 3
PPP2R1A 0.025 0.007 -10000 0 -10000 0 0
chromosome segregation 0.011 0.022 0.14 5 -10000 0 5
PRC1 0.026 0.003 -10000 0 -10000 0 0
ECT2 0.012 0.035 0.22 8 -10000 0 8
C13orf34 0.01 0.029 0.14 12 -0.082 1 13
NUDC 0.014 0.029 0.17 2 -0.23 3 5
regulation of attachment of spindle microtubules to kinetochore 0.015 0.037 0.22 8 -0.15 1 9
spindle assembly 0.015 0.041 0.17 17 -10000 0 17
spindle stabilization 0.016 0.028 0.18 9 -10000 0 9
APC/C/HCDH1 0.018 0.04 -10000 0 -0.34 4 4
MKLP2/PLK1 0.026 0.025 -10000 0 -10000 0 0
CCNB1 0.027 0.006 -10000 0 -10000 0 0
PPP1CB 0.026 0.005 -10000 0 -10000 0 0
BTRC 0.026 0.004 -10000 0 -10000 0 0
ROCK2 0.006 0.083 0.25 2 -0.37 15 17
TUBG1 0.015 0.032 0.19 8 -0.16 2 10
G2/M transition of mitotic cell cycle 0.012 0.008 -10000 0 -10000 0 0
MLF1IP 0.007 0.011 -10000 0 -10000 0 0
INCENP 0.026 0.005 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.026 0.005 -10000 0 -10000 0 0
NFATC1 0.033 0.093 0.44 8 -0.4 5 13
NFATC2 -0.015 0.09 0.28 9 -0.26 15 24
NFATC3 0.017 0.01 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.013 0.091 0.27 1 -0.37 9 10
Exportin 1/Ran/NUP214 0.045 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0 0.1 -10000 0 -0.42 7 7
BCL2/BAX 0.005 0.13 -10000 0 -0.5 22 22
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.007 0.02 -10000 0 -10000 0 0
BAX 0.025 0.007 -10000 0 -10000 0 0
MAPK14 0.024 0.005 -10000 0 -10000 0 0
BAD 0.026 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.002 0.097 0.38 3 -0.36 9 12
Calcineurin A alpha-beta B1/BCL2 -0.015 0.17 -10000 0 -0.68 22 22
FKBP8 0.025 0.007 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.002 0.096 0.35 9 -0.38 3 12
KPNB1 0.025 0.007 -10000 0 -10000 0 0
KPNA2 0.025 0.007 -10000 0 -10000 0 0
XPO1 0.025 0.005 -10000 0 -10000 0 0
SFN -0.075 0.11 -10000 0 -0.69 8 8
MAP3K8 0.016 0.074 -10000 0 -0.69 4 4
NFAT4/CK1 alpha 0.017 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.073 0.17 -10000 0 -0.34 84 84
CABIN1 -0.012 0.088 0.27 1 -0.36 8 9
CALM1 0.022 0.01 -10000 0 -10000 0 0
RAN 0.025 0.006 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.014 0.076 -10000 0 -0.69 4 4
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
MAPK3 0.025 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.035 0.012 -10000 0 -10000 0 0
YWHAB 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.053 -10000 0 -0.69 2 2
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.025 0.006 -10000 0 -10000 0 0
FKBP1A 0.026 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.016 0.08 0.28 1 -0.64 1 2
PRKCH 0.026 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.012 0.031 -10000 0 -10000 0 0
CASP3 0.024 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.013 -10000 0 -10000 0 0
apoptosis 0.011 0.041 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.049 -10000 0 -0.33 2 2
PRKCB 0.007 0.057 -10000 0 -0.69 1 1
PRKCE 0.02 0.064 -10000 0 -0.69 3 3
JNK2/NFAT4 0.03 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.038 0.009 -10000 0 -10000 0 0
PRKCD 0.026 0.004 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.023 0.008 -10000 0 -10000 0 0
PRKCA -0.013 0.16 -10000 0 -0.69 20 20
PRKCG 0.003 0.023 -10000 0 -10000 0 0
PRKCQ 0.015 0.085 -10000 0 -0.64 6 6
FKBP38/BCL2 0.005 0.13 -10000 0 -0.5 22 22
EP300 0.009 0.021 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.039 0.092 0.41 7 -0.38 5 12
CaM/Ca2+/FKBP38 0.018 0.026 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.004 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.057 -10000 0 -0.46 4 4
NFATc/ERK1 0.037 0.074 0.4 2 -0.38 5 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.004 0.1 -10000 0 -0.5 4 4
NR4A1 -0.18 0.3 -10000 0 -0.62 115 115
GSK3B 0.023 0.008 -10000 0 -10000 0 0
positive T cell selection 0.017 0.01 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.018 0.063 -10000 0 -0.34 3 3
RCH1/ KPNB1 0.037 0.01 -10000 0 -10000 0 0
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.026 0.005 -10000 0 -10000 0 0
MEF2D 0.012 0.022 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.004 -10000 0 -10000 0 0
NFATc/p38 alpha 0.045 0.093 0.41 9 -0.38 5 14
CREBBP 0.011 0.023 -10000 0 -10000 0 0
BCL2 -0.015 0.17 -10000 0 -0.68 22 22
S1P3 pathway

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
PDGFRB 0.026 0.006 -9999 0 -10000 0 0
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.014 0.046 -9999 0 -0.26 9 9
GNAO1 0.01 0.1 -9999 0 -0.69 8 8
S1P/S1P3/G12/G13 0.046 0.019 -9999 0 -10000 0 0
AKT1 0.023 0.032 -9999 0 -0.31 1 1
AKT3 0.019 0.062 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.006 -9999 0 -10000 0 0
GNAI2 0.028 0.004 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
GNAI1 0.025 0.038 -9999 0 -0.69 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.01 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.007 0.062 -9999 0 -0.29 8 8
MAPK3 0.004 0.058 -9999 0 -0.34 1 1
MAPK1 0.015 0.049 -9999 0 -0.33 1 1
JAK2 0.008 0.058 -9999 0 -0.34 1 1
CXCR4 0.004 0.057 -9999 0 -0.34 1 1
FLT1 0.027 0.007 -9999 0 -10000 0 0
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.005 -9999 0 -10000 0 0
SRC 0.004 0.058 -9999 0 -0.34 1 1
S1P/S1P3/Gi 0.007 0.063 -9999 0 -0.29 8 8
RAC1 0.025 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.012 0.066 -9999 0 -0.33 1 1
VEGFA 0.025 0.052 -9999 0 -0.69 2 2
S1P/S1P2/Gi 0.006 0.069 -9999 0 -0.33 9 9
VEGFR1 homodimer/VEGFA homodimer 0.04 0.043 -9999 0 -0.52 2 2
RHOA 0.026 0.004 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.059 0.15 -9999 0 -0.32 93 93
GNAQ 0.024 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.012 -9999 0 -10000 0 0
G12/G13 0.037 0.011 -9999 0 -10000 0 0
GNA14 -0.14 0.3 -9999 0 -0.66 91 91
GNA15 0.011 0.053 -9999 0 -0.69 1 1
GNA12 0.025 0.006 -9999 0 -10000 0 0
GNA13 0.025 0.007 -9999 0 -10000 0 0
GNA11 0.019 0.064 -9999 0 -0.69 3 3
Rac1/GTP 0.011 0.065 -9999 0 -0.33 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.022 0.097 -10000 0 -0.54 10 10
AKT1 0.035 0.081 0.32 2 -0.54 5 7
PTK2B 0.015 0.11 0.35 2 -0.54 12 14
VEGFR2 homodimer/Frs2 0.029 0.081 -10000 0 -0.73 4 4
CAV1 0.01 0.1 -10000 0 -0.69 8 8
CALM1 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.043 0.085 -10000 0 -0.59 6 6
endothelial cell proliferation 0.051 0.16 0.6 16 -0.59 3 19
mol:Ca2+ 0.022 0.076 -10000 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.057 0.082 -10000 0 -0.6 5 5
RP11-342D11.1 0.012 0.075 -10000 0 -0.54 6 6
CDH5 0.025 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.058 0.05 -10000 0 -0.37 4 4
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.021 0.053 -10000 0 -0.69 2 2
HRAS/GDP 0.039 0.063 -10000 0 -0.53 3 3
SH2D2A -0.013 0.15 -10000 0 -0.69 18 18
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.053 0.088 -10000 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.02 0.13 -10000 0 -0.46 23 23
VEGFR1 homodimer 0.025 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.065 0.074 -10000 0 -0.59 3 3
GRB10 0.022 0.074 -10000 0 -0.71 3 3
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
PAK1 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.066 0.08 -10000 0 -0.52 6 6
HRAS 0.025 0.009 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.024 0.069 -10000 0 -0.42 6 6
HIF1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.055 0.081 -10000 0 -0.59 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.018 0.074 -10000 0 -0.69 4 4
Nck/Pak 0.038 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.085 -10000 0 -0.59 6 6
mol:GDP 0.051 0.069 -10000 0 -0.57 3 3
mol:NADP 0.039 0.099 0.49 6 -0.47 3 9
eNOS/Hsp90 0.041 0.077 -10000 0 -0.44 3 3
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.022 0.077 -10000 0 -0.55 6 6
HIF1A/ARNT 0.036 0.012 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.024 0.052 -10000 0 -0.69 2 2
VEGFC 0.024 0.037 -10000 0 -0.69 1 1
FAK1/Vinculin 0.035 0.11 0.42 1 -0.64 6 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.044 0.12 -10000 0 -0.56 12 12
PTPN6 0.026 0.005 -10000 0 -10000 0 0
EPAS1 0.029 0.052 -10000 0 -0.45 4 4
mol:L-citrulline 0.039 0.099 0.49 6 -0.47 3 9
ITGAV 0.024 0.037 -10000 0 -0.69 1 1
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.056 0.083 -10000 0 -0.6 5 5
VEGFR2 homodimer/VEGFA homodimer 0.048 0.085 -10000 0 -0.59 6 6
VEGFR2/3 heterodimer 0.024 0.1 -10000 0 -0.66 7 7
VEGFB 0.026 0.005 -10000 0 -10000 0 0
MAPK11 0.007 0.081 0.38 1 -0.56 6 7
VEGFR2 homodimer 0.016 0.089 -10000 0 -0.82 4 4
FLT1 0.025 0.006 -10000 0 -10000 0 0
NEDD4 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.002 0.081 0.37 1 -0.61 4 5
MAPK1 -0.005 0.083 0.33 2 -0.62 4 6
VEGFA145/NRP2 0.039 0.043 -10000 0 -0.52 2 2
VEGFR1/2 heterodimer 0.028 0.081 -10000 0 -0.73 4 4
KDR 0.016 0.089 -10000 0 -0.82 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.082 -10000 0 -0.55 6 6
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.011 0.11 0.42 11 -0.57 5 16
PI3K 0.04 0.082 -10000 0 -0.64 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.044 0.085 -10000 0 -0.59 6 6
FES 0.023 0.079 -10000 0 -0.55 6 6
GAB1 0.027 0.077 -10000 0 -0.6 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.085 -10000 0 -0.59 6 6
