PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C12J68V0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C12J68V0
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 48 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 234
Signaling events mediated by Stem cell factor receptor (c-Kit) 152
Signaling events regulated by Ret tyrosine kinase 140
TCGA08_retinoblastoma 133
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 112
Reelin signaling pathway 104
Wnt signaling 100
PDGFR-alpha signaling pathway 93
IL4-mediated signaling events 92
FOXA2 and FOXA3 transcription factor networks 91
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 234 1638 7 -0.52 0 1000 -1000 -0.028 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 152 11882 78 -0.79 0.24 1000 -1000 -0.067 -1000
Signaling events regulated by Ret tyrosine kinase 140 11498 82 -0.47 0.013 1000 -1000 -0.085 -1000
TCGA08_retinoblastoma 133 1068 8 -0.13 0.073 1000 -1000 -0.017 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 112 7676 68 -0.91 0.37 1000 -1000 -0.11 -1000
Reelin signaling pathway 104 5828 56 -0.6 0.033 1000 -1000 -0.094 -1000
Wnt signaling 100 703 7 -0.42 0.013 1000 -1000 -0.032 -1000
PDGFR-alpha signaling pathway 93 4115 44 -0.51 0.033 1000 -1000 -0.063 -1000
IL4-mediated signaling events 92 8382 91 -1.3 0.66 1000 -1000 -0.13 -1000
FOXA2 and FOXA3 transcription factor networks 91 4226 46 -0.94 0.021 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 88 2292 26 -0.42 0.013 1000 -1000 -0.088 -1000
Signaling events mediated by the Hedgehog family 78 4059 52 -0.39 0.2 1000 -1000 -0.076 -1000
Nongenotropic Androgen signaling 78 4107 52 -0.34 0.17 1000 -1000 -0.066 -1000
Calcium signaling in the CD4+ TCR pathway 73 2292 31 -0.54 0.013 1000 -1000 -0.084 -1000
Nephrin/Neph1 signaling in the kidney podocyte 67 2305 34 -0.16 0.013 1000 -1000 -0.067 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 62 3374 54 -0.6 0.028 1000 -1000 -0.1 -1000
Glypican 1 network 60 2881 48 -0.38 0.029 1000 -1000 -0.049 -1000
Ephrin B reverse signaling 60 2891 48 -0.32 0.19 1000 -1000 -0.072 -1000
Endothelins 58 5593 96 -0.41 0.013 1000 -1000 -0.08 -1000
BMP receptor signaling 52 4286 81 -0.58 0.027 1000 -1000 -0.093 -1000
TCR signaling in naïve CD8+ T cells 52 4919 93 -0.19 0.089 1000 -1000 -0.072 -1000
IGF1 pathway 51 2947 57 -0.19 0.058 1000 -1000 -0.094 -1000
IL23-mediated signaling events 51 3107 60 -0.33 0.02 1000 -1000 -0.15 -1000
Glucocorticoid receptor regulatory network 49 5690 114 -0.57 0.37 1000 -1000 -0.078 -1000
HIF-1-alpha transcription factor network 48 3717 76 -0.57 0.043 1000 -1000 -0.099 -1000
Glypican 2 network 48 194 4 -0.087 -0.009 1000 -1000 -0.038 -1000
Arf6 signaling events 47 2951 62 -0.32 0.021 1000 -1000 -0.062 -1000
Coregulation of Androgen receptor activity 45 3446 76 -0.77 0.061 1000 -1000 -0.05 -1000
EPHB forward signaling 45 3831 85 -0.32 0.16 1000 -1000 -0.09 -1000
Syndecan-1-mediated signaling events 44 1515 34 -0.2 0.013 1000 -1000 -0.062 -1000
Signaling mediated by p38-alpha and p38-beta 39 1753 44 -0.24 0.013 1000 -1000 -0.05 -1000
IL12-mediated signaling events 37 3241 87 -0.42 0.024 1000 -1000 -0.12 -1000
Hedgehog signaling events mediated by Gli proteins 37 2419 65 -0.67 0.062 1000 -1000 -0.06 -1000
Syndecan-4-mediated signaling events 37 2540 67 -0.24 0.014 1000 -1000 -0.084 -1000
amb2 Integrin signaling 32 2691 82 -0.25 0.013 1000 -1000 -0.086 -1000
IL6-mediated signaling events 32 2466 75 -0.22 0.059 1000 -1000 -0.082 -1000
Thromboxane A2 receptor signaling 31 3294 105 -0.21 0.032 1000 -1000 -0.07 -1000
EGFR-dependent Endothelin signaling events 31 660 21 -0.11 0.013 1000 -1000 -0.068 -1000
Ras signaling in the CD4+ TCR pathway 31 537 17 -0.097 0.013 1000 -1000 -0.045 -1000
FAS signaling pathway (CD95) 29 1375 47 -0.26 0.03 1000 -1000 -0.044 -1000
Osteopontin-mediated events 27 1063 38 -0.27 0.013 1000 -1000 -0.11 -1000
Plasma membrane estrogen receptor signaling 27 2336 86 -0.18 0.019 1000 -1000 -0.082 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 26 2229 85 -0.29 0.013 1000 -1000 -0.084 -1000
Syndecan-2-mediated signaling events 25 1750 69 -0.22 0.038 1000 -1000 -0.062 -1000
Regulation of p38-alpha and p38-beta 25 1370 54 -0.47 0.013 1000 -1000 -0.051 -1000
Visual signal transduction: Rods 25 1322 52 -0.2 0.015 1000 -1000 -0.081 -1000
Regulation of Androgen receptor activity 25 1782 70 -0.48 0.034 1000 -1000 -0.059 -1000
ErbB2/ErbB3 signaling events 24 1591 65 -0.13 0.027 1000 -1000 -0.06 -1000
RXR and RAR heterodimerization with other nuclear receptor 23 1223 52 -0.28 0.053 1000 -1000 -0.062 -1000
BCR signaling pathway 23 2323 99 -0.19 0.022 1000 -1000 -0.086 -1000
JNK signaling in the CD4+ TCR pathway 22 383 17 -0.1 0.02 1000 -1000 -0.062 -1000
LPA receptor mediated events 22 2310 102 -0.26 0.031 1000 -1000 -0.085 -1000
Signaling events mediated by PTP1B 21 1607 76 -0.25 0.021 1000 -1000 -0.083 -1000
Integrins in angiogenesis 21 1840 84 -0.24 0.034 1000 -1000 -0.11 -1000
Angiopoietin receptor Tie2-mediated signaling 21 1932 88 -0.32 0.03 1000 -1000 -0.11 -1000
p75(NTR)-mediated signaling 20 2562 125 -0.36 0.067 1000 -1000 -0.096 -1000
Effects of Botulinum toxin 20 522 26 -0.17 0.019 1000 -1000 -0.064 -1000
IL27-mediated signaling events 20 1043 51 -0.17 0.065 1000 -1000 -0.084 -1000
Regulation of nuclear SMAD2/3 signaling 18 2519 136 -0.34 0.066 1000 -1000 -0.076 -1000
Visual signal transduction: Cones 18 685 38 -0.093 0.013 1000 -1000 -0.073 -1000
Fc-epsilon receptor I signaling in mast cells 18 1764 97 -0.22 0.031 1000 -1000 -0.092 -1000
Nectin adhesion pathway 18 1153 63 -0.26 0.033 1000 -1000 -0.066 -1000
ErbB4 signaling events 17 1228 69 -0.14 0.059 1000 -1000 -0.076 -1000
Aurora C signaling 17 122 7 -0.061 0.002 1000 -1000 -0.039 -1000
IL1-mediated signaling events 17 1061 62 -0.12 0.067 1000 -1000 -0.087 -1000
Syndecan-3-mediated signaling events 17 595 35 -0.17 0.013 1000 -1000 -0.063 -1000
Neurotrophic factor-mediated Trk receptor signaling 17 2061 120 -0.31 0.042 1000 -1000 -0.078 -1000
FOXM1 transcription factor network 17 906 51 -0.2 0.042 1000 -1000 -0.14 -1000
TCGA08_rtk_signaling 16 436 26 -0.25 0.025 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 15 920 61 -0.22 0.044 1000 -1000 -0.071 -1000
IFN-gamma pathway 15 1029 68 -0.11 0.042 1000 -1000 -0.089 -1000
Rapid glucocorticoid signaling 15 303 20 -0.092 0.015 1000 -1000 -0.035 -1000
Aurora B signaling 15 1025 67 -0.38 0.014 1000 -1000 -0.076 -1000
LPA4-mediated signaling events 14 170 12 -0.12 0.016 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 14 449 32 -0.21 0.04 1000 -1000 -0.066 -1000
VEGFR1 specific signals 14 791 56 -0.075 0.041 1000 -1000 -0.083 -1000
IL2 signaling events mediated by STAT5 13 307 22 -0.066 0.041 1000 -1000 -0.051 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 13 438 33 -0.16 0.035 1000 -1000 -0.07 -1000
Class IB PI3K non-lipid kinase events 13 39 3 -0.003 -1000 1000 -1000 -0.017 -1000
Ceramide signaling pathway 12 932 76 -0.18 0.024 1000 -1000 -0.063 -1000
Signaling events mediated by HDAC Class III 12 514 40 -0.36 0.024 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 12 740 58 -0.065 0.031 1000 -1000 -0.082 -1000
Insulin Pathway 12 955 74 -0.087 0.038 1000 -1000 -0.091 -1000
Signaling events mediated by PRL 12 415 34 -0.12 0.013 1000 -1000 -0.047 -1000
Sphingosine 1-phosphate (S1P) pathway 11 327 28 -0.18 0.031 1000 -1000 -0.052 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 11 523 45 -0.088 0.04 1000 -1000 -0.082 -1000
BARD1 signaling events 10 572 57 -0.034 0.053 1000 -1000 -0.065 -1000
a4b1 and a4b7 Integrin signaling 10 51 5 -0.027 0.005 1000 -1000 -0.04 -1000
Cellular roles of Anthrax toxin 10 396 39 -0.088 0.019 1000 -1000 -0.033 -1000
mTOR signaling pathway 10 546 53 -0.047 0.02 1000 -1000 -0.062 -1000
Stabilization and expansion of the E-cadherin adherens junction 10 753 74 -0.18 0.087 1000 -1000 -0.09 -1000
Class I PI3K signaling events 10 765 73 -0.25 0.023 1000 -1000 -0.058 -1000
Regulation of Telomerase 10 1095 102 -0.29 0.053 1000 -1000 -0.1 -1000
Caspase cascade in apoptosis 9 676 74 -0.088 0.03 1000 -1000 -0.055 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 9 815 83 -0.21 0.053 1000 -1000 -0.075 -1000
Retinoic acid receptors-mediated signaling 8 497 58 -0.12 0.034 1000 -1000 -0.072 -1000
S1P3 pathway 8 360 42 -0.18 0.049 1000 -1000 -0.055 -1000
Class I PI3K signaling events mediated by Akt 7 526 68 -0.21 0.052 1000 -1000 -0.063 -1000
TRAIL signaling pathway 7 344 48 -0.08 0.048 1000 -1000 -0.063 -1000
ceramide signaling pathway 7 380 49 -0.088 0.031 1000 -1000 -0.046 -1000
S1P1 pathway 7 266 36 -0.043 0.031 1000 -1000 -0.05 -1000
Canonical NF-kappaB pathway 6 259 39 -0.088 0.072 1000 -1000 -0.078 -1000
Arf6 downstream pathway 6 269 43 -0.18 0.094 1000 -1000 -0.046 -1000
FoxO family signaling 6 398 64 -0.21 0.16 1000 -1000 -0.064 -1000
Canonical Wnt signaling pathway 6 344 51 -0.049 0.069 1000 -1000 -0.055 -1000
Circadian rhythm pathway 5 120 22 -0.06 0.013 1000 -1000 -0.059 -1000
S1P5 pathway 5 93 17 -0.016 0.022 1000 -1000 -0.051 -1000
Signaling events mediated by HDAC Class I 5 616 104 -0.088 0.059 1000 -1000 -0.072 -1000
Paxillin-independent events mediated by a4b1 and a4b7 4 174 37 -0.029 0.041 1000 -1000 -0.058 -1000
Atypical NF-kappaB pathway 4 143 31 -0.038 0.047 1000 -1000 -0.055 -1000
E-cadherin signaling in the nascent adherens junction 4 351 76 -0.17 0.074 1000 -1000 -0.082 -1000
EPO signaling pathway 3 219 55 -0.036 0.063 1000 -1000 -0.087 -1000
PLK1 signaling events 3 280 85 -0.042 0.033 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 3 136 43 -0.2 0.2 1000 -1000 -0.074 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 479 125 -0.035 0.087 1000 -1000 -0.1 -1000
PDGFR-beta signaling pathway 3 346 97 -0.18 0.064 1000 -1000 -0.09 -1000
p38 MAPK signaling pathway 3 139 44 -0.037 0.027 1000 -1000 -0.057 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 2 55 23 -0.036 0.049 1000 -1000 -0.066 -1000
Signaling events mediated by HDAC Class II 2 169 75 -0.052 0.036 1000 -1000 -0.069 -1000
Aurora A signaling 2 166 60 -0.052 0.038 1000 -1000 -0.065 -1000
Signaling mediated by p38-gamma and p38-delta 2 40 15 0 0.032 1000 -1000 -0.032 -1000
Paxillin-dependent events mediated by a4b1 2 104 36 -0.027 0.024 1000 -1000 -0.075 -1000
E-cadherin signaling in keratinocytes 2 109 43 -0.004 0.053 1000 -1000 -0.064 -1000
S1P4 pathway 2 69 25 -0.016 0.032 1000 -1000 -0.055 -1000
PLK2 and PLK4 events 1 5 3 0.01 0.022 1000 -1000 -0.019 -1000
Arf6 trafficking events 1 73 71 -0.022 0.046 1000 -1000 -0.071 -1000
TCGA08_p53 0 0 7 -0.082 0.052 1000 -1000 -0.011 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.032 1000 -1000 -0.059 -1000
E-cadherin signaling events 0 0 5 0 0.013 1000 -1000 -0.035 -1000
Arf1 pathway 0 29 54 -0.005 0.035 1000 -1000 -0.044 -1000
Alternative NF-kappaB pathway 0 2 13 -0.001 0.013 1000 -1000 -0.058 -1000
Total 3790 209213 7203 -30 -990 131000 -131000 -9 -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 -0.43 0.32 -9999 0 -0.62 319 319
EFNA5 -0.12 0.3 -9999 0 -0.82 72 72
FYN -0.39 0.3 -9999 0 -0.57 319 319
neuron projection morphogenesis -0.43 0.32 -9999 0 -0.62 319 319
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.32 -9999 0 -0.62 319 319
EPHA5 -0.52 0.4 -9999 0 -0.83 290 290
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 0.22 -10000 0 -0.4 265 265
CRKL -0.21 0.24 -10000 0 -0.42 259 259
HRAS -0.19 0.22 -10000 0 -0.5 42 42
mol:PIP3 -0.21 0.22 -10000 0 -0.41 259 259
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.012 0.039 -10000 0 -0.83 1 1
GAB1 -0.23 0.25 -10000 0 -0.45 259 259
FOXO3 -0.19 0.22 -10000 0 -0.38 259 259
AKT1 -0.21 0.23 -10000 0 -0.41 259 259
BAD -0.19 0.22 -10000 0 -0.38 259 259
megakaryocyte differentiation -0.24 0.25 -10000 0 -0.45 266 266
GSK3B -0.19 0.22 -10000 0 -0.38 259 259
RAF1 -0.14 0.18 -10000 0 -0.45 24 24
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.23 0.25 -10000 0 -0.45 259 259
STAT1 -0.59 0.59 -10000 0 -1.1 260 260
HRAS/SPRED1 -0.17 0.15 -10000 0 -0.39 41 41
cell proliferation -0.24 0.25 -10000 0 -0.45 262 262
PIK3CA 0.007 0.068 -10000 0 -0.83 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.25 -10000 0 -0.45 259 259
HRAS/SPRED2 -0.17 0.15 -10000 0 -0.4 42 42
LYN/TEC/p62DOK -0.23 0.21 -10000 0 -0.41 259 259
MAPK3 -0.092 0.14 -10000 0 -0.32 19 19
STAP1 -0.26 0.25 -10000 0 -0.47 259 259
GRAP2 -0.042 0.2 -10000 0 -0.78 32 32
JAK2 -0.51 0.45 -10000 0 -0.9 260 260
STAT1 (dimer) -0.57 0.57 -10000 0 -1.1 260 260
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.24 0.21 -10000 0 -0.42 262 262
actin filament polymerization -0.23 0.24 -10000 0 -0.44 259 259
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.34 -10000 0 -0.64 259 259
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 249 249
PI3K -0.23 0.22 -10000 0 -0.42 260 260
PTEN 0.012 0.039 -10000 0 -0.83 1 1
SCF/KIT/EPO/EPOR -0.73 0.72 -10000 0 -1.4 259 259
MAPK8 -0.24 0.26 -10000 0 -0.46 262 262
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 259 259
positive regulation of transcription -0.073 0.11 -10000 0 -0.26 19 19
mol:GDP -0.23 0.19 -10000 0 -0.48 69 69
PIK3C2B -0.23 0.25 -10000 0 -0.45 259 259
CBL/CRKL -0.2 0.22 -10000 0 -0.39 258 258
FER -0.24 0.25 -10000 0 -0.45 260 260
SH2B3 -0.23 0.25 -10000 0 -0.45 259 259
PDPK1 -0.19 0.21 -10000 0 -0.37 260 260
SNAI2 -0.24 0.25 -10000 0 -0.45 260 260
positive regulation of cell proliferation -0.41 0.42 -10000 0 -0.77 260 260
KITLG -0.001 0.091 -10000 0 -0.86 5 5
cell motility -0.41 0.42 -10000 0 -0.77 260 260
PTPN6 0.02 0.018 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.56 7 7
STAT5A (dimer) -0.33 0.35 -10000 0 -0.63 259 259
SOCS1 0.009 0.049 -10000 0 -0.42 5 5
cell migration 0.24 0.25 0.45 261 -10000 0 261
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.003 0.033 -10000 0 -0.33 4 4
VAV1 -0.014 0.1 -10000 0 -0.36 34 34
GRB10 -0.23 0.25 -10000 0 -0.45 259 259
PTPN11 0.019 0.04 -10000 0 -0.81 1 1
SCF/KIT -0.25 0.26 -10000 0 -0.48 259 259
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.1 0.15 -10000 0 -0.35 21 21
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.79 0.75 -10000 0 -1.5 259 259
MAP2K2 -0.1 0.15 -10000 0 -0.35 21 21
SHC/Grb2/SOS1 -0.23 0.21 -10000 0 -0.41 259 259
STAT5A -0.34 0.36 -10000 0 -0.65 259 259
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.23 0.25 -10000 0 -0.44 260 260
SHC/GRAP2 -0.041 0.16 -10000 0 -0.64 29 29
PTPRO -0.25 0.25 -10000 0 -0.46 266 266
SH2B2 -0.23 0.25 -10000 0 -0.45 259 259
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.24 0.25 -10000 0 -0.46 261 261
CREBBP 0.018 0.021 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 34 34
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 -0.089 0.069 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.51 113 113
JUN -0.32 0.32 -9999 0 -0.7 152 152
HRAS 0.012 0.022 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.39 0.32 -9999 0 -0.61 286 286
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.39 0.32 -9999 0 -0.61 286 286
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.3 0.26 -9999 0 -0.52 263 263
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.35 0.3 -9999 0 -0.55 286 286
GRB7 -0.041 0.12 -9999 0 -0.31 77 77
RET51/GFRalpha1/GDNF -0.39 0.32 -9999 0 -0.61 286 286
MAPKKK cascade -0.31 0.26 -9999 0 -0.49 286 286
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.35 0.32 -9999 0 -0.59 275 275
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 264 264
RET51/GFRalpha1/GDNF/SHC -0.39 0.32 -9999 0 -0.61 286 286
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
RET9/GFRalpha1/GDNF/SHC -0.3 0.25 -9999 0 -0.52 263 263
RET9/GFRalpha1/GDNF/Shank3 -0.3 0.25 -9999 0 -0.52 263 263
MAPK3 -0.32 0.29 -9999 0 -0.52 286 286
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.83 72 72
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.31 0.29 -9999 0 -0.68 121 121
DOK5 -0.098 0.28 -9999 0 -0.83 61 61
GFRA1 -0.47 0.42 -9999 0 -0.83 264 264
MAPK8 -0.24 0.23 -9999 0 -0.59 84 84
HRAS/GTP -0.36 0.31 -9999 0 -0.57 286 286
tube development -0.28 0.24 -9999 0 -0.48 263 263
MAPK1 -0.32 0.29 -9999 0 -0.52 286 286
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.19 0.19 -9999 0 -0.34 263 263
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PDLIM7 0.01 0.03 -9999 0 -0.31 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.44 0.38 -9999 0 -0.67 296 296
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.39 0.33 -9999 0 -0.61 286 286
RET51/GFRalpha1/GDNF/Dok5 -0.45 0.39 -9999 0 -0.69 298 298
PRKCA -0.027 0.18 -9999 0 -0.83 22 22
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
CREB1 -0.24 0.24 -9999 0 -0.43 263 263
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 263 263
RET51/GFRalpha1/GDNF/Grb7 -0.42 0.33 -9999 0 -0.64 286 286
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.32 -9999 0 -0.65 125 125
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.68 152 152
RET9/GFRalpha1/GDNF/FRS2 -0.3 0.25 -9999 0 -0.52 263 263
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.19 0.18 -9999 0 -0.34 263 263
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.25 0.24 -9999 0 -0.41 286 286
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.25 0.24 -9999 0 -0.41 286 286
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.29 0.31 -9999 0 -0.47 286 286
PI3K -0.37 0.34 -9999 0 -0.63 264 264
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.28 0.24 -9999 0 -0.48 263 263
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.4 210 210
RET51/GFRalpha1/GDNF/FRS2 -0.39 0.32 -9999 0 -0.61 286 286
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.087 0.27 -9999 0 -0.83 55 55
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.29 0.31 -9999 0 -0.47 286 286
RET51/GFRalpha1/GDNF/PKC alpha -0.41 0.36 -9999 0 -0.64 288 288
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.042 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.45 0.37 -9999 0 -0.68 297 297
Rac1/GTP -0.29 0.23 -9999 0 -0.47 264 264
RET9/GFRalpha1/GDNF -0.32 0.28 -9999 0 -0.57 263 263
GFRalpha1/GDNF -0.37 0.32 -9999 0 -0.64 263 263
TCGA08_retinoblastoma

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
CDKN2B -0.13 0.16 -10000 0 -0.32 194 194
CDKN2C 0.026 0.037 -10000 0 -0.3 4 4
CDKN2A -0.12 0.16 -10000 0 -0.32 192 192
CCND2 0.07 0.073 0.17 135 -10000 0 135
RB1 -0.069 0.072 -10000 0 -0.17 135 135
CDK4 0.07 0.072 0.17 137 -10000 0 137
CDK6 0.073 0.077 0.18 135 -0.19 1 136
G1/S progression 0.061 0.08 0.17 135 -10000 0 135
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.044 0.16 -10000 0 -0.52 37 37
NFATC2 -0.23 0.38 -10000 0 -0.82 114 114
NFATC3 -0.086 0.13 -10000 0 -0.31 31 31
CD40LG -0.74 0.58 -10000 0 -1.2 260 260
ITCH 0.051 0.015 -10000 0 -10000 0 0
CBLB 0.051 0.015 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.53 0.52 -10000 0 -1.2 143 143
JUNB 0.002 0.095 -10000 0 -0.83 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.016 -10000 0 -0.34 1 1
T cell anergy 0.026 0.065 -10000 0 -0.5 1 1
TLE4 -0.24 0.44 -10000 0 -0.88 124 124
Jun/NFAT1-c-4/p21SNFT -0.67 0.61 -10000 0 -1.2 229 229
AP-1/NFAT1-c-4 -0.91 0.79 -10000 0 -1.5 256 256
IKZF1 -0.17 0.34 -10000 0 -0.74 94 94
T-helper 2 cell differentiation -0.31 0.35 -10000 0 -0.86 105 105
AP-1/NFAT1 -0.43 0.49 -10000 0 -0.91 205 205
CALM1 0.029 0.01 -10000 0 -10000 0 0
EGR2 -0.81 0.86 -10000 0 -1.7 218 218
EGR3 -0.58 0.75 -10000 0 -1.5 148 148
NFAT1/FOXP3 -0.22 0.34 -10000 0 -0.7 121 121
EGR1 -0.17 0.35 -10000 0 -0.83 101 101
JUN -0.19 0.35 -10000 0 -0.83 105 105
EGR4 -0.039 0.19 -10000 0 -0.71 31 31
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.16 0.32 -10000 0 -0.74 82 82
FOSL1 -0.03 0.12 -10000 0 -0.33 58 58
NFAT1-c-4/MAF/IRF4 -0.57 0.57 -10000 0 -1.1 230 230
DGKA -0.15 0.3 -10000 0 -0.68 85 85
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.56 0.56 -10000 0 -1.1 229 229
CTLA4 -0.23 0.38 -10000 0 -0.81 109 109
NFAT1-c-4 (dimer)/EGR1 -0.65 0.67 -10000 0 -1.2 231 231
NFAT1-c-4 (dimer)/EGR4 -0.58 0.57 -10000 0 -1.1 234 234
FOS -0.23 0.37 -10000 0 -0.83 125 125
IFNG -0.43 0.55 -10000 0 -1.2 136 136
T cell activation -0.44 0.43 -10000 0 -0.97 154 154
MAF 0.013 0 -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 0.37 0.43 0.76 217 -10000 0 217
TNF -0.6 0.58 -10000 0 -1.1 248 248
FASLG -0.76 0.79 -10000 0 -1.5 233 233
TBX21 -0.037 0.18 -10000 0 -0.72 28 28
BATF3 -0.007 0.085 -10000 0 -0.33 27 27
PRKCQ 0.002 0.096 -10000 0 -0.83 6 6
PTPN1 -0.15 0.3 -10000 0 -0.67 89 89
NFAT1-c-4/ICER1 -0.55 0.56 -10000 0 -1 229 229
GATA3 -0.031 0.19 -10000 0 -0.79 26 26
T-helper 1 cell differentiation -0.41 0.52 -10000 0 -1.1 137 137
IL2RA -0.48 0.46 -10000 0 -1 147 147
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.3 -10000 0 -0.67 92 92
E2F1 -0.078 0.15 -10000 0 -0.3 140 140
PPARG -0.001 0.1 -10000 0 -0.83 6 6
SLC3A2 -0.15 0.3 -10000 0 -0.67 89 89
IRF4 -0.099 0.23 -10000 0 -0.45 111 111
PTGS2 -0.72 0.57 -10000 0 -1.2 245 245
CSF2 -0.78 0.54 -10000 0 -1.2 258 258
JunB/Fra1/NFAT1-c-4 -0.54 0.54 -10000 0 -1 227 227
IL4 -0.33 0.37 -10000 0 -0.93 100 100
IL5 -0.7 0.55 -10000 0 -1.1 251 251
IL2 -0.45 0.44 -10000 0 -1 149 149
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.044 -10000 0 -0.88 1 1
NFATC1 -0.37 0.43 -10000 0 -0.76 217 217
CDK4 0.22 0.25 0.59 66 -10000 0 66
PTPRK -0.15 0.3 -10000 0 -0.67 89 89
IL8 -0.73 0.55 -10000 0 -1.2 244 244
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
Reelin signaling pathway

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.001 0.013 -9999 0 -10000 0 0
VLDLR -0.025 0.18 -9999 0 -0.83 21 21
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.01 0.034 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.42 0.27 -9999 0 -0.57 341 341
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.061 -9999 0 -0.47 8 8
AKT1 -0.24 0.18 -9999 0 -0.66 18 18
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.4 0.25 -9999 0 -0.54 340 340
LRPAP1/LRP8 -0.029 0.13 -9999 0 -0.64 21 21
RELN/LRP8/DAB1/Fyn -0.37 0.24 -9999 0 -0.5 340 340
DAB1/alpha3/beta1 Integrin -0.35 0.24 -9999 0 -0.87 34 34
long-term memory -0.37 0.25 -9999 0 -0.5 342 342
DAB1/LIS1 -0.36 0.24 -9999 0 -0.48 345 345
DAB1/CRLK/C3G -0.35 0.24 -9999 0 -0.91 30 30
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
DAB1/NCK2 -0.37 0.25 -9999 0 -0.49 345 345
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.024 0.16 -9999 0 -0.65 26 26
CDK5R1 0.012 0.022 -9999 0 -0.31 2 2
RELN -0.6 0.37 -9999 0 -0.83 336 336
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.42 0.27 -9999 0 -0.57 340 340
GRIN2A/RELN/LRP8/DAB1/Fyn -0.38 0.26 -9999 0 -0.52 342 342
MAPK8 -0.001 0.11 -9999 0 -0.83 8 8
RELN/VLDLR/DAB1 -0.4 0.25 -9999 0 -0.54 341 341
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.37 0.27 -9999 0 -0.51 345 345
RELN/LRP8 -0.42 0.27 -9999 0 -0.57 340 340
GRIN2B/RELN/LRP8/DAB1/Fyn -0.37 0.24 -9999 0 -0.5 340 340
PI3K -0.004 0.051 -9999 0 -0.64 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.021 -9999 0 -10000 0 0
RAP1A -0.31 0.24 -9999 0 -0.83 30 30
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.016 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.53 22 22
neuron adhesion -0.29 0.23 -9999 0 -0.74 34 34
LRP8 -0.025 0.18 -9999 0 -0.83 21 21
GSK3B -0.22 0.17 -9999 0 -0.62 18 18
RELN/VLDLR/DAB1/Fyn -0.37 0.24 -9999 0 -0.5 341 341
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.19 -9999 0 -0.36 342 342
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.09 -9999 0 -0.57 5 5
neuron migration -0.3 0.22 -9999 0 -0.67 31 31
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.54 22 22
RELN/VLDLR -0.41 0.27 -9999 0 -0.55 345 345
Wnt signaling

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
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.47 290 290
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.005 0.05 -9999 0 -0.31 11 11
WNT4 -0.27 0.4 -9999 0 -0.83 154 154
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.006 0.12 -9999 0 -0.78 11 11
WNT11 -0.42 0.42 -9999 0 -0.82 237 237
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 -0.26 0.39 -9999 0 -0.84 143 143
PDGF/PDGFRA/CRKL -0.2 0.29 -9999 0 -0.63 143 143
positive regulation of JUN kinase activity -0.15 0.23 -9999 0 -0.49 143 143
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.2 0.3 -9999 0 -0.64 143 143
AP1 -0.51 0.64 -9999 0 -1.5 131 131
mol:IP3 -0.2 0.31 -9999 0 -0.66 143 143
PLCG1 -0.2 0.31 -9999 0 -0.66 143 143
PDGF/PDGFRA/alphaV Integrin -0.2 0.3 -9999 0 -0.64 144 144
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.2 0.31 -9999 0 -0.65 143 143
CAV3 -0.001 0.03 -9999 0 -0.31 4 4
CAV1 -0.009 0.13 -9999 0 -0.83 12 12
SHC/Grb2/SOS1 -0.15 0.23 -9999 0 -0.49 143 143
PDGF/PDGFRA/Shf -0.2 0.29 -9999 0 -0.63 143 143
FOS -0.46 0.61 -9999 0 -1.4 131 131
JUN -0.18 0.29 -9999 0 -0.71 105 105
oligodendrocyte development -0.2 0.3 -9999 0 -0.64 144 144
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.31 -9999 0 -0.66 143 143
PDGF/PDGFRA -0.26 0.39 -9999 0 -0.84 143 143
actin cytoskeleton reorganization -0.2 0.29 -9999 0 -0.63 143 143
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.17 0.25 -9999 0 -0.54 146 146
PDGF/PDGFRA/Crk/C3G -0.17 0.25 -9999 0 -0.54 143 143
JAK1 -0.18 0.3 -9999 0 -0.63 143 143
ELK1/SRF -0.13 0.25 -9999 0 -0.49 143 143
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -0.31 1 1
CSNK2A1 0.028 0.028 -9999 0 -10000 0 0
GO:0007205 -0.2 0.32 -9999 0 -0.67 143 143
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.23 -9999 0 -0.49 143 143
PDGF/PDGFRA/SHB -0.2 0.29 -9999 0 -0.63 143 143
PDGF/PDGFRA/Caveolin-1 -0.21 0.32 -9999 0 -0.67 146 146
ITGAV 0.01 0.055 -9999 0 -0.83 2 2
ELK1 -0.18 0.28 -9999 0 -0.6 143 143
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
PDGF/PDGFRA/Crk -0.2 0.29 -9999 0 -0.63 143 143
JAK-STAT cascade -0.18 0.3 -9999 0 -0.63 143 143
cell proliferation -0.2 0.29 -9999 0 -0.63 143 143
IL4-mediated signaling events

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
BCL2L1 -0.59 0.44 -10000 0 -1.1 158 158
STAT6 (cleaved dimer) -0.65 0.45 -10000 0 -1 241 241
IGHG1 -0.2 0.14 -10000 0 -0.35 64 64
IGHG3 -0.58 0.42 -10000 0 -0.95 220 220
AKT1 -0.32 0.26 -10000 0 -0.68 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.25 0.25 -10000 0 -0.72 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.71 111 111
THY1 -0.59 0.44 -10000 0 -1.1 159 159
MYB -0.007 0.12 -10000 0 -0.62 15 15
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.41 0.31 -10000 0 -0.72 170 170
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.68 83 83
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.071 -10000 0 -0.31 23 23
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.44 -10000 0 -0.98 235 235
SOCS1 -0.4 0.29 -10000 0 -0.72 132 132
SOCS3 -0.38 0.36 -10000 0 -1.1 55 55
FCER2 -0.58 0.42 -10000 0 -0.98 189 189
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.48 -10000 0 -1.1 191 191
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.64 51 51
T cell proliferation -0.6 0.46 -10000 0 -1.1 179 179
IL4R/JAK1 -0.59 0.44 -10000 0 -1.1 164 164
EGR2 -0.94 0.73 -10000 0 -1.6 231 231
JAK2 -0.018 0.046 -10000 0 -0.87 1 1
JAK3 -0.065 0.14 -10000 0 -0.31 113 113
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.008 -10000 0 -10000 0 0
COL1A2 -0.19 0.16 -10000 0 -0.56 10 10
CCL26 -0.61 0.45 -10000 0 -1.1 162 162
IL4R -0.63 0.47 -10000 0 -1.1 166 166
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.7 0.57 -10000 0 -1.3 183 183
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.33 0.48 -10000 0 -1.2 85 85
ARG1 -0.14 0.11 -10000 0 -10000 0 0
CBL -0.38 0.3 -10000 0 -0.69 155 155
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
IL13RA1/JAK2 -0.024 0.045 -10000 0 -0.68 1 1
IRF4/BCL6 -0.31 0.43 -10000 0 -1.2 76 76
CD40LG -0.12 0.31 -10000 0 -0.8 75 75
MAPK14 -0.39 0.32 -10000 0 -0.77 124 124
mitosis -0.3 0.24 -10000 0 -0.64 84 84
STAT6 -0.68 0.51 -10000 0 -1.1 210 210
SPI1 0.002 0.07 -10000 0 -0.31 22 22
RPS6KB1 -0.29 0.24 -10000 0 -0.64 69 69
STAT6 (dimer) -0.68 0.52 -10000 0 -1.1 210 210
STAT6 (dimer)/PARP14 -0.63 0.47 -10000 0 -1.1 201 201
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.27 -10000 0 -0.7 88 88
FRAP1 -0.32 0.26 -10000 0 -0.68 84 84
LTA -0.61 0.46 -10000 0 -1.1 159 159
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.5 1.1 213 -10000 0 213
CCL11 -0.58 0.43 -10000 0 -1.1 154 154
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.68 89 89
IL2RG -0.043 0.19 -10000 0 -0.54 50 50
IL10 -0.61 0.47 -10000 0 -1.1 168 168
IRS1 -0.087 0.27 -10000 0 -0.83 55 55
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.096 -10000 0 -10000 0 0
IL5 -0.6 0.44 -10000 0 -1.1 158 158
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.34 -10000 0 -0.83 164 164
COL1A1 -0.25 0.23 -10000 0 -1.4 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.6 0.45 -10000 0 -1.1 140 140
IL2R gamma/JAK3 -0.079 0.18 -10000 0 -0.51 50 50
TFF3 -1.3 0.62 -10000 0 -1.6 376 376
ALOX15 -0.6 0.44 -10000 0 -1.1 154 154
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.51 0.36 -10000 0 -0.86 189 189
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.018 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.25 -10000 0 -0.66 80 80
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.68 84 84
PI3K -0.33 0.28 -10000 0 -0.74 83 83
DOK2 0 0.078 -10000 0 -0.38 16 16
ETS1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.24 0.21 -10000 0 -0.62 52 52
ITGB3 -0.62 0.48 -10000 0 -1.2 146 146
PIGR -0.64 0.5 -10000 0 -1.2 173 173
IGHE 0.051 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.61 52 52
BCL6 0.012 0.039 -10000 0 -0.83 1 1
OPRM1 -0.6 0.44 -10000 0 -1.1 152 152
RETNLB -0.6 0.44 -10000 0 -1.1 156 156
SELP -0.6 0.46 -10000 0 -1.1 159 159
AICDA -0.58 0.43 -10000 0 -1 170 170
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.52 0.55 -9999 0 -1.1 190 190
PCK1 -0.35 0.5 -9999 0 -1.2 82 82
HNF4A -0.68 0.66 -9999 0 -1.3 227 227
KCNJ11 -0.49 0.55 -9999 0 -1.1 189 189
AKT1 -0.041 0.12 -9999 0 -0.41 2 2
response to starvation -0.018 0.034 -9999 0 -10000 0 0
DLK1 -0.5 0.54 -9999 0 -1.1 181 181
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.52 0.55 -9999 0 -1.1 206 206
TAT -0.2 0.22 -9999 0 -0.66 10 10
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.087 -9999 0 -0.83 5 5
TTR -0.19 0.22 -9999 0 -0.74 32 32
PKLR -0.53 0.55 -9999 0 -1.1 195 195
APOA1 -0.94 0.9 -9999 0 -1.8 235 235
CPT1C -0.54 0.55 -9999 0 -1.1 188 188
ALAS1 -0.17 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.29 -9999 0 -0.74 32 32
FOXF1 -0.012 0.096 -9999 0 -0.76 7 7
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.52 0.55 -9999 0 -1.1 190 190
HMGCS1 -0.52 0.55 -9999 0 -1.1 180 180
NR3C1 0.02 0.016 -9999 0 -10000 0 0
CPT1B -0.52 0.55 -9999 0 -1.1 198 198
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.67 0.71 -9999 0 -1.3 213 213
CREB1 0 0.053 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.58 2 2
PDX1 -0.18 0.21 -9999 0 -10000 0 0
UCP2 -0.52 0.55 -9999 0 -1.1 191 191
ALDOB -0.49 0.54 -9999 0 -1.1 190 190
AFP -0.047 0.11 -9999 0 -0.47 11 11
BDH1 -0.52 0.55 -9999 0 -1.1 198 198
HADH -0.49 0.54 -9999 0 -1.1 189 189
F2 -0.64 0.64 -9999 0 -1.3 196 196
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.006 0.089 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.56 11 11
INS -0.008 0.018 -9999 0 -10000 0 0
FOXA1 -0.058 0.15 -9999 0 -0.34 90 90
FOXA3 -0.074 0.17 -9999 0 -0.35 108 108
FOXA2 -0.56 0.61 -9999 0 -1.2 200 200
ABCC8 -0.79 0.76 -9999 0 -1.4 248 248
ALB -0.1 0.33 -9999 0 -1.3 30 30
Noncanonical Wnt signaling pathway

