PARADIGM pathway analysis of mRNASeq expression data
Skin Cutaneous Melanoma (Metastatic)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1M044HJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1M044HJ
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 60 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
BCR signaling pathway 138
IL4-mediated signaling events 135
TCR signaling in naïve CD8+ T cells 104
IL23-mediated signaling events 102
Nephrin/Neph1 signaling in the kidney podocyte 91
IL12-mediated signaling events 80
Caspase cascade in apoptosis 74
FAS signaling pathway (CD95) 66
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 62
E-cadherin signaling events 62
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 367 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 367 ).

Pathway.Name Significance.Ratio 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
BCR signaling pathway 0.3760 138 13731 99 -0.76 0.026 1000 -1000 -0.056 -1000
IL4-mediated signaling events 0.3678 135 12285 91 -1.3 1 1000 -1000 -0.12 -1000
TCR signaling in naïve CD8+ T cells 0.2834 104 9697 93 -0.59 0.028 1000 -1000 -0.042 -1000
IL23-mediated signaling events 0.2779 102 6145 60 -0.74 0.019 1000 -1000 -0.064 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.2480 91 3110 34 -0.21 0.019 1000 -1000 -0.01 -1000
IL12-mediated signaling events 0.2180 80 7038 87 -0.68 0.11 1000 -1000 -0.087 -1000
Caspase cascade in apoptosis 0.2016 74 5507 74 -0.21 0.14 1000 -1000 -0.015 -1000
FAS signaling pathway (CD95) 0.1798 66 3130 47 -0.16 0.12 1000 -1000 -0.032 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1689 62 4273 68 -0.62 0.12 1000 -1000 -0.043 -1000
E-cadherin signaling events 0.1689 62 314 5 -0.13 0.019 1000 -1000 -0.005 -1000
Calcium signaling in the CD4+ TCR pathway 0.1580 58 1807 31 -0.43 0.019 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.1526 56 956 17 -0.17 0.037 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 0.1499 55 941 17 -0.2 0.019 1000 -1000 -0.021 -1000
S1P4 pathway 0.1444 53 1329 25 -0.16 0.028 1000 -1000 -0.011 -1000
IL27-mediated signaling events 0.1417 52 2665 51 -0.26 0.17 1000 -1000 -0.047 -1000
Signaling events regulated by Ret tyrosine kinase 0.1335 49 4057 82 -0.13 0.019 1000 -1000 -0.053 -1000
Glypican 1 network 0.1308 48 2317 48 -0.3 0.069 1000 -1000 -0.017 -1000
Wnt signaling 0.1308 48 342 7 -0.082 0.007 1000 -1000 -0.008 -1000
Glucocorticoid receptor regulatory network 0.1253 46 5259 114 -0.52 0.31 1000 -1000 -0.045 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.1226 45 3395 74 -0.13 0.05 1000 -1000 -0.047 -1000
a4b1 and a4b7 Integrin signaling 0.1199 44 222 5 -0.076 -0.019 1000 -1000 -0.002 -1000
amb2 Integrin signaling 0.1199 44 3630 82 -0.27 0.026 1000 -1000 -0.031 -1000
Endothelins 0.1172 43 4160 96 -0.18 0.02 1000 -1000 -0.049 -1000
E-cadherin signaling in the nascent adherens junction 0.1144 42 3224 76 -0.13 0.028 1000 -1000 -0.051 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.1117 41 1846 45 -0.28 0.046 1000 -1000 -0.052 -1000
TCGA08_retinoblastoma 0.1117 41 333 8 -0.11 0.03 1000 -1000 -0.004 -1000
Thromboxane A2 receptor signaling 0.1090 40 4262 105 -0.12 0.041 1000 -1000 -0.038 -1000
Syndecan-4-mediated signaling events 0.1090 40 2692 67 -0.26 0.025 1000 -1000 -0.018 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1090 40 3539 88 -0.22 0.03 1000 -1000 -0.054 -1000
Syndecan-1-mediated signaling events 0.1063 39 1331 34 -0.15 0.019 1000 -1000 -0.016 -1000
LPA receptor mediated events 0.1063 39 3994 102 -0.13 0.025 1000 -1000 -0.053 -1000
IL2 signaling events mediated by PI3K 0.1035 38 2221 58 -0.19 0.046 1000 -1000 -0.024 -1000
IL2 signaling events mediated by STAT5 0.1035 38 844 22 -0.2 0.02 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.1008 37 1390 37 -0.29 0.041 1000 -1000 -0.015 -1000
Regulation of p38-alpha and p38-beta 0.0981 36 1976 54 -0.34 0.049 1000 -1000 -0.038 -1000
Class I PI3K signaling events 0.0926 34 2552 73 -0.45 0.048 1000 -1000 -0.024 -1000
Fc-epsilon receptor I signaling in mast cells 0.0872 32 3163 97 -0.14 0.033 1000 -1000 -0.05 -1000
HIF-1-alpha transcription factor network 0.0845 31 2392 76 -0.11 0.084 1000 -1000 -0.056 -1000
Ephrin A reverse signaling 0.0817 30 213 7 -0.071 0.008 1000 -1000 -0.004 -1000
Visual signal transduction: Cones 0.0763 28 1088 38 -0.21 0.017 1000 -1000 -0.007 -1000
TRAIL signaling pathway 0.0763 28 1377 48 -0.057 0.022 1000 -1000 -0.023 -1000
Visual signal transduction: Rods 0.0763 28 1468 52 -0.21 0.019 1000 -1000 -0.043 -1000
TCGA08_p53 0.0736 27 190 7 -0.072 0.051 1000 -1000 -0.003 -1000
ceramide signaling pathway 0.0708 26 1317 49 -0.18 0.028 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 0.0708 26 810 31 -0.2 0.033 1000 -1000 -0.014 -1000
FOXA2 and FOXA3 transcription factor networks 0.0681 25 1158 46 -0.5 0.027 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 0.0654 24 628 26 -0.082 0.019 1000 -1000 -0.021 -1000
BMP receptor signaling 0.0654 24 1984 81 -0.23 0.059 1000 -1000 -0.057 -1000
IFN-gamma pathway 0.0654 24 1654 68 -0.18 0.028 1000 -1000 -0.055 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0654 24 1290 52 -0.19 0.031 1000 -1000 -0.025 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0627 23 663 28 -0.16 0.049 1000 -1000 -0.014 -1000
Aurora C signaling 0.0599 22 156 7 -0.098 0.017 1000 -1000 -0.008 -1000
Signaling events mediated by PTP1B 0.0545 20 1575 76 -0.34 0.032 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 0.0545 20 734 36 -0.077 0.059 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.0545 20 1700 84 -0.2 0.043 1000 -1000 -0.05 -1000
Osteopontin-mediated events 0.0518 19 735 38 -0.049 0.035 1000 -1000 -0.025 -1000
Syndecan-2-mediated signaling events 0.0518 19 1374 69 -0.26 0.046 1000 -1000 -0.005 -1000
Arf6 signaling events 0.0518 19 1218 62 -0.18 0.045 1000 -1000 -0.017 -1000
p75(NTR)-mediated signaling 0.0518 19 2420 125 -0.18 0.054 1000 -1000 -0.052 -1000
IL6-mediated signaling events 0.0518 19 1458 75 -0.19 0.068 1000 -1000 -0.034 -1000
Effects of Botulinum toxin 0.0463 17 448 26 -0.066 0.025 1000 -1000 -0.012 -1000
EGFR-dependent Endothelin signaling events 0.0463 17 362 21 -0.031 0.028 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0463 17 1360 78 -0.15 0.055 1000 -1000 -0.042 -1000
Signaling events mediated by the Hedgehog family 0.0436 16 839 52 -0.28 0.043 1000 -1000 -0.013 -1000
Cellular roles of Anthrax toxin 0.0436 16 629 39 -0.15 0.019 1000 -1000 -0.01 -1000
Nectin adhesion pathway 0.0409 15 954 63 -0.24 0.046 1000 -1000 -0.047 -1000
Ceramide signaling pathway 0.0409 15 1195 76 -0.18 0.042 1000 -1000 -0.015 -1000
EPHB forward signaling 0.0409 15 1301 85 -0.059 0.041 1000 -1000 -0.055 -1000
S1P5 pathway 0.0381 14 253 17 -0.093 0.019 1000 -1000 -0.005 -1000
Plasma membrane estrogen receptor signaling 0.0381 14 1286 86 -0.093 0.048 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0354 13 1112 85 -0.075 0.042 1000 -1000 -0.043 -1000
Ephrin B reverse signaling 0.0354 13 647 48 -0.12 0.021 1000 -1000 -0.032 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0354 13 1114 83 -0.16 0.084 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 0.0354 13 684 52 -0.093 0.037 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0354 13 1603 120 -0.12 0.078 1000 -1000 -0.044 -1000
E-cadherin signaling in keratinocytes 0.0354 13 572 43 -0.13 0.022 1000 -1000 -0.022 -1000
LPA4-mediated signaling events 0.0327 12 154 12 -0.056 0.02 1000 -1000 -0.01 -1000
EPO signaling pathway 0.0327 12 707 55 -0.079 0.029 1000 -1000 -0.052 -1000
Reelin signaling pathway 0.0327 12 705 56 -0.11 0.052 1000 -1000 -0.045 -1000
IL1-mediated signaling events 0.0327 12 755 62 -0.069 0.07 1000 -1000 -0.05 -1000
Coregulation of Androgen receptor activity 0.0300 11 849 76 -0.11 0.038 1000 -1000 -0.019 -1000
Syndecan-3-mediated signaling events 0.0300 11 412 35 -0.055 0.054 1000 -1000 -0.025 -1000
Glypican 2 network 0.0300 11 47 4 0.004 0.01 1000 -1000 -0.005 -1000
S1P3 pathway 0.0300 11 495 42 -0.091 0.037 1000 -1000 -0.013 -1000
ErbB4 signaling events 0.0272 10 702 69 -0.12 0.053 1000 -1000 -0.052 -1000
Presenilin action in Notch and Wnt signaling 0.0272 10 619 61 -0.11 0.055 1000 -1000 -0.024 -1000
S1P1 pathway 0.0272 10 392 36 -0.094 0.021 1000 -1000 -0.034 -1000
Canonical Wnt signaling pathway 0.0272 10 540 51 -0.078 0.071 1000 -1000 -0.027 -1000
ErbB2/ErbB3 signaling events 0.0245 9 630 65 -0.024 0.042 1000 -1000 -0.041 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0245 9 495 54 -0.13 0.033 1000 -1000 -0.057 -1000
PDGFR-beta signaling pathway 0.0245 9 951 97 -0.34 0.061 1000 -1000 -0.046 -1000
Regulation of Androgen receptor activity 0.0245 9 665 70 -0.14 0.056 1000 -1000 -0.027 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0218 8 269 33 -0.11 0.055 1000 -1000 -0.015 -1000
Rapid glucocorticoid signaling 0.0218 8 170 20 -0.02 0.02 1000 -1000 -0.007 -1000
Regulation of nuclear SMAD2/3 signaling 0.0191 7 1055 136 -0.11 0.082 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class I 0.0191 7 748 104 -0.095 0.063 1000 -1000 -0.021 -1000
Regulation of Telomerase 0.0191 7 714 102 -0.17 0.069 1000 -1000 -0.068 -1000
Hedgehog signaling events mediated by Gli proteins 0.0163 6 403 65 -0.093 0.085 1000 -1000 -0.043 -1000
Signaling mediated by p38-gamma and p38-delta 0.0163 6 103 15 -0.03 0.027 1000 -1000 -0.012 -1000
Signaling mediated by p38-alpha and p38-beta 0.0163 6 278 44 -0.039 0.028 1000 -1000 -0.015 -1000
Insulin Pathway 0.0163 6 459 74 -0.061 0.048 1000 -1000 -0.052 -1000
Signaling events mediated by PRL 0.0163 6 215 34 -0.089 0.049 1000 -1000 -0.01 -1000
Class IB PI3K non-lipid kinase events 0.0163 6 18 3 -0.01 0.01 1000 -1000 -0.005 -1000
Aurora B signaling 0.0163 6 444 67 -0.15 0.057 1000 -1000 -0.031 -1000
Canonical NF-kappaB pathway 0.0136 5 232 39 -0.095 0.085 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class III 0.0136 5 201 40 -0.094 0.035 1000 -1000 -0.006 -1000
TCGA08_rtk_signaling 0.0136 5 151 26 -0.055 0.05 1000 -1000 -0.005 -1000
FOXM1 transcription factor network 0.0136 5 274 51 -0.12 0.29 1000 -1000 -0.088 -1000
Retinoic acid receptors-mediated signaling 0.0109 4 233 58 -0.05 0.057 1000 -1000 -0.044 -1000
Insulin-mediated glucose transport 0.0082 3 118 32 -0.035 0.049 1000 -1000 -0.02 -1000
PDGFR-alpha signaling pathway 0.0082 3 174 44 -0.013 0.041 1000 -1000 -0.021 -1000
FoxO family signaling 0.0082 3 201 64 -0.43 0.18 1000 -1000 -0.023 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 3 421 125 -0.12 0.083 1000 -1000 -0.054 -1000
p38 MAPK signaling pathway 0.0082 3 152 44 -0.046 0.042 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class II 0.0054 2 175 75 -0.063 0.055 1000 -1000 -0.024 -1000
Arf6 downstream pathway 0.0054 2 93 43 -0.031 0.036 1000 -1000 -0.016 -1000
IGF1 pathway 0.0054 2 118 57 -0.046 0.054 1000 -1000 -0.052 -1000
Aurora A signaling 0.0027 1 103 60 -0.023 0.052 1000 -1000 -0.01 -1000
Class I PI3K signaling events mediated by Akt 0.0027 1 83 68 -0.044 0.059 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 0.0027 1 77 43 -0.16 0.16 1000 -1000 -0.049 -1000
Arf6 trafficking events 0.0027 1 114 71 -0.028 0.049 1000 -1000 -0.033 -1000
VEGFR1 specific signals 0.0027 1 110 56 -0.052 0.065 1000 -1000 -0.031 -1000
Arf1 pathway 0.0027 1 105 54 -0.034 0.034 1000 -1000 -0.011 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 0 23 0.015 0.056 1000 -1000 -0.015 -1000
BARD1 signaling events 0.0000 0 5 57 -0.047 0.08 1000 -1000 -0.017 -1000
PLK2 and PLK4 events 0.0000 0 2 3 0.017 0.025 1000 -1000 0 -1000
Circadian rhythm pathway 0.0000 0 12 22 -0.016 0.06 1000 -1000 -0.015 -1000
PLK1 signaling events 0.0000 0 45 85 -0.013 0.05 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0000 0 18 53 -0.005 0.041 1000 -1000 -0.039 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 -0.001 0.046 1000 -1000 -0.029 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.056 1000 -1000 -0.006 -1000
Total NA 3169 188858 7203 -22 7.6 131000 -131000 -4 -131000
BCR signaling pathway

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
JUN -0.32 0.28 -9999 0 -0.52 227 227
IKBKB -0.14 0.14 -9999 0 -0.25 197 197
AKT1 -0.18 0.15 -9999 0 -0.28 246 246
IKBKG -0.14 0.15 -9999 0 -0.27 178 178
CALM1 -0.37 0.37 -9999 0 -0.62 219 219
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
MAP3K1 -0.49 0.4 -9999 0 -0.76 241 241
MAP3K7 0.019 0 -9999 0 -10000 0 0
mol:Ca2+ -0.41 0.4 -9999 0 -0.68 219 219
DOK1 0.019 0 -9999 0 -10000 0 0
AP-1 -0.16 0.15 -9999 0 -0.27 225 225
LYN -0.004 0.11 -9999 0 -0.54 15 15
BLNK -0.19 0.27 -9999 0 -0.54 140 140
SHC1 0.019 0 -9999 0 -10000 0 0
BCR complex -0.39 0.33 -9999 0 -0.62 236 236
CD22 -0.62 0.51 -9999 0 -0.98 230 230
CAMK2G -0.33 0.33 -9999 0 -0.59 201 201
CSNK2A1 0.019 0 -9999 0 -10000 0 0
INPP5D -0.075 0.21 -9999 0 -0.54 62 62
SHC/GRB2/SOS1 -0.38 0.34 -9999 0 -0.65 203 203
GO:0007205 -0.42 0.42 -9999 0 -0.7 219 219
SYK -0.052 0.19 -9999 0 -0.54 47 47
ELK1 -0.38 0.38 -9999 0 -0.64 219 219
NFATC1 -0.43 0.36 -9999 0 -0.68 237 237
B-cell antigen/BCR complex -0.39 0.33 -9999 0 -0.62 236 236
PAG1/CSK 0.026 0.03 -9999 0 -0.38 2 2
NFKBIB -0.032 0.046 -9999 0 -0.082 57 57
HRAS -0.37 0.36 -9999 0 -0.62 219 219
NFKBIA -0.031 0.046 -9999 0 -0.08 57 57
NF-kappa-B/RelA/I kappa B beta -0.017 0.037 -9999 0 -10000 0 0
RasGAP/Csk -0.28 0.27 -9999 0 -0.47 237 237
mol:GDP -0.39 0.38 -9999 0 -0.65 219 219
PTEN 0.017 0.029 -9999 0 -0.54 1 1
CD79B -0.27 0.28 -9999 0 -0.54 192 192
NF-kappa-B/RelA/I kappa B alpha -0.016 0.037 -9999 0 -10000 0 0
GRB2 0.019 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.45 0.36 -9999 0 -0.7 237 237
PIK3R1 0.019 0 -9999 0 -10000 0 0
mol:IP3 -0.43 0.43 -9999 0 -0.72 219 219
CSK 0.019 0 -9999 0 -10000 0 0
FOS -0.34 0.34 -9999 0 -0.57 222 222
CHUK -0.14 0.15 -9999 0 -0.29 141 141
IBTK 0.019 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.34 0.34 -9999 0 -0.6 205 205
PTPN6 -0.62 0.52 -9999 0 -0.98 230 230
RELA 0.019 0 -9999 0 -10000 0 0
BCL2A1 -0.012 0.036 -9999 0 -0.1 24 24
VAV2 -0.66 0.52 -9999 0 -1 237 237
ubiquitin-dependent protein catabolic process -0.025 0.045 -9999 0 -0.076 19 19
BTK -0.17 0.41 -9999 0 -1 65 65
CD19 -0.66 0.52 -9999 0 -1 238 238
MAP4K1 -0.081 0.21 -9999 0 -0.54 66 66
CD72 -0.14 0.25 -9999 0 -0.54 105 105
PAG1 0.016 0.041 -9999 0 -0.54 2 2
MAPK14 -0.38 0.32 -9999 0 -0.61 239 239
SH3BP5 0.019 0 -9999 0 -10000 0 0
PIK3AP1 -0.46 0.47 -9999 0 -0.76 225 225
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.59 0.64 -9999 0 -1 219 219
RAF1 -0.33 0.33 -9999 0 -0.57 219 219
RasGAP/p62DOK/SHIP -0.31 0.31 -9999 0 -0.52 237 237
CD79A -0.31 0.27 -9999 0 -0.54 215 215
re-entry into mitotic cell cycle -0.16 0.15 -9999 0 -0.27 225 225
RASA1 0.017 0.029 -9999 0 -0.54 1 1
MAPK3 -0.26 0.26 -9999 0 -0.47 201 201
MAPK1 -0.26 0.26 -9999 0 -0.47 201 201
CD72/SHP1 -0.6 0.52 -9999 0 -0.96 230 230
NFKB1 0.019 0 -9999 0 -10000 0 0
MAPK8 -0.38 0.32 -9999 0 -0.6 241 241
actin cytoskeleton organization -0.5 0.4 -9999 0 -0.78 237 237
NF-kappa-B/RelA -0.026 0.072 -9999 0 -10000 0 0
Calcineurin -0.29 0.3 -9999 0 -0.52 201 201
PI3K -0.46 0.32 -9999 0 -0.67 246 246
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.49 0.5 -9999 0 -0.81 223 223
SOS1 0.019 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.63 0.53 -9999 0 -1 227 227
DAPP1 -0.76 0.65 -9999 0 -1.2 227 227
cytokine secretion -0.39 0.32 -9999 0 -0.61 237 237
mol:DAG -0.43 0.43 -9999 0 -0.72 219 219
PLCG2 -0.03 0.16 -9999 0 -0.54 32 32
MAP2K1 -0.3 0.3 -9999 0 -0.53 201 201
B-cell antigen/BCR complex/FcgammaRIIB -0.34 0.3 -9999 0 -0.55 237 237
mol:PI-3-4-5-P3 -0.3 0.2 -9999 0 -0.43 246 246
ETS1 -0.29 0.29 -9999 0 -0.52 201 201
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.42 0.41 -9999 0 -0.68 238 238
B-cell antigen/BCR complex/LYN -0.57 0.48 -9999 0 -0.88 237 237
MALT1 0.018 0.029 -9999 0 -0.54 1 1
TRAF6 0.019 0 -9999 0 -10000 0 0
RAC1 -0.56 0.45 -9999 0 -0.87 237 237
B-cell antigen/BCR complex/LYN/SYK -0.59 0.51 -9999 0 -0.95 229 229
CARD11 -0.44 0.44 -9999 0 -0.73 224 224
FCGR2B -0.005 0.11 -9999 0 -0.52 16 16
PPP3CA 0.019 0 -9999 0 -10000 0 0
BCL10 0.018 0.014 -9999 0 -0.24 1 1
IKK complex -0.044 0.056 -9999 0 -0.096 130 130
PTPRC -0.18 0.27 -9999 0 -0.54 131 131
PDPK1 -0.18 0.15 -9999 0 -0.28 246 246
PPP3CB 0.019 0 -9999 0 -10000 0 0
PPP3CC 0.019 0 -9999 0 -10000 0 0
POU2F2 -0.02 0.047 -9999 0 -0.11 62 62
IL4-mediated signaling events

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
BCL2L1 -0.89 0.59 -10000 0 -1.3 221 221
STAT6 (cleaved dimer) -0.99 0.6 -10000 0 -1.3 265 265
IGHG1 -0.25 0.16 -10000 0 -0.36 147 147
IGHG3 -0.87 0.56 -10000 0 -1.2 242 242
AKT1 -0.54 0.45 -10000 0 -0.98 152 152
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.58 0.61 -10000 0 -1.3 130 130
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.61 0.54 -10000 0 -1 179 179
THY1 -0.9 0.59 -10000 0 -1.3 231 231
MYB -0.01 0.12 -10000 0 -0.54 19 19
HMGA1 0.016 0.041 -10000 0 -0.54 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.66 0.54 -10000 0 -0.96 229 229
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.64 0.59 -10000 0 -1.1 171 171
SP1 0.022 0.013 -10000 0 -10000 0 0
INPP5D -0.075 0.21 -10000 0 -0.54 62 62
SOCS5 0.034 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.95 0.64 -10000 0 -1.3 245 245
SOCS1 -0.55 0.35 -10000 0 -0.79 224 224
SOCS3 -0.51 0.4 -10000 0 -0.97 127 127
FCER2 -1.3 0.69 -10000 0 -1.6 294 294
PARP14 0.007 0.051 -10000 0 -0.54 3 3
CCL17 -0.92 0.62 -10000 0 -1.3 230 230
GRB2 0.019 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.48 0.44 -10000 0 -0.98 129 129
T cell proliferation -0.94 0.64 -10000 0 -1.3 237 237
IL4R/JAK1 -0.9 0.59 -10000 0 -1.3 225 225
EGR2 -1 0.61 -10000 0 -1.3 257 257
JAK2 -0.036 0.076 -10000 0 -0.53 7 7
JAK3 -0.013 0.14 -10000 0 -0.51 25 25
PIK3R1 0.019 0 -10000 0 -10000 0 0
JAK1 0.005 0.013 -10000 0 -10000 0 0
COL1A2 -0.26 0.19 -10000 0 -0.58 42 42
CCL26 -0.9 0.59 -10000 0 -1.3 229 229
IL4R -0.96 0.64 -10000 0 -1.4 221 221
PTPN6 -0.1 0.24 -10000 0 -0.52 92 92
IL13RA2 -0.95 0.6 -10000 0 -1.3 237 237
IL13RA1 -0.026 0.03 -10000 0 -10000 0 0
IRF4 -0.7 0.61 -10000 0 -1.2 202 202
ARG1 -0.22 0.21 -10000 0 -0.73 35 35
CBL -0.61 0.49 -10000 0 -0.89 229 229
GTF3A 0.02 0.015 -10000 0 -10000 0 0
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
IL13RA1/JAK2 -0.041 0.065 -10000 0 -0.39 7 7
IRF4/BCL6 -0.61 0.56 -10000 0 -1.1 202 202
CD40LG -0.28 0.28 -10000 0 -0.54 195 195
MAPK14 -0.61 0.49 -10000 0 -0.92 210 210
mitosis -0.49 0.41 -10000 0 -0.9 151 151
STAT6 -1.1 0.81 -10000 0 -1.6 241 241
SPI1 -0.023 0.15 -10000 0 -0.54 28 28
RPS6KB1 -0.47 0.39 -10000 0 -0.89 137 137
STAT6 (dimer) -1.1 0.81 -10000 0 -1.6 241 241
STAT6 (dimer)/PARP14 -1.1 0.7 -10000 0 -1.4 261 261
mast cell activation 0.018 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.62 0.59 -10000 0 -1.2 161 161
FRAP1 -0.54 0.46 -10000 0 -0.98 152 152
LTA -1.1 0.73 -10000 0 -1.6 230 230
FES 0.007 0.081 -10000 0 -0.54 8 8
T-helper 1 cell differentiation 1 0.72 1.5 241 -10000 0 241
CCL11 -0.9 0.56 -10000 0 -1.3 237 237
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.61 0.57 -10000 0 -1.1 163 163
IL2RG -0.14 0.25 -10000 0 -0.52 112 112
IL10 -0.92 0.61 -10000 0 -1.3 222 222
IRS1 -0.002 0.071 -10000 0 -0.24 29 29
IRS2 0.019 0 -10000 0 -10000 0 0
IL4 -0.17 0.11 -10000 0 -10000 0 0
IL5 -0.9 0.59 -10000 0 -1.3 225 225
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.66 0.41 -10000 0 -0.92 234 234
COL1A1 -0.29 0.21 -10000 0 -0.59 69 69
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.93 0.63 -10000 0 -1.4 217 217
IL2R gamma/JAK3 -0.12 0.23 -10000 0 -0.44 112 112
TFF3 -0.97 0.65 -10000 0 -1.4 228 228
ALOX15 -0.9 0.6 -10000 0 -1.3 220 220
MYBL1 0.016 0.041 -10000 0 -0.54 2 2
T-helper 2 cell differentiation -0.83 0.58 -10000 0 -1.2 242 242
SHC1 0.019 0 -10000 0 -10000 0 0
CEBPB 0.02 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.59 0.54 -10000 0 -1 171 171
mol:PI-3-4-5-P3 -0.54 0.46 -10000 0 -0.98 152 152
PI3K -0.6 0.53 -10000 0 -1.1 152 152
DOK2 -0.037 0.17 -10000 0 -0.54 37 37
ETS1 0.037 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.44 0.4 -10000 0 -0.91 127 127
ITGB3 -0.92 0.6 -10000 0 -1.3 230 230
PIGR -0.99 0.66 -10000 0 -1.4 228 228
IGHE 0.057 0.039 0.28 2 -10000 0 2
MAPKKK cascade -0.43 0.39 -10000 0 -0.88 127 127
BCL6 0.024 0.008 -10000 0 -10000 0 0
OPRM1 -0.9 0.59 -10000 0 -1.3 221 221
RETNLB -0.9 0.59 -10000 0 -1.3 225 225
SELP -1 0.7 -10000 0 -1.5 229 229
AICDA -1.1 0.67 -10000 0 -1.5 266 266
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.27 0.4 -10000 0 -0.71 161 161
FYN -0.44 0.59 -10000 0 -1.1 163 163
LAT/GRAP2/SLP76 -0.33 0.38 -10000 0 -0.74 164 164
IKBKB 0.019 0 -10000 0 -10000 0 0
AKT1 -0.2 0.31 -10000 0 -0.54 163 163
B2M 0.004 0.082 -10000 0 -0.55 8 8
IKBKG -0.044 0.1 -10000 0 -0.16 154 154
MAP3K8 -0.003 0.11 -10000 0 -0.52 15 15
mol:Ca2+ -0.019 0.022 -10000 0 -0.077 11 11
integrin-mediated signaling pathway -0.02 0.12 -10000 0 -0.32 48 48
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.35 0.5 -10000 0 -0.89 163 163
TRPV6 -0.011 0.055 -10000 0 -0.26 17 17
CD28 -0.071 0.2 -10000 0 -0.54 58 58
SHC1 -0.4 0.55 -10000 0 -1 161 161
receptor internalization -0.48 0.64 -10000 0 -1.2 163 163
PRF1 -0.51 0.69 -10000 0 -1.3 149 149
KRAS 0.018 0.014 -10000 0 -0.24 1 1
GRB2 0.019 0 -10000 0 -10000 0 0
COT/AKT1 -0.15 0.25 -10000 0 -0.42 160 160
LAT -0.42 0.56 -10000 0 -1 162 162
EntrezGene:6955 -0.002 0.005 -10000 0 -10000 0 0
CD3D -0.22 0.28 -10000 0 -0.55 155 155
CD3E -0.19 0.28 -10000 0 -0.55 137 137
CD3G -0.18 0.27 -10000 0 -0.54 126 126
RASGRP2 -0.089 0.1 -10000 0 -0.19 186 186
RASGRP1 -0.22 0.34 -10000 0 -0.58 165 165
HLA-A 0.012 0.042 -10000 0 -0.55 2 2
RASSF5 -0.054 0.19 -10000 0 -0.54 48 48
RAP1A/GTP/RAPL -0.02 0.12 -10000 0 -0.32 48 48
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.095 -10000 0 -0.14 163 163
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.13 0.14 -10000 0 -0.29 157 157
PRKCA -0.13 0.16 -10000 0 -0.31 159 159
GRAP2 -0.046 0.18 -10000 0 -0.54 43 43
mol:IP3 -0.23 0.27 0.15 7 -0.52 163 170
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.59 0.78 -10000 0 -1.4 157 157
ORAI1 0.017 0.041 -10000 0 -0.38 1 1
CSK -0.42 0.57 -10000 0 -1 161 161
B7 family/CD28 -0.45 0.61 -10000 0 -1.1 161 161
CHUK 0.019 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.54 0.71 -10000 0 -1.3 161 161
PTPN6 -0.46 0.61 -10000 0 -1.1 159 159
VAV1 -0.42 0.57 -10000 0 -1 161 161
Monovalent TCR/CD3 -0.45 0.59 -10000 0 -1 169 169
CBL 0.019 0 -10000 0 -10000 0 0
LCK -0.51 0.67 -10000 0 -1.2 162 162
PAG1 -0.42 0.57 -10000 0 -1 161 161
RAP1A 0.019 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.55 0.72 -10000 0 -1.3 161 161
CD80 -0.099 0.23 -10000 0 -0.54 76 76
CD86 -0.053 0.19 -10000 0 -0.54 46 46
PDK1/CARD11/BCL10/MALT1 -0.16 0.18 -10000 0 -0.35 160 160
HRAS 0.019 0 -10000 0 -10000 0 0
GO:0035030 -0.32 0.44 -10000 0 -0.81 161 161
CD8A -0.19 0.27 -10000 0 -0.55 134 134
CD8B -0.19 0.28 -10000 0 -0.55 137 137
PTPRC -0.18 0.27 -10000 0 -0.54 131 131
PDK1/PKC theta -0.26 0.4 -10000 0 -0.7 163 163
CSK/PAG1 -0.4 0.55 -10000 0 -1 160 160
SOS1 0.019 0 -10000 0 -10000 0 0
peptide-MHC class I 0.009 0.069 -10000 0 -0.4 10 10
GRAP2/SLP76 -0.37 0.51 -10000 0 -0.92 163 163
STIM1 0.01 0.019 -10000 0 -10000 0 0
RAS family/GTP -0.045 0.13 -10000 0 -0.19 153 153
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.58 0.76 -10000 0 -1.4 163 163
mol:DAG -0.21 0.23 -10000 0 -0.46 163 163
RAP1A/GDP -0.016 0.042 -10000 0 -0.064 134 134
PLCG1 0.019 0 -10000 0 -10000 0 0
CD247 -0.18 0.27 -10000 0 -0.54 128 128
cytotoxic T cell degranulation -0.46 0.63 -10000 0 -1.2 149 149
RAP1A/GTP -0.035 0.033 -10000 0 -0.067 186 186
mol:PI-3-4-5-P3 -0.26 0.38 -10000 0 -0.67 163 163
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.32 0.37 0.17 7 -0.72 163 170
NRAS 0.019 0 -10000 0 -10000 0 0
ZAP70 -0.17 0.26 -10000 0 -0.54 126 126
GRB2/SOS1 0.028 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.32 0.37 -10000 0 -0.72 164 164
MALT1 0.017 0.029 -10000 0 -0.54 1 1
TRAF6 0.019 0 -10000 0 -10000 0 0
CD8 heterodimer -0.25 0.35 -10000 0 -0.66 149 149
CARD11 -0.14 0.25 -10000 0 -0.54 108 108
PRKCB -0.17 0.21 -10000 0 -0.38 166 166
PRKCE -0.13 0.16 -10000 0 -0.31 158 158
PRKCQ -0.33 0.47 -10000 0 -0.84 163 163
LCP2 -0.016 0.14 -10000 0 -0.54 23 23
BCL10 0.018 0.014 -10000 0 -0.24 1 1
regulation of survival gene product expression -0.16 0.26 -10000 0 -0.45 163 163
IKK complex -0.021 0.09 -10000 0 -0.12 153 153
RAS family/GDP -0.015 0.016 -10000 0 -10000 0 0
MAP3K14 -0.099 0.19 -10000 0 -0.31 157 157
PDPK1 -0.18 0.3 -10000 0 -0.51 163 163
TCR/CD3/MHC I/CD8/Fyn -0.57 0.74 -10000 0 -1.4 158 158
IL23-mediated signaling events

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
CCL2 -0.48 0.67 -9999 0 -1.2 150 150
IL23A -0.52 0.71 -9999 0 -1.3 151 151
NF kappa B1 p50/RelA/I kappa B alpha -0.6 0.65 -9999 0 -1.3 154 154
positive regulation of T cell mediated cytotoxicity -0.62 0.85 -9999 0 -1.5 155 155
ITGA3 -0.5 0.68 -9999 0 -1.2 152 152
IL17F -0.29 0.43 -9999 0 -0.75 153 153
IL12B -0.009 0.1 -9999 0 -0.57 9 9
STAT1 (dimer) -0.58 0.79 -9999 0 -1.4 155 155
CD4 -0.5 0.69 -9999 0 -1.3 151 151
IL23 -0.5 0.68 -9999 0 -1.3 151 151
IL23R -0.041 0.11 -9999 0 -10000 0 0
IL1B -0.54 0.74 -9999 0 -1.4 150 150
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.6 0.74 -9999 0 -1.3 182 182
TYK2 0.008 0.029 -9999 0 -10000 0 0
STAT4 -0.12 0.24 -9999 0 -0.54 92 92
STAT3 0.019 0 -9999 0 -10000 0 0
IL18RAP -0.17 0.26 -9999 0 -0.54 119 119
IL12RB1 -0.14 0.26 -9999 0 -0.57 97 97
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
IL12Rbeta1/TYK2 -0.097 0.2 -9999 0 -0.43 97 97
IL23R/JAK2 -0.047 0.15 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.62 0.85 -9999 0 -1.5 155 155
natural killer cell activation 0.005 0.01 -9999 0 -10000 0 0
JAK2 0 0.085 -9999 0 -0.53 7 7
PIK3R1 0.019 0 -9999 0 -10000 0 0
NFKB1 0.017 0.005 -9999 0 -10000 0 0
RELA 0.017 0.005 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.46 0.63 -9999 0 -1.2 152 152
ALOX12B -0.48 0.67 -9999 0 -1.2 152 152
CXCL1 -0.51 0.67 -9999 0 -1.2 154 154
T cell proliferation -0.62 0.85 -9999 0 -1.5 155 155
NFKBIA 0.017 0.005 -9999 0 -10000 0 0
IL17A -0.2 0.35 -9999 0 -0.58 140 140
PI3K -0.54 0.74 -9999 0 -1.3 154 154
IFNG -0.05 0.07 -9999 0 -0.12 175 175
STAT3 (dimer) -0.57 0.62 -9999 0 -1.2 154 154
IL18R1 -0.073 0.2 -9999 0 -0.54 58 58
IL23/IL23R/JAK2/TYK2/SOCS3 -0.28 0.44 -9999 0 -0.76 142 142
IL18/IL18R -0.23 0.33 -9999 0 -0.58 151 151
macrophage activation -0.023 0.02 -9999 0 -0.045 153 153
TNF -0.57 0.77 -9999 0 -1.4 153 153
STAT3/STAT4 -0.57 0.77 -9999 0 -1.4 157 157
STAT4 (dimer) -0.62 0.82 -9999 0 -1.5 159 159
IL18 -0.14 0.25 -9999 0 -0.54 99 99
IL19 -0.49 0.66 -9999 0 -1.2 146 146
STAT5A (dimer) -0.58 0.79 -9999 0 -1.4 155 155
STAT1 0.016 0.041 -9999 0 -0.54 2 2
SOCS3 0.014 0.05 -9999 0 -0.54 3 3
CXCL9 -0.65 0.81 -9999 0 -1.5 173 173
MPO -0.51 0.7 -9999 0 -1.3 158 158
positive regulation of humoral immune response -0.62 0.85 -9999 0 -1.5 155 155
IL23/IL23R/JAK2/TYK2 -0.74 1.1 -9999 0 -1.8 155 155
IL6 -0.5 0.69 -9999 0 -1.3 145 145
STAT5A 0.017 0.029 -9999 0 -0.54 1 1
IL2 0.002 0.021 -9999 0 -0.24 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.01 -9999 0 -10000 0 0
CD3E -0.6 0.8 -9999 0 -1.5 156 156
keratinocyte proliferation -0.62 0.85 -9999 0 -1.5 155 155
NOS2 -0.48 0.67 -9999 0 -1.2 151 151
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.14 0.2 0.39 148 -10000 0 148
KIRREL -0.004 0.047 -10000 0 -0.54 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.15 0.2 -10000 0 -0.39 148 148
PLCG1 0.019 0 -10000 0 -10000 0 0
ARRB2 0.019 0 -10000 0 -10000 0 0
WASL 0.019 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.095 0.15 -10000 0 -0.28 149 149
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.084 0.14 -10000 0 -0.26 148 148
FYN -0.095 0.14 -10000 0 -0.27 148 148
mol:Ca2+ -0.094 0.15 -10000 0 -0.27 148 148
mol:DAG -0.094 0.15 -10000 0 -0.28 148 148
NPHS2 -0.019 0.026 -10000 0 -10000 0 0
mol:IP3 -0.094 0.15 -10000 0 -0.28 148 148
regulation of endocytosis -0.079 0.14 -10000 0 -0.24 148 148
Nephrin/NEPH1/podocin/Cholesterol -0.1 0.15 -10000 0 -0.28 148 148
establishment of cell polarity -0.14 0.2 -10000 0 -0.39 148 148
Nephrin/NEPH1/podocin/NCK1-2 -0.076 0.14 -10000 0 -0.24 148 148
Nephrin/NEPH1/beta Arrestin2 -0.079 0.14 -10000 0 -0.25 148 148
NPHS1 -0.21 0.27 -10000 0 -0.54 146 146
Nephrin/NEPH1/podocin -0.096 0.14 -10000 0 -0.27 148 148
TJP1 0.019 0 -10000 0 -10000 0 0
NCK1 0.019 0 -10000 0 -10000 0 0
NCK2 0.019 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.095 0.15 -10000 0 -0.28 148 148
CD2AP 0.017 0.029 -10000 0 -0.54 1 1
Nephrin/NEPH1/podocin/GRB2 -0.095 0.15 -10000 0 -0.28 148 148
GRB2 0.019 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.098 0.14 -10000 0 -0.26 148 148
cytoskeleton organization -0.1 0.17 -10000 0 -0.31 148 148
Nephrin/NEPH1 -0.1 0.14 -10000 0 -0.27 148 148
Nephrin/NEPH1/ZO-1 -0.1 0.16 -10000 0 -0.3 148 148
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.27 -10000 0 -0.48 107 107
TBX21 -0.47 0.81 -10000 0 -1.5 133 133
B2M 0.008 0.081 -10000 0 -0.54 8 8
TYK2 0.014 0.03 -10000 0 -10000 0 0
IL12RB1 -0.13 0.27 -10000 0 -0.57 97 97
GADD45B -0.36 0.67 -10000 0 -1.2 126 126
IL12RB2 -0.058 0.13 -10000 0 -0.27 95 95
GADD45G -0.4 0.71 -10000 0 -1.3 136 136
natural killer cell activation -0.001 0.029 -10000 0 -10000 0 0
RELB 0.019 0 -10000 0 -10000 0 0
RELA 0.019 0 -10000 0 -10000 0 0
IL18 -0.13 0.25 -10000 0 -0.55 99 99
IL2RA -0.12 0.24 -10000 0 -0.54 93 93
IFNG -0.18 0.26 -10000 0 -0.54 129 129
STAT3 (dimer) -0.29 0.57 -10000 0 -1 134 134
HLA-DRB5 -0.014 0.13 -10000 0 -0.5 24 24
FASLG -0.5 0.83 -10000 0 -1.5 137 137
NF kappa B2 p52/RelB -0.51 0.68 -10000 0 -1.4 134 134
CD4 -0.034 0.16 -10000 0 -0.54 35 35
SOCS1 -0.01 0.12 -10000 0 -0.54 19 19
EntrezGene:6955 0.002 0.003 -10000 0 -10000 0 0
CD3D -0.21 0.28 -10000 0 -0.54 155 155
CD3E -0.19 0.27 -10000 0 -0.54 137 137
CD3G -0.17 0.26 -10000 0 -0.54 126 126
IL12Rbeta2/JAK2 -0.034 0.11 -10000 0 -0.29 35 35
CCL3 -0.41 0.74 -10000 0 -1.4 126 126
CCL4 -0.45 0.79 -10000 0 -1.5 129 129
HLA-A 0.017 0.041 -10000 0 -0.54 2 2
IL18/IL18R -0.19 0.36 -10000 0 -0.58 151 151
NOS2 -0.42 0.75 -10000 0 -1.4 129 129
IL12/IL12R/TYK2/JAK2/SPHK2 -0.098 0.24 -10000 0 -0.43 104 104
IL1R1 -0.4 0.72 -10000 0 -1.3 129 129
IL4 0.004 0.032 -10000 0 -0.27 1 1
JAK2 0.004 0.081 -10000 0 -0.53 7 7
EntrezGene:6957 0.002 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.6 0.83 -10000 0 -1.5 156 156
RAB7A -0.24 0.52 -10000 0 -0.92 126 126
lysosomal transport -0.22 0.48 -10000 0 -0.85 126 126
FOS -0.38 0.64 -10000 0 -1.2 131 131
STAT4 (dimer) -0.38 0.7 -10000 0 -1.2 139 139
STAT5A (dimer) -0.56 0.69 -10000 0 -1.3 153 153
GZMA -0.48 0.82 -10000 0 -1.6 129 129
GZMB -0.5 0.82 -10000 0 -1.5 141 141
HLX 0.017 0.019 -10000 0 -0.24 2 2
LCK -0.55 0.9 -10000 0 -1.6 145 145
TCR/CD3/MHC II/CD4 -0.46 0.66 -10000 0 -1.2 147 147
IL2/IL2R -0.18 0.32 -10000 0 -0.56 138 138
MAPK14 -0.37 0.7 -10000 0 -1.2 136 136
CCR5 -0.4 0.72 -10000 0 -1.3 130 130
IL1B -0.045 0.17 -10000 0 -0.5 43 43
STAT6 -0.042 0.16 -10000 0 -0.25 113 113
STAT4 -0.12 0.24 -10000 0 -0.54 92 92
STAT3 0.019 0 -10000 0 -10000 0 0
STAT1 0.016 0.041 -10000 0 -0.54 2 2
NFKB1 0.019 0 -10000 0 -10000 0 0
NFKB2 0.019 0 -10000 0 -10000 0 0
IL12B -0.001 0.094 -10000 0 -0.56 9 9
CD8A -0.18 0.27 -10000 0 -0.54 134 134
CD8B -0.19 0.27 -10000 0 -0.54 137 137
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.26 0.48 107 -10000 0 107
IL2RB -0.083 0.22 -10000 0 -0.54 67 67
proteasomal ubiquitin-dependent protein catabolic process -0.31 0.6 -10000 0 -1 139 139
IL2RG -0.15 0.26 -10000 0 -0.54 112 112
IL12 -0.01 0.13 -10000 0 -0.42 29 29
STAT5A 0.017 0.029 -10000 0 -0.54 1 1
CD247 -0.17 0.27 -10000 0 -0.54 128 128
IL2 0.005 0.016 -10000 0 -0.24 1 1
SPHK2 0.019 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.019 0.14 -10000 0 -0.55 21 21
IL12/IL12R/TYK2/JAK2 -0.68 1.2 -10000 0 -2.1 134 134
MAP2K3 -0.39 0.72 -10000 0 -1.3 135 135
RIPK2 0.019 0 -10000 0 -10000 0 0
MAP2K6 -0.4 0.72 -10000 0 -1.3 135 135
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.1 0.23 -10000 0 -0.54 81 81
IL18RAP -0.16 0.27 -10000 0 -0.54 119 119
IL12Rbeta1/TYK2 -0.088 0.21 -10000 0 -0.43 97 97
EOMES -0.15 0.41 -10000 0 -1.4 33 33
STAT1 (dimer) -0.38 0.58 -10000 0 -0.99 162 162
T cell proliferation -0.22 0.46 -10000 0 -0.79 138 138
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.067 0.21 -10000 0 -0.55 58 58
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.36 0.42 -10000 0 -0.86 141 141
ATF2 -0.31 0.61 -10000 0 -1.1 134 134
Caspase cascade in apoptosis