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.034 0.089 -10000 0 -0.51 4 4
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.085 -10000 0 -0.59 6 6
PI3K/GAB1 0.047 0.077 -10000 0 -0.54 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.067 0.083 -10000 0 -0.54 6 6
PRKACA 0.025 0.007 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.1 -10000 0 -0.67 7 7
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.074 -10000 0 -0.53 6 6
actin cytoskeleton reorganization 0.02 0.13 -10000 0 -0.45 23 23
PTK2 0.021 0.11 0.31 1 -0.69 6 7
EDG1 0.012 0.075 -10000 0 -0.54 6 6
mol:DAG 0.022 0.077 -10000 0 -0.55 6 6
CaM/Ca2+ 0.034 0.073 -10000 0 -0.5 6 6
MAP2K3 0.009 0.084 0.36 1 -0.49 8 9
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.051 0.083 -10000 0 -0.65 4 4
PLCG1 0.022 0.078 -10000 0 -0.55 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.054 0.084 -10000 0 -0.56 6 6
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
YES1 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.043 0.085 -10000 0 -0.59 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.043 0.085 -10000 0 -0.59 6 6
cell migration 0.04 0.089 0.33 1 -0.53 6 7
mol:PI-3-4-5-P3 0.039 0.076 -10000 0 -0.59 4 4
FYN 0.026 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.027 0.073 -10000 0 -0.51 6 6
mol:NO 0.039 0.099 0.49 6 -0.47 3 9
PXN 0.026 0.006 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.058 -10000 0 -0.53 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.041 0.079 -10000 0 -0.65 4 4
VHL 0.022 0.052 -10000 0 -0.69 2 2
ITGB3 0.007 0.11 -10000 0 -0.66 10 10
NOS3 0.038 0.11 0.5 6 -0.54 3 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.039 0.09 -10000 0 -0.56 7 7
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.007 0.12 0.36 1 -0.42 23 24
PRKCB 0.006 0.079 0.36 1 -0.53 6 7
VCL 0.026 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.029 0.078 -10000 0 -0.54 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.042 0.085 -10000 0 -0.59 6 6
VEGFA165/NRP2 0.039 0.043 -10000 0 -0.52 2 2
MAPKKK cascade 0.048 0.075 0.35 1 -0.53 3 4
NRP2 0.013 0.04 -10000 0 -10000 0 0
VEGFC homodimer 0.024 0.037 -10000 0 -0.69 1 1
NCK1 0.026 0.004 -10000 0 -10000 0 0
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.034 0.11 -10000 0 -0.64 6 6
MAP3K13 0.018 0.089 -10000 0 -0.48 10 10
PDPK1 0.024 0.072 -10000 0 -0.54 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.009 0.088 -10000 0 -0.39 16 16
CCNA2 0.023 0.021 -10000 0 -10000 0 0
PIK3CA 0.025 0.037 -10000 0 -0.69 1 1
JAK3 -0.006 0.056 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
JAK1 0.026 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.004 0.13 -10000 0 -0.57 13 13
SHC1 0.025 0.007 -10000 0 -10000 0 0
SP1 0.032 0.007 -10000 0 -10000 0 0
IL2RA -0.022 0.18 -10000 0 -0.89 16 16
IL2RB 0.001 0.1 -10000 0 -0.62 9 9
SOS1 0.026 0.005 -10000 0 -10000 0 0
IL2RG -0.013 0.14 -10000 0 -0.63 16 16
G1/S transition of mitotic cell cycle 0.032 0.061 0.43 5 -0.51 1 6
PTPN11 0.026 0.006 -10000 0 -10000 0 0
CCND2 0.022 0.005 -10000 0 -10000 0 0
LCK 0.012 0.079 -10000 0 -0.69 4 4
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.012 0.017 -10000 0 -10000 0 0
CDK6 0.023 0.037 -10000 0 -0.69 1 1
CCND3 0.008 0.11 -10000 0 -0.64 6 6
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.016 0.075 0.69 4 -10000 0 4
PI3K Class IB/PDE3B 0.016 0.075 -10000 0 -0.69 4 4
PDE3B 0.016 0.075 -10000 0 -0.69 4 4
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.017 0.04 -10000 0 -0.25 1 1
STMN1 0.003 0.039 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.063 0.04 -10000 0 -0.46 1 1
Chromosomal passenger complex/Cul3 protein complex 0.013 0.052 -10000 0 -0.26 9 9
BIRC5 0.013 0.053 -10000 0 -0.7 1 1
DES -0.33 0.3 -10000 0 -0.57 219 219
Aurora C/Aurora B/INCENP 0.059 0.027 -10000 0 -10000 0 0
Aurora B/TACC1 0.044 0.02 -10000 0 -10000 0 0
Aurora B/PP2A 0.048 0.021 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.005 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.011 0.056 -10000 0 -10000 0 0
Cul3 protein complex 0.038 0.071 -10000 0 -0.45 7 7
KIF2C 0.016 0.029 -10000 0 -0.48 1 1
PEBP1 0.026 0.006 -10000 0 -10000 0 0
KIF20A -0.001 0.053 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.048 0.021 -10000 0 -10000 0 0
SEPT1 0.024 0.016 -10000 0 -10000 0 0
SMC2 0.024 0.008 -10000 0 -10000 0 0
SMC4 0.026 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.014 0.089 -10000 0 -0.54 8 8
PSMA3 0.026 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.014 0.012 -10000 0 -10000 0 0
AURKB 0.006 0.058 -10000 0 -10000 0 0
AURKC 0.021 0.023 -10000 0 -10000 0 0
CDCA8 0.027 0.014 -10000 0 -10000 0 0
cytokinesis -0.018 0.049 -10000 0 -0.36 1 1
Aurora B/Septin1 0.048 0.061 -10000 0 -10000 0 0
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.028 0.007 -10000 0 -10000 0 0
KLHL13 0.008 0.099 -10000 0 -0.69 7 7
BUB1 -0.027 0.065 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.057 0.047 -10000 0 -0.42 1 1
EVI5 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.053 0.04 -10000 0 -10000 0 0
SGOL1 0.02 0.029 -10000 0 -10000 0 0
CENPA 0.019 0.04 0.2 1 -0.24 3 4
NCAPG 0.01 0.044 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.048 0.021 -10000 0 -10000 0 0
NCAPD2 0.026 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.047 0.022 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
NCAPH 0.004 0.05 -10000 0 -10000 0 0
NPM1 0.011 0.046 -10000 0 -0.33 2 2
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.021 -10000 0 -10000 0 0
PPP1CC 0.026 0.005 -10000 0 -10000 0 0
Centraspindlin 0.045 0.041 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.012 0.047 -10000 0 -0.32 3 3
MYLK 0.014 0.012 -10000 0 -10000 0 0
KIF23 0.02 0.032 -10000 0 -10000 0 0
VIM 0.001 0.034 -10000 0 -10000 0 0
RACGAP1 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.005 0.082 -10000 0 -0.9 2 2
Chromosomal passenger complex 0.017 0.031 -10000 0 -0.28 2 2
Chromosomal passenger complex/EVI5 0.11 0.058 -10000 0 -0.4 1 1
TACC1 0.026 0.004 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.026 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.04 0.071 0.37 1 -0.36 1 2
ERC1 0.026 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.046 -10000 0 -0.52 1 1
NFKBIA 0.02 0.015 -10000 0 -10000 0 0
BIRC2 0.026 0.005 -10000 0 -10000 0 0
IKBKB 0.026 0.004 -10000 0 -10000 0 0
RIPK2 0.026 0.004 -10000 0 -10000 0 0
IKBKG 0.032 0.022 -10000 0 -10000 0 0
IKK complex/A20 0.012 0.14 0.33 1 -0.55 3 4
NEMO/A20/RIP2 0.026 0.004 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.031 0.079 -10000 0 -0.45 3 3
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.034 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.042 0.072 -10000 0 -0.53 1 1
BCL10/MALT1/TRAF6 0.049 0.03 -10000 0 -0.45 1 1
NOD2 0.006 0.057 -10000 0 -0.69 1 1
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.028 0.005 -10000 0 -10000 0 0
MALT1 0.026 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.038 0.008 -10000 0 -10000 0 0
ATM 0.024 0.037 -10000 0 -0.69 1 1
TNF/TNFR1A -0.027 0.18 -10000 0 -0.52 42 42
TRAF6 0.024 0.037 -10000 0 -0.69 1 1
PRKCA -0.013 0.16 -10000 0 -0.69 20 20
CHUK 0.026 0.004 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
TNF -0.057 0.23 -10000 0 -0.69 42 42
NF kappa B1 p50/RelA 0.059 0.015 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.015 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.045 0.078 -10000 0 -0.49 2 2
CYLD 0.025 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.031 0.12 -10000 0 -0.49 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.026 0.004 -9999 0 -10000 0 0
ITGB7 0.005 0.1 -9999 0 -0.65 8 8
ITGA4 0.023 0.021 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.081 -9999 0 -0.49 8 8
alpha4/beta1 Integrin 0.036 0.018 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.022 0.1 -10000 0 -0.51 4 4
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.006 -10000 0 -10000 0 0
STXBP4 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.021 0.11 0.35 8 -0.42 8 16
YWHAZ 0.026 0.004 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
TBC1D4 -0.047 0.17 -10000 0 -0.51 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.026 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.049 0.016 -10000 0 -10000 0 0
YWHAG 0.025 0.006 -10000 0 -10000 0 0
ASIP 0.008 0.041 -10000 0 -10000 0 0
PRKCI 0.026 0.004 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
GYS1 0.016 0.013 0.24 1 -10000 0 1
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
TRIP10 0.025 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.033 0.01 -10000 0 -10000 0 0
AS160/14-3-3 -0.029 0.09 -10000 0 -0.34 11 11
VAMP2 0.025 0.007 -10000 0 -10000 0 0
SLC2A4 0.019 0.12 0.39 6 -0.48 8 14
STX4 0.025 0.006 -10000 0 -10000 0 0
GSK3B 0.022 0.007 -10000 0 -10000 0 0
SFN -0.075 0.11 -10000 0 -0.69 8 8
LNPEP 0.005 0.12 -10000 0 -0.69 11 11
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.015 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.043 0.014 -10000 0 -10000 0 0
CDKN1B 0.021 0.019 -10000 0 -10000 0 0