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
NFATC2 -0.12 0.31 -9999 0 -0.83 76 76
GNB1/GNG2 -0.26 0.24 -9999 0 -0.6 119 119
mol:DAG -0.22 0.24 -9999 0 -0.56 111 111
PLCG1 -0.22 0.25 -9999 0 -0.58 111 111
YES1 -0.26 0.27 -9999 0 -0.63 118 118
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.25 0.23 -9999 0 -0.58 113 113
MAP3K7 -0.18 0.2 -9999 0 -0.46 111 111
mol:Ca2+ -0.21 0.23 -9999 0 -0.54 111 111
mol:IP3 -0.22 0.24 -9999 0 -0.56 111 111
NLK -0.011 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.2 0.22 -9999 0 -0.49 124 124
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.47 290 290
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.26 0.27 -9999 0 -0.63 118 118
GO:0007205 -0.21 0.23 -9999 0 -0.54 111 111
WNT6 0.005 0.05 -9999 0 -0.31 11 11
WNT4 -0.27 0.4 -9999 0 -0.83 154 154
NFAT1/CK1 alpha -0.31 0.26 -9999 0 -0.63 141 141
GNG2 0.012 0.039 -9999 0 -0.83 1 1
WNT5A -0.006 0.12 -9999 0 -0.78 11 11
WNT11 -0.42 0.42 -9999 0 -0.82 237 237
CDC42 -0.24 0.25 -9999 0 -0.6 113 113
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.26 -10000 0 -0.7 33 33
IHH -0.21 0.38 -10000 0 -0.85 118 118
SHH Np/Cholesterol/GAS1 -0.11 0.21 -10000 0 -0.52 93 93
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.21 0.52 93 -10000 0 93
SMO/beta Arrestin2 -0.1 0.25 -10000 0 -0.49 121 121
SMO -0.11 0.26 -10000 0 -0.52 122 122
AKT1 -0.029 0.13 -10000 0 -1 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.003 0.12 -10000 0 -0.83 9 9
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.11 0.26 -10000 0 -0.51 122 122
STIL -0.082 0.2 -10000 0 -0.6 19 19
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 78 78
DHH N/PTCH1 -0.1 0.23 -10000 0 -0.46 124 124
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
DHH 0.008 0.068 -10000 0 -0.83 3 3
PTHLH -0.16 0.37 -10000 0 -1.2 33 33
determination of left/right symmetry -0.11 0.26 -10000 0 -0.51 122 122
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.16 0.37 -10000 0 -1.2 33 33
IHH N/Hhip -0.39 0.41 -10000 0 -0.75 244 244
DHH N/Hhip -0.25 0.31 -10000 0 -0.64 179 179
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.26 -10000 0 -0.51 122 122
pancreas development -0.32 0.41 -10000 0 -0.82 180 180
HHAT 0.012 0.039 -10000 0 -0.83 1 1
PI3K -0.004 0.051 -10000 0 -0.64 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.15 0.34 -10000 0 -0.83 92 92
somite specification -0.11 0.26 -10000 0 -0.51 122 122
SHH Np/Cholesterol/PTCH1 -0.093 0.21 -10000 0 -0.62 18 18
SHH Np/Cholesterol/PTCH2 -0.091 0.19 -10000 0 -0.52 77 77
SHH Np/Cholesterol/Megalin -0.15 0.23 -10000 0 -0.52 126 126
SHH 0.007 0.05 -10000 0 -0.64 1 1
catabolic process -0.12 0.26 -10000 0 -0.52 121 121
SMO/Vitamin D3 -0.096 0.23 -10000 0 -0.66 18 18
SHH Np/Cholesterol/Hhip -0.2 0.25 -10000 0 -0.52 179 179
LRP2 -0.22 0.37 -10000 0 -0.83 125 125
receptor-mediated endocytosis -0.21 0.24 -10000 0 -0.72 48 48
SHH Np/Cholesterol/BOC -0.016 0.08 -10000 0 -0.53 10 10
SHH Np/Cholesterol/CDO -0.16 0.24 -10000 0 -0.52 137 137
mesenchymal cell differentiation 0.2 0.25 0.51 179 -10000 0 179
mol:Vitamin D3 -0.092 0.21 -10000 0 -0.63 18 18
IHH N/PTCH2 -0.24 0.35 -10000 0 -0.67 172 172
CDON -0.24 0.38 -10000 0 -0.83 136 136
IHH N/PTCH1 -0.12 0.26 -10000 0 -0.52 121 121
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.64 125 125
PTCH2 -0.12 0.31 -10000 0 -0.83 76 76
SHH Np/Cholesterol -0.006 0.036 -10000 0 -0.52 1 1
PTCH1 -0.12 0.26 -10000 0 -0.52 121 121
HHIP -0.32 0.41 -10000 0 -0.82 180 180
Nongenotropic Androgen signaling

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
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.51 193 193
regulation of S phase of mitotic cell cycle -0.12 0.19 -10000 0 -0.34 194 194
GNAO1 -0.016 0.15 -10000 0 -0.74 18 18
HRAS 0.011 0.022 -10000 0 -0.32 2 2
SHBG/T-DHT -0.01 0.074 -10000 0 -0.57 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.17 0.24 -10000 0 -0.44 192 192
T-DHT/AR -0.27 0.32 -10000 0 -0.65 192 192
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 125 125
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.039 -10000 0 -0.83 1 1
mol:GDP -0.26 0.31 -10000 0 -0.62 192 192
cell proliferation -0.2 0.29 -10000 0 -0.68 77 77
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
FOS -0.25 0.4 -10000 0 -0.89 125 125
mol:Ca2+ -0.027 0.031 -10000 0 -0.072 89 89
MAPK3 -0.19 0.26 -10000 0 -0.6 83 83
MAPK1 -0.084 0.13 -10000 0 -0.31 74 74
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 125 125
cAMP biosynthetic process 0.015 0.078 -10000 0 -0.53 8 8
GNG2 0.012 0.039 -10000 0 -0.83 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 125 125
HRAS/GTP -0.2 0.23 -10000 0 -0.48 192 192
actin cytoskeleton reorganization -0.003 0.036 -10000 0 -0.45 3 3
SRC 0.012 0.016 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 125 125
PI3K -0.004 0.045 -10000 0 -0.56 3 3
apoptosis 0.17 0.26 0.53 125 -10000 0 125
T-DHT/AR/PELP1 -0.23 0.28 -10000 0 -0.56 192 192
HRAS/GDP -0.25 0.29 -10000 0 -0.59 193 193
CREB1 -0.18 0.28 -10000 0 -0.57 125 125
RAC1-CDC42/GTP -0.003 0.037 -10000 0 -0.46 3 3
AR -0.34 0.42 -10000 0 -0.83 192 192
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.18 0.24 -10000 0 -0.46 192 192
RAC1-CDC42/GDP -0.24 0.28 -10000 0 -0.56 192 192
T-DHT/AR/PELP1/Src -0.22 0.26 -10000 0 -0.52 192 192
MAP2K2 -0.17 0.24 -10000 0 -0.44 192 192
T-DHT/AR/PELP1/Src/PI3K -0.13 0.19 -10000 0 -0.34 194 194
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG -0.001 0.11 -10000 0 -0.83 8 8
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.56 15 15
mol:T-DHT 0 0.001 0.002 74 -0.003 49 123
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.043 -10000 0 -0.65 2 2
Gi family/GTP -0.095 0.13 -10000 0 -0.5 16 16
CDC42 0.013 0 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.079 -9999 0 -0.57 8 8
NFATC2 -0.098 0.22 -9999 0 -0.58 76 76
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.44 0.42 -9999 0 -0.88 189 189
PTGS2 -0.42 0.4 -9999 0 -0.86 176 176
JUNB 0.002 0.095 -9999 0 -0.83 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.83 105 105
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.03 0.12 -9999 0 -0.33 58 58
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.59 158 158
FOS -0.22 0.37 -9999 0 -0.84 125 125
IFNG -0.44 0.41 -9999 0 -0.86 192 192
AP-1/NFAT1-c-4 -0.54 0.51 -9999 0 -0.99 212 212
FASLG -0.42 0.39 -9999 0 -0.83 186 186
NFAT1-c-4/ICER1 -0.11 0.2 -9999 0 -0.51 83 83
IL2RA -0.41 0.38 -9999 0 -0.83 174 174
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.36 -9999 0 -0.77 253 253
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.51 90 90
IL4 -0.4 0.36 -9999 0 -0.8 173 173
IL2 -0.012 0.026 -9999 0 -10000 0 0
IL3 -0.033 0.03 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.007 0.085 -9999 0 -0.33 27 27
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.015 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.16 0.3 0.69 109 -10000 0 109
KIRREL -0.067 0.23 -10000 0 -0.85 37 37
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.16 0.3 -10000 0 -0.69 109 109
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.13 0.24 -10000 0 -0.54 109 109
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.073 0.19 -10000 0 -0.41 109 109
FYN -0.11 0.23 -10000 0 -0.51 109 109
mol:Ca2+ -0.13 0.24 -10000 0 -0.53 109 109
mol:DAG -0.13 0.24 -10000 0 -0.54 109 109
NPHS2 -0.015 0.034 -10000 0 -10000 0 0
mol:IP3 -0.13 0.24 -10000 0 -0.54 109 109
regulation of endocytosis -0.11 0.21 -10000 0 -0.48 109 109
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.55 109 109
establishment of cell polarity -0.16 0.3 -10000 0 -0.69 109 109
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 109 109
Nephrin/NEPH1/beta Arrestin2 -0.11 0.22 -10000 0 -0.48 109 109
NPHS1 -0.15 0.32 -10000 0 -0.83 84 84
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.51 109 109
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.24 -10000 0 -0.54 109 109
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 109 109
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.24 -10000 0 -0.51 113 113
cytoskeleton organization -0.098 0.25 -10000 0 -0.54 109 109
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.53 109 109
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.58 109 109
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.025 0.18 -9999 0 -0.83 21 21
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.42 0.27 -9999 0 -0.57 340 340
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.38 0.26 -9999 0 -0.52 340 340
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.1 0.29 -9999 0 -0.83 64 64
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.029 0.13 -9999 0 -0.64 21 21
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.012 0.022 -9999 0 -0.31 2 2
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.022 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.43 0.27 -9999 0 -0.58 341 341
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.28 0.21 -9999 0 -0.73 17 17
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.32 0.23 -9999 0 -0.45 340 340
RELN -0.6 0.37 -9999 0 -0.83 336 336
PAFAH/LIS1 -0.052 0.2 -9999 0 -0.55 64 64
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.22 0.14 -9999 0 -0.55 17 17
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.19 -9999 0 -0.72 20 20
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.3 0.22 -9999 0 -0.8 17 17
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.026 -9999 0 -0.31 3 3
PAFAH1B2 -0.001 0.11 -9999 0 -0.83 8 8
MAP1B/LIS1/Dynein heavy chain 0.027 0.004 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.28 0.18 -9999 0 -0.7 17 17
LRP8 -0.025 0.18 -9999 0 -0.83 21 21
NDEL1/Katanin 60 -0.28 0.21 -9999 0 -0.73 17 17
P39/CDK5 -0.33 0.23 -9999 0 -0.46 340 340
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.35 0.25 -9999 0 -0.48 340 340
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.36 0.23 -9999 0 -0.49 341 341
RELN/VLDLR -0.41 0.27 -9999 0 -0.55 345 345
CDC42 0 0 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.002 0.027 -10000 0 -0.55 1 1
fibroblast growth factor receptor signaling pathway -0.002 0.026 -10000 0 -0.55 1 1
LAMA1 -0.048 0.22 -10000 0 -0.81 34 34
PRNP 0.012 0.039 -10000 0 -0.83 1 1
GPC1/SLIT2 -0.093 0.22 -10000 0 -0.64 66 66
SMAD2 0.029 0.044 -10000 0 -0.5 2 2
GPC1/PrPc/Cu2+ -0.002 0.027 -10000 0 -0.56 1 1
GPC1/Laminin alpha1 -0.046 0.16 -10000 0 -0.64 33 33
TDGF1 -0.34 0.42 -10000 0 -0.83 194 194
CRIPTO/GPC1 -0.27 0.31 -10000 0 -0.64 194 194
APP/GPC1 0 0.009 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.28 -10000 0 -0.55 194 194
FLT1 0.012 0.039 -10000 0 -0.83 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.044 -10000 0 -0.55 2 2
SERPINC1 0.009 0.034 -10000 0 -0.31 5 5
FYN -0.21 0.28 -10000 0 -0.55 194 194
FGR -0.22 0.28 -10000 0 -0.55 194 194
positive regulation of MAPKKK cascade -0.28 0.32 -10000 0 -0.62 196 196
SLIT2 -0.11 0.3 -10000 0 -0.8 69 69
GPC1/NRG -0.065 0.19 -10000 0 -0.64 46 46
NRG1 -0.072 0.25 -10000 0 -0.81 48 48
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.061 -10000 0 -0.72 3 3
LYN -0.21 0.28 -10000 0 -0.55 194 194
mol:Spermine 0.012 0.01 -10000 0 -10000 0 0
cell growth -0.002 0.026 -10000 0 -0.55 1 1
BMP signaling pathway -0.013 0.015 0.31 1 -10000 0 1
SRC -0.21 0.28 -10000 0 -0.55 194 194
TGFBR1 0.006 0.05 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.37 -10000 0 -0.69 173 173
GPC1 0.013 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.006 0.05 -10000 0 -10000 0 0
VEGFA 0.008 0.068 -10000 0 -0.83 3 3
BLK -0.38 0.38 -10000 0 -0.68 263 263
HCK -0.22 0.28 -10000 0 -0.56 194 194
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.012 0.039 -10000 0 -0.83 1 1
VEGFR1 homodimer 0.011 0.039 -10000 0 -0.83 1 1
TGFBR2 0.01 0.055 -10000 0 -0.83 2 2
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.003 0.023 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.64 126 126
LCK -0.23 0.29 -10000 0 -0.55 199 199
neuron differentiation -0.065 0.19 -10000 0 -0.63 46 46
PrPc/Cu2+ -0.001 0.03 -10000 0 -0.64 1 1
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.01 0.055 -10000 0 -0.83 2 2
Ephrin B reverse signaling

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
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.007 0.068 -10000 0 -0.83 3 3
EFNB1 -0.003 0.12 -10000 0 -0.64 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.25 0.25 -10000 0 -0.53 195 195
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.51 182 182
neuron projection morphogenesis -0.24 0.24 -10000 0 -0.5 195 195
Ephrin B1/EPHB1-2/Tiam1 -0.27 0.27 -10000 0 -0.57 195 195
DNM1 -0.019 0.16 -10000 0 -0.8 18 18
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.006 0.086 -10000 0 -0.8 5 5
YES1 -0.009 0.11 -10000 0 -1 5 5
Ephrin B1/EPHB1-2/NCK2 -0.2 0.25 -10000 0 -0.48 195 195
PI3K 0.003 0.12 -10000 0 -1.1 5 5
mol:GDP -0.27 0.27 -10000 0 -0.56 195 195
ITGA2B -0.08 0.26 -10000 0 -0.83 51 51
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.009 0.11 -10000 0 -1 5 5
MAP3K7 -0.011 0.089 -10000 0 -0.86 5 5
FGR -0.011 0.11 -10000 0 -1 5 5
TIAM1 -0.17 0.16 -10000 0 -0.32 261 261
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.047 0.22 -10000 0 -0.55 62 62
LYN -0.009 0.11 -10000 0 -1 5 5
Ephrin B1/EPHB1-2/Src Family Kinases -0.013 0.1 -10000 0 -0.98 5 5
Ephrin B1/EPHB1-2 -0.019 0.095 -10000 0 -0.92 5 5
SRC -0.011 0.11 -10000 0 -1 5 5
ITGB3 -0.014 0.15 -10000 0 -0.83 15 15
EPHB1 -0.32 0.41 -10000 0 -0.83 180 180
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.089 0.24 -10000 0 -0.69 60 60
BLK -0.066 0.14 -10000 0 -1.1 5 5
HCK -0.012 0.11 -10000 0 -1 5 5
regulation of stress fiber formation 0.19 0.24 0.47 195 -10000 0 195
MAPK8 0.006 0.13 -10000 0 -0.82 9 9
Ephrin B1/EPHB1-2/RGS3 -0.2 0.25 -10000 0 -0.48 195 195
endothelial cell migration -0.006 0.078 -10000 0 -0.75 5 5
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.006 0.1 -10000 0 -0.95 5 5
regulation of focal adhesion formation 0.19 0.24 0.47 195 -10000 0 195
chemotaxis 0.19 0.24 0.47 195 -10000 0 195
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
Rac1/GTP -0.25 0.24 -10000 0 -0.52 195 195
angiogenesis -0.019 0.095 -10000 0 -0.91 5 5
LCK -0.014 0.11 -10000 0 -1.1 5 5
Endothelins

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
AKT1 -0.051 0.14 -9999 0 -0.55 9 9
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.68 60 60
EDN1 -0.043 0.12 -9999 0 -0.8 6 6
EDN3 -0.41 0.42 -9999 0 -0.82 231 231
EDN2 -0.015 0.12 -9999 0 -0.41 31 31
HRAS/GDP -0.1 0.24 -9999 0 -0.53 80 80
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.18 -9999 0 -0.39 89 89
ADCY4 -0.096 0.19 -9999 0 -0.51 64 64
ADCY5 -0.16 0.26 -9999 0 -0.57 109 109
ADCY6 -0.096 0.19 -9999 0 -0.5 65 65
ADCY7 -0.096 0.19 -9999 0 -0.5 65 65
ADCY1 -0.1 0.2 -9999 0 -0.53 67 67
ADCY2 -0.14 0.24 -9999 0 -0.55 95 95
ADCY3 -0.096 0.19 -9999 0 -0.5 65 65
ADCY8 -0.2 0.21 -9999 0 -0.55 89 89
ADCY9 -0.096 0.19 -9999 0 -0.51 64 64
arachidonic acid secretion -0.18 0.32 -9999 0 -0.64 127 127
ETB receptor/Endothelin-1/Gq/GTP -0.095 0.21 -9999 0 -0.44 103 103
GNAO1 -0.016 0.15 -9999 0 -0.74 18 18
HRAS 0.01 0.022 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.014 0.16 -9999 0 -0.53 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.083 0.22 -9999 0 -0.54 65 65
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.069 0.17 -9999 0 -0.5 35 35
EDNRB 0.004 0.089 -9999 0 -0.84 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.16 0.24 -9999 0 -0.7 36 36
CYSLTR1 -0.057 0.17 -9999 0 -0.73 12 12
SLC9A1 -0.022 0.075 -9999 0 -0.36 2 2
mol:GDP -0.12 0.26 -9999 0 -0.55 87 87
SLC9A3 -0.048 0.19 -9999 0 -0.78 20 20
RAF1 -0.16 0.3 -9999 0 -0.59 116 116
JUN -0.28 0.52 -9999 0 -1.2 111 111
JAK2 -0.053 0.14 -9999 0 -0.55 10 10
mol:IP3 -0.11 0.23 -9999 0 -0.49 98 98
ETA receptor/Endothelin-1 -0.035 0.2 -9999 0 -0.62 10 10
PLCB1 0.008 0.04 -9999 0 -0.83 1 1
PLCB2 0.005 0.044 -9999 0 -0.32 8 8
ETA receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.67 230 230
FOS -0.26 0.48 -9999 0 -1 127 127
Gai/GDP -0.003 0.13 -9999 0 -0.66 15 15
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.23 -9999 0 -0.61 49 49
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 98 98
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.092 0.28 -9999 0 -0.83 58 58
Gs family/GDP -0.19 0.25 -9999 0 -0.58 112 112
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.46 97 97
MAPK14 -0.063 0.17 -9999 0 -0.47 33 33
TRPC6 -0.14 0.29 -9999 0 -0.73 57 57
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.012 0.039 -9999 0 -0.83 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.18 -9999 0 -0.4 80 80
ETB receptor/Endothelin-2 -0.026 0.11 -9999 0 -0.64 11 11
ETB receptor/Endothelin-3 -0.32 0.32 -9999 0 -0.64 232 232
ETB receptor/Endothelin-1 -0.019 0.12 -9999 0 -0.63 11 11
MAPK3 -0.24 0.44 -9999 0 -0.88 133 133
MAPK1 -0.24 0.44 -9999 0 -0.88 133 133
Rac1/GDP -0.1 0.24 -9999 0 -0.53 76 76
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.56 72 72
MAPK8 -0.17 0.34 -9999 0 -0.69 99 99
SRC 0.012 0.015 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.009 0.078 -9999 0 -0.35 8 8
p130Cas/CRK/Src/PYK2 -0.13 0.29 -9999 0 -0.6 96 96
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.53 76 76
COL1A2 -0.037 0.16 -9999 0 -0.61 8 8
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.63 8 8
mol:DAG -0.11 0.23 -9999 0 -0.49 98 98
MAP2K2 -0.19 0.35 -9999 0 -0.68 135 135
MAP2K1 -0.19 0.35 -9999 0 -0.69 134 134
EDNRA -0.038 0.098 -9999 0 -0.55 4 4
positive regulation of muscle contraction -0.036 0.12 -9999 0 -0.5 8 8
Gq family/GDP -0.19 0.29 -9999 0 -0.66 114 114
HRAS/GTP -0.13 0.26 -9999 0 -0.55 98 98
PRKCH -0.1 0.22 -9999 0 -0.5 82 82
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.26 -9999 0 -0.56 94 94
PRKCB -0.12 0.23 -9999 0 -0.51 89 89
PRKCE -0.1 0.23 -9999 0 -0.52 83 83
PRKCD -0.1 0.22 -9999 0 -0.49 90 90
PRKCG -0.11 0.22 -9999 0 -0.51 82 82
regulation of vascular smooth muscle contraction -0.31 0.56 -9999 0 -1.2 127 127
PRKCQ -0.11 0.23 -9999 0 -0.52 86 86
PLA2G4A -0.2 0.36 -9999 0 -0.72 127 127
GNA14 -0.18 0.36 -9999 0 -0.84 107 107
GNA15 -0.015 0.092 -9999 0 -0.33 34 34
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.006 0.12 -9999 0 -0.83 9 9
Rac1/GTP -0.014 0.16 -9999 0 -0.53 8 8
MMP1 -0.096 0.16 -9999 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.27 0.33 -9999 0 -0.6 204 204
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.052 0.22 -9999 0 -0.7 42 42
SMAD9 -0.22 0.28 -9999 0 -0.59 156 156
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.094 0.2 -9999 0 -0.37 149 149
BMP7/USAG1 -0.33 0.32 -9999 0 -0.64 240 240
SMAD5/SKI -0.082 0.2 -9999 0 -0.54 27 27
SMAD1 0.02 0.045 -9999 0 -10000 0 0
BMP2 -0.021 0.17 -9999 0 -0.83 19 19
SMAD1/SMAD1/SMAD4 -0.001 0.001 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.26 0.39 -9999 0 -0.83 149 149
BMPR1A-1B/BAMBI -0.18 0.26 -9999 0 -0.56 149 149
AHSG -0.015 0.081 -9999 0 -0.31 31 31
CER1 0 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.041 0.14 -9999 0 -0.56 32 32
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.077 0.2 -9999 0 -0.64 31 31
BMP2-4 (homodimer) -0.047 0.16 -9999 0 -0.64 32 32
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.5 149 149
RGMA -0.018 0.16 -9999 0 -0.83 17 17
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.088 0.19 -9999 0 -0.34 114 114
BMP2-4/USAG1 -0.32 0.3 -9999 0 -0.59 255 255
SMAD6/SMURF1/SMAD5 -0.082 0.2 -9999 0 -0.54 27 27
SOSTDC1 -0.43 0.42 -9999 0 -0.82 241 241
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.5 149 149
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0.015 -9999 0 -0.31 1 1
HFE2 0.001 0.034 -9999 0 -0.31 5 5
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.05 0.16 -9999 0 -0.56 39 39
SMAD5/SMAD5/SMAD4 -0.082 0.2 -9999 0 -0.54 27 27
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.093 0.14 -9999 0 -0.5 28 28
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.014 0.053 -9999 0 -0.4 1 1
SMAD1/SKI 0.027 0.042 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.051 0.15 -9999 0 -0.57 32 32
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.35 -9999 0 -0.73 132 132
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.008 0.067 -9999 0 -0.55 7 7
BMPR1A-1B (homodimer) -0.2 0.3 -9999 0 -0.64 149 149
CHRDL1 -0.58 0.38 -9999 0 -0.83 324 324
ENDOFIN/SMAD1 0.027 0.042 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.008 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.082 -9999 0 -0.37 19 19
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.29 -9999 0 -0.59 330 330
BMP2-4/GREM1 -0.18 0.28 -9999 0 -0.62 124 124
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.19 0.28 -9999 0 -0.55 156 156
SMAD1/SMAD6 0.027 0.042 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.013 0.015 -9999 0 -0.31 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.066 0.16 -9999 0 -0.51 28 28
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.027 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.001 0.1 -9999 0 -0.83 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.2 0.32 -9999 0 -0.51 177 177
CHRD -0.001 0.11 -9999 0 -0.83 8 8
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.093 0.2 -9999 0 -0.35 123 123
BMP4 -0.015 0.14 -9999 0 -0.65 20 20
FST -0.2 0.36 -9999 0 -0.79 122 122
BMP2-4/NOG -0.082 0.19 -9999 0 -0.55 64 64
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.22 -9999 0 -0.47 149 149
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.6 76 76
FYN -0.1 0.34 -10000 0 -0.79 79 79
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.65 83 83
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.053 0.22 -10000 0 -0.47 83 83
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.03 0.05 -10000 0 -0.19 10 10
MAP3K8 -0.001 0.11 -10000 0 -0.83 8 8
mol:Ca2+ -0.031 0.051 -10000 0 -0.12 101 101
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.32 -10000 0 -0.72 86 86
TRPV6 -0.18 0.34 -10000 0 -0.81 104 104
CD28 -0.042 0.19 -10000 0 -0.58 43 43
SHC1 -0.11 0.34 -10000 0 -0.79 80 80
receptor internalization -0.14 0.38 -10000 0 -0.7 116 116
PRF1 -0.11 0.35 -10000 0 -0.88 66 66
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.036 0.18 -10000 0 -0.38 82 82
LAT -0.11 0.35 -10000 0 -0.8 80 80
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.093 0.27 -10000 0 -0.71 68 68
CD3E -0.068 0.24 -10000 0 -0.75 49 49
CD3G -0.15 0.33 -10000 0 -0.79 93 93
RASGRP2 0 0.03 -10000 0 -0.19 5 5
RASGRP1 -0.05 0.22 -10000 0 -0.46 88 88
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.068 -10000 0 -0.12 66 66
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.056 0.089 -10000 0 -0.25 56 56
PRKCA -0.061 0.13 -10000 0 -0.3 90 90
GRAP2 -0.042 0.2 -10000 0 -0.78 32 32
mol:IP3 -0.05 0.23 0.28 80 -0.46 82 162
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.92 82 82
ORAI1 0.089 0.16 0.39 98 -10000 0 98
CSK -0.12 0.35 -10000 0 -0.8 83 83
B7 family/CD28 -0.19 0.34 -10000 0 -0.74 106 106
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.15 0.42 -10000 0 -0.94 85 85
PTPN6 -0.12 0.36 -10000 0 -0.81 82 82
VAV1 -0.12 0.34 -10000 0 -0.76 89 89
Monovalent TCR/CD3 -0.16 0.41 -10000 0 -0.73 114 114
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.36 -10000 0 -0.8 84 84
PAG1 -0.12 0.35 -10000 0 -0.8 83 83
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.15 0.42 -10000 0 -0.91 89 89
CD80 -0.073 0.25 -10000 0 -0.81 48 48
CD86 -0.008 0.1 -10000 0 -0.41 23 23
PDK1/CARD11/BCL10/MALT1 -0.069 0.11 -10000 0 -0.3 64 64
HRAS 0.012 0.022 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.29 -10000 0 -0.59 106 106
CD8A -0.046 0.22 -10000 0 -0.83 32 32
CD8B -0.091 0.27 -10000 0 -0.73 65 65
PTPRC -0.032 0.17 -10000 0 -0.59 34 34
PDK1/PKC theta -0.067 0.27 -10000 0 -0.58 84 84
CSK/PAG1 -0.1 0.34 -10000 0 -0.78 80 80
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.015 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.15 0.32 -10000 0 -0.76 86 86
STIM1 0.048 0.082 -10000 0 -10000 0 0
RAS family/GTP 0.009 0.091 -10000 0 -0.18 55 55
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.78 116 116
mol:DAG -0.07 0.18 -10000 0 -0.41 82 82
RAP1A/GDP 0.006 0.03 -10000 0 -0.063 10 10
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.023 0.16 -10000 0 -0.64 26 26
cytotoxic T cell degranulation -0.1 0.33 -10000 0 -0.82 67 67
RAP1A/GTP -0.003 0.009 -10000 0 -0.07 4 4
mol:PI-3-4-5-P3 -0.072 0.26 -10000 0 -0.56 86 86
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.079 0.29 0.3 72 -0.61 82 154
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.024 0.16 -10000 0 -0.62 27 27
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.25 -10000 0 -0.62 82 82
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.055 -10000 0 -0.83 2 2
CD8 heterodimer -0.1 0.29 -10000 0 -0.77 68 68
CARD11 -0.074 0.17 -10000 0 -0.35 110 110
PRKCB -0.058 0.13 -10000 0 -0.3 83 83
PRKCE -0.051 0.12 -10000 0 -0.3 71 71
PRKCQ -0.089 0.31 -10000 0 -0.68 85 85
LCP2 0.008 0.04 -10000 0 -0.31 7 7
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.039 0.18 -10000 0 -0.39 83 83
IKK complex 0.013 0.069 -10000 0 -0.12 52 52
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.016 0.14 -10000 0 -0.31 59 59
PDPK1 -0.046 0.21 -10000 0 -0.44 83 83
TCR/CD3/MHC I/CD8/Fyn -0.16 0.45 -10000 0 -1.1 80 80
IGF1 pathway

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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.13 0.24 -10000 0 -0.46 145 145
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.022 -10000 0 -0.31 2 2
IRS1/Crk -0.13 0.24 -10000 0 -0.46 145 145
IGF-1R heterotetramer/IGF1/PTP1B -0.12 0.22 -10000 0 -0.53 102 102
AKT1 -0.09 0.22 -10000 0 -0.78 15 15
BAD -0.076 0.2 -10000 0 -0.71 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.24 -10000 0 -0.46 145 145
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.15 0.23 -10000 0 -0.46 145 145
RAF1 -0.066 0.19 -10000 0 -0.66 15 15
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.47 102 102
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.24 -10000 0 -0.5 145 145
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
RPS6KB1 -0.09 0.22 -10000 0 -0.78 15 15
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.17 -10000 0 -0.54 15 15
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.74 13 13
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.098 0.18 -10000 0 -0.43 102 102
IGF-1R heterotetramer -0.018 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.23 -10000 0 -0.46 145 145
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.44 102 102
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.35 -10000 0 -0.85 102 102
IRS2/Crk -0.11 0.23 -10000 0 -0.47 102 102
PI3K -0.14 0.22 -10000 0 -0.48 103 103
apoptosis 0.058 0.18 0.58 15 -10000 0 15
HRAS/GDP -0.001 0.014 -10000 0 -10000 0 0
PRKCD -0.1 0.24 -10000 0 -0.54 102 102
RAF1/14-3-3 E -0.049 0.17 -10000 0 -0.54 15 15
BAD/14-3-3 -0.062 0.19 -10000 0 -0.64 15 15
PRKCZ -0.09 0.22 -10000 0 -0.78 15 15
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.64 15 15
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.25 -10000 0 -0.57 102 102
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.47 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.24 -10000 0 -0.46 145 145
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.46 145 145
IRS1 -0.14 0.25 -10000 0 -0.5 145 145
IRS2 -0.13 0.24 -10000 0 -0.46 145 145
IGF-1R heterotetramer/IGF1 -0.16 0.27 -10000 0 -0.67 102 102
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.1 0.23 -10000 0 -0.46 103 103
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.1 0.24 -10000 0 -0.54 103 103
SHC1 0.013 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.21 0.55 -10000 0 -1.3 74 74
IL23A -0.23 0.56 -10000 0 -1.3 83 83
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.47 -10000 0 -1.2 83 83
positive regulation of T cell mediated cytotoxicity -0.25 0.61 -10000 0 -1.4 84 84
ITGA3 -0.2 0.51 -10000 0 -1.2 79 79
IL17F -0.11 0.34 -10000 0 -0.74 67 67
IL12B -0.004 0.11 -10000 0 -0.59 12 12
STAT1 (dimer) -0.24 0.58 -10000 0 -1.3 85 85
CD4 -0.2 0.5 -10000 0 -1.2 74 74
IL23 -0.23 0.54 -10000 0 -1.2 82 82
IL23R -0.004 0.099 -10000 0 -10000 0 0
IL1B -0.24 0.59 -10000 0 -1.4 75 75
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.2 0.5 -10000 0 -1.2 75 75
TYK2 0.013 0.023 -10000 0 -10000 0 0
STAT4 -0.027 0.15 -10000 0 -0.46 40 40
STAT3 0.013 0 -10000 0 -10000 0 0
IL18RAP -0.026 0.17 -10000 0 -0.8 21 21
IL12RB1 -0.02 0.12 -10000 0 -0.4 25 25
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
IL12Rbeta1/TYK2 -0.008 0.09 -10000 0 -0.68 3 3
IL23R/JAK2 -0.001 0.13 -10000 0 -0.68 1 1
positive regulation of chronic inflammatory response -0.25 0.61 -10000 0 -1.4 84 84
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.02 0.049 -10000 0 -0.87 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
NFKB1 0.011 0.04 -10000 0 -0.83 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.5 -10000 0 -1.1 83 83
ALOX12B -0.21 0.51 -10000 0 -1.2 77 77
CXCL1 -0.22 0.53 -10000 0 -1.2 78 78
T cell proliferation -0.25 0.61 -10000 0 -1.4 84 84
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.062 0.28 -10000 0 -0.58 56 56
PI3K -0.3 0.48 -10000 0 -1.2 81 81
IFNG -0.02 0.055 -10000 0 -0.13 67 67
STAT3 (dimer) -0.28 0.44 -10000 0 -1.1 81 81
IL18R1 -0.03 0.14 -10000 0 -0.41 45 45
IL23/IL23R/JAK2/TYK2/SOCS3 -0.1 0.33 -10000 0 -0.78 46 46
IL18/IL18R -0.067 0.18 -10000 0 -0.58 39 39
macrophage activation -0.015 0.018 -10000 0 -0.044 85 85
TNF -0.27 0.62 -10000 0 -1.4 95 95
STAT3/STAT4 -0.31 0.49 -10000 0 -1.2 87 87
STAT4 (dimer) -0.25 0.58 -10000 0 -1.3 86 86
IL18 -0.038 0.15 -10000 0 -0.42 50 50
IL19 -0.2 0.5 -10000 0 -1.1 79 79
STAT5A (dimer) -0.23 0.58 -10000 0 -1.3 83 83
STAT1 0.006 0.05 -10000 0 -0.31 11 11
SOCS3 -0.035 0.19 -10000 0 -0.83 26 26
CXCL9 -0.3 0.63 -10000 0 -1.4 105 105
MPO -0.2 0.51 -10000 0 -1.2 80 80
positive regulation of humoral immune response -0.25 0.61 -10000 0 -1.4 84 84
IL23/IL23R/JAK2/TYK2 -0.29 0.73 -10000 0 -1.6 83 83
IL6 -0.33 0.66 -10000 0 -1.4 115 115
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.001 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 0.036 1 -10000 0 1
CD3E -0.23 0.57 -10000 0 -1.3 85 85
keratinocyte proliferation -0.25 0.61 -10000 0 -1.4 84 84
NOS2 -0.21 0.51 -10000 0 -1.2 78 78
Glucocorticoid receptor regulatory network