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
TOP1 -0.12 0.26 0.19 1 -0.49 115 116
ACTA1 -0.16 0.31 0.2 41 -0.59 115 156
NUMA1 -0.12 0.26 0.19 1 -0.49 115 116
SPTAN1 -0.16 0.31 0.2 7 -0.58 115 122
LIMK1 -0.16 0.31 0.2 41 -0.58 115 156
BIRC3 -0.18 0.26 -10000 0 -0.54 128 128
BIRC2 0.013 0.052 -10000 0 -0.46 4 4
BAX 0.019 0 -10000 0 -10000 0 0
CASP10 -0.18 0.29 -10000 0 -0.54 137 137
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.019 0 -10000 0 -10000 0 0
PTK2 -0.12 0.26 -10000 0 -0.49 115 115
DIABLO 0.019 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.15 0.3 0.2 7 -0.57 115 122
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.018 0.014 -10000 0 -0.24 1 1
GSN -0.16 0.31 0.2 41 -0.59 115 156
MADD 0.019 0 -10000 0 -10000 0 0
TFAP2A -0.16 0.34 -10000 0 -0.79 81 81
BID -0.091 0.16 -10000 0 -0.29 137 137
MAP3K1 -0.036 0.1 -10000 0 -0.21 37 37
TRADD 0.019 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.029 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.18 0.35 0.2 38 -0.65 117 155
CASP9 0.019 0 -10000 0 -10000 0 0
DNA repair -0.019 0.08 0.15 31 -0.18 43 74
neuron apoptosis -0.003 0.091 -10000 0 -0.65 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.14 0.3 0.22 1 -0.56 115 116
APAF1 0.019 0 -10000 0 -10000 0 0
CASP6 -0.084 0.19 -10000 0 -0.41 76 76
TRAF2 0.019 0 -10000 0 -10000 0 0
ICAD/CAD -0.14 0.3 0.23 1 -0.56 115 116
CASP7 0.11 0.15 0.31 128 -10000 0 128
KRT18 -0.096 0.25 -10000 0 -0.69 49 49
apoptosis -0.1 0.25 0.22 41 -0.45 115 156
DFFA -0.16 0.31 0.2 41 -0.58 115 156
DFFB -0.16 0.31 0.2 41 -0.58 115 156
PARP1 0.019 0.081 0.18 43 -0.15 31 74
actin filament polymerization 0.14 0.29 0.53 115 -0.19 41 156
TNF -0.095 0.22 -10000 0 -0.54 75 75
CYCS -0.063 0.11 -10000 0 -0.2 137 137
SATB1 -0.091 0.21 -10000 0 -0.44 80 80
SLK -0.16 0.31 0.2 41 -0.58 115 156
p15 BID/BAX -0.073 0.14 -10000 0 -0.25 137 137
CASP2 -0.053 0.14 -10000 0 -0.34 53 53
JNK cascade 0.036 0.1 0.21 37 -10000 0 37
CASP3 -0.17 0.33 0.2 41 -0.62 115 156
LMNB2 -0.053 0.15 -10000 0 -0.32 64 64
RIPK1 0.019 0 -10000 0 -10000 0 0
CASP4 0.013 0.058 -10000 0 -0.54 4 4
Mammalian IAPs/DIABLO -0.069 0.16 -10000 0 -0.29 128 128
negative regulation of DNA binding -0.16 0.34 -10000 0 -0.78 81 81
stress fiber formation -0.15 0.3 0.19 41 -0.57 115 156
GZMB -0.21 0.32 -10000 0 -0.6 137 137
CASP1 -0.003 0.099 -10000 0 -0.37 22 22
LMNB1 -0.053 0.15 -10000 0 -0.29 84 84
APP -0.003 0.092 -10000 0 -0.66 5 5
TNFRSF1A 0.019 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.03 -10000 0 -0.39 2 2
VIM -0.1 0.25 0.21 41 -0.44 115 156
LMNA -0.054 0.15 -10000 0 -0.33 62 62
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.064 0.15 -10000 0 -0.37 53 53
LRDD 0.017 0.029 -10000 0 -0.54 1 1
SREBF1 -0.16 0.31 0.2 41 -0.58 115 156
APAF-1/Caspase 9 0.029 0.073 0.42 3 -10000 0 3
nuclear fragmentation during apoptosis -0.12 0.26 0.19 1 -0.48 115 116
CFL2 -0.14 0.3 0.2 7 -0.55 115 122
GAS2 -0.17 0.32 0.2 30 -0.59 121 151
positive regulation of apoptosis -0.048 0.15 -10000 0 -0.32 62 62
PRF1 -0.15 0.26 -10000 0 -0.54 110 110
FAS signaling pathway (CD95)

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
SPTAN1 0.066 0.086 0.19 117 -10000 0 117
RFC1 0.066 0.086 0.19 117 -10000 0 117
PRKDC 0.066 0.086 0.19 117 -10000 0 117
RIPK1 0.019 0.002 -10000 0 -10000 0 0
CASP7 0.064 0.11 0.25 57 -0.26 1 58
FASLG/FAS/FADD/FAF1 -0.006 0.15 0.22 60 -0.28 64 124
MAP2K4 -0.018 0.16 -10000 0 -0.41 20 20
mol:ceramide -0.073 0.19 -10000 0 -0.33 120 120
GSN 0.066 0.086 0.19 116 -10000 0 116
FASLG/FAS/FADD/FAF1/Caspase 8 -0.04 0.17 -10000 0 -0.32 66 66
FAS 0.007 0.081 -10000 0 -0.54 8 8
BID 0.1 0.13 0.3 117 -10000 0 117
MAP3K1 0.034 0.11 0.21 55 -0.25 14 69
MAP3K7 0.019 0.002 -10000 0 -10000 0 0
RB1 0.065 0.088 0.19 117 -0.31 1 118
CFLAR 0.019 0.002 -10000 0 -10000 0 0
HGF/MET -0.004 0.11 -10000 0 -0.34 31 31
ARHGDIB 0.034 0.13 0.19 107 -0.31 26 133
FADD 0.018 0.014 -10000 0 -0.24 1 1
actin filament polymerization -0.066 0.085 -10000 0 -0.19 116 116
NFKB1 -0.015 0.065 -10000 0 -0.27 8 8
MAPK8 -0.012 0.16 -10000 0 -0.44 23 23
DFFA 0.066 0.086 0.19 117 -10000 0 117
DNA fragmentation during apoptosis 0.066 0.086 0.19 117 -10000 0 117
FAS/FADD/MET 0.004 0.1 -10000 0 -0.33 29 29
CFLAR/RIP1 0.027 0.005 -10000 0 -10000 0 0
FAIM3 -0.16 0.26 -10000 0 -0.54 119 119
FAF1 0.019 0.005 -10000 0 -10000 0 0
PARP1 0.066 0.086 0.19 117 -10000 0 117
DFFB 0.066 0.086 0.19 117 -10000 0 117
CHUK -0.006 0.06 -10000 0 -0.24 8 8
FASLG -0.16 0.26 -10000 0 -0.54 120 120
FAS/FADD 0.019 0.061 -10000 0 -0.38 8 8
HGF 0 0.085 -10000 0 -0.34 19 19
LMNA 0.066 0.077 -10000 0 -10000 0 0
CASP6 0.066 0.086 0.19 117 -10000 0 117
CASP10 0.009 0.076 -10000 0 -0.54 7 7
CASP3 0.07 0.1 0.22 117 -10000 0 117
PTPN13 0.011 0.062 -10000 0 -0.41 7 7
CASP8 0.12 0.18 0.38 117 -10000 0 117
IL6 -0.044 0.27 -10000 0 -1.3 14 14
MET -0.024 0.14 -10000 0 -0.43 35 35
ICAD/CAD 0.067 0.078 0.18 112 -10000 0 112
FASLG/FAS/FADD/FAF1/Caspase 10 -0.074 0.19 -10000 0 -0.33 120 120
activation of caspase activity by cytochrome c 0.1 0.13 0.3 117 -10000 0 117
PAK2 0.066 0.086 0.19 117 -10000 0 117
BCL2 0.019 0 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.089 0.23 -10000 0 -0.59 62 62
NFATC2 -0.16 0.39 -10000 0 -0.68 109 109
NFATC3 -0.006 0.065 -10000 0 -0.22 5 5
CD40LG -0.51 0.55 -10000 0 -1 180 180
ITCH 0.004 0.066 -10000 0 -10000 0 0
CBLB 0.003 0.067 -10000 0 -0.35 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.5 0.7 -10000 0 -1.3 141 141
JUNB 0.017 0.019 -10000 0 -0.24 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.079 -10000 0 -0.28 2 2
T cell anergy -0.04 0.099 -10000 0 -0.31 8 8
TLE4 -0.13 0.35 -10000 0 -0.73 70 70
Jun/NFAT1-c-4/p21SNFT -0.28 0.46 -10000 0 -0.86 108 108
AP-1/NFAT1-c-4 -0.44 0.59 -10000 0 -1.1 142 142
IKZF1 -0.22 0.46 -10000 0 -0.9 106 106
T-helper 2 cell differentiation -0.24 0.42 -10000 0 -0.9 96 96
AP-1/NFAT1 -0.15 0.29 -10000 0 -0.52 106 106
CALM1 0.001 0.046 -10000 0 -10000 0 0
EGR2 -0.14 0.33 -10000 0 -0.8 40 40
EGR3 -0.17 0.39 -10000 0 -1.1 33 33
NFAT1/FOXP3 -0.19 0.41 -10000 0 -0.76 110 110
EGR1 -0.005 0.074 -10000 0 -0.25 31 31
JUN -0.031 0.087 -10000 0 -0.28 37 37
EGR4 0 0.062 -10000 0 -0.25 21 21
mol:Ca2+ -0.019 0.048 -10000 0 -0.17 2 2
GBP3 -0.14 0.36 -10000 0 -0.76 77 77
FOSL1 -0.014 0.12 -10000 0 -0.45 26 26
NFAT1-c-4/MAF/IRF4 -0.21 0.42 -10000 0 -0.87 79 79
DGKA -0.12 0.34 -10000 0 -0.74 64 64
CREM 0.018 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.21 0.43 -10000 0 -0.9 74 74
CTLA4 -0.21 0.43 -10000 0 -0.83 106 106
NFAT1-c-4 (dimer)/EGR1 -0.23 0.44 -10000 0 -0.88 87 87
NFAT1-c-4 (dimer)/EGR4 -0.22 0.44 -10000 0 -0.9 83 83
FOS -0.013 0.055 -10000 0 -0.28 12 12
IFNG -0.62 0.76 -10000 0 -1.4 178 178
T cell activation -0.14 0.27 -10000 0 -0.75 32 32
MAF 0.019 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 0.12 0.31 1.1 18 -10000 0 18
TNF -0.27 0.48 -10000 0 -0.99 99 99
FASLG -0.57 0.85 -10000 0 -1.7 126 126
TBX21 -0.16 0.25 -10000 0 -0.56 104 104
BATF3 0.007 0.081 -10000 0 -0.54 8 8
PRKCQ -0.17 0.27 -10000 0 -0.56 116 116
PTPN1 -0.1 0.3 -10000 0 -0.66 62 62
NFAT1-c-4/ICER1 -0.21 0.42 -10000 0 -0.88 75 75
GATA3 -0.1 0.23 -10000 0 -0.54 80 80
T-helper 1 cell differentiation -0.59 0.72 -10000 0 -1.3 179 179
IL2RA -0.45 0.64 -10000 0 -1.2 144 144
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.1 0.3 -10000 0 -0.66 62 62
E2F1 0.026 0.006 -10000 0 -10000 0 0
PPARG 0.011 0.064 -10000 0 -0.54 5 5
SLC3A2 -0.1 0.3 -10000 0 -0.65 64 64
IRF4 -0.033 0.16 -10000 0 -0.54 34 34
PTGS2 -0.4 0.49 -10000 0 -0.94 143 143
CSF2 -0.39 0.48 -10000 0 -0.92 142 142
JunB/Fra1/NFAT1-c-4 -0.2 0.41 -10000 0 -0.91 67 67
IL4 -0.26 0.45 -10000 0 -0.96 95 95
IL5 -0.39 0.48 -10000 0 -0.92 142 142
IL2 -0.14 0.27 -10000 0 -0.76 32 32
IL3 -0.067 0.06 -10000 0 -10000 0 0
RNF128 -0.05 0.14 -10000 0 -0.48 2 2
NFATC1 -0.12 0.31 -10000 0 -1.1 18 18
CDK4 0.1 0.21 0.66 13 -10000 0 13
PTPRK -0.11 0.3 -10000 0 -0.63 69 69
IL8 -0.41 0.48 -10000 0 -0.94 144 144
POU2F1 0.019 0 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.064 0.16 -9999 0 -0.32 101 101
E-cadherin/beta catenin -0.085 0.18 -9999 0 -0.38 101 101
CTNNB1 0.019 0 -9999 0 -10000 0 0
JUP 0.011 0.045 -9999 0 -0.24 11 11
CDH1 -0.13 0.25 -9999 0 -0.54 101 101
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.027 0.072 -9999 0 -0.4 9 9
NFATC2 -0.042 0.1 -9999 0 -0.37 25 25
NFATC3 -0.017 0.042 -9999 0 -10000 0 0
CD40LG -0.43 0.44 -9999 0 -0.75 222 222
PTGS2 -0.32 0.37 -9999 0 -0.65 183 183
JUNB 0.017 0.019 -9999 0 -0.24 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.012 0.027 -9999 0 -10000 0 0
CaM/Ca2+ -0.012 0.026 -9999 0 -10000 0 0
CALM1 0.005 0.016 -9999 0 -10000 0 0
JUN -0.022 0.082 -9999 0 -0.26 37 37
mol:Ca2+ -0.017 0.016 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.01 -9999 0 -10000 0 0
FOSL1 -0.014 0.12 -9999 0 -0.45 26 26
CREM 0.019 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.16 0.22 -9999 0 -0.41 125 125
FOS -0.004 0.051 -9999 0 -0.26 12 12
IFNG -0.39 0.43 -9999 0 -0.76 191 191
AP-1/NFAT1-c-4 -0.38 0.46 -9999 0 -0.79 180 180
FASLG -0.38 0.44 -9999 0 -0.77 179 179
NFAT1-c-4/ICER1 -0.082 0.15 -9999 0 -0.43 31 31
IL2RA -0.36 0.42 -9999 0 -0.74 179 179
FKBP12/FK506 0.014 0 -9999 0 -10000 0 0
CSF2 -0.31 0.36 -9999 0 -0.64 177 177
JunB/Fra1/NFAT1-c-4 -0.087 0.16 -9999 0 -0.4 45 45
IL4 -0.31 0.36 -9999 0 -0.64 176 176
IL2 -0.013 0.021 -9999 0 -10000 0 0
IL3 -0.029 0.026 -9999 0 -10000 0 0
FKBP1A 0.019 0 -9999 0 -10000 0 0
BATF3 0.007 0.081 -9999 0 -0.54 8 8
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.019 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.15 0.33 -9999 0 -0.66 98 98
MAP3K8 -0.003 0.11 -9999 0 -0.52 15 15
FOS -0.17 0.34 -9999 0 -0.69 99 99
PRKCA 0.014 0.044 -9999 0 -0.29 7 7
PTPN7 -0.12 0.24 -9999 0 -0.54 96 96
HRAS 0.019 0 -9999 0 -10000 0 0
PRKCB -0.15 0.26 -9999 0 -0.54 110 110
NRAS 0.019 0 -9999 0 -10000 0 0
RAS family/GTP 0.037 0.008 -9999 0 -10000 0 0
MAPK3 -0.17 0.33 -9999 0 -0.7 96 96
MAP2K1 -0.093 0.22 -9999 0 -0.42 110 110
ELK1 0.02 0.002 -9999 0 -10000 0 0
BRAF -0.095 0.21 -9999 0 -0.41 110 110
mol:GTP 0 0 -9999 0 -0.003 8 8
MAPK1 -0.17 0.33 -9999 0 -0.7 96 96
RAF1 -0.094 0.2 -9999 0 -0.4 110 110
KRAS 0.018 0.014 -9999 0 -0.24 1 1
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.1 0.27 -9999 0 -0.49 101 101
MAP4K1 -0.081 0.21 -9999 0 -0.54 66 66
MAP3K8 -0.003 0.11 -9999 0 -0.52 15 15
PRKCB -0.15 0.26 -9999 0 -0.54 110 110
DBNL 0.019 0 -9999 0 -10000 0 0
CRKL 0.018 0.014 -9999 0 -0.24 1 1
MAP3K1 -0.073 0.24 -9999 0 -0.6 53 53
JUN -0.2 0.35 -9999 0 -0.71 110 110
MAP3K7 -0.073 0.24 -9999 0 -0.6 53 53
GRAP2 -0.046 0.18 -9999 0 -0.54 43 43
CRK 0.019 0 -9999 0 -10000 0 0
MAP2K4 -0.07 0.25 -9999 0 -0.59 57 57
LAT -0.049 0.18 -9999 0 -0.54 45 45
LCP2 -0.016 0.14 -9999 0 -0.54 23 23
MAPK8 -0.2 0.37 -9999 0 -0.75 110 110
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.084 0.26 -9999 0 -0.64 53 53
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.086 0.26 -9999 0 -0.46 101 101
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.093 0.13 -9999 0 -0.25 155 155
CDC42/GTP -0.088 0.14 -9999 0 -0.27 121 121
PLCG1 -0.092 0.14 -9999 0 -0.28 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.019 0 -9999 0 -10000 0 0
GNAI3 0.019 0 -9999 0 -10000 0 0
G12/G13 0.028 0 -9999 0 -10000 0 0
cell migration -0.087 0.14 -9999 0 -0.26 121 121
S1PR5 0.008 0.052 -9999 0 -0.24 15 15
S1PR4 -0.16 0.26 -9999 0 -0.54 121 121
MAPK3 -0.092 0.14 -9999 0 -0.28 121 121
MAPK1 -0.092 0.14 -9999 0 -0.28 121 121
S1P/S1P5/Gi -0.017 0.065 -9999 0 -0.24 5 5
GNAI1 0.004 0.06 -9999 0 -0.24 20 20
CDC42/GDP 0.014 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.019 0.03 -9999 0 -10000 0 0
RHOA -0.063 0.14 -9999 0 -0.26 121 121
S1P/S1P4/Gi -0.1 0.15 -9999 0 -0.3 121 121
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.015 0.093 -9999 0 -0.26 45 45
S1P/S1P4/G12/G13 -0.07 0.15 -9999 0 -0.29 121 121
GNA12 0.019 0 -9999 0 -10000 0 0
GNA13 0.019 0 -9999 0 -10000 0 0
CDC42 0.019 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.016 0.041 -10000 0 -0.54 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.17 0.31 0.63 81 -10000 0 81
IL27/IL27R/JAK1 -0.17 0.35 -10000 0 -0.96 42 42
TBX21 -0.22 0.32 -10000 0 -0.66 115 115
IL12B -0.004 0.085 -10000 0 -0.54 9 9
IL12A -0.014 0.092 -10000 0 -0.38 21 21
IL6ST -0.001 0.082 -10000 0 -0.55 8 8
IL27RA/JAK1 -0.07 0.3 -10000 0 -1.3 20 20
IL27 -0.053 0.18 -10000 0 -0.55 40 40
TYK2 0.011 0.013 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.003 0.07 -10000 0 -0.67 1 1
T-helper 2 cell differentiation 0.17 0.31 0.63 81 -10000 0 81
T cell proliferation during immune response 0.17 0.31 0.63 81 -10000 0 81
MAPKKK cascade -0.17 0.31 -10000 0 -0.63 81 81
STAT3 0.019 0 -10000 0 -10000 0 0
STAT2 0.019 0 -10000 0 -10000 0 0
STAT1 0.015 0.041 -10000 0 -0.54 2 2
IL12RB1 -0.13 0.24 -10000 0 -0.54 97 97
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.2 0.27 -10000 0 -0.57 98 98
IL27/IL27R/JAK2/TYK2 -0.17 0.32 -10000 0 -0.64 81 81
positive regulation of T cell mediated cytotoxicity -0.17 0.31 -10000 0 -0.63 81 81
STAT1 (dimer) -0.26 0.37 -10000 0 -0.86 79 79
JAK2 0.006 0.073 -10000 0 -0.5 7 7
JAK1 0.018 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.15 0.3 -10000 0 -0.6 81 81
T cell proliferation -0.17 0.3 -10000 0 -0.61 84 84
IL12/IL12R/TYK2/JAK2 -0.17 0.28 -10000 0 -0.6 80 80
IL17A 0.003 0.07 -10000 0 -0.67 1 1
mast cell activation 0.17 0.31 0.63 81 -10000 0 81
IFNG -0.046 0.067 -10000 0 -0.12 145 145
T cell differentiation -0.01 0.011 0.012 1 -0.023 139 140
STAT3 (dimer) -0.15 0.3 -10000 0 -0.6 81 81
STAT5A (dimer) -0.15 0.3 -10000 0 -0.6 82 82
STAT4 (dimer) -0.22 0.36 -10000 0 -0.66 114 114
STAT4 -0.12 0.24 -10000 0 -0.54 92 92
T cell activation -0.003 0.032 0.13 20 -10000 0 20
IL27R/JAK2/TYK2 -0.08 0.3 -10000 0 -1.2 23 23
GATA3 -0.26 0.57 -10000 0 -1.3 80 80
IL18 -0.097 0.18 -10000 0 -0.39 99 99
positive regulation of mast cell cytokine production -0.15 0.28 -10000 0 -0.58 81 81
IL27/EBI3 -0.12 0.23 -10000 0 -0.48 99 99
IL27RA -0.083 0.32 -10000 0 -1.4 20 20
IL6 -0.008 0.11 -10000 0 -0.54 14 14
STAT5A 0.017 0.029 -10000 0 -0.54 1 1
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0.031 0.12 0.5 20 -10000 0 20
IL1B -0.03 0.12 -10000 0 -0.34 43 43
EBI3 -0.11 0.23 -10000 0 -0.55 82 82
TNF -0.071 0.16 -10000 0 -0.39 75 75
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0 0.048 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.069 0.11 -9999 0 -0.3 15 15
JUN -0.039 0.12 -9999 0 -0.31 14 14
HRAS 0.019 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.064 0.15 -9999 0 -0.29 106 106
RAP1A 0.019 0 -9999 0 -10000 0 0
FRS2 0.017 0.024 -9999 0 -0.24 3 3
RAP1A/GDP 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.063 0.15 -9999 0 -0.29 105 105
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.071 0.15 -9999 0 -0.29 103 103
RHOA 0.019 0 -9999 0 -10000 0 0
RAP1A/GTP -0.052 0.13 -9999 0 -0.25 102 102
GRB7 -0.004 0.068 -9999 0 -0.24 27 27
RET51/GFRalpha1/GDNF -0.063 0.15 -9999 0 -0.29 105 105
MAPKKK cascade -0.073 0.11 -9999 0 -0.37 4 4
BCAR1 0.019 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.081 0.15 -9999 0 -0.3 106 106
lamellipodium assembly -0.07 0.1 -9999 0 -0.24 101 101
RET51/GFRalpha1/GDNF/SHC -0.063 0.15 -9999 0 -0.29 105 105
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
RET9/GFRalpha1/GDNF/SHC -0.071 0.15 -9999 0 -0.29 103 103
RET9/GFRalpha1/GDNF/Shank3 -0.072 0.15 -9999 0 -0.29 103 103
MAPK3 -0.046 0.12 -9999 0 -0.23 102 102
DOK1 0.019 0 -9999 0 -10000 0 0
DOK6 -0.011 0.1 -9999 0 -0.3 34 34
PXN 0.019 0 -9999 0 -10000 0 0
neurite development -0.036 0.12 -9999 0 -0.32 12 12
DOK5 -0.05 0.12 -9999 0 -0.26 92 92
GFRA1 -0.13 0.24 -9999 0 -0.52 101 101
MAPK8 -0.036 0.12 -9999 0 -0.33 4 4
HRAS/GTP -0.062 0.14 -9999 0 -0.28 102 102
tube development -0.06 0.14 -9999 0 -0.27 103 103
MAPK1 -0.046 0.12 -9999 0 -0.23 102 102
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.051 0.12 -9999 0 -0.24 101 101
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
SRC 0.019 0 -9999 0 -10000 0 0
PDLIM7 0.019 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.065 0.15 -9999 0 -0.28 104 104
SHC1 0.019 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.063 0.15 -9999 0 -0.29 105 105
RET51/GFRalpha1/GDNF/Dok5 -0.098 0.16 -9999 0 -0.3 120 120
PRKCA 0.013 0.044 -9999 0 -0.29 7 7
HRAS/GDP 0.014 0 -9999 0 -10000 0 0
CREB1 -0.052 0.14 -9999 0 -0.27 101 101
PIK3R1 0.019 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.05 0.12 -9999 0 -0.24 101 101
RET51/GFRalpha1/GDNF/Grb7 -0.075 0.15 -9999 0 -0.29 110 110
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.014 0.04 -9999 0 -0.3 5 5
DOK4 0.019 0 -9999 0 -10000 0 0
JNK cascade -0.038 0.11 -9999 0 -0.3 14 14
RET9/GFRalpha1/GDNF/FRS2 -0.072 0.15 -9999 0 -0.29 103 103
SHANK3 0.017 0.019 -9999 0 -0.24 2 2
RASA1 0.017 0.029 -9999 0 -0.54 1 1
NCK1 0.019 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.12 -9999 0 -0.24 101 101
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.046 0.12 -9999 0 -0.23 102 102
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.046 0.12 -9999 0 -0.23 103 103
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.045 0.12 -9999 0 -0.23 102 102
PI3K -0.062 0.18 -9999 0 -0.34 101 101
SOS1 0.019 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.058 0.14 -9999 0 -0.27 103 103
GRB10 0.017 0.019 -9999 0 -0.24 2 2
activation of MAPKK activity -0.046 0.12 -9999 0 -0.33 11 11
RET51/GFRalpha1/GDNF/FRS2 -0.064 0.15 -9999 0 -0.28 106 106
GAB1 0.019 0 -9999 0 -10000 0 0
IRS1 -0.002 0.071 -9999 0 -0.24 29 29
IRS2 0.019 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.045 0.12 -9999 0 -0.23 102 102
RET51/GFRalpha1/GDNF/PKC alpha -0.066 0.15 -9999 0 -0.29 108 108
GRB2 0.019 0 -9999 0 -10000 0 0
PRKACA 0.019 0 -9999 0 -10000 0 0
GDNF -0.022 0.11 -9999 0 -0.3 43 43
RAC1 0.019 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.073 0.15 -9999 0 -0.3 108 108
Rac1/GTP -0.081 0.12 -9999 0 -0.28 101 101
RET9/GFRalpha1/GDNF -0.091 0.16 -9999 0 -0.33 103 103
GFRalpha1/GDNF -0.11 0.18 -9999 0 -0.39 103 103
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 -0.038 0.1 -10000 0 -0.28 27 27
fibroblast growth factor receptor signaling pathway -0.038 0.1 -10000 0 -0.28 27 27
LAMA1 -0.2 0.1 -10000 0 -0.24 302 302
PRNP 0.017 0.029 -10000 0 -0.54 1 1
GPC1/SLIT2 -0.052 0.11 -10000 0 -0.33 22 22
SMAD2 -0.007 0.062 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.025 0.072 -10000 0 -0.32 1 1
GPC1/Laminin alpha1 -0.17 0.1 -10000 0 -0.31 104 104
TDGF1 -0.088 0.21 -10000 0 -0.54 64 64
CRIPTO/GPC1 -0.11 0.16 -10000 0 -0.42 64 64
APP/GPC1 -0.035 0.09 -10000 0 -0.38 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.081 0.14 -10000 0 -0.35 64 64
FLT1 0.018 0.014 -10000 0 -0.24 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.013 0.073 -10000 0 -10000 0 0
SERPINC1 0.006 0.047 -10000 0 -0.24 12 12
FYN -0.081 0.14 -10000 0 -0.35 64 64
FGR -0.11 0.17 -10000 0 -0.37 95 95
positive regulation of MAPKKK cascade -0.3 0.29 -10000 0 -0.51 198 198
SLIT2 -0.012 0.095 -10000 0 -0.28 39 39
GPC1/NRG -0.044 0.1 -10000 0 -0.33 16 16
NRG1 -0.001 0.074 -10000 0 -0.29 20 20
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.021 0.083 -10000 0 -0.25 12 12
LYN -0.095 0.15 -10000 0 -0.36 77 77
mol:Spermine -0.045 0.083 -10000 0 -10000 0 0
cell growth -0.038 0.1 -10000 0 -0.28 27 27
BMP signaling pathway 0.069 0.12 0.24 122 -10000 0 122
SRC -0.081 0.14 -10000 0 -0.35 64 64
TGFBR1 0.019 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.061 0.16 -10000 0 -0.32 85 85
GPC1 -0.069 0.12 -10000 0 -0.24 122 122
TGFBR1 (dimer) 0.019 0 -10000 0 -10000 0 0
VEGFA 0.004 0.061 -10000 0 -0.24 21 21
BLK -0.3 0.21 -10000 0 -0.42 256 256
HCK -0.11 0.16 -10000 0 -0.36 91 91
FGF2 -0.004 0.08 -10000 0 -0.26 30 30
FGFR1 -0.003 0.073 -10000 0 -0.24 31 31
VEGFR1 homodimer 0.018 0.014 -10000 0 -0.24 1 1
TGFBR2 0.019 0 -10000 0 -10000 0 0
cell death -0.035 0.09 -10000 0 -0.38 3 3
ATIII/GPC1 -0.04 0.092 -10000 0 -0.31 7 7
PLA2G2A/GPC1 -0.086 0.14 -10000 0 -0.37 44 44
LCK -0.21 0.22 -10000 0 -0.41 180 180
neuron differentiation -0.044 0.1 -10000 0 -0.33 16 16
PrPc/Cu2+ 0.013 0.021 -10000 0 -0.39 1 1
APP 0.014 0.05 -10000 0 -0.54 3 3
TGFBR2 (dimer) 0.019 0 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.049 0.11 -9999 0 -0.33 31 31
FZD6 -0.01 0.12 -9999 0 -0.54 19 19
WNT6 0.007 0.052 -9999 0 -0.24 15 15
WNT4 -0.082 0.13 -9999 0 -0.24 140 140
FZD3 0.019 0 -9999 0 -10000 0 0
WNT5A -0.001 0.092 -9999 0 -0.37 19 19
WNT11 -0.066 0.12 -9999 0 -0.24 118 118
Glucocorticoid receptor regulatory network