CDKN1A 0.019 0.02 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.026 0.004 -10000 0 -10000 0 0
FOXO3 0.021 0.019 -10000 0 -10000 0 0
AKT1 0.021 0.017 -10000 0 -10000 0 0
BAD 0.026 0.005 -10000 0 -10000 0 0
AKT3 0.013 0.022 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.021 0.023 -10000 0 -10000 0 0
AKT1/ASK1 0.037 0.037 -10000 0 -0.34 1 1
BAD/YWHAZ 0.049 0.016 -10000 0 -10000 0 0
RICTOR 0.025 0.006 -10000 0 -10000 0 0
RAF1 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.035 0.035 0.33 1 -10000 0 1
TSC1 0.02 0.019 -10000 0 -10000 0 0
YWHAZ 0.026 0.004 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.036 0.28 1 -10000 0 1
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.021 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.02 0.018 -10000 0 -10000 0 0
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
TBC1D4 -0.042 0.14 -10000 0 -0.44 43 43
MAP3K5 0.024 0.037 -10000 0 -0.69 1 1
MAPKAP1 0.024 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.015 0.086 0.32 8 -0.43 6 14
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.023 0.029 -10000 0 -10000 0 0
CASP9 0.023 0.026 -10000 0 -10000 0 0
YWHAB 0.026 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.052 0.41 5 -10000 0 5
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.049 0.03 -10000 0 -0.45 1 1
YWHAE 0.025 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.021 0.023 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.009 -10000 0 -10000 0 0
CHUK 0.021 0.019 -10000 0 -10000 0 0
BAD/BCL-XL 0.045 0.031 -10000 0 -10000 0 0
mTORC2 0.03 0.011 -10000 0 -10000 0 0
AKT2 0.014 0.022 -10000 0 -0.4 1 1
FOXO1-3a-4/14-3-3 family 0.024 0.092 0.43 8 -0.34 4 12
PDPK1 0.023 0.038 -10000 0 -0.69 1 1
MDM2 0.021 0.021 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.035 -10000 0 -0.28 1 1
MDM2/Cbp/p300 0.038 0.03 -10000 0 -10000 0 0
TSC1/TSC2 0.022 0.036 0.44 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.028 -10000 0 -10000 0 0
glucose import -0.053 0.16 -10000 0 -0.43 52 52
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.024 0.026 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.055 0.16 -10000 0 -0.44 52 52
GSK3A 0.023 0.028 -10000 0 -10000 0 0
FOXO1 0.02 0.019 -10000 0 -10000 0 0
GSK3B 0.021 0.019 -10000 0 -10000 0 0
SFN -0.075 0.11 -10000 0 -0.69 8 8
G1/S transition of mitotic cell cycle 0.025 0.039 0.31 2 -10000 0 2
p27Kip1/14-3-3 family 0.018 0.05 0.26 1 -0.34 3 4
PRKACA 0.025 0.007 -10000 0 -10000 0 0
KPNA1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
YWHAG 0.025 0.006 -10000 0 -10000 0 0
RHEB 0.025 0.006 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.004 0.16 -10000 0 -0.45 42 42
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.14 -10000 0 -0.39 41 41
SUMO1 0.026 0.005 -10000 0 -10000 0 0
ZFPM1 0.025 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.008 -10000 0 -10000 0 0
FKBP3 0.026 0.005 -10000 0 -10000 0 0
Histones 0.034 0.083 -10000 0 -10000 0 0
YY1/LSF 0.006 0.065 -10000 0 -0.45 3 3
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.009 0.11 -10000 0 -0.32 40 40
I kappa B alpha/HDAC1 0.009 0.081 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
RELA -0.017 0.11 -10000 0 -0.32 42 42
HDAC1/Smad7 0.049 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.01 0.081 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.03 0.026 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA -0.024 0.12 0.32 1 -0.43 12 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.026 0.008 -10000 0 -10000 0 0
GATA1 0.011 0.02 -10000 0 -10000 0 0
Mad/Max 0.038 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.031 0.066 -10000 0 -0.46 4 4
RBBP7 0.025 0.007 -10000 0 -10000 0 0
NPC 0.015 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
MAX 0.026 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.004 0.084 -10000 0 -10000 0 0
KAT2B 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.019 -10000 0 -10000 0 0
SIN3 complex 0.06 0.033 -10000 0 -0.42 1 1
SMURF1 0.025 0.006 -10000 0 -10000 0 0
CHD3 0.025 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.037 -10000 0 -0.69 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.025 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.009 0.08 -10000 0 -10000 0 0
YY1/HDAC2 0.008 0.054 -10000 0 -0.28 1 1
YY1/HDAC1 0.009 0.052 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.03 0.023 -10000 0 -10000 0 0
PPARG -0.022 0.14 -10000 0 -0.39 45 45
HDAC8/hEST1B 0.045 0.021 -10000 0 -10000 0 0
UBE2I 0.025 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.01 0.081 -10000 0 -10000 0 0
MBD3L2 -0.016 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.016 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.034 0.057 -10000 0 -0.44 2 2
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 -0.004 0.084 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
YY1 0.018 0.011 -10000 0 -10000 0 0
HDAC8 0.025 0.007 -10000 0 -10000 0 0
SMAD7 0.026 0.004 -10000 0 -10000 0 0
NCOR2 0.026 0.006 -10000 0 -10000 0 0
MXD1 0.026 0.005 -10000 0 -10000 0 0
STAT3 0.017 0.011 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.018 0.065 -10000 0 -0.42 3 3
YY1/SAP30/HDAC1 0.02 0.057 -10000 0 -0.32 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.084 -10000 0 -10000 0 0
histone deacetylation 0.036 0.026 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.001 0.076 -10000 0 -10000 0 0
nuclear export -0.044 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.007 -10000 0 -10000 0 0
GATA2/HDAC3 0.01 0.081 -10000 0 -10000 0 0
GATA1/HDAC1 0.033 0.012 -10000 0 -10000 0 0
GATA1/HDAC3 0.007 0.08 -10000 0 -10000 0 0
CHD4 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.027 0.18 -10000 0 -0.52 42 42
SIN3/HDAC complex/Mad/Max 0.029 0.043 -10000 0 -0.67 1 1
NuRD Complex 0.04 0.048 -10000 0 -0.56 1 1
positive regulation of chromatin silencing 0.032 0.082 -10000 0 -10000 0 0
SIN3B 0.025 0.007 -10000 0 -10000 0 0
MTA2 0.026 0.005 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.013 0.057 -10000 0 -0.32 1 1
HDAC complex 0.062 0.021 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.013 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.051 0.014 -10000 0 -10000 0 0
TNF -0.057 0.23 -10000 0 -0.69 42 42
negative regulation of cell growth 0.032 0.044 -10000 0 -0.66 1 1
NuRD/MBD2/PRMT5 Complex 0.03 0.023 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.051 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.031 0.14 -10000 0 -0.41 41 41
SIN3/HDAC complex/NCoR1 0.028 0.046 -10000 0 -0.64 1 1
TFCP2 0.02 0.064 -10000 0 -0.69 3 3
NR2C1 0.026 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.007 -10000 0 -10000 0 0
MBD2 0.026 0.004 -10000 0 -10000 0 0
Canonical Wnt signaling 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
HDAC1 0.027 0.024 -10000 0 -10000 0 0
AES 0.025 0.019 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.01 -10000 0 -10000 0 0
SMAD4 0.026 0.004 -10000 0 -10000 0 0
DKK2 -0.008 0.15 -10000 0 -0.69 16 16
TLE1 0.021 0.055 0.24 1 -0.67 2 3
MACF1 0.026 0.006 -10000 0 -10000 0 0
CTNNB1 0.049 0.1 0.49 15 -10000 0 15
WIF1 -0.014 0.041 -10000 0 -10000 0 0
beta catenin/RanBP3 0.027 0.083 0.39 16 -10000 0 16
KREMEN2 0.015 0.035 -10000 0 -10000 0 0
DKK1 0.003 0.069 -10000 0 -0.69 2 2
beta catenin/beta TrCP1 0.044 0.048 0.38 2 -10000 0 2
FZD1 0.025 0.006 -10000 0 -10000 0 0
AXIN2 -0.034 0.3 0.62 9 -1.4 15 24
AXIN1 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.027 0.072 -10000 0 -0.51 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.036 0.091 -10000 0 -0.73 2 2
Axin1/APC/GSK3 0.031 0.045 0.36 3 -10000 0 3
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.046 0.51 2 -10000 0 2
HNF1A 0.026 0.02 0.23 1 -10000 0 1
CTBP1 0.026 0.019 0.24 1 -10000 0 1
MYC -0.034 0.22 0.6 2 -1.3 9 11
RANBP3 0.025 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.032 0.1 -10000 0 -0.45 15 15
NKD1 0.003 0.12 -10000 0 -0.69 11 11
TCF4 0.026 0.018 0.22 1 -10000 0 1
TCF3 0.025 0.023 0.25 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.062 0.02 -10000 0 -10000 0 0
Ran/GTP 0.019 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.021 0.11 0.47 17 -10000 0 17
LEF1 0.025 0.027 0.21 2 -10000 0 2
DVL1 0.026 0.014 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.1 -10000 0 -0.66 3 3
DKK1/LRP6/Kremen 2 0.048 0.048 -10000 0 -0.48 2 2
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.025 0.017 -10000 0 -10000 0 0
NLK 0.024 0.01 -10000 0 -10000 0 0
CCND1 -0.01 0.09 0.58 2 -0.72 2 4
WNT1 0.018 0.02 -10000 0 -10000 0 0
GSK3A 0.026 0.007 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
PPP2R5D 0.031 0.059 0.33 11 -0.33 1 12
APC 0.022 0.039 0.36 4 -10000 0 4
WNT1/LRP6/FZD1 0.028 0.017 -10000 0 -10000 0 0
CREBBP 0.026 0.02 0.23 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.008 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.011 -10000 0 -10000 0 0
STXBP1 0.024 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.009 0.045 -10000 0 -0.27 3 3
RAB3GAP2/RIMS1/UNC13B 0.047 0.018 -10000 0 -10000 0 0
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 0.021 0.016 -10000 0 -10000 0 0