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
PCK2 0.044 0.093 0.34 4 -10000 0 4
SMARCC2 0.014 0.014 -10000 0 -10000 0 0
SMARCC1 0.014 0.014 -10000 0 -10000 0 0
TBX21 -0.16 0.28 -10000 0 -0.83 46 46
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.051 -10000 0 -0.31 11 11
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.004 0.087 -10000 0 -0.83 5 5
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.36 34 -0.52 5 39
PRL -0.089 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.25 0.31 0.59 143 -0.5 20 163
RELA -0.035 0.088 -10000 0 -10000 0 0
FGG 0.25 0.19 0.52 94 -10000 0 94
GR beta/TIF2 0.085 0.23 0.35 61 -0.57 42 103
IFNG -0.5 0.51 -10000 0 -1.1 144 144
apoptosis 0.033 0.24 0.52 51 -0.56 2 53
CREB1 0.012 0.022 -10000 0 -10000 0 0
histone acetylation -0.072 0.17 -10000 0 -0.42 52 52
BGLAP -0.1 0.15 -10000 0 -0.53 12 12
GR/PKAc 0.13 0.1 0.37 18 -0.42 1 19
NF kappa B1 p50/RelA -0.073 0.16 -10000 0 -0.45 27 27
SMARCD1 0.014 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.094 0.27 93 -10000 0 93
GATA3 -0.028 0.19 -10000 0 -0.79 26 26
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.56 40 40
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.061 0.23 0.51 43 -0.74 5 48
CSN2 0.2 0.14 0.43 75 -10000 0 75
BRG1/BAF155/BAF170/BAF60A 0.015 0.048 -10000 0 -10000 0 0
NFATC1 0.001 0.11 -10000 0 -0.83 8 8
POU2F1 0.013 0.015 -10000 0 -0.3 1 1
CDKN1A 0.024 0.053 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.012 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 297 297
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.16 0.35 13 -0.47 13 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.082 0.45 0.49 43 -0.88 101 144
JUN -0.34 0.31 -10000 0 -0.74 140 140
IL4 -0.13 0.18 -10000 0 -0.69 19 19
CDK5R1 0.011 0.023 -10000 0 -0.32 2 2
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.38 0.41 -10000 0 -0.86 165 165
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.35 30 -0.47 5 35
cortisol/GR alpha (monomer) 0.37 0.3 0.7 164 -10000 0 164
NCOA2 -0.063 0.24 -10000 0 -0.83 42 42
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.26 0.36 -10000 0 -0.85 125 125
AP-1/NFAT1-c-4 -0.57 0.48 -10000 0 -1 201 201
AFP -0.22 0.22 -10000 0 -0.68 38 38
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.52 30 -10000 0 30
TP53 0.033 0.022 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.37 -10000 0 -0.84 165 165
KRT14 -0.24 0.18 -10000 0 -0.6 21 21
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.066 -10000 0 -10000 0 0
HDAC1 0.011 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.013 -10000 0 -10000 0 0
AP-1 -0.57 0.49 -10000 0 -1 201 201
MAPK14 0.014 0.011 -10000 0 -10000 0 0
MAPK10 0.012 0.041 -10000 0 -0.83 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.55 0.53 -10000 0 -1.1 159 159
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.052 -10000 0 -0.31 11 11
CGA -0.13 0.16 -10000 0 -0.53 24 24
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.4 132 -10000 0 132
MAPK3 0.014 0.012 -10000 0 -10000 0 0
MAPK1 0.014 0.011 -10000 0 -10000 0 0
ICAM1 -0.26 0.27 -10000 0 -0.64 111 111
NFKB1 -0.037 0.097 -10000 0 -0.95 1 1
MAPK8 -0.19 0.2 -10000 0 -0.52 84 84
MAPK9 0.014 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.028 0.24 0.52 51 -0.58 2 53
BAX 0.029 0.031 -10000 0 -10000 0 0
POMC -0.55 0.7 -10000 0 -1.6 127 127
EP300 0.065 0.066 -10000 0 -0.28 1 1
cortisol/GR alpha (dimer)/p53 0.33 0.24 0.61 154 -10000 0 154
proteasomal ubiquitin-dependent protein catabolic process 0.088 0.071 0.24 28 -10000 0 28
SGK1 0.1 0.23 -10000 0 -1.4 10 10
IL13 -0.3 0.25 -10000 0 -0.81 56 56
IL6 -0.4 0.53 -10000 0 -1.2 129 129
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.73 39 39
IL2 -0.37 0.27 -10000 0 -0.8 86 86
CDK5 0.013 0.007 -10000 0 -10000 0 0
PRKACB 0.012 0.039 -10000 0 -0.83 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.27 0.32 -10000 0 -0.82 71 71
CDK5R1/CDK5 0.007 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.031 0.12 -10000 0 -0.64 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.57 143 -10000 0 143
SMARCA4 0.014 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.41 100 -0.39 1 101
NF kappa B1 p50/RelA/Cbp 0.019 0.16 -10000 0 -0.51 5 5
JUN (dimer) -0.33 0.3 -10000 0 -0.74 140 140
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.42 -10000 0 -1.1 78 78
NR3C1 0.22 0.19 0.5 106 -10000 0 106
NR4A1 -0.32 0.42 -10000 0 -0.77 193 193
TIF2/SUV420H1 -0.058 0.18 -10000 0 -0.64 42 42
MAPKKK cascade 0.033 0.24 0.52 51 -0.56 2 53
cortisol/GR alpha (dimer)/Src-1 0.33 0.24 0.6 150 -10000 0 150
PBX1 0.012 0.039 -10000 0 -0.83 1 1
POU1F1 0.007 0.008 -10000 0 -10000 0 0
SELE -0.34 0.5 -10000 0 -1.2 94 94
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.42 100 -0.4 1 101
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.57 143 -10000 0 143
mol:cortisol 0.21 0.19 0.4 182 -10000 0 182
MMP1 -0.22 0.15 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.18 0.42 -9999 0 -0.97 46 46
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.34 -9999 0 -0.83 99 99
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.18 0.42 -9999 0 -0.96 48 48
AP1 -0.3 0.46 -9999 0 -0.93 147 147
ABCG2 -0.19 0.42 -9999 0 -1 41 41
HIF1A -0.009 0.068 -9999 0 -10000 0 0
TFF3 -0.57 0.52 -9999 0 -1 187 187
GATA2 0.014 0.016 -9999 0 -0.31 1 1
AKT1 -0.038 0.1 -9999 0 -10000 0 0
response to hypoxia -0.059 0.11 -9999 0 -0.24 21 21
MCL1 -0.18 0.42 -9999 0 -0.96 48 48
NDRG1 -0.18 0.42 -9999 0 -0.95 50 50
SERPINE1 -0.2 0.43 -9999 0 -0.96 54 54
FECH -0.18 0.42 -9999 0 -0.98 44 44
FURIN -0.18 0.42 -9999 0 -0.95 50 50
NCOA2 -0.062 0.24 -9999 0 -0.83 42 42
EP300 -0.063 0.18 -9999 0 -0.34 101 101
HMOX1 -0.19 0.42 -9999 0 -0.98 47 47
BHLHE40 -0.19 0.43 -9999 0 -0.99 47 47
BHLHE41 -0.18 0.42 -9999 0 -0.98 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.016 0.036 -9999 0 -10000 0 0
ENG 0.043 0.093 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.83 105 105
RORA -0.19 0.42 -9999 0 -0.99 46 46
ABCB1 -0.072 0.18 -9999 0 -1.5 6 6
TFRC -0.18 0.42 -9999 0 -0.97 47 47
CXCR4 -0.18 0.42 -9999 0 -0.95 50 50
TF -0.24 0.49 -9999 0 -1.1 77 77
CITED2 -0.22 0.47 -9999 0 -1.1 59 59
HIF1A/ARNT -0.29 0.38 -9999 0 -1 61 61
LDHA -0.039 0.05 -9999 0 -10000 0 0
ETS1 -0.18 0.42 -9999 0 -0.97 46 46
PGK1 -0.18 0.42 -9999 0 -0.97 45 45
NOS2 -0.2 0.43 -9999 0 -0.98 50 50
ITGB2 -0.19 0.42 -9999 0 -0.99 47 47
ALDOA -0.18 0.42 -9999 0 -0.97 46 46
Cbp/p300/CITED2 -0.32 0.51 -9999 0 -1.1 98 98
FOS -0.21 0.37 -9999 0 -0.83 125 125
HK2 -0.19 0.42 -9999 0 -0.95 52 52
SP1 0.023 0.006 -9999 0 -10000 0 0
GCK -0.4 0.72 -9999 0 -1.5 130 130
HK1 -0.18 0.42 -9999 0 -0.97 46 46
NPM1 -0.18 0.42 -9999 0 -0.99 41 41
EGLN1 -0.18 0.42 -9999 0 -0.95 52 52
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.18 0.42 -9999 0 -0.97 46 46
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.17 0.32 -9999 0 -0.74 63 63
IGFBP1 -0.2 0.42 -9999 0 -0.97 48 48
VEGFA -0.16 0.39 -9999 0 -0.76 72 72
HIF1A/JAB1 -0.011 0.02 -9999 0 -10000 0 0
CP -0.35 0.56 -9999 0 -1.1 134 134
CXCL12 -0.23 0.48 -9999 0 -1.1 70 70
COPS5 0.014 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.18 0.42 -9999 0 -0.97 46 46
EGLN3 -0.2 0.44 -9999 0 -1 53 53
CA9 -0.2 0.42 -9999 0 -0.98 48 48
TERT -0.2 0.42 -9999 0 -0.96 49 49
ENO1 -0.18 0.42 -9999 0 -0.98 43 43
PFKL -0.18 0.42 -9999 0 -0.98 44 44
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.22 0.44 -9999 0 -1 52 52
ARNT -0.009 0.068 -9999 0 -10000 0 0
HNF4A -0.026 0.064 -9999 0 -0.34 9 9
ADFP -0.2 0.42 -9999 0 -0.92 61 61
SLC2A1 -0.15 0.38 -9999 0 -0.75 71 71
LEP -0.2 0.42 -9999 0 -0.99 45 45
HIF1A/ARNT/Cbp/p300 -0.29 0.36 -9999 0 -0.86 102 102
EPO -0.14 0.33 -9999 0 -0.89 27 27
CREBBP -0.063 0.18 -9999 0 -0.34 101 101
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.83 97 97
PFKFB3 -0.18 0.42 -9999 0 -1 41 41
NT5E -0.19 0.43 -9999 0 -0.99 47 47
Glypican 2 network

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
MDK -0.087 0.15 -9999 0 -0.31 142 142
GPC2 -0.009 0.083 -9999 0 -0.31 32 32
GPC2/Midkine -0.076 0.11 -9999 0 -0.4 10 10
neuron projection morphogenesis -0.076 0.11 -9999 0 -0.4 10 10
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 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.043 0.11 -9999 0 -0.48 12 12
EGFR 0.006 0.078 -9999 0 -0.83 4 4
EPHA2 0.011 0.026 -9999 0 -0.31 3 3
USP6 0.011 0.026 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.099 0.23 -9999 0 -0.64 70 70
ARRB2 -0.044 0.15 -9999 0 -0.45 56 56
mol:GTP 0.021 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0.039 -9999 0 -0.83 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.009 0.055 -9999 0 -0.83 2 2
EGF -0.11 0.3 -9999 0 -0.78 72 72
somatostatin receptor activity 0 0 -9999 0 -0.001 133 133
ARAP2 0.01 0.055 -9999 0 -0.83 2 2
mol:GDP -0.12 0.15 -9999 0 -0.3 142 142
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 116 116
ITGA2B -0.08 0.26 -9999 0 -0.83 51 51
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.011 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.17 0.24 -9999 0 -0.69 67 67
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.31 134 134
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.086 0.2 -9999 0 -0.55 70 70
ADRB2 -0.009 0.13 -9999 0 -0.83 12 12
receptor agonist activity 0 0 -9999 0 0 141 141
actin filament binding 0 0 -9999 0 -0.001 133 133
SRC 0.012 0.015 -9999 0 -0.31 1 1
ITGB3 -0.014 0.15 -9999 0 -0.83 15 15
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 126 126
ARF6/GDP 0.001 0.07 -9999 0 -0.34 2 2
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.5 111 111
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.071 0.19 -9999 0 -0.55 60 60
ACAP1 0 0.077 -9999 0 -0.38 15 15
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.082 0.22 -9999 0 -0.68 56 56
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.83 67 67
CYTH3 0.009 0.043 -9999 0 -0.65 2 2
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 126 126
endosomal lumen acidification 0 0 -9999 0 -0.001 135 135
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.33 -9999 0 -0.83 85 85
GNAQ/ARNO 0.009 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 37 37
MET -0.11 0.16 -9999 0 -0.31 174 174
GNA14 -0.18 0.36 -9999 0 -0.83 107 107
GNA15 -0.012 0.093 -9999 0 -0.33 34 34
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 132 132
GNA11 -0.003 0.12 -9999 0 -0.83 9 9
LHCGR -0.098 0.27 -9999 0 -0.78 62 62
AGTR1 -0.32 0.41 -9999 0 -0.82 185 185
desensitization of G-protein coupled receptor protein signaling pathway -0.081 0.22 -9999 0 -0.68 56 56
IPCEF1/ARNO -0.058 0.16 -9999 0 -0.44 70 70
alphaIIb/beta3 Integrin -0.089 0.24 -9999 0 -0.69 60 60
Coregulation of Androgen receptor activity

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
NRIP1 -0.014 0.063 -10000 0 -0.35 12 12
SVIL -0.006 0.031 -10000 0 -10000 0 0
ZNF318 0.061 0.093 0.24 1 -0.83 1 2
JMJD2C -0.064 0.069 -10000 0 -0.12 262 262
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.63 192 192
CARM1 0.012 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.026 0.019 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.051 0.13 0.22 2 -0.8 6 8
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.062 -10000 0 -0.83 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.065 0.24 -10000 0 -0.83 42 42
NCOA6 -0.007 0.048 -10000 0 -0.83 1 1
DNA-PK 0.059 0.084 0.26 1 -10000 0 1
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.011 0.15 -10000 0 -1.1 6 6
XRCC5 0.025 0.018 -10000 0 -10000 0 0
UBE3A -0.016 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.31 0.34 -10000 0 -0.67 198 198
FHL2 -0.15 0.36 -10000 0 -1.4 35 35
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.003 0.037 -10000 0 -0.12 33 33
CDK6 0.011 0.055 -10000 0 -0.83 2 2
TGFB1I1 -0.006 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.3 0.3 -10000 0 -0.64 194 194
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.32 -10000 0 -0.64 215 215
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.046 0.05 -10000 0 -10000 0 0
BRCA1 -0.006 0.031 -10000 0 -10000 0 0
TCF4 0.036 0.034 -10000 0 -10000 0 0
CDKN2A -0.1 0.16 -10000 0 -0.31 132 132
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1.3 4 4
KLK3 -0.44 0.71 -10000 0 -1.6 130 130
TMF1 0.005 0.055 -10000 0 -0.83 2 2
HNRNPA1 0.031 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 130 130
APPL1 0.052 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.28 0.3 -10000 0 -0.62 192 192
AR -0.38 0.42 -10000 0 -0.87 192 192
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.031 0.028 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.025 0.018 -10000 0 -10000 0 0
PA2G4 0.036 0.035 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.28 -10000 0 -0.57 192 192
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.3 -10000 0 -0.63 192 192
LATS2 0.029 0.048 -10000 0 -0.83 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.57 192 192
Cyclin D3/CDK11 p58 0 0.003 -10000 0 -10000 0 0
VAV3 -0.011 0.089 -10000 0 -0.83 5 5
KLK2 -0.77 0.63 -10000 0 -1.3 261 261
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.35 -10000 0 -0.68 198 198
TMPRSS2 -0.18 0.31 -10000 0 -1.2 33 33
CCND1 0.002 0.048 -10000 0 -0.31 10 10
PIAS1 -0.016 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.04 -10000 0 -0.081 154 154
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.036 0.077 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.28 0.3 -10000 0 -0.63 193 193
CMTM2 0.014 0.027 -10000 0 -0.31 3 3
SNURF -0.031 0.19 -10000 0 -0.83 24 24
ZMIZ1 -0.012 0.052 -10000 0 -0.81 1 1
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.031 0.028 -10000 0 -10000 0 0
FKBP4 -0.005 0.029 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 -0.09 0.21 -10000 0 -0.56 73 73
cell-cell adhesion 0.16 0.19 0.54 9 -10000 0 9
Ephrin B/EPHB2/RasGAP -0.013 0.067 -10000 0 -0.47 9 9
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.081 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.22 0.27 -10000 0 -0.56 180 180
HRAS/GDP -0.14 0.17 -10000 0 -0.48 11 11
Ephrin B/EPHB1/GRB7 -0.22 0.25 -10000 0 -0.51 185 185
Endophilin/SYNJ1 0.026 0.071 -10000 0 -0.44 9 9
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.19 0.23 -10000 0 -0.48 185 185
endothelial cell migration -0.003 0.038 -10000 0 -0.47 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.041 0.12 -10000 0 -0.31 77 77
PAK1 0.034 0.072 -10000 0 -0.44 9 9
HRAS 0.012 0.022 -10000 0 -0.31 2 2
RRAS 0.025 0.073 -10000 0 -0.44 9 9
DNM1 -0.018 0.16 -10000 0 -0.8 18 18
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.24 -10000 0 -0.45 185 185
lamellipodium assembly -0.16 0.19 -10000 0 -0.54 9 9
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.11 0.18 -10000 0 -0.33 180 180
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.068 -10000 0 -0.83 3 3
EPHB3 -0.19 0.16 -10000 0 -0.31 284 284
EPHB1 -0.32 0.41 -10000 0 -0.83 180 180
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.072 0.17 -10000 0 -0.44 10 10
Ephrin B/EPHB2 -0.014 0.069 -10000 0 -0.48 9 9
Ephrin B/EPHB3 -0.086 0.086 -10000 0 -0.59 6 6
JNK cascade -0.16 0.25 -10000 0 -0.46 182 182
Ephrin B/EPHB1 -0.2 0.24 -10000 0 -0.48 185 185
RAP1/GDP -0.055 0.16 -10000 0 -0.45 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.11 -10000 0 -0.45 23 23
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.51 182 182
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.19 -10000 0 -0.56 9 9
Rap1/GTP -0.16 0.19 -10000 0 -0.55 9 9
axon guidance -0.089 0.21 -10000 0 -0.56 73 73
MAPK3 -0.081 0.16 -10000 0 -0.37 9 9
MAPK1 -0.081 0.16 -10000 0 -0.54 1 1
Rac1/GDP -0.047 0.17 -10000 0 -0.43 6 6
actin cytoskeleton reorganization -0.11 0.13 -10000 0 -0.44 5 5
CDC42/GDP -0.047 0.17 -10000 0 -0.43 6 6
PI3K -0.003 0.038 -10000 0 -0.48 3 3
EFNA5 -0.12 0.3 -10000 0 -0.82 72 72
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.054 -10000 0 -0.33 9 9
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.15 0.18 -10000 0 -0.52 10 10
PTK2 0.042 0.052 -10000 0 -10000 0 0
MAP4K4 -0.16 0.25 -10000 0 -0.47 182 182
SRC 0.013 0.015 -10000 0 -0.31 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.072 0.18 -10000 0 -0.55 2 2
MAP2K1 -0.093 0.17 -10000 0 -0.39 9 9
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.2 0.25 -10000 0 -0.5 182 182
cell migration -0.09 0.19 -10000 0 -0.42 9 9
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.072 -10000 0 -0.44 9 9
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.023 0.17 -10000 0 -0.45 59 59
HRAS/GTP -0.17 0.2 -10000 0 -0.41 187 187
Ephrin B1/EPHB1-2 -0.2 0.25 -10000 0 -0.51 182 182
cell adhesion mediated by integrin 0.013 0.075 0.52 6 -10000 0 6
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.22 -10000 0 -0.44 187 187
RAC1-CDC42/GTP -0.21 0.21 -10000 0 -0.49 141 141
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.055 0.16 -10000 0 -0.49 2 2
ruffle organization -0.12 0.22 -10000 0 -0.55 9 9
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.016 0.12 -10000 0 -0.46 24 24
Ephrin B/EPHB2/KALRN -0.013 0.067 -10000 0 -0.47 9 9
ROCK1 -0.075 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.085 0.11 -10000 0 -0.52 2 2
Rac1/GTP -0.16 0.2 -10000 0 -0.58 9 9
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.34 185 185
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.043 -9999 0 -0.31 8 8
CCL5 -0.04 0.2 -9999 0 -0.71 34 34
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.16 -9999 0 -0.48 48 48
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.093 0.16 -9999 0 -0.57 27 27
Syndecan-1/Syntenin -0.093 0.16 -9999 0 -0.64 21 21
MAPK3 -0.07 0.14 -9999 0 -0.61 18 18
HGF/MET -0.17 0.24 -9999 0 -0.69 67 67
TGFB1/TGF beta receptor Type II 0.008 0.043 -9999 0 -0.31 8 8
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.092 0.15 -9999 0 -0.56 27 27
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.68 45 45
Syndecan-1/CD147 -0.082 0.15 -9999 0 -0.63 20 20
Syndecan-1/Syntenin/PIP2 -0.1 0.14 -9999 0 -0.62 21 21
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.098 0.14 -9999 0 -0.6 21 21
MMP7 -0.18 0.22 -9999 0 -0.37 234 234
HGF -0.11 0.3 -9999 0 -0.83 67 67
Syndecan-1/CASK -0.1 0.16 -9999 0 -0.47 46 46
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.65 80 80
regulation of cell adhesion -0.06 0.14 -9999 0 -0.58 18 18
HPSE -0.017 0.14 -9999 0 -0.5 27 27
positive regulation of cell migration -0.11 0.16 -9999 0 -0.48 48 48
SDC1 -0.11 0.17 -9999 0 -0.5 46 46
Syndecan-1/Collagen -0.11 0.16 -9999 0 -0.48 48 48
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.11 0.16 -9999 0 -0.31 174 174
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.57 76 76
MAPK1 -0.07 0.14 -9999 0 -0.61 18 18
homophilic cell adhesion -0.1 0.16 -9999 0 -0.48 48 48
MMP1 -0.14 0.16 -9999 0 -0.31 219 219
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.4 -9999 0 -1.3 43 43
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.038 0.11 -9999 0 -0.39 19 19
ATF2/c-Jun -0.22 0.42 -9999 0 -0.98 106 106
MAPK11 -0.038 0.11 -9999 0 -0.39 19 19
MITF -0.032 0.14 -9999 0 -0.4 43 43
MAPKAPK5 -0.032 0.14 -9999 0 -0.4 43 43
KRT8 -0.032 0.14 -9999 0 -0.4 43 43
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.053 0.17 -9999 0 -0.52 43 43
CEBPB -0.032 0.14 -9999 0 -0.4 43 43
SLC9A1 -0.032 0.14 -9999 0 -0.4 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.072 0.19 -9999 0 -0.46 58 58
p38alpha-beta/MNK1 -0.028 0.14 -9999 0 -0.5 19 19
JUN -0.22 0.42 -9999 0 -0.97 106 106
PPARGC1A -0.24 0.25 -9999 0 -0.46 244 244
USF1 -0.032 0.14 -9999 0 -0.4 43 43
RAB5/GDP/GDI1 -0.04 0.086 -9999 0 -0.35 19 19
NOS2 -0.052 0.16 -9999 0 -0.66 8 8
DDIT3 -0.034 0.14 -9999 0 -0.41 43 43
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.015 0.11 -9999 0 -0.39 19 19
p38alpha-beta/HBP1 -0.028 0.14 -9999 0 -0.5 19 19
CREB1 -0.052 0.16 -9999 0 -0.46 43 43
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.018 0.12 -9999 0 -0.44 18 18
RPS6KA4 -0.032 0.14 -9999 0 -0.4 43 43
PLA2G4A -0.051 0.2 -9999 0 -0.61 42 42
GDI1 -0.032 0.14 -9999 0 -0.4 43 43
TP53 -0.041 0.16 -9999 0 -0.5 43 43
RPS6KA5 -0.081 0.21 -9999 0 -0.47 84 84
ESR1 -0.07 0.22 -9999 0 -0.54 58 58
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.033 0.14 -9999 0 -0.4 44 44
MEF2A -0.033 0.14 -9999 0 -0.4 44 44
EIF4EBP1 -0.052 0.16 -9999 0 -0.46 44 44
KRT19 -0.11 0.21 -9999 0 -0.54 56 56
ELK4 -0.032 0.14 -9999 0 -0.4 43 43
ATF6 -0.032 0.14 -9999 0 -0.4 43 43
ATF1 -0.053 0.17 -9999 0 -0.47 44 44
p38alpha-beta/MAPKAPK2 -0.028 0.14 -9999 0 -0.5 19 19
p38alpha-beta/MAPKAPK3 -0.028 0.14 -9999 0 -0.5 19 19
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.025 0.16 -10000 0 -0.44 29 29
TBX21 -0.12 0.43 -10000 0 -1.1 58 58
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.018 0.12 -10000 0 -0.4 27 27
GADD45B -0.093 0.38 -10000 0 -0.96 55 55
IL12RB2 -0.016 0.16 -10000 0 -0.73 20 20
GADD45G -0.073 0.34 -10000 0 -0.87 48 48
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.034 0.15 -10000 0 -0.47 34 34
IL2RA -0.043 0.19 -10000 0 -0.56 45 45
IFNG -0.11 0.29 -10000 0 -0.73 76 76
STAT3 (dimer) -0.072 0.32 -10000 0 -0.73 62 62
HLA-DRB5 -0.041 0.13 -10000 0 -0.34 67 67
FASLG -0.14 0.48 -10000 0 -1.2 67 67
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.87 63 63
CD4 0 0.059 -10000 0 -0.32 15 15
SOCS1 0.009 0.049 -10000 0 -0.42 5 5
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.097 0.27 -10000 0 -0.72 68 68
CD3E -0.071 0.24 -10000 0 -0.75 49 49
CD3G -0.15 0.33 -10000 0 -0.8 93 93
IL12Rbeta2/JAK2 -0.001 0.13 -10000 0 -0.64 17 17
CCL3 -0.11 0.43 -10000 0 -1.2 47 47
CCL4 -0.15 0.52 -10000 0 -1.3 61 61
HLA-A 0.011 0.023 -10000 0 -0.31 2 2
IL18/IL18R -0.03 0.19 -10000 0 -0.58 40 40
NOS2 -0.088 0.34 -10000 0 -0.89 46 46
IL12/IL12R/TYK2/JAK2/SPHK2 -0.023 0.15 -10000 0 -0.42 27 27
IL1R1 -0.087 0.37 -10000 0 -0.97 48 48
IL4 0.001 0.022 -10000 0 -10000 0 0
JAK2 0.014 0.045 -10000 0 -0.86 1 1
EntrezGene:6957 -0.006 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.25 0.57 -10000 0 -1.2 100 100
RAB7A -0.04 0.29 -10000 0 -0.72 36 36
lysosomal transport -0.035 0.28 -10000 0 -0.66 42 42
FOS -0.42 0.66 -10000 0 -1.3 155 155
STAT4 (dimer) -0.078 0.35 -10000 0 -0.82 58 58
STAT5A (dimer) -0.22 0.36 -10000 0 -0.86 88 88
GZMA -0.1 0.4 -10000 0 -1 49 49
GZMB -0.1 0.39 -10000 0 -0.94 59 59
HLX 0.003 0.056 -10000 0 -0.31 14 14
LCK -0.11 0.43 -10000 0 -0.97 67 67
TCR/CD3/MHC II/CD4 -0.19 0.35 -10000 0 -0.59 136 136
IL2/IL2R -0.078 0.22 -10000 0 -0.69 41 41
MAPK14 -0.069 0.35 -10000 0 -0.79 62 62
CCR5 -0.096 0.4 -10000 0 -1.1 44 44
IL1B -0.052 0.23 -10000 0 -0.79 40 40
STAT6 -0.004 0.11 -10000 0 -0.25 19 19
STAT4 -0.027 0.15 -10000 0 -0.46 40 40
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.31 11 11
NFKB1 0.012 0.039 -10000 0 -0.83 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.003 0.11 -10000 0 -0.61 11 11
CD8A -0.046 0.22 -10000 0 -0.83 32 32
CD8B -0.092 0.27 -10000 0 -0.73 65 65
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.024 0.16 0.44 29 -10000 0 29
IL2RB -0.014 0.13 -10000 0 -0.5 25 25
proteasomal ubiquitin-dependent protein catabolic process -0.066 0.32 -10000 0 -0.75 57 57
IL2RG -0.047 0.19 -10000 0 -0.54 50 50
IL12 -0.061 0.22 -10000 0 -0.64 55 55
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.027 0.16 -10000 0 -0.64 26 26
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.077 0.26 -10000 0 -0.81 52 52
IL12/IL12R/TYK2/JAK2 -0.12 0.48 -10000 0 -1 68 68
MAP2K3 -0.071 0.34 -10000 0 -0.78 62 62
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.077 0.36 -10000 0 -0.8 64 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.026 0.13 -10000 0 -0.39 42 42
IL18RAP -0.022 0.17 -10000 0 -0.81 21 21
IL12Rbeta1/TYK2 -0.002 0.09 -10000 0 -0.64 3 3
EOMES -0.15 0.44 -10000 0 -1.5 43 43
STAT1 (dimer) -0.14 0.37 -10000 0 -0.76 89 89
T cell proliferation -0.049 0.27 -10000 0 -0.61 53 53
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.025 0.14 -10000 0 -0.41 45 45
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.24 -10000 0 -0.69 57 57
ATF2 -0.07 0.33 -10000 0 -0.74 60 60
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.049 -9999 0 -1 1 1
forebrain development -0.32 0.29 -9999 0 -0.56 244 244
GNAO1 -0.019 0.15 -9999 0 -0.74 18 18
SMO/beta Arrestin2 0.011 0.033 -9999 0 -0.64 1 1
SMO 0.006 0.04 -9999 0 -0.83 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.045 0.056 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.03 -9999 0 -0.5 1 1
GNAI1 0.008 0.04 -9999 0 -0.84 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.25 0.2 -9999 0 -0.51 130 130
SAP30 0.012 0.039 -9999 0 -0.83 1 1
mol:GDP 0.006 0.04 -9999 0 -0.83 1 1
MIM/GLI2A -0.007 0.043 -9999 0 -0.31 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GLI2 0.034 0.06 -9999 0 -10000 0 0
GLI3 0.039 0.059 -9999 0 -0.3 11 11
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.012 0.039 -9999 0 -0.83 1 1
Gi family/GTP 0.007 0.071 -9999 0 -0.34 17 17
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.058 -9999 0 -10000 0 0
FOXA2 -0.67 0.66 -9999 0 -1.3 226 226
neural tube patterning -0.32 0.29 -9999 0 -0.56 244 244
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.022 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.007 0.043 -9999 0 -0.31 1 1
embryonic limb morphogenesis -0.32 0.29 -9999 0 -0.56 244 244
SUFU 0.016 0.022 -9999 0 -10000 0 0
LGALS3 -0.1 0.16 -9999 0 -0.31 166 166
catabolic process 0.062 0.066 -9999 0 -10000 0 0
GLI3A/CBP -0.2 0.2 -9999 0 -0.39 243 243
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.33 0.3 -9999 0 -0.57 244 244
RAB23 0.008 0.068 -9999 0 -0.83 3 3
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.036 0.079 -9999 0 -0.4 1 1
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.068 -9999 0 -0.83 3 3
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.056 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.063 -9999 0 -0.42 2 2
PTCH1 -0.29 0.27 -9999 0 -0.62 130 130
MIM/GLI1 -0.46 0.39 -9999 0 -0.76 240 240
CREBBP -0.2 0.2 -9999 0 -0.38 243 243
Su(fu)/SIN3/HDAC complex 0.056 0.027 -9999 0 -10000 0 0
Syndecan-4-mediated 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
PTK2 -0.082 0.062 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.18 -9999 0 -0.65 38 38
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.6 66 66
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.65 39 39
CCL5 -0.04 0.2 -9999 0 -0.71 34 34
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG 0.001 0.03 -9999 0 -0.31 3 3
ADAM12 -0.071 0.14 -9999 0 -0.31 119 119
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.064 0.045 -9999 0 -0.23 4 4
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.62 62 62
Syndecan-4/CXCL12/CXCR4 -0.17 0.22 -9999 0 -0.64 66 66
Syndecan-4/Laminin alpha3 -0.15 0.19 -9999 0 -0.64 47 47
MDK -0.087 0.15 -9999 0 -0.31 142 142
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 40 40
Syndecan-4/Midkine -0.18 0.19 -9999 0 -0.65 39 39
FZD7 0.006 0.078 -9999 0 -0.83 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 39 39
THBS1 -0.011 0.086 -9999 0 -0.31 34 34
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.66 39 39
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.6 66 66
Syndecan-4/TACI -0.24 0.26 -9999 0 -0.62 129 129
CXCR4 0.012 0.022 -9999 0 -0.31 2 2
cell adhesion -0.073 0.094 -9999 0 -0.45 22 22
Syndecan-4/Dynamin -0.13 0.18 -9999 0 -0.65 38 38
Syndecan-4/TSP1 -0.14 0.18 -9999 0 -0.65 38 38
Syndecan-4/GIPC -0.13 0.18 -9999 0 -0.65 38 38
Syndecan-4/RANTES -0.16 0.22 -9999 0 -0.7 53 53
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.048 0.22 -9999 0 -0.81 34 34
LAMA3 -0.023 0.16 -9999 0 -0.59 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.014 0.17 -9999 0 -0.75 22 22
Syndecan-4/alpha-Actinin -0.13 0.18 -9999 0 -0.65 38 38
TFPI -0.03 0.19 -9999 0 -0.83 24 24
F2 -0.004 0.045 -9999 0 -0.32 9 9
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.17 0.21 -9999 0 -0.67 51 51
ACTN1 0.013 0.015 -9999 0 -0.31 1 1
TNC -0.12 0.17 -9999 0 -0.32 177 177
Syndecan-4/CXCL12 -0.18 0.23 -9999 0 -0.64 78 78
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.076 0.26 -9999 0 -0.83 49 49
TNFRSF13B -0.19 0.35 -9999 0 -0.83 107 107
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.039 -9999 0 -0.83 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 333 333
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.008 0.015 -9999 0 -10000 0 0
vasculogenesis -0.14 0.17 -9999 0 -0.62 38 38
SDC4 -0.15 0.19 -9999 0 -0.7 38 38
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.69 39 39
Syndecan-4/PI-4-5-P2/PKC alpha -0.051 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.18 -9999 0 -0.65 38 38
MMP9 -0.085 0.24 -9999 0 -0.57 76 76
Rac1/GTP -0.075 0.096 -9999 0 -0.46 22 22
cytoskeleton organization -0.13 0.17 -9999 0 -0.62 38 38
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.2 -9999 0 -0.62 60 60
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.042 0.12 -9999 0 -0.54 16 16
alphaM/beta2 Integrin/GPIbA -0.055 0.14 -9999 0 -0.57 26 26
alphaM/beta2 Integrin/proMMP-9 -0.094 0.2 -9999 0 -0.59 52 52
PLAUR -0.091 0.15 -9999 0 -10000 0 0
HMGB1 0.003 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.035 0.1 -9999 0 -0.52 11 11
AGER -0.062 0.22 -9999 0 -0.81 36 36
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.008 0.081 -9999 0 -0.31 30 30
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.12 0.2 -9999 0 -0.62 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.57 76 76
CYR61 -0.25 0.39 -9999 0 -0.83 143 143
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.072 0.092 -9999 0 -0.44 9 9
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.004 0.11 -9999 0 -0.59 13 13
MYH2 -0.1 0.12 -9999 0 -0.43 25 25
MST1R 0 0.099 -9999 0 -0.66 9 9
leukocyte activation during inflammatory response -0.039 0.094 -9999 0 -0.61 5 5
APOB -0.008 0.075 -9999 0 -0.31 26 26
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.002 0.091 -9999 0 -0.64 8 8
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.63 23 23
alphaM/beta2 Integrin/CTGF -0.12 0.22 -9999 0 -0.6 76 76
alphaM/beta2 Integrin -0.095 0.11 -9999 0 -0.36 41 41
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.084 0.15 -9999 0 -0.31 137 137
phagocytosis triggered by activation of immune response cell surface activating receptor -0.094 0.11 -9999 0 -0.36 41 41
cell adhesion -0.054 0.14 -9999 0 -0.57 26 26
NFKB1 -0.13 0.3 -9999 0 -0.74 58 58
THY1 0.01 0.03 -9999 0 -0.31 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.013 0.048 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/LRP/tPA -0.036 0.11 -9999 0 -0.58 10 10
IL6 -0.23 0.46 -9999 0 -1.1 96 96
ITGB2 -0.019 0.088 -9999 0 -0.34 28 28
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.54 34 34
alphaM/beta2 Integrin/JAM2/JAM3 -0.033 0.1 -9999 0 -0.64 8 8
JAM2 0.005 0.079 -9999 0 -0.83 4 4
alphaM/beta2 Integrin/ICAM1 -0.069 0.13 -9999 0 -0.5 22 22
alphaM/beta2 Integrin/uPA/Plg -0.1 0.12 -9999 0 -0.51 20 20
RhoA/GTP -0.11 0.12 -9999 0 -0.42 37 37
positive regulation of phagocytosis -0.07 0.12 -9999 0 -0.49 17 17
Ron/MSP -0.011 0.08 -9999 0 -0.64 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.54 34 34
alphaM/beta2 Integrin/uPAR -0.086 0.13 -9999 0 -0.57 18 18
PLAU -0.14 0.16 -9999 0 -0.31 218 218
PLAT 0 0.088 -9999 0 -0.48 12 12
actin filament polymerization -0.099 0.11 -9999 0 -0.41 25 25
MST1 0.011 0.042 -9999 0 -0.57 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.04 0.095 -9999 0 -0.62 5 5
TNF -0.18 0.4 -9999 0 -0.98 74 74
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.54 21 21
fibrinolysis -0.099 0.12 -9999 0 -0.51 20 20
HCK -0.008 0.081 -9999 0 -0.31 30 30
dendritic cell antigen processing and presentation -0.094 0.11 -9999 0 -0.36 41 41
VTN -0.067 0.24 -9999 0 -0.83 42 42
alphaM/beta2 Integrin/CYR61 -0.21 0.28 -9999 0 -0.6 146 146
LPA -0.002 0.044 -9999 0 -0.31 9 9
LRP1 0.012 0.039 -9999 0 -0.83 1 1
cell migration -0.088 0.2 -9999 0 -0.57 54 54
FN1 -0.22 0.15 -9999 0 -0.31 333 333
alphaM/beta2 Integrin/Thy1 -0.036 0.1 -9999 0 -0.52 11 11
MPO -0.001 0.099 -9999 0 -0.66 9 9
KNG1 -0.013 0.075 -9999 0 -0.31 27 27
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.094 0.12 -9999 0 -0.4 35 35
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.03 -9999 0 -0.31 4 4
CTGF -0.11 0.3 -9999 0 -0.83 67 67
alphaM/beta2 Integrin/Hck -0.046 0.12 -9999 0 -0.56 19 19
ITGAM -0.024 0.11 -9999 0 -0.39 30 30
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.047 0.13 -9999 0 -0.52 26 26
HP -0.079 0.16 -9999 0 -0.34 120 120
leukocyte adhesion -0.092 0.16 -9999 0 -0.61 25 25
SELP -0.004 0.11 -9999 0 -0.59 13 13
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.053 0.21 -10000 0 -0.64 22 22
CRP -0.059 0.21 -10000 0 -0.71 14 14
cell cycle arrest -0.075 0.23 -10000 0 -0.72 28 28
TIMP1 -0.15 0.21 -10000 0 -0.59 39 39
IL6ST -0.11 0.29 -10000 0 -0.83 65 65
Rac1/GDP -0.084 0.25 -10000 0 -0.6 56 56
AP1 -0.2 0.33 -10000 0 -0.72 113 113
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.096 0.22 -10000 0 -0.67 18 18
HSP90B1 0.023 0.042 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.094 0.3 -10000 0 -0.8 49 49
AKT1 0.053 0.058 -10000 0 -1.1 1 1
FOXO1 0.059 0.055 -10000 0 -0.98 1 1
MAP2K6 -0.098 0.28 -10000 0 -0.7 57 57
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.073 0.23 -10000 0 -0.63 41 41
MITF -0.086 0.26 -10000 0 -0.63 52 52
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.013 0 -10000 0 -10000 0 0
A2M 0.025 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.023 0.084 -10000 0 -0.5 1 1
STAT3 -0.088 0.24 -10000 0 -0.78 28 28
STAT1 -0.011 0.023 -10000 0 -10000 0 0
CEBPD -0.053 0.21 -10000 0 -0.69 14 14
PIK3CA 0.01 0.068 -10000 0 -0.83 3 3
PI3K 0.019 0.053 -10000 0 -0.64 3 3
JUN -0.18 0.35 -10000 0 -0.83 105 105
PIAS3/MITF -0.074 0.24 -10000 0 -0.61 48 48
MAPK11 -0.094 0.3 -10000 0 -0.8 49 49
STAT3 (dimer)/FOXO1 -0.005 0.2 -10000 0 -0.6 15 15
GRB2/SOS1/GAB family -0.11 0.19 -10000 0 -0.7 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.25 -10000 0 -0.49 104 104
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.012 0.039 -10000 0 -0.83 1 1
LBP -0.059 0.19 -10000 0 -0.61 13 13
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.005 -10000 0 -10000 0 0
MYC -0.067 0.26 -10000 0 -0.9 23 23
FGG -0.062 0.21 -10000 0 -0.68 17 17
macrophage differentiation -0.075 0.23 -10000 0 -0.72 28 28
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.28 -10000 0 -0.56 144 144
JUNB -0.06 0.23 -10000 0 -0.78 20 20
FOS -0.22 0.37 -10000 0 -0.83 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.097 0.27 -10000 0 -0.56 79 79
STAT1/PIAS1 -0.079 0.24 -10000 0 -0.53 63 63
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.063 -10000 0 -0.74 2 2
STAT3 (dimer) -0.085 0.24 -10000 0 -0.75 28 28
PRKCD -0.06 0.22 -10000 0 -0.62 36 36
IL6R -0.012 0.14 -10000 0 -0.83 14 14
SOCS3 -0.11 0.37 -10000 0 -1.2 39 39
gp130 (dimer)/JAK1/JAK1/LMO4 -0.058 0.2 -10000 0 -0.55 65 65
Rac1/GTP -0.11 0.23 -10000 0 -0.6 56 56
HCK -0.008 0.081 -10000 0 -0.31 30 30
MAPKKK cascade 0.01 0.077 -10000 0 -0.98 1 1
bone resorption -0.091 0.21 -10000 0 -0.64 18 18
IRF1 -0.054 0.21 -10000 0 -0.69 14 14
mol:GDP -0.096 0.26 -10000 0 -0.58 70 70
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.099 0.26 -10000 0 -0.59 69 69
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.29 -10000 0 -0.79 51 51
PTPN11 -0.011 0.06 -10000 0 -1.2 1 1
IL6/IL6RA -0.14 0.28 -10000 0 -0.66 100 100
gp130 (dimer)/TYK2/TYK2/LMO4 -0.065 0.2 -10000 0 -0.55 65 65
gp130 (dimer)/JAK2/JAK2/LMO4 -0.066 0.2 -10000 0 -0.56 65 65
IL6 -0.17 0.33 -10000 0 -0.72 115 115
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.085 0.15 -10000 0 -0.83 1 1
PIAS1 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.1 0.26 -10000 0 -0.45 131 131
LMO4 0.012 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.23 0.38 1 -0.78 27 28
MCL1 0.059 0.05 -10000 0 -0.88 1 1
Thromboxane A2 receptor signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.035 0.11 -10000 0 -0.32 65 65
GNB1/GNG2 -0.044 0.067 -10000 0 -0.19 56 56
AKT1 -0.013 0.1 -10000 0 -0.21 41 41
EGF -0.11 0.3 -10000 0 -0.78 72 72
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.031 0.078 -10000 0 -0.65 2 2
mol:Ca2+ -0.043 0.14 -10000 0 -0.31 70 70
LYN 0.032 0.077 -10000 0 -0.65 2 2
RhoA/GTP -0.031 0.045 -10000 0 -0.13 14 14
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.043 0.16 -10000 0 -0.34 70 70
GNG2 0.011 0.039 -10000 0 -0.83 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.026 0.12 -10000 0 -0.55 11 11
G beta5/gamma2 -0.059 0.091 -10000 0 -0.27 43 43
PRKCH -0.051 0.16 -10000 0 -0.36 68 68
DNM1 -0.018 0.16 -10000 0 -0.8 18 18
TXA2/TP beta/beta Arrestin3 -0.014 0.058 -10000 0 -0.3 17 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.023 0.17 -10000 0 -0.83 20 20
G12 family/GTP -0.077 0.11 -10000 0 -0.3 69 69
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.1 0.36 15 -10000 0 15
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.21 0.37 -10000 0 -0.83 124 124
mol:IP3 -0.058 0.17 -10000 0 -0.38 70 70
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.086 0.22 -10000 0 -0.52 69 69
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.099 0.21 -10000 0 -0.4 136 136
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.023 0.082 -10000 0 -0.65 2 2
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.002 0.095 -10000 0 -0.83 6 6
PRKCB1 -0.059 0.17 -10000 0 -0.38 71 71
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.083 0.23 -10000 0 -0.54 70 70
LCK 0.022 0.099 -10000 0 -0.55 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.02 0.092 -10000 0 -0.97 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.031 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.019 0.09 -10000 0 -0.96 2 2
MAPK14 -0.018 0.11 -10000 0 -0.23 65 65
TGM2/GTP -0.071 0.2 -10000 0 -0.43 73 73
MAPK11 -0.018 0.11 -10000 0 -0.23 65 65
ARHGEF1 -0.015 0.088 -10000 0 -0.18 41 41
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.056 0.18 -10000 0 -0.39 71 71
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.051 0.15 -10000 0 -0.3 78 78
cAMP biosynthetic process -0.058 0.16 -10000 0 -0.36 72 72
Gq family/GTP/EBP50 -0.043 0.12 -10000 0 -0.35 21 21
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.032 0.077 -10000 0 -0.65 2 2
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.019 0.1 -10000 0 -0.35 9 9
VCAM1 -0.037 0.14 -10000 0 -0.3 71 71
TP beta/Gq family/GDP/G beta5/gamma2 -0.026 0.12 -10000 0 -0.55 11 11
platelet activation -0.025 0.15 -10000 0 -0.3 66 66
PGI2/IP -0.008 0.073 -10000 0 -0.64 6 6
PRKACA -0.001 0.11 -10000 0 -0.44 24 24
Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.5 11 11
TXA2/TP beta/beta Arrestin2 -0.026 0.12 -10000 0 -0.66 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.006 0.11 -10000 0 -0.42 24 24
mol:DAG -0.067 0.19 -10000 0 -0.43 70 70
EGFR 0.006 0.078 -10000 0 -0.83 4 4
TXA2/TP alpha -0.081 0.22 -10000 0 -0.49 71 71
Gq family/GTP -0.076 0.13 -10000 0 -0.3 114 114
YES1 0.032 0.077 -10000 0 -0.65 2 2
GNAI2/GTP -0.017 0.079 -10000 0 -0.81 2 2
PGD2/DP -0.028 0.13 -10000 0 -0.64 20 20
SLC9A3R1 0.012 0.022 -10000 0 -0.31 2 2
FYN 0.032 0.077 -10000 0 -0.65 2 2
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.012 0.093 -10000 0 -0.33 34 34
PGK/cGMP -0.15 0.25 -10000 0 -0.56 124 124
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.032 0.1 -10000 0 -0.66 6 6
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.063 0.18 -10000 0 -0.39 80 80
PRKCB -0.06 0.17 -10000 0 -0.37 71 71
PRKCE -0.053 0.17 -10000 0 -0.37 70 70
PRKCD -0.054 0.17 -10000 0 -0.38 68 68
PRKCG -0.058 0.17 -10000 0 -0.39 69 69
muscle contraction -0.073 0.21 -10000 0 -0.49 71 71
PRKCZ -0.043 0.16 -10000 0 -0.34 70 70
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.02 0.093 -10000 0 -0.99 2 2
PRKCQ -0.052 0.17 -10000 0 -0.36 74 74
MAPKKK cascade -0.073 0.2 -10000 0 -0.46 72 72
SELE -0.057 0.18 -10000 0 -0.43 67 67
TP beta/GNAI2/GDP/G beta/gamma -0.019 0.096 -10000 0 -1.1 2 2
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.36 -10000 0 -0.83 107 107
chemotaxis -0.095 0.26 -10000 0 -0.62 70 70
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.003 0.12 -10000 0 -0.83 9 9
Rac1/GTP 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.022 -9999 0 -0.31 2 2
EGFR 0.006 0.078 -9999 0 -0.83 4 4
EGF/EGFR -0.078 0.17 -9999 0 -0.46 76 76
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.072 0.17 -9999 0 -0.47 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.047 -9999 0 -0.44 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.78 72 72
EGF/EGFR dimer/SHC -0.086 0.2 -9999 0 -0.55 70 70
mol:GDP -0.072 0.17 -9999 0 -0.46 70 70
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.004 0.088 -9999 0 -0.74 6 6
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.066 0.15 -9999 0 -0.43 70 70
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.067 0.16 -9999 0 -0.43 70 70
FRAP1 -0.036 0.17 -9999 0 -0.44 70 70
EGF/EGFR dimer -0.099 0.23 -9999 0 -0.64 70 70
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.074 -9999 0 -0.64 6 6
Ras signaling in the CD4+ TCR pathway