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
PCK2 0.069 0.11 0.34 10 -10000 0 10
SMARCC2 0.021 0 -10000 0 -10000 0 0
SMARCC1 0.021 0 -10000 0 -10000 0 0
TBX21 -0.28 0.41 -10000 0 -0.83 121 121
SUMO2 0.021 0.009 -10000 0 -10000 0 0
STAT1 (dimer) -0.012 0.12 -10000 0 -0.33 39 39
FKBP4 0.018 0.014 -10000 0 -0.24 1 1
FKBP5 -0.021 0.14 -10000 0 -0.54 26 26
GR alpha/HSP90/FKBP51/HSP90 0.1 0.14 0.3 84 -0.27 8 92
PRL -0.11 0.17 -10000 0 -0.55 19 19
cortisol/GR alpha (dimer)/TIF2 0.27 0.29 0.56 152 -0.35 1 153
RELA -0.006 0.066 -10000 0 -0.22 5 5
FGG 0.2 0.23 0.5 102 -0.47 1 103
GR beta/TIF2 0.14 0.14 0.32 107 -10000 0 107
IFNG -0.52 0.6 -10000 0 -1.2 145 145
apoptosis 0.086 0.16 0.49 37 -10000 0 37
CREB1 0.019 0.016 -10000 0 -10000 0 0
histone acetylation -0.079 0.17 -10000 0 -0.35 77 77
BGLAP -0.091 0.17 -10000 0 -0.44 37 37
GR/PKAc 0.13 0.11 0.3 83 -10000 0 83
NF kappa B1 p50/RelA -0.006 0.12 -10000 0 -0.32 17 17
SMARCD1 0.021 0 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.24 118 -10000 0 118
GATA3 -0.1 0.23 -10000 0 -0.54 80 80
AKT1 0.01 0.001 -10000 0 -10000 0 0
CSF2 -0.1 0.18 -10000 0 -0.55 20 20
GSK3B 0.021 0.009 -10000 0 -10000 0 0
NR1I3 0.096 0.14 0.48 34 -10000 0 34
CSN2 0.16 0.18 0.4 95 -0.32 1 96
BRG1/BAF155/BAF170/BAF60A 0.058 0.001 -10000 0 -10000 0 0
NFATC1 0.007 0.086 -10000 0 -0.54 9 9
POU2F1 0.013 0.027 -10000 0 -10000 0 0
CDKN1A 0.033 0.032 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.009 -10000 0 -10000 0 0
SFN -0.035 0.11 -10000 0 -0.24 74 74
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.084 0.14 0.3 62 -0.3 9 71
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.083 0.15 0.45 36 -10000 0 36
JUN -0.2 0.22 -10000 0 -0.45 123 123
IL4 -0.12 0.19 -10000 0 -0.5 42 42
CDK5R1 0.018 0.029 -10000 0 -0.54 1 1
PRKACA 0.019 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.096 0.17 0.22 19 -0.39 60 79
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.3 81 -0.24 5 86
cortisol/GR alpha (monomer) 0.31 0.36 0.68 152 -0.42 1 153
NCOA2 0.018 0.014 -10000 0 -0.24 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.036 0.075 -10000 0 -0.29 12 12
AP-1/NFAT1-c-4 -0.27 0.31 -10000 0 -0.62 130 130
AFP -0.14 0.15 -10000 0 -0.59 1 1
SUV420H1 0.019 0 -10000 0 -10000 0 0
IRF1 0.061 0.34 0.46 59 -0.76 43 102
TP53 0.043 0.013 -10000 0 -10000 0 0
PPP5C 0.019 0 -10000 0 -10000 0 0
KRT17 -0.27 0.3 -10000 0 -0.68 98 98
KRT14 -0.18 0.19 -10000 0 -0.55 40 40
TBP 0.03 0.007 -10000 0 -10000 0 0
CREBBP 0.044 0.044 -10000 0 -10000 0 0
HDAC1 0.017 0.029 -10000 0 -0.54 1 1
HDAC2 0.017 0.005 -10000 0 -10000 0 0
AP-1 -0.28 0.32 -10000 0 -0.62 130 130
MAPK14 0.021 0.008 -10000 0 -10000 0 0
MAPK10 -0.031 0.1 -10000 0 -0.24 71 71
MAPK11 0.021 0.009 -10000 0 -10000 0 0
KRT5 -0.33 0.42 -10000 0 -0.86 111 111
interleukin-1 receptor activity -0.002 0.005 -10000 0 -10000 0 0
NCOA1 0.023 0.002 -10000 0 -10000 0 0
STAT1 -0.012 0.12 -10000 0 -0.33 39 39
CGA -0.11 0.17 -10000 0 -0.47 35 35
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.14 0.35 86 -10000 0 86
MAPK3 0.021 0.009 -10000 0 -10000 0 0
MAPK1 0.021 0.008 -10000 0 -10000 0 0
ICAM1 -0.15 0.26 -10000 0 -0.59 70 70
NFKB1 -0.006 0.066 -10000 0 -0.21 7 7
MAPK8 -0.17 0.21 -10000 0 -0.42 119 119
MAPK9 0.021 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.082 0.16 0.49 37 -10000 0 37
BAX 0.034 0.019 -10000 0 -10000 0 0
POMC -0.27 0.53 -10000 0 -1.4 53 53
EP300 0.044 0.044 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.28 0.29 0.58 151 -10000 0 151
proteasomal ubiquitin-dependent protein catabolic process 0.07 0.085 0.2 80 -10000 0 80
SGK1 0.1 0.064 -10000 0 -10000 0 0
IL13 -0.29 0.36 -10000 0 -0.88 76 76
IL6 -0.17 0.3 -10000 0 -0.78 48 48
PRKACG 0.002 0.02 -10000 0 -0.24 2 2
IL5 -0.26 0.31 -10000 0 -0.78 73 73
IL2 -0.25 0.29 -10000 0 -0.69 76 76
CDK5 0.02 0.004 -10000 0 -10000 0 0
PRKACB 0.018 0.014 -10000 0 -0.24 1 1
HSP90AA1 0.017 0.029 -10000 0 -0.54 1 1
IL8 -0.18 0.27 -10000 0 -0.61 77 77
CDK5R1/CDK5 0.029 0.024 -10000 0 -0.38 1 1
NF kappa B1 p50/RelA/PKAc 0.021 0.09 -10000 0 -0.28 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.27 0.54 151 -10000 0 151
SMARCA4 0.021 0 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.17 0.4 112 -10000 0 112
NF kappa B1 p50/RelA/Cbp 0.046 0.11 0.32 1 -0.31 2 3
JUN (dimer) -0.19 0.22 -10000 0 -0.45 123 123
YWHAH 0.019 0 -10000 0 -10000 0 0
VIPR1 -0.25 0.39 -10000 0 -0.79 116 116
NR3C1 0.19 0.23 0.45 128 -10000 0 128
NR4A1 -0.029 0.15 -10000 0 -0.41 46 46
TIF2/SUV420H1 0.028 0.009 -10000 0 -10000 0 0
MAPKKK cascade 0.086 0.16 0.49 37 -10000 0 37
cortisol/GR alpha (dimer)/Src-1 0.27 0.29 0.57 152 -0.35 1 153
PBX1 -0.006 0.081 -10000 0 -0.28 26 26
POU1F1 -0.002 0.028 -10000 0 -10000 0 0
SELE -0.23 0.41 -10000 0 -0.95 74 74
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.17 0.4 112 -10000 0 112
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.27 0.54 151 -10000 0 151
mol:cortisol 0.18 0.23 0.41 146 -0.24 1 147
MMP1 -0.17 0.34 -10000 0 -0.86 52 52
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization -0.037 0.12 -10000 0 -0.23 101 101
epithelial cell differentiation -0.042 0.14 -10000 0 -0.26 101 101
CYFIP2 -0.01 0.12 -10000 0 -0.54 19 19
ENAH 0.005 0.095 -10000 0 -0.31 2 2
EGFR -0.007 0.087 -10000 0 -0.27 33 33
EPHA2 0.013 0.058 -10000 0 -0.54 4 4
MYO6 -0.039 0.13 -10000 0 -0.24 101 101
CTNNB1 0.019 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.02 0.079 -10000 0 -0.32 19 19
AQP5 -0.043 0.12 -10000 0 -0.32 15 15
CTNND1 0.019 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.037 0.12 -10000 0 -0.24 101 101
regulation of calcium-dependent cell-cell adhesion -0.046 0.13 -10000 0 -0.24 110 110
EGF -0.031 0.15 -10000 0 -0.42 41 41
NCKAP1 0.019 0 -10000 0 -10000 0 0
AQP3 -0.085 0.2 -10000 0 -0.52 49 49
cortical microtubule organization -0.042 0.14 -10000 0 -0.26 101 101
GO:0000145 -0.037 0.12 -10000 0 -0.23 101 101
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.04 0.14 -10000 0 -0.26 101 101
MLLT4 0.001 0.066 -10000 0 -0.24 25 25
ARF6/GDP -0.055 0.089 -10000 0 -0.43 2 2
ARF6 0.019 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.034 -10000 0 -0.28 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.024 0.12 -10000 0 -0.29 2 2
PVRL2 0.019 0 -10000 0 -10000 0 0
ZYX -0.038 0.13 -10000 0 -0.25 101 101
ARF6/GTP 0.05 0.032 -10000 0 -0.25 4 4
CDH1 -0.13 0.25 -10000 0 -0.54 101 101
EGFR/EGFR/EGF/EGF -0.092 0.13 -10000 0 -0.27 119 119
RhoA/GDP -0.036 0.13 -10000 0 -0.24 101 101
actin cytoskeleton organization -0.032 0.12 -10000 0 -0.23 101 101
IGF-1R heterotetramer 0.016 0.027 -10000 0 -0.24 4 4
GIT1 0.019 0 -10000 0 -10000 0 0
IGF1R 0.016 0.027 -10000 0 -0.24 4 4
IGF1 0.008 0.066 -10000 0 -0.36 10 10
DIAPH1 -0.026 0.14 -10000 0 -0.63 19 19
Wnt receptor signaling pathway 0.042 0.14 0.26 101 -10000 0 101
RHOA 0.019 0 -10000 0 -10000 0 0
RhoA/GTP -0.055 0.09 -10000 0 -0.43 2 2
CTNNA1 0.019 0 -10000 0 -10000 0 0
VCL -0.033 0.13 -10000 0 -0.24 101 101
EFNA1 0.019 0 -10000 0 -10000 0 0
LPP -0.03 0.12 -10000 0 -0.23 102 102
Ephrin A1/EPHA2 -0.066 0.11 -10000 0 -0.23 103 103
SEC6/SEC8 -0.061 0.094 -10000 0 -0.3 7 7
MGAT3 -0.046 0.13 -10000 0 -0.25 110 110
HGF/MET -0.088 0.14 -10000 0 -0.27 115 115
HGF 0 0.085 -10000 0 -0.34 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.038 0.12 -10000 0 -0.23 101 101
actin cable formation 0.021 0.097 -10000 0 -0.22 10 10
KIAA1543 -0.059 0.14 -10000 0 -0.32 34 34
KIFC3 -0.038 0.13 -10000 0 -0.24 101 101
NCK1 0.019 0 -10000 0 -10000 0 0
EXOC3 0.018 0.014 -10000 0 -0.24 1 1
ACTN1 -0.038 0.13 -10000 0 -0.24 102 102
NCK1/GIT1 0.028 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.14 -10000 0 -0.26 101 101
EXOC4 0.019 0 -10000 0 -10000 0 0
STX4 -0.038 0.13 -10000 0 -0.24 101 101
PIP5K1C -0.038 0.13 -10000 0 -0.24 101 101
LIMA1 0.019 0 -10000 0 -10000 0 0
ABI1 0.019 0 -10000 0 -10000 0 0
ROCK1 -0.003 0.11 -10000 0 -0.37 2 2
adherens junction assembly -0.039 0.14 -10000 0 -0.36 19 19
IGF-1R heterotetramer/IGF1 -0.068 0.11 -10000 0 -0.36 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0.045 -10000 0 -10000 0 0
MET -0.024 0.14 -10000 0 -0.43 35 35
PLEKHA7 -0.048 0.14 -10000 0 -0.25 112 112
mol:GTP 0.043 0.034 -10000 0 -0.28 4 4
establishment of epithelial cell apical/basal polarity -0.015 0.12 -10000 0 -0.29 7 7
cortical actin cytoskeleton stabilization -0.037 0.12 -10000 0 -0.23 101 101
regulation of cell-cell adhesion -0.032 0.12 -10000 0 -0.23 101 101
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.038 0.12 -10000 0 -0.23 101 101
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.017 0.019 -9999 0 -0.24 2 2
ITGB7 -0.063 0.2 -9999 0 -0.54 54 54
ITGA4 -0.043 0.18 -9999 0 -0.54 41 41
alpha4/beta7 Integrin -0.076 0.2 -9999 0 -0.42 84 84
alpha4/beta1 Integrin -0.019 0.13 -9999 0 -0.38 41 41
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.048 0.17 -9999 0 -0.42 53 53
alphaM/beta2 Integrin/GPIbA -0.2 0.25 -9999 0 -0.4 202 202
alphaM/beta2 Integrin/proMMP-9 -0.086 0.23 -9999 0 -0.47 86 86
PLAUR 0.013 0.044 -9999 0 -0.29 7 7
HMGB1 0.011 0.021 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.027 0.16 -9999 0 -0.44 44 44
AGER 0.009 0.031 -9999 0 -0.24 3 3
RAP1A 0.019 0 -9999 0 -10000 0 0
SELPLG -0.036 0.16 -9999 0 -0.54 36 36
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.038 0.2 -9999 0 -0.47 48 48
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.082 0.21 -9999 0 -0.52 68 68
CYR61 0.011 0.054 -9999 0 -0.31 9 9
TLN1 0.019 0 -9999 0 -10000 0 0
Rap1/GTP -0.11 0.19 -9999 0 -0.48 60 60
RHOA 0.019 0 -9999 0 -10000 0 0
P-selectin oligomer -0.17 0.26 -9999 0 -0.54 123 123
MYH2 -0.12 0.22 -9999 0 -0.44 81 81
MST1R -0.014 0.13 -9999 0 -0.48 24 24
leukocyte activation during inflammatory response -0.04 0.14 -9999 0 -0.4 44 44
APOB -0.013 0.071 -9999 0 -0.24 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.019 0.097 -9999 0 -0.26 50 50
JAM3 -0.007 0.078 -9999 0 -0.24 36 36
GP1BA -0.27 0.28 -9999 0 -0.54 191 191
alphaM/beta2 Integrin/CTGF -0.034 0.16 -9999 0 -0.43 46 46
alphaM/beta2 Integrin -0.12 0.24 -9999 0 -0.52 70 70
JAM3 homodimer -0.007 0.078 -9999 0 -0.24 36 36
ICAM2 -0.019 0.14 -9999 0 -0.54 25 25
ICAM1 0.008 0.076 -9999 0 -0.54 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.24 -9999 0 -0.51 70 70
cell adhesion -0.2 0.25 -9999 0 -0.4 202 202
NFKB1 -0.066 0.25 -9999 0 -0.46 87 87
THY1 0.015 0.043 -9999 0 -0.44 3 3
RhoA/GDP 0.014 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.006 0.039 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.019 0.15 -9999 0 -0.39 46 46
IL6 -0.07 0.26 -9999 0 -0.67 45 45
ITGB2 -0.057 0.19 -9999 0 -0.57 44 44
elevation of cytosolic calcium ion concentration -0.02 0.16 -9999 0 -0.4 46 46
alphaM/beta2 Integrin/JAM2/JAM3 -0.027 0.16 -9999 0 -0.42 45 45
JAM2 0.015 0.043 -9999 0 -0.44 3 3
alphaM/beta2 Integrin/ICAM1 -0.026 0.18 -9999 0 -0.38 63 63
alphaM/beta2 Integrin/uPA/Plg -0.027 0.15 -9999 0 -0.41 44 44
RhoA/GTP -0.13 0.23 -9999 0 -0.38 123 123
positive regulation of phagocytosis -0.099 0.25 -9999 0 -0.58 62 62
Ron/MSP 0.002 0.096 -9999 0 -0.38 21 21
alphaM/beta2 Integrin/uPAR/uPA -0.019 0.16 -9999 0 -0.4 46 46
alphaM/beta2 Integrin/uPAR -0.03 0.17 -9999 0 -0.45 44 44
PLAU 0.012 0.048 -9999 0 -0.28 9 9
PLAT 0.012 0.051 -9999 0 -0.33 7 7
actin filament polymerization -0.11 0.21 -9999 0 -0.42 81 81
MST1 0.016 0.035 -9999 0 -0.34 3 3
alphaM/beta2 Integrin/lipoprotein(a) -0.038 0.15 -9999 0 -0.4 44 44
TNF -0.14 0.38 -9999 0 -0.83 79 79
RAP1B 0.019 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.17 -9999 0 -0.45 44 44
fibrinolysis -0.028 0.15 -9999 0 -0.41 44 44
HCK -0.028 0.16 -9999 0 -0.54 31 31
dendritic cell antigen processing and presentation -0.12 0.24 -9999 0 -0.51 70 70
VTN -0.058 0.19 -9999 0 -0.5 54 54
alphaM/beta2 Integrin/CYR61 -0.031 0.16 -9999 0 -0.44 46 46
LPA 0 0 -9999 0 -10000 0 0
LRP1 0.014 0.036 -9999 0 -0.24 7 7
cell migration -0.09 0.22 -9999 0 -0.43 89 89
FN1 0 0.1 -9999 0 -0.52 13 13
alphaM/beta2 Integrin/Thy1 -0.029 0.16 -9999 0 -0.44 46 46
MPO -0.033 0.16 -9999 0 -0.53 34 34
KNG1 -0.004 0.049 -9999 0 -0.24 14 14
RAP1/GDP 0.026 0 -9999 0 -10000 0 0
ROCK1 -0.11 0.22 -9999 0 -0.45 74 74
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0 -9999 0 -10000 0 0
CTGF 0.007 0.059 -9999 0 -0.26 16 16
alphaM/beta2 Integrin/Hck -0.052 0.23 -9999 0 -0.62 46 46
ITGAM -0.006 0.099 -9999 0 -0.56 11 11
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.29 -9999 0 -0.45 139 139
HP -0.12 0.23 -9999 0 -0.5 94 94
leukocyte adhesion -0.035 0.19 -9999 0 -0.51 38 38
SELP -0.17 0.26 -9999 0 -0.54 123 123
Endothelins

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
AKT1 -0.026 0.18 0.29 21 -0.42 33 54
PTK2B 0.008 0.076 -10000 0 -0.54 7 7
mol:Ca2+ -0.031 0.18 -10000 0 -0.5 13 13
EDN1 -0.017 0.13 0.24 21 -0.33 24 45
EDN3 -0.063 0.15 -10000 0 -0.31 86 86
EDN2 0 0 -10000 0 -10000 0 0
HRAS/GDP -0.07 0.22 -10000 0 -0.46 61 61
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.04 0.18 0.21 13 -0.43 44 57
ADCY4 -0.038 0.16 -10000 0 -0.34 50 50
ADCY5 -0.096 0.19 -10000 0 -0.33 110 110
ADCY6 -0.036 0.15 -10000 0 -0.34 47 47
ADCY7 -0.036 0.15 -10000 0 -0.34 48 48
ADCY1 -0.078 0.18 -10000 0 -0.33 89 89
ADCY2 -0.089 0.16 -10000 0 -0.34 76 76
ADCY3 -0.035 0.15 -10000 0 -0.34 46 46
ADCY8 -0.05 0.16 -10000 0 -0.34 54 54
ADCY9 -0.035 0.15 -10000 0 -0.34 46 46
arachidonic acid secretion -0.037 0.18 -10000 0 -0.4 46 46
ETB receptor/Endothelin-1/Gq/GTP -0.039 0.14 -10000 0 -0.3 68 68
GNAO1 -0.093 0.13 -10000 0 -0.25 155 155
HRAS 0.019 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.005 0.18 0.37 23 -0.38 33 56
ETA receptor/Endothelin-1/Gs/GTP -0.026 0.18 0.33 23 -0.36 47 70
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.046 0.2 0.29 21 -0.4 54 75
EDNRB -0.024 0.094 -10000 0 -0.25 50 50
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.065 0.25 0.29 21 -0.61 48 69
CYSLTR1 -0.073 0.27 0.29 20 -0.6 60 80
SLC9A1 -0.006 0.1 0.21 20 -0.23 27 47
mol:GDP -0.085 0.23 0.23 6 -0.49 65 71
SLC9A3 -0.18 0.3 -10000 0 -0.59 103 103
RAF1 -0.067 0.21 -10000 0 -0.47 54 54
JUN -0.035 0.19 -10000 0 -0.52 12 12
JAK2 -0.032 0.19 0.29 20 -0.42 37 57
mol:IP3 -0.054 0.2 -10000 0 -0.42 59 59
ETA receptor/Endothelin-1 -0.029 0.23 0.44 23 -0.46 38 61
PLCB1 -0.002 0.11 -10000 0 -0.54 14 14
PLCB2 0.001 0.099 -10000 0 -0.54 12 12
ETA receptor/Endothelin-3 -0.055 0.14 -10000 0 -0.3 60 60
FOS -0.031 0.17 -10000 0 -0.5 16 16
Gai/GDP -0.034 0.091 -10000 0 -0.62 2 2
CRK 0.019 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.07 0.23 0.27 12 -0.49 58 70
BCAR1 0.019 0.001 -10000 0 -10000 0 0
PRKCB1 -0.05 0.19 -10000 0 -0.4 59 59
GNAQ 0.02 0.005 -10000 0 -10000 0 0
GNAZ -0.015 0.093 -10000 0 -0.26 45 45
GNAL -0.02 0.1 -10000 0 -0.28 49 49
Gs family/GDP -0.094 0.21 -10000 0 -0.46 63 63
ETA receptor/Endothelin-1/Gq/GTP -0.041 0.17 0.23 15 -0.39 48 63
MAPK14 -0.028 0.15 -10000 0 -0.4 31 31
TRPC6 -0.033 0.19 -10000 0 -0.52 13 13
GNAI2 0.019 0 -10000 0 -10000 0 0
GNAI3 0.019 0 -10000 0 -10000 0 0
GNAI1 0.004 0.06 -10000 0 -0.24 20 20
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.037 0.16 -10000 0 -0.35 50 50
ETB receptor/Endothelin-2 -0.014 0.064 -10000 0 -0.25 5 5
ETB receptor/Endothelin-3 -0.058 0.12 -10000 0 -0.27 49 49
ETB receptor/Endothelin-1 -0.026 0.12 -10000 0 -0.31 24 24
MAPK3 -0.044 0.2 -10000 0 -0.48 33 33
MAPK1 -0.044 0.2 -10000 0 -0.48 33 33
Rac1/GDP -0.071 0.22 -10000 0 -0.47 59 59
cAMP biosynthetic process -0.091 0.18 0.22 3 -0.37 72 75
MAPK8 -0.039 0.19 -10000 0 -0.44 41 41
SRC 0.019 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.027 0.079 -10000 0 -0.26 11 11
p130Cas/CRK/Src/PYK2 -0.074 0.23 -10000 0 -0.49 59 59
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.071 0.22 -10000 0 -0.46 61 61
COL1A2 -0.057 0.2 -10000 0 -0.5 29 29
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.012 0.088 -10000 0 -0.25 14 14
mol:DAG -0.054 0.2 -10000 0 -0.42 59 59
MAP2K2 -0.052 0.2 -10000 0 -0.46 44 44
MAP2K1 -0.052 0.2 -10000 0 -0.47 42 42
EDNRA -0.023 0.13 0.24 21 -0.31 29 50
positive regulation of muscle contraction -0.014 0.15 0.25 21 -0.37 29 50
Gq family/GDP -0.12 0.22 -10000 0 -0.52 67 67
HRAS/GTP -0.082 0.22 -10000 0 -0.45 69 69
PRKCH -0.044 0.19 -10000 0 -0.42 52 52
RAC1 0.019 0 -10000 0 -10000 0 0
PRKCA -0.045 0.19 -10000 0 -0.42 52 52
PRKCB -0.12 0.26 -10000 0 -0.49 92 92
PRKCE -0.041 0.19 -10000 0 -0.42 49 49
PRKCD -0.043 0.19 -10000 0 -0.41 51 51
PRKCG -0.046 0.19 -10000 0 -0.42 52 52
regulation of vascular smooth muscle contraction -0.04 0.2 -10000 0 -0.61 15 15
PRKCQ -0.13 0.26 -10000 0 -0.45 107 107
PLA2G4A -0.041 0.2 -10000 0 -0.43 46 46
GNA14 -0.083 0.22 -10000 0 -0.53 69 69
GNA15 0.003 0.095 -10000 0 -0.54 11 11
GNA12 0.019 0 -10000 0 -10000 0 0
GNA11 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.18 0.38 23 -0.38 33 56
MMP1 -0.058 0.26 0.29 2 -0.66 43 45
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.09 0.22 -9999 0 -0.44 101 101
KLHL20 -0.002 0.089 -9999 0 -0.22 8 8
CYFIP2 -0.01 0.12 -9999 0 -0.54 19 19
Rac1/GDP -0.021 0.14 -9999 0 -0.25 99 99
ENAH -0.09 0.22 -9999 0 -0.44 101 101
AP1M1 0.019 0 -9999 0 -10000 0 0
RAP1B 0.019 0 -9999 0 -10000 0 0
RAP1A 0.019 0 -9999 0 -10000 0 0
CTNNB1 0.019 0 -9999 0 -10000 0 0
CDC42/GTP -0.048 0.079 -9999 0 -0.24 7 7
ABI1/Sra1/Nap1 -0.032 0.046 -9999 0 -0.17 15 15
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.088 0.19 -9999 0 -0.32 134 134
RAPGEF1 -0.064 0.19 -9999 0 -0.38 101 101
CTNND1 0.019 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.098 0.23 -9999 0 -0.46 101 101
CRK -0.077 0.21 -9999 0 -0.41 101 101
E-cadherin/gamma catenin/alpha catenin -0.064 0.16 -9999 0 -0.32 101 101
alphaE/beta7 Integrin -0.032 0.14 -9999 0 -0.38 54 54
IQGAP1 0.019 0 -9999 0 -10000 0 0
NCKAP1 0.019 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.027 0.035 -9999 0 -10000 0 0
DLG1 -0.089 0.22 -9999 0 -0.44 101 101
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.057 -9999 0 -0.17 8 8
MLLT4 0.001 0.066 -9999 0 -0.24 25 25
ARF6/GTP/NME1/Tiam1 0.017 0.077 -9999 0 -0.29 22 22
PI3K -0.044 0.072 -9999 0 -0.22 8 8
ARF6 0.019 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.09 0.19 -9999 0 -0.39 101 101
TIAM1 -0.014 0.13 -9999 0 -0.54 22 22
E-cadherin(dimer)/Ca2+ -0.04 0.14 -9999 0 -0.26 101 101
AKT1 -0.025 0.042 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
CDH1 -0.13 0.25 -9999 0 -0.54 101 101
RhoA/GDP -0.021 0.14 -9999 0 -0.25 99 99
actin cytoskeleton organization 0.001 0.068 -9999 0 -0.16 7 7
CDC42/GDP -0.021 0.14 -9999 0 -0.25 99 99
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.048 0.12 -9999 0 -0.25 101 101
ITGB7 -0.063 0.2 -9999 0 -0.54 54 54
RAC1 0.019 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.042 0.15 -9999 0 -0.28 101 101
E-cadherin/Ca2+/beta catenin/alpha catenin -0.05 0.14 -9999 0 -0.27 101 101
mol:GDP -0.038 0.16 -9999 0 -0.29 101 101
CDC42/GTP/IQGAP1 0.026 0 -9999 0 -10000 0 0
JUP 0.011 0.045 -9999 0 -0.24 11 11
p120 catenin/RhoA/GDP -0.022 0.14 -9999 0 -0.25 99 99
RAC1/GTP/IQGAP1 0.026 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.028 0 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
CDC42 0.019 0 -9999 0 -10000 0 0
CTNNA1 0.019 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.004 0.05 -9999 0 -0.12 6 6
NME1 0.019 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.089 0.22 -9999 0 -0.44 101 101
regulation of cell-cell adhesion -0.043 0.07 -9999 0 -0.21 7 7
WASF2 -0.016 0.025 -9999 0 -0.11 2 2
Rap1/GTP -0.015 0.12 -9999 0 -0.28 7 7
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.077 0.18 -9999 0 -0.3 134 134
CCND1 0.003 0.06 -9999 0 -0.15 6 6
VAV2 -0.073 0.22 -9999 0 -0.41 102 102
RAP1/GDP -0.019 0.12 -9999 0 -0.28 7 7
adherens junction assembly -0.086 0.21 -9999 0 -0.43 101 101
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.019 0 -9999 0 -10000 0 0
PIP5K1C 0.019 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.069 0.18 -9999 0 -0.29 134 134
E-cadherin/beta catenin -0.086 0.17 -9999 0 -0.36 101 101
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.089 0.22 -9999 0 -0.44 101 101
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
Rac1/GTP -0.066 0.095 -9999 0 -0.35 8 8
E-cadherin/beta catenin/alpha catenin -0.059 0.16 -9999 0 -0.32 101 101
ITGAE 0.019 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.1 0.23 -9999 0 -0.48 101 101
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.017 0.029 -9999 0 -0.54 1 1
Caspase 8 (4 units) -0.037 0.13 -9999 0 -0.44 11 11
NEF -0.029 0.054 -9999 0 -0.19 19 19
NFKBIA -0.017 0.054 -9999 0 -10000 0 0
BIRC3 -0.16 0.29 -9999 0 -0.56 128 128
CYCS -0.049 0.14 -9999 0 -0.44 11 11
RIPK1 0.019 0 -9999 0 -10000 0 0
CD247 -0.23 0.33 -9999 0 -0.67 128 128
MAP2K7 -0.042 0.14 -9999 0 -0.38 15 15
protein ubiquitination -0.011 0.12 -9999 0 -0.39 11 11
CRADD 0.018 0.014 -9999 0 -0.24 1 1
DAXX 0.019 0 -9999 0 -10000 0 0
FAS 0.007 0.081 -9999 0 -0.54 8 8
BID -0.058 0.15 -9999 0 -0.25 121 121
NF-kappa-B/RelA/I kappa B alpha -0.059 0.15 -9999 0 -0.27 128 128
TRADD 0.019 0 -9999 0 -10000 0 0
MAP3K5 0.016 0.041 -9999 0 -0.54 2 2
CFLAR 0.019 0 -9999 0 -10000 0 0
FADD 0.018 0.014 -9999 0 -0.24 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.06 0.15 -9999 0 -0.27 128 128
MAPK8 -0.033 0.13 -9999 0 -0.36 15 15
APAF1 0.019 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.098 -9999 0 -0.46 15 15
TRAF2 0.019 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.069 0.15 -9999 0 -0.27 121 121
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.034 0.15 -9999 0 -0.33 58 58
CHUK -0.014 0.13 -9999 0 -0.43 11 11
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.046 0.056 -9999 0 -0.26 12 12
TCRz/NEF -0.21 0.31 -9999 0 -0.57 147 147
TNF -0.095 0.22 -9999 0 -0.54 75 75
FASLG -0.28 0.4 -9999 0 -0.74 147 147
NFKB1 -0.017 0.054 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.035 0.14 -9999 0 -0.32 76 76
CASP6 -0.01 0.11 -9999 0 -0.4 11 11
CASP7 -0.15 0.3 -9999 0 -0.55 128 128
RELA -0.017 0.054 -9999 0 -10000 0 0
CASP2 0.019 0 -9999 0 -10000 0 0
CASP3 -0.15 0.3 -9999 0 -0.55 128 128
TNFRSF1A 0.019 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.027 0.021 -9999 0 -0.38 1 1
CASP8 0.016 0.041 -9999 0 -0.54 2 2
CASP9 0.019 0 -9999 0 -10000 0 0
MAP3K14 -0.024 0.14 -9999 0 -0.31 48 48
APAF-1/Caspase 9 -0.16 0.2 -9999 0 -0.43 128 128
BCL2 -0.023 0.12 -9999 0 -0.36 10 10
TCGA08_retinoblastoma

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
CDKN2B -0.008 0.088 -10000 0 -0.28 31 31
CDKN2C 0.029 0.012 -10000 0 -10000 0 0
CDKN2A -0.11 0.14 -10000 0 -0.25 172 172
CCND2 0.022 0.065 0.18 23 -0.13 14 37
RB1 -0.026 0.063 -10000 0 -0.18 23 23
CDK4 0.03 0.063 0.19 23 -10000 0 23
CDK6 0.028 0.066 0.2 23 -0.16 1 24
G1/S progression 0.026 0.063 0.18 23 -10000 0 23
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.014 0.04 -10000 0 -0.3 5 5
GNB1/GNG2 -0.057 0.085 -10000 0 -0.2 93 93
AKT1 -0.011 0.12 -10000 0 -0.2 92 92
EGF -0.031 0.15 -10000 0 -0.42 41 41
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.097 -10000 0 -0.25 38 38
mol:Ca2+ -0.04 0.17 -10000 0 -0.31 94 94
LYN 0.027 0.08 -10000 0 -0.29 16 16
RhoA/GTP -0.035 0.055 -10000 0 -0.13 93 93
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.064 0.21 -10000 0 -0.38 104 104
GNG2 0.01 0.071 -10000 0 -0.54 6 6
ARRB2 0.019 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.001 0.11 -10000 0 -0.48 12 12
G beta5/gamma2 -0.073 0.11 -10000 0 -0.26 93 93
PRKCH -0.046 0.18 -10000 0 -0.34 95 95
DNM1 -0.009 0.081 -10000 0 -0.24 39 39
TXA2/TP beta/beta Arrestin3 -0.006 0.024 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.002 0.095 -10000 0 -0.54 11 11
G12 family/GTP -0.087 0.13 -10000 0 -0.31 94 94
ADRBK1 0.019 0 -10000 0 -10000 0 0
ADRBK2 0.014 0.05 -10000 0 -0.54 3 3
RhoA/GTP/ROCK1 0.025 0.001 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 0.37 12 -10000 0 12
mol:NADP 0.014 0.042 -10000 0 -0.29 6 6
RAB11A 0.019 0 -10000 0 -10000 0 0
PRKG1 -0.088 0.13 -10000 0 -0.24 148 148
mol:IP3 -0.058 0.2 -10000 0 -0.39 94 94
cell morphogenesis 0.025 0.001 -10000 0 -10000 0 0
PLCB2 -0.091 0.27 -10000 0 -0.53 94 94
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.12 0.13 -10000 0 -0.24 113 113
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.017 0.095 -10000 0 -0.27 28 28
RHOA 0.019 0 -10000 0 -10000 0 0
PTGIR 0.014 0.05 -10000 0 -0.54 3 3
PRKCB1 -0.055 0.2 -10000 0 -0.37 94 94
GNAQ 0.019 0 -10000 0 -10000 0 0
mol:L-citrulline 0.014 0.042 -10000 0 -0.29 6 6
TXA2/TXA2-R family -0.097 0.28 -10000 0 -0.55 94 94
LCK -0.058 0.14 -10000 0 -0.23 135 135
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.024 0.05 -10000 0 -0.26 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.034 0.029 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.033 0.051 -10000 0 -0.26 2 2
MAPK14 -0.029 0.14 -10000 0 -0.25 95 95
TGM2/GTP -0.082 0.22 -10000 0 -0.44 94 94
MAPK11 -0.029 0.14 -10000 0 -0.24 101 101
ARHGEF1 -0.014 0.1 -10000 0 -0.18 93 93
GNAI2 0.019 0 -10000 0 -10000 0 0
JNK cascade -0.061 0.21 -10000 0 -0.4 94 94
RAB11/GDP 0.019 0.002 -10000 0 -10000 0 0
ICAM1 -0.036 0.16 -10000 0 -0.29 93 93
cAMP biosynthetic process -0.059 0.19 -10000 0 -0.37 94 94
Gq family/GTP/EBP50 -0.012 0.095 -10000 0 -0.33 11 11
actin cytoskeleton reorganization 0.025 0.001 -10000 0 -10000 0 0
SRC 0.037 0.05 -10000 0 -0.25 2 2
GNB5 0.017 0.029 -10000 0 -0.54 1 1
GNB1 0.019 0 -10000 0 -10000 0 0
EGF/EGFR -0.11 0.15 -10000 0 -0.28 127 127
VCAM1 -0.059 0.2 -10000 0 -0.38 93 93
TP beta/Gq family/GDP/G beta5/gamma2 0.001 0.11 -10000 0 -0.48 12 12
platelet activation -0.034 0.18 -10000 0 -0.32 94 94
PGI2/IP 0.011 0.037 -10000 0 -0.39 3 3
PRKACA 0.015 0.055 -10000 0 -0.26 14 14
Gq family/GDP/G beta5/gamma2 0 0.11 -10000 0 -0.46 12 12
TXA2/TP beta/beta Arrestin2 -0.011 0.031 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.018 0.056 -10000 0 -0.25 15 15
mol:DAG -0.064 0.22 -10000 0 -0.42 94 94
EGFR -0.007 0.087 -10000 0 -0.27 33 33
TXA2/TP alpha -0.089 0.26 -10000 0 -0.51 94 94
Gq family/GTP -0.045 0.097 -10000 0 -0.24 72 72
YES1 0.037 0.05 -10000 0 -0.25 2 2
GNAI2/GTP -0.01 0.044 -10000 0 -0.24 5 5
PGD2/DP 0.002 0.069 -10000 0 -0.39 11 11
SLC9A3R1 0.019 0 -10000 0 -10000 0 0
FYN 0.037 0.05 -10000 0 -0.25 2 2
mol:NO 0.014 0.042 -10000 0 -0.29 6 6
GNA15 0.002 0.095 -10000 0 -0.54 11 11
PGK/cGMP -0.038 0.078 -10000 0 -0.32 3 3
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.039 0.066 -10000 0 -0.37 2 2
NOS3 0.014 0.042 -10000 0 -0.3 6 6
RAC1 0.019 0 -10000 0 -10000 0 0
PRKCA -0.047 0.18 -10000 0 -0.34 94 94
PRKCB -0.087 0.23 -10000 0 -0.44 94 94
PRKCE -0.039 0.18 -10000 0 -0.34 94 94
PRKCD -0.054 0.2 -10000 0 -0.38 94 94
PRKCG -0.057 0.2 -10000 0 -0.38 94 94
muscle contraction -0.092 0.26 -10000 0 -0.52 94 94
PRKCZ -0.048 0.19 -10000 0 -0.35 93 93
ARR3 0.004 0.008 -10000 0 -10000 0 0
TXA2/TP beta 0.032 0.06 -10000 0 -0.24 9 9
PRKCQ -0.09 0.23 -10000 0 -0.44 95 95
MAPKKK cascade -0.089 0.25 -10000 0 -0.5 94 94
SELE -0.056 0.19 -10000 0 -0.36 93 93
TP beta/GNAI2/GDP/G beta/gamma 0.041 0.064 -10000 0 -0.32 3 3
ROCK1 0.019 0 -10000 0 -10000 0 0
GNA14 -0.084 0.22 -10000 0 -0.53 69 69
chemotaxis -0.12 0.32 -10000 0 -0.64 93 93
GNA12 0.019 0 -10000 0 -10000 0 0
GNA13 0.019 0 -10000 0 -10000 0 0
GNA11 0.019 0 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.002 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.003 0.11 -9999 0 -0.56 12 12
Syndecan-4/Syndesmos -0.055 0.21 -9999 0 -0.49 65 65
positive regulation of JNK cascade -0.07 0.22 -9999 0 -0.5 68 68
Syndecan-4/ADAM12 -0.063 0.21 -9999 0 -0.49 65 65
CCL5 -0.15 0.26 -9999 0 -0.54 110 110
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
DNM2 0.019 0 -9999 0 -10000 0 0
ITGA5 0.015 0.031 -9999 0 -0.24 5 5
SDCBP 0.019 0 -9999 0 -10000 0 0
PLG 0 0.006 -9999 0 -10000 0 0
ADAM12 -0.001 0.07 -9999 0 -0.24 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.019 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.005 0.01 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.2 -9999 0 -0.56 66 66
Syndecan-4/CXCL12/CXCR4 -0.074 0.24 -9999 0 -0.54 68 68
Syndecan-4/Laminin alpha3 -0.064 0.21 -9999 0 -0.5 66 66
MDK 0.004 0.07 -9999 0 -0.3 17 17
Syndecan-4/FZD7 -0.056 0.21 -9999 0 -0.5 65 65
Syndecan-4/Midkine -0.061 0.21 -9999 0 -0.5 65 65
FZD7 0.015 0.037 -9999 0 -0.32 4 4
Syndecan-4/FGFR1/FGF -0.064 0.2 -9999 0 -0.46 65 65
THBS1 -0.006 0.077 -9999 0 -0.24 34 34
integrin-mediated signaling pathway -0.061 0.21 -9999 0 -0.49 67 67
positive regulation of MAPKKK cascade -0.07 0.22 -9999 0 -0.5 68 68
Syndecan-4/TACI -0.19 0.25 -9999 0 -0.61 73 73
CXCR4 -0.024 0.15 -9999 0 -0.54 28 28
cell adhesion 0.019 0.059 -9999 0 -0.27 13 13
Syndecan-4/Dynamin -0.055 0.21 -9999 0 -0.49 65 65
Syndecan-4/TSP1 -0.065 0.21 -9999 0 -0.49 66 66
Syndecan-4/GIPC -0.055 0.21 -9999 0 -0.49 65 65
Syndecan-4/RANTES -0.13 0.26 -9999 0 -0.63 67 67
ITGB1 0.017 0.019 -9999 0 -0.24 2 2
LAMA1 -0.2 0.1 -9999 0 -0.24 302 302
LAMA3 0 0.1 -9999 0 -0.52 13 13
RAC1 0.019 0 -9999 0 -10000 0 0
PRKCA 0.018 0.053 -9999 0 -0.27 6 6
Syndecan-4/alpha-Actinin -0.056 0.21 -9999 0 -0.49 65 65
TFPI 0.014 0.04 -9999 0 -0.3 5 5
F2 -0.01 0.052 -9999 0 -0.25 16 16
alpha5/beta1 Integrin 0.025 0.029 -9999 0 -0.31 2 2
positive regulation of cell adhesion -0.14 0.2 -9999 0 -0.52 75 75
ACTN1 0.017 0.029 -9999 0 -0.54 1 1
TNC -0.001 0.1 -9999 0 -0.48 15 15
Syndecan-4/CXCL12 -0.067 0.22 -9999 0 -0.5 66 66
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
CXCL12 -0.005 0.11 -9999 0 -0.54 16 16
TNFRSF13B -0.26 0.28 -9999 0 -0.54 180 180
FGF2 -0.004 0.08 -9999 0 -0.26 30 30
FGFR1 -0.003 0.073 -9999 0 -0.24 31 31
Syndecan-4/PI-4-5-P2 -0.066 0.2 -9999 0 -0.49 65 65
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.001 0.096 -9999 0 -0.5 13 13
cell migration 0.002 0.006 -9999 0 -10000 0 0
PRKCD 0.02 0.005 -9999 0 -10000 0 0
vasculogenesis -0.062 0.2 -9999 0 -0.47 66 66
SDC4 -0.069 0.22 -9999 0 -0.52 65 65
Syndecan-4/Tenascin C -0.064 0.22 -9999 0 -0.51 67 67
Syndecan-4/PI-4-5-P2/PKC alpha -0.004 0.008 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.055 0.21 -9999 0 -0.49 65 65
MMP9 -0.081 0.21 -9999 0 -0.52 68 68
Rac1/GTP 0.019 0.06 -9999 0 -0.28 13 13
cytoskeleton organization -0.052 0.2 -9999 0 -0.47 65 65
GIPC1 0.019 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.057 0.21 -9999 0 -0.49 65 65
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.083 0.36 -10000 0 -0.84 63 63
NCK1/PAK1/Dok-R -0.087 0.16 -10000 0 -0.42 64 64
NCK1/Dok-R -0.16 0.44 -10000 0 -1.1 63 63
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
mol:beta2-estradiol 0.03 0.089 0.22 62 -10000 0 62
RELA 0.019 0 -10000 0 -10000 0 0
SHC1 0.019 0.002 -10000 0 -10000 0 0
Rac/GDP 0.014 0 -10000 0 -10000 0 0
F2 0.022 0.11 0.24 43 -0.26 15 58
TNIP2 0.019 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.4 -10000 0 -0.99 63 63
FN1 0 0.1 -10000 0 -0.52 13 13
PLD2 -0.15 0.44 -10000 0 -1.1 63 63
PTPN11 0.019 0 -10000 0 -10000 0 0
GRB14 -0.027 0.096 -10000 0 -0.24 59 59
ELK1 -0.12 0.4 -10000 0 -0.97 63 63
GRB7 -0.004 0.068 -10000 0 -0.24 27 27
PAK1 0.018 0.014 -10000 0 -0.24 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.14 0.42 -10000 0 -1 63 63
CDKN1A -0.02 0.23 -10000 0 -0.5 61 61
ITGA5 0.015 0.031 -10000 0 -0.24 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.16 0.44 -10000 0 -1.1 63 63
CRK 0.019 0 -10000 0 -10000 0 0
mol:NO -0.046 0.28 -10000 0 -0.63 63 63
PLG -0.16 0.44 -10000 0 -1.1 63 63
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.081 0.35 -10000 0 -0.83 63 63
GRB2 0.019 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.002 -10000 0 -10000 0 0
ANGPT2 -0.035 0.18 -10000 0 -0.4 60 60
BMX -0.2 0.45 -10000 0 -1.1 63 63
ANGPT1 -0.22 0.52 -10000 0 -1.3 63 63
tube development -0.034 0.25 -10000 0 -0.55 63 63
ANGPT4 0.001 0.002 -10000 0 -10000 0 0
response to hypoxia -0.01 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.18 0.45 -10000 0 -1.1 63 63
alpha5/beta1 Integrin 0.025 0.029 -10000 0 -0.31 2 2
FGF2 -0.005 0.08 -10000 0 -0.26 30 30
STAT5A (dimer) -0.035 0.28 -10000 0 -0.62 62 62
mol:L-citrulline -0.046 0.28 -10000 0 -0.63 63 63
AGTR1 0.001 0.003 -10000 0 -10000 0 0
MAPK14 -0.13 0.41 -10000 0 -1 63 63
Tie2/SHP2 -0.004 0.14 -10000 0 -1.2 2 2
TEK -0.012 0.16 -10000 0 -1.4 2 2
RPS6KB1 -0.077 0.34 -10000 0 -0.81 63 63
Angiotensin II/AT1 0.004 0.005 -10000 0 -10000 0 0
Tie2/Ang1/GRB2 -0.16 0.45 -10000 0 -1.1 63 63
MAPK3 -0.13 0.4 -10000 0 -1 63 63
MAPK1 -0.13 0.4 -10000 0 -1 63 63
Tie2/Ang1/GRB7 -0.16 0.45 -10000 0 -1.1 63 63
NFKB1 0.019 0 -10000 0 -10000 0 0
MAPK8 -0.15 0.44 -10000 0 -1.1 63 63
PI3K -0.11 0.4 -10000 0 -0.96 63 63
FES -0.13 0.42 -10000 0 -1 63 63
Crk/Dok-R -0.16 0.44 -10000 0 -1.1 63 63
Tie2/Ang1/ABIN2 -0.16 0.45 -10000 0 -1.1 63 63
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.069 0.32 -10000 0 -0.75 63 63
STAT5A 0.018 0.029 -10000 0 -0.54 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.077 0.34 -10000 0 -0.81 63 63
Tie2/Ang2 -0.062 0.31 -10000 0 -0.71 63 63
Tie2/Ang1 -0.17 0.47 -10000 0 -1.2 63 63
FOXO1 -0.067 0.32 -10000 0 -0.76 63 63
ELF1 0.027 0.011 -10000 0 -10000 0 0
ELF2 -0.15 0.43 -10000 0 -1.1 63 63
mol:Choline -0.14 0.42 -10000 0 -1 63 63
cell migration -0.049 0.088 -10000 0 -0.23 64 64
FYN -0.043 0.28 -10000 0 -0.62 63 63
DOK2 -0.037 0.17 -10000 0 -0.54 37 37
negative regulation of cell cycle -0.014 0.22 -10000 0 -0.46 61 61
ETS1 -0.012 0.087 -10000 0 -0.22 40 40
PXN -0.051 0.29 -10000 0 -0.67 63 63
ITGB1 0.017 0.019 -10000 0 -0.24 2 2
NOS3 -0.059 0.31 -10000 0 -0.71 63 63
RAC1 0.019 0 -10000 0 -10000 0 0
TNF -0.13 0.25 -10000 0 -0.46 115 115
MAPKKK cascade -0.14 0.42 -10000 0 -1 63 63
RASA1 0.017 0.029 -10000 0 -0.54 1 1
Tie2/Ang1/Shc -0.15 0.45 -10000 0 -1.1 63 63
NCK1 0.019 0 -10000 0 -10000 0 0
vasculogenesis -0.035 0.25 -10000 0 -0.56 63 63
mol:Phosphatidic acid -0.14 0.42 -10000 0 -1 63 63
mol:Angiotensin II 0.001 0.003 -10000 0 -10000 0 0
mol:NADP -0.046 0.28 -10000 0 -0.63 63 63
Rac1/GTP -0.14 0.28 -10000 0 -0.76 63 63
MMP2 -0.17 0.44 -10000 0 -1.1 63 63
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 0.016 0.041 -9999 0 -0.54 2 2
CCL5 -0.15 0.26 -9999 0 -0.54 110 110
SDCBP 0.019 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.06 0.17 -9999 0 -0.32 89 89
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 -0.049 0.17 -9999 0 -0.51 29 29
Syndecan-1/Syntenin -0.048 0.17 -9999 0 -0.5 29 29
MAPK3 -0.031 0.15 -9999 0 -0.44 29 29
HGF/MET -0.016 0.12 -9999 0 -0.4 27 27
TGFB1/TGF beta receptor Type II 0.016 0.041 -9999 0 -0.54 2 2
BSG 0.018 0.014 -9999 0 -0.24 1 1
keratinocyte migration -0.048 0.17 -9999 0 -0.5 29 29
Syndecan-1/RANTES -0.13 0.23 -9999 0 -0.4 122 122
Syndecan-1/CD147 -0.038 0.16 -9999 0 -0.48 29 29
Syndecan-1/Syntenin/PIP2 -0.047 0.16 -9999 0 -0.48 29 29
LAMA5 0.017 0.029 -9999 0 -0.54 1 1
positive regulation of cell-cell adhesion -0.047 0.16 -9999 0 -0.47 29 29
MMP7 -0.016 0.11 -9999 0 -0.33 35 35
HGF 0 0.085 -9999 0 -0.34 19 19
Syndecan-1/CASK -0.059 0.16 -9999 0 -0.31 89 89
Syndecan-1/HGF/MET -0.066 0.19 -9999 0 -0.49 45 45
regulation of cell adhesion -0.024 0.15 -9999 0 -0.46 25 25
HPSE 0.019 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.06 0.17 -9999 0 -0.32 89 89
SDC1 -0.061 0.18 -9999 0 -0.32 89 89
Syndecan-1/Collagen -0.06 0.17 -9999 0 -0.32 89 89
PPIB 0.019 0 -9999 0 -10000 0 0
MET -0.024 0.14 -9999 0 -0.43 35 35
PRKACA 0.019 0 -9999 0 -10000 0 0
MMP9 -0.082 0.21 -9999 0 -0.52 68 68
MAPK1 -0.031 0.15 -9999 0 -0.47 26 26
homophilic cell adhesion -0.059 0.17 -9999 0 -0.32 89 89
MMP1 -0.058 0.16 -9999 0 -0.35 76 76
LPA receptor mediated events