mol:ACh 0.003 0.045 0.14 17 -0.14 17 34
RAB3GAP2 0.025 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.054 -10000 0 -0.26 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.009 0.045 -10000 0 -0.27 3 3
UNC13B 0.025 0.007 -10000 0 -10000 0 0
CHRNA1 0.007 0.053 -10000 0 -0.69 1 1
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.044 0.12 -10000 0 -0.5 21 21
SNAP25 -0.014 0.074 -10000 0 -0.34 18 18
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.071 0.16 -10000 0 -0.69 21 21
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.054 -10000 0 -0.26 1 1
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.023 0.039 0.31 1 -10000 0 1
PDGFB-D/PDGFRB/SLAP 0.037 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.051 0.015 -10000 0 -10000 0 0
AKT1 0.028 0.084 0.46 10 -10000 0 10
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.028 0.045 0.35 2 -10000 0 2
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
FGR 0.017 0.042 0.36 1 -0.66 1 2
mol:Ca2+ 0.033 0.074 0.4 9 -10000 0 9
MYC 0.031 0.17 0.57 14 -0.78 8 22
SHC1 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.033 0.013 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.038 0.036 -10000 0 -0.46 1 1
GRB10 0.025 0.006 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0.033 0.074 0.4 9 -10000 0 9
PTEN 0.025 0.022 -10000 0 -0.38 1 1
GRB2 0.025 0.007 -10000 0 -10000 0 0
GRB7 0.006 0.047 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.038 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.038 0.01 -10000 0 -10000 0 0
cell cycle arrest 0.037 0.012 -10000 0 -10000 0 0
HRAS 0.025 0.009 -10000 0 -10000 0 0
HIF1A 0.019 0.082 0.44 10 -10000 0 10
GAB1 0.026 0.083 0.41 9 -0.41 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.031 0.1 0.48 13 -0.33 1 14
PDGFB-D/PDGFRB 0.054 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.01 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.019 0.045 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.038 0.009 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.033 0.074 0.41 9 -10000 0 9
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.022 0.039 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.15 0.26 -10000 0 -0.56 110 110
PTPN2 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.009 -10000 0 -10000 0 0
BCAR1 0.025 0.006 -10000 0 -10000 0 0
VAV2 0.031 0.11 0.46 12 -0.48 2 14
CBL 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.009 -10000 0 -10000 0 0
LCK 0.012 0.063 -10000 0 -0.57 4 4
PDGFRB 0.027 0.006 -10000 0 -10000 0 0
ACP1 0.026 0.005 -10000 0 -10000 0 0
HCK 0.024 0.017 -10000 0 -10000 0 0
ABL1 0.025 0.09 0.39 12 -0.5 1 13
PDGFB-D/PDGFRB/CBL 0.021 0.073 0.39 4 -0.46 1 5
PTPN1 0.027 0.005 -10000 0 -10000 0 0
SNX15 0.026 0.005 -10000 0 -10000 0 0
STAT3 0.025 0.007 -10000 0 -10000 0 0
STAT1 0.022 0.022 -10000 0 -10000 0 0
cell proliferation 0.032 0.16 0.53 16 -0.68 8 24
SLA 0.025 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.032 0.019 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
PI3K 0.014 0.022 -10000 0 -0.35 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.05 0.022 -10000 0 -10000 0 0
SH2B2 0.025 0.009 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.028 0.045 0.35 2 -10000 0 2
LYN 0.017 0.034 -10000 0 -0.45 1 1
LRP1 0.024 0.037 -10000 0 -0.69 1 1
SOS1 0.026 0.005 -10000 0 -10000 0 0
STAT5B 0.025 0.007 -10000 0 -10000 0 0
STAT5A 0.025 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.077 0.025 -10000 0 -10000 0 0
SPHK1 0.023 0.019 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.033 0.074 0.41 9 -10000 0 9
PLCG1 0.033 0.075 0.41 9 -10000 0 9
NHERF/PDGFRB 0.05 0.016 -10000 0 -10000 0 0
YES1 0.014 0.059 0.36 1 -0.49 4 5
cell migration 0.049 0.016 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.071 0.031 -10000 0 -10000 0 0
SLC9A3R2 0.025 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.025 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.061 0.026 -10000 0 -10000 0 0
FYN 0.016 0.05 0.38 1 -0.52 2 3
DOK1 0.021 0.016 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.006 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.038 0.14 0.53 16 -0.47 5 21
PRKCD 0.023 0.022 -10000 0 -10000 0 0
FER 0.019 0.037 -10000 0 -0.42 2 2
MAPKKK cascade 0.013 0.055 0.37 1 -10000 0 1
RASA1 0.021 0.017 -10000 0 -10000 0 0
NCK1 0.026 0.004 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.037 0.021 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.036 0.013 -10000 0 -10000 0 0
chemotaxis 0.025 0.089 0.39 12 -0.49 1 13
STAT1-3-5/STAT1-3-5 0.063 0.021 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.019 0.005 -10000 0 -10000 0 0
PTPRJ 0.026 0.005 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.025 0.007 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0.082 -10000 0 -0.69 5 5
CDKN1A -0.01 0.074 -10000 0 -0.62 1 1
PRL-3/alpha Tubulin 0.029 0.029 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.078 0.22 2 -0.53 8 10
AGT 0.004 0.11 -10000 0 -0.69 8 8
CCNA2 -0.072 0.16 -10000 0 -10000 0 0
TUBA1B 0.026 0.006 -10000 0 -10000 0 0
EGR1 -0.09 0.21 -10000 0 -0.51 76 76
CDK2/Cyclin E1 0.016 0.079 -10000 0 -0.55 1 1
MAPK3 0.009 0.022 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.038 0.008 -10000 0 -10000 0 0
MAPK1 0.008 0.019 -10000 0 -10000 0 0
PTP4A1 -0.074 0.17 -10000 0 -10000 0 0
PTP4A3 0.016 0.035 -10000 0 -10000 0 0
PTP4A2 0.026 0.005 -10000 0 -10000 0 0
ITGB1 0.009 0.022 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.014 0.082 -10000 0 -0.62 1 1
Rab GGTase beta/Rab GGTase alpha 0.037 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.055 0.16 -10000 0 -10000 0 0
RABGGTA 0.026 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.008 -10000 0 -10000 0 0
RHOC -0.014 0.084 -10000 0 -0.75 1 1
RHOA -0.015 0.086 -10000 0 -0.63 2 2
cell motility -0.008 0.098 0.3 3 -0.6 2 5
PRL-1/alpha Tubulin -0.055 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.022 0.072 -10000 0 -0.54 5 5
ROCK1 -0.01 0.095 0.28 2 -0.6 2 4
RABGGTB 0.026 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.006 -10000 0 -10000 0 0
mitosis -0.073 0.16 -10000 0 -10000 0 0
ATF5 0.02 0.027 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.009 0.1 -10000 0 -0.69 8 8
CDC42/GTP 0.008 0.07 -10000 0 -0.32 8 8
PLCG1 -0.002 0.064 -10000 0 -0.33 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.011 -10000 0 -10000 0 0
cell migration 0.008 0.068 -10000 0 -0.31 8 8
S1PR5 0.024 0.014 -10000 0 -10000 0 0
S1PR4 0.023 0.017 -10000 0 -10000 0 0
MAPK3 -0.002 0.064 -10000 0 -0.33 8 8
MAPK1 0.01 0.056 -10000 0 -0.33 8 8
S1P/S1P5/Gi 0.001 0.069 -10000 0 -0.33 10 10
GNAI1 0.023 0.037 -10000 0 -0.69 1 1
CDC42/GDP 0.019 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.011 -10000 0 -10000 0 0
RHOA 0.031 0.067 0.44 7 -10000 0 7
S1P/S1P4/Gi 0.001 0.069 -10000 0 -0.33 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.046 0.017 -10000 0 -10000 0 0
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.032 0.089 -10000 0 -10000 0 0
CRKL 0.015 0.049 0.45 3 -10000 0 3
mol:DAG 0.027 0.044 -10000 0 -10000 0 0
HRAS 0.031 0.059 0.4 3 -10000 0 3
MAPK8 0.018 0.046 -10000 0 -0.45 2 2
RAP1A 0.025 0.067 0.48 6 -10000 0 6
GAB1 0.022 0.056 0.45 4 -10000 0 4
MAPK14 0.02 0.03 -10000 0 -10000 0 0
EPO 0.02 0.016 -10000 0 -10000 0 0
PLCG1 0.027 0.045 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.024 0.019 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.015 0.12 -10000 0 -0.44 23 23
GAB1/SHC/GRB2/SOS1 0.047 0.039 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.033 0.021 -10000 0 -10000 0 0
IRS2 0.023 0.062 0.46 5 -10000 0 5
STAT1 0.03 0.065 -10000 0 -10000 0 0
STAT5B 0.028 0.055 -10000 0 -10000 0 0
cell proliferation 0.014 0.057 0.34 5 -0.42 2 7
GAB1/SHIP/PIK3R1/SHP2/SHC 0.038 0.032 -10000 0 -10000 0 0
TEC 0.022 0.056 0.45 4 -10000 0 4
SOCS3 -0.019 0.17 -10000 0 -0.69 23 23
STAT1 (dimer) 0.03 0.065 -10000 0 -10000 0 0
JAK2 0.027 0.014 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.048 -10000 0 -10000 0 0
EPO/EPOR 0.033 0.021 -10000 0 -10000 0 0
LYN 0.025 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.031 0.036 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.024 0.019 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.03 -10000 0 -10000 0 0
mol:IP3 0.027 0.044 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.046 0.041 -10000 0 -10000 0 0
SH2B3 0.026 0.01 -10000 0 -10000 0 0
NFKB1 0.02 0.028 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.069 -10000 0 -0.26 22 22
PTPN6 0.022 0.043 0.3 1 -10000 0 1
TEC/VAV2/GRB2 0.041 0.039 -10000 0 -10000 0 0
EPOR 0.024 0.019 -10000 0 -10000 0 0
INPP5D 0.016 0.035 -10000 0 -10000 0 0
mol:GDP 0.046 0.039 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG2 0.025 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.031 0.038 -10000 0 -10000 0 0
VAV2 0.025 0.064 0.46 6 -10000 0 6
CBL 0.022 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.036 0.035 -10000 0 -10000 0 0
STAT5A 0.028 0.055 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.041 0.088 -10000 0 -0.43 1 1
LYN/PLCgamma2 0.037 0.011 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