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.097 0.22 -9999 0 -0.41 140 140
MAP3K8 -0.004 0.11 -9999 0 -0.83 8 8
FOS -0.06 0.16 -9999 0 -0.5 31 31
PRKCA -0.029 0.18 -9999 0 -0.83 22 22
PTPN7 -0.045 0.17 -9999 0 -0.46 55 55
HRAS 0.011 0.022 -9999 0 -0.32 2 2
PRKCB -0.027 0.12 -9999 0 -0.35 48 48
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.032 0.12 -9999 0 -0.52 16 16
MAP2K1 -0.024 0.14 -9999 0 -0.56 25 25
ELK1 0.008 0.011 -9999 0 -10000 0 0
BRAF -0.043 0.12 -9999 0 -0.55 25 25
mol:GTP -0.002 0.003 -9999 0 -0.006 124 124
MAPK1 -0.032 0.12 -9999 0 -0.52 16 16
RAF1 -0.043 0.12 -9999 0 -0.55 25 25
KRAS 0.013 0.002 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.025 0.078 0.29 37 -10000 0 37
RFC1 0.025 0.078 0.29 34 -10000 0 34
PRKDC 0.025 0.078 0.29 37 -10000 0 37
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.014 0.045 0.2 3 -10000 0 3
FASLG/FAS/FADD/FAF1 -0.031 0.11 0.26 4 -0.37 34 38
MAP2K4 -0.024 0.16 -10000 0 -0.4 37 37
mol:ceramide -0.025 0.15 -10000 0 -0.48 35 35
GSN 0.025 0.078 0.29 34 -10000 0 34
FASLG/FAS/FADD/FAF1/Caspase 8 -0.022 0.14 -10000 0 -0.47 34 34
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.033 0.081 0.32 3 -10000 0 3
MAP3K1 0.004 0.098 -10000 0 -0.28 16 16
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.024 0.079 0.29 33 -0.32 1 34
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.14 0.22 -10000 0 -0.62 69 69
ARHGDIB 0.022 0.082 0.29 37 -10000 0 37
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.025 0.078 -10000 0 -0.29 34 34
NFKB1 -0.053 0.094 -10000 0 -0.79 1 1
MAPK8 -0.057 0.22 -10000 0 -0.45 94 94
DFFA 0.025 0.078 0.29 37 -10000 0 37
DNA fragmentation during apoptosis 0.025 0.078 0.29 34 -10000 0 34
FAS/FADD/MET -0.06 0.077 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.003 0.09 -10000 0 -0.39 19 19
FAF1 0.011 0.006 -10000 0 -10000 0 0
PARP1 0.025 0.078 0.29 34 -10000 0 34
DFFB 0.025 0.078 0.29 34 -10000 0 34
CHUK -0.045 0.083 -10000 0 -0.73 1 1
FASLG -0.065 0.23 -10000 0 -0.67 51 51
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.83 67 67
LMNA 0.023 0.071 0.26 34 -10000 0 34
CASP6 0.025 0.078 0.29 37 -10000 0 37
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.03 0.095 0.35 37 -10000 0 37
PTPN13 0.004 0.087 -10000 0 -0.83 5 5
CASP8 0.008 0.045 0.46 3 -10000 0 3
IL6 -0.26 0.56 -10000 0 -1.4 91 91
MET -0.11 0.16 -10000 0 -0.31 174 174
ICAD/CAD 0.024 0.073 0.27 34 -10000 0 34
FASLG/FAS/FADD/FAF1/Caspase 10 -0.025 0.15 -10000 0 -0.49 35 35
activation of caspase activity by cytochrome c -0.033 0.081 0.32 3 -10000 0 3
PAK2 0.025 0.078 0.29 34 -10000 0 34
BCL2 -0.048 0.22 -10000 0 -0.83 34 34
Osteopontin-mediated 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
IKK alpha homodimer -0.035 0.15 -9999 0 -0.48 35 35
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.12 -9999 0 -0.57 8 8
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.15 -9999 0 -0.62 22 22
AP1 -0.27 0.36 -9999 0 -0.87 102 102
ILK -0.034 0.16 -9999 0 -0.51 35 35
bone resorption -0.05 0.16 -9999 0 -0.67 12 12
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.053 0.13 -9999 0 -0.63 7 7
ITGAV 0.01 0.055 -9999 0 -0.82 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.026 0.13 -9999 0 -0.64 19 19
alphaV/beta3 Integrin/Osteopontin -0.072 0.16 -9999 0 -0.57 35 35
MAP3K1 -0.035 0.16 -9999 0 -0.52 35 35
JUN -0.18 0.35 -9999 0 -0.83 105 105
MAPK3 -0.035 0.15 -9999 0 -0.48 35 35
MAPK1 -0.035 0.15 -9999 0 -0.48 35 35
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
MAPK8 -0.032 0.17 -9999 0 -0.53 39 39
ITGB3 -0.014 0.15 -9999 0 -0.82 15 15
NFKBIA -0.028 0.15 -9999 0 -0.65 7 7
FOS -0.22 0.37 -9999 0 -0.83 125 125
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.11 0.18 -9999 0 -0.72 5 5
NF kappa B1 p50/RelA -0.062 0.11 -9999 0 -0.64 4 4
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.023 0.13 -9999 0 -0.69 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.035 0.16 -9999 0 -0.52 35 35
VAV3 -0.028 0.16 -9999 0 -0.49 39 39
MAP3K14 -0.042 0.16 -9999 0 -0.52 35 35
ROCK2 -0.021 0.17 -9999 0 -0.83 19 19
SPP1 -0.082 0.2 -9999 0 -0.41 104 104
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.055 0.13 -9999 0 -0.45 39 39
MMP2 -0.18 0.29 -9999 0 -0.67 94 94
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.037 0.12 -10000 0 -0.51 26 26
ER alpha/Gai/GDP/Gbeta gamma 0.004 0.15 -10000 0 -0.48 35 35
AKT1 -0.019 0.21 -10000 0 -0.86 26 26
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.018 0.21 -10000 0 -0.87 26 26
mol:Ca2+ -0.1 0.23 -10000 0 -0.5 109 109
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.073 0.18 -10000 0 -0.58 50 50
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.016 0.2 0.82 26 -10000 0 26
RhoA/GTP -0.028 0.094 -10000 0 -0.41 24 24
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.039 0.14 -10000 0 -0.59 24 24
regulation of stress fiber formation -0.013 0.12 0.36 19 -10000 0 19
E2/ERA-ERB (dimer) -0.043 0.14 -10000 0 -0.58 26 26
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.036 0.12 -10000 0 -0.51 24 24
pseudopodium formation 0.013 0.12 -10000 0 -0.36 19 19
E2/ER alpha (dimer)/PELP1 -0.04 0.13 -10000 0 -0.56 24 24
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.012 0.039 -10000 0 -0.83 1 1
GNAO1 -0.016 0.15 -10000 0 -0.74 18 18
HRAS 0.012 0.022 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.01 0.16 -10000 0 -0.6 25 25
E2/ER beta (dimer) -0.004 0.052 -10000 0 -0.64 3 3
mol:GDP -0.038 0.13 -10000 0 -0.57 26 26
mol:NADP 0.01 0.16 -10000 0 -0.6 25 25
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.1 0.24 -10000 0 -0.52 109 109
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.24 -10000 0 -0.54 109 109
PLCB2 -0.12 0.25 -10000 0 -0.54 108 108
IGF1 -0.18 0.35 -10000 0 -0.8 108 108
mol:L-citrulline 0.01 0.16 -10000 0 -0.6 25 25
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.027 0.14 -10000 0 -0.79 15 15
JNK cascade -0.004 0.052 -10000 0 -0.64 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.008 0.068 -10000 0 -0.83 3 3
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.052 0.2 -10000 0 -0.54 54 54
Gq family/GDP/Gbeta gamma -0.056 0.18 -10000 0 -0.53 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.085 -10000 0 -0.36 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.039 0.14 -10000 0 -0.59 24 24
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.047 0.15 -10000 0 -0.64 24 24
STRN -0.038 0.2 -10000 0 -0.83 28 28
GNAL -0.092 0.28 -10000 0 -0.83 58 58
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.016 0.046 -10000 0 -0.56 3 3
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.039 -10000 0 -0.83 1 1
HBEGF -0.005 0.16 -10000 0 -0.5 31 31
cAMP biosynthetic process -0.092 0.19 -10000 0 -0.49 80 80
SRC 0.012 0.14 -10000 0 -0.5 25 25
PI3K -0.004 0.051 -10000 0 -0.64 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.033 0.12 -10000 0 -0.51 26 26
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.55 35 35
Gs family/GTP -0.094 0.2 -10000 0 -0.5 80 80
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation 0.011 0.15 -10000 0 -0.56 25 25
mol:DAG -0.1 0.24 -10000 0 -0.52 109 109
Gs family/GDP/Gbeta gamma -0.075 0.16 -10000 0 -0.42 80 80
MSN 0.011 0.12 -10000 0 -0.39 19 19
Gq family/GTP -0.15 0.24 -10000 0 -0.57 108 108
mol:PI-3-4-5-P3 -0.016 0.2 -10000 0 -0.83 26 26
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.011 0.15 0.56 25 -10000 0 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.034 0.12 -10000 0 -0.53 26 26
NOS3 0.008 0.16 -10000 0 -0.63 25 25
GNA11 -0.003 0.12 -10000 0 -0.83 9 9
MAPKKK cascade -0.01 0.2 -10000 0 -0.55 50 50
E2/ER alpha (dimer)/PELP1/Src -0.042 0.15 -10000 0 -0.63 24 24
ruffle organization 0.013 0.12 -10000 0 -0.36 19 19
ROCK2 0.002 0.13 -10000 0 -0.4 42 42
GNA14 -0.18 0.36 -10000 0 -0.83 107 107
GNA15 -0.012 0.093 -10000 0 -0.33 34 34
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.029 0.2 -10000 0 -0.49 59 59
MMP2 0.015 0.15 -10000 0 -0.73 9 9
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.076 0.098 -10000 0 -10000 0 0
CRKL -0.031 0.11 -10000 0 -0.33 24 24
mol:PIP3 -0.019 0.034 0.69 1 -10000 0 1
AKT1 0 0.041 0.45 1 -0.54 2 3
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.021 0.11 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
HGF/MET/SHIP2 -0.14 0.21 -10000 0 -0.6 67 67
MAP3K5 -0.018 0.11 -10000 0 -0.48 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.55 67 67
AP1 -0.29 0.42 -10000 0 -0.88 147 147
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.27 0.4 -10000 0 -0.85 147 147
STAT3 (dimer) -0.039 0.13 -10000 0 -0.34 67 67
GAB1/CRKL/SHP2/PI3K -0.042 0.095 -10000 0 -0.7 2 2
INPP5D -0.003 0.071 -10000 0 -0.31 23 23
CBL/CRK -0.022 0.11 -10000 0 -10000 0 0
PTPN11 0.012 0.039 -10000 0 -0.83 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.039 -10000 0 -0.83 1 1
ELK1 -0.05 0.062 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.039 0.072 -10000 0 -0.25 25 25
PAK1 0.009 0.039 0.42 1 -0.5 2 3
HGF/MET/RANBP10 -0.14 0.21 -10000 0 -0.6 67 67
HRAS -0.058 0.16 -10000 0 -0.43 67 67
DOCK1 -0.025 0.12 -10000 0 -0.56 4 4
GAB1 -0.041 0.12 -10000 0 -0.3 67 67
CRK -0.031 0.11 -10000 0 -0.33 24 24
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 67 67
JUN -0.18 0.35 -10000 0 -0.83 105 105
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.07 0.1 -10000 0 -0.29 67 67
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.011 0.14 -10000 0 -0.65 2 2
GRB2/SHC -0.038 0.096 -10000 0 -0.3 24 24
FOS -0.22 0.37 -10000 0 -0.83 125 125
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.05 0.062 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.61 67 67
cell migration -0.054 0.083 -10000 0 -0.3 24 24
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.076 0.098 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.051 0.14 -10000 0 -0.36 67 67
MET/MUC20 -0.081 0.1 -10000 0 -0.21 174 174
RAP1B -0.012 0.1 -10000 0 -10000 0 0
RAP1A -0.012 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.21 -10000 0 -0.6 67 67
RAF1 -0.047 0.15 -10000 0 -0.46 25 25
STAT3 -0.039 0.13 -10000 0 -0.34 67 67
cell proliferation -0.046 0.17 -10000 0 -0.45 67 67
RPS6KB1 -0.015 0.039 -10000 0 -10000 0 0
MAPK3 -0.051 0.057 -10000 0 -10000 0 0
MAPK1 -0.051 0.057 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.005 0.13 -10000 0 -0.69 8 8
SRC -0.039 0.13 -10000 0 -0.39 24 24
PI3K -0.041 0.1 -10000 0 -0.54 3 3
MET/Glomulin -0.06 0.094 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.036 0.14 -10000 0 -0.42 25 25
MET -0.11 0.16 -10000 0 -0.31 174 174
MAP4K1 -0.027 0.12 -10000 0 -0.54 4 4
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.036 0.14 -10000 0 -0.42 25 25
BAD 0.009 0.039 0.42 1 -0.5 2 3
MAP2K4 -0.009 0.1 -10000 0 -0.43 5 5
SHP2/GRB2/SOS1/GAB1 -0.057 0.09 -10000 0 -0.39 1 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.048 0.1 -10000 0 -0.32 24 24
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.83 67 67
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.04 0.11 -10000 0 -0.33 24 24
PDPK1 -0.009 0.045 0.52 1 -0.58 2 3
HGF/MET/SHIP -0.15 0.21 -10000 0 -0.57 76 76
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.12 0.11 -9999 0 -0.66 7 7
EPHB2 0.008 0.068 -9999 0 -0.83 3 3
Syndecan-2/TACI -0.13 0.25 -9999 0 -0.56 111 111
LAMA1 -0.048 0.22 -9999 0 -0.81 34 34
Syndecan-2/alpha2 ITGB1 -0.072 0.11 -9999 0 -0.47 22 22
HRAS 0.012 0.022 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.068 -9999 0 -0.56 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.025 0.097 -9999 0 -0.5 15 15
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.008 0.061 -9999 0 -0.5 7 7
LAMA3 -0.023 0.16 -9999 0 -0.59 28 28
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.055 -9999 0 -0.83 2 2
Syndecan-2/MMP2 0.01 0.098 -9999 0 -0.59 11 11
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.081 0.099 -9999 0 -10000 0 0
dendrite morphogenesis 0.013 0.083 -9999 0 -0.55 10 10
Syndecan-2/GM-CSF -0.11 0.099 -9999 0 -0.57 7 7
determination of left/right symmetry 0.011 0.08 -9999 0 -0.63 7 7
Syndecan-2/PKC delta 0.017 0.07 -9999 0 -0.55 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.088 0.093 -9999 0 -0.52 7 7
MAPK1 -0.088 0.093 -9999 0 -0.52 7 7
Syndecan-2/RACK1 -0.008 0.058 -9999 0 -0.47 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.011 0.08 -9999 0 -0.63 7 7
ITGA2 -0.12 0.16 -9999 0 -0.31 184 184
MAPK8 0.018 0.1 -9999 0 -0.55 15 15
Syndecan-2/alpha2/beta1 Integrin -0.087 0.14 -9999 0 -0.52 37 37
Syndecan-2/Kininogen -0.007 0.08 -9999 0 -0.55 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.06 -9999 0 -0.44 7 7
Syndecan-2/CASK/Protein 4.1 -0.008 0.062 -9999 0 -0.51 7 7
extracellular matrix organization 0.014 0.073 -9999 0 -0.54 7 7
actin cytoskeleton reorganization -0.12 0.11 -9999 0 -0.65 7 7
Syndecan-2/Caveolin-2/Ras -0.01 0.076 -9999 0 -0.56 8 8
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.55 22 22
Syndecan-2/RasGAP -0.007 0.055 -9999 0 -0.45 7 7
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.084 -9999 0 -0.55 10 10
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.059 -9999 0 -0.43 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.19 0.35 -9999 0 -0.83 107 107
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.081 0.099 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.017 0.07 -9999 0 -0.55 7 7
TGFB1 0.008 0.043 -9999 0 -0.31 8 8
CASP3 0.027 0.065 -9999 0 -0.5 7 7
FN1 -0.22 0.15 -9999 0 -0.31 333 333
Syndecan-2/IL8 -0.039 0.13 -9999 0 -0.55 17 17
SDC2 0.011 0.08 -9999 0 -0.64 7 7
KNG1 -0.013 0.075 -9999 0 -0.31 27 27
Syndecan-2/Neurofibromin 0.017 0.07 -9999 0 -0.55 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 313 313
Syndecan-2/TGFB1 0.014 0.074 -9999 0 -0.55 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.008 0.062 -9999 0 -0.51 7 7
Syndecan-2/Ezrin -0.008 0.061 -9999 0 -0.5 7 7
PRKACA 0.027 0.065 -9999 0 -0.5 7 7
angiogenesis -0.039 0.13 -9999 0 -0.55 17 17
MMP2 0.002 0.091 -9999 0 -0.64 8 8
IL8 -0.083 0.18 -9999 0 -0.36 120 120
calcineurin-NFAT signaling pathway -0.12 0.25 -9999 0 -0.56 111 111
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.002 0.11 -9999 0 -0.77 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.15 -9999 0 -0.28 266 266
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.01 0.03 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.047 0.068 -9999 0 -0.3 6 6
PRKG1 -0.21 0.37 -9999 0 -0.83 124 124
DUSP8 0.002 0.086 -9999 0 -0.52 10 10
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.47 127 127
apoptosis -0.046 0.066 -9999 0 -0.3 5 5
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.31 -9999 0 -0.83 75 75
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 0 0.006 -9999 0 -10000 0 0
TRAF6 0.01 0.055 -9999 0 -0.83 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0.015 -9999 0 -0.31 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.06 0.13 -9999 0 -0.38 13 13
BLK -0.25 0.38 -9999 0 -0.76 156 156
HCK -0.008 0.081 -9999 0 -0.31 30 30
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.01 0.045 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.002 0.034 -9999 0 -0.52 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.027 0.092 -9999 0 -0.32 6 6
positive regulation of innate immune response -0.058 0.14 -9999 0 -0.4 13 13
LCK -0.011 0.11 -9999 0 -0.44 25 25
p38alpha-beta/MKP7 -0.049 0.13 -9999 0 -0.4 10 10
p38alpha-beta/MKP5 -0.05 0.13 -9999 0 -0.44 10 10
PGK/cGMP -0.17 0.29 -9999 0 -0.64 124 124
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.47 82 82
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.47 0.42 -9999 0 -0.83 266 266
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.017 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.011 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.017 0.063 -9999 0 -0.56 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.026 -9999 0 -0.31 3 3
GRK1 -0.07 0.25 -9999 0 -0.82 46 46
CNG Channel -0.027 0.083 -9999 0 -0.54 7 7
mol:Na + -0.023 0.083 -9999 0 -0.46 13 13
mol:ADP -0.07 0.25 -9999 0 -0.82 46 46
RGS9-1/Gbeta5/R9AP -0.093 0.21 -9999 0 -0.56 76 76
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.024 0.086 -9999 0 -0.47 13 13
CNGB1 -0.001 0.063 -9999 0 -0.31 18 18
RDH5 -0.2 0.16 -9999 0 -0.31 300 300
SAG 0.002 0.016 -9999 0 -0.31 1 1
mol:Ca2+ 0.015 0.09 -9999 0 -0.81 1 1
Na + (4 Units) -0.021 0.077 -9999 0 -0.77 1 1
RGS9 -0.077 0.26 -9999 0 -0.81 51 51
GNB1/GNGT1 -0.003 0.025 -9999 0 -10000 0 0
GNAT1/GDP -0.082 0.18 -9999 0 -0.49 76 76
GUCY2D -0.01 0.11 -9999 0 -0.44 24 24
GNGT1 -0.004 0.039 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.068 -9999 0 -0.48 3 3
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 300 300
mol:cGMP -0.016 0.073 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.14 0.098 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.001 0.093 -9999 0 -0.57 10 10
Metarhodopsin II -0.051 0.15 -9999 0 -0.52 45 45
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.077 -9999 0 -0.51 9 9
RGS9BP -0.04 0.2 -9999 0 -0.83 29 29
Metarhodopsin II/Transducin 0.011 0.016 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.044 -9999 0 -0.52 3 3
PDE6A/B -0.012 0.047 -9999 0 -10000 0 0
mol:Pi -0.093 0.21 -9999 0 -0.56 76 76
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.023 -9999 0 -0.3 1 1
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.008 0.076 -9999 0 -0.31 27 27
PDE6G -0.015 0.11 -9999 0 -0.36 35 35
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.092 0.18 -9999 0 -0.48 78 78
GUCA1A 0.004 0.03 -9999 0 -0.31 4 4
GC2/GCAP Family -0.005 0.044 -9999 0 -0.52 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.068 -9999 0 -0.83 3 3
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.032 0.2 -9999 0 -0.82 28 28
HDAC7 -0.028 0.14 -9999 0 -0.61 13 13
JUN -0.18 0.35 -9999 0 -0.83 105 105
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.013 0.001 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 0.001 0.088 -9999 0 -0.65 8 8
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.041 0.14 -9999 0 -0.62 15 15
MAP2K6 -0.007 0.11 -9999 0 -0.78 9 9
BRM/BAF57 -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 0.009 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.012 0.055 -9999 0 -10000 0 0
NCOA2 -0.07 0.24 -9999 0 -0.83 42 42
CEBPA 0.005 0.087 -9999 0 -0.83 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.064 0.14 -9999 0 -0.5 16 16
NR0B1 -0.002 0.039 -9999 0 -0.31 7 7
EGR1 -0.18 0.35 -9999 0 -0.83 101 101
RXRs/9cRA -0.13 0.058 -9999 0 -0.51 3 3
AR/RACK1/Src -0.11 0.15 -9999 0 -0.64 15 15
AR/GR -0.12 0.19 -9999 0 -0.37 121 121
GNB2L1 0.007 0.007 -9999 0 -10000 0 0
PKN1 0.013 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 0.001 0.087 -9999 0 -0.64 8 8
T-DHT/AR/TIF2/CARM1 -0.12 0.22 -9999 0 -0.68 49 49
SRC 0 0.1 -9999 0 -0.52 15 15
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 130 130
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.051 0.14 -9999 0 -0.64 15 15
TMPRSS2 -0.056 0.31 -9999 0 -1.3 29 29
RXRG -0.28 0.12 -9999 0 -0.32 406 406
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.007 0.007 -9999 0 -10000 0 0
NR2C2 -0.004 0.12 -9999 0 -0.83 9 9
KLK2 -0.48 0.43 -9999 0 -0.83 269 269
AR -0.15 0.21 -9999 0 -0.38 193 193
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.022 0.014 -9999 0 -10000 0 0
SRY 0.009 0.015 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.015 0.055 -9999 0 -0.32 13 13
T-DHT/AR/RACK1/Src -0.073 0.14 -9999 0 -0.63 15 15
positive regulation of transcription 0.013 0.015 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.005 -9999 0 -10000 0 0
NCOA1 0.013 0.009 -9999 0 -10000 0 0
SPDEF -0.027 0.1 -9999 0 -0.32 51 51
T-DHT/AR/TIF2 -0.051 0.15 -9999 0 -0.44 43 43
T-DHT/AR/Hsp90 -0.052 0.14 -9999 0 -0.64 15 15
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.003 0.11 -9999 0 -0.55 15 15
SIRT1 0.011 0.039 -9999 0 -0.83 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.02 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.072 0.13 -9999 0 -0.64 15 15
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.043 0.1 -9999 0 -0.38 21 21
NFATC4 -0.003 0.12 -9999 0 -0.31 54 54
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.048 0.13 -9999 0 -0.41 54 54
JUN 0.001 0.096 -9999 0 -0.28 10 10
HRAS 0.011 0.022 -9999 0 -0.32 2 2
DOCK7 -0.018 0.14 -9999 0 -0.39 57 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.059 0.16 -9999 0 -0.5 54 54
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.024 0.065 -9999 0 -0.32 3 3
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.028 0.16 -9999 0 -0.44 54 54
RAF1 -0.005 0.13 -9999 0 -0.6 2 2
ErbB2/ErbB3/neuregulin 2 -0.069 0.18 -9999 0 -0.52 60 60
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.021 0.084 -9999 0 -0.29 6 6
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.13 0.33 -9999 0 -0.68 110 110
FOS -0.11 0.29 -9999 0 -0.52 147 147
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.048 0.13 -9999 0 -0.41 54 54
MAPK3 -0.087 0.26 -9999 0 -0.52 94 94
MAPK1 -0.087 0.26 -9999 0 -0.52 91 91
JAK2 -0.016 0.14 -9999 0 -0.39 55 55
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.018 0.14 -9999 0 -0.38 54 54
NRG1 -0.074 0.25 -9999 0 -0.81 48 48
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.015 0.14 -9999 0 -0.35 61 61
MAPK9 -0.024 0.063 -9999 0 -0.26 2 2
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.008 0.12 -9999 0 -0.74 11 11
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.034 0.09 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.059 0.2 -9999 0 -0.45 31 31
myelination 0.007 0.12 -9999 0 -0.3 54 54
PPP3CB -0.013 0.13 -9999 0 -0.36 54 54
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.032 0.11 -9999 0 -0.65 2 2
NRG2 -0.082 0.26 -9999 0 -0.8 54 54
mol:GDP -0.018 0.13 -9999 0 -0.38 54 54
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.008 0.14 -9999 0 -0.41 21 21
SRC 0.013 0.015 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.017 0.14 -9999 0 -0.38 55 55
MAP2K1 -0.08 0.23 -9999 0 -0.58 33 33
heart morphogenesis -0.048 0.13 -9999 0 -0.41 54 54
RAS family/GDP -0.037 0.1 -9999 0 -0.64 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.01 0.034 -9999 0 -0.13 16 16
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.048 0.13 -9999 0 -0.41 54 54
CDC42 0.013 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.038 -9999 0 -10000 0 0
VDR 0.013 0.015 -9999 0 -10000 0 0
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.057 0.1 -9999 0 -0.35 44 44
RXRs/LXRs/DNA/Oxysterols -0.046 0.15 -9999 0 -0.46 53 53
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.023 0.077 -9999 0 -0.33 21 21
RXRs/NUR77 -0.26 0.25 -9999 0 -0.64 137 137
RXRs/PPAR -0.053 0.062 -9999 0 -0.4 9 9
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.012 0.075 -9999 0 -0.49 11 11
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.011 0.074 -9999 0 -0.48 11 11
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.053 0.032 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.023 0.077 -9999 0 -0.33 21 21
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0.01 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.08 -9999 0 -0.58 3 3
NR1H4 0 0.033 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.096 0.09 -9999 0 -0.57 3 3
NR1H2 0.016 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.1 0.066 -9999 0 -0.52 3 3
NR4A1 -0.23 0.38 -9999 0 -0.82 136 136
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.046 0.047 -9999 0 -0.32 3 3
RXRG -0.28 0.12 -9999 0 -0.32 406 406
RXR alpha/CCPG 0.021 0.009 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.014 -9999 0 -10000 0 0
THRB -0.005 0.12 -9999 0 -0.83 10 10
PPARG -0.001 0.1 -9999 0 -0.83 6 6
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 53 53
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.045 0.15 -9999 0 -0.45 53 53
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.007 0.13 -9999 0 -0.83 11 11
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.45 159 159
SREBF1 -0.035 0.14 -9999 0 -0.62 2 2
RXRs/RXRs/DNA/9cRA -0.12 0.081 -9999 0 -0.58 3 3
ABCA1 -0.035 0.14 -9999 0 -0.62 2 2
RARs/THRs -0.021 0.097 -9999 0 -0.47 21 21
RXRs/FXR -0.12 0.069 -9999 0 -0.55 3 3
BCL2 -0.049 0.22 -9999 0 -0.83 34 34
BCR signaling 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
JUN -0.11 0.18 -9999 0 -0.46 58 58
IKBKB -0.018 0.071 -9999 0 -0.3 6 6
AKT1 -0.04 0.1 -9999 0 -0.26 22 22
IKBKG -0.017 0.075 -9999 0 -0.32 6 6
CALM1 -0.035 0.085 -9999 0 -0.35 2 2
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
MAP3K1 -0.073 0.18 -9999 0 -0.65 15 15
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.045 0.089 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.084 0.13 -9999 0 -0.28 105 105
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.17 0.24 -9999 0 -0.53 130 130
CD22 -0.15 0.22 -9999 0 -0.52 97 97
CAMK2G -0.025 0.081 -9999 0 -0.32 2 2
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 23 23
SHC/GRB2/SOS1 -0.097 0.15 -9999 0 -10000 0 0
GO:0007205 -0.045 0.09 -9999 0 -0.38 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.035 0.086 -9999 0 -0.36 2 2
NFATC1 -0.069 0.16 -9999 0 -0.55 18 18
B-cell antigen/BCR complex -0.17 0.24 -9999 0 -0.53 130 130
PAG1/CSK -0.001 0.03 -9999 0 -0.64 1 1
NFKBIB 0.002 0.028 -9999 0 -0.11 3 3
HRAS -0.037 0.099 -9999 0 -0.35 2 2
NFKBIA 0.003 0.028 -9999 0 -0.11 3 3
NF-kappa-B/RelA/I kappa B beta 0.008 0.025 -9999 0 -0.2 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.49 90 90
mol:GDP -0.041 0.083 -9999 0 -0.36 2 2
PTEN 0.012 0.039 -9999 0 -0.83 1 1
CD79B -0.029 0.11 -9999 0 -0.31 60 60
NF-kappa-B/RelA/I kappa B alpha 0.009 0.024 -9999 0 -0.2 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.086 0.18 -9999 0 -0.43 71 71
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.051 0.087 -9999 0 -0.39 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.15 0.22 -9999 0 -0.48 127 127
CHUK -0.017 0.075 -9999 0 -0.32 6 6
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.067 0.095 -9999 0 -0.5 8 8
PTPN6 -0.14 0.21 -9999 0 -0.6 49 49
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.004 0.035 -9999 0 -0.14 18 18
VAV2 -0.13 0.19 -9999 0 -0.5 40 40
ubiquitin-dependent protein catabolic process 0.007 0.027 -9999 0 -0.11 3 3
BTK -0.017 0.15 -9999 0 -1.2 7 7
CD19 -0.15 0.2 -9999 0 -0.45 94 94
MAP4K1 -0.02 0.13 -9999 0 -0.41 36 36
CD72 0.012 0.022 -9999 0 -0.31 2 2
PAG1 0.012 0.039 -9999 0 -0.83 1 1
MAPK14 -0.054 0.16 -9999 0 -0.52 15 15
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.035 0.088 -9999 0 -0.32 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.061 0.17 -9999 0 -0.43 68 68
RAF1 -0.028 0.095 -9999 0 -0.34 1 1
RasGAP/p62DOK/SHIP -0.14 0.2 -9999 0 -0.48 89 89
CD79A -0.19 0.3 -9999 0 -0.52 176 176
re-entry into mitotic cell cycle -0.082 0.13 -9999 0 -0.28 104 104
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.009 0.084 -9999 0 -10000 0 0
MAPK1 -0.009 0.084 -9999 0 -10000 0 0
CD72/SHP1 -0.1 0.21 -9999 0 -0.58 43 43
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
MAPK8 -0.061 0.17 -9999 0 -0.52 23 23
actin cytoskeleton organization -0.086 0.18 -9999 0 -0.68 10 10
NF-kappa-B/RelA 0.022 0.045 -9999 0 -0.2 1 1
Calcineurin -0.035 0.059 -9999 0 -10000 0 0
PI3K -0.13 0.16 -9999 0 -0.53 30 30
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.055 0.086 -9999 0 -0.35 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.24 -9999 0 -1 19 19
DAPP1 -0.13 0.26 -9999 0 -1.3 16 16
cytokine secretion -0.064 0.15 -9999 0 -0.5 18 18
mol:DAG -0.051 0.087 -9999 0 -0.39 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.018 0.09 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.17 0.24 -9999 0 -0.58 90 90
mol:PI-3-4-5-P3 -0.095 0.12 -9999 0 -0.37 28 28
ETS1 -0.016 0.076 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.17 -9999 0 -0.47 71 71
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.49 78 78
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.055 -9999 0 -0.83 2 2
RAC1 -0.092 0.19 -9999 0 -0.75 10 10
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.56 77 77
CARD11 -0.075 0.13 -9999 0 -0.54 11 11
FCGR2B -0.03 0.18 -9999 0 -0.75 26 26
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0 0.035 -9999 0 -0.14 2 2
PTPRC -0.031 0.17 -9999 0 -0.59 34 34
PDPK1 -0.043 0.1 -9999 0 -0.27 22 22
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.024 -9999 0 -0.089 1 1
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.055 0.16 -9999 0 -0.56 38 38
MAP4K1 -0.02 0.13 -9999 0 -0.41 36 36
MAP3K8 -0.001 0.11 -9999 0 -0.83 8 8
PRKCB -0.024 0.12 -9999 0 -0.35 48 48
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.014 0.11 -9999 0 -0.56 5 5
JUN -0.1 0.24 -9999 0 -0.51 113 113
MAP3K7 0.014 0.11 -9999 0 -0.56 5 5
GRAP2 -0.042 0.2 -9999 0 -0.78 32 32
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.02 0.11 -9999 0 -0.52 7 7
LAT 0.005 0.079 -9999 0 -0.72 5 5
LCP2 0.008 0.04 -9999 0 -0.31 7 7
MAPK8 0.002 0.12 -9999 0 -0.71 11 11
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.11 -9999 0 -0.37 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.051 0.15 -9999 0 -0.52 38 38
LPA receptor mediated events