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.034 0.14 -9999 0 -0.31 66 66
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.092 -9999 0 -0.3 11 11
AP1 -0.082 0.11 -9999 0 -0.28 71 71
mol:PIP3 -0.068 0.096 -9999 0 -0.24 70 70
AKT1 0.012 0.1 -9999 0 -0.32 11 11
PTK2B -0.035 0.12 -9999 0 -0.26 70 70
RHOA 0.01 0.045 -9999 0 -0.29 1 1
PIK3CB 0.019 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.008 0.077 -9999 0 -0.33 7 7
MAGI3 0.019 0 -9999 0 -10000 0 0
RELA 0.019 0 -9999 0 -10000 0 0
apoptosis -0.061 0.13 -9999 0 -0.29 73 73
HRAS/GDP 0.014 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.071 0.12 -9999 0 -0.3 64 64
NF kappa B1 p50/RelA -0.062 0.11 -9999 0 -0.31 44 44
endothelial cell migration -0.066 0.16 -9999 0 -0.3 107 107
ADCY4 -0.086 0.18 -9999 0 -0.44 69 69
ADCY5 -0.13 0.22 -9999 0 -0.46 91 91
ADCY6 -0.084 0.18 -9999 0 -0.43 69 69
ADCY7 -0.085 0.18 -9999 0 -0.44 68 68
ADCY1 -0.12 0.2 -9999 0 -0.44 86 86
ADCY2 -0.11 0.18 -9999 0 -0.44 75 75
ADCY3 -0.084 0.18 -9999 0 -0.43 68 68
ADCY8 -0.093 0.18 -9999 0 -0.42 72 72
ADCY9 -0.084 0.18 -9999 0 -0.43 68 68
GSK3B -0.026 0.12 -9999 0 -0.27 49 49
arachidonic acid secretion -0.077 0.17 -9999 0 -0.4 69 69
GNG2 0.01 0.07 -9999 0 -0.54 6 6
TRIP6 0.025 0.022 -9999 0 -10000 0 0
GNAO1 -0.11 0.16 -9999 0 -0.38 77 77
HRAS 0.019 0 -9999 0 -10000 0 0
NFKBIA -0.018 0.099 -9999 0 -0.32 16 16
GAB1 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.023 0.23 -9999 0 -0.94 22 22
JUN -0.008 0.079 -9999 0 -0.24 37 37
LPA/LPA2/NHERF2 0.018 0.038 -9999 0 -0.32 3 3
TIAM1 -0.06 0.27 -9999 0 -1.1 22 22
PIK3R1 0.019 0.001 -9999 0 -10000 0 0
mol:IP3 -0.008 0.079 -9999 0 -0.34 7 7
PLCB3 0.022 0.033 -9999 0 -0.28 3 3
FOS 0.01 0.047 -9999 0 -0.24 12 12
positive regulation of mitosis -0.077 0.17 -9999 0 -0.4 69 69
LPA/LPA1-2-3 -0.063 0.14 -9999 0 -0.3 75 75
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.019 0 -9999 0 -10000 0 0
stress fiber formation -0.035 0.12 -9999 0 -0.27 67 67
GNAZ -0.066 0.15 -9999 0 -0.34 70 70
EGFR/PI3K-beta/Gab1 -0.07 0.1 -9999 0 -0.25 70 70
positive regulation of dendritic cell cytokine production -0.064 0.14 -9999 0 -0.3 75 75
LPA/LPA2/MAGI-3 0.019 0.037 -9999 0 -0.32 3 3
ARHGEF1 -0.025 0.12 -9999 0 -0.26 65 65
GNAI2 -0.047 0.14 -9999 0 -0.32 65 65
GNAI3 -0.047 0.14 -9999 0 -0.32 65 65
GNAI1 -0.055 0.14 -9999 0 -0.33 69 69
LPA/LPA3 -0.033 0.076 -9999 0 -0.16 85 85
LPA/LPA2 0.006 0.042 -9999 0 -0.39 3 3
LPA/LPA1 -0.068 0.16 -9999 0 -0.29 108 108
HB-EGF/EGFR -0.046 0.14 -9999 0 -0.32 68 68
HBEGF -0.049 0.16 -9999 0 -0.38 65 65
mol:DAG -0.008 0.079 -9999 0 -0.34 7 7
cAMP biosynthetic process -0.11 0.18 -9999 0 -0.44 74 74
NFKB1 0.019 0 -9999 0 -10000 0 0
SRC 0.019 0 -9999 0 -10000 0 0
GNB1 0.019 0.001 -9999 0 -10000 0 0
LYN -0.036 0.15 -9999 0 -0.44 28 28
GNAQ -0.007 0.056 -9999 0 -0.25 4 4
LPAR2 0.014 0.05 -9999 0 -0.54 3 3
LPAR3 -0.044 0.11 -9999 0 -0.24 85 85
LPAR1 -0.085 0.21 -9999 0 -0.52 66 66
IL8 -0.094 0.17 -9999 0 -0.36 64 64
PTK2 -0.056 0.13 -9999 0 -0.28 75 75
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
CASP3 -0.062 0.13 -9999 0 -0.29 73 73
EGFR -0.008 0.087 -9999 0 -0.27 33 33
PLCG1 -0.025 0.087 -9999 0 -0.25 27 27
PLD2 -0.056 0.13 -9999 0 -0.28 75 75
G12/G13 -0.028 0.13 -9999 0 -0.29 65 65
PI3K-beta -0.042 0.086 -9999 0 -0.37 11 11
cell migration -0.006 0.091 -9999 0 -0.27 23 23
SLC9A3R2 0.018 0.014 -9999 0 -0.24 1 1
PXN -0.036 0.12 -9999 0 -0.27 67 67
HRAS/GTP -0.079 0.17 -9999 0 -0.41 69 69
RAC1 0.019 0 -9999 0 -10000 0 0
MMP9 -0.082 0.21 -9999 0 -0.52 68 68
PRKCE 0.019 0 -9999 0 -10000 0 0
PRKCD -0.001 0.075 -9999 0 -0.34 6 6
Gi(beta/gamma) -0.077 0.17 -9999 0 -0.4 69 69
mol:LPA -0.008 0.035 -9999 0 -0.18 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.029 0.14 -9999 0 -0.31 44 44
MAPKKK cascade -0.077 0.17 -9999 0 -0.4 69 69
contractile ring contraction involved in cytokinesis 0.01 0.045 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.064 0.14 -9999 0 -0.32 69 69
GNA15 -0.017 0.083 -9999 0 -0.35 13 13
GNA12 0.019 0 -9999 0 -10000 0 0
GNA13 0.019 0 -9999 0 -10000 0 0
MAPT -0.073 0.13 -9999 0 -0.3 64 64
GNA11 -0.007 0.056 -9999 0 -0.25 4 4
Rac1/GTP -0.025 0.25 -9999 0 -1 22 22
MMP2 -0.066 0.16 -9999 0 -0.3 107 107
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.15 0.32 -10000 0 -0.72 71 71
UGCG -0.011 0.082 -10000 0 -0.78 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT -0.061 0.21 -10000 0 -0.38 97 97
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.011 0.081 -10000 0 -0.76 2 2
mol:DAG -0.011 0.079 -10000 0 -1.1 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.16 0.22 -10000 0 -0.47 112 112
FRAP1 -0.12 0.31 -10000 0 -0.55 112 112
FOXO3 -0.12 0.3 -10000 0 -0.55 112 112
AKT1 -0.14 0.33 -10000 0 -0.6 112 112
GAB2 0.016 0.031 -10000 0 -0.24 5 5
SMPD1 -0.007 0.058 -10000 0 -10000 0 0
SGMS1 -0.012 0.096 -10000 0 -1 2 2
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 0.023 0.008 -10000 0 -10000 0 0
CALM1 0.019 0 -10000 0 -10000 0 0
cell proliferation -0.032 0.14 -10000 0 -0.32 19 19
EIF3A 0.019 0 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
RPS6KB1 0.005 0.063 -10000 0 -0.25 13 13
mol:sphingomyelin -0.011 0.079 -10000 0 -1.1 2 2
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.016 0.14 -10000 0 -0.54 25 25
PIK3R1 0.022 0.002 -10000 0 -10000 0 0
JAK1 0.022 0.002 -10000 0 -10000 0 0
NFKB1 0.019 0 -10000 0 -10000 0 0
MYC -0.099 0.27 -10000 0 -0.52 94 94
MYB -0.031 0.29 -10000 0 -1.3 19 19
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.17 0.36 -10000 0 -0.66 121 121
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.061 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.16 0.35 -10000 0 -0.64 121 121
Rac1/GDP 0.034 0.007 -10000 0 -10000 0 0
T cell proliferation -0.15 0.32 -10000 0 -0.58 121 121
SHC1 0.02 0.001 -10000 0 -10000 0 0
RAC1 0.019 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.016 -10000 0 -0.066 19 19
PRKCZ -0.16 0.34 -10000 0 -0.61 121 121
NF kappa B1 p50/RelA -0.086 0.27 -10000 0 -0.47 112 112
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.17 0.35 -10000 0 -0.65 112 112
HSP90AA1 0.017 0.029 -10000 0 -0.54 1 1
RELA 0.019 0 -10000 0 -10000 0 0
IL2RA -0.12 0.24 -10000 0 -0.54 93 93
IL2RB -0.08 0.22 -10000 0 -0.54 67 67
TERT 0.001 0.072 -10000 0 -0.27 22 22
E2F1 0.007 0.11 -10000 0 -0.45 19 19
SOS1 0.02 0.001 -10000 0 -10000 0 0
RPS6 0.019 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.008 0.031 19 -10000 0 19
PTPN11 0.02 0.001 -10000 0 -10000 0 0
IL2RG -0.15 0.26 -10000 0 -0.54 112 112
actin cytoskeleton organization -0.15 0.32 -10000 0 -0.58 121 121
GRB2 0.02 0.001 -10000 0 -10000 0 0
IL2 0.008 0.016 -10000 0 -0.24 1 1
PIK3CA 0.021 0.014 -10000 0 -0.24 1 1
Rac1/GTP 0.046 0.013 -10000 0 -10000 0 0
LCK -0.19 0.27 -10000 0 -0.54 142 142
BCL2 -0.075 0.24 -10000 0 -0.44 95 95
IL2 signaling events mediated by STAT5

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
GAB2 0.016 0.031 -9999 0 -0.24 5 5
ELF1 -0.063 0.16 -9999 0 -0.34 93 93
CCNA2 0.017 0.029 -9999 0 -0.54 1 1
PIK3CA 0.019 0.014 -9999 0 -0.24 1 1
JAK3 -0.018 0.14 -9999 0 -0.54 25 25
PIK3R1 0.019 0 -9999 0 -10000 0 0
JAK1 0.02 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.18 0.37 -9999 0 -0.68 121 121
SHC1 0.02 0 -9999 0 -10000 0 0
SP1 0.003 0.094 -9999 0 -0.34 26 26
IL2RA -0.17 0.36 -9999 0 -0.78 93 93
IL2RB -0.082 0.22 -9999 0 -0.54 67 67
SOS1 0.019 0 -9999 0 -10000 0 0
IL2RG -0.15 0.26 -9999 0 -0.54 112 112
G1/S transition of mitotic cell cycle -0.032 0.24 -9999 0 -0.81 30 30
PTPN11 0.02 0 -9999 0 -10000 0 0
CCND2 -0.022 0.21 -9999 0 -0.76 27 27
LCK -0.2 0.27 -9999 0 -0.54 142 142
GRB2 0.019 0 -9999 0 -10000 0 0
IL2 0.005 0.016 -9999 0 -0.24 1 1
CDK6 0.014 0.052 -9999 0 -0.46 4 4
CCND3 -0.14 0.31 -9999 0 -0.61 96 96
Paxillin-independent events mediated by a4b1 and a4b7

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 -0.053 0.17 -9999 0 -0.35 84 84
CRKL 0.018 0.014 -9999 0 -0.24 1 1
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
DOCK1 0.019 0 -9999 0 -10000 0 0
ITGA4 -0.043 0.18 -9999 0 -0.54 41 41
alpha4/beta7 Integrin/MAdCAM1 -0.21 0.22 -9999 0 -0.36 237 237
EPO 0.011 0.021 -9999 0 -0.24 2 2
alpha4/beta7 Integrin -0.076 0.2 -9999 0 -0.42 84 84
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.13 -9999 0 -0.38 41 41
EPO/EPOR (dimer) 0.022 0.017 -9999 0 -10000 0 0
lamellipodium assembly 0.041 0.01 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
PI3K 0.028 0.009 -9999 0 -10000 0 0
ARF6 0.019 0 -9999 0 -10000 0 0
JAK2 -0.002 0.12 -9999 0 -0.31 41 41
PXN 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
MADCAM1 -0.29 0.27 -9999 0 -0.54 204 204
cell adhesion -0.21 0.22 -9999 0 -0.35 237 237
CRKL/CBL 0.028 0.009 -9999 0 -10000 0 0
ITGB1 0.017 0.019 -9999 0 -0.24 2 2
SRC -0.051 0.18 -9999 0 -0.38 76 76
ITGB7 -0.063 0.2 -9999 0 -0.54 54 54
RAC1 0.019 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.059 0.2 -9999 0 -0.43 76 76
p130Cas/Crk/Dock1 -0.018 0.16 -9999 0 -0.47 28 28
VCAM1 -0.077 0.21 -9999 0 -0.54 63 63
RHOA 0.019 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.011 0.1 -9999 0 -0.28 41 41
BCAR1 -0.041 0.17 -9999 0 -0.35 76 76
EPOR 0.018 0.014 -9999 0 -0.24 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.019 0 -9999 0 -10000 0 0
GIT1 0.019 0 -9999 0 -10000 0 0
Rac1/GTP 0.041 0.01 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.019 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.008 0.076 -9999 0 -0.54 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.019 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.021 0.025 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.019 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 0.019 0 -9999 0 -10000 0 0
FYN 0.019 0 -9999 0 -10000 0 0
MAP3K12 0.019 0 -9999 0 -10000 0 0
FGR -0.036 0.16 -9999 0 -0.54 36 36
p38 alpha/TAB1 -0.13 0.15 -9999 0 -0.3 122 122
PRKG1 -0.088 0.13 -9999 0 -0.24 148 148
DUSP8 -0.026 0.1 -9999 0 -0.24 63 63
PGK/cGMP/p38 alpha -0.16 0.16 -9999 0 -0.35 119 119
apoptosis -0.12 0.14 -9999 0 -0.28 122 122
RAL/GTP 0.026 0 -9999 0 -10000 0 0
LYN -0.004 0.11 -9999 0 -0.54 15 15
DUSP1 0.014 0.036 -9999 0 -0.24 7 7
PAK1 0.018 0.014 -9999 0 -0.24 1 1
SRC 0.019 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.049 0 -9999 0 -10000 0 0
TRAF6 0.019 0 -9999 0 -10000 0 0
RAC1 0.019 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 0.019 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.026 0 -9999 0 -10000 0 0
MAPK11 -0.16 0.21 -9999 0 -0.39 122 122
BLK -0.34 0.26 -9999 0 -0.54 236 236
HCK -0.028 0.16 -9999 0 -0.54 31 31
MAP2K3 0.019 0 -9999 0 -10000 0 0
DUSP16 0.019 0 -9999 0 -10000 0 0
DUSP10 0.013 0.058 -9999 0 -0.54 4 4
TRAF6/MEKK3 0.024 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.12 0.18 -9999 0 -0.32 122 122
positive regulation of innate immune response -0.17 0.23 -9999 0 -0.42 124 124
LCK -0.2 0.27 -9999 0 -0.54 142 142
p38alpha-beta/MKP7 -0.16 0.22 -9999 0 -0.4 121 121
p38alpha-beta/MKP5 -0.16 0.22 -9999 0 -0.4 124 124
PGK/cGMP -0.057 0.087 -9999 0 -0.16 148 148
PAK2 0.019 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.16 0.22 -9999 0 -0.4 122 122
CDC42 0.019 0 -9999 0 -10000 0 0
RALB 0.019 0 -9999 0 -10000 0 0
RALA 0.019 0 -9999 0 -10000 0 0
PAK3 -0.014 0.081 -9999 0 -0.24 40 40
Class I PI3K 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
ARF5/GTP 0.042 0.014 0.25 1 -10000 0 1
DAPP1 -0.34 0.43 -10000 0 -0.75 154 154
Src family/SYK family/BLNK-LAT/BTK-ITK -0.42 0.46 -10000 0 -0.86 167 167
mol:DAG -0.13 0.16 -10000 0 -0.31 145 145
HRAS 0.02 0.001 -10000 0 -10000 0 0
RAP1A 0.02 0.001 -10000 0 -10000 0 0
ARF5/GDP -0.005 0.12 -10000 0 -0.36 22 22
PLCG2 -0.03 0.16 -10000 0 -0.54 32 32
PLCG1 0.019 0 -10000 0 -10000 0 0
ARF5 0.019 0 -10000 0 -10000 0 0
mol:GTP 0.026 0.013 0.23 1 -10000 0 1
ARF1/GTP 0.04 0.013 0.24 1 -10000 0 1
RHOA 0.019 0 -10000 0 -10000 0 0
YES1 0.019 0 -10000 0 -10000 0 0
RAP1A/GTP 0.031 0.013 0.23 1 -10000 0 1
ADAP1 0.023 0.049 -10000 0 -0.24 12 12
ARAP3 0.026 0.013 0.23 1 -10000 0 1
INPPL1 0.019 0 -10000 0 -10000 0 0
PREX1 0.016 0.041 -10000 0 -0.54 2 2
ARHGEF6 -0.005 0.11 -10000 0 -0.54 16 16
ARHGEF7 0.019 0 -10000 0 -10000 0 0
ARF1 0.019 0 -10000 0 -10000 0 0
NRAS 0.02 0.001 -10000 0 -10000 0 0
FYN 0.019 0 -10000 0 -10000 0 0
ARF6 0.019 0 -10000 0 -10000 0 0
FGR -0.036 0.16 -10000 0 -0.54 36 36
mol:Ca2+ -0.053 0.081 -10000 0 -0.15 87 87
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.014 0.13 -10000 0 -0.54 22 22
ZAP70 -0.17 0.26 -10000 0 -0.54 126 126
mol:IP3 -0.079 0.11 -10000 0 -0.21 137 137
LYN -0.004 0.11 -10000 0 -0.54 15 15
ARF1/GDP -0.005 0.12 -10000 0 -0.36 22 22
RhoA/GDP 0.029 0.062 -10000 0 -0.34 2 2
PDK1/Src/Hsp90 0.037 0.019 -10000 0 -0.32 1 1
BLNK -0.19 0.27 -10000 0 -0.54 140 140
actin cytoskeleton reorganization 0.02 0.099 -10000 0 -0.48 3 3
SRC 0.019 0 -10000 0 -10000 0 0
PLEKHA2 -0.03 0.14 -10000 0 -0.33 62 62
RAC1 0.019 0 -10000 0 -10000 0 0
PTEN 0.013 0.028 -10000 0 -0.51 1 1
HSP90AA1 0.017 0.029 -10000 0 -0.54 1 1
ARF6/GTP 0.042 0.013 0.25 1 -10000 0 1
RhoA/GTP 0.037 0.012 0.23 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.45 0.54 -10000 0 -0.94 167 167
BLK -0.34 0.26 -10000 0 -0.54 236 236
PDPK1 0.019 0 -10000 0 -10000 0 0
CYTH1 0.032 0.012 0.23 1 -10000 0 1
HCK -0.028 0.16 -10000 0 -0.54 31 31
CYTH3 0.032 0.014 0.23 1 -10000 0 1
CYTH2 0.032 0.012 0.23 1 -10000 0 1
KRAS 0.019 0.014 -10000 0 -0.24 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.048 0.015 -10000 0 -10000 0 0
SGK1 0.043 0.016 -10000 0 -10000 0 0
INPP5D -0.075 0.21 -10000 0 -0.54 62 62
mol:GDP -0.016 0.12 -10000 0 -0.31 34 34
SOS1 0.019 0 -10000 0 -10000 0 0
SYK -0.052 0.19 -10000 0 -0.54 47 47
ARF6/GDP 0.027 0.061 -10000 0 -0.34 2 2
mol:PI-3-4-5-P3 0 0.016 0.28 1 -10000 0 1
ARAP3/RAP1A/GTP 0.031 0.013 0.23 1 -10000 0 1
VAV1 -0.09 0.22 -10000 0 -0.54 72 72
mol:PI-3-4-P2 -0.043 0.15 -10000 0 -0.38 62 62
RAS family/GTP/PI3K Class I 0.04 0.012 0.19 1 -10000 0 1
PLEKHA1 -0.028 0.13 -10000 0 -0.32 62 62
Rac1/GDP -0.005 0.12 -10000 0 -0.36 22 22
LAT -0.049 0.18 -10000 0 -0.54 45 45
Rac1/GTP -0.027 0.16 -10000 0 -0.44 35 35
ITK -0.047 0.12 -10000 0 -0.24 105 105
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.19 0.24 -10000 0 -0.47 145 145
LCK -0.2 0.27 -10000 0 -0.54 142 142
BTK -0.016 0.1 -10000 0 -0.24 64 64
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.019 0 -9999 0 -10000 0 0
LAT2 -0.063 0.24 -9999 0 -0.54 60 60
AP1 -0.087 0.28 -9999 0 -0.6 77 77
mol:PIP3 -0.082 0.27 -9999 0 -0.58 75 75
IKBKB -0.04 0.15 -9999 0 -0.3 73 73
AKT1 0.026 0.078 -9999 0 -0.26 7 7
IKBKG -0.04 0.15 -9999 0 -0.3 72 72
MS4A2 0.009 0.04 -9999 0 -0.25 8 8
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
MAP3K1 -0.057 0.23 -9999 0 -0.51 69 69
mol:Ca2+ -0.05 0.2 -9999 0 -0.41 75 75
LYN -0.005 0.11 -9999 0 -0.55 15 15
CBLB -0.028 0.17 -9999 0 -0.44 41 41
SHC1 0.019 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.033 0.025 -9999 0 -0.29 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.075 0.21 -9999 0 -0.54 62 62
PLD2 0.006 0.084 -9999 0 -0.25 31 31
PTPN13 -0.022 0.17 -9999 0 -0.5 30 30
PTPN11 0.016 0.011 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.021 0.11 -9999 0 -0.29 27 27
SYK -0.054 0.19 -9999 0 -0.55 47 47
GRB2 0.019 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.25 -9999 0 -0.6 73 73
LAT -0.061 0.22 -9999 0 -0.47 66 66
PAK2 -0.076 0.27 -9999 0 -0.59 69 69
NFATC2 -0.03 0.14 -9999 0 -0.56 23 23
HRAS -0.094 0.3 -9999 0 -0.66 70 70
GAB2 0.015 0.031 -9999 0 -0.24 5 5
PLA2G1B 0.03 0.015 -9999 0 -10000 0 0
Fc epsilon R1 -0.007 0.11 -9999 0 -0.32 34 34
Antigen/IgE/Fc epsilon R1 -0.006 0.097 -9999 0 -0.29 34 34
mol:GDP -0.12 0.32 -9999 0 -0.68 81 81
JUN -0.008 0.079 -9999 0 -0.24 37 37
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.019 0.001 -9999 0 -10000 0 0
FOS 0.01 0.047 -9999 0 -0.24 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.036 0.18 -9999 0 -0.39 57 57
CHUK -0.04 0.15 -9999 0 -0.3 72 72
KLRG1 -0.033 0.17 -9999 0 -0.38 56 56
VAV1 -0.077 0.25 -9999 0 -0.52 74 74
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.028 0.17 -9999 0 -0.44 41 41
negative regulation of mast cell degranulation -0.065 0.23 -9999 0 -0.5 70 70
BTK -0.13 0.35 -9999 0 -0.78 75 75
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.039 0.18 -9999 0 -0.41 50 50
GAB2/PI3K/SHP2 -0.024 0.065 -9999 0 -0.25 14 14
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.046 0.21 -9999 0 -0.45 61 61
RAF1 0.018 0.018 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.047 0.19 -9999 0 -0.39 75 75
FCER1G -0.029 0.16 -9999 0 -0.54 31 31
FCER1A 0.004 0.06 -9999 0 -0.26 16 16
Antigen/IgE/Fc epsilon R1/Fyn 0.006 0.091 -9999 0 -0.26 34 34
MAPK3 0.029 0.016 -9999 0 -10000 0 0
MAPK1 0.029 0.016 -9999 0 -10000 0 0
NFKB1 0.019 0 -9999 0 -10000 0 0
MAPK8 0.01 0.072 -9999 0 -10000 0 0
DUSP1 0.014 0.036 -9999 0 -0.24 7 7
NF-kappa-B/RelA -0.043 0.07 -9999 0 -0.2 38 38
actin cytoskeleton reorganization -0.026 0.17 -9999 0 -0.5 33 33
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.067 0.26 -9999 0 -0.57 68 68
FER -0.028 0.17 -9999 0 -0.44 41 41
RELA 0.019 0 -9999 0 -10000 0 0
ITK -0.12 0.22 -9999 0 -0.46 106 106
SOS1 0.019 0 -9999 0 -10000 0 0
PLCG1 -0.11 0.32 -9999 0 -0.7 72 72
cytokine secretion -0.032 0.051 -9999 0 -0.16 1 1
SPHK1 -0.031 0.17 -9999 0 -0.45 42 42
PTK2 -0.028 0.18 -9999 0 -0.53 32 32
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.13 0.26 -9999 0 -0.62 71 71
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.065 0.25 -9999 0 -0.55 69 69
MAP2K2 0.024 0.016 -9999 0 -10000 0 0
MAP2K1 0.024 0.016 -9999 0 -10000 0 0
MAP2K7 0.019 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.028 0.16 -9999 0 -0.42 40 40
MAP2K4 0.025 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.006 0.13 -9999 0 -0.33 42 42
mol:Choline 0.006 0.083 -9999 0 -0.25 31 31
SHC/Grb2/SOS1 -0.007 0.16 -9999 0 -0.43 38 38
FYN 0.019 0 -9999 0 -10000 0 0
DOK1 0.019 0 -9999 0 -10000 0 0
PXN -0.018 0.16 -9999 0 -0.52 27 27
HCLS1 -0.073 0.25 -9999 0 -0.55 65 65
PRKCB -0.073 0.2 -9999 0 -0.41 83 83
FCGR2B -0.005 0.11 -9999 0 -0.52 16 16
IGHE -0.001 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.067 0.24 -9999 0 -0.51 70 70
LCP2 -0.016 0.14 -9999 0 -0.54 23 23
PLA2G4A -0.032 0.17 -9999 0 -0.44 45 45
RASA1 0.017 0.029 -9999 0 -0.54 1 1
mol:Phosphatidic acid 0.006 0.083 -9999 0 -0.25 31 31
IKK complex -0.015 0.11 -9999 0 -0.22 65 65
WIPF1 0.011 0.064 -9999 0 -0.54 5 5
HIF-1-alpha transcription factor network

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
PKM2 -0.001 0.38 -9999 0 -0.79 43 43
HDAC7 0.021 0.004 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0 0.36 -9999 0 -0.76 29 29
SMAD4 0.02 0 -9999 0 -10000 0 0
ID2 -0.001 0.38 -9999 0 -0.79 43 43
AP1 0.007 0.069 -9999 0 -0.3 7 7
ABCG2 -0.021 0.41 -9999 0 -0.84 47 47
HIF1A 0.026 0.074 -9999 0 -10000 0 0
TFF3 -0.059 0.43 -9999 0 -0.82 62 62
GATA2 0.016 0.036 -9999 0 -0.24 7 7
AKT1 0.018 0.092 -9999 0 -0.22 5 5
response to hypoxia -0.001 0.094 -9999 0 -0.2 22 22
MCL1 -0.001 0.38 -9999 0 -0.79 43 43
NDRG1 -0.003 0.38 -9999 0 -0.8 43 43
SERPINE1 -0.01 0.39 -9999 0 -0.8 45 45
FECH -0.001 0.38 -9999 0 -0.79 43 43
FURIN -0.001 0.38 -9999 0 -0.79 43 43
NCOA2 0.02 0.014 -9999 0 -0.24 1 1
EP300 0.025 0.15 -9999 0 -0.28 39 39
HMOX1 -0.003 0.38 -9999 0 -0.79 43 43
BHLHE40 -0.002 0.38 -9999 0 -0.79 43 43
BHLHE41 -0.006 0.39 -9999 0 -0.81 44 44
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.084 0.11 -9999 0 -10000 0 0
ENG 0.074 0.093 -9999 0 -10000 0 0
JUN -0.007 0.079 -9999 0 -0.24 37 37
RORA -0.003 0.38 -9999 0 -0.78 44 44
ABCB1 -0.11 0.34 -9999 0 -1.3 29 29
TFRC -0.001 0.38 -9999 0 -0.79 43 43
CXCR4 -0.021 0.41 -9999 0 -0.84 50 50
TF -0.081 0.42 -9999 0 -0.84 56 56
CITED2 -0.001 0.38 -9999 0 -0.79 43 43
HIF1A/ARNT -0.006 0.45 -9999 0 -0.89 42 42
LDHA -0.017 0.077 -9999 0 -1.3 1 1
ETS1 -0.001 0.38 -9999 0 -0.79 43 43
PGK1 -0.001 0.38 -9999 0 -0.79 43 43
NOS2 -0.011 0.38 -9999 0 -0.8 44 44
ITGB2 -0.033 0.43 -9999 0 -0.87 52 52
ALDOA -0.001 0.38 -9999 0 -0.79 43 43
Cbp/p300/CITED2 -0.015 0.42 -9999 0 -0.87 42 42
FOS 0.011 0.047 -9999 0 -0.24 12 12
HK2 -0.001 0.38 -9999 0 -0.79 43 43
SP1 0.025 0.022 -9999 0 -10000 0 0
GCK -0.089 0.48 -9999 0 -1.3 43 43
HK1 -0.001 0.38 -9999 0 -0.79 43 43
NPM1 -0.001 0.38 -9999 0 -0.79 43 43
EGLN1 -0.001 0.38 -9999 0 -0.79 43 43
CREB1 0.028 0.001 -9999 0 -10000 0 0
PGM1 -0.001 0.38 -9999 0 -0.79 43 43
SMAD3 0.02 0 -9999 0 -10000 0 0
EDN1 0.022 0.21 -9999 0 -0.63 14 14
IGFBP1 -0.012 0.38 -9999 0 -0.8 43 43
VEGFA 0.021 0.33 -9999 0 -0.65 30 30
HIF1A/JAB1 0.033 0.05 -9999 0 -10000 0 0
CP -0.11 0.46 -9999 0 -0.86 68 68
CXCL12 -0.013 0.4 -9999 0 -0.82 49 49
COPS5 0.02 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0.031 0.001 -9999 0 -10000 0 0
BNIP3 -0.002 0.38 -9999 0 -0.79 43 43
EGLN3 -0.004 0.38 -9999 0 -0.79 44 44
CA9 -0.034 0.39 -9999 0 -0.82 46 46
TERT -0.011 0.39 -9999 0 -0.79 46 46
ENO1 -0.001 0.38 -9999 0 -0.79 43 43
PFKL -0.001 0.38 -9999 0 -0.79 43 43
NCOA1 0.019 0.001 -9999 0 -10000 0 0
ADM -0.042 0.39 -9999 0 -0.8 49 49
ARNT 0.026 0.074 -9999 0 -10000 0 0
HNF4A -0.024 0.083 -9999 0 -0.25 34 34
ADFP -0.012 0.38 -9999 0 -0.79 44 44
SLC2A1 0.027 0.32 -9999 0 -0.65 28 28
LEP -0.034 0.38 -9999 0 -0.81 43 43
HIF1A/ARNT/Cbp/p300 -0.01 0.37 -9999 0 -0.75 35 35
EPO 0.056 0.26 -9999 0 -0.55 5 5
CREBBP 0.025 0.15 -9999 0 -0.3 32 32
HIF1A/ARNT/Cbp/p300/HDAC7 0.017 0.37 -9999 0 -0.76 29 29
PFKFB3 -0.001 0.38 -9999 0 -0.79 43 43
NT5E -0.028 0.38 -9999 0 -0.8 47 47
Ephrin A reverse signaling

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
MAPKKK cascade -0.034 0.1 -9999 0 -0.33 26 26
EFNA5 0.008 0.076 -9999 0 -0.54 7 7
FYN -0.024 0.092 -9999 0 -0.3 26 26
neuron projection morphogenesis -0.034 0.1 -9999 0 -0.33 26 26
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.034 0.1 -9999 0 -0.33 26 26
EPHA5 -0.071 0.15 -9999 0 -0.3 102 102
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.033 0.12 -9999 0 -0.27 78 78
RGS9BP 0.017 0.019 -9999 0 -0.24 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.001 0.023 -9999 0 -10000 0 0
mol:ADP 0.007 0.011 -9999 0 -0.16 1 1
GNAT2 0.017 0.015 -9999 0 -0.24 1 1
RGS9-1/Gbeta5/R9AP -0.11 0.18 -9999 0 -0.32 150 150
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.013 0.021 -9999 0 -10000 0 0
GRK7 0.01 0.016 -9999 0 -0.24 1 1
CNGB3 0 0.042 -9999 0 -0.24 10 10
Cone Metarhodopsin II/X-Arrestin 0.003 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.001 0.02 -9999 0 -10000 0 0
Cone PDE6 -0.091 0.15 -9999 0 -0.27 150 150
Cone Metarhodopsin II 0.007 0.009 -9999 0 -0.12 1 1
Na + (4 Units) 0.001 0.021 -9999 0 -10000 0 0
GNAT2/GDP -0.084 0.15 -9999 0 -0.26 150 150
GNB5 0.017 0.029 -9999 0 -0.54 1 1
mol:GMP (4 units) 0.008 0.017 -9999 0 -10000 0 0
Cone Transducin -0.035 0.13 -9999 0 -0.29 78 78
SLC24A2 0 0 -9999 0 -10000 0 0
GNB3/GNGT2 -0.06 0.17 -9999 0 -0.38 78 78
GNB3 0.013 0.054 -9999 0 -0.42 5 5
GNAT2/GTP 0.012 0.01 -9999 0 -0.16 1 1
CNGA3 0 0 -9999 0 -10000 0 0
ARR3 0.004 0.008 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.001 0.023 -9999 0 -10000 0 0
mol:Pi -0.11 0.18 -9999 0 -0.32 150 150
Cone CNG Channel 0.01 0.024 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0 0 -9999 0 -10000 0 0
RGS9 -0.21 0.27 -9999 0 -0.54 150 150
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.095 0.22 -9999 0 -0.54 75 75
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.033 -9999 0 -0.24 6 6
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.036 0.16 -10000 0 -0.54 36 36
positive regulation of NF-kappaB transcription factor activity -0.027 0.13 -10000 0 -0.3 62 62
MAP2K4 0.009 0.1 -10000 0 -0.36 15 15
IKBKB 0.019 0 -10000 0 -10000 0 0
TNFRSF10B 0.008 0.076 -10000 0 -0.54 7 7
TNFRSF10A -0.046 0.18 -10000 0 -0.54 43 43
SMPD1 -0.002 0.073 -10000 0 -0.21 41 41
IKBKG 0.019 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.003 0.075 -10000 0 -0.26 29 29
TRAIL/TRAILR2 -0.02 0.14 -10000 0 -0.4 41 41
TRAIL/TRAILR3 -0.038 0.16 -10000 0 -0.41 55 55
TRAIL/TRAILR1 -0.057 0.19 -10000 0 -0.46 64 64
TRAIL/TRAILR4 -0.027 0.13 -10000 0 -0.3 62 62
TRAIL/TRAILR1/DAP3/GTP -0.032 0.16 -10000 0 -0.36 64 64
IKK complex 0.022 0.064 -10000 0 -10000 0 0
RIPK1 0.019 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0 -10000 0 -10000 0 0
MAPK3 -0.014 0.12 -10000 0 -0.38 36 36
MAP3K1 0.002 0.11 -10000 0 -0.29 39 39
TRAILR4 (trimer) -0.003 0.075 -10000 0 -0.26 29 29
TRADD 0.019 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.046 0.18 -10000 0 -0.54 43 43
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.014 0.13 -10000 0 -0.29 64 64
CFLAR 0.019 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.12 -10000 0 -0.38 36 36
TRAIL/TRAILR1/FADD/TRADD/RIP -0.01 0.15 -10000 0 -0.32 64 64
mol:ceramide -0.002 0.072 -10000 0 -0.2 41 41
FADD 0.018 0.014 -10000 0 -0.24 1 1
MAPK8 0.015 0.1 -10000 0 -0.34 15 15
TRAF2 0.019 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.018 0.14 -10000 0 -0.54 24 24
CHUK 0.019 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.036 0.17 -10000 0 -0.39 64 64
DAP3 0.019 0 -10000 0 -10000 0 0
CASP10 -0.033 0.17 0.26 1 -0.44 42 43
JNK cascade -0.027 0.13 -10000 0 -0.3 62 62
TRAIL (trimer) -0.036 0.16 -10000 0 -0.54 36 36
TNFRSF10C -0.018 0.14 -10000 0 -0.54 24 24
TRAIL/TRAILR1/DAP3/GTP/FADD -0.021 0.15 -10000 0 -0.33 64 64
TRAIL/TRAILR2/FADD -0.003 0.12 -10000 0 -0.33 41 41
cell death -0.002 0.072 -10000 0 -0.2 41 41
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.012 0.091 -10000 0 -0.24 41 41
TRAILR2 (trimer) 0.008 0.076 -10000 0 -0.54 7 7
CASP8 0.005 0.075 -10000 0 -0.88 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.019 0.1 -10000 0 -0.27 41 41
Visual signal transduction: Rods