BTK 0.014 0.046 -10000 0 -0.37 2 2
BCL2 -0.004 0.23 -10000 0 -0.91 22 22
S1P5 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
telencephalon oligodendrocyte cell migration -0.008 0.069 0.31 8 -10000 0 8
GNAI2 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.009 0.1 -10000 0 -0.69 8 8
RhoA/GTP 0.008 0.07 -10000 0 -0.32 8 8
negative regulation of cAMP metabolic process 0.001 0.068 -10000 0 -0.33 10 10
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.006 -10000 0 -10000 0 0
S1PR5 0.024 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.069 -10000 0 -0.33 10 10
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
GNAI1 0.023 0.037 -10000 0 -0.69 1 1
FoxO family signaling

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
G6PC 0.026 0.12 0.67 9 -10000 0 9
PLK1 0.072 0.1 0.57 3 -0.57 1 4
CDKN1B 0.073 0.095 0.55 4 -10000 0 4
FOXO3 0.068 0.094 -10000 0 -0.62 1 1
KAT2B 0.032 0.017 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.053 0.4 2 -10000 0 2
CAT 0.068 0.094 0.53 1 -10000 0 1
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.033 0.018 -10000 0 -10000 0 0
FOXO1 0.019 0.086 0.44 11 -10000 0 11
MAPK10 0.033 0.027 -10000 0 -10000 0 0
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.072 0.082 0.52 8 -0.4 1 9
response to oxidative stress 0.01 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.084 0.063 -10000 0 -0.42 1 1
XPO1 0.026 0.005 -10000 0 -10000 0 0
EP300 0.021 0.012 -10000 0 -10000 0 0
BCL2L11 0.025 0.1 -10000 0 -0.66 7 7
FOXO1/SKP2 0.016 0.046 -10000 0 -0.38 1 1
mol:GDP 0.01 0.01 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
GADD45A 0.098 0.092 0.5 5 -0.55 2 7
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.002 0.099 -10000 0 -0.45 4 4
MST1 0.03 0.041 -10000 0 -0.68 1 1
CSNK1D 0.025 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.002 0.11 -10000 0 -0.5 8 8
YWHAB 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.031 0.044 0.21 2 -0.41 2 4
MAPK9 0.029 0.018 -10000 0 -10000 0 0
YWHAG 0.025 0.006 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
YWHAZ 0.026 0.004 -10000 0 -10000 0 0
SIRT1 0.026 0.018 -10000 0 -10000 0 0
SOD2 0.1 0.1 0.55 11 -10000 0 11
RBL2 0.081 0.12 0.5 2 -0.68 5 7
RAL/GDP 0.044 0.014 -10000 0 -10000 0 0
CHUK 0.032 0.017 -10000 0 -10000 0 0
Ran/GTP 0.022 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.007 -10000 0 -10000 0 0
RAL/GTP 0.048 0.015 -10000 0 -10000 0 0
CSNK1G1 0.026 0.003 -10000 0 -10000 0 0
FASLG -0.058 0.36 -10000 0 -1.3 27 27
SKP2 0.023 0.037 -10000 0 -0.69 1 1
USP7 0.026 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.017 -10000 0 -10000 0 0
CCNB1 0.072 0.1 0.57 3 -10000 0 3
FOXO1-3a-4/beta catenin 0.097 0.092 0.42 6 -0.41 2 8
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.046 -10000 0 -0.38 1 1
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.018 0.098 -10000 0 -0.68 7 7
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.01 -10000 0 -10000 0 0
ZFAND5 0.079 0.11 0.63 11 -10000 0 11
SFN -0.075 0.11 -10000 0 -0.69 8 8
CDK2 0.026 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.013 0.096 -10000 0 -0.46 8 8
CREBBP 0.025 0.006 -10000 0 -10000 0 0
FBXO32 0.067 0.098 0.55 2 -0.55 1 3
BCL6 0.083 0.13 0.52 2 -0.82 4 6
RALB 0.027 0.005 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.007 0.002 -10000 0 -10000 0 0
SNTA1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.007 0.004 -10000 0 -10000 0 0
MAPK12 0 0.047 -10000 0 -0.4 5 5
CCND1 0.008 0.039 -10000 0 -0.34 3 3
p38 gamma/SNTA1 0.02 0.058 -10000 0 -0.36 6 6
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
G2/M transition checkpoint 0.003 0.053 0.21 6 -0.4 5 11
MAP2K6 0.003 0.055 -10000 0 -0.42 6 6
MAPT 0.01 0.052 0.32 6 -0.37 2 8
MAPK13 0.015 0.004 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.004 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.037 0.012 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.01 0.098 -10000 0 -0.46 16 16
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.036 -10000 0 -10000 0 0
NFKBIA 0.013 0.026 -10000 0 -0.25 3 3
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.007 -10000 0 -10000 0 0
ARRB2 0.015 0.004 -10000 0 -10000 0 0
REL -0.005 0.14 -10000 0 -0.69 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.007 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
NF kappa B1 p50 dimer 0.025 0.028 0.25 6 -10000 0 6
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.016 0.003 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.018 0.037 -10000 0 -0.33 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.038 0.038 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.03 -10000 0 -0.52 1 1
NF kappa B1 p50/RelA 0.018 0.038 -10000 0 -0.34 3 3
IKBKB 0.026 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.024 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.034 -10000 0 -10000 0 0
cell death 0.036 0.037 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.01 0.098 -10000 0 -0.46 16 16
LCK 0.011 0.079 -10000 0 -0.69 4 4
BCL3 0.025 0.009 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.029 0.068 -10000 0 -10000 0 0
CDKN2C 0.03 0.017 -10000 0 -10000 0 0
CDKN2A -0.029 0.069 -10000 0 -10000 0 0
CCND2 0.007 0.019 -10000 0 -10000 0 0
RB1 -0.01 0.043 0.33 1 -0.24 8 9
CDK4 0.005 0.019 -10000 0 -10000 0 0
CDK6 0.007 0.021 -10000 0 -0.16 1 1
G1/S progression 0.011 0.044 0.24 9 -0.33 1 10
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.018 0.03 -10000 0 -0.35 2 2
TRAF2/ASK1 0.031 0.028 -10000 0 -0.45 1 1
ATM 0.024 0.037 -10000 0 -0.69 1 1
MAP2K3 0.038 0.1 0.41 14 -0.39 3 17
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.093 0.34 13 -0.45 3 16
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.083 -10000 0 -0.69 5 5
TXN 0.007 0.003 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
GADD45A 0.026 0.005 -10000 0 -10000 0 0
GADD45B 0 0.13 -10000 0 -0.65 14 14
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
MAP3K4 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.036 0.03 -10000 0 -0.52 1 1
TAK1/TAB family 0.011 0.032 -10000 0 -0.19 2 2
RAC1/OSM/MEKK3 0.048 0.014 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.035 0.055 -10000 0 -0.4 1 1
TRAF6 0.007 0.021 -10000 0 -0.4 1 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.018 0.074 -10000 0 -0.69 4 4
CCM2 0.025 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.029 0.051 -10000 0 -0.45 4 4
MAPK11 0.02 0.012 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.042 0.061 -10000 0 -0.51 4 4
OSM/MEKK3 0.037 0.011 -10000 0 -10000 0 0
TAOK1 -0.023 0.12 -10000 0 -0.41 33 33
TAOK2 0.014 0.022 -10000 0 -0.4 1 1
TAOK3 0.014 0.022 -10000 0 -0.4 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.024 0.037 -10000 0 -0.69 1 1
MAP3K10 0.025 0.006 -10000 0 -10000 0 0
MAP3K3 0.025 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.015 0.039 -10000 0 -0.44 1 1
GADD45/MTK1/MTK1 0.033 0.099 -10000 0 -0.42 15 15
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.026 0.004 -9999 0 -10000 0 0
SMAD2 -0.015 0.044 -9999 0 -0.24 1 1
SMAD3 0.02 0.015 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.041 -9999 0 -0.45 2 2
SMAD4/Ubc9/PIASy 0.048 0.018 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.026 0.062 -9999 0 -10000 0 0
PPM1A 0.026 0.005 -9999 0 -10000 0 0
CALM1 0.026 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.003 0.057 -9999 0 -0.39 2 2
MAP3K1 0.026 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.014 0.11 -9999 0 -0.52 16 16
MAPK3 0.025 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.024 0.008 -9999 0 -10000 0 0
CTDSP1 0.026 0.005 -9999 0 -10000 0 0
CTDSP2 0.026 0.006 -9999 0 -10000 0 0
CTDSPL 0.026 0.004 -9999 0 -10000 0 0
KPNB1 0.025 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.005 0.14 -9999 0 -0.69 16 16
UBE2I 0.025 0.007 -9999 0 -10000 0 0
NUP153 0.027 0.003 -9999 0 -10000 0 0
KPNA2 0.025 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.007 -9999 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.045 0.03 -9999 0 -10000 0 0
CLOCK 0.006 0.12 -9999 0 -0.69 11 11
TIMELESS/CRY2 0.032 0.029 -9999 0 -10000 0 0
DEC1/BMAL1 0.017 0.036 -9999 0 -10000 0 0
ATR 0.026 0.004 -9999 0 -10000 0 0
NR1D1 0.008 0.028 -9999 0 -10000 0 0
ARNTL 0.01 0.045 -9999 0 -10000 0 0
TIMELESS 0.016 0.022 -9999 0 -10000 0 0
NPAS2 0.026 0.024 -9999 0 -0.38 1 1
CRY2 0.026 0.005 -9999 0 -10000 0 0
mol:CO -0.006 0.007 -9999 0 -10000 0 0
CHEK1 0.026 0.005 -9999 0 -10000 0 0
mol:HEME 0.006 0.007 -9999 0 -10000 0 0
PER1 0.025 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.045 0.091 -9999 0 -0.46 11 11
BMAL1/CLOCK 0.015 0.08 -9999 0 -0.44 6 6
S phase of mitotic cell cycle 0.045 0.03 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.045 0.031 -9999 0 -10000 0 0
mol:NADPH 0.006 0.007 -9999 0 -10000 0 0
PER1/TIMELESS 0.031 0.026 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.013 0.013 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.025 -10000 0 -10000 0 0
BIRC5 0.011 0.053 -10000 0 -0.69 1 1
NFKBIA 0.014 0.027 0.25 4 -10000 0 4
CPEB1 -0.024 0.18 -10000 0 -0.67 27 27
AKT1 0.015 0.029 0.25 5 -10000 0 5