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
GNB1/GNG2 -0.046 0.16 -9999 0 -0.54 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.6 1 1
AP1 -0.26 0.37 -9999 0 -0.69 170 170
mol:PIP3 -0.041 0.13 -9999 0 -0.64 7 7
AKT1 -0.028 0.096 -9999 0 -0.6 4 4
PTK2B 0.001 0.085 -9999 0 -0.33 11 11
RHOA 0.031 0.046 -9999 0 -0.26 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.074 -9999 0 -10000 0 0
MAGI3 0.012 0.039 -9999 0 -0.83 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.015 0.13 -9999 0 -0.44 39 39
HRAS/GDP -0.001 0.014 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.009 0.089 -9999 0 -0.42 5 5
NF kappa B1 p50/RelA -0.045 0.12 -9999 0 -0.56 11 11
endothelial cell migration -0.027 0.2 -9999 0 -0.63 39 39
ADCY4 -0.015 0.19 -9999 0 -0.62 38 38
ADCY5 -0.047 0.21 -9999 0 -0.65 41 41
ADCY6 -0.015 0.19 -9999 0 -0.62 38 38
ADCY7 -0.015 0.19 -9999 0 -0.62 38 38
ADCY1 -0.018 0.2 -9999 0 -0.63 38 38
ADCY2 -0.038 0.21 -9999 0 -0.66 39 39
ADCY3 -0.015 0.19 -9999 0 -0.62 38 38
ADCY8 -0.057 0.19 -9999 0 -0.64 41 41
ADCY9 -0.015 0.19 -9999 0 -0.62 38 38
GSK3B 0.009 0.082 -9999 0 -0.34 4 4
arachidonic acid secretion -0.008 0.18 -9999 0 -0.58 38 38
GNG2 0.012 0.039 -9999 0 -0.82 1 1
TRIP6 0.027 0.008 -9999 0 -10000 0 0
GNAO1 -0.041 0.2 -9999 0 -0.6 51 51
HRAS 0.012 0.022 -9999 0 -0.31 2 2
NFKBIA 0.011 0.078 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.034 0.1 -9999 0 -0.97 5 5
JUN -0.18 0.35 -9999 0 -0.83 105 105
LPA/LPA2/NHERF2 0 0.005 -9999 0 -10000 0 0
TIAM1 -0.044 0.12 -9999 0 -1.2 5 5
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.004 0.075 -9999 0 -10000 0 0
PLCB3 0.03 0.007 -9999 0 -10000 0 0
FOS -0.22 0.37 -9999 0 -0.83 125 125
positive regulation of mitosis -0.008 0.18 -9999 0 -0.58 38 38
LPA/LPA1-2-3 -0.051 0.15 -9999 0 -0.54 38 38
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.11 -9999 0 -0.35 38 38
GNAZ -0.021 0.17 -9999 0 -0.57 39 39
EGFR/PI3K-beta/Gab1 -0.043 0.13 -9999 0 -0.68 7 7
positive regulation of dendritic cell cytokine production -0.05 0.15 -9999 0 -0.53 38 38
LPA/LPA2/MAGI-3 -0.002 0.028 -9999 0 -0.6 1 1
ARHGEF1 -0.001 0.15 -9999 0 -0.49 38 38
GNAI2 -0.021 0.17 -9999 0 -0.57 39 39
GNAI3 -0.021 0.17 -9999 0 -0.57 39 39
GNAI1 -0.022 0.17 -9999 0 -0.57 40 40
LPA/LPA3 -0.01 0.043 -9999 0 -0.21 16 16
LPA/LPA2 -0.001 0.008 -9999 0 -10000 0 0
LPA/LPA1 -0.057 0.19 -9999 0 -0.66 39 39
HB-EGF/EGFR -0.054 0.17 -9999 0 -0.54 44 44
HBEGF -0.061 0.19 -9999 0 -0.62 40 40
mol:DAG 0.004 0.075 -9999 0 -10000 0 0
cAMP biosynthetic process -0.028 0.2 -9999 0 -0.57 50 50
NFKB1 0.011 0.039 -9999 0 -0.83 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.011 0.078 -9999 0 -10000 0 0
GNAQ 0.02 0.028 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.065 -9999 0 -0.31 19 19
LPAR1 -0.053 0.24 -9999 0 -0.84 38 38
IL8 -0.13 0.2 -9999 0 -0.48 56 56
PTK2 -0.01 0.15 -9999 0 -0.5 38 38
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.015 0.14 -9999 0 -0.44 39 39
EGFR 0.006 0.078 -9999 0 -0.83 4 4
PLCG1 -0.015 0.085 -9999 0 -0.31 9 9
PLD2 -0.01 0.15 -9999 0 -0.5 38 38
G12/G13 -0.045 0.15 -9999 0 -0.53 38 38
PI3K-beta -0.033 0.11 -9999 0 -0.43 24 24
cell migration -0.016 0.059 -9999 0 -0.26 9 9
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.11 -9999 0 -0.36 38 38
HRAS/GTP -0.01 0.19 -9999 0 -0.6 38 38
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.57 76 76
PRKCE 0.006 0.078 -9999 0 -0.83 4 4
PRKCD 0.012 0.072 -9999 0 -10000 0 0
Gi(beta/gamma) -0.009 0.19 -9999 0 -0.59 38 38
mol:LPA 0.003 0.015 -9999 0 -0.22 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.03 0.13 -9999 0 -0.45 38 38
MAPKKK cascade -0.008 0.18 -9999 0 -0.58 38 38
contractile ring contraction involved in cytokinesis 0.031 0.046 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.086 0.2 -9999 0 -0.44 107 107
GNA15 0.009 0.054 -9999 0 -0.44 1 1
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.008 0.091 -9999 0 -0.44 5 5
GNA11 0.011 0.068 -9999 0 -0.43 9 9
Rac1/GTP -0.035 0.11 -9999 0 -1 5 5
MMP2 -0.027 0.2 -9999 0 -0.63 39 39
Signaling events mediated by PTP1B

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
PDGFRB 0.012 0.039 -10000 0 -0.83 1 1
Jak2/Leptin Receptor -0.022 0.096 0.21 4 -0.38 17 21
PTP1B/AKT1 -0.004 0.065 -10000 0 -0.31 4 4
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.013 0.071 -10000 0 -0.32 6 6
EGFR 0.004 0.079 -10000 0 -0.84 4 4
EGF/EGFR -0.085 0.18 -10000 0 -0.5 70 70
CSF1 0.001 0.1 -10000 0 -0.83 7 7
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.014 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.1 0.12 -10000 0 -0.41 27 27
Insulin Receptor/Insulin -0.014 0.042 -10000 0 -10000 0 0
HCK -0.008 0.081 -10000 0 -0.31 30 30
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.004 0.068 -10000 0 -0.32 4 4
EGF -0.11 0.3 -10000 0 -0.79 72 72
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.019 0.1 -10000 0 -0.37 6 6
TXN 0.011 0.016 -10000 0 -0.32 1 1
PTP1B/IRS1/GRB2 -0.057 0.17 -10000 0 -0.5 56 56
cell migration 0.013 0.071 0.32 6 -10000 0 6
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.04 0.19 -10000 0 -0.59 41 41
ITGA2B -0.08 0.26 -10000 0 -0.83 51 51
CSF1R 0.008 0.052 -10000 0 -0.4 6 6
Prolactin Receptor/Prolactin -0.036 0.14 -10000 0 -0.64 22 22
FGR 0.01 0.03 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.005 0.067 -10000 0 -0.32 4 4
Crk/p130 Cas 0 0.062 -10000 0 -0.35 2 2
DOK1 0.005 0.063 -10000 0 -0.28 5 5
JAK2 -0.011 0.088 -10000 0 -0.37 13 13
Jak2/Leptin Receptor/Leptin -0.057 0.14 -10000 0 -0.58 27 27
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.013 0.072 -10000 0 -0.32 6 6
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.19 0.2 -10000 0 -0.34 262 262
SRC 0.011 0.03 -10000 0 -10000 0 0
ITGB3 -0.016 0.15 -10000 0 -0.83 15 15
CAT1/PTP1B -0.092 0.15 -10000 0 -0.38 60 60
CAPN1 0.013 0.003 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.016 0.057 -10000 0 -0.62 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.056 0.15 -10000 0 -0.63 26 26
negative regulation of transcription -0.01 0.087 -10000 0 -0.37 13 13
FCGR2A -0.008 0.086 -10000 0 -0.33 28 28
FER 0.006 0.068 -10000 0 -0.84 3 3
alphaIIb/beta3 Integrin -0.088 0.24 -10000 0 -0.69 60 60
BLK -0.25 0.38 -10000 0 -0.76 156 156
Insulin Receptor/Insulin/Shc 0 0.001 -10000 0 -10000 0 0
RHOA 0.013 0.003 -10000 0 -10000 0 0
LEPR 0.003 0.089 -10000 0 -0.68 7 7
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.5 47 47
PRL 0.001 0.016 -10000 0 -0.31 1 1
SOCS3 -0.072 0.35 -10000 0 -1.5 26 26
SPRY2 0.009 0.058 -10000 0 -0.66 3 3
Insulin Receptor/Insulin/IRS1 -0.067 0.18 -10000 0 -0.56 55 55
CSF1/CSF1R -0.01 0.095 -10000 0 -0.53 9 9
Ras protein signal transduction 0.021 0.023 -10000 0 -10000 0 0
IRS1 -0.087 0.27 -10000 0 -0.83 55 55
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.008 0.067 -10000 0 -0.31 21 21
STAT5B -0.008 0.071 -10000 0 -0.27 9 9
STAT5A -0.008 0.071 -10000 0 -0.27 9 9
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.07 -10000 0 -0.35 5 5
CSN2 -0.005 0.053 -10000 0 -10000 0 0
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
LAT 0.001 0.067 -10000 0 -0.54 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.011 0.11 -10000 0 -0.44 25 25
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 205 205
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.079 -9999 0 -0.74 5 5
alphaV beta3 Integrin -0.02 0.11 -9999 0 -0.62 15 15
PTK2 0.015 0.16 -9999 0 -0.66 9 9
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.025 0.1 -9999 0 -0.31 54 54
SRC 0.013 0.015 -9999 0 -0.31 1 1
CDKN1B -0.063 0.18 -9999 0 -0.62 42 42
VEGFA 0.008 0.068 -9999 0 -0.83 3 3
ILK -0.063 0.18 -9999 0 -0.62 42 42
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.058 0.17 -9999 0 -0.57 42 42
PTK2B 0.017 0.12 -9999 0 -0.53 20 20
alphaV/beta3 Integrin/JAM-A -0.061 0.16 -9999 0 -0.49 56 56
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.021 0.12 -9999 0 -0.62 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.26 -9999 0 -0.54 145 145
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.003 0.11 -9999 0 -0.54 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.021 0.11 -9999 0 -0.62 15 15
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.24 0.26 -9999 0 -0.63 110 110
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
alphaV/beta3 Integrin/Osteopontin -0.072 0.16 -9999 0 -0.59 35 35
RPS6KB1 -0.2 0.25 -9999 0 -0.58 110 110
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.096 0.16 -9999 0 -0.8 15 15
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.096 0.16 -9999 0 -0.8 15 15
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.038 0.16 -9999 0 -0.64 27 27
cell adhesion -0.031 0.11 -9999 0 -0.57 15 15
ANGPTL3 0.006 0.022 -9999 0 -0.31 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.071 -9999 0 -0.65 5 5
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.01 0.055 -9999 0 -0.83 2 2
ITGB3 -0.014 0.15 -9999 0 -0.83 15 15
IGF1 -0.18 0.35 -9999 0 -0.8 108 108
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.02 0.11 -9999 0 -0.61 15 15
apoptosis 0.01 0.055 -9999 0 -0.82 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.02 0.11 -9999 0 -0.62 15 15
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.038 0.14 -9999 0 -0.65 20 20
CSF1 0.001 0.1 -9999 0 -0.83 7 7
PIK3C2A -0.065 0.18 -9999 0 -0.62 43 43
PI4 Kinase/Pyk2 -0.055 0.14 -9999 0 -0.79 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.12 -9999 0 -0.57 20 20
FAK1/Vinculin 0.024 0.13 -9999 0 -0.49 9 9
alphaV beta3/Integrin/ppsTEM5 -0.02 0.11 -9999 0 -0.62 15 15
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.067 0.24 -9999 0 -0.83 42 42
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.038 0.12 -9999 0 -0.62 15 15
alphaV/beta3 Integrin/TGFBR2 -0.022 0.12 -9999 0 -0.61 17 17
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.076 -9999 0 -0.56 8 8
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.019 0.11 -9999 0 -0.57 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 333 333
alphaV/beta3 Integrin/Pyk2 -0.023 0.11 -9999 0 -0.54 20 20
SDC1 0.01 0.03 -9999 0 -0.31 4 4
VAV3 0.027 0.097 -9999 0 -0.54 12 12
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
IRS1 -0.087 0.27 -9999 0 -0.83 55 55
FAK1/Paxillin 0.024 0.13 -9999 0 -0.49 9 9
cell migration 0.034 0.12 -9999 0 -0.44 9 9
ITGAV 0.01 0.055 -9999 0 -0.83 2 2
PI3K -0.057 0.16 -9999 0 -0.95 4 4
SPP1 -0.083 0.2 -9999 0 -0.41 104 104
KDR 0.008 0.068 -9999 0 -0.83 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.055 -9999 0 -0.83 2 2
COL4A3 -0.014 0.15 -9999 0 -0.83 15 15
angiogenesis -0.084 0.19 -9999 0 -0.68 24 24
Rac1/GTP -0.013 0.083 -9999 0 -0.49 12 12
EDIL3 -0.021 0.13 -9999 0 -0.41 37 37
cell proliferation -0.022 0.12 -9999 0 -0.6 17 17
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.011 0.22 -10000 0 -0.95 20 20
NCK1/PAK1/Dok-R -0.028 0.091 -10000 0 -0.43 20 20
NCK1/Dok-R -0.067 0.24 -10000 0 -1.2 20 20
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
mol:beta2-estradiol -0.003 0.047 0.24 17 -10000 0 17
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.008 0.064 0.26 3 -0.33 8 11
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.059 0.22 -10000 0 -1.1 20 20
FN1 -0.22 0.15 -10000 0 -0.31 333 333
PLD2 0.001 0.27 -10000 0 -1.2 20 20
PTPN11 0.012 0.039 -10000 0 -0.83 1 1
GRB14 -0.012 0.14 -10000 0 -0.83 14 14
ELK1 0.017 0.24 -10000 0 -1.1 20 20
GRB7 -0.041 0.12 -10000 0 -0.31 77 77
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.1 0.24 -10000 0 -1.2 20 20
CDKN1A -0.009 0.17 -10000 0 -0.64 19 19
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.067 0.24 -10000 0 -1.2 20 20
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.027 0.17 -10000 0 -0.68 20 20
PLG -0.007 0.27 -10000 0 -1.2 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.01 0.21 -10000 0 -0.92 20 20
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
ANGPT2 -0.11 0.22 -10000 0 -0.87 16 16
BMX -0.012 0.28 -10000 0 -1.2 21 21
ANGPT1 -0.038 0.29 -10000 0 -1.5 17 17
tube development -0.016 0.18 -10000 0 -0.72 20 20
ANGPT4 -0.057 0.23 -10000 0 -0.73 44 44
response to hypoxia 0 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.018 0.29 -10000 0 -1.3 20 20
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.018 0.21 -10000 0 -0.83 20 20
mol:L-citrulline 0.027 0.17 -10000 0 -0.68 20 20
AGTR1 -0.32 0.41 -10000 0 -0.82 185 185
MAPK14 -0.01 0.26 -10000 0 -1.2 20 20
Tie2/SHP2 -0.023 0.14 -10000 0 -1.4 4 4
TEK 0.019 0.16 -10000 0 -1.5 4 4
RPS6KB1 0.011 0.21 -10000 0 -0.91 20 20
Angiotensin II/AT1 -0.25 0.32 -10000 0 -0.64 185 185
Tie2/Ang1/GRB2 -0.004 0.28 -10000 0 -1.3 20 20
MAPK3 0.012 0.25 -10000 0 -1.1 20 20
MAPK1 0.012 0.25 -10000 0 -1.1 20 20
Tie2/Ang1/GRB7 -0.028 0.28 -10000 0 -1.3 20 20
NFKB1 0.012 0.039 -10000 0 -0.83 1 1
MAPK8 -0.006 0.28 -10000 0 -1.2 21 21
PI3K -0.004 0.25 -10000 0 -1.1 20 20
FES -0.01 0.26 -10000 0 -1.2 20 20
Crk/Dok-R -0.067 0.24 -10000 0 -1.2 20 20
Tie2/Ang1/ABIN2 -0.004 0.28 -10000 0 -1.3 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.016 0.2 -10000 0 -0.84 20 20
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.011 0.21 -10000 0 -0.91 20 20
Tie2/Ang2 -0.038 0.24 -10000 0 -1 20 20
Tie2/Ang1 -0.01 0.29 -10000 0 -1.3 20 20
FOXO1 0.022 0.2 -10000 0 -0.84 20 20
ELF1 0.015 0.081 -10000 0 -0.85 4 4
ELF2 -0.002 0.26 -10000 0 -1.2 20 20
mol:Choline 0.004 0.26 -10000 0 -1.1 20 20
cell migration -0.024 0.056 -10000 0 -0.24 20 20
FYN -0.022 0.21 -10000 0 -0.84 20 20
DOK2 0 0.078 -10000 0 -0.38 16 16
negative regulation of cell cycle -0.006 0.16 -10000 0 -0.58 19 19
ETS1 0.016 0.044 -10000 0 -10000 0 0
PXN 0.024 0.18 -10000 0 -0.74 20 20
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.024 0.19 -10000 0 -0.79 20 20
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.086 0.28 -10000 0 -0.77 60 60
MAPKKK cascade 0.004 0.26 -10000 0 -1.1 20 20
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.007 0.28 -10000 0 -1.3 20 20
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.03 0.15 -10000 0 -0.61 20 20
mol:Phosphatidic acid 0.004 0.26 -10000 0 -1.1 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.027 0.17 -10000 0 -0.68 20 20
Rac1/GTP -0.05 0.17 -10000 0 -0.84 20 20
MMP2 -0.004 0.28 -10000 0 -1.2 20 20
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.003 0.042 -10000 0 -0.64 2 2
Necdin/E2F1 -0.068 0.12 -10000 0 -0.76 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.036 0.1 -10000 0 -0.49 19 19
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.28 -10000 0 -0.58 220 220
NT-4/5 (dimer)/p75(NTR) -0.075 0.18 -10000 0 -0.68 34 34
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.004 0.12 -10000 0 -0.5 22 22
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.62 20 20
MGDIs/NGR/p75(NTR)/LINGO1 -0.049 0.12 -10000 0 -0.54 20 20
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.058 0.14 -10000 0 -0.56 29 29
LINGO1 -0.004 0.073 -10000 0 -0.31 24 24
Sortilin/TRAF6/NRIF -0.002 0.027 -10000 0 -10000 0 0
proBDNF (dimer) -0.014 0.14 -10000 0 -0.62 20 20
NTRK1 0 0.058 -10000 0 -0.31 15 15
RTN4R 0.013 0 -10000 0 -10000 0 0
neuron apoptosis -0.01 0.14 -10000 0 -0.5 23 23
IRAK1 0.013 0 -10000 0 -10000 0 0
SHC1 -0.021 0.13 -10000 0 -0.57 19 19
ARHGDIA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.04 0.11 -10000 0 -0.52 19 19
MAGEH1 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.045 0.12 -10000 0 -0.52 24 24
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.5 23 23
proNGF (dimer) 0.006 0.072 -10000 0 -0.57 6 6
MAGED1 0.013 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -10000 0 -0.64 25 25
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.037 0.11 -10000 0 -0.49 19 19
NGF 0.006 0.072 -10000 0 -0.57 6 6
cell cycle arrest 0.043 0.16 -10000 0 -0.48 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.087 -10000 0 -0.35 21 21
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.16 -10000 0 -0.59 36 36
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.046 0.13 -10000 0 -0.57 20 20
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.01 0.12 -10000 0 -0.52 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.071 -10000 0 -0.44 2 2
p75(NTR)/beta APP -0.05 0.13 -10000 0 -0.64 17 17
BEX1 -0.36 0.42 -10000 0 -0.83 206 206
mol:GDP -0.031 0.13 -10000 0 -0.58 19 19
NGF (dimer) -0.097 0.13 -10000 0 -0.51 29 29
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.11 -10000 0 -0.53 17 17
PIK3R1 0.013 0 -10000 0 -10000 0 0
RAC1/GTP -0.039 0.11 -10000 0 -0.5 19 19
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.046 0.13 -10000 0 -0.57 20 20
RHOB 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.061 0.093 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.62 44 44
TP53 -0.006 0.13 -10000 0 -0.46 30 30
PRDM4 -0.01 0.12 -10000 0 -0.52 19 19
BDNF (dimer) -0.13 0.16 -10000 0 -0.55 38 38
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
SORT1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.035 0.1 -10000 0 -0.48 19 19
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.042 0.12 -10000 0 -0.53 21 21
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
MAPK10 0.023 0.12 -10000 0 -0.45 19 19
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.01 0.12 -10000 0 -0.52 19 19
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.045 0.12 -10000 0 -0.58 19 19
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.03 -10000 0 -0.64 1 1
NT3 (dimer)/p75(NTR) -0.093 0.2 -10000 0 -0.67 42 42
MAPK8 0.018 0.13 -10000 0 -0.46 19 19
MAPK9 0.023 0.12 -10000 0 -0.44 18 18
APAF1 0.012 0.039 -10000 0 -0.83 1 1
NTF3 -0.047 0.2 -10000 0 -0.62 44 44
NTF4 -0.022 0.16 -10000 0 -0.64 25 25
NDN 0.004 0.087 -10000 0 -0.83 5 5
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.033 0.097 -10000 0 -0.45 20 20
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.056 -10000 0 -0.66 3 3
RhoA-B-C/GTP -0.046 0.12 -10000 0 -0.57 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.048 0.12 -10000 0 -0.49 30 30
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.13 -10000 0 -0.52 30 30
PRKACB 0.012 0.039 -10000 0 -0.83 1 1
proBDNF (dimer)/p75 ECD -0.023 0.11 -10000 0 -0.64 14 14
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.67 33 33
BIRC2 0.013 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.067 0.17 0.24 176 -0.48 19 195
BAD 0.029 0.12 -10000 0 -0.44 19 19
RIPK2 0.013 0 -10000 0 -10000 0 0
NGFR -0.06 0.19 -10000 0 -0.43 77 77
CYCS -0.001 0.12 -10000 0 -0.49 19 19
ADAM17 0.01 0.055 -10000 0 -0.83 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.042 0.12 -10000 0 -0.53 21 21
BCL2L11 0.029 0.12 -10000 0 -0.44 19 19
BDNF (dimer)/p75(NTR) -0.069 0.17 -10000 0 -0.64 29 29
PI3K -0.043 0.12 -10000 0 -0.53 22 22
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.04 0.11 -10000 0 -0.52 19 19
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.055 0.15 -10000 0 -0.66 19 19
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.04 0.11 -10000 0 -0.52 19 19
TRAF6 0.01 0.055 -10000 0 -0.83 2 2
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
PLG -0.001 0.03 -10000 0 -0.31 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.017 0.14 -10000 0 -0.5 30 30
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0 -10000 0 -10000 0 0
CASP3 0.031 0.11 -10000 0 -0.41 19 19
E2F1 -0.086 0.15 -10000 0 -0.31 140 140
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.013 0.06 -10000 0 -0.54 3 3
NGF (dimer)/TRKA -0.012 0.064 -10000 0 -0.64 3 3
MMP7 -0.18 0.22 -10000 0 -0.37 234 234
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.11 -10000 0 -0.5 21 21
MMP3 -0.04 0.11 -10000 0 -0.31 65 65
APAF-1/Caspase 9 -0.041 0.11 -10000 0 -0.6 6 6
Effects of Botulinum toxin

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
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.013 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.015 0.063 -9999 0 -0.29 2 2
RAB3GAP2/RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.01 0.022 -9999 0 -0.31 2 2
mol:ACh -0.007 0.041 -9999 0 -0.15 28 28
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.045 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.014 0.063 -9999 0 -0.29 2 2
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.017 0.092 -9999 0 -0.31 40 40
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.11 0.16 -9999 0 -0.25 210 210
SNAP25 -0.032 0.098 -9999 0 -0.38 28 28
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.17 0.23 -9999 0 -0.38 210 210
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.045 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.043 -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 0.065 0.15 0.46 18 -10000 0 18
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.58 46 46
TBX21 -0.09 0.22 -10000 0 -0.65 32 32
IL12B -0.007 0.1 -10000 0 -0.57 12 12
IL12A -0.061 0.2 -10000 0 -0.62 52 52
IL6ST -0.11 0.29 -10000 0 -0.83 65 65
IL27RA/JAK1 0.013 0.026 -10000 0 -10000 0 0
IL27 0.002 0.035 -10000 0 -0.32 5 5
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.061 0.15 -10000 0 -0.51 1 1
T-helper 2 cell differentiation 0.065 0.15 0.46 18 -10000 0 18
T cell proliferation during immune response 0.065 0.15 0.46 18 -10000 0 18
MAPKKK cascade -0.065 0.15 -10000 0 -0.46 18 18
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.32 11 11
IL12RB1 -0.021 0.11 -10000 0 -0.83 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.09 0.21 -10000 0 -0.63 29 29
IL27/IL27R/JAK2/TYK2 -0.066 0.15 -10000 0 -0.49 14 14
positive regulation of T cell mediated cytotoxicity -0.065 0.15 -10000 0 -0.46 18 18
STAT1 (dimer) -0.12 0.24 0.52 15 -0.75 17 32
JAK2 0.012 0.04 -10000 0 -0.84 1 1
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.054 0.14 -10000 0 -0.52 9 9
T cell proliferation -0.16 0.24 -10000 0 -0.53 99 99
IL12/IL12R/TYK2/JAK2 -0.059 0.18 -10000 0 -0.73 14 14
IL17A -0.061 0.15 -10000 0 -0.51 1 1
mast cell activation 0.065 0.15 0.46 18 -10000 0 18
IFNG -0.021 0.049 -10000 0 -0.13 63 63
T cell differentiation -0.005 0.008 -10000 0 -0.022 55 55
STAT3 (dimer) -0.054 0.14 -10000 0 -0.52 9 9
STAT5A (dimer) -0.054 0.14 -10000 0 -0.52 9 9
STAT4 (dimer) -0.075 0.16 -10000 0 -0.52 23 23
STAT4 -0.027 0.15 -10000 0 -0.46 40 40
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.063 0.18 -10000 0 -0.54 26 26
GATA3 -0.045 0.34 -10000 0 -1.5 24 24
IL18 -0.024 0.11 -10000 0 -0.65 10 10
positive regulation of mast cell cytokine production -0.054 0.14 -10000 0 -0.51 9 9
IL27/EBI3 -0.098 0.12 -10000 0 -0.44 6 6
IL27RA 0.003 0.027 -10000 0 -10000 0 0
IL6 -0.17 0.33 -10000 0 -0.71 115 115
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.014 -10000 0 -10000 0 0
IL1B -0.041 0.18 -10000 0 -0.59 40 40
EBI3 -0.15 0.17 -10000 0 -0.36 21 21
TNF -0.067 0.21 -10000 0 -0.6 59 59
Regulation of nuclear SMAD2/3 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
EP300 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.004 0.078 -10000 0 -0.83 4 4
SMAD3/SMAD4/ER alpha -0.055 0.14 -10000 0 -0.59 25 25
AKT1 0.008 0.01 -10000 0 -10000 0 0
GSC -0.21 0.56 -10000 0 -1.6 67 67
NKX2-5 0.002 0.03 -10000 0 -0.31 4 4
muscle cell differentiation 0.025 0.05 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.004 0.08 -10000 0 -10000 0 0
SMAD4 -0.012 0.059 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.012 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.079 -10000 0 -0.55 5 5
SMAD3/SMAD4/VDR 0.01 0.044 -10000 0 -10000 0 0
MYC 0.003 0.13 -10000 0 -0.83 11 11
CDKN2B -0.078 0.14 -10000 0 -10000 0 0
AP1 -0.26 0.51 -10000 0 -1 125 125
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.031 0.057 -10000 0 -0.72 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.063 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.01 0.07 -10000 0 -0.3 18 18
SMAD3/SMAD4/GR -0.017 0.045 -10000 0 -10000 0 0
GATA3 -0.032 0.19 -10000 0 -0.78 26 26
SKI/SIN3/HDAC complex/NCoR1 0.04 0.03 -10000 0 -10000 0 0
MEF2C/TIF2 -0.053 0.16 -10000 0 -0.54 30 30
endothelial cell migration -0.01 0.1 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.011 0.004 -10000 0 -10000 0 0
RBBP4 0.006 0.068 -10000 0 -0.83 3 3
RUNX2 -0.076 0.15 -10000 0 -0.32 123 123
RUNX3 -0.008 0.12 -10000 0 -0.6 16 16
RUNX1 -0.13 0.16 -10000 0 -0.31 205 205
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -10000 0 0
CDKN1A 0.024 0.07 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.037 0.092 -10000 0 -0.42 2 2
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.009 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.037 0.11 -10000 0 -0.59 16 16
SMAD3/SMAD4/ATF3 -0.16 0.27 -10000 0 -0.63 110 110
SAP30 0.01 0.039 -10000 0 -0.83 1 1
Cbp/p300/PIAS3 0.034 0.045 -10000 0 -10000 0 0
JUN -0.26 0.5 -10000 0 -1.1 112 112
SMAD3/SMAD4/IRF7 -0.017 0.045 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.001 0.092 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.066 0.095 0.47 4 -10000 0 4
DLX1 -0.034 0.19 -10000 0 -0.83 26 26
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.23 0.4 -10000 0 -0.89 125 125
SMAD3/SMAD4/Max -0.017 0.045 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.042 -10000 0 -0.55 2 2
ZBTB17 0.021 0.012 -10000 0 -10000 0 0
LAMC1 0.025 0.053 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.044 -10000 0 -10000 0 0
IRF7 0.014 0.016 -10000 0 -0.31 1 1
ESR1 -0.052 0.2 -10000 0 -0.54 54 54
HNF4A -0.003 0.044 -10000 0 -0.31 9 9
MEF2C 0.004 0.098 -10000 0 -1 1 1
SMAD2-3/SMAD4 -0.032 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.025 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.017 0.024 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.018 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.039 -10000 0 -0.83 1 1
HDAC1 0.011 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
SNIP1 0.008 0.055 -10000 0 -0.83 2 2
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.011 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.11 -10000 0 -0.69 9 9
SMAD2 -0.003 0.04 -10000 0 -10000 0 0
SMAD3 -0.005 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.009 0.076 -10000 0 -0.41 7 7
SMAD2/SMAD2/SMAD4 0.014 0.028 -10000 0 -10000 0 0
NCOR1 0.011 0.004 -10000 0 -10000 0 0
NCOA2 -0.063 0.24 -10000 0 -0.83 42 42
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.013 0.076 -10000 0 -10000 0 0
IFNB1 0.014 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.098 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.32 382 382
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.009 0.13 -10000 0 -0.83 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.007 0.082 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.083 0.11 -10000 0 -0.58 9 9
SMAD7 -0.11 0.28 -10000 0 -0.6 86 86
MYC/MIZ-1 0.015 0.11 -10000 0 -0.64 11 11
SMAD3/SMAD4 0.064 0.1 0.31 41 -0.35 1 42
IL10 -0.027 0.19 -10000 0 -0.62 36 36
PIASy/HDAC complex 0.007 0.01 -10000 0 -10000 0 0
PIAS3 0.016 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.017 0.14 -10000 0 -0.51 24 24
CDK4 0.019 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.19 0.36 -10000 0 -0.8 117 117
SMAD3/SMAD4/SP1 -0.016 0.054 -10000 0 -10000 0 0
FOXG1 -0.003 0.074 -10000 0 -0.39 13 13
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.004 0.097 -10000 0 -1 1 1
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.051 0.14 -10000 0 -0.61 26 26
MYOD1 -0.002 0.029 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.052 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.052 0.14 -10000 0 -0.55 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.011 0.039 -10000 0 -0.83 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.076 0.11 -10000 0 -0.55 11 11
SMAD3/SMAD4/SP1-3 -0.003 0.049 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.021 -10000 0 -10000 0 0
SIN3B 0.011 0.004 -10000 0 -10000 0 0
SIN3A 0.012 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.017 0.093 -10000 0 -0.62 1 1
ITGB5 0.035 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.29 -10000 0 -0.6 192 192
AR -0.34 0.41 -10000 0 -0.83 192 192
negative regulation of cell growth -0.042 0.13 -10000 0 -0.54 5 5
SMAD3/SMAD4/MYOD -0.023 0.049 -10000 0 -10000 0 0
E2F5 0.012 0.039 -10000 0 -0.83 1 1
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.012 0.065 -10000 0 -0.37 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0 0.067 -10000 0 -10000 0 0
TFDP1 0.012 0.039 -10000 0 -0.83 1 1
SMAD3/SMAD4/AP1 -0.28 0.52 -10000 0 -1.1 110 110
SMAD3/SMAD4/RUNX2 -0.066 0.096 -10000 0 -0.47 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.016 0.15 -10000 0 -0.83 16 16
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.087 -9999 0 -0.48 15 15
RGS9BP -0.04 0.2 -9999 0 -0.83 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.07 0.25 -9999 0 -0.82 46 46
mol:Na + -0.021 0.056 -9999 0 -10000 0 0
mol:ADP -0.047 0.2 -9999 0 -0.64 45 45
GNAT2 0.009 0.022 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.093 0.21 -9999 0 -0.56 76 76
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.062 -9999 0 -0.3 2 2
Cone PDE6 -0.081 0.18 -9999 0 -0.49 76 76
Cone Metarhodopsin II -0.051 0.15 -9999 0 -0.52 45 45
Na + (4 Units) -0.024 0.057 -9999 0 -0.3 2 2
GNAT2/GDP -0.081 0.18 -9999 0 -0.49 76 76
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.018 0.091 -9999 0 -0.51 15 15
SLC24A2 -0.009 0.064 -9999 0 -0.31 19 19
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.64 15 15
GNB3 -0.012 0.14 -9999 0 -0.83 14 14
GNAT2/GTP -0.001 0.014 -9999 0 -0.21 2 2
CNGA3 -0.026 0.11 -9999 0 -0.31 55 55
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.056 -9999 0 -10000 0 0
mol:Pi -0.093 0.21 -9999 0 -0.56 76 76
Cone CNG Channel -0.016 0.042 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.063 -9999 0 -0.31 19 19
RGS9 -0.077 0.26 -9999 0 -0.81 51 51
PDE6C 0.003 0.016 -9999 0 -0.31 1 1
GNGT2 0.009 0.047 -9999 0 -0.44 4 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.019 0.1 -9999 0 -0.38 6 6
AP1 -0.21 0.28 -9999 0 -0.64 121 121
mol:PIP3 -0.018 0.15 -9999 0 -0.52 14 14
IKBKB 0.003 0.094 -9999 0 -0.28 14 14
AKT1 -0.018 0.14 -9999 0 -0.59 6 6
IKBKG 0.003 0.094 -9999 0 -0.29 13 13
MS4A2 -0.066 0.14 -9999 0 -0.32 107 107
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
MAP3K1 0.009 0.1 -9999 0 -0.47 7 7
mol:Ca2+ -0.009 0.12 -9999 0 -0.38 14 14
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.011 0.091 -9999 0 -0.35 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.083 0.19 -9999 0 -0.51 75 75
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 23 23
PLD2 -0.05 0.15 -9999 0 -0.45 40 40
PTPN13 -0.002 0.1 -9999 0 -0.59 5 5
PTPN11 0.01 0.041 -9999 0 -0.86 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.017 0.1 -9999 0 -0.37 4 4
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.064 0.13 -9999 0 -0.54 14 14
LAT -0.016 0.1 -9999 0 -0.43 8 8
PAK2 0.001 0.11 -9999 0 -0.51 8 8
NFATC2 -0.15 0.28 -9999 0 -0.76 76 76
HRAS -0.009 0.12 -9999 0 -0.5 11 11
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.031 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.17 -9999 0 -0.51 52 52
Antigen/IgE/Fc epsilon R1 -0.092 0.16 -9999 0 -0.47 52 52
mol:GDP -0.017 0.13 -9999 0 -0.52 14 14
JUN -0.18 0.35 -9999 0 -0.83 105 105
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.22 0.37 -9999 0 -0.83 125 125
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.045 0.081 -9999 0 -0.35 6 6
CHUK 0.003 0.094 -9999 0 -0.28 15 15
KLRG1 -0.023 0.11 -9999 0 -0.42 14 14
VAV1 -0.024 0.12 -9999 0 -0.49 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.011 0.091 -9999 0 -0.35 4 4
negative regulation of mast cell degranulation -0.021 0.11 -9999 0 -0.38 14 14
BTK -0.048 0.11 -9999 0 -0.6 11 11
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.05 0.19 -9999 0 -0.52 46 46
GAB2/PI3K/SHP2 -0.067 0.13 -9999 0 -0.67 6 6
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.019 0.096 -9999 0 -0.29 34 34
RAF1 0.018 0.021 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.2 -9999 0 -0.59 54 54
FCER1G -0.009 0.083 -9999 0 -0.32 30 30
FCER1A -0.078 0.23 -9999 0 -0.56 72 72
Antigen/IgE/Fc epsilon R1/Fyn -0.082 0.14 -9999 0 -0.48 40 40
MAPK3 0.029 0.018 -9999 0 -10000 0 0
MAPK1 0.029 0.018 -9999 0 -10000 0 0
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
MAPK8 0.007 0.1 -9999 0 -0.71 8 8
DUSP1 -0.12 0.31 -9999 0 -0.83 75 75
NF-kappa-B/RelA -0.019 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.005 0.085 -9999 0 -0.38 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.043 0.11 -9999 0 -0.56 10 10
FER -0.014 0.1 -9999 0 -0.43 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.073 0.18 -9999 0 -0.54 56 56
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.013 0.13 -9999 0 -0.55 11 11
cytokine secretion -0.014 0.032 -9999 0 -0.23 1 1
SPHK1 -0.015 0.094 -9999 0 -0.38 5 5
PTK2 -0.006 0.087 -9999 0 -0.39 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.067 0.14 -9999 0 -0.44 38 38
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.012 0.15 -9999 0 -0.49 14 14
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.049 0.096 -9999 0 -0.43 13 13
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.21 -9999 0 -0.63 51 51
mol:Choline -0.049 0.15 -9999 0 -0.44 40 40
SHC/Grb2/SOS1 -0.032 0.067 -9999 0 -0.4 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.002 0.083 -9999 0 -0.36 1 1
HCLS1 -0.013 0.095 -9999 0 -0.38 5 5
PRKCB -0.011 0.12 -9999 0 -0.38 21 21
FCGR2B -0.03 0.18 -9999 0 -0.75 26 26
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.022 0.11 -9999 0 -0.39 14 14
LCP2 0.008 0.04 -9999 0 -0.32 7 7
PLA2G4A -0.042 0.16 -9999 0 -0.52 33 33
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.049 0.15 -9999 0 -0.44 40 40
IKK complex 0.018 0.076 -9999 0 -0.22 5 5
WIPF1 0.013 0 -9999 0 -10000 0 0
Nectin adhesion pathway