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
mol:K + 0.019 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0 0 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.041 0.12 -9999 0 -0.33 57 57
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.085 0.15 -9999 0 -0.32 95 95
mol:Na + -0.008 0.06 -9999 0 -0.27 10 10
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.11 0.18 -9999 0 -0.32 150 150
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.005 0.066 -9999 0 -0.28 10 10
CNGB1 0.01 0.009 -9999 0 -10000 0 0
RDH5 0.008 0.066 -9999 0 -0.36 10 10
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.062 -9999 0 -0.26 10 10
Na + (4 Units) -0.019 0.048 -9999 0 -0.25 10 10
RGS9 -0.21 0.27 -9999 0 -0.54 150 150
GNB1/GNGT1 -0.016 0.069 -9999 0 -10000 0 0
GNAT1/GDP -0.092 0.15 -9999 0 -0.27 150 150
GUCY2D 0.009 0.041 -9999 0 -0.24 9 9
GNGT1 -0.044 0.1 -9999 0 -0.24 75 75
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0.017 0.029 -9999 0 -0.54 1 1
mol:GMP (4 units) -0.068 0.18 -9999 0 -0.36 91 91
mol:11-cis-retinal 0.008 0.066 -9999 0 -0.36 10 10
mol:cGMP 0.001 0.062 -9999 0 -0.3 6 6
GNB1 0.019 0 -9999 0 -10000 0 0
Rhodopsin 0.007 0.047 -9999 0 -0.39 4 4
SLC24A1 0.019 0 -9999 0 -10000 0 0
CNGA1 0.006 0.068 -9999 0 -0.43 8 8
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.002 0.066 -9999 0 -0.32 6 6
RGS9BP 0.017 0.019 -9999 0 -0.24 2 2
Metarhodopsin II/Transducin -0.008 0.036 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.004 0.061 -9999 0 -0.32 5 5
PDE6A/B -0.046 0.15 -9999 0 -0.36 69 69
mol:Pi -0.11 0.18 -9999 0 -0.32 150 150
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.009 0.052 -9999 0 -10000 0 0
PDE6B -0.074 0.21 -9999 0 -0.54 61 61
PDE6A 0.011 0.039 -9999 0 -0.24 8 8
PDE6G -0.068 0.2 -9999 0 -0.54 57 57
RHO 0 0 -9999 0 -10000 0 0
PDE6 -0.16 0.24 -9999 0 -0.36 186 186
GUCA1A -0.027 0.095 -9999 0 -0.24 58 58
GC2/GCAP Family -0.004 0.061 -9999 0 -0.32 5 5
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.011 0.064 -9999 0 -0.54 5 5
TCGA08_p53

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
CDKN2A -0.072 0.093 -10000 0 -0.17 172 172
TP53 -0.027 0.033 -10000 0 -0.15 4 4
Senescence -0.028 0.032 -10000 0 -0.14 4 4
Apoptosis -0.028 0.032 -10000 0 -0.14 4 4
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.051 0.06 0.25 4 -0.17 2 6
MDM4 0.019 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.083 0.19 -9999 0 -0.43 53 53
BAG4 0.017 0.029 -9999 0 -0.54 1 1
BAD -0.012 0.063 -9999 0 -0.13 53 53
NFKBIA 0.019 0 -9999 0 -10000 0 0
BIRC3 -0.18 0.26 -9999 0 -0.54 128 128
BAX -0.012 0.063 -9999 0 -0.13 53 53
EnzymeConsortium:3.1.4.12 -0.017 0.046 -9999 0 -0.1 53 53
IKBKB -0.072 0.18 -9999 0 -0.4 53 53
MAP2K2 0.001 0.062 -9999 0 -10000 0 0
MAP2K1 0.001 0.062 -9999 0 -10000 0 0
SMPD1 -0.011 0.046 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 -0.073 0.18 -9999 0 -0.41 56 56
MAP2K4 -0.004 0.061 -9999 0 -10000 0 0
protein ubiquitination -0.072 0.18 -9999 0 -0.41 53 53
EnzymeConsortium:2.7.1.37 0.005 0.066 -9999 0 -10000 0 0
response to UV 0 0.001 -9999 0 -0.002 53 53
RAF1 -0.005 0.063 -9999 0 -10000 0 0
CRADD 0.018 0.014 -9999 0 -0.24 1 1
mol:ceramide -0.02 0.065 -9999 0 -0.14 53 53
I-kappa-B-alpha/RELA/p50/ubiquitin 0.026 0 -9999 0 -10000 0 0
MADD 0.019 0 -9999 0 -10000 0 0
MAP3K1 -0.012 0.063 -9999 0 -10000 0 0
TRADD 0.019 0 -9999 0 -10000 0 0
RELA/p50 0.019 0 -9999 0 -10000 0 0
MAPK3 0.005 0.061 -9999 0 -10000 0 0
MAPK1 0.005 0.061 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.028 0 -9999 0 -10000 0 0
FADD -0.083 0.19 -9999 0 -0.43 54 54
KSR1 -0.012 0.064 -9999 0 -0.13 53 53
MAPK8 0.003 0.058 -9999 0 -10000 0 0
TRAF2 0.019 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK -0.072 0.18 -9999 0 -0.4 53 53
TNF R/SODD 0.027 0.021 -9999 0 -0.38 1 1
TNF -0.095 0.22 -9999 0 -0.54 75 75
CYCS -0.01 0.061 -9999 0 -0.12 53 53
IKBKG -0.072 0.18 -9999 0 -0.4 53 53
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.094 0.19 -9999 0 -0.34 128 128
RELA 0.019 0 -9999 0 -10000 0 0
RIPK1 0.019 0.001 -9999 0 -10000 0 0
AIFM1 -0.01 0.061 -9999 0 -0.12 53 53
TNF/TNF R/SODD -0.035 0.14 -9999 0 -0.32 76 76
TNFRSF1A 0.019 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 -0.001 0.075 -9999 0 -0.78 2 2
NSMAF -0.081 0.18 -9999 0 -0.42 53 53
response to hydrogen peroxide 0 0.001 -9999 0 -0.002 53 53
BCL2 0.019 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.026 0.03 -9999 0 -0.38 2 2
FBXW11 0.019 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.033 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.065 0.18 -9999 0 -0.46 47 47
NFKBIA -0.1 0.2 -9999 0 -0.31 142 142
MAPK14 0.019 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.033 0 -9999 0 -10000 0 0
ARRB2 0.02 0 -9999 0 -10000 0 0
REL 0.019 0.001 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.026 -9999 0 -0.32 2 2
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
NF kappa B1 p50 dimer 0.025 0 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
NFKB1 0.026 0 -9999 0 -10000 0 0
RELA 0.019 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.08 0.16 -9999 0 -0.27 142 142
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.059 0.17 -9999 0 -0.45 47 47
SRC 0.019 0 -9999 0 -10000 0 0
PI3K 0.028 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.08 0.16 -9999 0 -0.27 142 142
IKBKB 0.019 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -10000 0 0
SYK -0.052 0.19 -9999 0 -0.54 47 47
I kappa B alpha/PIK3R1 -0.086 0.19 -9999 0 -0.5 47 47
cell death -0.056 0.17 -9999 0 -0.43 47 47
NF kappa B1 p105/c-Rel 0.033 0.001 -9999 0 -10000 0 0
LCK -0.2 0.27 -9999 0 -0.54 142 142
BCL3 0.016 0.041 -9999 0 -0.54 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.15 0.3 -9999 0 -0.79 35 35
PCK1 -0.11 0.19 -9999 0 -0.52 23 23
HNF4A -0.17 0.32 -9999 0 -0.92 30 30
KCNJ11 -0.2 0.38 -9999 0 -0.92 53 53
AKT1 -0.088 0.16 -9999 0 -0.38 26 26
response to starvation -0.001 0.011 -9999 0 -10000 0 0
DLK1 -0.2 0.37 -9999 0 -0.9 53 53
NKX2-1 -0.075 0.17 -9999 0 -0.47 2 2
ACADM -0.15 0.3 -9999 0 -0.76 39 39
TAT -0.08 0.16 -9999 0 -0.6 4 4
CEBPB 0.017 0.009 -9999 0 -10000 0 0
CEBPA -0.029 0.16 -9999 0 -0.54 31 31
TTR -0.13 0.28 -9999 0 -0.78 38 38
PKLR -0.5 0.53 -9999 0 -0.94 205 205
APOA1 -0.19 0.35 -9999 0 -1 28 28
CPT1C -0.17 0.34 -9999 0 -0.89 39 39
ALAS1 -0.052 0.16 -9999 0 -0.59 1 1
TFRC -0.1 0.21 -9999 0 -0.71 7 7
FOXF1 -0.021 0.14 -9999 0 -0.51 28 28
NF1 0.027 0.003 -9999 0 -10000 0 0
HNF1A (dimer) 0.019 0 -9999 0 -10000 0 0
CPT1A -0.15 0.3 -9999 0 -0.78 37 37
HMGCS1 -0.15 0.3 -9999 0 -0.78 37 37
NR3C1 0.019 0 -9999 0 -10000 0 0
CPT1B -0.16 0.31 -9999 0 -0.78 43 43
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.019 0 -9999 0 -10000 0 0
GCK -0.22 0.41 -9999 0 -0.96 65 65
CREB1 0.009 0.029 -9999 0 -10000 0 0
IGFBP1 -0.062 0.14 -9999 0 -10000 0 0
PDX1 -0.064 0.16 -9999 0 -10000 0 0
UCP2 -0.22 0.41 -9999 0 -0.98 62 62
ALDOB -0.16 0.32 -9999 0 -0.84 36 36
AFP -0.012 0.071 -9999 0 -10000 0 0
BDH1 -0.16 0.31 -9999 0 -0.84 34 34
HADH -0.16 0.32 -9999 0 -0.83 36 36
F2 -0.19 0.35 -9999 0 -1 27 27
HNF1A 0.019 0 -9999 0 -10000 0 0
G6PC -0.014 0.096 -9999 0 -0.47 1 1
SLC2A2 -0.09 0.19 -9999 0 -0.54 3 3
INS -0.008 0.003 -9999 0 -10000 0 0
FOXA1 0.006 0.057 -9999 0 -0.27 12 12
FOXA3 -0.026 0.13 -9999 0 -0.39 33 33
FOXA2 -0.2 0.37 -9999 0 -0.83 53 53
ABCC8 -0.17 0.32 -9999 0 -0.82 37 37
ALB -0.014 0.086 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.019 0.14 -9999 0 -0.49 27 27
GNB1/GNG2 -0.031 0.12 -9999 0 -0.38 22 22
mol:DAG -0.024 0.11 -9999 0 -0.38 17 17
PLCG1 -0.025 0.11 -9999 0 -0.39 17 17
YES1 -0.039 0.1 -9999 0 -0.36 19 19
FZD3 0.019 0 -9999 0 -10000 0 0
FZD6 -0.01 0.12 -9999 0 -0.54 19 19
G protein -0.023 0.11 -9999 0 -0.36 22 22
MAP3K7 -0.023 0.1 -9999 0 -0.35 17 17
mol:Ca2+ -0.023 0.1 -9999 0 -0.34 22 22
mol:IP3 -0.024 0.11 -9999 0 -0.38 17 17
NLK 0.012 0.01 -9999 0 -10000 0 0
GNB1 0.019 0 -9999 0 -10000 0 0
CAMK2A -0.031 0.11 -9999 0 -0.38 17 17
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.049 0.11 -9999 0 -0.33 31 31
CSNK1A1 0.019 0 -9999 0 -10000 0 0
GNAS -0.039 0.1 -9999 0 -0.36 19 19
GO:0007205 -0.024 0.1 -9999 0 -0.37 17 17
WNT6 0.007 0.052 -9999 0 -0.24 15 15
WNT4 -0.082 0.13 -9999 0 -0.24 140 140
NFAT1/CK1 alpha -0.029 0.13 -9999 0 -0.36 29 29
GNG2 0.01 0.07 -9999 0 -0.54 6 6
WNT5A -0.001 0.092 -9999 0 -0.37 19 19
WNT11 -0.066 0.12 -9999 0 -0.24 118 118
CDC42 -0.03 0.1 -9999 0 -0.34 18 18
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.11 0.13 -9999 0 -0.33 60 60
SMAD6-7/SMURF1 0.035 0.022 -9999 0 -10000 0 0
NOG -0.15 0.25 -9999 0 -0.53 112 112
SMAD9 -0.006 0.087 -9999 0 -0.47 10 10
SMAD4 0.019 0 -9999 0 -10000 0 0
SMAD5 -0.016 0.063 -9999 0 -0.3 2 2
BMP7/USAG1 -0.22 0.21 -9999 0 -0.42 168 168
SMAD5/SKI -0.007 0.062 -9999 0 -0.28 2 2
SMAD1 0.036 0.014 -9999 0 -10000 0 0
BMP2 -0.003 0.089 -9999 0 -0.32 24 24
SMAD1/SMAD1/SMAD4 -0.001 0.006 -9999 0 -10000 0 0
BMPR1A 0.018 0.014 -9999 0 -0.24 1 1
BMPR1B -0.14 0.13 -9999 0 -0.24 215 215
BMPR1A-1B/BAMBI -0.06 0.09 -9999 0 -0.39 8 8
AHSG -0.01 0.064 -9999 0 -0.24 25 25
CER1 0.002 0.03 -9999 0 -0.24 5 5
BMP2-4/CER1 0.005 0.079 -9999 0 -0.32 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.071 -9999 0 -0.29 8 8
BMP2-4 (homodimer) 0.002 0.09 -9999 0 -0.39 15 15
RGMB 0.002 0.064 -9999 0 -0.24 23 23
BMP6/BMPR2/BMPR1A-1B -0.038 0.072 -9999 0 -0.22 3 3
RGMA -0.006 0.082 -9999 0 -0.26 32 32
SMURF1 0.019 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.025 0.075 -9999 0 -0.3 13 13
BMP2-4/USAG1 -0.14 0.18 -9999 0 -0.33 158 158
SMAD6/SMURF1/SMAD5 -0.007 0.062 -9999 0 -0.28 2 2
SOSTDC1 -0.23 0.26 -9999 0 -0.48 182 182
BMP7/BMPR2/BMPR1A-1B -0.092 0.11 -9999 0 -0.25 78 78
SKI 0.019 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.015 0.033 -9999 0 -0.24 6 6
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.019 0 -9999 0 -10000 0 0
MAP3K7 0.019 0 -9999 0 -10000 0 0
BMP2-4/CHRD 0.006 0.085 -9999 0 -0.32 16 16
SMAD5/SMAD5/SMAD4 -0.007 0.062 -9999 0 -0.28 2 2
MAPK1 0.019 0 -9999 0 -10000 0 0
TAK1/TAB family -0.024 0.052 -9999 0 -0.28 8 8
BMP7 (homodimer) -0.09 0.16 -9999 0 -0.29 128 128
NUP214 0.019 0 -9999 0 -10000 0 0
BMP6/FETUA 0.005 0.05 -9999 0 -0.31 1 1
SMAD1/SKI 0.046 0.013 -9999 0 -10000 0 0
SMAD6 0.013 0.039 -9999 0 -0.24 8 8
CTDSP2 0.019 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.002 0.085 -9999 0 -0.33 16 16
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.02 0.13 -9999 0 -0.37 37 37
BMPR2 (homodimer) 0.019 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.038 0.008 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.078 0.089 -9999 0 -10000 0 0
CHRDL1 -0.062 0.18 -9999 0 -0.39 72 72
ENDOFIN/SMAD1 0.046 0.013 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.059 0.02 -9999 0 -10000 0 0
SMAD6/SMURF1 0.019 0 -9999 0 -10000 0 0
BAMBI 0.007 0.081 -9999 0 -0.54 8 8
SMURF2 0.019 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.033 0.14 -9999 0 -0.36 48 48
BMP2-4/GREM1 -0.008 0.11 -9999 0 -0.32 35 35
SMAD7 0.019 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.005 0.082 -9999 0 -0.44 10 10
SMAD1/SMAD6 0.046 0.013 -9999 0 -10000 0 0
TAK1/SMAD6 0.028 0 -9999 0 -10000 0 0
BMP7 -0.091 0.16 -9999 0 -0.29 128 128
BMP6 0.015 0.033 -9999 0 -0.24 6 6
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.013 0.067 -9999 0 -0.26 13 13
PPM1A 0.019 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.046 0.013 -9999 0 -10000 0 0
SMAD7/SMURF1 0.028 0 -9999 0 -10000 0 0
CTDSPL 0.019 0 -9999 0 -10000 0 0
PPP1CA 0.019 0 -9999 0 -10000 0 0
XIAP 0.019 0 -9999 0 -10000 0 0
CTDSP1 0.019 0 -9999 0 -10000 0 0
PPP1R15A 0.018 0.014 -9999 0 -0.24 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.1 -9999 0 -0.32 28 28
CHRD 0.002 0.064 -9999 0 -0.24 23 23
BMPR2 0.019 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.029 0.078 -9999 0 -0.32 13 13
BMP4 0.004 0.085 -9999 0 -0.44 12 12
FST -0.045 0.15 -9999 0 -0.36 61 61
BMP2-4/NOG -0.093 0.17 -9999 0 -0.33 121 121
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.078 0.1 -9999 0 -0.33 21 21
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.06 0.15 -9999 0 -0.25 126 126
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.018 0.014 -9999 0 -0.24 1 1
STAT1 (dimer)/Cbp/p300 -0.052 0.17 -9999 0 -0.37 40 40
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.006 0.06 -9999 0 -0.35 6 6
antigen processing and presentation of peptide antigen via MHC class I -0.045 0.077 -9999 0 -0.28 20 20
CaM/Ca2+ -0.051 0.14 -9999 0 -0.23 126 126
RAP1A 0.019 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.058 0.14 -9999 0 -0.33 27 27
AKT1 -0.039 0.12 -9999 0 -0.29 16 16
MAP2K1 -0.044 0.13 -9999 0 -0.3 16 16
MAP3K11 -0.055 0.13 -9999 0 -0.28 27 27
IFNGR1 0.008 0.017 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.1 -9999 0 -0.42 6 6
Rap1/GTP -0.059 0.082 -9999 0 -0.35 3 3
CRKL/C3G 0.028 0.009 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.057 0.15 -9999 0 -0.26 132 132
CEBPB 0.001 0.12 -9999 0 -0.36 3 3
STAT3 0.019 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.11 0.31 -9999 0 -1.2 22 22
STAT1 -0.06 0.14 -9999 0 -0.33 27 27
CALM1 0.019 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.18 0.26 -9999 0 -0.54 129 129
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
STAT1 (dimer)/PIAS1 -0.048 0.14 -9999 0 -0.33 21 21
CEBPB/PTGES2/Cbp/p300 -0.036 0.051 -9999 0 -10000 0 0
mol:Ca2+ -0.061 0.14 -9999 0 -0.25 126 126
MAPK3 -0.019 0.12 -9999 0 -0.37 3 3
STAT1 (dimer) -0.058 0.11 -9999 0 -0.4 20 20
MAPK1 -0.019 0.12 -9999 0 -0.37 3 3
JAK2 -0.001 0.074 -9999 0 -0.51 7 7
PIK3R1 0.019 0 -9999 0 -10000 0 0
JAK1 0.008 0.017 -9999 0 -10000 0 0
CAMK2D 0.019 0 -9999 0 -10000 0 0
DAPK1 0.018 0.09 -9999 0 -10000 0 0
SMAD7 0.012 0.064 -9999 0 -0.16 10 10
CBL/CRKL/C3G -0.036 0.13 -9999 0 -0.29 16 16
PI3K -0.048 0.13 -9999 0 -0.31 16 16
IFNG -0.18 0.26 -9999 0 -0.54 129 129
apoptosis 0.006 0.082 -9999 0 -0.24 1 1
CAMK2G 0.019 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.019 0 -9999 0 -10000 0 0
CAMK2A -0.018 0.1 -9999 0 -0.28 46 46
CAMK2B -0.011 0.1 -9999 0 -0.33 31 31
FRAP1 -0.038 0.12 -9999 0 -0.27 16 16
PRKCD -0.038 0.12 -9999 0 -0.29 16 16
RAP1B 0.019 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.045 0.077 -9999 0 -0.28 20 20
PTPN2 0.019 0 -9999 0 -10000 0 0
EP300 0.019 0.002 -9999 0 -10000 0 0
IRF1 -0.077 0.23 -9999 0 -0.56 54 54
STAT1 (dimer)/PIASy -0.048 0.14 -9999 0 -0.36 18 18
SOCS1 -0.048 0.32 -9999 0 -1.4 19 19
mol:GDP -0.036 0.12 -9999 0 -0.28 16 16
CASP1 0.003 0.092 -9999 0 -0.31 20 20
PTGES2 0.019 0 -9999 0 -10000 0 0
IRF9 0.026 0.052 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.078 0.1 -9999 0 -0.3 16 16
RAP1/GDP -0.06 0.082 -9999 0 -0.35 3 3
CBL -0.057 0.13 -9999 0 -0.23 126 126
MAP3K1 -0.055 0.13 -9999 0 -0.28 27 27
PIAS1 0.019 0 -9999 0 -10000 0 0
PIAS4 0.019 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.045 0.077 -9999 0 -0.28 20 20
PTPN11 -0.067 0.14 -9999 0 -0.25 126 126
CREBBP 0.019 0.002 -9999 0 -10000 0 0
RAPGEF1 0.019 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.014 0.099 -10000 0 -1.3 2 2
VDR 0.016 0.041 -10000 0 -0.54 2 2
FAM120B 0.019 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.048 0.17 -10000 0 -0.46 20 20
RXRs/LXRs/DNA/Oxysterols -0.06 0.21 -10000 0 -0.42 75 75
MED1 0.019 0 -10000 0 -10000 0 0
mol:9cRA -0.003 0.022 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.017 0.065 -10000 0 -0.24 15 15
RXRs/NUR77 -0.031 0.15 -10000 0 -0.29 82 82
RXRs/PPAR -0.025 0.12 -10000 0 -0.23 87 87
NCOR2 0.019 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.012 0.03 -10000 0 -0.39 2 2
RARs/VDR/DNA/Vit D3 0.031 0.063 -10000 0 -0.26 16 16
RARA 0.019 0 -10000 0 -10000 0 0
NCOA1 0.019 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.016 0.041 -10000 0 -0.54 2 2
RARs/RARs/DNA/9cRA 0.02 0.061 -10000 0 -0.28 14 14
RARG 0.019 0 -10000 0 -10000 0 0
RPS6KB1 0.028 0.052 -10000 0 -0.41 2 2
RARs/THRs/DNA/SMRT 0.017 0.065 -10000 0 -0.24 15 15
THRA 0.019 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.012 0.03 -10000 0 -0.39 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.044 0.15 0.3 1 -0.3 82 83
NR1H4 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.026 0.16 -10000 0 -0.27 84 84
NR1H2 0.017 0.019 -10000 0 -10000 0 0
NR1H3 0.013 0.047 -10000 0 -0.55 2 2
RXRs/VDR/DNA/Vit D3 -0.03 0.14 -10000 0 -0.27 84 84
NR4A1 0.016 0.035 -10000 0 -0.34 3 3
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.033 0.11 -10000 0 -0.21 82 82
RXRG -0.11 0.23 -10000 0 -0.54 82 82
RXR alpha/CCPG 0.026 0.014 -10000 0 -10000 0 0
RXRA 0.016 0.019 -10000 0 -10000 0 0
RXRB 0.016 0.022 -10000 0 -10000 0 0
THRB -0.026 0.1 -10000 0 -0.26 60 60
PPARG 0.011 0.064 -10000 0 -0.54 5 5
PPARD 0.017 0.019 -10000 0 -0.24 2 2
TNF -0.19 0.46 -10000 0 -1.1 75 75
mol:Oxysterols -0.002 0.02 -10000 0 -10000 0 0
cholesterol transport -0.06 0.21 -10000 0 -0.42 75 75
PPARA 0.019 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.003 0.11 -10000 0 -0.52 15 15
RXRs/NUR77/BCL2 -0.027 0.12 -10000 0 -0.24 82 82
SREBF1 -0.046 0.19 -10000 0 -0.53 20 20
RXRs/RXRs/DNA/9cRA -0.044 0.15 0.3 1 -0.3 82 83
ABCA1 -0.046 0.19 -10000 0 -0.53 20 20
RARs/THRs 0.021 0.08 -10000 0 -0.28 15 15
RXRs/FXR -0.04 0.14 -10000 0 -0.3 82 82
BCL2 0.019 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.019 0 -9999 0 -10000 0 0
SPHK1 0.011 0.058 -9999 0 -0.36 8 8
GNAI2 0.019 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.034 -9999 0 -0.28 4 4
GNAO1 -0.093 0.13 -9999 0 -0.25 155 155
mol:Sphinganine-1-P 0.02 0.042 -9999 0 -0.38 3 3
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.049 0.026 -9999 0 -0.18 4 4
GNAI3 0.019 0 -9999 0 -10000 0 0
G12/G13 0.028 0 -9999 0 -10000 0 0
S1PR3 0.014 0.052 -9999 0 -0.46 4 4
S1PR2 0.019 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.014 0.028 -9999 0 -0.24 4 4
S1PR5 0.008 0.052 -9999 0 -0.24 15 15
S1PR4 -0.16 0.26 -9999 0 -0.54 121 121
GNAI1 0.004 0.06 -9999 0 -0.24 20 20
S1P/S1P5/G12 0.033 0.037 -9999 0 -0.2 4 4
S1P/S1P3/Gq -0.017 0.13 -9999 0 -0.27 73 73
S1P/S1P4/Gi -0.095 0.15 -9999 0 -0.29 122 122
GNAQ 0.019 0 -9999 0 -10000 0 0
GNAZ -0.015 0.093 -9999 0 -0.26 45 45
GNA14 -0.084 0.22 -9999 0 -0.53 69 69
GNA15 0.002 0.095 -9999 0 -0.54 11 11
GNA12 0.019 0 -9999 0 -10000 0 0
GNA13 0.019 0 -9999 0 -10000 0 0
GNA11 0.019 0 -9999 0 -10000 0 0
ABCC1 0.017 0.029 -9999 0 -0.54 1 1
Aurora C signaling

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
INCENP 0.019 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.032 0.13 -9999 0 -0.29 78 78
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.002 0.043 -9999 0 -10000 0 0
AURKB 0.017 0.029 -9999 0 -0.54 1 1
AURKC -0.098 0.23 -9999 0 -0.54 77 77
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 0.015 0.031 -10000 0 -0.24 5 5
Jak2/Leptin Receptor -0.002 0.076 0.21 1 -0.46 6 7
PTP1B/AKT1 0.021 0.043 -10000 0 -0.23 3 3
FYN 0.019 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.012 0.046 -10000 0 -0.26 3 3
EGFR -0.008 0.087 -10000 0 -0.27 33 33
EGF/EGFR -0.005 0.098 -10000 0 -0.29 32 32
CSF1 0.01 0.07 -10000 0 -0.54 6 6
AKT1 0.019 0 -10000 0 -10000 0 0
INSR 0.019 0.014 -10000 0 -0.24 1 1
PTP1B/N-cadherin -0.02 0.1 -10000 0 -0.27 42 42
Insulin Receptor/Insulin 0.028 0.034 -10000 0 -10000 0 0
HCK -0.028 0.16 -10000 0 -0.54 31 31
CRK 0.019 0 -10000 0 -10000 0 0
TYK2 0.019 0.044 -10000 0 -0.24 3 3
EGF -0.031 0.15 -10000 0 -0.43 41 41
YES1 0.019 0 -10000 0 -10000 0 0
CAV1 0.018 0.06 -10000 0 -0.22 5 5
TXN 0.018 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.023 0.056 -10000 0 -0.23 3 3
cell migration -0.012 0.046 0.26 3 -10000 0 3
STAT3 0.019 0.001 -10000 0 -10000 0 0
PRLR -0.048 0.11 -10000 0 -0.24 92 92
ITGA2B -0.005 0.073 -10000 0 -0.24 31 31
CSF1R -0.013 0.13 -10000 0 -0.54 21 21
Prolactin Receptor/Prolactin -0.046 0.096 -10000 0 -0.3 16 16
FGR -0.036 0.16 -10000 0 -0.54 36 36
PTP1B/p130 Cas 0.021 0.045 -10000 0 -0.24 3 3
Crk/p130 Cas 0.032 0.044 -10000 0 -0.23 3 3
DOK1 0.026 0.041 -10000 0 -0.21 2 2
JAK2 -0.009 0.078 -10000 0 -0.48 6 6
Jak2/Leptin Receptor/Leptin 0.002 0.071 -10000 0 -0.34 8 8
PIK3R1 0.019 0 -10000 0 -10000 0 0
PTPN1 0.012 0.047 -10000 0 -0.26 3 3
LYN -0.004 0.11 -10000 0 -0.54 15 15
CDH2 -0.063 0.18 -10000 0 -0.41 69 69
SRC 0.027 0.02 -10000 0 -10000 0 0
ITGB3 -0.033 0.14 -10000 0 -0.36 50 50
CAT1/PTP1B -0.17 0.23 -10000 0 -0.42 131 131
CAPN1 0.019 0.001 -10000 0 -10000 0 0
CSK 0.019 0 -10000 0 -10000 0 0
PI3K 0.012 0.025 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) 0.011 0.072 -10000 0 -0.34 7 7
negative regulation of transcription -0.009 0.078 -10000 0 -0.48 6 6
FCGR2A 0.013 0.058 -10000 0 -0.54 4 4
FER 0.018 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.025 0.11 -10000 0 -0.37 25 25
BLK -0.34 0.26 -10000 0 -0.54 236 236
Insulin Receptor/Insulin/Shc 0.026 0.008 -10000 0 -10000 0 0
RHOA 0.019 0.001 -10000 0 -10000 0 0
LEPR 0.018 0.001 -10000 0 -10000 0 0
BCAR1 0.019 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.019 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.29 0.32 -10000 0 -0.61 142 142
PRL -0.023 0.083 -10000 0 -0.24 45 45
SOCS3 0.006 0.13 -10000 0 -1.4 3 3
SPRY2 0.017 0.02 -10000 0 -0.24 2 2
Insulin Receptor/Insulin/IRS1 0.014 0.042 -10000 0 -10000 0 0
CSF1/CSF1R 0.012 0.098 -10000 0 -0.31 25 25
Ras protein signal transduction 0.011 0.015 -10000 0 -10000 0 0
IRS1 -0.002 0.071 -10000 0 -0.24 29 29
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.035 0.1 -10000 0 -0.24 70 70
STAT5B 0.008 0.052 -10000 0 -0.27 4 4
STAT5A 0.007 0.053 -10000 0 -0.27 4 4
GRB2 0.019 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.048 -10000 0 -0.24 3 3
CSN2 -0.02 0.036 -10000 0 -10000 0 0
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
LAT -0.038 0.18 -10000 0 -0.5 45 45
YBX1 0.029 0.001 -10000 0 -10000 0 0
LCK -0.2 0.27 -10000 0 -0.54 142 142
SHC1 0.019 0 -10000 0 -10000 0 0
NOX4 -0.04 0.12 -10000 0 -0.26 78 78
Paxillin-dependent events mediated by a4b1