NDEL1 0.025 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.025 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.041 0.023 -10000 0 -10000 0 0
GADD45A 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.029 0.024 -10000 0 -10000 0 0
MDM2 0.026 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.006 0.027 -10000 0 -10000 0 0
TP53 0.024 0.011 -10000 0 -10000 0 0
DLG7 0.012 0.011 -10000 0 -10000 0 0
AURKAIP1 0.026 0.005 -10000 0 -10000 0 0
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.043 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.025 0.021 -10000 0 -10000 0 0
AURKA 0.019 0.015 -10000 0 -10000 0 0
AURKB 0.013 0.024 -10000 0 -0.16 3 3
CDC25B 0.02 0.012 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.019 -10000 0 -10000 0 0
mRNA polyadenylation -0.004 0.11 -10000 0 -0.41 25 25
Aurora A/CPEB -0.004 0.11 -10000 0 -0.41 25 25
Aurora A/TACC1/TRAP/chTOG 0.053 0.033 -10000 0 -10000 0 0
BRCA1 0.025 0.007 -10000 0 -10000 0 0
centrosome duplication 0.029 0.024 -10000 0 -10000 0 0
regulation of centrosome cycle 0.04 0.023 -10000 0 -10000 0 0
spindle assembly 0.052 0.032 -10000 0 -10000 0 0
TDRD7 0.024 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.053 0.036 -10000 0 -0.37 1 1
CENPA 0.016 0.032 -10000 0 -0.25 5 5
Aurora A/PP2A 0.029 0.025 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.02 0.016 -10000 0 -10000 0 0
negative regulation of DNA binding 0.023 0.016 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.009 0.019 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.015 -10000 0 -10000 0 0
TACC1 0.026 0.004 -10000 0 -10000 0 0
TACC3 0.026 0.008 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.044 0.02 -10000 0 -10000 0 0
Aurora A/RasGAP 0.029 0.025 -10000 0 -10000 0 0
OAZ1 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.01 -10000 0 -10000 0 0
GIT1 0.025 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.049 0.017 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.006 0.027 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.032 0.22 1 -10000 0 1
PAK1 0.026 0.005 -10000 0 -10000 0 0
CKAP5 0.026 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.015 0.054 -9999 0 -0.36 7 7
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.005 -9999 0 -10000 0 0
DOCK1 0.024 0.037 -9999 0 -0.69 1 1
ITGA4 0.023 0.021 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.054 0.07 -9999 0 -0.42 7 7
EPO 0.004 0.022 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.081 -9999 0 -0.49 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.031 0.016 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.028 -9999 0 -0.42 1 1
PIK3CA 0.024 0.037 -9999 0 -0.69 1 1
PI3K 0.036 0.03 -9999 0 -0.52 1 1
ARF6 0.026 0.005 -9999 0 -10000 0 0
JAK2 0.025 0.011 -9999 0 -10000 0 0
PXN 0.026 0.006 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.006 0.037 -9999 0 -10000 0 0
cell adhesion 0.051 0.069 -9999 0 -0.42 7 7
CRKL/CBL 0.029 0.018 -9999 0 -10000 0 0
ITGB1 0.026 0.004 -9999 0 -10000 0 0
SRC 0.018 0.05 -9999 0 -0.42 3 3
ITGB7 0.005 0.1 -9999 0 -0.65 8 8
RAC1 0.025 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.047 0.048 -9999 0 -0.45 3 3
p130Cas/Crk/Dock1 0.035 0.051 -9999 0 -0.36 4 4
VCAM1 0.018 0.066 -9999 0 -0.69 3 3
RHOA 0.026 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.021 -9999 0 -10000 0 0
BCAR1 0.009 0.046 -9999 0 -0.39 3 3
EPOR 0.024 0.014 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.026 0.005 -9999 0 -10000 0 0
GIT1 0.025 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.028 -9999 0 -0.43 1 1
HIF-2-alpha transcription factor network

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
MMP14 0.013 0.04 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.007 -10000 0 -10000 0 0
TCEB1 0.026 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.095 0.077 -10000 0 -0.39 1 1
EPO 0.12 0.097 -10000 0 -10000 0 0
FIH (dimer) 0.035 0.013 -10000 0 -10000 0 0
APEX1 0.034 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.1 -10000 0 -0.52 1 1
FLT1 0.023 0.11 -10000 0 -0.64 6 6
ADORA2A 0.1 0.1 0.43 1 -10000 0 1
germ cell development 0.12 0.097 -10000 0 -10000 0 0
SLC11A2 0.12 0.099 -10000 0 -10000 0 0
BHLHE40 0.13 0.098 -10000 0 -10000 0 0
HIF1AN 0.035 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.083 0.35 1 -10000 0 1
ETS1 0.037 0.013 -10000 0 -10000 0 0
CITED2 -0.033 0.3 -10000 0 -1.1 27 27
KDR 0.027 0.12 -10000 0 -1.1 4 4
PGK1 0.12 0.098 -10000 0 -10000 0 0
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.12 -10000 0 -10000 0 0
EPAS1 0.059 0.064 -10000 0 -10000 0 0
SP1 0.031 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.11 -10000 0 -0.57 3 3
EFNA1 0.12 0.096 -10000 0 -10000 0 0
FXN 0.12 0.11 0.55 2 -10000 0 2
POU5F1 0.12 0.099 -10000 0 -10000 0 0
neuron apoptosis -0.16 0.12 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.013 0.11 -10000 0 -0.68 8 8
EGLN2 0.034 0.015 -10000 0 -10000 0 0
EGLN1 0.034 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.048 0.039 -10000 0 -0.45 2 2
VHL 0.022 0.052 -10000 0 -0.69 2 2
ARNT 0.034 0.014 -10000 0 -10000 0 0
SLC2A1 0.13 0.11 0.48 5 -10000 0 5
TWIST1 0.12 0.12 0.4 1 -0.58 4 5
ELK1 0.021 0.035 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.087 0.09 -10000 0 -10000 0 0
VEGFA 0.12 0.11 -10000 0 -0.56 2 2
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
DOCK1 0.024 0.037 -9999 0 -0.69 1 1
ITGA4 0.023 0.021 -9999 0 -10000 0 0
RAC1 0.025 0.006 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.081 -9999 0 -0.49 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.05 0.016 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.035 0.065 -9999 0 -0.42 7 7
lamellipodium assembly 0.025 0.053 -9999 0 -0.48 3 3
PIK3CA 0.024 0.037 -9999 0 -0.69 1 1
PI3K 0.036 0.03 -9999 0 -0.52 1 1
ARF6 0.026 0.005 -9999 0 -10000 0 0
TLN1 0.025 0.007 -9999 0 -10000 0 0
PXN 0.015 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.053 0.02 -9999 0 -10000 0 0
cell adhesion 0.052 0.022 -9999 0 -10000 0 0
CRKL/CBL 0.029 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.043 0.015 -9999 0 -10000 0 0
ITGB1 0.026 0.004 -9999 0 -10000 0 0
ITGB7 0.005 0.1 -9999 0 -0.65 8 8
ARF6/GDP 0.023 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.052 0.045 -9999 0 -0.39 3 3
p130Cas/Crk/Dock1 0.047 0.031 -9999 0 -0.45 1 1
VCAM1 0.018 0.066 -9999 0 -0.69 3 3
alpha4/beta1 Integrin/Paxillin/Talin 0.053 0.023 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.021 -9999 0 -10000 0 0
BCAR1 0.025 0.006 -9999 0 -10000 0 0
mol:GDP -0.053 0.02 -9999 0 -10000 0 0
CBL 0.026 0.005 -9999 0 -10000 0 0
PRKACA 0.025 0.007 -9999 0 -10000 0 0
GIT1 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.053 0.023 -9999 0 -10000 0 0
Rac1/GTP 0.026 0.06 -9999 0 -0.54 3 3
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.028 0.03 -10000 0 -10000 0 0
KLHL20 0.013 0.049 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.035 0.04 -10000 0 -10000 0 0
ENAH 0.026 0.027 -10000 0 -10000 0 0
AP1M1 0.025 0.007 -10000 0 -10000 0 0
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.033 0.015 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.031 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.069 -10000 0 -0.42 7 7
RAPGEF1 0.025 0.04 0.35 1 -10000 0 1
CTNND1 0.026 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.035 -10000 0 -10000 0 0
CRK 0.023 0.029 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.049 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.021 0.079 -10000 0 -0.52 7 7
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
NCKAP1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.014 -10000 0 -10000 0 0
DLG1 0.027 0.035 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.012 -10000 0 -10000 0 0
MLLT4 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.058 0.034 -10000 0 -0.42 1 1
PI3K 0.016 0.016 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.036 0.011 -10000 0 -10000 0 0
TIAM1 -0.049 0.074 -10000 0 -0.69 1 1
E-cadherin(dimer)/Ca2+ 0.059 0.017 -10000 0 -10000 0 0
AKT1 0.016 0.02 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.076 0.47 7 -10000 0 7
actin cytoskeleton organization 0.012 0.039 0.2 2 -10000 0 2
CDC42/GDP 0.047 0.083 0.52 8 -10000 0 8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.021 0.007 -10000 0 -10000 0 0
ITGB7 0.005 0.1 -10000 0 -0.65 8 8
RAC1 0.025 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.064 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.044 0.013 -10000 0 -10000 0 0
mol:GDP 0.036 0.091 0.56 8 -10000 0 8
CDC42/GTP/IQGAP1 0.035 0.008 -10000 0 -10000 0 0
JUP 0.025 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.043 0.043 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1 0.034 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.011 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.037 0.25 3 -10000 0 3
NME1 0.025 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.027 0.035 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.023 0.011 -10000 0 -10000 0 0
WASF2 0.007 0.021 -10000 0 -10000 0 0
Rap1/GTP 0.04 0.026 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.063 0.069 -10000 0 -0.4 7 7