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.039 -9999 0 -0.83 1 1
alphaV beta3 Integrin -0.023 0.13 -9999 0 -0.7 15 15
PTK2 -0.039 0.15 -9999 0 -0.62 26 26
positive regulation of JNK cascade -0.02 0.08 -9999 0 -0.35 26 26
CDC42/GDP 0.032 0.12 -9999 0 -0.47 26 26
Rac1/GDP 0.033 0.12 -9999 0 -0.47 26 26
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.025 0.1 -9999 0 -0.43 26 26
nectin-3/I-afadin -0.036 0.15 -9999 0 -0.64 26 26
RAPGEF1 0.024 0.14 -9999 0 -0.54 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0.16 -9999 0 -0.64 26 26
PDGFB-D/PDGFRB 0.011 0.039 -9999 0 -0.83 1 1
TLN1 0.02 0.075 -9999 0 -0.94 1 1
Rap1/GTP -0.021 0.086 -9999 0 -0.37 26 26
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.036 0.15 -9999 0 -0.64 26 26
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.025 0.15 -9999 0 -0.6 26 26
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
PI3K -0.03 0.13 -9999 0 -0.52 27 27
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.031 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.021 0.084 -9999 0 -0.36 26 26
PVRL1 0.006 0.05 -9999 0 -0.31 11 11
PVRL3 -0.034 0.19 -9999 0 -0.83 26 26
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.26 0.15 -9999 0 -0.33 376 376
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.58 36 36
SRC -0.042 0.17 -9999 0 -0.72 26 26
ITGB3 -0.014 0.15 -9999 0 -0.83 15 15
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.031 -9999 0 -10000 0 0
FARP2 0.02 0.15 -9999 0 -0.58 26 26
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.031 0.13 -9999 0 -0.55 26 26
nectin-1/I-afadin -0.005 0.031 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.035 0.13 -9999 0 -0.55 26 26
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.02 0.08 -9999 0 -0.35 26 26
alphaV/beta3 Integrin/Talin 0.016 0.14 -9999 0 -0.63 15 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0.08 -9999 0 -0.28 26 26
VAV2 0.018 0.15 -9999 0 -0.6 26 26
RAP1/GDP -0.025 0.1 -9999 0 -0.43 26 26
ITGAV 0.01 0.055 -9999 0 -0.83 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.031 0.13 -9999 0 -0.55 26 26
nectin-3(dimer)/I-afadin/I-afadin -0.036 0.15 -9999 0 -0.64 26 26
Rac1/GTP -0.026 0.1 -9999 0 -0.45 26 26
PTPRM -0.018 0.083 -9999 0 -0.32 26 26
E-cadherin/beta catenin/alpha catenin -0.002 0.015 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.094 -10000 0 -0.35 6 6
epithelial cell differentiation -0.046 0.099 -10000 0 -0.48 11 11
ITCH 0.024 0.02 -10000 0 -10000 0 0
WWP1 -0.001 0.08 -10000 0 -0.44 1 1
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.006 0.078 -10000 0 -0.83 4 4
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0 0.15 -10000 0 -0.52 10 10
PTPRZ1 -0.015 0.13 -10000 0 -0.55 22 22
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.062 0.14 -10000 0 -0.45 47 47
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.048 0.18 -10000 0 -0.53 48 48
ADAM17 0.02 0.059 -10000 0 -0.82 2 2
ErbB4/ErbB4 -0.011 0.1 -10000 0 -0.52 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.048 0.17 -10000 0 -0.56 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.071 0.15 -10000 0 -0.5 48 48
GRIN2B -0.033 0.16 -10000 0 -0.47 47 47
ErbB4/ErbB2/betacellulin -0.037 0.11 -10000 0 -0.62 13 13
STAT1 0.006 0.05 -10000 0 -0.31 11 11
HBEGF -0.004 0.074 -10000 0 -0.31 25 25
PRLR -0.04 0.19 -10000 0 -0.59 41 41
E4ICDs/ETO2 -0.006 0.092 -10000 0 -0.49 3 3
axon guidance -0.002 0.088 -10000 0 -0.39 5 5
NEDD4 0.02 0.059 -10000 0 -0.81 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.04 0.14 -10000 0 -0.64 22 22
CBFA2T3 0.011 0.042 -10000 0 -0.57 2 2
ErbB4/ErbB2/HBEGF -0.03 0.062 -10000 0 -0.5 3 3
MAPK3 -0.009 0.15 -10000 0 -0.53 11 11
STAT1 (dimer) -0.009 0.091 -10000 0 -0.35 5 5
MAPK1 -0.009 0.15 -10000 0 -0.53 11 11
JAK2 0.012 0.039 -10000 0 -0.83 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.15 -10000 0 -0.5 48 48
NRG1 -0.04 0.21 -10000 0 -0.65 47 47
NRG3 -0.053 0.23 -10000 0 -0.83 36 36
NRG2 -0.082 0.26 -10000 0 -0.8 54 54
NRG4 0.008 0.037 -10000 0 -10000 0 0
heart development -0.002 0.088 -10000 0 -0.39 5 5
neural crest cell migration -0.07 0.15 -10000 0 -0.49 48 48
ERBB2 0.028 0.044 -10000 0 -0.62 2 2
WWOX/E4ICDs -0.006 0.094 -10000 0 -0.95 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.037 0.086 -10000 0 -0.66 4 4
apoptosis 0.059 0.14 0.47 37 -10000 0 37
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.067 0.19 -10000 0 -0.55 53 53
ErbB4/ErbB2/epiregulin -0.079 0.088 -10000 0 -0.55 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.019 0.13 -10000 0 -0.65 13 13
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.059 0.12 -10000 0 -0.47 24 24
MDM2 -0.001 0.088 -10000 0 -0.46 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.066 0.15 -10000 0 -0.51 47 47
STAT5A 0.006 0.082 -10000 0 -0.41 3 3
ErbB4/EGFR/neuregulin 1 beta -0.075 0.16 -10000 0 -0.52 50 50
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.033 0.064 -10000 0 -0.43 1 1
STAT5A (dimer) -0.049 0.11 -10000 0 -0.51 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.004 0.081 -10000 0 -0.41 3 3
LRIG1 0.001 0.1 -10000 0 -0.83 7 7
EREG -0.14 0.16 -10000 0 -0.31 214 214
BTC -0.009 0.13 -10000 0 -0.83 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.003 0.088 -10000 0 -0.4 5 5
ERBB4 -0.011 0.1 -10000 0 -0.52 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.02 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.058 -10000 0 -0.51 2 2
glial cell differentiation 0.033 0.064 0.42 1 -10000 0 1
WWOX 0.012 0.039 -10000 0 -0.83 1 1
cell proliferation -0.026 0.18 -10000 0 -0.46 54 54
Aurora C signaling

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
INCENP 0.012 0.039 -9999 0 -0.83 1 1
Aurora C/Aurora B/INCENP -0.038 0.072 -9999 0 -0.65 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.019 -9999 0 -10000 0 0
AURKB -0.061 0.14 -9999 0 -0.31 104 104
AURKC 0.002 0.06 -9999 0 -0.31 16 16
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.03 0.067 -9999 0 -0.32 7 7
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.25 -9999 0 -0.68 71 71
IL1A -0.055 0.23 -9999 0 -0.79 39 39
IL1B -0.032 0.18 -9999 0 -0.64 37 37
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.028 -9999 0 -0.43 2 2
IL1R2 -0.082 0.24 -9999 0 -0.83 40 40
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.068 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.004 0.087 -9999 0 -0.83 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.067 0.028 -9999 0 -10000 0 0
JUN -0.072 0.21 -9999 0 -0.43 111 111
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.067 0.13 -9999 0 -0.48 39 39
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.074 0.14 -9999 0 -0.52 36 36
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.067 0.13 -9999 0 -0.48 36 36
IL1 beta fragment/IL1R1/IL1RAP -0.077 0.15 -9999 0 -0.54 36 36
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
MAPK8 0.023 0.1 -9999 0 -0.5 15 15
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.045 0.11 -9999 0 -0.64 10 10
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.055 -9999 0 -0.83 2 2
PI3K -0.004 0.051 -9999 0 -0.64 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.087 -9999 0 -0.34 7 7
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.077 0.15 -9999 0 -0.54 36 36
IL1 beta/IL1R2 -0.1 0.23 -9999 0 -0.6 72 72
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.029 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.058 0.12 -9999 0 -0.56 7 7
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.069 0.14 -9999 0 -0.49 41 41
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.1 -9999 0 -0.34 36 36
IL1 alpha/IL1R1/IL1RAP -0.085 0.16 -9999 0 -0.55 38 38
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.022 0.036 -9999 0 -0.48 2 2
IL1RAP -0.072 0.14 -9999 0 -0.31 120 120
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.054 0.12 -9999 0 -0.5 11 11
CASP1 0.008 0.061 -9999 0 -0.52 5 5
IL1RN/IL1R2 -0.11 0.22 -9999 0 -0.63 58 58
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.069 0.14 -9999 0 -0.5 36 36
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.082 -9999 0 -0.34 4 4
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
IL1RN -0.055 0.16 -9999 0 -0.38 81 81
TRAF6/TAK1/TAB1/TAB2 -0.002 0.031 -9999 0 -0.47 2 2
MAP2K6 0.024 0.07 -9999 0 -0.44 10 10
Syndecan-3-mediated signaling events

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
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.04 0.12 -9999 0 -0.43 42 42
Syndecan-3/Neurocan -0.036 0.12 -9999 0 -0.47 34 34
POMC -0.17 0.34 -9999 0 -0.81 100 100
EGFR 0.006 0.078 -9999 0 -0.83 4 4
Syndecan-3/EGFR -0.005 0.044 -9999 0 -0.47 4 4
AGRP -0.004 0.061 -9999 0 -0.31 17 17
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.052 0.22 -9999 0 -0.77 38 38
long-term memory -0.001 0.006 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.04 0.083 -9999 0 -0.47 10 10
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0 0.009 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.008 -9999 0 -10000 0 0
MC4R 0.001 0.04 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PTN -0.064 0.24 -9999 0 -0.82 43 43
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.069 0.15 -9999 0 -0.42 75 75
Syndecan-3/AgRP -0.005 0.024 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.007 0.026 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.04 0.081 -9999 0 -0.46 10 10
IL8 -0.083 0.18 -9999 0 -0.36 120 120
Syndecan-3/Fyn/Cortactin -0.001 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.26 -9999 0 -0.64 97 97
Gamma Secretase 0 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.064 0.082 -10000 0 -0.34 22 22
NT3 (dimer)/TRKC -0.088 0.19 -10000 0 -0.68 37 37
NT3 (dimer)/TRKB -0.082 0.18 -10000 0 -0.58 46 46
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.03 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.62 20 20
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 0 0.058 -10000 0 -0.31 15 15
NTRK2 0.006 0.078 -10000 0 -0.83 4 4
NTRK3 -0.055 0.17 -10000 0 -0.39 78 78
NT-4/5 (dimer)/TRKB -0.067 0.16 -10000 0 -0.58 38 38
neuron apoptosis 0.04 0.093 0.42 15 -10000 0 15
SHC 2-3/Grb2 -0.043 0.1 -10000 0 -0.46 15 15
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.029 0.094 -10000 0 -0.64 6 6
SHC3 -0.048 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.024 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.083 0.18 -10000 0 -0.57 44 44
RIN/GDP -0.009 0.063 -10000 0 -0.28 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.093 -10000 0 -0.42 22 22
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.026 0.043 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.012 0.039 -10000 0 -0.83 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -10000 0 -0.64 25 25
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.018 0.08 -10000 0 -0.53 9 9
TRKA/NEDD4-2 -0.007 0.036 -10000 0 -10000 0 0
ELMO1 -0.31 0.41 -10000 0 -0.83 177 177
RhoG/GTP/ELMO1/DOCK1 -0.22 0.28 -10000 0 -0.57 178 178
NGF 0.006 0.072 -10000 0 -0.57 6 6
HRAS 0.012 0.022 -10000 0 -0.31 2 2
DOCK1 0.006 0.078 -10000 0 -0.83 4 4
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.018 0.16 -10000 0 -0.8 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.2 0.23 -10000 0 -0.47 193 193
mol:GDP -0.015 0.091 -10000 0 -0.4 4 4
NGF (dimer) 0.006 0.072 -10000 0 -0.57 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.64 177 177
RIT1/GDP -0.004 0.064 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 261 261
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.022 0.11 -10000 0 -0.62 14 14
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.026 -10000 0 -0.55 1 1
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.62 44 44
RAP1/GDP -0.018 0.043 -10000 0 -0.25 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.014 0.14 -10000 0 -0.62 20 20
ubiquitin-dependent protein catabolic process -0.01 0.053 -10000 0 -0.55 3 3
Schwann cell development -0.042 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.017 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.066 0.15 -10000 0 -0.69 12 12
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.037 -10000 0 -10000 0 0
STAT3 0.018 0.024 -10000 0 -10000 0 0
axon guidance -0.063 0.14 -10000 0 -0.61 14 14
MAPK3 0.016 0.079 -10000 0 -0.5 8 8
MAPK1 0.016 0.079 -10000 0 -0.5 8 8
CDC42/GDP -0.004 0.064 -10000 0 -0.28 2 2
NTF3 -0.047 0.2 -10000 0 -0.62 44 44
NTF4 -0.022 0.16 -10000 0 -0.64 25 25
NGF (dimer)/TRKA/FAIM -0.01 0.053 -10000 0 -0.55 3 3
PI3K -0.004 0.051 -10000 0 -0.64 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.11 -10000 0 -0.46 29 29
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.051 0.18 -10000 0 -0.59 37 37
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.048 -10000 0 -0.43 1 1
Rac1/GDP -0.004 0.064 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.01 0.055 -10000 0 -0.56 3 3
neuron projection morphogenesis 0.001 0.095 -10000 0 -0.52 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.053 -10000 0 -0.55 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.06 0.19 -10000 0 -0.43 77 77
NGF (dimer)/TRKA/GIPC/GAIP 0.018 0.081 -10000 0 -0.35 19 19
RAS family/GTP/PI3K 0.03 0.033 -10000 0 -0.37 3 3
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.022 -10000 0 -0.47 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.058 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.036 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.02 0.1 -10000 0 -0.57 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.043 -10000 0 -0.47 3 3
MATK -0.001 0.095 -10000 0 -0.53 12 12
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.035 0.1 -10000 0 -0.45 22 22
Rac1/GTP -0.19 0.15 -10000 0 -0.36 181 181
FRS2 family/SHP2/CRK family -0.001 0.022 -10000 0 -0.47 1 1
FOXM1 transcription factor network

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
NFATC3 0.041 0.35 -9999 0 -0.91 13 13
PLK1 0.042 0.071 -9999 0 -10000 0 0
BIRC5 0.022 0.12 -9999 0 -1.6 1 1
HSPA1B 0.041 0.35 -9999 0 -0.91 13 13
MAP2K1 0.031 0.037 -9999 0 -10000 0 0
BRCA2 0.035 0.36 -9999 0 -0.98 16 16
FOXM1 0.029 0.39 -9999 0 -0.98 20 20
XRCC1 0.041 0.35 -9999 0 -0.91 13 13
FOXM1B/p19 -0.1 0.3 -9999 0 -0.88 25 25
Cyclin D1/CDK4 0.028 0.33 -9999 0 -0.85 13 13
CDC2 0.034 0.36 -9999 0 -0.88 20 20
TGFA 0.01 0.34 -9999 0 -0.84 16 16
SKP2 0.033 0.36 -9999 0 -0.98 16 16
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.041 0.35 -9999 0 -0.91 13 13
RB1 -0.055 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.026 0.36 -9999 0 -0.96 19 19
AURKB -0.007 0.13 -9999 0 -10000 0 0
CENPF 0.035 0.36 -9999 0 -0.93 14 14
CDK4 0.018 0.015 -9999 0 -10000 0 0
MYC 0.036 0.35 -9999 0 -0.91 19 19
CHEK2 0.031 0.037 -9999 0 -10000 0 0
ONECUT1 0.024 0.34 -9999 0 -0.87 16 16
CDKN2A -0.13 0.16 -9999 0 -0.32 167 167
LAMA4 0.041 0.35 -9999 0 -0.91 13 13
FOXM1B/HNF6 0.017 0.37 -9999 0 -0.99 16 16
FOS -0.2 0.66 -9999 0 -1.2 126 126
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.041 0.35 -9999 0 -0.92 13 13
response to radiation 0.014 0.034 -9999 0 -10000 0 0
CENPB 0.041 0.35 -9999 0 -0.91 13 13
CENPA 0.028 0.37 -9999 0 -0.96 18 18
NEK2 0.031 0.36 -9999 0 -0.93 15 15
HIST1H2BA 0.032 0.35 -9999 0 -0.92 13 13
CCNA2 0.009 0.048 -9999 0 -0.33 9 9
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.029 0.37 -9999 0 -0.98 16 16
CCNB2 0.038 0.36 -9999 0 -0.95 13 13
CCNB1 0.036 0.36 -9999 0 -0.91 16 16
ETV5 0.04 0.35 -9999 0 -0.91 14 14
ESR1 -0.012 0.44 -9999 0 -1.1 35 35
CCND1 0.031 0.34 -9999 0 -0.87 13 13
GSK3A 0.029 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.035 0.051 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.017 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.13 0.23 -9999 0 -0.88 20 20
GAS1 -0.14 0.61 -9999 0 -1.2 100 100
MMP2 0.033 0.37 -9999 0 -1.1 15 15
RB1/FOXM1C 0.039 0.34 -9999 0 -0.92 13 13
CREBBP 0.013 0 -9999 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.25 0.39 -10000 0 -0.83 143 143
HRAS 0.012 0.022 -10000 0 -0.31 2 2
EGFR 0.006 0.078 -10000 0 -0.83 4 4
AKT 0.018 0.025 -10000 0 -10000 0 0
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.11 0.16 -10000 0 -0.31 174 174
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.008 0.13 -10000 0 -0.66 15 15
PIK3R3 0.012 0.039 -10000 0 -0.83 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.06 0.1 -10000 0 -0.26 42 42
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.19 1 -0.17 1 2
PI3K -0.04 0.096 0.23 1 -0.23 47 48
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.025 0.027 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.039 -10000 0 -0.83 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.018 0.12 -10000 0 -0.8 10 10
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.001 0.1 -10000 0 -0.83 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.007 0.068 -10000 0 -0.83 3 3
AP1 -0.15 0.26 -10000 0 -0.52 137 137
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.005 0.12 -10000 0 -0.83 10 10
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.052 -10000 0 -10000 0 0
NICD/RBPSUH -0.016 0.11 -10000 0 -0.74 10 10
WIF1 -0.033 0.1 -10000 0 -0.31 55 55
NOTCH1 -0.017 0.11 -10000 0 -0.77 10 10
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.011 0.085 -10000 0 -0.31 34 34
DKK1 -0.04 0.13 -10000 0 -0.33 72 72
beta catenin/beta TrCP1 0.037 0.038 0.23 13 -10000 0 13
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.035 -10000 0 -0.22 10 10
CtBP/CBP/TCF1/TLE1/AES 0.023 0.037 -10000 0 -0.35 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.37 -10000 0 -0.83 125 125
JUN -0.18 0.35 -10000 0 -0.83 105 105
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.03 0.041 0.24 14 -10000 0 14
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.036 0.12 -10000 0 -0.57 18 18
HNF1A 0.012 0.002 -10000 0 -10000 0 0
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.011 0.24 -10000 0 -1.5 11 11
NKD1 -0.015 0.15 -10000 0 -0.74 17 17
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.023 0.12 -10000 0 -0.62 17 17
apoptosis -0.15 0.26 -10000 0 -0.52 137 137
Delta 1/NOTCHprecursor -0.017 0.11 -10000 0 -0.77 10 10
DLL1 0.011 0.042 -10000 0 -0.57 2 2
PPARD 0.024 0.016 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.001 0.061 -10000 0 -0.3 10 10
DVL1 0.003 0.01 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.038 0.082 -10000 0 -0.4 9 9
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.015 0.007 -10000 0 -10000 0 0
CCND1 0.019 0.042 -10000 0 -10000 0 0
WNT1 0.01 0.022 -10000 0 -0.31 2 2
Axin1/APC/beta catenin 0.044 0.052 -10000 0 -0.67 1 1
DKK2 -0.026 0.17 -10000 0 -0.66 27 27
NOTCH1 precursor/DVL1 -0.011 0.096 -10000 0 -0.65 10 10
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.023 0.12 -10000 0 -0.63 17 17
PPP2R5D 0.012 0.065 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.016 0.044 -10000 0 -10000 0 0
RBPJ 0.013 0.015 -10000 0 -0.31 1 1
CREBBP 0.017 0.004 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.029 0.17 -9999 0 -0.44 62 62
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.051 0.12 -9999 0 -0.75 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.01 0.038 -9999 0 -0.65 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.3 2 2
CaM/Ca2+ -0.057 0.14 -9999 0 -0.41 62 62
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.022 0.16 -9999 0 -0.41 62 62
AKT1 -0.004 0.15 -9999 0 -0.63 3 3
MAP2K1 -0.007 0.15 -9999 0 -0.39 61 61
MAP3K11 -0.018 0.16 -9999 0 -0.41 62 62
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.067 -9999 0 -0.64 1 1
Rap1/GTP -0.042 0.1 -9999 0 -0.6 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.065 0.16 -9999 0 -0.46 61 61
CEBPB 0.017 0.17 -9999 0 -0.84 4 4
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.061 0.15 -9999 0 -1.1 2 2
STAT1 -0.021 0.16 -9999 0 -0.41 62 62
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.11 0.28 -9999 0 -0.72 76 76
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
STAT1 (dimer)/PIAS1 -0.013 0.15 -9999 0 -0.38 61 61
CEBPB/PTGES2/Cbp/p300 -0.035 0.081 -9999 0 -0.45 4 4
mol:Ca2+ -0.062 0.15 -9999 0 -0.44 62 62
MAPK3 0.009 0.14 -9999 0 -0.55 4 4
STAT1 (dimer) -0.031 0.082 -9999 0 -0.42 2 2
MAPK1 0.009 0.14 -9999 0 -0.55 4 4
JAK2 0.007 0.044 -9999 0 -0.88 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.017 0.18 -9999 0 -0.66 21 21
SMAD7 0.041 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.052 0.13 -9999 0 -0.77 1 1
PI3K -0.058 0.14 -9999 0 -0.54 7 7
IFNG -0.11 0.28 -9999 0 -0.72 76 76
apoptosis 0.013 0.13 -9999 0 -0.45 21 21
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.004 0.068 -9999 0 -0.31 21 21
CAMK2B 0.004 0.087 -9999 0 -0.83 5 5
FRAP1 -0.002 0.14 -9999 0 -0.57 3 3
PRKCD -0.003 0.15 -9999 0 -0.64 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.061 -9999 0 -0.3 2 2
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.028 0.12 -9999 0 -0.53 1 1
STAT1 (dimer)/PIASy -0.056 0.14 -9999 0 -0.51 4 4
SOCS1 0.001 0.076 -9999 0 -1.5 1 1
mol:GDP -0.049 0.12 -9999 0 -0.72 1 1
CASP1 0.039 0.063 -9999 0 -0.35 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.042 0.058 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.056 0.14 -9999 0 -0.52 7 7
RAP1/GDP -0.042 0.1 -9999 0 -0.61 1 1
CBL -0.019 0.16 -9999 0 -0.41 62 62
MAP3K1 -0.018 0.16 -9999 0 -0.41 62 62
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.061 -9999 0 -0.3 2 2
PTPN11 -0.028 0.16 -9999 0 -0.44 62 62
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
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 -0.062 0.16 -10000 0 -0.48 59 59
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.055 -10000 0 -0.21 30 30
GNB1/GNG2 -0.001 0.026 -10000 0 -0.56 1 1
GNB1 0.013 0 -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 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.066 0.17 -10000 0 -0.52 58 58
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 0.015 0.039 0.12 58 -10000 0 58
GNAL -0.092 0.28 -10000 0 -0.83 58 58
GNG2 0.012 0.039 -10000 0 -0.83 1 1
CRH -0.013 0.08 -10000 0 -0.31 30 30
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.061 -10000 0 -0.46 8 8
MAPK11 0.009 0 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0 0.08 -9999 0 -10000 0 0
STMN1 -0.022 0.095 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.027 0.11 -9999 0 -0.55 1 1
Chromosomal passenger complex/Cul3 protein complex 0.008 0.069 -9999 0 -0.35 4 4
BIRC5 -0.018 0.1 -9999 0 -0.33 42 42
DES -0.38 0.3 -9999 0 -0.61 279 279
Aurora C/Aurora B/INCENP -0.014 0.084 -9999 0 -0.42 3 3
Aurora B/TACC1 -0.022 0.082 -9999 0 -0.72 1 1
Aurora B/PP2A -0.027 0.092 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.026 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.051 0.15 -9999 0 -0.39 59 59
Cul3 protein complex -0.016 0.083 -9999 0 -0.55 10 10
KIF2C -0.001 0.042 -9999 0 -0.16 1 1
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.042 0.12 -9999 0 -0.31 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.092 -9999 0 -10000 0 0
SEPT1 0.008 0.043 -9999 0 -0.31 8 8
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.006 0.045 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
H3F3B -0.007 0.055 -9999 0 -10000 0 0
AURKB -0.052 0.14 -9999 0 -0.31 104 104
AURKC 0.002 0.06 -9999 0 -0.31 16 16
CDCA8 0.01 0.028 -9999 0 -10000 0 0
cytokinesis -0.066 0.082 -9999 0 -0.44 4 4
Aurora B/Septin1 -0.027 0.1 -9999 0 -0.5 3 3
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.01 0.04 -9999 0 -0.84 1 1
KLHL13 -0.013 0.13 -9999 0 -0.56 21 21
BUB1 -0.1 0.16 -9999 0 -0.32 163 163
hSgo1/Aurora B/Survivin -0.028 0.12 -9999 0 -0.45 17 17
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.073 -9999 0 -0.36 3 3
SGOL1 0.001 0.063 -9999 0 -0.31 18 18
CENPA -0.008 0.071 -9999 0 -0.24 6 6
NCAPG -0.02 0.099 -9999 0 -0.31 47 47
Aurora B/HC8 Proteasome -0.027 0.092 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.027 0.092 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.035 0.12 -9999 0 -0.31 68 68
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.091 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.036 0.082 -9999 0 -0.35 18 18
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.007 0.055 -9999 0 -10000 0 0
KIF23 -0.004 0.074 -9999 0 -0.32 24 24
VIM -0.021 0.093 -9999 0 -10000 0 0
RACGAP1 0.013 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.014 0.084 -9999 0 -0.26 21 21
Chromosomal passenger complex/EVI5 0.009 0.12 -9999 0 -0.54 3 3
TACC1 0.012 0.039 -9999 0 -0.83 1 1
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.016 0.054 -9999 0 -0.56 4 4
ADCY5 -0.06 0.2 -9999 0 -0.56 63 63
ADCY6 0.016 0.054 -9999 0 -0.56 4 4
ADCY7 0.016 0.054 -9999 0 -0.56 4 4
ADCY1 0.009 0.081 -9999 0 -0.58 8 8
ADCY2 -0.038 0.17 -9999 0 -0.57 42 42
ADCY3 0.016 0.054 -9999 0 -0.56 4 4
ADCY8 -0.12 0.099 -9999 0 -0.71 4 4
PRKCE 0.006 0.061 -9999 0 -0.65 4 4
ADCY9 0.016 0.054 -9999 0 -0.56 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.1 -9999 0 -0.37 29 29
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.005 0.075 -10000 0 -0.36 6 6
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.039 -10000 0 -0.83 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.04 0.077 0.24 12 -10000 0 12
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.063 0.22 -10000 0 -0.64 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.026 -10000 0 -0.55 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.028 0.11 -10000 0 -0.31 56 56
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.038 0.1 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.04 0.081 0.26 2 -10000 0 2
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 297 297
LNPEP -0.01 0.14 -10000 0 -0.83 13 13
YWHAE 0.013 0 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.045 -9999 0 -0.93 1 1
VEGFR1 homodimer/NRP1 -0.002 0.044 -9999 0 -0.94 1 1
mol:DAG -0.015 0.17 -9999 0 -0.5 49 49
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.07 -9999 0 -0.78 3 3
CaM/Ca2+ -0.007 0.16 -9999 0 -0.46 49 49
HIF1A 0.021 0.019 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.006 0.17 -9999 0 -1.2 2 2
PLCG1 -0.015 0.17 -9999 0 -0.5 49 49
NOS3 0.014 0.16 -9999 0 -0.91 1 1
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.015 0.15 -9999 0 -0.85 1 1
FLT1 0.03 0.05 -9999 0 -1 1 1
PGF -0.075 0.26 -9999 0 -0.82 49 49
VEGFR1 homodimer/NRP2/VEGFR121 -0.015 0.077 -9999 0 -0.77 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
eNOS/Hsp90 0.022 0.15 -9999 0 -0.81 1 1
endothelial cell proliferation -0.03 0.19 -9999 0 -0.52 49 49
mol:Ca2+ -0.014 0.17 -9999 0 -0.49 49 49
MAPK3 -0.019 0.18 -9999 0 -0.49 22 22
MAPK1 -0.019 0.18 -9999 0 -1 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.075 0.26 -9999 0 -0.82 49 49
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.009 0.13 -9999 0 -0.83 12 12
VEGFA homodimer 0.008 0.067 -9999 0 -0.83 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.077 -9999 0 -0.83 3 3
platelet activating factor biosynthetic process -0.011 0.18 -9999 0 -0.96 2 2
PI3K -0.053 0.15 -9999 0 -0.48 51 51
PRKCA -0.029 0.19 -9999 0 -0.47 69 69
PRKCB -0.023 0.17 -9999 0 -0.48 51 51
VEGFR1 homodimer/PLGF homodimer -0.028 0.18 -9999 0 -0.55 49 49
VEGFA 0.008 0.068 -9999 0 -0.83 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.015 0.17 -9999 0 -0.5 49 49
RASA1 0.041 0.042 -9999 0 -0.86 1 1
NRP2 -0.014 0.09 -9999 0 -0.31 38 38
VEGFR1 homodimer 0.03 0.05 -9999 0 -1 1 1
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.01 0.17 -9999 0 -0.81 4 4
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
mol:PI-3-4-5-P3 -0.052 0.15 -9999 0 -0.47 51 51
mol:L-citrulline 0.015 0.15 -9999 0 -0.85 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.005 0.066 -9999 0 -0.73 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.07 -9999 0 -0.77 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.049 0.14 -9999 0 -1.2 1 1
PDPK1 -0.003 0.17 -9999 0 -1.2 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.087 -9999 0 -0.91 3 3
mol:NADP 0.015 0.15 -9999 0 -0.85 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.005 0.064 -9999 0 -0.71 3 3
VEGFR1 homodimer/NRP2 0.017 0.067 -9999 0 -0.93 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.012 0.12 -9999 0 -0.45 26 26
CCNA2 0.007 0.045 -9999 0 -0.31 9 9
PIK3CA 0.009 0.068 -9999 0 -0.83 3 3
JAK3 -0.066 0.14 -9999 0 -0.31 113 113
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.019 0.15 -9999 0 -0.57 18 18
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.038 0.24 -9999 0 -0.97 26 26
IL2RB -0.014 0.13 -9999 0 -0.5 25 25
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.046 0.19 -9999 0 -0.54 50 50
G1/S transition of mitotic cell cycle 0.041 0.048 -9999 0 -0.6 2 2
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.01 0.11 -9999 0 -0.44 25 25
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.01 0.055 -9999 0 -0.83 2 2
CCND3 0.029 0.13 -9999 0 -0.64 7 7
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.34 -9999 0 -0.83 95 95
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.026 -9999 0 -0.31 3 3
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.024 -9999 0 -10000 0 0
HIF1A 0.022 0.025 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.004 0.042 -9999 0 -0.51 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.16 -9999 0 -0.31 193 193
ARNT/IPAS -0.13 0.26 -9999 0 -0.64 95 95
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.024 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.013 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.024 -9999 0 -10000 0 0
PHD1-3/OS9 -0.019 0.091 -9999 0 -0.54 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.018 -9999 0 -10000 0 0
VHL 0.008 0.068 -9999 0 -0.83 3 3
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.024 -9999 0 -10000 0 0
EGLN3 -0.019 0.14 -9999 0 -0.52 28 28
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.01 0.055 -9999 0 -0.83 2 2
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.053 -9999 0 -0.6 3 3
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.031 0.073 -9999 0 -0.29 1 1
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.003 0.1 0.55 13 -10000 0 13
PI3K Class IB/PDE3B -0.003 0.1 -10000 0 -0.55 13 13
PDE3B -0.003 0.1 -10000 0 -0.55 13 13
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.001 0.14 -10000 0 -0.71 9 9
BAG4 0.012 0.039 -10000 0 -0.83 1 1
PKC zeta/ceramide -0.018 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.67 33 33
BAX -0.005 0.02 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.009 -10000 0 -10000 0 0
BAD -0.017 0.041 -10000 0 -10000 0 0
SMPD1 -0.005 0.095 -10000 0 -0.26 53 53
RB1 -0.018 0.047 -10000 0 -0.5 1 1
FADD/Caspase 8 0.011 0.13 -10000 0 -0.67 9 9
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.051 -10000 0 -0.52 2 2
EGF -0.11 0.3 -10000 0 -0.78 72 72
mol:ceramide -0.029 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.031 -10000 0 -0.64 1 1
ASAH1 0.012 0.039 -10000 0 -0.83 1 1
negative regulation of cell cycle -0.019 0.046 -10000 0 -0.5 1 1
cell proliferation -0.097 0.16 -10000 0 -0.39 103 103
BID -0.016 0.09 -10000 0 -0.4 9 9
MAP3K1 -0.017 0.041 -10000 0 -10000 0 0
EIF2A 0 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.002 0.048 -10000 0 -0.48 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.048 -10000 0 -0.48 2 2
Cathepsin D/ceramide -0.018 0.041 -10000 0 -10000 0 0
FADD -0.001 0.14 -10000 0 -0.71 9 9
KSR1 -0.02 0.054 -10000 0 -0.56 2 2
MAPK8 -0.009 0.055 -10000 0 -0.32 8 8
PRKRA -0.017 0.041 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.8 108 108
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -10000 0 0
CTSD 0.013 0.015 -10000 0 -0.31 1 1
regulation of nitric oxide biosynthetic process -0.001 0.029 -10000 0 -0.63 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.083 0.19 -10000 0 -0.42 103 103
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.031 -10000 0 -0.64 1 1
RelA/NF kappa B1 -0.001 0.03 -10000 0 -0.64 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.01 0.15 -10000 0 -0.75 9 9
TNFR1A/BAG4/TNF-alpha -0.066 0.18 -10000 0 -0.55 54 54
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.002 0.049 -10000 0 -0.49 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.004 0.052 0.18 25 -10000 0 25
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.039 -10000 0 -0.83 1 1
TNFR1A/BAG4 -0.001 0.03 -10000 0 -0.64 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.065 0.18 -10000 0 -0.55 53 53
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.078 -10000 0 -0.33 9 9
MAP2K2 -0.002 0.049 -10000 0 -0.49 2 2
SMPD3 -0.011 0.12 -10000 0 -0.3 58 58
TNF -0.088 0.27 -10000 0 -0.78 59 59
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.024 0.11 0.28 66 -10000 0 66
NF kappa B1/RelA/I kappa B alpha -0.001 0.022 -10000 0 -0.47 1 1
AIFM1 0.003 0.052 0.18 25 -10000 0 25
BCL2 -0.049 0.22 -10000 0 -0.83 34 34
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.031 0.64 1 -10000 0 1
CDKN1A -0.006 0.036 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
FOXO3 0 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.024 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.007 0.022 -10000 0 -0.31 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.02 -10000 0 -10000 0 0
PPARGC1A -0.36 0.42 -10000 0 -0.83 203 203
FHL2 -0.051 0.22 -10000 0 -0.83 35 35
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.032 -10000 0 -0.64 1 1
HIST2H4A 0.021 0.031 -10000 0 -0.64 1 1
SIRT1/FOXO3a 0 0.027 -10000 0 -0.56 1 1
SIRT1 0 0.041 -10000 0 -0.83 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.028 -10000 0 -0.55 1 1
SIRT1/Histone H1b -0.006 0.052 -10000 0 -0.33 10 10
apoptosis -0.001 0.029 0.55 1 -10000 0 1
SIRT1/PGC1A -0.25 0.28 -10000 0 -0.56 203 203
p53/SIRT1 0.004 0.044 -10000 0 -0.64 1 1
SIRT1/FOXO4 0.001 0.028 -10000 0 -0.54 1 1
FOXO1/FHL2/SIRT1 -0.038 0.14 -10000 0 -0.51 36 36
HIST1H1E 0.015 0.056 -10000 0 -0.37 9 9
SIRT1/p300 0.001 0.032 -10000 0 -0.64 1 1
muscle cell differentiation 0.001 0.032 0.56 1 -10000 0 1
TP53 0.002 0.012 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.029 -10000 0 -0.55 1 1
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0 0.034 -10000 0 -0.64 1 1
ACSS2 0.021 0.031 -10000 0 -0.64 1 1
SIRT1/PCAF/MYOD -0.001 0.032 -10000 0 -0.56 1 1
IL2 signaling events mediated by PI3K