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
CRKL 0.018 0.014 -10000 0 -0.24 1 1
Rac1/GDP 0.015 0.014 -10000 0 -10000 0 0
DOCK1 0.019 0 -10000 0 -10000 0 0
ITGA4 -0.043 0.18 -10000 0 -0.54 41 41
RAC1 0.019 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.076 0.2 -10000 0 -0.42 84 84
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.11 -10000 0 -0.32 41 41
alpha4/beta7 Integrin/Paxillin -0.039 0.16 -10000 0 -0.32 84 84
lamellipodium assembly 0.057 0.007 -10000 0 -10000 0 0
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
PI3K 0.028 0.009 -10000 0 -10000 0 0
ARF6 0.019 0 -10000 0 -10000 0 0
TLN1 0.019 0 -10000 0 -10000 0 0
PXN 0.026 0 -10000 0 -10000 0 0
PIK3R1 0.019 0 -10000 0 -10000 0 0
ARF6/GTP 0.017 0.088 -10000 0 -0.23 41 41
cell adhesion 0.017 0.096 -10000 0 -0.25 41 41
CRKL/CBL 0.028 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.006 0.1 -10000 0 -0.28 41 41
ITGB1 0.017 0.019 -10000 0 -0.24 2 2
ITGB7 -0.063 0.2 -10000 0 -0.54 54 54
ARF6/GDP 0.015 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.033 0.18 -10000 0 -0.36 76 76
p130Cas/Crk/Dock1 0.038 0 -10000 0 -10000 0 0
VCAM1 -0.077 0.21 -10000 0 -0.54 63 63
alpha4/beta1 Integrin/Paxillin/Talin 0.018 0.098 -10000 0 -0.26 41 41
alpha4/beta1 Integrin/Paxillin/GIT1 0.018 0.098 -10000 0 -0.26 41 41
BCAR1 0.019 0 -10000 0 -10000 0 0
mol:GDP -0.017 0.096 0.25 41 -10000 0 41
CBL 0.019 0 -10000 0 -10000 0 0
PRKACA 0.019 0 -10000 0 -10000 0 0
GIT1 0.019 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.018 0.098 -10000 0 -0.26 41 41
Rac1/GTP 0.059 0.007 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.049 -9999 0 -0.31 1 1
alphaV beta3 Integrin -0.006 0.1 -9999 0 -0.29 32 32
PTK2 -0.063 0.15 -9999 0 -0.4 36 36
IGF1R 0.016 0.027 -9999 0 -0.24 4 4
PI4KB 0.019 0 -9999 0 -10000 0 0
MFGE8 0.004 0.06 -9999 0 -0.24 20 20
SRC 0.019 0 -9999 0 -10000 0 0
CDKN1B -0.05 0.18 -9999 0 -0.48 48 48
VEGFA 0.004 0.061 -9999 0 -0.24 21 21
ILK -0.05 0.18 -9999 0 -0.48 48 48
ROCK1 0.019 0 -9999 0 -10000 0 0
AKT1 -0.04 0.17 -9999 0 -0.45 48 48
PTK2B 0.001 0.088 -9999 0 -0.26 26 26
alphaV/beta3 Integrin/JAM-A -0.032 0.14 -9999 0 -0.3 69 69
CBL 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.006 0.086 -9999 0 -0.32 20 20
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.03 0.056 -9999 0 -0.27 5 5
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.007 0.1 -9999 0 -0.32 12 12
alphaV/beta3 Integrin/Syndecan-1 -0.001 0.1 -9999 0 -0.34 26 26
PI4KA 0.018 0.014 -9999 0 -0.24 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.042 0.089 -9999 0 -0.28 32 32
PI4 Kinase 0.028 0.009 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
alphaV/beta3 Integrin/Osteopontin -0.03 0.14 -9999 0 -0.35 53 53
RPS6KB1 0.002 0.1 -9999 0 -0.41 8 8
TLN1 0.019 0 -9999 0 -10000 0 0
MAPK3 -0.024 0.14 -9999 0 -0.47 25 25
GPR124 0.016 0.027 -9999 0 -0.24 4 4
MAPK1 -0.024 0.14 -9999 0 -0.48 24 24
PXN 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.13 0.19 -9999 0 -0.35 151 151
cell adhesion 0.004 0.088 -9999 0 -0.32 19 19
ANGPTL3 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.027 0.042 -9999 0 -0.25 1 1
IGF-1R heterotetramer 0.016 0.027 -9999 0 -0.24 4 4
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
TGFBR2 0.019 0 -9999 0 -10000 0 0
ITGB3 -0.032 0.14 -9999 0 -0.36 50 50
IGF1 0.008 0.066 -9999 0 -0.36 10 10
RAC1 0.019 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.005 0.089 -9999 0 -0.32 20 20
apoptosis 0.018 0.014 -9999 0 -0.24 1 1
CD47 0.019 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.007 0.088 -9999 0 -0.31 20 20
VCL 0.019 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.036 0.11 -9999 0 -0.29 41 41
CSF1 0.01 0.07 -9999 0 -0.54 6 6
PIK3C2A -0.05 0.18 -9999 0 -0.48 48 48
PI4 Kinase/Pyk2 -0.059 0.1 -9999 0 -0.37 17 17
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.009 0.089 -9999 0 -0.26 26 26
FAK1/Vinculin -0.043 0.13 -9999 0 -0.33 32 32
alphaV beta3/Integrin/ppsTEM5 0.005 0.09 -9999 0 -0.32 20 20
RHOA 0.019 0 -9999 0 -10000 0 0
VTN -0.058 0.19 -9999 0 -0.5 54 54
BCAR1 0.019 0 -9999 0 -10000 0 0
FGF2 -0.004 0.08 -9999 0 -0.26 30 30
F11R 0.004 0.078 -9999 0 -0.42 8 8
alphaV/beta3 Integrin/Lactadherin -0.001 0.095 -9999 0 -0.32 23 23
alphaV/beta3 Integrin/TGFBR2 0.007 0.088 -9999 0 -0.31 20 20
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.043 0.042 -9999 0 -0.28 6 6
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
alphaV/beta3 Integrin/Talin 0.008 0.08 -9999 0 -0.28 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0 0.1 -9999 0 -0.52 13 13
alphaV/beta3 Integrin/Pyk2 0.008 0.091 -9999 0 -0.26 26 26
SDC1 0.005 0.08 -9999 0 -0.43 11 11
VAV3 0.032 0.054 -9999 0 -0.29 8 8
PTPN11 0.019 0 -9999 0 -10000 0 0
IRS1 -0.002 0.071 -9999 0 -0.24 29 29
FAK1/Paxillin -0.043 0.13 -9999 0 -0.34 27 27
cell migration -0.033 0.12 -9999 0 -0.32 23 23
ITGAV 0.018 0.014 -9999 0 -0.24 1 1
PI3K -0.019 0.13 -9999 0 -0.41 15 15
SPP1 -0.04 0.17 -9999 0 -0.52 40 40
KDR 0.014 0.036 -9999 0 -0.24 7 7
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.018 0.014 -9999 0 -0.24 1 1
COL4A3 -0.2 0.27 -9999 0 -0.54 144 144
angiogenesis -0.032 0.16 -9999 0 -0.46 31 31
Rac1/GTP 0.039 0.05 -9999 0 -0.26 8 8
EDIL3 -0.056 0.12 -9999 0 -0.24 104 104
cell proliferation 0.006 0.087 -9999 0 -0.31 20 20
Osteopontin-mediated events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.005 0.12 -9999 0 -0.42 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.12 -9999 0 -0.39 10 10
alphaV/beta3 Integrin/Osteopontin/Src -0.007 0.12 -9999 0 -0.37 38 38
AP1 0.008 0.14 -9999 0 -0.44 9 9
ILK -0.009 0.13 -9999 0 -0.44 11 11
bone resorption -0.017 0.16 -9999 0 -0.44 25 25
PTK2B 0.008 0.076 -9999 0 -0.54 7 7
PYK2/p130Cas -0.026 0.17 -9999 0 -0.43 32 32
ITGAV 0.022 0.014 -9999 0 -0.24 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.027 0.021 -9999 0 -0.38 1 1
alphaV/beta3 Integrin/Osteopontin -0.013 0.14 -9999 0 -0.34 53 53
MAP3K1 -0.009 0.13 -9999 0 -0.3 51 51
JUN -0.008 0.08 -9999 0 -0.25 37 37
MAPK3 0.004 0.12 -9999 0 -0.43 11 11
MAPK1 0.004 0.12 -9999 0 -0.43 11 11
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
NFKB1 0.019 0 -9999 0 -10000 0 0
MAPK8 -0.002 0.12 -9999 0 -0.27 51 51
ITGB3 -0.028 0.14 -9999 0 -0.35 50 50
NFKBIA 0.015 0.12 -9999 0 -0.44 10 10
FOS 0.01 0.047 -9999 0 -0.25 12 12
CD44 0.017 0.029 -9999 0 -0.54 1 1
CHUK 0.019 0 -9999 0 -10000 0 0
PLAU 0.02 0.13 -9999 0 -0.84 2 2
NF kappa B1 p50/RelA 0.035 0.11 -9999 0 -0.4 9 9
BCAR1 0.019 0 -9999 0 -10000 0 0
RELA 0.019 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0 0.1 -9999 0 -0.37 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.049 0.17 -9999 0 -0.33 86 86
VAV3 -0.044 0.17 -9999 0 -0.36 55 55
MAP3K14 -0.006 0.13 -9999 0 -0.3 51 51
ROCK2 0.019 0 -9999 0 -10000 0 0
SPP1 -0.036 0.17 -9999 0 -0.51 40 40
RAC1 0.019 0 -9999 0 -10000 0 0
Rac1/GTP -0.032 0.16 -9999 0 -0.45 25 25
MMP2 -0.005 0.14 -9999 0 -0.38 15 15
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.013 0.077 -9999 0 -0.34 15 15
EPHB2 -0.005 0.11 -9999 0 -0.54 16 16
Syndecan-2/TACI -0.15 0.17 -9999 0 -0.32 183 183
LAMA1 -0.2 0.1 -9999 0 -0.24 302 302
Syndecan-2/alpha2 ITGB1 0.031 0.076 -9999 0 -0.28 17 17
HRAS 0.019 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.01 0.04 -9999 0 -0.32 4 4
ITGA5 0.015 0.031 -9999 0 -0.24 5 5
BAX 0.037 0.037 -9999 0 -10000 0 0
EPB41 0.017 0.029 -9999 0 -0.54 1 1
positive regulation of cell-cell adhesion 0.022 0.037 -9999 0 -0.28 4 4
LAMA3 0 0.1 -9999 0 -0.52 13 13
EZR 0.011 0.064 -9999 0 -0.54 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.019 0 -9999 0 -10000 0 0
Syndecan-2/MMP2 0.003 0.068 -9999 0 -0.3 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.022 0.04 -9999 0 -0.21 9 9
dendrite morphogenesis 0.009 0.081 -9999 0 -0.32 20 20
Syndecan-2/GM-CSF 0.018 0.046 -9999 0 -0.32 5 5
determination of left/right symmetry 0.015 0.049 -9999 0 -0.23 12 12
Syndecan-2/PKC delta 0.024 0.041 -9999 0 -0.31 4 4
GNB2L1 0.019 0 -9999 0 -10000 0 0
MAPK3 0.025 0.041 -9999 0 -0.28 5 5
MAPK1 0.025 0.041 -9999 0 -0.28 5 5
Syndecan-2/RACK1 0.033 0.036 -9999 0 -0.26 4 4
NF1 0.019 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.015 0.049 -9999 0 -0.23 12 12
ITGA2 0.012 0.048 -9999 0 -0.28 9 9
MAPK8 0.03 0.041 -9999 0 -0.31 4 4
Syndecan-2/alpha2/beta1 Integrin -0.067 0.062 -9999 0 -0.26 14 14
Syndecan-2/Kininogen 0.009 0.048 -9999 0 -0.32 4 4
ITGB1 0.017 0.019 -9999 0 -0.24 2 2
SRC 0.035 0.034 -9999 0 -0.24 4 4
Syndecan-2/CASK/Protein 4.1 0.021 0.041 -9999 0 -0.29 5 5
extracellular matrix organization 0.022 0.048 -9999 0 -0.31 6 6
actin cytoskeleton reorganization 0.013 0.077 -9999 0 -0.34 15 15
Syndecan-2/Caveolin-2/Ras 0.035 0.038 -9999 0 -0.28 4 4
Syndecan-2/Laminin alpha3 0.013 0.08 -9999 0 -0.36 14 14
Syndecan-2/RasGAP 0.041 0.038 -9999 0 -0.24 5 5
alpha5/beta1 Integrin 0.025 0.029 -9999 0 -0.31 2 2
PRKCD 0.019 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.009 0.081 -9999 0 -0.32 20 20
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.046 0.037 -9999 0 -0.23 5 5
RHOA 0.019 0 -9999 0 -10000 0 0
SDCBP 0.019 0 -9999 0 -10000 0 0
TNFRSF13B -0.26 0.28 -9999 0 -0.54 180 180
RASA1 0.017 0.029 -9999 0 -0.54 1 1
alpha2/beta1 Integrin 0.022 0.04 -9999 0 -0.21 9 9
Syndecan-2/Synbindin 0.024 0.041 -9999 0 -0.31 4 4
TGFB1 0.016 0.041 -9999 0 -0.54 2 2
CASP3 0.03 0.037 -9999 0 -0.28 4 4
FN1 0 0.1 -9999 0 -0.52 13 13
Syndecan-2/IL8 -0.015 0.078 -9999 0 -0.3 9 9
SDC2 0.015 0.049 -9999 0 -0.23 12 12
KNG1 -0.004 0.049 -9999 0 -0.24 14 14
Syndecan-2/Neurofibromin 0.024 0.041 -9999 0 -0.31 4 4
TRAPPC4 0.019 0 -9999 0 -10000 0 0
CSF2 0.01 0.033 -9999 0 -0.39 2 2
Syndecan-2/TGFB1 0.022 0.048 -9999 0 -0.32 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.037 -9999 0 -0.28 4 4
Syndecan-2/Ezrin 0.03 0.053 -9999 0 -0.28 9 9
PRKACA 0.03 0.037 -9999 0 -0.28 4 4
angiogenesis -0.015 0.078 -9999 0 -0.3 9 9
MMP2 -0.019 0.097 -9999 0 -0.26 50 50
IL8 -0.05 0.12 -9999 0 -0.25 93 93
calcineurin-NFAT signaling pathway -0.15 0.17 -9999 0 -0.32 183 183
Arf6 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
CENTA1/KIF3B 0.013 0.065 -9999 0 -0.32 13 13
ARNO/beta Arrestin1-2 0.032 0.027 -9999 0 -10000 0 0
EGFR -0.007 0.087 -9999 0 -0.27 33 33
EPHA2 0.013 0.058 -9999 0 -0.54 4 4
USP6 0.019 0 -9999 0 -10000 0 0
IQSEC1 0.019 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.026 0.12 -9999 0 -0.38 31 31
ARRB2 0.01 0 -9999 0 -10000 0 0
mol:GTP -0.021 0.066 -9999 0 -0.21 19 19
ARRB1 0.019 0 -9999 0 -10000 0 0
FBXO8 0.019 0 -9999 0 -10000 0 0
TSHR -0.03 0.16 -9999 0 -0.53 32 32
EGF -0.031 0.15 -9999 0 -0.42 41 41
somatostatin receptor activity 0 0 -9999 0 -0.001 33 33
ARAP2 0.007 0.081 -9999 0 -0.54 8 8
mol:GDP -0.001 0.07 -9999 0 -0.24 18 18
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 23 23
ITGA2B -0.004 0.073 -9999 0 -0.24 31 31
ARF6 0.019 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.034 -9999 0 -0.28 4 4
ADAP1 -0.001 0.1 -9999 0 -0.54 13 13
KIF13B 0.019 0 -9999 0 -10000 0 0
HGF/MET -0.016 0.12 -9999 0 -0.4 27 27
PXN 0.019 0 -9999 0 -10000 0 0
ARF6/GTP -0.018 0.1 -9999 0 -0.25 32 32
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.008 0.11 -9999 0 -0.32 31 31
ADRB2 0.013 0.058 -9999 0 -0.54 4 4
receptor agonist activity 0 0 -9999 0 0 34 34
actin filament binding 0 0 -9999 0 0 33 33
SRC 0.019 0 -9999 0 -10000 0 0
ITGB3 -0.032 0.14 -9999 0 -0.36 50 50
GNAQ 0.019 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 27 27
ARF6/GDP -0.066 0.18 -9999 0 -0.3 128 128
ARF6/GDP/GULP/ACAP1 -0.077 0.18 -9999 0 -0.31 106 106
alphaIIb/beta3 Integrin/paxillin/GIT1 0.007 0.089 -9999 0 -0.27 25 25
ACAP1 -0.18 0.26 -9999 0 -0.54 128 128
ACAP2 0.019 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0 0 -9999 0 -10000 0 0
EFNA1 0.019 0 -9999 0 -10000 0 0
HGF 0 0.085 -9999 0 -0.34 19 19
CYTH3 0.012 0.009 -9999 0 -0.16 1 1
CYTH2 0.014 0.002 -9999 0 -10000 0 0
NCK1 0.019 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 43 43
endosomal lumen acidification 0 0 -9999 0 0 33 33
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.007 0.12 -9999 0 -0.54 17 17
GNAQ/ARNO 0.024 0.004 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 8 8
MET -0.024 0.14 -9999 0 -0.43 35 35
GNA14 -0.084 0.22 -9999 0 -0.53 69 69
GNA15 0.002 0.095 -9999 0 -0.54 11 11
GIT1 0.019 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 27 27
GNA11 0.019 0 -9999 0 -10000 0 0
LHCGR 0 0 -9999 0 -10000 0 0
AGTR1 0 0 -9999 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0 0 -9999 0 -10000 0 0
IPCEF1/ARNO -0.001 0.08 -9999 0 -0.34 2 2
alphaIIb/beta3 Integrin -0.024 0.11 -9999 0 -0.36 25 25
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.024 0.043 -9999 0 -0.38 4 4
Necdin/E2F1 0.016 0.07 -9999 0 -0.38 11 11
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.005 0.086 -9999 0 -0.3 8 8
NGF (dimer)/p75(NTR)/BEX1 -0.025 0.1 -9999 0 -0.29 29 29
NT-4/5 (dimer)/p75(NTR) -0.017 0.074 -9999 0 -0.39 4 4
IKBKB 0.019 0 -9999 0 -10000 0 0
AKT1 0.013 0.063 -9999 0 -0.25 4 4
IKBKG 0.019 0 -9999 0 -10000 0 0
BDNF -0.12 0.24 -9999 0 -0.54 88 88
MGDIs/NGR/p75(NTR)/LINGO1 -0.029 0.1 -9999 0 -0.28 30 30
FURIN 0.019 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.077 0.16 -9999 0 -0.34 93 93
LINGO1 -0.026 0.1 -9999 0 -0.25 61 61
Sortilin/TRAF6/NRIF -0.004 0.029 -9999 0 -10000 0 0
proBDNF (dimer) -0.12 0.24 -9999 0 -0.54 88 88
NTRK1 -0.001 0.1 -9999 0 -0.5 14 14
RTN4R -0.007 0.089 -9999 0 -0.28 32 32
neuron apoptosis -0.031 0.13 -9999 0 -0.37 11 11
IRAK1 0.019 0 -9999 0 -10000 0 0
SHC1 -0.003 0.075 -9999 0 -0.27 14 14
ARHGDIA 0.019 0 -9999 0 -10000 0 0
RhoA/GTP 0.014 0 -9999 0 -10000 0 0
Gamma Secretase 0.054 0.028 -9999 0 -0.26 3 3
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.011 0.078 -9999 0 -0.24 18 18
MAGEH1 0.019 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.002 0.095 -9999 0 -0.27 29 29
Mammalian IAPs/DIABLO -0.069 0.16 -9999 0 -0.29 128 128
proNGF (dimer) 0.002 0.062 -9999 0 -0.24 22 22
MAGED1 0.019 0 -9999 0 -10000 0 0
APP 0.014 0.05 -9999 0 -0.54 3 3
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.019 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI 0.01 0.065 -9999 0 -0.22 14 14
NGF 0.002 0.063 -9999 0 -0.24 22 22
cell cycle arrest 0.004 0.071 -9999 0 -0.22 18 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.021 0.052 -9999 0 -0.23 5 5
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.001 0.063 -9999 0 -0.32 4 4
NCSTN 0.019 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.077 -9999 0 -0.27 14 14
PSENEN 0.019 0 -9999 0 -10000 0 0
mol:ceramide 0.002 0.076 -9999 0 -0.25 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.03 0.047 -9999 0 -0.28 1 1
p75(NTR)/beta APP -0.007 0.084 -9999 0 -0.4 7 7
BEX1 -0.029 0.099 -9999 0 -0.24 64 64
mol:GDP -0.015 0.073 -9999 0 -0.28 14 14
NGF (dimer) 0.008 0.071 -9999 0 -0.3 11 11
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.014 0.097 -9999 0 -0.25 30 30
PIK3R1 0.019 0 -9999 0 -10000 0 0
RAC1/GTP 0.003 0.065 -9999 0 -0.23 14 14
MYD88 0.017 0.029 -9999 0 -0.54 1 1
CHUK 0.019 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.002 0.078 -9999 0 -0.27 14 14
RHOB 0.017 0.019 -9999 0 -0.24 2 2
RHOA 0.019 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.028 0 -9999 0 -10000 0 0
NT3 (dimer) -0.004 0.068 -9999 0 -0.24 27 27
TP53 -0.044 0.13 -9999 0 -0.25 93 93
PRDM4 0.002 0.074 -9999 0 -0.24 18 18
BDNF (dimer) -0.12 0.15 -9999 0 -0.32 114 114
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
SORT1 0.013 0.058 -9999 0 -0.54 4 4
activation of caspase activity 0.002 0.083 -9999 0 -0.3 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.011 0.078 -9999 0 -0.24 18 18
RHOC 0.019 0 -9999 0 -10000 0 0
XIAP 0.019 0 -9999 0 -10000 0 0
MAPK10 -0.029 0.11 -9999 0 -0.37 7 7
DIABLO 0.019 0 -9999 0 -10000 0 0
SMPD2 0.002 0.076 -9999 0 -0.25 19 19
APH1B 0.014 0.05 -9999 0 -0.54 3 3
APH1A 0.019 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.002 0.084 -9999 0 -0.28 18 18
PSEN1 0.019 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.028 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.019 0.091 -9999 0 -0.34 12 12
MAPK8 -0.014 0.11 -9999 0 -0.37 7 7
MAPK9 -0.014 0.11 -9999 0 -0.37 7 7
APAF1 0.019 0 -9999 0 -10000 0 0
NTF3 -0.004 0.068 -9999 0 -0.24 27 27
NTF4 0 0 -9999 0 -10000 0 0
NDN 0.002 0.095 -9999 0 -0.54 11 11
RAC1/GDP 0.014 0 -9999 0 -10000 0 0
RhoA-B-C/GDP 0.021 0.061 -9999 0 -0.23 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.045 0.034 -9999 0 -0.28 4 4
RhoA-B-C/GTP 0.001 0.077 -9999 0 -0.27 14 14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.045 0.14 -9999 0 -0.28 93 93
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.058 0.15 -9999 0 -0.3 93 93
PRKACB 0.018 0.014 -9999 0 -0.24 1 1
proBDNF (dimer)/p75 ECD -0.071 0.18 -9999 0 -0.38 88 88
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.18 0.26 -9999 0 -0.54 128 128
BIRC2 0.014 0.052 -9999 0 -0.46 4 4
neuron projection morphogenesis -0.014 0.07 -9999 0 -0.27 7 7
BAD -0.014 0.11 -9999 0 -0.37 7 7
RIPK2 0.019 0 -9999 0 -10000 0 0
NGFR -0.027 0.11 -9999 0 -0.26 59 59
CYCS 0.01 0.069 -9999 0 -0.26 8 8
ADAM17 0.019 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.015 0.072 -9999 0 -0.24 14 14
BCL2L11 -0.014 0.11 -9999 0 -0.37 7 7
BDNF (dimer)/p75(NTR) -0.1 0.18 -9999 0 -0.4 90 90
PI3K 0.015 0.072 -9999 0 -0.23 14 14
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.011 0.078 -9999 0 -0.24 18 18
NDNL2 0.019 0 -9999 0 -10000 0 0
YWHAE 0.019 0 -9999 0 -10000 0 0
PRKCI 0.019 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.014 0.09 -9999 0 -0.33 14 14
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.011 0.078 -9999 0 -0.24 18 18
TRAF6 0.019 0 -9999 0 -10000 0 0
RAC1 0.019 0 -9999 0 -10000 0 0
PRKCZ 0.016 0.041 -9999 0 -0.54 2 2
PLG 0 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.06 0.14 -9999 0 -0.27 93 93
SQSTM1 0.019 0 -9999 0 -10000 0 0
NGFRAP1 -0.013 0.086 -9999 0 -0.24 44 44
CASP3 -0.01 0.1 -9999 0 -0.34 7 7
E2F1 0.019 0 -9999 0 -10000 0 0
CASP9 0.019 0 -9999 0 -10000 0 0
IKK complex -0.011 0.047 -9999 0 -0.32 2 2
NGF (dimer)/TRKA 0.002 0.083 -9999 0 -0.38 12 12
MMP7 -0.016 0.11 -9999 0 -0.33 35 35
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.021 0.074 -9999 0 -0.26 8 8
MMP3 -0.1 0.13 -9999 0 -0.24 162 162
APAF-1/Caspase 9 -0.079 0.1 -9999 0 -0.31 28 28
IL6-mediated signaling events

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
BCL2L1 -0.044 0.27 -10000 0 -0.69 25 25
CRP -0.052 0.27 -10000 0 -0.72 24 24
cell cycle arrest -0.065 0.3 -10000 0 -0.68 48 48
TIMP1 -0.022 0.22 -10000 0 -0.55 20 20
IL6ST 0.008 0.082 -10000 0 -0.54 8 8
Rac1/GDP -0.03 0.19 -10000 0 -0.42 51 51
AP1 0.032 0.088 -10000 0 -0.31 1 1
GAB2 0.016 0.031 -10000 0 -0.24 5 5
TNFSF11 -0.18 0.49 -10000 0 -1.1 79 79
HSP90B1 0.029 0.055 -10000 0 -10000 0 0
GAB1 0.019 0.001 -10000 0 -10000 0 0
MAPK14 0.031 0.12 -10000 0 -0.66 5 5
AKT1 0.063 0.017 -10000 0 -10000 0 0
FOXO1 0.068 0.016 -10000 0 -10000 0 0
MAP2K6 0.02 0.12 -10000 0 -0.4 14 14
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.032 0.22 -10000 0 -0.48 51 51
MITF 0.007 0.13 -10000 0 -0.33 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.019 0 -10000 0 -10000 0 0
A2M 0.019 0.031 -10000 0 -10000 0 0
CEBPB 0.025 0.008 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.028 0.064 -10000 0 -10000 0 0
STAT3 -0.068 0.31 -10000 0 -0.71 48 48
STAT1 0.003 0.071 -10000 0 -0.92 2 2
CEBPD -0.047 0.28 -10000 0 -0.73 25 25
PIK3CA 0.02 0.014 -10000 0 -0.24 1 1
PI3K 0.031 0.009 -10000 0 -10000 0 0
JUN -0.008 0.079 -10000 0 -0.24 37 37
PIAS3/MITF 0.015 0.12 -10000 0 -0.33 22 22
MAPK11 0.031 0.12 -10000 0 -0.66 5 5
STAT3 (dimer)/FOXO1 0.008 0.24 -10000 0 -0.55 24 24
GRB2/SOS1/GAB family 0.023 0.12 -10000 0 -0.48 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0 0.14 -10000 0 -0.34 42 42
GRB2 0.019 0.001 -10000 0 -10000 0 0
JAK2 0.009 0.072 -10000 0 -0.5 7 7
LBP -0.19 0.44 -10000 0 -0.91 87 87
PIK3R1 0.02 0 -10000 0 -10000 0 0
JAK1 0.02 0.006 -10000 0 -10000 0 0
MYC -0.044 0.27 -10000 0 -0.7 25 25
FGG -0.057 0.27 -10000 0 -0.72 25 25
macrophage differentiation -0.065 0.3 -10000 0 -0.68 48 48
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.026 0.11 -10000 0 -0.32 30 30
JUNB -0.043 0.26 -10000 0 -0.69 22 22
FOS 0.01 0.047 -10000 0 -0.24 12 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.12 -10000 0 -0.37 21 21
STAT1/PIAS1 0.01 0.13 -10000 0 -0.35 21 21
GRB2/SOS1/GAB family/SHP2/PI3K 0.052 0.018 -10000 0 -10000 0 0
STAT3 (dimer) -0.067 0.31 -10000 0 -0.71 48 48
PRKCD -0.036 0.25 -10000 0 -0.54 51 51
IL6R 0.012 0.067 -10000 0 -0.56 5 5
SOCS3 0.035 0.14 -10000 0 -1.2 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.032 0.062 -10000 0 -0.32 9 9
Rac1/GTP -0.035 0.2 -10000 0 -0.44 53 53
HCK -0.029 0.16 -10000 0 -0.54 31 31
MAPKKK cascade 0.04 0.054 -10000 0 -10000 0 0
bone resorption -0.16 0.45 -10000 0 -0.98 79 79
IRF1 -0.11 0.41 -10000 0 -1.1 47 47
mol:GDP -0.039 0.19 -10000 0 -0.4 58 58
SOS1 0.019 0.002 -10000 0 -10000 0 0
VAV1 -0.04 0.19 -10000 0 -0.41 58 58
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.031 0.12 -10000 0 -0.54 8 8
PTPN11 0.016 0.022 -10000 0 -10000 0 0
IL6/IL6RA 0.005 0.1 -10000 0 -0.42 18 18
gp130 (dimer)/TYK2/TYK2/LMO4 0.031 0.058 -10000 0 -0.32 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.025 0.083 -10000 0 -0.4 12 12
IL6 -0.007 0.11 -10000 0 -0.43 22 22
PIAS3 0.019 0 -10000 0 -10000 0 0
PTPRE 0.008 0.07 -10000 0 -0.52 6 6
PIAS1 0.019 0 -10000 0 -10000 0 0
RAC1 0.019 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.012 0.094 0.2 1 -0.29 27 28
LMO4 0.018 0.032 -10000 0 -0.55 1 1
STAT3 (dimer)/PIAS3 -0.058 0.3 -10000 0 -0.7 39 39
MCL1 0.068 0.016 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.004 0.039 -9999 0 -0.16 19 19
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.013 0.038 -9999 0 -0.39 1 1
STXBP1 0.019 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.047 0.13 -9999 0 -0.31 64 64
RAB3GAP2/RIMS1/UNC13B 0.025 0.032 -9999 0 -0.32 1 1
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 0.046 -9999 0 -0.24 12 12
mol:ACh -0.007 0.024 -9999 0 -0.077 6 6
RAB3GAP2 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.012 0.043 -9999 0 -0.27 1 1
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.047 0.13 -9999 0 -0.31 64 64
UNC13B 0.017 0.029 -9999 0 -0.54 1 1
CHRNA1 -0.066 0.19 -9999 0 -0.46 64 64
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.016 0.064 -9999 0 -0.16 52 52
SNAP25 -0.024 0.049 -9999 0 -0.099 110 110
VAMP2 0.008 0 -9999 0 -10000 0 0
SYT1 -0.021 0.098 -9999 0 -0.26 52 52
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.016 0.033 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.012 0.043 -9999 0 -0.27 1 1
EGFR-dependent Endothelin signaling events