CCND1 0.012 0.038 0.22 2 -10000 0 2
VAV2 0.007 0.14 -10000 0 -0.54 17 17
RAP1/GDP 0.045 0.039 0.3 3 -10000 0 3
adherens junction assembly 0.027 0.034 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.007 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.051 0.064 -10000 0 -0.38 7 7
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.028 0.03 -10000 0 -10000 0 0
PIK3CA 0.024 0.037 -10000 0 -0.69 1 1
Rac1/GTP -0.004 0.074 -10000 0 -0.32 1 1
E-cadherin/beta catenin/alpha catenin 0.051 0.014 -10000 0 -10000 0 0
ITGAE 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.036 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.004 0.14 -10000 0 -0.67 15 15
CLTC 0.026 0.02 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.017 0.2 1 -10000 0 1
Dynamin 2/GTP 0.026 0.01 -10000 0 -10000 0 0
EXOC4 0.025 0.006 -10000 0 -10000 0 0
CD59 0.02 0.011 -10000 0 -10000 0 0
CPE 0.007 0.063 -10000 0 -0.45 7 7
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
membrane fusion 0.016 0.006 -10000 0 -10000 0 0
CTNND1 0.02 0.036 0.36 2 -10000 0 2
DNM2 0.025 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.029 0.19 1 -10000 0 1
TSHR 0.013 0.034 -10000 0 -0.46 2 2
INS 0.008 0.062 -10000 0 -0.46 6 6
BIN1 0.026 0.005 -10000 0 -10000 0 0
mol:Choline 0.016 0.006 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.004 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.009 -10000 0 -10000 0 0
JUP 0.02 0.01 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.048 0.027 -10000 0 -0.42 1 1
ARF6/GTP 0.019 0.004 -10000 0 -10000 0 0
CDH1 0.019 0.01 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.019 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.004 -10000 0 -10000 0 0
EXOC2 0.026 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.031 0.013 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.025 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.044 0.024 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.015 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.01 -10000 0 -10000 0 0
ACAP1 0.022 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.016 0.009 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.026 0.021 -10000 0 -10000 0 0
JIP4/KLC1 0.048 0.014 -10000 0 -10000 0 0
EXOC1 0.026 0.004 -10000 0 -10000 0 0
exocyst 0.031 0.013 -10000 0 -10000 0 0
RALA/GTP 0.019 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.01 -10000 0 -10000 0 0
receptor recycling 0.019 0.004 -10000 0 -10000 0 0
CTNNA1 0.018 0.029 0.36 1 -10000 0 1
NME1 0.015 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0.03 0.038 0.33 3 -10000 0 3
IL2RA 0.008 0.051 -10000 0 -10000 0 0
VAMP3 0.015 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.023 0.072 -10000 0 -0.33 14 14
EXOC6 0.026 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.005 -10000 0 -10000 0 0
PLD2 0.016 0.005 -10000 0 -10000 0 0
EXOC5 0.026 0.005 -10000 0 -10000 0 0
PIP5K1C 0.02 0.015 0.19 1 -10000 0 1
SDC1 0.019 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.024 0.007 -10000 0 -10000 0 0
EXOC7 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.048 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.016 0.006 -10000 0 -10000 0 0
endocytosis -0.046 0.026 0.41 1 -10000 0 1
SCAMP2 0.026 0.003 -10000 0 -10000 0 0
ADRB2 0.027 0.089 0.42 8 -0.35 8 16
EXOC3 0.025 0.007 -10000 0 -10000 0 0
ASAP2 0.024 0.037 -10000 0 -0.69 1 1
Dynamin 2/GDP 0.029 0.011 -10000 0 -10000 0 0
KLC1 0.026 0.005 -10000 0 -10000 0 0
AVPR2 0.028 0.09 0.48 7 -0.35 8 15
RALA 0.025 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.042 0.023 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.027 0.033 0.29 2 -0.38 1 3
adherens junction organization 0.021 0.043 0.24 4 -0.31 1 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.049 -10000 0 -10000 0 0
FMN1 0.012 0.07 -10000 0 -0.36 12 12
mol:IP3 0.027 0.026 -10000 0 -0.34 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.027 0.026 -10000 0 -0.3 1 1
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.032 0.031 0.25 1 -0.34 1 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.034 -10000 0 -10000 0 0
CTNND1 0.027 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.018 -10000 0 -10000 0 0
VASP 0.022 0.024 -10000 0 -10000 0 0
ZYX 0.023 0.024 -10000 0 -0.29 1 1
JUB 0.023 0.024 -10000 0 -0.28 1 1
EGFR(dimer) 0.035 0.054 -10000 0 -0.34 6 6
E-cadherin/beta catenin-gamma catenin 0.049 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.047 0.033 -10000 0 -0.35 1 1
PIK3CA 0.026 0.038 -10000 0 -0.69 1 1
PI3K 0.049 0.034 -10000 0 -0.36 1 1
FYN 0.024 0.03 0.28 2 -10000 0 2
mol:Ca2+ 0.026 0.025 -10000 0 -0.34 1 1
JUP 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
mol:DAG 0.027 0.026 -10000 0 -0.34 1 1
CDH1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.049 -10000 0 -0.33 6 6
establishment of polarity of embryonic epithelium 0.022 0.024 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
EGFR 0.016 0.082 -10000 0 -0.69 5 5
CASR 0.018 0.028 0.29 1 -0.33 1 2
RhoA/GTP 0.038 0.025 -10000 0 -0.31 1 1
AKT2 0.03 0.028 -10000 0 -0.34 1 1
actin cable formation 0.009 0.067 -10000 0 -0.35 11 11
apoptosis -0.027 0.032 0.35 1 -0.37 1 2
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.018 0.049 -10000 0 -0.34 6 6
PIP5K1A 0.023 0.018 -10000 0 -10000 0 0
PLCG1 0.027 0.026 -10000 0 -0.35 1 1
Rac1/GTP 0.044 0.053 -10000 0 -0.33 5 5
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.062 0.021 -9999 0 -10000 0 0
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.034 0.011 -9999 0 -10000 0 0
GATA1/HDAC5 0.033 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.037 0.01 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.047 0.031 -9999 0 -0.45 1 1
HDAC9 0.011 0.042 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.049 0.016 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.037 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.008 -9999 0 -10000 0 0
GATA2 0.026 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.036 0.011 -9999 0 -10000 0 0
BCOR 0.025 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.012 -9999 0 -10000 0 0
HDAC5 0.025 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.01 -9999 0 -10000 0 0
Histones 0.007 0.048 -9999 0 -10000 0 0
ADRBK1 0.026 0.005 -9999 0 -10000 0 0
HDAC4 0.026 0.005 -9999 0 -10000 0 0
XPO1 0.026 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.037 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.037 0.011 -9999 0 -10000 0 0
HDAC7 0.026 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.037 0.011 -9999 0 -10000 0 0
TUBA1B 0.026 0.006 -9999 0 -10000 0 0
HDAC6 0.025 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.012 -9999 0 -10000 0 0
CAMK4 0.014 0.076 -9999 0 -0.69 4 4
Tubulin/HDAC6 0.045 0.05 -9999 0 -0.41 4 4
SUMO1 0.026 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.026 0.005 -9999 0 -10000 0 0
GATA1 0.011 0.02 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.025 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.3 1 1
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.038 0.009 -9999 0 -10000 0 0
Tubulin 0.032 0.058 -9999 0 -0.52 4 4
HDAC4/14-3-3 E 0.036 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.005 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.035 0.031 -9999 0 -0.52 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.051 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.046 0.054 -9999 0 -0.45 4 4
HDAC4/ER alpha 0.006 0.12 -9999 0 -0.51 17 17
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.007 0.048 -9999 0 -10000 0 0
cell motility 0.044 0.05 -9999 0 -0.4 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.025 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.038 0.009 -9999 0 -10000 0 0
BCL6 0.024 0.037 -9999 0 -0.69 1 1
HDAC4/CaMK II delta B 0.026 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.036 0.012 -9999 0 -10000 0 0
ESR1 -0.016 0.15 -9999 0 -0.67 17 17
HDAC6/HDAC11 0.036 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.051 -9999 0 -10000 0 0
NPC 0.015 0.003 -9999 0 -10000 0 0
MEF2C 0.026 0.005 -9999 0 -10000 0 0
RAN 0.026 0.006 -9999 0 -10000 0 0
HDAC4/MEF2C 0.072 0.024 -9999 0 -10000 0 0
GNG2 0.026 0.005 -9999 0 -10000 0 0
NCOR2 0.026 0.006 -9999 0 -10000 0 0
TUBB2A 0.019 0.074 -9999 0 -0.69 4 4
HDAC11 0.026 0.004 -9999 0 -10000 0 0
HSP90AA1 0.026 0.005 -9999 0 -10000 0 0
RANBP2 0.026 0.005 -9999 0 -10000 0 0
ANKRA2 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.007 -9999 0 -10000 0 0
nuclear import -0.034 0.011 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.024 0.016 -9999 0 -9999 0 0
PLK4 0.026 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.014 0.01 -9999 0 -9999 0 0
Arf6 downstream 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
PLAUR 0.002 0.033 -10000 0 -10000 0 0
regulation of axonogenesis -0.013 0.008 -10000 0 -10000 0 0
myoblast fusion -0.014 0.023 -10000 0 -10000 0 0
mol:GTP 0.016 0.01 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.053 0.043 0.43 1 -10000 0 1
ARF1/GTP 0.03 0.013 -10000 0 -10000 0 0
mol:GM1 0.006 0.009 -10000 0 -10000 0 0