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
BCL2L1 0.011 0.12 -10000 0 -0.57 9 9
UGCG -0.042 0.18 -10000 0 -0.83 21 21
AKT1/mTOR/p70S6K/Hsp90/TERT 0.022 0.13 -10000 0 -0.41 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.02 0.18 -10000 0 -0.81 21 21
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.058 0.14 -10000 0 -0.46 32 32
FRAP1 0.004 0.2 -10000 0 -0.49 47 47
FOXO3 0.022 0.16 -10000 0 -0.61 16 16
AKT1 0.013 0.18 -10000 0 -0.61 20 20
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.005 0.022 -10000 0 -10000 0 0
SGMS1 -0.005 0.022 -10000 0 -10000 0 0
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 0.019 0.048 -10000 0 -0.57 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.001 0.16 -10000 0 -0.54 24 24
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.054 -10000 0 -0.64 3 3
RPS6KB1 0.017 0.041 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 5 5
JAK3 -0.065 0.14 -10000 0 -0.31 113 113
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.039 -10000 0 -0.83 1 1
MYC 0.011 0.21 -10000 0 -0.92 16 16
MYB -0.014 0.19 -10000 0 -1.3 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.01 0.16 -10000 0 -0.57 22 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.037 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.011 0.16 -10000 0 -0.55 22 22
Rac1/GDP 0.024 0.045 -10000 0 -0.51 3 3
T cell proliferation 0.019 0.15 -10000 0 -0.53 19 19
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.05 15 15
PRKCZ 0.018 0.15 -10000 0 -0.55 19 19
NF kappa B1 p50/RelA -0.057 0.14 -10000 0 -0.46 29 29
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.001 0.13 -10000 0 -0.6 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.043 0.19 -10000 0 -0.56 45 45
IL2RB -0.013 0.13 -10000 0 -0.5 25 25
TERT 0.001 0.03 -10000 0 -0.31 4 4
E2F1 -0.003 0.075 -10000 0 -0.45 9 9
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.024 15 -10000 0 15
PTPN11 0.011 0.04 -10000 0 -0.83 1 1
IL2RG -0.044 0.19 -10000 0 -0.54 50 50
actin cytoskeleton organization 0.019 0.15 -10000 0 -0.53 19 19
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.068 -10000 0 -0.83 3 3
Rac1/GTP 0.031 0.044 -10000 0 -0.49 3 3
LCK -0.009 0.11 -10000 0 -0.44 25 25
BCL2 -0.024 0.28 -10000 0 -0.84 44 44
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 -0.055 0.15 -9999 0 -0.44 57 57
TC10/GTP -0.003 0.034 -9999 0 -0.42 3 3
Insulin Receptor/Insulin/IRS1/Shp2 -0.063 0.17 -9999 0 -0.53 55 55
HRAS 0.012 0.022 -9999 0 -0.31 2 2
APS homodimer 0.013 0.015 -9999 0 -0.31 1 1
GRB14 -0.012 0.14 -9999 0 -0.83 14 14
FOXO3 -0.025 0.11 -9999 0 -0.73 10 10
AKT1 -0.014 0.17 -9999 0 -0.89 2 2
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.008 0.068 -9999 0 -0.83 3 3
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.038 0 -9999 0 -10000 0 0
CAV1 -0.046 0.18 -9999 0 -0.48 67 67
CBL/APS/CAP/Crk-II/C3G -0.003 0.038 -9999 0 -0.47 3 3
Insulin Receptor/Insulin/IRS1/NCK2 -0.062 0.17 -9999 0 -0.52 55 55
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.057 0.15 -9999 0 -0.46 57 57
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.003 0.1 -9999 0 -10000 0 0
RPS6KB1 -0.003 0.15 -9999 0 -0.77 2 2
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.057 0.14 -9999 0 -0.79 2 2
HRAS/GTP -0.051 0.13 -9999 0 -0.51 3 3
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.057 0.16 -9999 0 -0.48 55 55
PRKCI -0.015 0.035 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.066 0.16 -9999 0 -0.49 18 18
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.058 0.16 -9999 0 -0.47 57 57
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
AKT2 -0.014 0.17 -9999 0 -0.89 2 2
PRKCZ -0.015 0.035 -9999 0 -10000 0 0
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
SHC/SHIP -0.03 0.16 -9999 0 -0.46 55 55
F2RL2 -0.082 0.16 -9999 0 -0.32 131 131
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.004 0.041 -9999 0 -0.5 3 3
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.04 0.17 -9999 0 -0.49 55 55
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.027 0.15 -9999 0 -1 10 10
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
IRS1 -0.087 0.27 -9999 0 -0.83 55 55
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.04 0.17 -9999 0 -0.48 55 55
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.005 0.16 -9999 0 -0.64 4 4
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.055 -9999 0 -0.83 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.008 0.12 -9999 0 -0.33 55 55
Insulin Receptor/Insulin/IRS1 -0.063 0.17 -9999 0 -0.52 55 55
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.036 0.062 -9999 0 -0.48 2 2
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.006 0.078 -9999 0 -0.83 4 4
CDKN1A -0.014 0.09 -9999 0 -10000 0 0
PRL-3/alpha Tubulin -0.016 0.055 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.099 -9999 0 -0.65 7 7
AGT -0.016 0.12 -9999 0 -0.83 7 7
CCNA2 -0.066 0.21 -9999 0 -0.59 4 4
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.12 0.27 -9999 0 -0.63 101 101
CDK2/Cyclin E1 0.003 0.078 -9999 0 -10000 0 0
MAPK3 0.006 0.061 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.006 0.061 -9999 0 -10000 0 0
PTP4A1 -0.076 0.22 -9999 0 -0.49 101 101
PTP4A3 -0.013 0.089 -9999 0 -0.31 37 37
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.006 0.061 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1 -0.018 0.093 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.071 0.21 -9999 0 -0.59 4 4
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.012 0.04 -9999 0 -10000 0 0
RHOC -0.018 0.093 -9999 0 -10000 0 0
RHOA -0.018 0.093 -9999 0 -10000 0 0
cell motility -0.016 0.1 -9999 0 -0.26 13 13
PRL-1/alpha Tubulin -0.065 0.2 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.022 0.082 -9999 0 -0.68 4 4
ROCK1 -0.016 0.1 -9999 0 -0.27 13 13
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.075 0.22 -9999 0 -0.48 101 101
ATF5 0.001 0.063 -9999 0 -0.31 18 18
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.05 -9999 0 -0.31 11 11
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.017 -9999 0 -10000 0 0
GNAO1 -0.016 0.15 -9999 0 -0.74 18 18
mol:Sphinganine-1-P 0.019 0.035 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.002 0.013 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.01 0.03 -9999 0 -0.31 4 4
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.011 -9999 0 -10000 0 0
S1PR5 0.007 0.054 -9999 0 -0.39 7 7
S1PR4 0.01 0.034 -9999 0 -0.31 5 5
GNAI1 0.012 0.039 -9999 0 -0.83 1 1
S1P/S1P5/G12 -0.004 0.029 -9999 0 -0.49 1 1
S1P/S1P3/Gq -0.049 0.15 -9999 0 -0.31 114 114
S1P/S1P4/Gi 0.031 0.068 -9999 0 -0.32 16 16
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.36 -9999 0 -0.83 107 107
GNA15 -0.012 0.093 -9999 0 -0.33 34 34
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.83 9 9
ABCC1 0.013 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.039 -9999 0 -0.83 1 1
Caspase 8 (4 units) -0.022 0.063 -9999 0 -10000 0 0
NEF -0.013 0.057 -9999 0 -0.22 28 28
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.004 0.2 -9999 0 -0.82 24 24
CYCS -0.007 0.1 -9999 0 -0.4 6 6
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.037 0.18 -9999 0 -0.71 26 26
MAP2K7 0.023 0.081 -9999 0 -0.31 2 2
protein ubiquitination 0.04 0.086 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.016 0.11 -9999 0 -0.42 6 6
NF-kappa-B/RelA/I kappa B alpha -0.021 0.08 -9999 0 -0.35 24 24
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.039 -9999 0 -0.83 1 1
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.08 -9999 0 -0.35 24 24
MAPK8 0.023 0.097 -9999 0 -0.42 8 8
APAF1 0.012 0.039 -9999 0 -0.83 1 1
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.099 -9999 0 -0.3 36 36
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.025 0.1 -9999 0 -0.37 9 9
CHUK 0.04 0.091 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.022 -9999 0 -0.47 1 1
TCRz/NEF -0.061 0.18 -9999 0 -0.51 50 50
TNF -0.088 0.27 -9999 0 -0.78 59 59
FASLG -0.073 0.29 -9999 0 -0.85 50 50
NFKB1 0.007 0.048 -9999 0 -0.82 1 1
TNFR1A/BAG4/TNF-alpha -0.066 0.18 -9999 0 -0.55 54 54
CASP6 -0.005 0.047 -9999 0 -10000 0 0
CASP7 0.029 0.16 -9999 0 -0.63 23 23
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.029 0.16 -9999 0 -0.63 23 23
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.03 -9999 0 -0.64 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.033 0.097 -9999 0 -0.37 2 2
APAF-1/Caspase 9 -0.047 0.12 -9999 0 -0.53 23 23
BCL2 -0.003 0.14 -9999 0 -0.4 40 40
BARD1 signaling events

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
BARD1/CSTF1 -0.033 0.14 -10000 0 -0.64 24 24
ATM 0.012 0.039 -10000 0 -0.83 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.012 0.039 -10000 0 -0.83 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.031 -10000 0 -0.44 2 2
protein ubiquitination -0.025 0.1 -10000 0 -0.46 25 25
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.004 0.044 -10000 0 -0.55 3 3
MRE11A 0.008 0.068 -10000 0 -0.83 3 3
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.033 0.14 -10000 0 -0.64 24 24
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.002 0.068 -10000 0 -0.31 21 21
DNA repair 0.053 0.1 -10000 0 -0.42 1 1
BRCA1/BARD1/ubiquitin -0.033 0.14 -10000 0 -0.64 24 24
BARD1/DNA-PK -0.026 0.11 -10000 0 -0.5 24 24
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.033 0.14 0.63 24 -10000 0 24
BRCA1/BARD1/CTIP/M/R/N Complex 0.02 0.091 -10000 0 -0.33 28 28
BRCA1/BACH1/BARD1/TopBP1 -0.029 0.12 -10000 0 -0.55 24 24
BRCA1/BARD1/P53 -0.027 0.11 -10000 0 -0.5 25 25
BARD1/CSTF1/BRCA1 -0.029 0.12 -10000 0 -0.55 24 24
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.031 0.19 -10000 0 -0.83 24 24
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.029 0.12 -10000 0 -0.55 24 24
BRCA1/BARD1/UbcH7 -0.029 0.12 -10000 0 -0.55 24 24
BRCA1/BARD1/RAD51/PCNA -0.027 0.11 -10000 0 -0.5 24 24
BARD1/DNA-PK/P53 -0.024 0.1 -10000 0 -0.47 24 24
BRCA1/BARD1/Ubiquitin -0.033 0.14 -10000 0 -0.64 24 24
BRCA1/BARD1/CTIP -0.027 0.11 -10000 0 -0.5 25 25
FA complex 0.038 0.025 -10000 0 -10000 0 0
BARD1/EWS -0.033 0.14 -10000 0 -0.64 24 24
RBBP8 0.023 0.031 -10000 0 -0.64 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.027 0.11 0.5 25 -10000 0 25
BRCA1/BARD1 -0.025 0.11 -10000 0 -0.47 25 25
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.034 0.14 -10000 0 -0.64 24 24
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0.022 -10000 0 -0.31 2 2
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.033 0.14 -10000 0 -0.64 24 24
EWSR1 0.013 0 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.018 0.14 -9999 0 -0.5 28 28
ITGA4 0.005 0.06 -9999 0 -0.36 10 10
alpha4/beta7 Integrin -0.027 0.11 -9999 0 -0.62 12 12
alpha4/beta1 Integrin -0.005 0.041 -9999 0 -0.64 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.12 -10000 0 -0.83 9 9
ANTXR2 0.008 0.068 -10000 0 -0.83 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 12 12
monocyte activation -0.045 0.17 -10000 0 -0.49 55 55
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.011 0.068 -10000 0 -0.51 8 8
CYAA 0.003 0.08 -10000 0 -0.49 12 12
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.024 0.13 -10000 0 -0.47 37 37
Channel -0.013 0.082 -10000 0 -0.52 12 12
NLRP1 -0.004 0.035 -10000 0 -0.5 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 12 -10000 0 12
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.023 0.088 -10000 0 -0.46 15 15
PA/Cellular Receptors -0.015 0.089 -10000 0 -0.56 12 12
apoptosis -0.003 0.016 -10000 0 -0.1 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.08 -10000 0 -0.48 12 12
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.088 0.27 -10000 0 -0.78 59 59
VCAM1 -0.046 0.17 -10000 0 -0.49 55 55
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.023 0.11 8 -10000 0 8
IL18 -0.01 0.085 -10000 0 -0.46 11 11
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 12 12
LEF -0.003 0.016 -10000 0 -0.1 12 12
CASP1 -0.004 0.021 -10000 0 -0.23 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.078 -10000 0 -0.49 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.044 0.12 0.34 1 -0.36 57 58
FRAP1 0.008 0.027 -10000 0 -10000 0 0
AKT1 -0.037 0.1 0.25 1 -0.66 3 4
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.028 0.079 -10000 0 -0.51 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.008 0.023 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.067 -10000 0 -0.46 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.036 0.14 -10000 0 -0.42 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.009 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.061 -10000 0 -0.35 3 3
MAP3K5 0.011 0.022 -10000 0 -0.45 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.022 -10000 0 -0.45 1 1
mol:LY294002 0 0.001 0.001 2 -0.002 54 56
EIF4B 0.017 0.056 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.014 0.04 -10000 0 -0.32 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.026 0.14 -10000 0 -0.39 57 57
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.041 0.18 1 -0.28 2 3
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.023 0.066 -10000 0 -0.45 3 3
mol:Amino Acids 0 0.001 0.001 2 -0.002 54 56
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.041 0.12 0.26 1 -0.34 57 58
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.035 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.002 -10000 0 -10000 0 0
TSC1/TSC2 -0.03 0.085 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 54 -0.001 2 56
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.047 0.15 -10000 0 -0.46 55 55
INS 0 0 -10000 0 -10000 0 0
PTEN 0.011 0.039 -10000 0 -0.83 1 1
PDK2 -0.04 0.11 0.26 1 -0.32 57 58
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
PPP2R5D 0.015 0.025 -10000 0 -10000 0 0
peptide biosynthetic process 0.018 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 3 4
EEF2 0.018 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.019 0.008 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.071 0.009 -9999 0 -10000 0 0
EGFR 0.006 0.078 -9999 0 -0.83 4 4
EPHA2 0.011 0.026 -9999 0 -0.31 3 3
MYO6 0.041 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.038 0.13 -9999 0 -0.6 23 23
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.074 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.78 72 72
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.072 0.19 -9999 0 -0.6 56 56
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.005 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.011 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.05 0.028 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.041 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.009 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.067 0.15 -9999 0 -0.43 70 70
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.35 -9999 0 -0.8 108 108
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.005 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.048 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.042 0.05 -9999 0 -0.43 5 5
Ephrin A1/EPHA2 -0.001 0.008 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.038 0.075 -9999 0 -10000 0 0
HGF/MET -0.1 0.16 -9999 0 -0.48 67 67
HGF -0.11 0.3 -9999 0 -0.83 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.087 0.018 -9999 0 -10000 0 0
KIAA1543 0.047 0.022 -9999 0 -0.42 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.041 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.02 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.096 0.18 -9999 0 -0.43 102 102
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.11 0.16 -9999 0 -0.31 174 174
PLEKHA7 0.04 0.023 -9999 0 -0.45 1 1
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.033 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.002 0.035 0.3 1 -0.48 2 3
DAPP1 -0.054 0.14 -10000 0 -0.5 12 12
Src family/SYK family/BLNK-LAT/BTK-ITK -0.059 0.18 -10000 0 -0.5 29 29
mol:DAG -0.005 0.097 -10000 0 -0.28 15 15
HRAS 0.013 0.021 -10000 0 -0.31 2 2
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.023 0.035 -10000 0 -0.46 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.014 0.27 1 -10000 0 1
ARF1/GTP -0.001 0.023 0.28 1 -10000 0 1
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.014 0.26 1 -10000 0 1
ADAP1 0 0.013 0.26 1 -10000 0 1
ARAP3 0 0.014 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.013 0 -10000 0 -10000 0 0
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.01 0.03 -10000 0 -0.31 4 4
mol:Ca2+ 0.007 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.32 261 261
ZAP70 -0.024 0.16 -10000 0 -0.62 27 27
mol:IP3 0.005 0.072 -10000 0 -0.21 1 1
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.035 -10000 0 -0.46 1 1
RhoA/GDP -0.001 0.02 0.28 1 -10000 0 1
PDK1/Src/Hsp90 -0.003 0.037 -10000 0 -0.55 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.039 0.038 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
PLEKHA2 0.023 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.037 -10000 0 -0.8 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.015 0.3 1 -10000 0 1
RhoA/GTP 0 0.013 0.26 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.051 0.16 -10000 0 -0.61 13 13
BLK -0.25 0.38 -10000 0 -0.76 156 156
PDPK1 0.01 0.055 -10000 0 -0.83 2 2
CYTH1 0 0.013 0.26 1 -10000 0 1
HCK -0.008 0.081 -10000 0 -0.31 30 30
CYTH3 -0.002 0.035 0.26 1 -0.5 2 3
CYTH2 0 0.013 0.26 1 -10000 0 1
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.013 0.095 -10000 0 -0.63 10 10
SGK1 -0.015 0.11 -10000 0 -0.7 10 10
INPP5D -0.003 0.071 -10000 0 -0.31 23 23
mol:GDP 0.016 0.037 -10000 0 -0.5 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.02 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.018 0.37 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.014 0.26 1 -10000 0 1
VAV1 -0.014 0.1 -10000 0 -0.36 34 34
mol:PI-3-4-P2 0.013 0.049 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.007 -10000 0 -10000 0 0
PLEKHA1 0.023 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.035 -10000 0 -0.46 1 1
LAT 0.005 0.079 -10000 0 -0.72 5 5
Rac1/GTP -0.006 0.054 -10000 0 -0.6 1 1
ITK -0.055 0.14 -10000 0 -0.44 55 55
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.014 0.13 -10000 0 -0.4 15 15
LCK -0.011 0.11 -10000 0 -0.44 25 25
BTK -0.013 0.06 0.26 1 -0.44 7 8
Regulation of Telomerase