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
HRAS 0.019 0 -9999 0 -10000 0 0
EGFR -0.007 0.087 -9999 0 -0.27 33 33
EGF/EGFR -0.009 0.096 -9999 0 -0.24 47 47
EGF/EGFR dimer/SHC/GRB2/SOS1 0.015 0.093 -9999 0 -0.26 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.006 0.057 -9999 0 -0.24 18 18
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.031 0.15 -9999 0 -0.42 41 41
EGF/EGFR dimer/SHC -0.008 0.11 -9999 0 -0.32 31 31
mol:GDP 0.011 0.091 -9999 0 -0.26 31 31
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.012 0.055 -9999 0 -0.39 6 6
GRB2/SOS1 0.028 0 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.066 -9999 0 -0.24 28 28
SHC1 0.019 0 -9999 0 -10000 0 0
HRAS/GDP 0.013 0.084 -9999 0 -0.24 28 28
FRAP1 0 0.082 -9999 0 -0.24 31 31
EGF/EGFR dimer -0.026 0.12 -9999 0 -0.38 31 31
SOS1 0.019 0 -9999 0 -10000 0 0
GRB2 0.019 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.015 0.059 -9999 0 -0.34 6 6
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.003 0.13 -10000 0 -0.37 15 15
CRKL 0.04 0.11 -10000 0 -0.36 8 8
HRAS -0.005 0.15 -10000 0 -0.38 37 37
mol:PIP3 0.025 0.1 0.35 1 -0.35 8 9
SPRED1 0.016 0.041 -10000 0 -0.54 2 2
SPRED2 0.019 0 -10000 0 -10000 0 0
GAB1 0.035 0.12 0.22 1 -0.39 8 9
FOXO3 0.046 0.1 0.26 1 -0.36 6 7
AKT1 0.04 0.11 0.26 1 -0.39 6 7
BAD 0.046 0.1 0.26 1 -0.36 6 7
megakaryocyte differentiation 0.007 0.13 -10000 0 -0.32 26 26
GSK3B 0.046 0.1 0.26 1 -0.36 6 7
RAF1 0.005 0.13 -10000 0 -0.32 29 29
SHC1 0.019 0 -10000 0 -10000 0 0
STAT3 0.035 0.12 -10000 0 -0.39 8 8
STAT1 0.021 0.2 -10000 0 -0.87 10 10
HRAS/SPRED1 0.005 0.13 -10000 0 -0.31 38 38
cell proliferation 0.035 0.12 0.22 1 -0.38 8 9
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
TEC 0.005 0.086 -10000 0 -0.54 9 9
RPS6KB1 0.039 0.12 0.24 1 -0.38 8 9
HRAS/SPRED2 0.006 0.13 -10000 0 -0.3 37 37
LYN/TEC/p62DOK 0.035 0.12 -10000 0 -0.38 13 13
MAPK3 0.018 0.098 0.19 13 -0.24 20 33
STAP1 -0.15 0.16 -10000 0 -0.28 192 192
GRAP2 -0.046 0.18 -10000 0 -0.54 43 43
JAK2 0.022 0.18 -10000 0 -0.76 10 10
STAT1 (dimer) 0.022 0.19 -10000 0 -0.85 10 10
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.016 0.14 -10000 0 -0.37 26 26
actin filament polymerization 0.03 0.12 -10000 0 -0.32 13 13
LYN -0.004 0.11 -10000 0 -0.54 15 15
STAP1/STAT5A (dimer) -0.13 0.18 -10000 0 -0.44 50 50
PIK3R1 0.019 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.055 0.1 -10000 0 -0.35 6 6
PI3K 0.053 0.11 0.24 1 -0.39 6 7
PTEN 0.017 0.029 -10000 0 -0.54 1 1
SCF/KIT/EPO/EPOR -0.014 0.2 -10000 0 -1.2 7 7
MAPK8 0.035 0.12 -10000 0 -0.39 8 8
STAT3 (dimer) 0.035 0.12 -10000 0 -0.38 8 8
positive regulation of transcription 0.02 0.084 0.17 13 -0.2 20 33
mol:GDP -0.02 0.16 -10000 0 -0.39 42 42
PIK3C2B 0.036 0.12 -10000 0 -0.39 8 8
CBL/CRKL 0.048 0.11 -10000 0 -0.34 8 8
FER 0.035 0.12 -10000 0 -0.39 8 8
SH2B3 0.035 0.12 -10000 0 -0.39 8 8
PDPK1 0.031 0.1 0.34 1 -0.32 8 9
SNAI2 0.032 0.12 -10000 0 -0.39 9 9
positive regulation of cell proliferation 0.032 0.16 -10000 0 -0.63 10 10
KITLG 0.018 0.037 -10000 0 -0.35 3 3
cell motility 0.032 0.16 -10000 0 -0.63 10 10
PTPN6 -0.12 0.24 -10000 0 -0.53 92 92
EPOR 0.039 0.074 -10000 0 -10000 0 0
STAT5A (dimer) 0.035 0.14 -10000 0 -0.52 10 10
SOCS1 -0.01 0.12 -10000 0 -0.54 19 19
cell migration -0.001 0.13 0.31 24 -10000 0 24
SOS1 0.019 0 -10000 0 -10000 0 0
EPO 0.013 0.021 -10000 0 -0.24 2 2
VAV1 -0.09 0.22 -10000 0 -0.54 72 72
GRB10 0.035 0.12 -10000 0 -0.39 8 8
PTPN11 0.017 0.005 -10000 0 -10000 0 0
SCF/KIT 0.031 0.12 0.22 59 -0.38 10 69
GO:0007205 0 0.006 -10000 0 -10000 0 0
MAP2K1 0.014 0.1 -10000 0 -0.26 24 24
CBL 0.019 0 -10000 0 -10000 0 0
KIT -0.022 0.22 -10000 0 -1.3 7 7
MAP2K2 0.014 0.1 -10000 0 -0.26 26 26
SHC/Grb2/SOS1 0.052 0.11 -10000 0 -0.35 8 8
STAT5A 0.035 0.14 -10000 0 -0.54 10 10
GRB2 0.019 0 -10000 0 -10000 0 0
response to radiation 0.033 0.12 -10000 0 -0.38 9 9
SHC/GRAP2 -0.02 0.13 -10000 0 -0.38 43 43
PTPRO 0.006 0.13 -10000 0 -0.32 26 26
SH2B2 0.03 0.12 -10000 0 -0.33 13 13
DOK1 0.019 0 -10000 0 -10000 0 0
MATK 0.001 0.13 -10000 0 -0.31 24 24
CREBBP 0.035 0.027 -10000 0 -10000 0 0
BCL2 0.04 0.071 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.027 0.12 -10000 0 -0.49 13 13
IHH 0.014 0.052 -10000 0 -0.24 10 10
SHH Np/Cholesterol/GAS1 0.017 0.035 -10000 0 -0.3 4 4
LRPAP1 0.019 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.017 0.035 0.29 4 -10000 0 4
SMO/beta Arrestin2 0.039 0.094 -10000 0 -0.5 4 4
SMO 0.031 0.097 -10000 0 -0.53 4 4
AKT1 0.043 0.049 -10000 0 -10000 0 0
ARRB2 0.019 0 -10000 0 -10000 0 0
BOC 0.015 0.031 -10000 0 -0.24 5 5
ADRBK1 0.019 0 -10000 0 -10000 0 0
heart looping 0.031 0.096 -10000 0 -0.52 4 4
STIL 0.034 0.065 -10000 0 -0.36 4 4
DHH N/PTCH2 0.002 0.084 -10000 0 -0.38 12 12
DHH N/PTCH1 0.019 0.1 -10000 0 -0.32 18 18
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
DHH -0.011 0.11 -10000 0 -0.36 29 29
PTHLH 0.02 0.16 -10000 0 -0.69 13 13
determination of left/right symmetry 0.031 0.096 -10000 0 -0.52 4 4
PIK3R1 0.019 0 -10000 0 -10000 0 0
skeletal system development 0.021 0.16 -10000 0 -0.68 13 13
IHH N/Hhip 0.011 0.028 -10000 0 -0.18 1 1
DHH N/Hhip -0.007 0.078 -10000 0 -0.39 11 11
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.031 0.096 -10000 0 -0.52 4 4
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.017 0.032 -10000 0 -0.39 2 2
PI3K 0.028 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.013 0.054 -10000 0 -0.42 5 5
somite specification 0.031 0.096 -10000 0 -0.52 4 4
SHH Np/Cholesterol/PTCH1 0.03 0.069 -10000 0 -0.38 4 4
SHH Np/Cholesterol/PTCH2 0.017 0.03 -10000 0 -0.3 2 2
SHH Np/Cholesterol/Megalin -0.15 0.16 -10000 0 -0.3 195 195
SHH 0.011 0.023 -10000 0 -0.28 2 2
catabolic process 0.029 0.085 -10000 0 -0.36 9 9
SMO/Vitamin D3 0.035 0.081 -10000 0 -0.52 3 3
SHH Np/Cholesterol/Hhip 0.008 0.017 -10000 0 -0.3 1 1
LRP2 -0.28 0.28 -10000 0 -0.54 195 195
receptor-mediated endocytosis -0.084 0.15 -10000 0 -0.41 21 21
SHH Np/Cholesterol/BOC 0.019 0.023 -10000 0 -0.29 1 1
SHH Np/Cholesterol/CDO 0.02 0.018 -10000 0 -0.29 1 1
mesenchymal cell differentiation -0.007 0.017 0.3 1 -10000 0 1
mol:Vitamin D3 0.034 0.071 -10000 0 -0.38 4 4
IHH N/PTCH2 0.021 0.046 -10000 0 -0.2 9 9
CDON 0.019 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.032 0.087 -10000 0 -0.36 9 9
Megalin/LRPAP1 -0.19 0.2 -10000 0 -0.38 195 195
PTCH2 0.012 0.046 -10000 0 -0.28 8 8
SHH Np/Cholesterol 0.011 0.018 -10000 0 -0.3 1 1
PTCH1 0.029 0.085 -10000 0 -0.36 9 9
HHIP 0 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.005 0.058 -10000 0 -0.24 19 19
ANTXR2 0.013 0.049 -10000 0 -0.34 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.009 -10000 0 -0.065 3 3
monocyte activation -0.15 0.29 -10000 0 -0.56 105 105
MAP2K2 0.015 0.005 -10000 0 -10000 0 0
MAP2K1 0.01 0.009 -10000 0 -10000 0 0
MAP2K7 0.01 0.009 -10000 0 -10000 0 0
MAP2K6 0.004 0.041 -10000 0 -0.28 7 7
CYAA 0.006 0.036 -10000 0 -0.26 3 3
MAP2K4 0.01 0.009 -10000 0 -10000 0 0
IL1B -0.038 0.12 -10000 0 -0.28 64 64
Channel 0.014 0.041 -10000 0 -0.27 3 3
NLRP1 -0.023 0.094 -10000 0 -0.29 41 41
CALM1 0.019 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.014 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.009 0.065 3 -10000 0 3
MAPK3 0.01 0.009 -10000 0 -10000 0 0
MAPK1 0.01 0.009 -10000 0 -10000 0 0
PGR 0.008 0.016 -10000 0 -0.12 4 4
PA/Cellular Receptors 0.014 0.045 -10000 0 -0.15 24 24
apoptosis -0.002 0.009 -10000 0 -0.065 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.014 0.037 -10000 0 -0.26 3 3
macrophage activation 0.016 0.009 -10000 0 -10000 0 0
TNF -0.095 0.22 -10000 0 -0.54 75 75
VCAM1 -0.15 0.29 -10000 0 -0.57 105 105
platelet activation 0.014 0.012 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.014 -10000 0 -10000 0 0
IL18 -0.085 0.18 -10000 0 -0.34 103 103
negative regulation of macrophage activation -0.002 0.009 -10000 0 -0.065 3 3
LEF -0.002 0.009 -10000 0 -0.065 3 3
CASP1 -0.018 0.081 -10000 0 -0.2 46 46
mol:cAMP 0.014 0.012 -10000 0 -10000 0 0
necrosis -0.002 0.009 -10000 0 -0.065 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.014 0.038 -10000 0 -0.26 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.015 0.031 -9999 0 -0.24 5 5
alphaV beta3 Integrin -0.009 0.1 -9999 0 -0.38 20 20
PTK2 0.018 0.079 -9999 0 -0.36 8 8
positive regulation of JNK cascade -0.011 0.043 -9999 0 -0.28 8 8
CDC42/GDP 0.044 0.076 -9999 0 -0.37 8 8
Rac1/GDP 0.046 0.076 -9999 0 -0.37 8 8
RAP1B 0.019 0 -9999 0 -10000 0 0
RAP1A 0.019 0 -9999 0 -10000 0 0
CTNNB1 0.019 0 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.054 -9999 0 -0.34 8 8
nectin-3/I-afadin -0.004 0.084 -9999 0 -0.37 10 10
RAPGEF1 0.034 0.08 -9999 0 -0.4 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.028 0.088 -9999 0 -0.45 9 9
PDGFB-D/PDGFRB 0.015 0.031 -9999 0 -0.24 5 5
TLN1 0.021 0.036 -9999 0 -10000 0 0
Rap1/GTP -0.01 0.045 -9999 0 -0.29 8 8
IQGAP1 0.019 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.027 0.035 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.004 0.084 -9999 0 -0.37 10 10
PVR 0.017 0.029 -9999 0 -0.54 1 1
Necl-5(dimer) 0.017 0.029 -9999 0 -0.54 1 1
mol:GDP 0.039 0.088 -9999 0 -0.43 9 9
MLLT4 0.001 0.066 -9999 0 -0.24 25 25
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
PI3K 0.03 0.066 -9999 0 -0.24 11 11
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.014 0.049 -9999 0 -0.31 1 1
positive regulation of lamellipodium assembly -0.013 0.05 -9999 0 -0.28 11 11
PVRL1 0.017 0.024 -9999 0 -0.24 3 3
PVRL3 -0.009 0.1 -9999 0 -0.32 30 30
PVRL2 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
CDH1 -0.13 0.25 -9999 0 -0.54 101 101
CLDN1 -0.24 0.28 -9999 0 -0.54 173 173
JAM-A/CLDN1 -0.14 0.18 -9999 0 -0.31 179 179
SRC 0.021 0.095 -9999 0 -0.5 9 9
ITGB3 -0.032 0.14 -9999 0 -0.36 50 50
nectin-1(dimer)/I-afadin/I-afadin 0.014 0.049 -9999 0 -0.31 1 1
FARP2 0.035 0.085 -9999 0 -0.45 8 8
RAC1 0.019 0 -9999 0 -10000 0 0
CTNNA1 0.019 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.01 0.076 -9999 0 -0.32 11 11
nectin-1/I-afadin 0.014 0.049 -9999 0 -0.31 1 1
nectin-2/I-afadin 0.016 0.045 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.026 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.01 0.074 -9999 0 -0.3 11 11
CDC42/GTP/IQGAP1/filamentous actin 0.026 0 -9999 0 -10000 0 0
F11R 0.01 0.07 -9999 0 -0.54 6 6
positive regulation of filopodium formation -0.011 0.043 -9999 0 -0.28 8 8
alphaV/beta3 Integrin/Talin 0.016 0.075 -9999 0 -0.23 19 19
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0.045 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.016 0.045 -9999 0 -10000 0 0
PIP5K1C 0.015 0.039 -9999 0 -0.17 8 8
VAV2 0.03 0.096 -9999 0 -0.45 11 11
RAP1/GDP 0.045 0.07 -9999 0 -0.34 8 8
ITGAV 0.018 0.014 -9999 0 -0.24 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.011 0.072 -9999 0 -0.3 10 10
nectin-3(dimer)/I-afadin/I-afadin -0.004 0.084 -9999 0 -0.37 10 10
Rac1/GTP -0.013 0.061 -9999 0 -0.33 11 11
PTPRM 0.007 0.043 -9999 0 -0.2 8 8
E-cadherin/beta catenin/alpha catenin -0.034 0.14 -9999 0 -0.25 101 101
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.019 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.015 0.064 -10000 0 -0.38 9 9
MAP4K4 -0.082 0.19 -10000 0 -0.48 53 53
BAG4 0.017 0.029 -10000 0 -0.54 1 1
PKC zeta/ceramide 0 0.038 0.14 8 -0.29 2 10
NFKBIA 0.019 0 -10000 0 -10000 0 0
BIRC3 -0.18 0.26 -10000 0 -0.54 128 128
BAX 0.005 0.017 -10000 0 -10000 0 0
RIPK1 0.019 0 -10000 0 -10000 0 0
AKT1 0.019 0.007 -10000 0 -10000 0 0
BAD -0.004 0.032 0.15 9 -10000 0 9
SMPD1 -0.032 0.099 -10000 0 -0.22 75 75
RB1 -0.004 0.035 0.15 9 -0.29 1 10
FADD/Caspase 8 -0.069 0.19 -10000 0 -0.46 56 56
MAP2K4 0.004 0.03 0.15 8 -10000 0 8
NSMAF 0.019 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.03 0.15 8 -10000 0 8
EGF -0.031 0.15 -10000 0 -0.42 41 41
mol:ceramide -0.012 0.034 0.15 9 -10000 0 9
MADD 0.019 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.064 -10000 0 -0.38 9 9
ASAH1 0.019 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.004 0.035 0.15 9 -0.29 1 10
cell proliferation 0.025 0.034 -10000 0 -0.23 3 3
BID -0.047 0.13 -10000 0 -0.31 49 49
MAP3K1 -0.004 0.032 0.15 9 -10000 0 9
EIF2A 0.01 0.029 -10000 0 -10000 0 0
TRADD 0.019 0 -10000 0 -10000 0 0
CRADD 0.018 0.014 -10000 0 -0.24 1 1
MAPK3 0.015 0.028 0.15 8 -10000 0 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.015 0.028 0.15 8 -10000 0 8
Cathepsin D/ceramide 0 0.034 0.14 9 -0.12 4 13
FADD -0.082 0.19 -10000 0 -0.48 54 54
KSR1 -0.004 0.032 0.15 9 -10000 0 9
MAPK8 0.01 0.034 0.15 8 -0.22 2 10
PRKRA -0.004 0.032 0.15 9 -10000 0 9
PDGFA 0.004 0.088 -10000 0 -0.48 11 11
TRAF2 0.019 0 -10000 0 -10000 0 0
IGF1 0.008 0.066 -10000 0 -0.36 10 10
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.034 0.15 9 -10000 0 9
CTSD 0.016 0.027 -10000 0 -0.24 4 4
regulation of nitric oxide biosynthetic process 0.028 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.031 0.04 -10000 0 -0.24 3 3
PRKCD 0.019 0 -10000 0 -10000 0 0
PRKCZ 0.016 0.041 -10000 0 -0.54 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.064 -10000 0 -0.38 9 9
RelA/NF kappa B1 0.028 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.004 0.11 -10000 0 -0.54 15 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.094 0.2 -10000 0 -0.52 53 53
TNFR1A/BAG4/TNF-alpha -0.035 0.14 -10000 0 -0.32 76 76
mol:Sphingosine-1-phosphate 0.015 0.064 -10000 0 -0.38 9 9
MAP2K1 0.01 0.029 0.15 8 -10000 0 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.019 0 -10000 0 -10000 0 0
CYCS 0.001 0.023 0.11 8 -10000 0 8
TNFRSF1A 0.019 0 -10000 0 -10000 0 0
NFKB1 0.019 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.021 -10000 0 -0.38 1 1
EIF2AK2 0.004 0.03 0.15 8 -10000 0 8
TNF-alpha/TNFR1A/FAN -0.034 0.14 -10000 0 -0.32 75 75
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.03 0.12 -10000 0 -0.26 55 55
MAP2K2 0.01 0.029 0.15 8 -10000 0 8
SMPD3 -0.04 0.12 -10000 0 -0.25 75 75
TNF -0.095 0.22 -10000 0 -0.54 75 75
PKC zeta/PAR4 0.009 0.086 -10000 0 -0.38 17 17
mol:PHOSPHOCHOLINE -0.001 0.066 0.19 30 -10000 0 30
NF kappa B1/RelA/I kappa B alpha 0.042 0.066 -10000 0 -0.26 17 17
AIFM1 0.001 0.023 0.11 8 -10000 0 8
BCL2 0.019 0 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.004 0.085 -10000 0 -0.32 23 23
cell-cell adhesion 0.032 0.076 0.32 8 -10000 0 8
Ephrin B/EPHB2/RasGAP 0.014 0.1 -10000 0 -0.26 40 40
ITSN1 0.019 0 -10000 0 -10000 0 0
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
SHC1 0.019 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.009 0.049 -10000 0 -0.26 2 2
Ephrin B1/EPHB1 0.006 0.066 -10000 0 -0.3 11 11
HRAS/GDP -0.024 0.073 -10000 0 -0.26 25 25
Ephrin B/EPHB1/GRB7 0.004 0.1 -10000 0 -0.28 33 33
Endophilin/SYNJ1 0.003 0.091 -10000 0 -0.24 39 39
KRAS 0.018 0.014 -10000 0 -0.24 1 1
Ephrin B/EPHB1/Src 0.016 0.098 -10000 0 -0.27 32 32
endothelial cell migration 0.037 0.022 -10000 0 -10000 0 0
GRB2 0.019 0 -10000 0 -10000 0 0
GRB7 -0.004 0.068 -10000 0 -0.24 27 27
PAK1 0.008 0.098 -10000 0 -0.26 39 39
HRAS 0.019 0 -10000 0 -10000 0 0
RRAS 0.003 0.092 -10000 0 -0.25 39 39
DNM1 -0.009 0.081 -10000 0 -0.24 39 39
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.005 0.089 -10000 0 -0.26 32 32
lamellipodium assembly -0.032 0.076 -10000 0 -0.32 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.074 -10000 0 -0.24 9 9
PIK3R1 0.019 0 -10000 0 -10000 0 0
EPHB2 -0.005 0.11 -10000 0 -0.54 16 16
EPHB3 -0.001 0.069 -10000 0 -0.24 27 27
EPHB1 -0.005 0.094 -10000 0 -0.33 25 25
EPHB4 0.018 0.014 -10000 0 -0.24 1 1
mol:GDP 0.012 0.092 -10000 0 -0.27 25 25
Ephrin B/EPHB2 0.004 0.1 -10000 0 -0.26 42 42
Ephrin B/EPHB3 0.008 0.088 -10000 0 -0.27 27 27
JNK cascade 0.013 0.085 -10000 0 -0.27 25 25
Ephrin B/EPHB1 0.005 0.097 -10000 0 -0.27 34 34
RAP1/GDP 0.029 0.086 -10000 0 -0.3 4 4
EFNB2 0.012 0.041 -10000 0 -0.24 9 9
EFNB3 -0.016 0.14 -10000 0 -0.54 23 23
EFNB1 0.009 0.051 -10000 0 -0.24 14 14
Ephrin B2/EPHB1-2 0.006 0.091 -10000 0 -0.31 23 23
RAP1B 0.019 0 -10000 0 -10000 0 0
RAP1A 0.019 0 -10000 0 -10000 0 0
CDC42/GTP -0.037 0.088 -10000 0 -0.4 6 6
Rap1/GTP -0.031 0.075 -10000 0 -0.35 6 6
axon guidance 0.003 0.085 -10000 0 -0.32 23 23
MAPK3 0.029 0.067 -10000 0 -0.28 2 2
MAPK1 0.029 0.067 -10000 0 -0.32 1 1
Rac1/GDP 0.022 0.088 -10000 0 -0.25 24 24
actin cytoskeleton reorganization -0.026 0.064 -10000 0 -0.3 6 6
CDC42/GDP 0.022 0.088 -10000 0 -0.25 24 24
PI3K 0.041 0.023 -10000 0 -10000 0 0
EFNA5 0.008 0.076 -10000 0 -0.54 7 7
Ephrin B2/EPHB4 0.022 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.01 0.087 -10000 0 -0.23 39 39
CDC42 0.019 0 -10000 0 -10000 0 0
RAS family/GTP -0.031 0.073 -10000 0 -0.34 6 6
PTK2 0.008 0.022 -10000 0 -10000 0 0
MAP4K4 0.013 0.086 -10000 0 -0.28 25 25
SRC 0.019 0 -10000 0 -10000 0 0
KALRN 0.014 0.045 -10000 0 -0.39 4 4
Intersectin/N-WASP 0.028 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.032 0.097 -10000 0 -0.32 8 8
MAP2K1 0.024 0.07 -10000 0 -0.3 2 2
WASL 0.019 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.016 0.095 -10000 0 -0.3 25 25
cell migration 0.026 0.082 -10000 0 -0.35 2 2
NRAS 0.019 0 -10000 0 -10000 0 0
SYNJ1 0.003 0.092 -10000 0 -0.25 39 39
PXN 0.019 0 -10000 0 -10000 0 0
TF -0.059 0.14 -10000 0 -0.27 97 97
HRAS/GTP 0.005 0.1 -10000 0 -0.35 8 8
Ephrin B1/EPHB1-2 0.005 0.094 -10000 0 -0.31 25 25
cell adhesion mediated by integrin 0.022 0.072 0.26 26 -10000 0 26
RAC1 0.019 0 -10000 0 -10000 0 0
mol:GTP 0.006 0.11 -10000 0 -0.26 47 47
RAC1-CDC42/GTP -0.035 0.077 -10000 0 -0.34 8 8
RASA1 0.017 0.029 -10000 0 -0.54 1 1
RAC1-CDC42/GDP 0.029 0.086 -10000 0 -0.3 4 4
ruffle organization 0.018 0.097 -10000 0 -0.35 6 6
NCK1 0.019 0 -10000 0 -10000 0 0
receptor internalization -0.003 0.094 -10000 0 -0.24 40 40
Ephrin B/EPHB2/KALRN 0.013 0.11 -10000 0 -0.28 39 39
ROCK1 0.014 0.043 -10000 0 -0.22 2 2
RAS family/GDP -0.026 0.064 -10000 0 -0.29 6 6
Rac1/GTP -0.034 0.08 -10000 0 -0.34 8 8
Ephrin B/EPHB1/Src/Paxillin 0.012 0.082 -10000 0 -0.24 32 32
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.007 0.059 0.22 4 -10000 0 4
GNAI2 0.019 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.019 0.03 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.093 0.13 -10000 0 -0.25 155 155
RhoA/GTP -0.007 0.06 -10000 0 -0.23 4 4
negative regulation of cAMP metabolic process -0.017 0.065 -10000 0 -0.24 5 5
GNAZ -0.015 0.093 -10000 0 -0.26 45 45
GNAI3 0.019 0 -10000 0 -10000 0 0
GNA12 0.019 0 -10000 0 -10000 0 0
S1PR5 0.008 0.052 -10000 0 -0.24 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.017 0.065 -10000 0 -0.24 5 5
RhoA/GDP 0.014 0 -10000 0 -10000 0 0
RHOA 0.019 0 -10000 0 -10000 0 0
GNAI1 0.004 0.06 -10000 0 -0.24 20 20
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.023 0.081 -10000 0 -0.28 24 24
ER alpha/Gai/GDP/Gbeta gamma -0.007 0.09 -10000 0 -0.37 12 12
AKT1 0.023 0.12 -10000 0 -0.79 7 7
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.019 0.12 -10000 0 -0.81 7 7
mol:Ca2+ -0.052 0.19 -10000 0 -0.4 73 73
IGF1R 0.016 0.027 -10000 0 -0.24 4 4
E2/ER alpha (dimer)/Striatin 0.019 0.048 -10000 0 -0.32 7 7
SHC1 0.019 0 -10000 0 -10000 0 0
apoptosis -0.023 0.11 0.76 7 -10000 0 7
RhoA/GTP -0.004 0.031 -10000 0 -0.22 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.01 0.073 -10000 0 -0.41 9 9
regulation of stress fiber formation -0.047 0.031 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) 0.007 0.078 -10000 0 -0.32 19 19
KRAS 0.018 0.014 -10000 0 -0.24 1 1
G13/GTP 0.018 0.044 -10000 0 -0.29 7 7
pseudopodium formation 0.047 0.031 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 0.019 0.048 -10000 0 -0.32 7 7
GRB2 0.019 0 -10000 0 -10000 0 0
GNG2 0.01 0.07 -10000 0 -0.54 6 6
GNAO1 -0.093 0.13 -10000 0 -0.25 155 155
HRAS 0.019 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.094 -10000 0 -0.5 8 8
E2/ER beta (dimer) 0 0.073 -10000 0 -0.36 14 14
mol:GDP -0.017 0.071 -10000 0 -0.32 19 19
mol:NADP 0.014 0.094 -10000 0 -0.5 8 8
PIK3R1 0.019 0 -10000 0 -10000 0 0
mol:IP3 -0.055 0.2 -10000 0 -0.42 73 73
IGF-1R heterotetramer 0.016 0.027 -10000 0 -0.24 4 4
PLCB1 -0.055 0.19 -10000 0 -0.42 69 69
PLCB2 -0.054 0.2 -10000 0 -0.42 71 71
IGF1 0.008 0.066 -10000 0 -0.36 10 10
mol:L-citrulline 0.014 0.094 -10000 0 -0.5 8 8
RHOA 0.019 0 -10000 0 -10000 0 0
Gai/GDP -0.022 0.081 -10000 0 -0.5 2 2
JNK cascade 0 0.073 -10000 0 -0.36 14 14
BCAR1 0.019 0 -10000 0 -10000 0 0
ESR2 -0.001 0.1 -10000 0 -0.5 14 14
GNAQ 0.019 0 -10000 0 -10000 0 0
ESR1 0.008 0.076 -10000 0 -0.54 7 7
Gq family/GDP/Gbeta gamma -0.012 0.14 -10000 0 -0.57 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.034 0.042 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.01 0.073 -10000 0 -0.41 9 9
GNAZ -0.015 0.093 -10000 0 -0.26 45 45
E2/ER alpha (dimer) 0.006 0.055 -10000 0 -0.39 7 7
STRN 0.019 0 -10000 0 -10000 0 0
GNAL -0.02 0.1 -10000 0 -0.28 49 49
PELP1 0.019 0 -10000 0 -10000 0 0
MAPK11 0.01 0.062 -10000 0 -0.32 12 12
GNAI2 0.019 0 -10000 0 -10000 0 0
GNAI3 0.019 0 -10000 0 -10000 0 0
GNAI1 0.004 0.06 -10000 0 -0.24 20 20
HBEGF -0.023 0.1 -10000 0 -0.36 13 13
cAMP biosynthetic process -0.01 0.08 -10000 0 -0.27 25 25
SRC 0.001 0.086 -10000 0 -0.39 9 9
PI3K 0.028 0.009 -10000 0 -10000 0 0
GNB1 0.019 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.027 0.08 -10000 0 -0.28 19 19
SOS1 0.019 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.013 0.063 -10000 0 -0.35 9 9
Gs family/GTP -0.006 0.083 -10000 0 -0.27 25 25
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.007 -10000 0 -10000 0 0
vasodilation 0.014 0.091 -10000 0 -0.48 8 8
mol:DAG -0.055 0.2 -10000 0 -0.42 73 73
Gs family/GDP/Gbeta gamma -0.025 0.073 -10000 0 -0.29 19 19
MSN 0.048 0.033 -10000 0 -10000 0 0
Gq family/GTP -0.054 0.19 -10000 0 -0.43 67 67
mol:PI-3-4-5-P3 0.02 0.11 -10000 0 -0.78 7 7
NRAS 0.019 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.014 0.091 0.48 8 -10000 0 8
GRB2/SOS1 0.028 0 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.076 -10000 0 -0.3 19 19
NOS3 0.013 0.098 -10000 0 -0.53 8 8
GNA11 0.019 0 -10000 0 -10000 0 0
MAPKKK cascade 0.032 0.094 -10000 0 -0.59 7 7
E2/ER alpha (dimer)/PELP1/Src 0.015 0.088 -10000 0 -0.43 9 9
ruffle organization 0.047 0.031 -10000 0 -10000 0 0
ROCK2 0.045 0.035 -10000 0 -10000 0 0
GNA14 -0.084 0.22 -10000 0 -0.53 69 69
GNA15 0.002 0.095 -10000 0 -0.54 11 11
GNA13 0.019 0 -10000 0 -10000 0 0
MMP9 -0.04 0.14 -10000 0 -0.33 45 45
MMP2 -0.008 0.09 -10000 0 -0.37 9 9
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.003 0.1 -10000 0 -0.38 22 22
CRKL 0.017 0.079 -10000 0 -0.26 23 23
mol:PIP3 -0.019 0.028 0.51 1 -10000 0 1
AKT1 0.001 0.019 0.36 1 -10000 0 1
PTK2B 0.008 0.076 -10000 0 -0.54 7 7
RAPGEF1 0.024 0.076 -10000 0 -0.32 4 4
RANBP10 0.019 0 -10000 0 -10000 0 0
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
HGF/MET/SHIP2 0.001 0.1 -10000 0 -0.33 27 27
MAP3K5 -0.013 0.14 -10000 0 -0.37 28 28
HGF/MET/CIN85/CBL/ENDOPHILINS 0.014 0.095 -10000 0 -0.3 27 27
AP1 -0.004 0.066 -10000 0 -0.26 11 11
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0 -10000 0 -10000 0 0
apoptosis 0.003 0.056 -10000 0 -10000 0 0
STAT3 (dimer) 0.016 0.091 -10000 0 -0.47 4 4
GAB1/CRKL/SHP2/PI3K 0.041 0.075 -10000 0 -0.33 3 3
INPP5D -0.075 0.21 -10000 0 -0.54 62 62
CBL/CRK 0.028 0.077 -10000 0 -0.32 4 4
PTPN11 0.019 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0 -10000 0 -10000 0 0
PTEN 0.017 0.029 -10000 0 -0.54 1 1
ELK1 -0.017 0.049 -10000 0 -0.2 22 22
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.019 0.051 -10000 0 -0.24 3 3
PAK1 0.008 0.019 0.34 1 -10000 0 1
HGF/MET/RANBP10 0.001 0.1 -10000 0 -0.33 27 27
HRAS -0.005 0.16 -10000 0 -0.61 22 22
DOCK1 0.024 0.076 -10000 0 -0.32 4 4
GAB1 0.011 0.083 -10000 0 -0.28 23 23
CRK 0.018 0.079 -10000 0 -0.26 23 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.16 -10000 0 -0.55 27 27
JUN -0.008 0.079 -10000 0 -0.24 37 37
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.008 0.075 -10000 0 -0.26 27 27
PIK3R1 0.019 0 -10000 0 -10000 0 0
cell morphogenesis 0.042 0.092 -10000 0 -0.43 4 4
GRB2/SHC 0.015 0.07 -10000 0 -0.23 22 22
FOS 0.01 0.047 -10000 0 -0.24 12 12
GLMN -0.003 0.027 -10000 0 -0.26 4 4
cell motility -0.017 0.049 -10000 0 -0.2 22 22
HGF/MET/MUC20 -0.012 0.1 -10000 0 -0.34 27 27
cell migration 0.015 0.069 -10000 0 -0.23 22 22
GRB2 0.019 0 -10000 0 -10000 0 0
CBL 0.019 0 -10000 0 -10000 0 0
MET/RANBP10 -0.003 0.1 -10000 0 -0.38 22 22
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.011 0.092 -10000 0 -0.26 33 33
MET/MUC20 -0.017 0.1 -10000 0 -0.31 35 35
RAP1B 0.03 0.072 -10000 0 -0.32 3 3
RAP1A 0.03 0.072 -10000 0 -0.32 3 3
HGF/MET/RANBP9 0.001 0.1 -10000 0 -0.33 27 27
RAF1 0.003 0.15 -10000 0 -0.57 22 22
STAT3 0.016 0.092 -10000 0 -0.48 4 4
cell proliferation 0.019 0.12 -10000 0 -0.37 27 27
RPS6KB1 0.006 0.034 -10000 0 -0.19 2 2
MAPK3 -0.023 0.045 -10000 0 -0.19 2 2
MAPK1 -0.023 0.045 -10000 0 -10000 0 0
RANBP9 0.019 0 -10000 0 -10000 0 0
MAPK8 0.018 0.11 -10000 0 -0.33 14 14
SRC 0.017 0.086 -10000 0 -0.44 4 4
PI3K 0.015 0.07 -10000 0 -0.23 22 22
MET/Glomulin -0.012 0.092 -10000 0 -0.26 38 38
SOS1 0.019 0 -10000 0 -10000 0 0
MAP2K1 0.011 0.14 -10000 0 -0.52 22 22
MET -0.024 0.14 -10000 0 -0.43 35 35
MAP4K1 -0.02 0.14 -10000 0 -0.38 27 27
PTK2 0.019 0 -10000 0 -10000 0 0
MAP2K2 0.011 0.14 -10000 0 -0.52 22 22
BAD 0.008 0.018 0.34 1 -10000 0 1
MAP2K4 -0.004 0.13 -10000 0 -0.36 22 22
SHP2/GRB2/SOS1/GAB1 -0.025 0.083 -10000 0 -0.34 22 22
INPPL1 0.019 0 -10000 0 -10000 0 0
PXN 0.019 0 -10000 0 -10000 0 0
SH3KBP1 0.019 0 -10000 0 -10000 0 0
HGS 0 0.07 -10000 0 -0.23 27 27
PLCgamma1/PKC 0.014 0 -10000 0 -10000 0 0
HGF 0 0.085 -10000 0 -0.34 19 19
RASA1 0.017 0.029 -10000 0 -0.54 1 1
NCK1 0.019 0 -10000 0 -10000 0 0
PTPRJ 0.019 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.017 0.071 -10000 0 -0.23 22 22
PDPK1 -0.008 0.022 0.4 1 -10000 0 1
HGF/MET/SHIP -0.058 0.17 -10000 0 -0.37 78 78
Ephrin B reverse 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
EFNB2 0.012 0.041 -10000 0 -0.24 9 9
EPHB2 -0.006 0.12 -10000 0 -0.54 16 16
EFNB1 -0.001 0.069 -10000 0 -0.31 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.004 0.12 -10000 0 -0.3 41 41
Ephrin B2/EPHB1-2 0.005 0.093 -10000 0 -0.32 23 23
neuron projection morphogenesis -0.025 0.11 -10000 0 -0.29 41 41
Ephrin B1/EPHB1-2/Tiam1 -0.012 0.13 -10000 0 -0.33 41 41
DNM1 -0.01 0.082 -10000 0 -0.25 39 39
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 0.002 0.077 -10000 0 -0.7 4 4
YES1 -0.002 0.1 -10000 0 -0.94 4 4
Ephrin B1/EPHB1-2/NCK2 0.006 0.1 -10000 0 -0.31 23 23
PI3K 0.011 0.079 -10000 0 -0.7 4 4
mol:GDP -0.013 0.13 -10000 0 -0.32 41 41
ITGA2B -0.004 0.073 -10000 0 -0.24 31 31
endothelial cell proliferation 0.021 0.024 -10000 0 -10000 0 0
FYN -0.002 0.1 -10000 0 -0.94 4 4
MAP3K7 -0.005 0.081 -10000 0 -0.74 4 4
FGR -0.019 0.12 -10000 0 -0.95 4 4
TIAM1 -0.014 0.13 -10000 0 -0.54 22 22
PIK3R1 0.019 0 -10000 0 -10000 0 0
RGS3 0.019 0 -10000 0 -10000 0 0
cell adhesion -0.01 0.12 -10000 0 -0.55 8 8
LYN -0.009 0.11 -10000 0 -0.94 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.013 0.093 -10000 0 -0.88 4 4
Ephrin B1/EPHB1-2 -0.019 0.085 -10000 0 -0.8 4 4
SRC -0.002 0.099 -10000 0 -0.92 4 4
ITGB3 -0.032 0.14 -10000 0 -0.36 50 50
EPHB1 -0.006 0.094 -10000 0 -0.33 25 25
EPHB4 0.018 0.014 -10000 0 -0.24 1 1
RAC1 0.019 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.021 0.025 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.024 0.11 -10000 0 -0.36 25 25
BLK -0.12 0.12 -10000 0 -0.99 4 4
HCK -0.021 0.11 -10000 0 -0.96 4 4
regulation of stress fiber formation -0.005 0.1 0.31 23 -10000 0 23
MAPK8 0.009 0.073 -10000 0 -0.66 4 4
Ephrin B1/EPHB1-2/RGS3 0.006 0.1 -10000 0 -0.31 23 23
endothelial cell migration -0.002 0.073 -10000 0 -0.63 4 4
NCK2 0.019 0 -10000 0 -10000 0 0
PTPN13 0.018 0.077 -10000 0 -0.49 7 7
regulation of focal adhesion formation -0.005 0.1 0.31 23 -10000 0 23
chemotaxis -0.005 0.1 0.31 23 -10000 0 23
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
Rac1/GTP -0.009 0.12 -10000 0 -0.29 41 41
angiogenesis -0.019 0.085 -10000 0 -0.8 4 4
LCK -0.069 0.14 -10000 0 -0.99 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.018 0.014 -10000 0 -0.24 1 1
NFATC1 0.056 0.055 -10000 0 -0.27 9 9
NFATC2 0.032 0.047 -10000 0 -0.25 2 2
NFATC3 0.027 0.03 -10000 0 -0.38 2 2
YWHAE 0.019 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.099 0.2 -10000 0 -0.44 81 81
Exportin 1/Ran/NUP214 0.039 0.001 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.1 0.22 -10000 0 -0.44 99 99
BCL2/BAX 0.028 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.016 0.002 -10000 0 -10000 0 0
CaM/Ca2+ 0.016 0.002 -10000 0 -10000 0 0
BAX 0.019 0 -10000 0 -10000 0 0
MAPK14 0.019 0.001 -10000 0 -10000 0 0
BAD 0.019 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.085 0.19 -10000 0 -0.42 81 81
Calcineurin A alpha-beta B1/BCL2 0.019 0 -10000 0 -10000 0 0
FKBP8 0.019 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.084 0.19 0.41 81 -10000 0 81
KPNB1 0.019 0 -10000 0 -10000 0 0
KPNA2 0.019 0 -10000 0 -10000 0 0
XPO1 0.019 0 -10000 0 -10000 0 0
SFN -0.035 0.11 -10000 0 -0.24 74 74
MAP3K8 -0.003 0.11 -10000 0 -0.52 15 15
NFAT4/CK1 alpha 0.041 0.019 -10000 0 -0.21 2 2
MEF2D/NFAT1/Cbp/p300 0.069 0.049 -10000 0 -0.24 1 1
CABIN1 -0.1 0.2 -10000 0 -0.45 81 81
CALM1 0.019 0.001 -10000 0 -10000 0 0
RAN 0.019 0 -10000 0 -10000 0 0
MAP3K1 0.019 0 -10000 0 -10000 0 0
CAMK4 -0.063 0.2 -10000 0 -0.54 54 54
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.019 0 -10000 0 -10000 0 0
YWHAH 0.019 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.042 0.16 -10000 0 -0.38 63 63
YWHAB 0.019 0 -10000 0 -10000 0 0
MAPK8 0.019 0.001 -10000 0 -10000 0 0
MAPK9 0.019 0 -10000 0 -10000 0 0
YWHAG 0.019 0 -10000 0 -10000 0 0
FKBP1A 0.019 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.074 0.055 -10000 0 -0.27 2 2
PRKCH 0.016 0.041 -10000 0 -0.54 2 2
CABIN1/Cbp/p300 0.029 0.002 -10000 0 -10000 0 0
CASP3 0.019 0.001 -10000 0 -10000 0 0
PIM1 0.019 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.001 -10000 0 -10000 0 0
apoptosis 0 0.005 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.027 -10000 0 -10000 0 0
PRKCB -0.15 0.26 -10000 0 -0.54 110 110
PRKCE 0.019 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.035 0.028 -10000 0 -0.34 2 2
BAD/BCL-XL 0.028 0.009 -10000 0 -10000 0 0
PRKCD 0.019 0 -10000 0 -10000 0 0
NUP214 0.019 0 -10000 0 -10000 0 0
PRKCZ 0.016 0.041 -10000 0 -0.54 2 2
PRKCA 0.013 0.044 -10000 0 -0.29 7 7
PRKCG 0.01 0.025 -10000 0 -0.24 3 3
PRKCQ -0.16 0.26 -10000 0 -0.54 116 116
FKBP38/BCL2 0.028 0 -10000 0 -10000 0 0
EP300 0.02 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.019 0 -10000 0 -10000 0 0
NFATc/JNK1 0.065 0.053 -10000 0 -0.27 1 1
CaM/Ca2+/FKBP38 0.027 0.002 -10000 0 -10000 0 0
FKBP12/FK506 0.014 0 -10000 0 -10000 0 0
CSNK1A1 0.024 0.002 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.025 0.12 -10000 0 -0.32 54 54
NFATc/ERK1 0.064 0.053 -10000 0 -0.27 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.1 0.22 -10000 0 -0.44 99 99
NR4A1 0.062 0.051 -10000 0 -0.49 1 1
GSK3B 0.019 0.001 -10000 0 -10000 0 0
positive T cell selection 0.027 0.03 -10000 0 -0.38 2 2
NFAT1/CK1 alpha 0.031 0.039 -10000 0 -0.22 2 2
RCH1/ KPNB1 0.028 0 -10000 0 -10000 0 0
YWHAQ 0.019 0 -10000 0 -10000 0 0
PRKACA 0.019 0.001 -10000 0 -10000 0 0
AKAP5 -0.077 0.21 -10000 0 -0.54 63 63
MEF2D 0.02 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.065 0.053 -10000 0 -0.27 1 1
CREBBP 0.02 0.001 -10000 0 -10000 0 0
BCL2 0.019 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.024 0.076 -9999 0 -0.31 6 6
regulation of S phase of mitotic cell cycle 0 0.045 -9999 0 -10000 0 0
GNAO1 -0.093 0.13 -9999 0 -0.25 155 155
HRAS 0.019 0 -9999 0 -10000 0 0
SHBG/T-DHT 0.003 0.036 -9999 0 -0.13 24 24
PELP1 0.019 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
MAP2K1 0.007 0.053 -9999 0 -10000 0 0
T-DHT/AR -0.056 0.085 -9999 0 -0.16 144 144
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
mol:GTP 0 0.001 -9999 0 -0.004 12 12
GNAI2 0.019 0 -9999 0 -10000 0 0
GNAI3 0.019 0 -9999 0 -10000 0 0
GNAI1 0.005 0.06 -9999 0 -0.24 20 20
mol:GDP -0.039 0.049 -9999 0 -10000 0 0
cell proliferation 0.022 0.056 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
FOS 0.03 0.055 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.019 -9999 0 -0.051 19 19
MAPK3 0.016 0.053 -9999 0 -10000 0 0
MAPK1 0.018 0.03 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
mol:IP3 0 0 -9999 0 -0.002 12 12
cAMP biosynthetic process 0.009 0.037 -9999 0 -0.13 16 16
GNG2 0.01 0.07 -9999 0 -0.54 6 6
potassium channel inhibitor activity 0 0 -9999 0 -0.002 12 12
HRAS/GTP -0.009 0.058 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.029 0.006 -9999 0 -10000 0 0
SRC 0.019 0 -9999 0 -10000 0 0
voltage-gated calcium channel activity 0 0 -9999 0 -0.002 12 12
PI3K 0.025 0.008 -9999 0 -10000 0 0
apoptosis -0.028 0.046 -9999 0 -10000 0 0
T-DHT/AR/PELP1 -0.034 0.072 -9999 0 -10000 0 0
HRAS/GDP -0.013 0.059 -9999 0 -10000 0 0
CREB1 0.028 0.047 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.037 0.006 -9999 0 -10000 0 0
AR -0.086 0.13 -9999 0 -0.24 144 144
GNB1 0.019 0 -9999 0 -10000 0 0
RAF1 -0.001 0.055 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.003 0.059 -9999 0 -10000 0 0
T-DHT/AR/PELP1/Src -0.018 0.067 -9999 0 -10000 0 0
MAP2K2 0.007 0.053 -9999 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0 0.045 -9999 0 -10000 0 0
GNAZ -0.015 0.093 -9999 0 -0.26 45 45
SHBG 0.001 0.065 -9999 0 -0.24 24 24
Gi family/GNB1/GNG2/GDP -0.018 0.076 -9999 0 -0.3 7 7
mol:T-DHT 0 0 -9999 0 -10000 0 0
RAC1 0.019 0 -9999 0 -10000 0 0
GNRH1 0.005 0.055 -9999 0 -0.39 7 7
Gi family/GTP -0.038 0.065 -9999 0 -0.19 18 18
CDC42 0.019 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.018 0.014 -10000 0 -0.24 1 1
RAS family/GTP/Tiam1 0.004 0.08 -10000 0 -0.23 24 24
NT3 (dimer)/TRKC -0.019 0.12 -10000 0 -0.39 28 28
NT3 (dimer)/TRKB -0.023 0.1 -10000 0 -0.29 28 28
SHC/Grb2/SOS1/GAB1/PI3K 0.044 0.005 -10000 0 -10000 0 0
RAPGEF1 0.019 0 -10000 0 -10000 0 0
BDNF -0.12 0.24 -10000 0 -0.54 88 88
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
DYNLT1 0.019 0 -10000 0 -10000 0 0
NTRK1 -0.001 0.1 -10000 0 -0.5 14 14
NTRK2 -0.019 0.1 -10000 0 -0.28 47 47
NTRK3 -0.025 0.14 -10000 0 -0.49 31 31
NT-4/5 (dimer)/TRKB -0.022 0.09 -10000 0 -0.29 21 21
neuron apoptosis 0.078 0.12 0.3 42 -10000 0 42
SHC 2-3/Grb2 -0.083 0.12 -10000 0 -0.32 42 42
SHC1 0.019 0 -10000 0 -10000 0 0
SHC2 -0.072 0.12 -10000 0 -0.32 33 33
SHC3 -0.063 0.11 -10000 0 -0.3 26 26
STAT3 (dimer) 0.024 0.029 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.014 0.1 -10000 0 -0.33 23 23
RIN/GDP 0.015 0.053 -10000 0 -0.18 1 1
GIPC1 0.019 0 -10000 0 -10000 0 0
KRAS 0.018 0.014 -10000 0 -0.24 1 1
DNAJA3 -0.003 0.072 -10000 0 -0.26 15 15
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.027 0.05 -10000 0 -10000 0 0
MAGED1 0.019 0 -10000 0 -10000 0 0
PTPN11 0.019 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.038 0 -10000 0 -10000 0 0
GRB2 0.019 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.026 0.14 -10000 0 -0.36 51 51
TRKA/NEDD4-2 0.01 0.084 -10000 0 -0.39 15 15
ELMO1 -0.007 0.12 -10000 0 -0.54 17 17
RhoG/GTP/ELMO1/DOCK1 0.009 0.074 -10000 0 -0.32 17 17
NGF 0.002 0.063 -10000 0 -0.24 22 22
HRAS 0.019 0 -10000 0 -10000 0 0
DOCK1 0.019 0 -10000 0 -10000 0 0
GAB2 0.015 0.031 -10000 0 -0.24 5 5
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.019 0 -10000 0 -10000 0 0
FRS2 0.017 0.024 -10000 0 -0.24 3 3
DNM1 -0.009 0.081 -10000 0 -0.24 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.012 0.089 -10000 0 -0.26 32 32
mol:GDP 0.02 0.073 -10000 0 -0.26 1 1
NGF (dimer) 0.002 0.062 -10000 0 -0.24 22 22
RhoG/GDP -0.005 0.085 -10000 0 -0.39 17 17
RIT1/GDP 0.023 0.055 -10000 0 -10000 0 0
TIAM1 -0.014 0.13 -10000 0 -0.54 22 22
PIK3R1 0.019 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.069 0.16 -10000 0 -0.33 92 92
KIDINS220/CRKL/C3G 0.028 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.027 0.021 -10000 0 -0.38 1 1
FRS2 family/SHP2 0.037 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.049 0 -10000 0 -10000 0 0
RIT1/GTP 0.014 0 -10000 0 -10000 0 0
NT3 (dimer) -0.004 0.068 -10000 0 -0.24 27 27
RAP1/GDP -0.008 0.028 -10000 0 -10000 0 0
KIDINS220/CRKL 0.018 0.014 -10000 0 -0.24 1 1
BDNF (dimer) -0.12 0.24 -10000 0 -0.54 88 88
ubiquitin-dependent protein catabolic process 0.013 0.079 -10000 0 -0.32 15 15
Schwann cell development -0.023 0.026 -10000 0 -10000 0 0
EHD4 0.019 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.048 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.045 0.013 -10000 0 -10000 0 0
RAP1B 0.019 0 -10000 0 -10000 0 0
RAP1A 0.019 0 -10000 0 -10000 0 0
CDC42/GTP -0.095 0.15 -10000 0 -0.36 52 52
ABL1 0.019 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.028 0 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.07 -10000 0 -10000 0 0
STAT3 0.024 0.029 -10000 0 -10000 0 0
axon guidance -0.11 0.13 -10000 0 -0.35 52 52
MAPK3 -0.02 0.13 -10000 0 -0.32 51 51
MAPK1 -0.02 0.13 -10000 0 -0.32 51 51
CDC42/GDP 0.023 0.055 -10000 0 -10000 0 0
NTF3 -0.004 0.068 -10000 0 -0.24 27 27
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.013 0.078 -10000 0 -0.32 15 15
PI3K 0.028 0.009 -10000 0 -10000 0 0
FRS3 0.019 0 -10000 0 -10000 0 0
FAIM 0.014 0.05 -10000 0 -0.54 3 3
GAB1 0.019 0 -10000 0 -10000 0 0
RASGRF1 -0.029 0.11 -10000 0 -0.28 42 42
SOS1 0.019 0 -10000 0 -10000 0 0
MCF2L -0.055 0.11 -10000 0 -0.32 35 35
RGS19 0.019 0 -10000 0 -10000 0 0
CDC42 0.019 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.046 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.055 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT 0.004 0.071 -10000 0 -0.32 12 12
neuron projection morphogenesis 0.014 0.069 -10000 0 -0.5 1 1
NGF (dimer)/TRKA/NEDD4-2 0.013 0.079 -10000 0 -0.32 15 15
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.027 0.11 -10000 0 -0.26 59 59
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.06 -10000 0 -0.23 12 12
RAS family/GTP/PI3K 0.036 0.007 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.055 0.012 -10000 0 -10000 0 0
NRAS 0.019 0 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0 -10000 0 -10000 0 0
PRKCI 0.019 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0 -10000 0 -10000 0 0
PRKCZ 0.016 0.041 -10000 0 -0.54 2 2
MAPKKK cascade -0.031 0.12 -10000 0 -0.56 15 15
RASA1 0.017 0.029 -10000 0 -0.54 1 1
TRKA/c-Abl 0.014 0.074 -10000 0 -0.38 12 12
SQSTM1 0.019 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.051 0.14 -10000 0 -0.29 92 92
NGF (dimer)/TRKA/p62/Atypical PKCs 0.035 0.067 -10000 0 -0.26 14 14
MATK -0.049 0.18 -10000 0 -0.53 45 45
NEDD4L 0.014 0.05 -10000 0 -0.54 3 3
RAS family/GDP -0.01 0.025 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.011 0.075 -10000 0 -0.28 15 15
Rac1/GTP -0.04 0.074 -10000 0 -0.25 24 24
FRS2 family/SHP2/CRK family 0.055 0.014 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.01 0.072 -9999 0 -10000 0 0
adherens junction organization -0.029 0.13 -9999 0 -0.31 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.007 0.085 -9999 0 -0.3 2 2
FMN1 -0.034 0.13 -9999 0 -0.34 13 13
mol:IP3 0.002 0.073 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.037 0.13 -9999 0 -0.24 101 101
CTNNB1 0.022 0.005 -9999 0 -10000 0 0
AKT1 0.001 0.086 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.069 0.19 -9999 0 -0.38 101 101
CTNND1 0.019 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.027 0.12 -9999 0 -0.3 5 5
VASP -0.028 0.12 -9999 0 -0.31 5 5
ZYX -0.029 0.12 -9999 0 -0.31 7 7
JUB -0.028 0.12 -9999 0 -0.31 6 6
EGFR(dimer) -0.036 0.13 -9999 0 -0.32 22 22
E-cadherin/beta catenin-gamma catenin -0.06 0.15 -9999 0 -0.3 101 101
mol:PI-3-4-5-P3 -0.005 0.09 -9999 0 -0.23 5 5
PIK3CA 0.019 0.014 -9999 0 -0.25 1 1
PI3K -0.005 0.092 -9999 0 -0.24 5 5
FYN 0.014 0.063 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.072 -9999 0 -10000 0 0
JUP 0.014 0.045 -9999 0 -0.24 11 11
PIK3R1 0.019 0.001 -9999 0 -10000 0 0
mol:DAG 0.002 0.073 -9999 0 -10000 0 0
CDH1 -0.13 0.25 -9999 0 -0.54 101 101
RhoA/GDP 0.007 0.085 -9999 0 -0.3 2 2
establishment of polarity of embryonic epithelium -0.027 0.12 -9999 0 -0.3 5 5
SRC 0.019 0 -9999 0 -10000 0 0
RAC1 0.019 0 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
EGFR -0.007 0.087 -9999 0 -0.27 33 33
CASR 0.002 0.069 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.068 -9999 0 -10000 0 0
AKT2 0.001 0.086 -9999 0 -10000 0 0
actin cable formation -0.026 0.13 -9999 0 -0.37 9 9
apoptosis 0 0.082 -9999 0 -10000 0 0
CTNNA1 0.019 0.001 -9999 0 -10000 0 0
mol:GDP -0.003 0.087 -9999 0 -0.33 2 2
PIP5K1A -0.028 0.12 -9999 0 -0.31 5 5
PLCG1 0.001 0.074 -9999 0 -10000 0 0
Rac1/GTP -0.027 0.12 -9999 0 -0.3 20 20
homophilic cell adhesion 0 0.002 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.016 0.036 -9999 0 -0.33 4 4
ADCY5 -0.056 0.14 -9999 0 -0.33 80 80
ADCY6 0.019 0.013 -9999 0 -10000 0 0
ADCY7 0.018 0.025 -9999 0 -0.33 2 2
ADCY1 -0.034 0.13 -9999 0 -0.33 58 58
ADCY2 -0.046 0.071 -9999 0 -10000 0 0
ADCY3 0.02 0 -9999 0 -10000 0 0
ADCY8 0.001 0.042 -9999 0 -10000 0 0
PRKCE 0.013 0 -9999 0 -10000 0 0
ADCY9 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.029 0.057 -9999 0 -0.19 10 10
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0.12 -9999 0 -0.43 13 13
CRKL -0.014 0.11 -9999 0 -0.36 6 6
mol:DAG -0.002 0.12 -9999 0 -0.42 18 18
HRAS 0.014 0.1 -9999 0 -0.38 3 3
MAPK8 0.019 0.07 -9999 0 -0.31 15 15
RAP1A -0.014 0.11 -9999 0 -0.42 4 4
GAB1 -0.014 0.11 -9999 0 -0.36 6 6
MAPK14 0.019 0.07 -9999 0 -0.31 15 15
EPO 0.007 0.026 -9999 0 -0.26 2 2
PLCG1 -0.003 0.12 -9999 0 -0.43 18 18
EPOR/TRPC2/IP3 Receptors 0.013 0.02 -9999 0 -0.24 1 1
RAPGEF1 0.019 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.028 0.041 -9999 0 -0.35 3 3
GAB1/SHC/GRB2/SOS1 0.008 0.1 -9999 0 -0.36 4 4
EPO/EPOR (dimer) 0.016 0.029 -9999 0 -10000 0 0
IRS2 -0.014 0.11 -9999 0 -0.42 4 4
STAT1 0.006 0.13 -9999 0 -0.47 16 16
STAT5B 0.003 0.13 -9999 0 -0.45 15 15
cell proliferation 0.024 0.065 -9999 0 -0.28 15 15
GAB1/SHIP/PIK3R1/SHP2/SHC -0.079 0.14 -9999 0 -0.39 59 59
TEC -0.02 0.13 -9999 0 -0.35 16 16
SOCS3 0.014 0.05 -9999 0 -0.54 3 3
STAT1 (dimer) 0.007 0.13 -9999 0 -0.46 16 16
JAK2 0.004 0.074 -9999 0 -0.51 7 7
PIK3R1 0.019 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.004 0.13 -9999 0 -0.33 9 9
EPO/EPOR 0.016 0.029 -9999 0 -10000 0 0
LYN -0.002 0.11 -9999 0 -0.54 15 15
TEC/VAV2 -0.011 0.13 -9999 0 -0.43 11 11
elevation of cytosolic calcium ion concentration 0.013 0.02 -9999 0 -0.24 1 1
SHC1 0.019 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.025 0.081 -9999 0 -0.35 15 15
mol:IP3 -0.002 0.12 -9999 0 -0.42 18 18
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.038 0.19 -9999 0 -0.43 59 59
SH2B3 0.013 0.014 -9999 0 -10000 0 0
NFKB1 0.019 0.07 -9999 0 -0.31 15 15
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.044 -9999 0 -0.26 7 7
PTPN6 -0.023 0.12 -9999 0 -0.33 9 9
TEC/VAV2/GRB2 -0.002 0.13 -9999 0 -0.41 11 11
EPOR 0.013 0.02 -9999 0 -0.24 1 1
INPP5D -0.075 0.21 -9999 0 -0.54 62 62
mol:GDP 0.007 0.11 -9999 0 -0.37 4 4
SOS1 0.019 0 -9999 0 -10000 0 0
PLCG2 -0.03 0.16 -9999 0 -0.54 32 32
CRKL/CBL/C3G 0.006 0.11 -9999 0 -0.39 4 4
VAV2 -0.016 0.12 -9999 0 -0.37 9 9
CBL -0.014 0.11 -9999 0 -0.34 7 7
SHC/Grb2/SOS1 -0.046 0.081 -9999 0 -0.39 4 4
STAT5A 0.002 0.13 -9999 0 -0.43 19 19
GRB2 0.019 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.02 0.13 -9999 0 -0.43 16 16
LYN/PLCgamma2 -0.022 0.15 -9999 0 -0.42 42 42
PTPN11 0.019 0 -9999 0 -10000 0 0
BTK -0.062 0.2 -9999 0 -0.45 65 65
BCL2 0.029 0.12 -9999 0 -0.43 13 13
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.027 0.021 -9999 0 -0.38 1 1
VLDLR 0.005 0.086 -9999 0 -0.54 9 9
CRKL 0.018 0.014 -9999 0 -0.24 1 1
LRPAP1 0.019 0 -9999 0 -10000 0 0
FYN 0.019 0 -9999 0 -10000 0 0
ITGA3 0.002 0.069 -9999 0 -0.26 23 23
RELN/VLDLR/Fyn -0.009 0.085 -9999 0 -0.34 9 9
MAPK8IP1/MKK7/MAP3K11/JNK1 0.052 0.027 -9999 0 -0.26 1 1
AKT1 -0.002 0.068 -9999 0 -0.27 10 10
MAP2K7 0.019 0 -9999 0 -10000 0 0
RAPGEF1 0.019 0 -9999 0 -10000 0 0
DAB1 -0.028 0.089 -9999 0 -0.24 52 52
RELN/LRP8/DAB1 -0.023 0.08 -9999 0 -0.22 27 27
LRPAP1/LRP8 0.028 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.011 0.076 -9999 0 -0.2 27 27
DAB1/alpha3/beta1 Integrin -0.039 0.067 -9999 0 -0.34 6 6
long-term memory -0.024 0.097 -9999 0 -0.3 17 17
DAB1/LIS1 -0.004 0.086 -9999 0 -0.3 9 9
DAB1/CRLK/C3G -0.033 0.062 -9999 0 -0.4 3 3
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
DAB1/NCK2 -0.004 0.086 -9999 0 -0.3 9 9
ARHGEF2 0.017 0.029 -9999 0 -0.54 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.002 0.07 -9999 0 -0.24 28 28
CDK5R1 0.017 0.029 -9999 0 -0.54 1 1
RELN -0.047 0.11 -9999 0 -0.24 91 91
PIK3R1 0.019 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn 0 0.066 -9999 0 -10000 0 0
GRIN2A/RELN/LRP8/DAB1/Fyn -0.012 0.087 -9999 0 -0.31 6 6
MAPK8 0.019 0.001 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.03 0.095 -9999 0 -0.26 34 34
ITGB1 0.017 0.019 -9999 0 -0.24 2 2
MAP1B -0.019 0.087 -9999 0 -0.31 12 12
RELN/LRP8 0 0.066 -9999 0 -10000 0 0
GRIN2B/RELN/LRP8/DAB1/Fyn -0.022 0.094 -9999 0 -0.31 12 12
PI3K 0.028 0.009 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.015 0.05 -9999 0 -0.34 2 2
RAP1A 0.006 0.078 -9999 0 -0.37 3 3
PAFAH1B1 0.019 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0.041 -9999 0 -0.24 9 9
CRLK/C3G 0.028 0.009 -9999 0 -10000 0 0
GRIN2B -0.025 0.088 -9999 0 -0.24 50 50
NCK2 0.019 0 -9999 0 -10000 0 0
neuron differentiation 0.019 0.045 -9999 0 -10000 0 0
neuron adhesion 0.011 0.08 -9999 0 -0.33 4 4
LRP8 0.019 0 -9999 0 -10000 0 0
GSK3B 0.005 0.065 -9999 0 -0.36 3 3
RELN/VLDLR/DAB1/Fyn -0.019 0.09 -9999 0 -0.24 34 34
MAP3K11 0.019 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.01 0.073 -9999 0 -0.29 10 10
CDK5 0.019 0 -9999 0 -10000 0 0
MAPT -0.11 0.12 -9999 0 -0.22 186 186
neuron migration 0.021 0.077 -9999 0 -0.35 3 3
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.019 0.046 -9999 0 -10000 0 0
RELN/VLDLR 0.005 0.079 -9999 0 -0.31 9 9
IL1-mediated signaling events