mol:Choline 0.008 0.011 -10000 0 -10000 0 0
lamellipodium assembly 0.017 0.022 -10000 0 -10000 0 0
MAPK3 0.011 0.022 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.054 0.043 -10000 0 -0.43 1 1
ARF1 0.025 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.014 0.023 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.027 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.026 0.003 -10000 0 -10000 0 0
TIAM1 -0.05 0.075 -10000 0 -0.69 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.02 -10000 0 -10000 0 0
actin filament bundle formation -0.026 0.026 -10000 0 -10000 0 0
KALRN 0.012 0.016 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.037 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.026 -10000 0 -10000 0 0
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.022 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.016 0.01 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.017 0.023 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
liver development 0.016 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.016 0.01 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.011 0.016 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.015 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
PLD1 0.018 0.008 -10000 0 -10000 0 0
RAB11FIP3 0.025 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.022 -10000 0 -10000 0 0
ruffle organization 0.013 0.008 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.016 0.01 -10000 0 -10000 0 0
PLD2 0.018 0.008 -10000 0 -10000 0 0
PIP5K1A 0.013 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.011 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.023 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.026 0.005 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.051 0.023 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.011 0.019 -9999 0 -0.34 1 1
AURKB -0.003 0.054 -9999 0 -10000 0 0
AURKC 0.021 0.023 -9999 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.024 0.038 -10000 0 -0.69 1 1
positive regulation of NF-kappaB transcription factor activity 0.037 0.03 -10000 0 -0.52 1 1
MAP2K4 0.026 0.043 -10000 0 -0.3 2 2
IKBKB 0.026 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.004 -10000 0 -10000 0 0
TNFRSF10A 0.024 0.037 -10000 0 -0.69 1 1
SMPD1 0.015 0.014 -10000 0 -0.25 1 1
IKBKG 0.024 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.026 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.03 -10000 0 -0.52 1 1
TRAIL/TRAILR3 0.005 0.057 -10000 0 -0.52 1 1
TRAIL/TRAILR1 0.035 0.042 -10000 0 -0.52 2 2
TRAIL/TRAILR4 0.037 0.03 -10000 0 -0.52 1 1
TRAIL/TRAILR1/DAP3/GTP 0.044 0.037 -10000 0 -0.42 2 2
IKK complex 0.022 0.048 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.018 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.028 -10000 0 -0.52 1 1
MAP3K1 0.027 0.038 -10000 0 -0.3 3 3
TRAILR4 (trimer) 0.026 0.004 -10000 0 -10000 0 0
TRADD 0.025 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.024 0.037 -10000 0 -0.69 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.029 0.027 -10000 0 -0.29 2 2
CFLAR 0.026 0.005 -10000 0 -10000 0 0
MAPK1 0.01 0.029 -10000 0 -0.52 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.04 -10000 0 -0.4 2 2
mol:ceramide 0.015 0.014 -10000 0 -0.25 1 1
FADD 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.02 0.054 0.28 1 -0.34 2 3
TRAF2 0.024 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.061 -10000 0 -10000 0 0
CHUK 0.026 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.049 0.039 -10000 0 -0.45 2 2
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.011 0.029 -10000 0 -0.44 1 1
JNK cascade 0.037 0.03 -10000 0 -0.52 1 1
TRAIL (trimer) 0.024 0.038 -10000 0 -0.69 1 1
TNFRSF10C -0.014 0.062 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.055 0.039 -10000 0 -0.4 2 2
TRAIL/TRAILR2/FADD 0.051 0.029 -10000 0 -0.45 1 1
cell death 0.015 0.014 -10000 0 -0.25 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.021 -10000 0 -0.29 1 1
TRAILR2 (trimer) 0.026 0.004 -10000 0 -10000 0 0
CASP8 0.013 0.012 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.073 0.032 -10000 0 -0.4 1 1
Glypican 2 network

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
MDK -0.014 0.061 -9999 0 -9999 0 0
GPC2 0.014 0.037 -9999 0 -9999 0 0
GPC2/Midkine -0.001 0.055 -9999 0 -9999 0 0
neuron projection morphogenesis -0.001 0.055 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.026 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.053 -9999 0 -10000 0 0
HDAC4 0.026 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.014 -9999 0 -10000 0 0
SUMO1 0.026 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.038 -9999 0 -0.25 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.011 0.007 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.3 1 1
SUMO1/HDAC1 0.013 0.057 -9999 0 -0.32 1 1
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.065 0.017 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.008 -9999 0 -10000 0 0
Ran/GTP 0.006 0.047 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.026 0.005 -9999 0 -10000 0 0
UBE2I 0.025 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.045 -9999 0 -10000 0 0
NPC 0.015 0.003 -9999 0 -10000 0 0
PIAS2 0.026 0.004 -9999 0 -10000 0 0
PIAS1 0.026 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.049 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.037 0.01 -9999 0 -9999 0 0
CTNNB1 0.026 0.004 -9999 0 -9999 0 0
JUP 0.025 0.007 -9999 0 -9999 0 0
CDH1 0.025 0.006 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.019 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0.03 -9999 0 -0.22 1 1
AP2 0.037 0.01 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.034 0.011 -9999 0 -10000 0 0
CLTB 0.026 0.006 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.009 -9999 0 -10000 0 0
CD4 0.021 0.024 -9999 0 -10000 0 0
CLTA 0.025 0.007 -9999 0 -10000 0 0
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ARFGAP1 0.008 0.002 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.004 -9999 0 -10000 0 0
ARF1/GTP 0.029 0.012 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.014 0.006 -9999 0 -10000 0 0
mol:Choline 0.007 0.003 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.026 0.008 -9999 0 -10000 0 0
DDEF1 0.007 0.01 -9999 0 -10000 0 0
ARF1/GDP 0.005 0.015 -9999 0 -10000 0 0
AP2M1 0.026 0.004 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.013 0.006 -9999 0 -10000 0 0
Rac/GTP 0.021 0.007 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.035 0.015 -9999 0 -10000 0 0
ARFIP2 0.021 0.013 -9999 0 -10000 0 0
COPA 0.025 0.007 -9999 0 -10000 0 0
RAC1 0.025 0.006 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.035 -9999 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.017 0.007 -9999 0 -10000 0 0
GGA3 0.025 0.007 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.015 -9999 0 -10000 0 0
AP2A1 0.025 0.007 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.018 0.008 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.018 -9999 0 -0.2 1 1
Arfaptin 2/Rac/GDP 0.033 0.011 -9999 0 -10000 0 0
CYTH2 0.027 0.009 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.032 0.013 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.019 0.005 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.023 0.023 -9999 0 -10000 0 0
PLD2 0.007 0.003 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.008 0.002 -9999 0 -10000 0 0
PIP5K1A 0.007 0.004 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.023 0.013 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.003 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.002 -9999 0 -10000 0 0
GOSR2 0.014 0.008 -9999 0 -10000 0 0
USO1 0.014 0.008 -9999 0 -10000 0 0
GBF1 0.012 0.024 -9999 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.034 0.013 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.051 0.016 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.037 0.01 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.026 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.071 0.025 -9999 0 -9999 0 0
NFKB1 0.026 0.004 -9999 0 -9999 0 0
MAP3K14 0.025 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.037 0.01 -9999 0 -9999 0 0
RELB 0.025 0.006 -9999 0 -9999 0 0
NFKB2 0.026 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.033 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 375 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.J8.A3YH TCGA.J8.A3YG TCGA.J8.A3YE TCGA.J8.A3YD
109_MAP3K5 0.041 0.041 -0.2 0.049
47_PPARGC1A -0.69 -0.69 0.027 0.027
105_BMP4 0.027 0 -0.69 0.027
105_BMP6 0.027 0.027 0.027 0.027
105_BMP7 0.027 0.027 0.027 0.027
105_BMP2 0.027 0.027 0.027 0.027
131_RELN/VLDLR -0.42 -0.4 -0.42 0.069
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.035 -0.14 -0.068 0.11
84_STAT5A 0.035 -0.14 -0.068 0.11
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2398258/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/THCA-TP/2403693/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

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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