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
Telomerase catalytic core complex -0.023 0.091 -9999 0 -0.52 1 1
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.29 0.46 -9999 0 -0.93 147 147
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.002 0.073 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.047 0.15 -9999 0 -0.4 54 54
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.78 72 72
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.006 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.036 0.067 -9999 0 -10000 0 0
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.004 0.044 -9999 0 -0.55 3 3
WT1 -0.026 0.1 -9999 0 -0.31 51 51
WRN 0.012 0.039 -9999 0 -0.83 1 1
SP1 0.015 0.003 -9999 0 -10000 0 0
SP3 0.014 0.001 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.028 0.052 -9999 0 -10000 0 0
Mad/Max 0.005 0.009 -9999 0 -10000 0 0
TERT -0.024 0.092 -9999 0 -10000 0 0
CCND1 -0.015 0.091 -9999 0 -10000 0 0
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.008 0.068 -9999 0 -0.83 3 3
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
Telomerase/911 0.036 0.019 -9999 0 -10000 0 0
CDKN1B -0.042 0.19 -9999 0 -0.53 61 61
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.039 -9999 0 -0.83 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.001 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.83 105 105
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.006 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.83 125 125
IFN-gamma/IRF1 -0.088 0.21 -9999 0 -0.62 62 62
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.013 0.015 -9999 0 -0.31 1 1
Telomerase 0.014 0.073 -9999 0 -0.49 5 5
IRF1 0.018 0.015 -9999 0 -0.3 1 1
ESR1 -0.051 0.2 -9999 0 -0.54 54 54
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.026 -9999 0 -0.56 1 1
ubiquitin-dependent protein catabolic process 0.052 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.053 0.028 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC2 0.015 0.003 -9999 0 -10000 0 0
ATM -0.001 0.026 -9999 0 -0.56 1 1
SMAD3 0.02 0.03 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.014 0.002 -9999 0 -10000 0 0
MRE11A 0.008 0.068 -9999 0 -0.83 3 3
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.031 0.064 -9999 0 -10000 0 0
NR2F2 0.012 0.002 -9999 0 -10000 0 0
MAPK3 0.017 0.006 -9999 0 -10000 0 0
MAPK1 0.017 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.007 0.043 -9999 0 -0.31 8 8
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.026 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.006 0.078 -9999 0 -0.83 4 4
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.099 0.23 -9999 0 -0.64 70 70
MYC -0.006 0.13 -9999 0 -0.83 11 11
IL2 0.006 0.007 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.007 0.043 -9999 0 -0.31 8 8
TRF2/BLM 0 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.024 0.073 -9999 0 -10000 0 0
SP1/HDAC2 0.021 0.008 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.028 0.052 -9999 0 -10000 0 0
Smad3/Myc 0.011 0.093 -9999 0 -0.56 11 11
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.1 0.28 -9999 0 -0.72 76 76
Telomerase/PinX1 -0.028 0.052 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.021 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.028 0.052 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.003 0.037 -9999 0 -0.46 3 3
TRF2/WRN -0.001 0.028 -9999 0 -0.6 1 1
Telomerase/hnRNP C1/C2 -0.028 0.052 -9999 0 -10000 0 0
E2F1 -0.085 0.15 -9999 0 -0.31 140 140
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.001 0.092 -9999 0 -0.6 9 9
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.02 0.087 -10000 0 -0.45 10 10
ACTA1 0.012 0.11 0.24 6 -0.55 10 16
NUMA1 0.02 0.087 -10000 0 -0.45 10 10
SPTAN1 0.017 0.1 -10000 0 -0.55 10 10
LIMK1 0.017 0.1 -10000 0 -0.57 9 9
BIRC3 -0.036 0.19 -10000 0 -0.67 33 33
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
CASP10 0.001 0.12 -10000 0 -0.59 12 12
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.02 0.087 -10000 0 -0.45 10 10
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.017 0.1 -10000 0 -0.54 10 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.017 0.11 -10000 0 -0.61 8 8
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.055 0.22 -10000 0 -0.65 55 55
BID -0.01 0.066 -10000 0 -0.3 10 10
MAP3K1 0.015 0.04 -10000 0 -0.23 2 2
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.03 -10000 0 -0.64 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.014 0.11 -10000 0 -0.53 11 11
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.016 0.05 -10000 0 -0.23 20 20
neuron apoptosis 0.024 0.015 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.023 0.1 -10000 0 -0.58 8 8
APAF1 0.011 0.039 -10000 0 -0.83 1 1
CASP6 0.023 0.062 -10000 0 -0.43 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.024 0.1 -10000 0 -0.58 8 8
CASP7 0.009 0.079 0.34 23 -10000 0 23
KRT18 0.017 0.018 -10000 0 -10000 0 0
apoptosis 0.027 0.11 0.26 20 -0.55 10 30
DFFA 0.017 0.1 -10000 0 -0.55 10 10
DFFB 0.017 0.1 -10000 0 -0.55 10 10
PARP1 0.016 0.051 0.23 20 -10000 0 20
actin filament polymerization -0.024 0.098 0.55 8 -10000 0 8
TNF -0.088 0.27 -10000 0 -0.78 59 59
CYCS 0.005 0.043 -10000 0 -0.22 10 10
SATB1 0.03 0.06 -10000 0 -0.4 4 4
SLK 0.014 0.12 -10000 0 -0.59 12 12
p15 BID/BAX -0.002 0.058 -10000 0 -0.34 3 3
CASP2 0.007 0.11 -10000 0 -0.46 9 9
JNK cascade -0.015 0.04 0.23 2 -10000 0 2
CASP3 0.009 0.11 0.25 8 -0.58 10 18
LMNB2 0.021 0.076 -10000 0 -0.32 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.5 23 23
negative regulation of DNA binding -0.054 0.22 -10000 0 -0.64 55 55
stress fiber formation 0.014 0.12 -10000 0 -0.58 12 12
GZMB -0.011 0.13 -10000 0 -0.68 12 12
CASP1 0.015 0.033 -10000 0 -0.45 2 2
LMNB1 0.021 0.076 -10000 0 -0.32 4 4
APP 0.024 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.024 0.092 0.25 20 -0.49 8 28
LMNA 0.021 0.076 -10000 0 -0.32 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.001 0.12 -10000 0 -0.49 9 9
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.016 0.11 -10000 0 -0.55 10 10
APAF-1/Caspase 9 0.005 0.041 -10000 0 -0.4 1 1
nuclear fragmentation during apoptosis 0.02 0.085 -10000 0 -0.44 10 10
CFL2 0.024 0.1 -10000 0 -0.57 8 8
GAS2 0.011 0.12 -10000 0 -0.54 15 15
positive regulation of apoptosis 0.024 0.078 -10000 0 -0.31 4 4
PRF1 0.001 0.098 -10000 0 -0.7 8 8
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.047 0.058 -10000 0 -0.38 8 8
NFATC2 -0.017 0.092 -10000 0 -0.3 21 21
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.091 -10000 0 -0.31 24 24
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.025 0.094 -10000 0 -0.61 7 7
BCL2/BAX -0.047 0.17 -10000 0 -0.64 34 34
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.005 0.01 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.015 0.086 -10000 0 -0.6 3 3
Calcineurin A alpha-beta B1/BCL2 -0.049 0.22 -10000 0 -0.83 34 34
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.015 0.085 0.59 3 -10000 0 3
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 297 297
MAP3K8 -0.005 0.11 -10000 0 -0.83 8 8
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.11 0.15 -10000 0 -0.49 17 17
CABIN1 0.011 0.091 -10000 0 -0.31 24 24
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.1 -10000 0 -0.52 15 15
mol:Ca2+ -0.005 0.01 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.005 0.11 -10000 0 -0.83 8 8
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.005 0.048 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.015 0.051 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.048 -10000 0 -10000 0 0
PRKCB -0.024 0.12 -10000 0 -0.35 48 48
PRKCE 0.006 0.078 -10000 0 -0.83 4 4
JNK2/NFAT4 0.022 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.027 0.18 -10000 0 -0.83 22 22
PRKCG 0.005 0.022 -10000 0 -0.31 2 2
PRKCQ 0.002 0.095 -10000 0 -0.83 6 6
FKBP38/BCL2 -0.047 0.17 -10000 0 -0.64 34 34
EP300 0.01 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.033 0.084 -10000 0 -0.4 8 8
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.068 -10000 0 -0.57 6 6
NFATc/ERK1 0.053 0.055 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.092 -10000 0 -0.6 7 7
NR4A1 -0.19 0.36 -10000 0 -0.73 137 137
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.035 0.06 -10000 0 -0.43 3 3
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.01 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.061 -10000 0 -10000 0 0
CREBBP 0.01 0.007 -10000 0 -10000 0 0
BCL2 -0.049 0.22 -10000 0 -0.83 34 34
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.058 -10000 0 -0.35 5 5
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0.083 0.24 6 -0.41 12 18
RAR alpha/9cRA/Cyclin H -0.024 0.095 -10000 0 -0.41 22 22
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.064 -10000 0 -0.4 5 5
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.014 0.11 -10000 0 -0.73 8 8
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.019 0.16 -10000 0 -0.66 23 23
NCOA2 -0.063 0.24 -10000 0 -0.83 42 42
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -10000 0 -10000 0 0
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0 0.11 -10000 0 -0.83 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.038 0.15 -10000 0 -0.67 22 22
RARA 0.007 0.092 -10000 0 -0.34 28 28
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.002 0.13 -10000 0 -0.52 14 14
PRKCA -0.024 0.18 -10000 0 -0.83 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.029 0.16 -10000 0 -0.68 23 23
RXRG -0.12 0.11 -10000 0 -0.54 25 25
RXRA 0.013 0.094 -10000 0 -0.35 28 28
RXRB 0.004 0.1 -10000 0 -0.45 22 22
VDR/Vit D3/DNA 0 0.01 -10000 0 -10000 0 0
RBP1 -0.002 0.11 -10000 0 -0.64 11 11
CRBP1/9-cic-RA -0.012 0.081 -10000 0 -0.64 7 7
RARB -0.005 0.13 -10000 0 -0.83 11 11
PRKCG 0.008 0.022 -10000 0 -0.31 2 2
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.025 0.17 -10000 0 -0.71 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.007 0.14 -10000 0 -0.57 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.086 -10000 0 -0.5 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.029 0.16 -10000 0 -0.68 23 23
positive regulation of DNA binding -0.022 0.089 -10000 0 -0.39 22 22
NRIP1 -0.025 0.15 -10000 0 -0.82 7 7
RXRs/RARs -0.037 0.16 -10000 0 -0.67 23 23
RXRs/RXRs/DNA/9cRA -0.049 0.15 -10000 0 -0.7 22 22
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.013 0.054 -10000 0 -0.53 2 2
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.039 -9999 0 -0.83 1 1
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.058 -9999 0 -0.28 16 16
GNAO1 -0.014 0.15 -9999 0 -0.74 18 18
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.029 -9999 0 -0.47 1 1
AKT3 0.049 0.05 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.039 -9999 0 -0.83 1 1
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.013 0.039 -9999 0 -0.83 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.01 0.03 -9999 0 -0.31 4 4
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.036 0.067 -9999 0 -0.32 15 15
MAPK3 0.043 0.064 -9999 0 -10000 0 0
MAPK1 0.043 0.064 -9999 0 -10000 0 0
JAK2 0.046 0.065 -9999 0 -0.43 1 1
CXCR4 0.042 0.064 -9999 0 -10000 0 0
FLT1 0.015 0.039 -9999 0 -0.83 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.042 0.064 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.036 0.067 -9999 0 -0.32 15 15
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.052 -9999 0 -10000 0 0
VEGFA 0.011 0.068 -9999 0 -0.83 3 3
S1P/S1P2/Gi 0.031 0.068 -9999 0 -0.33 15 15
VEGFR1 homodimer/VEGFA homodimer 0.024 0.07 -9999 0 -0.81 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.066 0.17 -9999 0 -0.36 114 114
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.36 -9999 0 -0.83 107 107
GNA15 -0.012 0.093 -9999 0 -0.33 34 34
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.83 9 9
Rac1/GTP -0.01 0.052 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.017 -10000 0 -10000 0 0
CDKN1A 0.034 0.031 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.017 -10000 0 -10000 0 0
AKT1 -0.001 0.015 -10000 0 -0.28 1 1
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.016 0.031 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.017 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.024 -10000 0 -0.43 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.012 0.039 -10000 0 -0.83 1 1
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.024 0.42 1 -10000 0 1
TSC1 0.039 0.017 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.016 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.001 0.015 -10000 0 -0.28 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.017 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.051 0.2 -10000 0 -0.56 61 61
MAP3K5 0.012 0.039 -10000 0 -0.83 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.036 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.017 -10000 0 -10000 0 0
CASP9 0.039 0.017 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.016 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.003 0.037 -10000 0 -0.55 2 2
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
AKT2/p21CIP1 -0.005 0.03 -10000 0 -0.37 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.039 0.017 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.016 -10000 0 -10000 0 0
mTORC2 -0.001 0.024 -10000 0 -0.52 1 1
AKT2 0.016 0.031 -10000 0 -0.45 2 2
FOXO1-3a-4/14-3-3 family 0.024 0.041 -10000 0 -10000 0 0
PDPK1 0.01 0.055 -10000 0 -0.83 2 2
MDM2 0.039 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.016 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.015 -10000 0 -10000 0 0
TSC1/TSC2 0.046 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.012 -10000 0 -10000 0 0
glucose import -0.06 0.21 -10000 0 -0.53 75 75
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.06 0.21 -10000 0 -0.53 75 75
GSK3A 0.039 0.017 -10000 0 -10000 0 0
FOXO1 0.039 0.017 -10000 0 -10000 0 0
GSK3B 0.039 0.017 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 297 297
G1/S transition of mitotic cell cycle 0.046 0.016 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.052 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.009 0.057 -9999 0 -0.66 3 3
positive regulation of NF-kappaB transcription factor activity -0.003 0.043 -9999 0 -0.63 2 2
MAP2K4 0.048 0.027 -9999 0 -0.3 2 2
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.068 -9999 0 -0.83 3 3
SMPD1 -0.001 0.02 -9999 0 -0.29 2 2
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.003 0.043 -9999 0 -0.64 2 2
TRAIL/TRAILR3 -0.06 0.1 -9999 0 -0.72 2 2
TRAIL/TRAILR1 -0.007 0.066 -9999 0 -0.64 5 5
TRAIL/TRAILR4 -0.003 0.043 -9999 0 -0.64 2 2
TRAIL/TRAILR1/DAP3/GTP -0.006 0.053 -9999 0 -0.51 5 5
IKK complex -0.002 0.016 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.021 0.045 -9999 0 -0.63 2 2
MAP3K1 -0.002 0.024 -9999 0 -0.32 2 2
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.067 -9999 0 -0.83 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.036 0.039 -9999 0 -0.33 5 5
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.021 0.045 -9999 0 -0.63 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP -0.005 0.049 -9999 0 -0.47 5 5
mol:ceramide -0.001 0.019 -9999 0 -0.29 2 2
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.046 0.074 -9999 0 -0.48 8 8
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.08 0.15 -9999 0 -0.31 131 131
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.006 0.057 -9999 0 -0.55 5 5
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.004 0.041 -9999 0 -0.52 2 2
JNK cascade -0.003 0.043 -9999 0 -0.63 2 2
TRAIL (trimer) 0.009 0.057 -9999 0 -0.66 3 3
TNFRSF10C -0.08 0.15 -9999 0 -0.31 131 131
TRAIL/TRAILR1/DAP3/GTP/FADD -0.005 0.049 -9999 0 -0.48 5 5
TRAIL/TRAILR2/FADD -0.003 0.037 -9999 0 -0.55 2 2
cell death 0.02 0.021 -9999 0 -0.29 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.038 0.025 -9999 0 -0.33 2 2
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.011 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.031 -9999 0 -0.47 2 2
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.006 0.13 -10000 0 -0.56 9 9
BAG4 0.012 0.039 -10000 0 -0.83 1 1
BAD 0.018 0.045 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.67 33 33
BAX 0.018 0.046 -10000 0 -0.22 1 1
EnzymeConsortium:3.1.4.12 0.004 0.033 -10000 0 -0.12 9 9
IKBKB 0.014 0.12 -10000 0 -0.52 9 9
MAP2K2 0.028 0.056 -10000 0 -0.37 2 2
MAP2K1 0.028 0.056 -10000 0 -0.37 2 2
SMPD1 0.01 0.033 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.014 0.12 -10000 0 -0.54 9 9
MAP2K4 0.025 0.046 -10000 0 -10000 0 0
protein ubiquitination 0.016 0.12 -10000 0 -0.53 9 9
EnzymeConsortium:2.7.1.37 0.031 0.061 -10000 0 -0.38 2 2
response to UV 0 0.001 -10000 0 -0.003 2 2
RAF1 0.022 0.057 -10000 0 -0.4 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.047 -10000 0 -0.17 9 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.018 0.047 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.056 -10000 0 -0.36 2 2
MAPK1 0.03 0.056 -10000 0 -0.36 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.006 0.13 -10000 0 -0.56 9 9
KSR1 0.016 0.056 -10000 0 -0.43 2 2
MAPK8 0.024 0.075 -10000 0 -0.44 8 8
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.014 0.12 -10000 0 -0.52 9 9
TNF R/SODD -0.001 0.03 -10000 0 -0.64 1 1
TNF -0.088 0.27 -10000 0 -0.78 59 59
CYCS 0.028 0.056 0.16 29 -10000 0 29
IKBKG 0.014 0.12 -10000 0 -0.52 9 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.13 -10000 0 -0.44 23 23
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.028 0.056 0.16 29 -10000 0 29
TNF/TNF R/SODD -0.066 0.18 -10000 0 -0.55 54 54
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.033 -10000 0 -10000 0 0
NSMAF 0.006 0.13 -10000 0 -0.55 9 9
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 2 2
BCL2 -0.049 0.22 -10000 0 -0.83 34 34
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.08 -9999 0 -0.74 5 5
PDGFRB 0.011 0.039 -9999 0 -0.83 1 1
SPHK1 -0.008 0.022 -9999 0 -10000 0 0
mol:S1P -0.01 0.027 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.15 -9999 0 -0.67 11 11
GNAO1 -0.016 0.15 -9999 0 -0.75 18 18
PDGFB-D/PDGFRB/PLCgamma1 0.021 0.14 -9999 0 -0.57 11 11
PLCG1 0.018 0.14 -9999 0 -0.64 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.039 -9999 0 -0.83 1 1
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.011 0.04 -9999 0 -0.83 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.072 -9999 0 -0.65 5 5
S1P1/S1P -0.017 0.066 -9999 0 -0.52 5 5
negative regulation of cAMP metabolic process 0.012 0.15 -9999 0 -0.54 17 17
MAPK3 0.003 0.2 -9999 0 -0.59 44 44
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.007 0.068 -9999 0 -0.83 3 3
PLCB2 0.029 0.072 -9999 0 -0.45 5 5
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.054 -9999 0 -0.42 5 5
receptor internalization -0.016 0.061 -9999 0 -0.47 5 5
PTGS2 -0.043 0.35 -9999 0 -1.1 44 44
Rac1/GTP -0.014 0.054 -9999 0 -0.42 5 5
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.007 0.068 -9999 0 -0.83 3 3
negative regulation of T cell proliferation 0.012 0.15 -9999 0 -0.54 17 17
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 0.003 0.2 -9999 0 -0.59 44 44
S1P1/S1P/PDGFB-D/PDGFRB 0.031 0.088 -9999 0 -0.51 6 6
ABCC1 0.014 0.002 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.072 0.055 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.027 0.073 -9999 0 -0.64 1 1
NFKBIA 0.049 0.025 -9999 0 -0.48 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.005 0.017 -9999 0 -10000 0 0
IKK complex/A20 -0.048 0.13 -9999 0 -0.4 53 53
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.043 0.037 -9999 0 -0.43 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.001 0.011 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.036 -9999 0 -0.55 2 2
NOD2 -0.03 0.12 -9999 0 -0.32 60 60
NFKB1 0.015 0.039 -9999 0 -0.82 1 1
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.012 0.039 -9999 0 -0.83 1 1
TNF/TNFR1A -0.076 0.2 -9999 0 -0.64 53 53
TRAF6 0.01 0.055 -9999 0 -0.83 2 2
PRKCA -0.027 0.18 -9999 0 -0.83 22 22
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.088 0.27 -9999 0 -0.78 59 59
NF kappa B1 p50/RelA -0.001 0.025 -9999 0 -0.53 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.024 -9999 0 -0.47 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.002 0.013 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.02 0.086 -9999 0 -0.54 1 1
Arf6 downstream 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
PLAUR -0.062 0.13 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.038 0.33 2 -10000 0 2
myoblast fusion 0.024 0.052 -10000 0 -10000 0 0
mol:GTP -0.027 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.094 0.11 0.52 1 -10000 0 1
ARF1/GTP -0.016 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.034 -10000 0 -10000 0 0
mol:Choline 0.011 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.064 -10000 0 -10000 0 0
MAPK3 -0.018 0.065 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.094 0.11 -10000 0 -0.53 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.031 0.047 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.059 -10000 0 -10000 0 0
ARF6 -0.002 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.18 0.17 -10000 0 -0.32 261 261
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.065 -10000 0 -10000 0 0
actin filament bundle formation 0.025 0.038 -10000 0 -10000 0 0
KALRN -0.006 0.051 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.038 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.027 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.003 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.027 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.016 0.023 -10000 0 -10000 0 0
mol:GDP -0.011 0.065 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.014 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0 0.033 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.003 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.038 -10000 0 -0.33 2 2
regulation of epithelial cell migration -0.027 0.039 -10000 0 -10000 0 0
PLD2 0 0.033 -10000 0 -10000 0 0
PIP5K1A 0.01 0.038 -10000 0 -0.33 2 2
mol:Phosphatidic acid 0.011 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.065 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.039 0.02 -9999 0 -10000 0 0
PLK1 0.1 0.11 -9999 0 -0.73 1 1
CDKN1B 0.15 0.049 -9999 0 -0.39 1 1
FOXO3 0.1 0.12 -9999 0 -0.62 3 3
KAT2B 0.025 0.01 -9999 0 -10000 0 0
FOXO1/SIRT1 0.01 0.039 -9999 0 -0.6 1 1
CAT 0.1 0.15 -9999 0 -1.4 3 3
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.011 -9999 0 -10000 0 0
FOXO1 0.042 0.014 -9999 0 -10000 0 0
MAPK10 0.043 0.027 -9999 0 -0.51 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.064 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.014 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.011 0.089 -9999 0 -0.72 3 3
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.002 -9999 0 -10000 0 0
BCL2L11 0.04 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 0.039 0.052 -9999 0 -0.5 4 4
mol:GDP 0.015 0.014 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.063 -9999 0 -0.72 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.04 0.041 -9999 0 -10000 0 0
MST1 0.022 0.043 -9999 0 -0.56 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.065 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.036 0.071 -9999 0 -0.5 8 8
MAPK9 0.044 0.007 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.006 0.044 -9999 0 -0.82 1 1
SOD2 0.16 0.075 -9999 0 -0.79 1 1
RBL2 0.11 0.16 -9999 0 -1.4 4 4
RAL/GDP 0.033 0.013 -9999 0 -10000 0 0
CHUK 0.025 0.01 -9999 0 -10000 0 0
Ran/GTP 0.015 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.042 0.01 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.081 0.42 -9999 0 -1.5 35 35
SKP2 0.006 0.078 -9999 0 -0.83 4 4
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.01 -9999 0 -10000 0 0
CCNB1 0.11 0.11 -9999 0 -0.73 1 1
FOXO1-3a-4/beta catenin -0.004 0.05 -9999 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.052 -9999 0 -0.5 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.007 0.12 -9999 0 -0.82 10 10
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.003 -9999 0 -10000 0 0
ZFAND5 0.11 0.054 -9999 0 -0.47 1 1
SFN -0.21 0.19 -9999 0 -0.34 297 297
CDK2 0.014 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.016 0.063 -9999 0 -10000 0 0
CREBBP 0.014 0.002 -9999 0 -10000 0 0
FBXO32 0.1 0.11 -9999 0 -0.73 1 1
BCL6 0.11 0.11 -9999 0 -0.94 2 2
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Canonical Wnt signaling 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
HDAC1 0.006 0.023 -10000 0 -10000 0 0
AES 0.005 0.02 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.026 0.17 -10000 0 -0.66 27 27
TLE1 0 0.068 -10000 0 -0.81 3 3
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.04 -10000 0 -10000 0 0
WIF1 -0.033 0.1 -10000 0 -0.31 55 55
beta catenin/RanBP3 0.021 0.091 0.37 24 -10000 0 24
KREMEN2 -0.011 0.085 -10000 0 -0.31 34 34
DKK1 -0.04 0.13 -10000 0 -0.33 72 72
beta catenin/beta TrCP1 0.053 0.038 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.049 0.32 -10000 0 -1.6 18 18
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.063 0.044 0.29 1 -0.41 1 2
Axin1/APC/GSK3 0.007 0.032 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.019 -10000 0 -10000 0 0
HNF1A 0.006 0.021 -10000 0 -10000 0 0
CTBP1 0.006 0.021 -10000 0 -10000 0 0
MYC -0.028 0.25 -10000 0 -1.6 11 11
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.036 0.12 -10000 0 -0.57 18 18
NKD1 -0.015 0.15 -10000 0 -0.74 17 17
TCF4 0.006 0.021 -10000 0 -10000 0 0
TCF3 0.006 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.009 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.12 0.48 26 -10000 0 26
LEF1 -0.001 0.057 -10000 0 -0.38 8 8
DVL1 0.017 0.028 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.069 0.072 -10000 0 -0.52 2 2
DKK1/LRP6/Kremen 2 -0.038 0.082 -10000 0 -0.4 9 9
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.006 0.023 -10000 0 -10000 0 0
NLK 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.001 0.075 -10000 0 -0.81 1 1
WNT1 0.01 0.022 -10000 0 -0.31 2 2
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.031 0.062 0.37 14 -10000 0 14
APC 0.038 0.027 -10000 0 -0.47 1 1
WNT1/LRP6/FZD1 0.035 0.036 -10000 0 -10000 0 0
CREBBP 0.006 0.021 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification -0.026 0.048 -9999 0 -0.64 1 1
CLOCK -0.037 0.2 -9999 0 -0.83 26 26
TIMELESS/CRY2 -0.006 0.064 -9999 0 -10000 0 0
DEC1/BMAL1 -0.022 0.065 -9999 0 -10000 0 0
ATR 0.012 0.039 -9999 0 -0.83 1 1
NR1D1 -0.06 0.13 -9999 0 -10000 0 0
ARNTL -0.022 0.098 -9999 0 -0.32 46 46
TIMELESS -0.014 0.073 -9999 0 -10000 0 0
NPAS2 0.007 0.057 -9999 0 -0.65 3 3
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.008 0.031 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.008 0.031 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.03 0.15 -9999 0 -0.56 28 28
BMAL1/CLOCK -0.055 0.15 -9999 0 -0.62 12 12
S phase of mitotic cell cycle -0.026 0.048 -9999 0 -0.64 1 1
TIMELESS/CHEK1/ATR -0.027 0.048 -9999 0 -0.65 1 1
mol:NADPH -0.008 0.031 -9999 0 -10000 0 0
PER1/TIMELESS -0.006 0.064 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.015 -9999 0 -0.31 1 1
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 0.012 0.055 0.3 16 -10000 0 16
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.032 -10000 0 -0.56 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.016 0.15 -10000 0 -0.74 18 18
RhoA/GTP -0.012 0.056 -10000 0 -0.3 16 16
negative regulation of cAMP metabolic process 0.022 0.071 -10000 0 -0.33 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.007 0.054 -10000 0 -0.39 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.071 -10000 0 -0.33 17 17
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.039 -10000 0 -0.83 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.06 0.16 -9999 0 -0.51 54 54
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.14 -9999 0 -0.42 54 54
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.024 0.066 -9999 0 -10000 0 0
YY1/LSF 0.029 0.045 -9999 0 -0.53 3 3
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.012 0.13 -9999 0 -0.37 53 53
I kappa B alpha/HDAC1 0.001 0.09 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.002 0.12 -9999 0 -0.32 53 53
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0.001 0.09 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.021 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.11 -9999 0 -0.48 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.009 0.006 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.023 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.008 0.068 -9999 0 -0.83 3 3
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.007 0.1 -9999 0 -0.28 53 53
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.028 -9999 0 -10000 0 0
SIN3 complex -0.001 0.023 -9999 0 -0.5 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.039 -9999 0 -0.83 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.016 0.084 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0 -9999 0 -10000 0 0
YY1/HDAC1 0.033 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.049 0.021 -9999 0 -10000 0 0
PPARG -0.059 0.16 -9999 0 -0.46 57 57
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.001 0.09 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.022 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.1 -9999 0 -0.28 53 53
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.028 0 -9999 0 -10000 0 0
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.003 0.039 -9999 0 -0.49 3 3
YY1/SAP30/HDAC1 -0.001 0.023 -9999 0 -0.49 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.028 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.1 -9999 0 -0.28 53 53
histone deacetylation 0.049 0.02 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.084 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 0 0.09 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.009 0.089 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.076 0.2 -9999 0 -0.64 53 53
SIN3/HDAC complex/Mad/Max 0.049 0.024 -9999 0 -10000 0 0
NuRD Complex 0.058 0.022 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.024 0.065 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.04 -9999 0 -0.5 3 3
GATA1/Fog1 0 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.088 0.27 -9999 0 -0.78 59 59
negative regulation of cell growth 0.049 0.024 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.049 0.021 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.052 0.14 -9999 0 -0.44 53 53
SIN3/HDAC complex/NCoR1 0.046 0.027 -9999 0 -10000 0 0
TFCP2 0.008 0.068 -9999 0 -0.83 3 3
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.014 0.078 -9999 0 -0.44 11 11
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.006 0.078 -9999 0 -0.83 4 4
ITGA4 0.005 0.06 -9999 0 -0.36 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.029 0.093 -9999 0 -0.5 13 13
EPO 0.004 0.03 -9999 0 -0.31 4 4
alpha4/beta7 Integrin -0.027 0.11 -9999 0 -0.62 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.005 0.041 -9999 0 -0.64 1 1
EPO/EPOR (dimer) -0.005 0.032 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.039 -9999 0 -0.47 3 3
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
PI3K -0.004 0.051 -9999 0 -0.64 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.026 0.043 -9999 0 -0.51 2 2
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.012 0.092 -9999 0 -0.35 28 28
cell adhesion -0.029 0.092 -9999 0 -0.5 13 13
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.024 0.064 -9999 0 -0.5 5 5
ITGB7 -0.018 0.14 -9999 0 -0.5 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.011 0.065 -9999 0 -0.49 7 7
p130Cas/Crk/Dock1 0.041 0.071 -9999 0 -10000 0 0
VCAM1 0.002 0.086 -9999 0 -0.52 10 10
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.029 -9999 0 -0.5 1 1
BCAR1 0.033 0.061 -9999 0 -0.46 5 5
EPOR 0.008 0.043 -9999 0 -0.31 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.04 -9999 0 -0.49 3 3
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 0.009 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.008 0.14 -9999 0 -0.57 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.04 -9999 0 -0.42 1 1
NFKBIA 0.024 0.038 -9999 0 -0.28 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.027 -9999 0 -0.55 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.038 0.2 -9999 0 -0.83 28 28
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.028 -9999 0 -0.55 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.027 -9999 0 -0.55 1 1
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
NF kappa B1 p50 dimer 0.02 0.031 -9999 0 -0.64 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.031 -9999 0 -0.64 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.039 -9999 0 -0.27 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.039 -9999 0 -0.4 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
PI3K -0.004 0.051 -9999 0 -0.64 3 3
NF kappa B1 p50/RelA 0.031 0.04 -9999 0 -0.27 6 6
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.03 0.036 -9999 0 -10000 0 0
cell death -0.004 0.029 -9999 0 -0.39 1 1
NF kappa B1 p105/c-Rel -0.008 0.14 -9999 0 -0.57 28 28
LCK -0.011 0.11 -9999 0 -0.44 25 25
BCL3 0.013 0.015 -9999 0 -0.31 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.044 0.007 -9999 0 -10000 0 0
KLHL20 -0.009 0.02 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.074 0.009 -9999 0 -10000 0 0
ENAH 0.044 0.007 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.076 -9999 0 -0.5 10 10
RAPGEF1 0.058 0.006 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.052 0.006 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.022 0.099 -9999 0 -0.64 10 10
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.045 0.007 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.017 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.08 0.072 -9999 0 -0.51 1 1
PI3K -0.002 0.022 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.17 0.16 -9999 0 -0.32 261 261
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.012 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.074 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.015 -9999 0 -10000 0 0
CDC42/GDP 0.074 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.027 0 -9999 0 -10000 0 0
ITGB7 -0.018 0.14 -9999 0 -0.5 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.073 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.032 -9999 0 -0.15 9 9
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.044 0.007 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.008 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.015 0.071 -9999 0 -0.47 10 10
CCND1 0.015 0.038 -9999 0 -0.18 9 9
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.013 0.067 -9999 0 -0.44 10 10
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.009 -9999 0 -10000 0 0
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
Rac1/GTP -0.017 0.032 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.053 0.1 -9999 0 -10000 0 0
CRKL 0.039 0.045 -9999 0 -0.54 1 1
mol:DAG 0.042 0.049 -9999 0 -0.38 1 1
HRAS 0.063 0.041 -9999 0 -0.43 1 1
MAPK8 0.022 0.084 -9999 0 -0.58 8 8
RAP1A 0.039 0.045 -9999 0 -0.54 1 1
GAB1 0.039 0.045 -9999 0 -0.54 1 1
MAPK14 0.032 0.028 -9999 0 -10000 0 0
EPO 0.007 0.03 -9999 0 -0.3 4 4
PLCG1 0.043 0.05 -9999 0 -0.39 1 1
EPOR/TRPC2/IP3 Receptors 0.01 0.044 -9999 0 -0.32 8 8
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.036 0.14 -9999 0 -0.58 26 26
GAB1/SHC/GRB2/SOS1 -0.005 0.025 -9999 0 -0.46 1 1
EPO/EPOR (dimer) 0.015 0.037 -9999 0 -0.28 1 1
IRS2 0.039 0.045 -9999 0 -0.54 1 1
STAT1 0.043 0.077 -9999 0 -0.38 1 1
STAT5B 0.044 0.065 -9999 0 -0.38 1 1
cell proliferation 0.03 0.079 -9999 0 -0.54 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.008 0.034 -9999 0 -0.44 2 2
TEC 0.039 0.045 -9999 0 -0.54 1 1
SOCS3 -0.035 0.19 -9999 0 -0.83 26 26
STAT1 (dimer) 0.043 0.076 -9999 0 -0.37 1 1
JAK2 0.013 0.04 -9999 0 -0.84 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.044 0.05 -9999 0 -0.57 1 1
EPO/EPOR 0.015 0.037 -9999 0 -0.28 1 1
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.047 0.044 -9999 0 -0.51 1 1
elevation of cytosolic calcium ion concentration 0.01 0.044 -9999 0 -0.32 8 8
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.029 0.032 -9999 0 -10000 0 0
mol:IP3 0.042 0.049 -9999 0 -0.38 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.009 0.032 -9999 0 -0.48 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.031 0.037 -9999 0 -0.51 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.07 -9999 0 -0.29 27 27
PTPN6 0.032 0.047 -9999 0 -0.56 1 1
TEC/VAV2/GRB2 0.052 0.042 -9999 0 -0.49 1 1
EPOR 0.01 0.044 -9999 0 -0.32 8 8
INPP5D -0.003 0.071 -9999 0 -0.31 23 23
mol:GDP -0.005 0.026 -9999 0 -0.47 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.052 0.042 -9999 0 -0.49 1 1
VAV2 0.039 0.045 -9999 0 -0.54 1 1
CBL 0.039 0.045 -9999 0 -0.54 1 1
SHC/Grb2/SOS1 -0.006 0.028 -9999 0 -0.49 1 1
STAT5A 0.044 0.065 -9999 0 -0.38 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.054 0.098 -9999 0 -0.42 1 1
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
BTK 0.023 0.087 -9999 0 -0.52 7 7
BCL2 0.003 0.28 -9999 0 -0.98 34 34
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.009 0.018 -9999 0 -10000 0 0
BUB1B 0.017 0.028 -9999 0 -10000 0 0
PLK1 0.017 0.012 -9999 0 -10000 0 0
PLK1S1 0.015 0.008 -9999 0 -10000 0 0
KIF2A 0.023 0.03 -9999 0 -0.6 1 1
regulation of mitotic centrosome separation 0.017 0.012 -9999 0 -10000 0 0
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.003 0.077 -9999 0 -0.28 16 16
WEE1 0.023 0.011 -9999 0 -10000 0 0
cytokinesis 0.002 0.069 -9999 0 -0.3 4 4
PP2A-alpha B56 -0.017 0.051 -9999 0 -0.73 2 2
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.018 -9999 0 -10000 0 0
CENPE 0.02 0.044 -9999 0 -0.55 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.03 -9999 0 -0.59 1 1
PPP2CA 0.013 0 -9999 0 -10000 0 0
FZR1 0.013 0 -9999 0 -10000 0 0
TPX2 0.009 0.022 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.009 0.082 -9999 0 -0.31 31 31
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.031 -9999 0 -0.34 1 1
GORASP1 0.013 0 -9999 0 -10000 0 0
metaphase 0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.009 0.008 -9999 0 -0.066 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.013 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -9999 0 -10000 0 0
spindle elongation 0.017 0.012 -9999 0 -10000 0 0
ODF2 0.013 0.001 -9999 0 -10000 0 0
BUB1 -0.025 0.06 -9999 0 -0.8 2 2
TPT1 0.015 0.008 -9999 0 -10000 0 0
CDC25C 0.011 0.023 -9999 0 -10000 0 0
CDC25B 0.012 0.021 -9999 0 -0.31 2 2
SGOL1 0.009 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.006 0.012 -9999 0 -10000 0 0
CDC14B 0.005 0.069 -9999 0 -0.66 5 5
CDC20 0.008 0.04 -9999 0 -0.31 7 7
PLK1/PBIP1 0.002 0.024 -9999 0 -10000 0 0
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.022 -9999 0 -0.4 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.035 0.12 -9999 0 -0.31 68 68
metaphase plate congression 0.015 0.007 -9999 0 -10000 0 0
ERCC6L 0.007 0.015 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.013 0.009 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -0.011 3 3
PPP1R12A 0.013 0 -9999 0 -10000 0 0
interphase 0 0.001 -9999 0 -0.011 3 3
PLK1/PRC1-2 0.004 0.061 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.005 -9999 0 -10000 0 0
RAB1A 0.013 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.018 0.041 -9999 0 -0.48 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.035 -9999 0 -0.31 3 3
microtubule-based process -0.005 0.064 -9999 0 -10000 0 0
Golgi organization 0.017 0.012 -9999 0 -10000 0 0
Cohesin/SA2 -0.001 0.005 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.042 0.12 -9999 0 -0.31 78 78
APC/C/CDC20 0.021 0.025 -9999 0 -10000 0 0
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.002 0.023 -9999 0 -10000 0 0
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.022 0.04 -9999 0 -0.56 2 2
C13orf34 0.018 0.041 -9999 0 -0.48 3 3
NUDC 0.016 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.028 -9999 0 -10000 0 0
spindle assembly 0.017 0.011 -9999 0 -10000 0 0
spindle stabilization 0.015 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.013 0.06 -9999 0 -0.56 5 5
MKLP2/PLK1 -0.005 0.064 -9999 0 -10000 0 0
CCNB1 0.014 0.001 -9999 0 -10000 0 0
PPP1CB 0.013 0 -9999 0 -10000 0 0
BTRC 0.013 0 -9999 0 -10000 0 0
ROCK2 0.002 0.11 -9999 0 -0.52 19 19
TUBG1 0.015 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.008 -9999 0 -10000 0 0
MLF1IP 0.007 0.035 -9999 0 -0.22 11 11
INCENP 0.011 0.039 -9999 0 -0.83 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.001 0.023 -10000 0 -10000 0 0
oxygen homeostasis 0.016 0.011 -10000 0 -10000 0 0
TCEB2 0.011 0.026 -10000 0 -0.31 3 3
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.012 0.076 -10000 0 -0.7 4 4
EPO 0.18 0.14 -10000 0 -0.8 2 2
FIH (dimer) 0.029 0.011 -10000 0 -10000 0 0
APEX1 0.027 0.011 -10000 0 -10000 0 0
SERPINE1 0.18 0.17 -10000 0 -0.81 3 3
FLT1 -0.002 0.074 -10000 0 -1.6 1 1
ADORA2A 0.19 0.14 -10000 0 -0.86 2 2
germ cell development 0.19 0.14 -10000 0 -0.85 2 2
SLC11A2 0.19 0.15 -10000 0 -0.9 2 2
BHLHE40 0.18 0.16 -10000 0 -0.9 2 2
HIF1AN 0.029 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.003 0.078 -10000 0 -0.97 2 2
ETS1 0.03 0.002 -10000 0 -10000 0 0
CITED2 -0.09 0.32 -10000 0 -1.2 35 35
KDR -0.007 0.11 -10000 0 -1.4 3 3
PGK1 0.19 0.15 -10000 0 -0.9 2 2
SIRT1 0.012 0.039 -10000 0 -0.83 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.2 0.17 -10000 0 -1.2 2 2
EPAS1 0.11 0.11 -10000 0 -0.56 4 4
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.19 0.16 -10000 0 -0.88 4 4
EFNA1 0.19 0.15 -10000 0 -0.9 2 2
FXN 0.19 0.14 -10000 0 -0.86 2 2
POU5F1 0.19 0.15 -10000 0 -0.9 2 2
neuron apoptosis -0.2 0.16 1.1 2 -10000 0 2
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.003 0.14 -10000 0 -0.5 28 28
EGLN2 0.029 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.057 -10000 0 -0.83 2 2
VHL/Elongin B/Elongin C -0.005 0.05 -10000 0 -0.6 3 3
VHL 0.008 0.068 -10000 0 -0.83 3 3
ARNT 0.027 0.011 -10000 0 -10000 0 0
SLC2A1 0.19 0.14 -10000 0 -0.86 2 2
TWIST1 0.18 0.18 -10000 0 -0.66 10 10
ELK1 0.015 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.001 0.067 -10000 0 -0.77 2 2
VEGFA 0.19 0.16 -10000 0 -0.85 4 4
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.023 0.13 -9999 0 -0.7 15 15
AKT1 0.085 0.087 -9999 0 -0.7 4 4
PTK2B 0.035 0.14 -9999 0 -0.94 5 5
VEGFR2 homodimer/Frs2 0.032 0.09 -9999 0 -1.1 3 3
CAV1 -0.009 0.13 -9999 0 -0.83 12 12
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.009 0.1 -9999 0 -0.87 5 5
endothelial cell proliferation 0.077 0.098 -9999 0 -0.7 3 3
mol:Ca2+ 0.051 0.1 -9999 0 -1 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.009 0.096 -9999 0 -0.83 5 5
RP11-342D11.1 0.042 0.099 -9999 0 -0.73 6 6
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.065 -9999 0 -0.59 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.068 -9999 0 -0.83 3 3
HRAS/GDP -0.008 0.08 -9999 0 -0.77 4 4
SH2D2A -0.033 0.18 -9999 0 -0.83 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.007 0.066 -9999 0 -0.73 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.035 0.14 -9999 0 -0.56 26 26
VEGFR1 homodimer 0.011 0.039 -9999 0 -0.83 1 1
SHC/GRB2/SOS1 -0.009 0.093 -9999 0 -1 3 3
GRB10 0.052 0.1 -9999 0 -1 3 3
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.009 0.092 -9999 0 -1 3 3
HRAS 0.012 0.022 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.08 -9999 0 -0.52 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.009 0.092 -9999 0 -0.8 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.004 0.087 -9999 0 -0.83 5 5
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.1 -9999 0 -0.87 5 5
mol:GDP -0.009 0.085 -9999 0 -0.93 3 3
mol:NADP 0.077 0.064 -9999 0 -0.58 3 3
eNOS/Hsp90 0.08 0.06 -9999 0 -0.54 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.051 0.1 -9999 0 -1.1 3 3
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.01 0.068 -9999 0 -0.82 3 3
VEGFC 0.012 0.039 -9999 0 -0.83 1 1
FAK1/Vinculin 0.058 0.11 -9999 0 -0.77 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.026 0.14 -9999 0 -1 5 5
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.02 0.063 -9999 0 -0.66 3 3
mol:L-citrulline 0.077 0.064 -9999 0 -0.58 3 3
ITGAV 0.01 0.055 -9999 0 -0.83 2 2
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.009 0.096 -9999 0 -0.83 5 5
VEGFR2 homodimer/VEGFA homodimer -0.011 0.12 -9999 0 -0.86 6 6
VEGFR2/3 heterodimer 0.026 0.12 -9999 0 -0.95 6 6
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.053 0.11 -9999 0 -0.78 6 6
VEGFR2 homodimer 0.031 0.099 -9999 0 -1.2 3 3
FLT1 0.012 0.039 -9999 0 -0.83 1 1
NEDD4 0.012 0.055 -9999 0 -0.82 2 2
MAPK3 0.044 0.1 -9999 0 -0.97 3 3
MAPK1 0.044 0.1 -9999 0 -0.97 3 3
VEGFA145/NRP2 -0.021 0.074 -9999 0 -0.63 3 3
VEGFR1/2 heterodimer 0.031 0.1 -9999 0 -1.2 3 3
KDR 0.031 0.099 -9999 0 -1.2 3 3
VEGFA165/NRP1/VEGFR2 homodimer -0.017 0.11 -9999 0 -1.2 3 3
SRC 0.013 0.015 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.047 0.1 -9999 0 -1 3 3
PI3K -0.011 0.091 -9999 0 -0.96 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.1 -9999 0 -0.87 5 5
FES 0.051 0.11 -9999 0 -0.78 6 6
GAB1 -0.009 0.09 -9999 0 -1 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.01 0.1 -9999 0 -0.87 5 5
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.07 0.091 -9999 0 -0.63 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.1 -9999 0 -0.87 5 5
PI3K/GAB1 0.087 0.081 -9999 0 -0.72 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.009 0.092 -9999 0 -1 3 3
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.013 0.12 -9999 0 -0.83 7 7
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.051 0.11 -9999 0 -1.1 3 3
actin cytoskeleton reorganization -0.034 0.14 -9999 0 -0.56 26 26
PTK2 0.053 0.12 -9999 0 -0.76 7 7
EDG1 0.042 0.099 -9999 0 -0.73 6 6
mol:DAG 0.051 0.1 -9999 0 -1.1 3 3
CaM/Ca2+ -0.009 0.086 -9999 0 -0.94 3 3
MAP2K3 0.051 0.12 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.011 0.11 -9999 0 -1.2 3 3
PLCG1 0.051 0.11 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.009 0.096 -9999 0 -1.1 3 3
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.01 0.11 -9999 0 -0.94 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.1 -9999 0 -0.87 5 5
cell migration 0.083 0.096 -9999 0 -0.72 3 3
mol:PI-3-4-5-P3 -0.01 0.079 -9999 0 -0.82 3 3
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.009 0.087 -9999 0 -0.95 3 3
mol:NO 0.077 0.064 -9999 0 -0.58 3 3
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.079 -9999 0 -0.76 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.05 0.11 -9999 0 -1.2 3 3
VHL 0.008 0.068 -9999 0 -0.83 3 3
ITGB3 -0.014 0.15 -9999 0 -0.83 15 15
NOS3 0.079 0.073 -9999 0 -0.69 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.013 0.11 -9999 0 -0.73 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.035 0.15 -9999 0 -1.2 3 3
PRKCB 0.041 0.11 -9999 0 -0.94 3 3
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.041 0.11 -9999 0 -0.78 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.01 0.11 -9999 0 -0.94 5 5
VEGFA165/NRP2 -0.021 0.074 -9999 0 -0.63 3 3
MAPKKK cascade -0.008 0.078 -9999 0 -0.85 3 3
NRP2 -0.014 0.09 -9999 0 -0.31 38 38
VEGFC homodimer 0.011 0.039 -9999 0 -0.83 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.058 0.11 -9999 0 -0.77 5 5
MAP3K13 0.043 0.13 -9999 0 -1.2 3 3
PDPK1 0.077 0.089 -9999 0 -0.74 4 4
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.001 0.041 -9999 0 -0.74 1 1
PDGFB-D/PDGFRB/SLAP -0.002 0.031 -9999 0 -0.64 1 1
PDGFB-D/PDGFRB/APS/CBL -0.002 0.027 -9999 0 -0.55 1 1
AKT1 0.059 0.045 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.052 -9999 0 -0.79 1 1
PIK3CA 0.008 0.068 -9999 0 -0.83 3 3
FGR 0.002 0.029 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.049 -9999 0 -0.83 1 1
MYC 0.02 0.15 -9999 0 -0.84 12 12
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.029 -9999 0 -0.46 1 1
LRP1/PDGFRB/PDGFB -0.002 0.036 -9999 0 -0.55 2 2
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.039 -9999 0 -0.83 1 1
GO:0007205 0.02 0.05 -9999 0 -0.85 1 1
PTEN 0.012 0.039 -9999 0 -0.83 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.041 0.12 -9999 0 -0.31 77 77
PDGFB-D/PDGFRB/SHP2 -0.003 0.042 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/GRB10 -0.001 0.03 -9999 0 -0.64 1 1
cell cycle arrest -0.002 0.031 -9999 0 -0.64 1 1
HRAS 0.012 0.022 -9999 0 -0.31 2 2
HIF1A 0.064 0.041 -9999 0 -10000 0 0
GAB1 0.013 0.064 -9999 0 -0.87 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.06 -9999 0 -0.79 1 1
PDGFB-D/PDGFRB 0.012 0.032 -9999 0 -0.57 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.03 -9999 0 -0.64 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.048 -9999 0 -0.75 1 1
positive regulation of MAPKKK cascade -0.003 0.042 -9999 0 -0.64 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.051 -9999 0 -0.86 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.035 0.084 -9999 0 -0.8 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 136 136
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.03 -9999 0 -0.64 1 1
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.017 0.071 -9999 0 -0.87 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.001 0.03 -9999 0 -0.64 1 1
LCK -0.009 0.09 -9999 0 -0.74 6 6
PDGFRB 0.012 0.04 -9999 0 -0.84 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.036 -9999 0 -0.55 1 1
ABL1 0.009 0.062 -9999 0 -0.84 1 1
PDGFB-D/PDGFRB/CBL 0.009 0.068 -9999 0 -0.95 1 1
PTPN1 0.014 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.006 0.05 -9999 0 -0.31 11 11
cell proliferation 0.022 0.13 -9999 0 -0.73 12 12
SLA 0.013 0.015 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.052 0.025 -9999 0 -10000 0 0
SRC 0.005 0.029 -9999 0 -0.56 1 1
PI3K -0.005 0.042 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.027 0.066 -9999 0 -0.7 1 1
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.024 0.054 -9999 0 -0.83 1 1
LYN 0.006 0.029 -9999 0 -0.56 1 1
LRP1 0.012 0.039 -9999 0 -0.83 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.022 -9999 0 -0.45 1 1
SPHK1 0.006 0.05 -9999 0 -0.31 11 11
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.051 -9999 0 -0.86 1 1
PLCG1 0.02 0.052 -9999 0 -0.9 1 1
NHERF/PDGFRB -0.002 0.028 -9999 0 -0.55 1 1
YES1 0.004 0.028 -9999 0 -0.56 1 1
cell migration -0.002 0.027 -9999 0 -0.55 1 1
SHC/Grb2/SOS1 0 0.022 -9999 0 -0.45 1 1
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.022 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.003 0.034 -9999 0 -0.5 2 2
FYN 0.006 0.029 -9999 0 -0.56 1 1
DOK1 0.034 0.026 -9999 0 -0.51 1 1
HRAS/GTP -0.001 0.014 -9999 0 -10000 0 0
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.028 0.087 -9999 0 -0.44 12 12
PRKCD 0.034 0.026 -9999 0 -0.51 1 1
FER 0.031 0.051 -9999 0 -0.51 4 4
MAPKKK cascade -0.001 0.021 -9999 0 -0.44 1 1
RASA1 0.034 0.026 -9999 0 -0.51 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.017 0.03 -9999 0 -0.46 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.03 -9999 0 -0.64 1 1
chemotaxis 0.009 0.06 -9999 0 -0.8 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.024 -9999 0 -0.43 1 1
Bovine Papilomavirus E5/PDGFRB 0.001 0.031 -9999 0 -0.65 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.003 0.032 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.026 -9999 0 -0.56 1 1
ATM 0.012 0.039 -9999 0 -0.83 1 1
MAP2K3 0.027 0.057 -9999 0 -0.53 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.026 0.076 -9999 0 -0.41 6 6
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0 0.099 -9999 0 -0.66 9 9
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.016 0.15 -9999 0 -0.83 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.03 -9999 0 -0.64 1 1
TAK1/TAB family -0.001 0.014 -9999 0 -0.22 2 2
RAC1/OSM/MEKK3 0 0.007 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.033 -9999 0 -0.39 2 2
TRAF6 0.007 0.031 -9999 0 -0.46 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.004 0.087 -9999 0 -0.83 5 5
CCM2 0.013 0.015 -9999 0 -0.31 1 1
CaM/Ca2+/CAMKIIB -0.006 0.058 -9999 0 -0.56 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.007 0.066 -9999 0 -0.6 5 5
OSM/MEKK3 0 0.009 -9999 0 -10000 0 0
TAOK1 -0.037 0.16 -9999 0 -0.46 53 53
TAOK2 0.017 0.022 -9999 0 -0.45 1 1
TAOK3 0.017 0.022 -9999 0 -0.45 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.039 -9999 0 -0.83 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.027 -9999 0 -0.55 1 1
GADD45/MTK1/MTK1 -0.023 0.11 -9999 0 -0.5 21 21
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.045 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.021 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.02 -9999 0 -0.43 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.036 0.15 -9999 0 -0.64 26 26
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.034 0.19 -9999 0 -0.83 26 26
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.039 -9999 0 -0.83 1 1
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.023 -9999 0 -0.5 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.026 -9999 0 -0.55 1 1
HDAC9 -0.017 0.095 -9999 0 -0.31 43 43
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
HDAC4/RFXANK -0.001 0.013 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.03 -9999 0 -0.64 1 1
Histones 0.036 0.023 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -9999 0 -10000 0 0
CAMK4 -0.004 0.1 -9999 0 -0.52 15 15
Tubulin/HDAC6 -0.005 0.051 -9999 0 -0.55 4 4
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.009 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.006 0.059 -9999 0 -0.64 4 4
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.03 -9999 0 -0.64 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.066 -9999 0 -0.55 6 6
HDAC4/ER alpha -0.046 0.15 -9999 0 -0.64 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.036 0.023 -9999 0 -10000 0 0
cell motility -0.005 0.051 -9999 0 -0.55 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.012 0.039 -9999 0 -0.83 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.052 0.2 -9999 0 -0.54 54 54
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0.039 -9999 0 -0.83 1 1
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.022 -9999 0 -0.47 1 1
GNG2 0.012 0.039 -9999 0 -0.83 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.006 0.078 -9999 0 -0.83 4 4
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.022 -9999 0 -0.31 2 2
nuclear import 0 0 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.028 0.007 -9999 0 -10000 0 0
BIRC5 -0.018 0.1 -9999 0 -0.33 42 42
NFKBIA 0.032 0.008 -9999 0 -10000 0 0
CPEB1 -0.052 0.23 -9999 0 -0.83 36 36
AKT1 0.032 0.008 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.011 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.014 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.013 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.028 0.007 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.012 0.039 -9999 0 -0.83 1 1
TPX2 0.001 0.069 -9999 0 -10000 0 0
TP53 0.032 0.006 -9999 0 -10000 0 0
DLG7 0.021 0.008 -9999 0 -10000 0 0
AURKAIP1 0.012 0.022 -9999 0 -0.31 2 2
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.011 -9999 0 -10000 0 0
AURKA 0.026 0.011 -9999 0 -10000 0 0
AURKB -0.014 0.027 -9999 0 -0.14 3 3
CDC25B 0.007 0.018 -9999 0 -10000 0 0
G2/M transition checkpoint 0.002 0.026 -9999 0 -0.5 1 1
mRNA polyadenylation -0.037 0.14 -9999 0 -0.5 36 36
Aurora A/CPEB -0.037 0.14 -9999 0 -0.51 36 36
Aurora A/TACC1/TRAP/chTOG 0.003 0.026 -9999 0 -0.47 1 1
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.028 0.007 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.011 -9999 0 -10000 0 0
spindle assembly 0.002 0.025 -9999 0 -0.46 1 1
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.011 0.037 -9999 0 -0.45 1 1
CENPA -0.009 0.026 -9999 0 -0.26 3 3
Aurora A/PP2A 0.028 0.007 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.008 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.006 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.002 0.026 -9999 0 -0.51 1 1
mitotic prometaphase 0.006 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.011 -9999 0 -10000 0 0
TACC1 0.012 0.039 -9999 0 -0.83 1 1
TACC3 0.013 0.015 -9999 0 -0.31 1 1
Aurora A/Antizyme1 0.003 0.016 -9999 0 -10000 0 0
Aurora A/RasGAP 0.028 0.007 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.005 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.001 0.068 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.019 0.05 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.032 0.009 -9999 0 -10000 0 0
MAPK12 0.021 0.073 -9999 0 -0.48 9 9
CCND1 0.018 0.032 -9999 0 -0.26 1 1
p38 gamma/SNTA1 0.027 0.068 -9999 0 -0.46 8 8
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.021 0.072 -9999 0 -0.48 9 9
MAP2K6 0.015 0.077 -9999 0 -0.53 9 9
MAPT 0.025 0.045 -9999 0 -0.4 3 3
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.022 -9999 0 -0.45 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.005 -10000 0 -10000 0 0
DOCK1 0.006 0.078 -10000 0 -0.83 4 4
ITGA4 0.005 0.06 -10000 0 -0.36 10 10
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.027 0.11 -10000 0 -0.62 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.004 0.033 -10000 0 -0.55 1 1
alpha4/beta7 Integrin/Paxillin -0.02 0.082 -10000 0 -0.5 11 11
lamellipodium assembly -0.005 0.059 -10000 0 -0.65 3 3
PIK3CA 0.008 0.068 -10000 0 -0.83 3 3
PI3K -0.004 0.051 -10000 0 -0.64 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.024 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP -0.003 0.024 -10000 0 -0.42 1 1
cell adhesion -0.003 0.026 -10000 0 -0.46 1 1
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.004 0.029 -10000 0 -0.5 1 1
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.018 0.14 -10000 0 -0.5 28 28
ARF6/GDP 0.001 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.009 0.054 -10000 0 -0.47 5 5
p130Cas/Crk/Dock1 -0.005 0.051 -10000 0 -0.55 4 4
VCAM1 0.002 0.086 -10000 0 -0.52 10 10
alpha4/beta1 Integrin/Paxillin/Talin -0.003 0.027 -10000 0 -0.47 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 -0.003 0.027 -10000 0 -0.47 1 1
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.026 0.46 1 -10000 0 1
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.003 0.027 -10000 0 -0.47 1 1
Rac1/GTP -0.006 0.069 -10000 0 -0.77 3 3
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.051 0.04 -10000 0 -0.44 3 3
adherens junction organization 0.042 0.036 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.053 0.059 -10000 0 -0.75 1 1
FMN1 0.023 0.1 -10000 0 -0.44 22 22
mol:IP3 -0.003 0.033 -10000 0 -0.41 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.049 0.037 -10000 0 -0.4 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.037 -10000 0 -0.49 2 2
VASP 0.047 0.012 -10000 0 -10000 0 0
ZYX 0.047 0.012 -10000 0 -10000 0 0
JUB 0.046 0.025 -10000 0 -0.44 1 1
EGFR(dimer) 0.041 0.049 -10000 0 -0.47 4 4
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.035 -10000 0 -0.43 3 3
PIK3CA 0.009 0.068 -10000 0 -0.83 3 3
PI3K -0.003 0.035 -10000 0 -0.44 3 3
FYN 0.05 0.036 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.032 -10000 0 -0.4 3 3
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.003 0.033 -10000 0 -0.41 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.053 0.059 -10000 0 -0.75 1 1
establishment of polarity of embryonic epithelium 0.046 0.012 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.006 0.078 -10000 0 -0.83 4 4
CASR 0.042 0.039 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.029 -10000 0 -0.36 3 3
AKT2 0.049 0.037 -10000 0 -0.4 3 3
actin cable formation 0.031 0.1 -10000 0 -0.42 22 22
apoptosis 0.003 0.033 0.42 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.047 0.063 -10000 0 -0.48 6 6
PIP5K1A 0.045 0.038 -10000 0 -0.51 2 2
PLCG1 -0.003 0.034 -10000 0 -0.42 3 3
Rac1/GTP -0.004 0.04 -10000 0 -0.43 4 4
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.016 0.15 -9999 0 -0.74 18 18
CDC42/GTP -0.011 0.054 -9999 0 -0.32 1 1
PLCG1 0.031 0.065 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.011 0.054 -9999 0 -0.32 1 1
S1PR5 0.007 0.054 -9999 0 -0.39 7 7
S1PR4 0.01 0.034 -9999 0 -0.31 5 5
MAPK3 0.031 0.065 -9999 0 -0.33 1 1
MAPK1 0.031 0.065 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.071 -9999 0 -0.33 17 17
GNAI1 0.012 0.039 -9999 0 -0.83 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.032 -9999 0 -0.56 1 1
RHOA 0.032 0.016 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.023 0.069 -9999 0 -0.33 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.002 0.014 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.01 0.034 -9999 0 -0.31 5 5
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.023 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.022 0.16 -10000 0 -0.73 22 22
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.011 0.071 -10000 0 -0.56 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.017 0.038 -10000 0 -0.56 2 2
INS 0.013 0 -10000 0 -10000 0 0
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.024 -10000 0 -0.51 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.027 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.026 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.012 0.067 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.017 0.08 -10000 0 -0.41 18 18
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.001 0.023 0.5 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.028 0.077 -10000 0 -0.44 12 12
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.012 0.039 -10000 0 -0.83 1 1
Dynamin 2/GDP 0.027 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.067 -10000 0 -0.44 9 9
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.082 0.11 -9999 0 -9999 0 0
TP53 -0.028 0.033 -9999 0 -9999 0 0
Senescence -0.028 0.033 -9999 0 -9999 0 0
Apoptosis -0.028 0.033 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.052 0.062 -9999 0 -9999 0 0
MDM4 0.013 0 -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 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 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 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -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 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.015 -9999 0 -0.21 2 2
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.004 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.003 0.058 -9999 0 -0.31 15 15
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.028 -9999 0 -0.43 2 2
ARF1/GTP -0.001 0.017 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.002 0.028 -9999 0 -0.42 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 -0.002 0.028 -9999 0 -0.43 2 2
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.003 -9999 0 -10000 0 0
ARFIP2 0 0.005 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.008 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.01 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin -0.001 0.01 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.004 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -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 0.035 0.014 -9999 0 -10000 0 0
PLD2 -0.002 0.028 -9999 0 -0.43 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.028 -9999 0 -0.43 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.016 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.028 -9999 0 -0.42 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 -0.001 0.011 -9999 0 -10000 0 0
USO1 -0.001 0.011 -9999 0 -10000 0 0
GBF1 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.028 -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 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.039 -9999 0 -0.83 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.03 -9999 0 -0.64 1 1
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 461 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU TCGA.L6.A4ET
109_MAP3K5 -0.017 -0.017 -0.017 -0.21
47_PPARGC1A -0.83 -0.83 0.013 -0.83
105_BMP4 -0.31 0.013 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.5 -0.5 -0.5 -0.51
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B -0.097 0 -0.098 -0.17
84_STAT5A -0.097 0 -0.098 -0.17
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/3033031/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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