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
UBC13/UEV1A 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.016 0.041 -10000 0 -0.54 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.019 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.002 0.08 -10000 0 -0.32 9 9
IRAK/TOLLIP 0.032 0 -10000 0 -10000 0 0
IKBKB 0.019 0 -10000 0 -10000 0 0
IKBKG 0.019 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.041 0.15 -10000 0 -0.34 67 67
IL1A 0.004 0.054 -10000 0 -0.24 16 16
IL1B -0.037 0.16 -10000 0 -0.42 48 48
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.021 -10000 0 -10000 0 0
IL1R2 -0.062 0.2 -10000 0 -0.54 53 53
IL1R1 0.016 0.041 -10000 0 -0.54 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.014 0.075 0.21 4 -0.28 9 13
TOLLIP 0.019 0 -10000 0 -10000 0 0
TICAM2 0.009 0.07 -10000 0 -0.54 6 6
MAP3K3 0.019 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.013 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.07 0.007 -10000 0 -10000 0 0
JUN 0.026 0.047 -10000 0 -0.31 1 1
MAP3K7 0.019 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.003 0.12 -10000 0 -0.28 49 49
IL1 alpha/IL1R1/IL1RAP/MYD88 0.028 0.055 -10000 0 -0.25 6 6
PIK3R1 0.019 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.037 0.053 -10000 0 -0.23 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.018 0.13 -10000 0 -0.32 50 50
NFKB1 0.019 0 -10000 0 -10000 0 0
MAPK8 0.032 0.036 -10000 0 -0.23 7 7
IRAK1 0.022 0 -10000 0 -10000 0 0
IL1RN/IL1R1 0.013 0.073 -10000 0 -0.38 11 11
IRAK4 0.019 0 -10000 0 -10000 0 0
PRKCI 0.019 0 -10000 0 -10000 0 0
TRAF6 0.019 0 -10000 0 -10000 0 0
PI3K 0.028 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.089 -10000 0 -0.34 10 10
CHUK 0.019 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.018 0.13 -10000 0 -0.32 50 50
IL1 beta/IL1R2 -0.069 0.19 -10000 0 -0.39 86 86
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.038 0.092 -10000 0 -0.45 8 8
IRAK3 0.011 0.064 -10000 0 -0.54 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.001 0.13 -10000 0 -0.3 52 52
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.03 0.04 -10000 0 -0.23 3 3
IL1 alpha/IL1R1/IL1RAP 0.017 0.057 -10000 0 -0.28 5 5
RELA 0.019 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.019 0 -10000 0 -10000 0 0
MYD88 0.017 0.029 -10000 0 -0.54 1 1
IRAK/TRAF6/MEKK3 0.043 0 -10000 0 -10000 0 0
IL1RAP 0.001 0.066 -10000 0 -0.24 25 25
UBE2N 0.019 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.038 0.093 -10000 0 -0.44 10 10
CASP1 -0.011 0.13 -10000 0 -0.54 20 20
IL1RN/IL1R2 -0.043 0.16 -10000 0 -0.39 60 60
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.13 -10000 0 -0.31 49 49
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.037 0.04 -10000 0 -0.3 3 3
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
IL1RN 0.002 0.091 -10000 0 -0.43 14 14
TRAF6/TAK1/TAB1/TAB2 0.028 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.038 -10000 0 -0.25 7 7
Coregulation of Androgen receptor activity

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
NRIP1 0.019 0 -9999 0 -10000 0 0
SVIL 0.017 0.029 -9999 0 -0.54 1 1
ZNF318 0.019 0 -9999 0 -10000 0 0
JMJD2C -0.005 0.027 -9999 0 -0.064 61 61
T-DHT/AR/Ubc9 -0.038 0.084 -9999 0 -0.22 19 19
CARM1 0.019 0 -9999 0 -10000 0 0
PRDX1 0.011 0.064 -9999 0 -0.54 5 5
PELP1 0.019 0 -9999 0 -10000 0 0
CTNNB1 0.019 0 -9999 0 -10000 0 0
AKT1 0.019 0 -9999 0 -10000 0 0
PTK2B 0.008 0.076 -9999 0 -0.54 7 7
MED1 0.019 0 -9999 0 -10000 0 0
MAK 0.016 0.027 -9999 0 -0.24 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.016 0.027 -9999 0 -0.24 4 4
GSN 0.018 0.014 -9999 0 -0.24 1 1
NCOA2 0.018 0.014 -9999 0 -0.24 1 1
NCOA6 0.019 0 -9999 0 -10000 0 0
DNA-PK 0.038 0 -9999 0 -10000 0 0
NCOA4 0.019 0 -9999 0 -10000 0 0
PIAS3 0.019 0 -9999 0 -10000 0 0
cell proliferation -0.006 0.025 -9999 0 -10000 0 0
XRCC5 0.019 0 -9999 0 -10000 0 0
UBE3A 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.051 0.1 -9999 0 -0.27 33 33
FHL2 -0.003 0.14 -9999 0 -1.1 6 6
RANBP9 0.019 0 -9999 0 -10000 0 0
JMJD1A 0.001 0.046 -9999 0 -0.13 38 38
CDK6 0.014 0.052 -9999 0 -0.46 4 4
TGFB1I1 0.017 0.032 -9999 0 -0.39 2 2
T-DHT/AR/CyclinD1 -0.043 0.087 -9999 0 -0.22 26 26
XRCC6 0.019 0 -9999 0 -10000 0 0
T-DHT/AR -0.037 0.11 -9999 0 -0.3 21 21
CTDSP1 0.019 0 -9999 0 -10000 0 0
CTDSP2 0.019 0 -9999 0 -10000 0 0
BRCA1 0.019 0 -9999 0 -10000 0 0
TCF4 0.011 0.057 -9999 0 -0.37 7 7
CDKN2A -0.11 0.14 -9999 0 -0.25 172 172
SRF 0.026 0.017 -9999 0 -10000 0 0
NKX3-1 -0.055 0.24 -9999 0 -0.92 22 22
KLK3 0.011 0.017 -9999 0 -10000 0 0
TMF1 0.019 0 -9999 0 -10000 0 0
HNRNPA1 0.019 0 -9999 0 -10000 0 0
AOF2 0 0 -9999 0 -10000 0 0
APPL1 0.026 0 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.04 0.088 -9999 0 -0.23 22 22
AR -0.091 0.13 -9999 0 -0.25 144 144
UBA3 0.019 0 -9999 0 -10000 0 0
PATZ1 0.019 0 -9999 0 -10000 0 0
PAWR -0.004 0.11 -9999 0 -0.54 15 15
PRKDC 0.019 0 -9999 0 -10000 0 0
PA2G4 0.019 0 -9999 0 -10000 0 0
UBE2I 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.033 0.076 -9999 0 -0.2 20 20
RPS6KA3 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.038 0.084 -9999 0 -0.22 19 19
LATS2 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.037 0.081 -9999 0 -0.21 25 25
Cyclin D3/CDK11 p58 0.014 0 -9999 0 -10000 0 0
VAV3 0.008 0.064 -9999 0 -0.32 12 12
KLK2 -0.048 0.11 -9999 0 -0.31 26 26
CASP8 0.016 0.041 -9999 0 -0.54 2 2
T-DHT/AR/TIF2/CARM1 -0.023 0.079 -9999 0 -0.26 3 3
TMPRSS2 -0.049 0.22 -9999 0 -0.92 18 18
CCND1 0.01 0.047 -9999 0 -0.24 12 12
PIAS1 0.019 0 -9999 0 -10000 0 0
mol:T-DHT -0.005 0.025 -9999 0 -0.063 45 45
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.041 0.089 -9999 0 -0.24 24 24
CMTM2 0.007 0.05 -9999 0 -0.24 14 14
SNURF -0.001 0.1 -9999 0 -0.54 13 13
ZMIZ1 0.015 0.024 -9999 0 -10000 0 0
CCND3 0.019 0 -9999 0 -10000 0 0
TGIF1 0.019 0 -9999 0 -10000 0 0
FKBP4 0.018 0.014 -9999 0 -0.24 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.017 0.024 -9999 0 -0.24 3 3
Syndecan-3/Src/Cortactin 0.021 0.052 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.017 0.028 -9999 0 -10000 0 0
POMC -0.049 0.18 -9999 0 -0.52 46 46
EGFR -0.007 0.087 -9999 0 -0.27 33 33
Syndecan-3/EGFR 0.019 0.042 -9999 0 -0.26 3 3
AGRP 0.003 0.045 -9999 0 -0.24 11 11
NCSTN 0.019 0 -9999 0 -10000 0 0
PSENEN 0.019 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0.05 -9999 0 -0.54 3 3
APH1A 0.019 0 -9999 0 -10000 0 0
NCAN 0.001 0.055 -9999 0 -0.24 17 17
long-term memory 0.04 0.014 -9999 0 -10000 0 0
Syndecan-3/IL8 0 0.057 -9999 0 -0.28 3 3
PSEN1 0.019 0 -9999 0 -10000 0 0
Src/Cortactin 0.027 0.016 -9999 0 -10000 0 0
FYN 0.019 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.008 -9999 0 -10000 0 0
MC4R -0.031 0.095 -9999 0 -0.24 60 60
SRC 0.019 0 -9999 0 -10000 0 0
PTN -0.046 0.11 -9999 0 -0.24 90 90
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis 0.015 0.052 -9999 0 -10000 0 0
Syndecan-3/AgRP 0.014 0.027 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.008 0.048 -9999 0 -10000 0 0
Fyn/Cortactin 0.027 0.016 -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 0.057 -9999 0 -0.28 3 3
IL8 -0.05 0.12 -9999 0 -0.25 93 93
Syndecan-3/Fyn/Cortactin 0.041 0.014 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.055 0.14 -9999 0 -0.4 44 44
Gamma Secretase 0.054 0.028 -9999 0 -0.26 3 3
Glypican 2 network

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
MDK 0.004 0.07 -9999 0 -0.3 17 17
GPC2 0.008 0.073 -9999 0 -0.46 8 8
GPC2/Midkine 0.01 0.074 -9999 0 -0.37 11 11
neuron projection morphogenesis 0.01 0.074 -9999 0 -0.37 11 11
S1P3 pathway

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.015 0.031 -9999 0 -0.24 5 5
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.011 0.06 -9999 0 -0.24 4 4
GNAO1 -0.091 0.13 -9999 0 -0.24 155 155
S1P/S1P3/G12/G13 0.037 0.03 -9999 0 -0.29 3 3
AKT1 0.019 0.03 -9999 0 -10000 0 0
AKT3 0.026 0.043 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.031 -9999 0 -0.24 5 5
GNAI2 0.021 0 -9999 0 -10000 0 0
GNAI3 0.021 0 -9999 0 -10000 0 0
GNAI1 0.006 0.06 -9999 0 -0.24 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.016 0.052 -9999 0 -0.46 4 4
S1PR2 0.019 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.003 0.067 -9999 0 -0.26 6 6
MAPK3 0.004 0.063 -9999 0 -0.25 5 5
MAPK1 0.004 0.063 -9999 0 -0.29 3 3
JAK2 -0.006 0.091 -9999 0 -0.35 12 12
CXCR4 -0.018 0.11 -9999 0 -0.32 31 31
FLT1 0.022 0.014 -9999 0 -0.24 1 1
RhoA/GDP 0.014 0 -9999 0 -10000 0 0
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
SRC 0.004 0.063 -9999 0 -0.29 3 3
S1P/S1P3/Gi -0.004 0.068 -9999 0 -0.26 6 6
RAC1 0.019 0 -9999 0 -10000 0 0
RhoA/GTP 0.005 0.062 -9999 0 -0.24 5 5
VEGFA 0.007 0.062 -9999 0 -0.24 21 21
S1P/S1P2/Gi -0.006 0.062 -9999 0 -0.22 4 4
VEGFR1 homodimer/VEGFA homodimer 0.027 0.046 -9999 0 -0.3 1 1
RHOA 0.019 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.022 0.13 -9999 0 -0.26 73 73
GNAQ 0.019 0 -9999 0 -10000 0 0
GNAZ -0.013 0.093 -9999 0 -0.26 45 45
G12/G13 0.028 0 -9999 0 -10000 0 0
GNA14 -0.084 0.22 -9999 0 -0.53 69 69
GNA15 0.002 0.095 -9999 0 -0.54 11 11
GNA12 0.019 0 -9999 0 -10000 0 0
GNA13 0.019 0 -9999 0 -10000 0 0
GNA11 0.019 0 -9999 0 -10000 0 0
Rac1/GTP 0.005 0.062 -9999 0 -0.28 3 3
ErbB4 signaling events

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.019 0.058 -10000 0 -10000 0 0
epithelial cell differentiation -0.024 0.043 -10000 0 -10000 0 0
ITCH 0.026 0.014 -10000 0 -10000 0 0
WWP1 0.02 0.052 -10000 0 -10000 0 0
FYN 0.019 0 -10000 0 -10000 0 0
EGFR -0.007 0.087 -10000 0 -0.27 33 33
PRL -0.023 0.084 -10000 0 -0.24 45 45
neuron projection morphogenesis 0.047 0.052 -10000 0 -0.28 1 1
PTPRZ1 -0.055 0.18 -10000 0 -0.43 60 60
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.043 0.058 -10000 0 -0.32 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.016 0.061 -10000 0 -0.31 3 3
ADAM17 0.026 0.014 -10000 0 -10000 0 0
ErbB4/ErbB4 0.014 0.067 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.058 0.13 -10000 0 -0.32 48 48
NCOR1 0.019 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.025 0.058 -10000 0 -0.36 1 1
GRIN2B 0.011 0.066 -10000 0 -0.31 2 2
ErbB4/ErbB2/betacellulin 0.015 0.056 -10000 0 -10000 0 0
STAT1 0.016 0.041 -10000 0 -0.54 2 2
HBEGF 0.017 0.019 -10000 0 -0.24 2 2
PRLR -0.048 0.11 -10000 0 -0.24 92 92
E4ICDs/ETO2 -0.007 0.1 -10000 0 -0.3 30 30
axon guidance 0.042 0.061 -10000 0 -10000 0 0
NEDD4 0.024 0.024 -10000 0 -0.24 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.045 0.097 -10000 0 -0.31 16 16
CBFA2T3 -0.028 0.15 -10000 0 -0.52 32 32
ErbB4/ErbB2/HBEGF 0.034 0.042 -10000 0 -10000 0 0
MAPK3 0.042 0.053 -10000 0 -0.3 1 1
STAT1 (dimer) 0.018 0.062 -10000 0 -0.29 2 2
MAPK1 0.042 0.053 -10000 0 -0.3 1 1
JAK2 0.009 0.072 -10000 0 -0.5 7 7
ErbB4/ErbB2/neuregulin 1 beta 0.023 0.057 -10000 0 -0.36 1 1
NRG1 0.016 0.053 -10000 0 -0.38 3 3
NRG3 -0.12 0.2 -10000 0 -0.34 142 142
NRG2 0.011 0.057 -10000 0 -0.37 7 7
NRG4 -0.002 0.094 -10000 0 -0.54 11 11
heart development 0.042 0.061 -10000 0 -10000 0 0
neural crest cell migration 0.023 0.057 -10000 0 -0.35 1 1
ERBB2 0.03 0.009 -10000 0 -10000 0 0
WWOX/E4ICDs 0.02 0.058 -10000 0 -10000 0 0
SHC1 0.019 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.006 0.089 -10000 0 -0.31 14 14
apoptosis 0.053 0.14 0.37 48 -10000 0 48
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.016 0.067 -10000 0 -0.33 3 3
ErbB4/ErbB2/epiregulin 0.02 0.054 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.002 0.071 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.008 0.087 -10000 0 -10000 0 0
MDM2 0.018 0.06 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.024 0.051 -10000 0 -0.28 3 3
STAT5A 0.046 0.058 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.013 0.075 -10000 0 -0.29 4 4
DLG4 0.017 0.029 -10000 0 -0.54 1 1
GRB2/SHC 0.028 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.018 0.052 -10000 0 -10000 0 0
STAT5A (dimer) -0.012 0.058 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.048 0.054 -10000 0 -10000 0 0
LRIG1 0.017 0.029 -10000 0 -0.54 1 1
EREG -0.01 0.072 -10000 0 -0.24 31 31
BTC -0.021 0.083 -10000 0 -0.24 44 44
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.042 0.061 -10000 0 -10000 0 0
ERBB4 0.014 0.068 -10000 0 -10000 0 0
STAT5B 0.019 0 -10000 0 -10000 0 0
YAP1 0.015 0.022 -10000 0 -0.19 1 1
GRB2 0.019 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.023 0.07 -10000 0 -0.36 5 5
glial cell differentiation -0.018 0.052 -10000 0 -10000 0 0
WWOX 0.019 0 -10000 0 -10000 0 0
cell proliferation 0.03 0.062 -10000 0 -0.31 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.038 0.027 -10000 0 -10000 0 0
HDAC1 0.013 0.029 -10000 0 -0.54 1 1
AES 0.018 0.001 -10000 0 -10000 0 0
FBXW11 0.019 0 -10000 0 -10000 0 0
DTX1 -0.11 0.23 -10000 0 -0.54 85 85
LRP6/FZD1 0.025 0.023 -10000 0 -10000 0 0
TLE1 0.016 0.029 -10000 0 -0.54 1 1
AP1 0.009 0.056 -10000 0 -0.27 8 8
NCSTN 0.019 0 -10000 0 -10000 0 0
ADAM10 0.019 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.052 0.024 -10000 0 -10000 0 0
NICD/RBPSUH 0.043 0.007 -10000 0 -10000 0 0
WIF1 -0.025 0.087 -10000 0 -0.24 49 49
NOTCH1 0.034 0.007 -10000 0 -10000 0 0
PSENEN 0.019 0 -10000 0 -10000 0 0
KREMEN2 -0.057 0.19 -10000 0 -0.54 50 50
DKK1 -0.078 0.2 -10000 0 -0.44 78 78
beta catenin/beta TrCP1 0.039 0.03 0.24 1 -10000 0 1
APH1B 0.014 0.05 -10000 0 -0.54 3 3
APH1A 0.019 0 -10000 0 -10000 0 0
AXIN1 0.008 0.016 0.26 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.027 0.024 -10000 0 -0.25 2 2
PSEN1 0.019 0 -10000 0 -10000 0 0
FOS 0.01 0.047 -10000 0 -0.24 12 12
JUN -0.008 0.079 -10000 0 -0.24 37 37
MAP3K7 0.017 0.002 -10000 0 -10000 0 0
CTNNB1 0.029 0.033 0.25 1 -10000 0 1
MAPK3 0.019 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.13 -10000 0 -0.33 52 52
HNF1A 0.018 0.001 -10000 0 -10000 0 0
CTBP1 0.018 0.001 -10000 0 -10000 0 0
MYC 0.026 0.028 -10000 0 -10000 0 0
NKD1 -0.005 0.093 -10000 0 -0.33 24 24
FZD1 0.015 0.033 -10000 0 -0.24 6 6
NOTCH1 precursor/Deltex homolog 1 -0.024 0.12 -10000 0 -0.31 1 1
apoptosis 0.009 0.055 -10000 0 -0.27 8 8
Delta 1/NOTCHprecursor 0.04 0.028 -10000 0 -10000 0 0
DLL1 0.014 0.052 -10000 0 -0.46 4 4
PPARD 0.027 0.024 -10000 0 -0.3 1 1
Gamma Secretase 0.055 0.028 -10000 0 -0.26 3 3
APC 0.008 0.016 0.26 1 -10000 0 1
DVL1 0.029 0.023 -10000 0 -10000 0 0
CSNK2A1 0.019 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.069 0.17 -10000 0 -0.35 92 92
LRP6 0.019 0 -10000 0 -10000 0 0
CSNK1A1 0.019 0.001 -10000 0 -10000 0 0
NLK 0.016 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.053 -10000 0 -10000 0 0
WNT1 -0.031 0.15 -10000 0 -0.52 32 32
Axin1/APC/beta catenin 0.05 0.025 0.3 1 -10000 0 1
DKK2 0.001 0.076 -10000 0 -0.28 22 22
NOTCH1 precursor/DVL1 0.053 0.018 -10000 0 -10000 0 0
GSK3B 0.018 0 -10000 0 -10000 0 0
FRAT1 0.016 0.029 -10000 0 -0.54 1 1
NOTCH/Deltex homolog 1 -0.026 0.12 -10000 0 -0.31 1 1
PPP2R5D 0.027 0.047 0.29 7 -10000 0 7
MAPK1 0.019 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.006 0.1 -10000 0 -0.29 34 34
RBPJ 0.019 0 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.014 0.05 -9999 0 -0.32 1 1
PDGFRB 0.015 0.031 -9999 0 -0.25 5 5
SPHK1 -0.008 0.078 -9999 0 -0.84 3 3
mol:S1P 0.008 0.075 -9999 0 -0.63 4 4
S1P1/S1P/Gi -0.019 0.096 -9999 0 -0.31 15 15
GNAO1 -0.094 0.13 -9999 0 -0.25 155 155
PDGFB-D/PDGFRB/PLCgamma1 -0.006 0.089 -9999 0 -0.35 7 7
PLCG1 -0.012 0.091 -9999 0 -0.34 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.031 -9999 0 -0.24 5 5
GNAI2 0.018 0.004 -9999 0 -10000 0 0
GNAI3 0.018 0.003 -9999 0 -10000 0 0
GNAI1 0.004 0.06 -9999 0 -0.25 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.008 0.041 -9999 0 -0.27 1 1
S1P1/S1P 0.014 0.071 -9999 0 -0.42 5 5
negative regulation of cAMP metabolic process -0.018 0.094 -9999 0 -0.3 15 15
MAPK3 -0.017 0.11 -9999 0 -0.4 11 11
calcium-dependent phospholipase C activity -0.001 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.014 0 -9999 0 -10000 0 0
RhoA/GDP 0.014 0 -9999 0 -10000 0 0
KDR 0.014 0.036 -9999 0 -0.24 7 7
PLCB2 0.013 0.083 -9999 0 -0.33 12 12
RAC1 0.019 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.049 -9999 0 -0.35 5 5
receptor internalization 0.014 0.066 -9999 0 -0.39 5 5
PTGS2 -0.024 0.15 -9999 0 -0.93 4 4
Rac1/GTP -0.013 0.049 -9999 0 -0.35 5 5
RHOA 0.019 0 -9999 0 -10000 0 0
VEGFA 0.004 0.062 -9999 0 -0.25 21 21
negative regulation of T cell proliferation -0.018 0.094 -9999 0 -0.3 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.016 0.094 -9999 0 -0.26 45 45
MAPK1 -0.017 0.11 -9999 0 -0.4 11 11
S1P1/S1P/PDGFB-D/PDGFRB 0.021 0.074 -9999 0 -0.4 5 5
ABCC1 0.017 0.029 -9999 0 -0.54 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0.03 -10000 0 -0.54 1 1
AES 0.015 0.007 -10000 0 -10000 0 0
FBXW11 0.019 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.026 0.023 -10000 0 -10000 0 0
SMAD4 0.019 0 -10000 0 -10000 0 0
DKK2 0.001 0.076 -10000 0 -0.28 22 22
TLE1 0.013 0.03 -10000 0 -0.54 1 1
MACF1 0.019 0 -10000 0 -10000 0 0
CTNNB1 0.018 0.073 -10000 0 -0.27 4 4
WIF1 -0.025 0.087 -10000 0 -0.24 49 49
beta catenin/RanBP3 -0.012 0.066 0.31 4 -10000 0 4
KREMEN2 -0.057 0.19 -10000 0 -0.54 50 50
DKK1 -0.078 0.2 -10000 0 -0.44 78 78
beta catenin/beta TrCP1 0.027 0.071 -10000 0 -0.25 3 3
FZD1 0.015 0.033 -10000 0 -0.24 6 6
AXIN2 0.012 0.09 -10000 0 -1.5 1 1
AXIN1 0.019 0.001 -10000 0 -10000 0 0
RAN 0.019 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.038 0.017 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.057 0.057 -10000 0 -0.4 1 1
Axin1/APC/GSK3 0.038 0.04 0.2 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.032 0.084 -10000 0 -10000 0 0
HNF1A 0.014 0.007 -10000 0 -10000 0 0
CTBP1 0.014 0.007 -10000 0 -10000 0 0
MYC 0.017 0.036 -10000 0 -10000 0 0
RANBP3 0.019 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.13 -10000 0 -0.33 52 52
NKD1 -0.004 0.093 -10000 0 -0.33 24 24
TCF4 0.007 0.057 -10000 0 -0.37 7 7
TCF3 0.014 0.007 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.017 0.091 -10000 0 -0.28 30 30
Ran/GTP 0.014 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.007 0.065 0.36 4 -10000 0 4
LEF1 -0.004 0.099 -10000 0 -0.54 12 12
DVL1 0.033 0.026 -10000 0 -10000 0 0
CSNK2A1 0.019 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.071 0.059 -10000 0 -0.38 1 1
DKK1/LRP6/Kremen 2 -0.069 0.17 -10000 0 -0.35 92 92
LRP6 0.019 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.008 -10000 0 -10000 0 0
NLK 0.02 0.002 -10000 0 -10000 0 0
CCND1 0.012 0.059 -10000 0 -10000 0 0
WNT1 -0.03 0.15 -10000 0 -0.52 32 32
GSK3A 0.019 0.001 -10000 0 -10000 0 0
GSK3B 0.019 0 -10000 0 -10000 0 0
FRAT1 0.017 0.029 -10000 0 -0.54 1 1
PPP2R5D 0.029 0.047 0.27 8 -10000 0 8
APC 0.015 0.082 -10000 0 -0.25 30 30
WNT1/LRP6/FZD1 0.025 0.071 -10000 0 -0.2 26 26
CREBBP 0.014 0.007 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.021 0.003 -9999 0 -10000 0 0
RAS family/GTP 0.034 0.076 -9999 0 -0.29 10 10
NFATC4 0.018 0.068 -9999 0 -0.26 9 9
ERBB2IP 0.018 0.002 -9999 0 -10000 0 0
HSP90 (dimer) 0.017 0.029 -9999 0 -0.54 1 1
mammary gland morphogenesis 0.021 0.069 -9999 0 -0.26 17 17
JUN 0.042 0.074 -9999 0 -0.21 6 6
HRAS 0.019 0.001 -9999 0 -10000 0 0
DOCK7 0.026 0.066 -9999 0 -0.27 10 10
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.016 0.075 -9999 0 -0.3 17 17
AKT1 0.013 0.002 -9999 0 -10000 0 0
BAD 0.021 0.001 -9999 0 -10000 0 0
MAPK10 0.017 0.051 -9999 0 -0.18 7 7
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.023 0.074 -9999 0 -0.28 17 17
RAF1 0.036 0.085 -9999 0 -0.31 9 9
ErbB2/ErbB3/neuregulin 2 0.01 0.073 -9999 0 -0.32 16 16
STAT3 0.028 0.005 -9999 0 -10000 0 0
cell migration 0.032 0.045 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation -0.007 0.25 -9999 0 -0.58 52 52
FOS 0.024 0.16 -9999 0 -0.33 52 52
NRAS 0.019 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.069 -9999 0 -0.26 17 17
MAPK3 0.005 0.2 -9999 0 -0.45 52 52
MAPK1 0.005 0.2 -9999 0 -0.45 52 52
JAK2 0.022 0.072 -9999 0 -0.29 6 6
NF2 0.007 0.011 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.015 0.07 -9999 0 -0.29 17 17
NRG1 -0.001 0.074 -9999 0 -0.29 20 20
GRB2/SOS1 0.028 0.001 -9999 0 -10000 0 0
MAPK8 0.032 0.069 -9999 0 -0.26 17 17
MAPK9 0.033 0.038 -9999 0 -0.16 2 2
ERBB2 -0.001 0.002 -9999 0 -10000 0 0
ERBB3 -0.002 0.11 -9999 0 -0.54 14 14
SHC1 0.019 0.001 -9999 0 -10000 0 0
RAC1 0.019 0 -9999 0 -10000 0 0
apoptosis -0.019 0.009 -9999 0 -10000 0 0
STAT3 (dimer) 0.028 0.005 -9999 0 -10000 0 0
RNF41 0.026 0.004 -9999 0 -10000 0 0
FRAP1 0.01 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.009 0.038 -9999 0 -0.23 4 4
ErbB2/ErbB2/HSP90 (dimer) 0.013 0.018 -9999 0 -0.33 1 1
CHRNA1 -0.024 0.26 -9999 0 -0.64 52 52
myelination 0.018 0.064 -9999 0 -0.25 9 9
PPP3CB 0.025 0.062 -9999 0 -0.25 10 10
KRAS 0.018 0.014 -9999 0 -0.25 1 1
RAC1-CDC42/GDP 0.035 0.064 -9999 0 -0.24 17 17
NRG2 0.011 0.057 -9999 0 -0.37 7 7
mol:GDP 0.015 0.07 -9999 0 -0.29 17 17
SOS1 0.019 0.001 -9999 0 -10000 0 0
MAP2K2 0.035 0.097 -9999 0 -0.34 8 8
SRC 0.019 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.029 0.065 -9999 0 -0.26 10 10
MAP2K1 0.013 0.17 -9999 0 -0.48 13 13
heart morphogenesis 0.021 0.069 -9999 0 -0.26 17 17
RAS family/GDP 0.04 0.069 -9999 0 -0.28 9 9
GRB2 0.019 0.001 -9999 0 -10000 0 0
PRKACA 0 0.004 -9999 0 -10000 0 0
CHRNE 0.018 0.031 -9999 0 -0.1 17 17
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
activation of caspase activity -0.013 0.002 -9999 0 -10000 0 0
nervous system development 0.021 0.069 -9999 0 -0.26 17 17
CDC42 0.019 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.019 0 -9999 0 -10000 0 0
VLDLR 0.005 0.086 -9999 0 -0.54 9 9
LRPAP1 0.019 0 -9999 0 -10000 0 0
NUDC 0.019 0 -9999 0 -10000 0 0
RELN/LRP8 0 0.066 -9999 0 -10000 0 0
CaM/Ca2+ 0.014 0 -9999 0 -10000 0 0
KATNA1 0.019 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.004 0.057 -9999 0 -10000 0 0
IQGAP1/CaM 0.028 0 -9999 0 -10000 0 0
DAB1 -0.028 0.089 -9999 0 -0.24 52 52
IQGAP1 0.019 0 -9999 0 -10000 0 0
PLA2G7 -0.13 0.24 -9999 0 -0.54 96 96
CALM1 0.019 0 -9999 0 -10000 0 0
DYNLT1 0.019 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.028 0 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.019 0 -9999 0 -10000 0 0
CDK5R1 0.017 0.029 -9999 0 -0.54 1 1
LIS1/Poliovirus Protein 3A 0.019 0 -9999 0 -10000 0 0
CDK5R2 -0.042 0.11 -9999 0 -0.24 83 83
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.035 0.1 -9999 0 -0.28 34 34
YWHAE 0.019 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E 0.018 0.062 -9999 0 -0.27 1 1
MAP1B 0.006 0.017 -9999 0 -10000 0 0
RAC1 0.025 0 -9999 0 -10000 0 0
p35/CDK5 0.02 0.054 -9999 0 -0.34 1 1
RELN -0.047 0.11 -9999 0 -0.24 91 91
PAFAH/LIS1 -0.058 0.15 -9999 0 -0.32 96 96
LIS1/CLIP170 0.033 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.007 0.025 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0 0.073 -9999 0 -0.29 10 10
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.008 0.062 -9999 0 -0.29 1 1
LIS1/IQGAP1 0.033 0 -9999 0 -10000 0 0
RHOA 0.025 0 -9999 0 -10000 0 0
PAFAH1B1 0.026 0 -9999 0 -10000 0 0
PAFAH1B3 0.017 0.029 -9999 0 -0.54 1 1
PAFAH1B2 0.019 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.03 0.012 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.061 -9999 0 -10000 0 0
LRP8 0.019 0 -9999 0 -10000 0 0
NDEL1/Katanin 60 0.018 0.062 -9999 0 -0.27 1 1
P39/CDK5 -0.007 0.072 -9999 0 -10000 0 0
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0 -9999 0 -10000 0 0
CDK5 0.011 0.052 -9999 0 -10000 0 0
PPP2R5D 0.019 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0 -9999 0 -10000 0 0
CSNK2A1 0.019 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.011 0.09 -9999 0 -0.32 9 9
RELN/VLDLR 0.005 0.079 -9999 0 -0.31 9 9
CDC42 0.025 0 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.008 0.07 -9999 0 -0.41 3 3
PDGFB-D/PDGFRB/SLAP -0.051 0.16 -9999 0 -0.39 68 68
PDGFB-D/PDGFRB/APS/CBL 0.03 0.052 -9999 0 -0.32 7 7
AKT1 0.054 0.019 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.011 0.07 -9999 0 -0.41 3 3
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
FGR -0.048 0.17 -9999 0 -0.56 36 36
mol:Ca2+ -0.018 0.06 -9999 0 -0.24 2 2
MYC -0.014 0.085 -9999 0 -0.38 2 2
SHC1 0.019 0 -9999 0 -10000 0 0
HRAS/GDP 0.04 0.021 -9999 0 -0.26 1 1
LRP1/PDGFRB/PDGFB 0.034 0.031 -9999 0 -0.25 2 2
GRB10 0.017 0.019 -9999 0 -0.24 2 2
PTPN11 0.019 0 -9999 0 -10000 0 0
GO:0007205 -0.018 0.061 -9999 0 -0.26 1 1
PTEN 0.017 0.029 -9999 0 -0.54 1 1
GRB2 0.019 0 -9999 0 -10000 0 0
GRB7 -0.004 0.068 -9999 0 -0.24 27 27
PDGFB-D/PDGFRB/SHP2 0.026 0.021 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.025 0.025 -9999 0 -10000 0 0
cell cycle arrest -0.051 0.16 -9999 0 -0.39 68 68
HRAS 0.019 0 -9999 0 -10000 0 0
HIF1A 0.057 0.018 -9999 0 -10000 0 0
GAB1 -0.046 0.095 -9999 0 -0.28 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.034 0.088 -9999 0 -0.33 6 6
PDGFB-D/PDGFRB 0.043 0.019 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.026 0.021 -9999 0 -0.15 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.025 0.075 -9999 0 -0.48 3 3
positive regulation of MAPKKK cascade 0.026 0.021 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
mol:IP3 -0.018 0.061 -9999 0 -0.26 1 1
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.019 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.01 0.052 -9999 0 -0.3 1 1
SHB 0.006 0.071 -9999 0 -0.33 14 14
BLK -0.34 0.26 -9999 0 -0.53 236 236
PTPN2 0.019 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.026 0.021 -9999 0 -10000 0 0
BCAR1 0.019 0 -9999 0 -10000 0 0
VAV2 -0.042 0.11 -9999 0 -0.31 25 25
CBL 0.019 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.026 0.021 -9999 0 -10000 0 0
LCK -0.2 0.27 -9999 0 -0.53 142 142
PDGFRB 0.016 0.031 -9999 0 -0.25 5 5
ACP1 0.019 0 -9999 0 -10000 0 0
HCK -0.031 0.16 -9999 0 -0.56 31 31
ABL1 -0.065 0.11 -9999 0 -0.31 39 39
PDGFB-D/PDGFRB/CBL -0.054 0.1 -9999 0 -0.3 25 25
PTPN1 0.019 0.001 -9999 0 -10000 0 0
SNX15 0.019 0 -9999 0 -10000 0 0
STAT3 0.019 0 -9999 0 -10000 0 0
STAT1 0.016 0.041 -9999 0 -0.54 2 2
cell proliferation -0.013 0.081 -9999 0 -0.34 3 3
SLA -0.084 0.22 -9999 0 -0.54 68 68
actin cytoskeleton reorganization 0.048 0.038 -9999 0 -0.24 4 4
SRC 0.006 0.019 -9999 0 -10000 0 0
PI3K -0.002 0.013 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.023 0.045 -9999 0 -0.24 1 1
SH2B2 0.008 0.076 -9999 0 -0.54 7 7
PLCgamma1/SPHK1 -0.011 0.072 -9999 0 -0.43 3 3
LYN -0.013 0.11 -9999 0 -0.56 15 15
LRP1 0.014 0.036 -9999 0 -0.24 7 7
SOS1 0.019 0 -9999 0 -10000 0 0
STAT5B 0.019 0 -9999 0 -10000 0 0
STAT5A 0.017 0.029 -9999 0 -0.54 1 1
NCK1-2/p130 Cas 0.061 0.016 -9999 0 -10000 0 0
SPHK1 0.011 0.059 -9999 0 -0.36 8 8
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG -0.018 0.061 -9999 0 -0.26 1 1
PLCG1 -0.018 0.062 -9999 0 -0.26 1 1
NHERF/PDGFRB 0.036 0.019 -9999 0 -10000 0 0
YES1 0.008 0.018 -9999 0 -10000 0 0
cell migration 0.036 0.019 -9999 0 -10000 0 0
SHC/Grb2/SOS1 0.061 0.016 -9999 0 -10000 0 0
SLC9A3R2 0.018 0.014 -9999 0 -0.24 1 1
SLC9A3R1 0.019 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.046 0.025 -9999 0 -0.28 1 1
FYN 0.009 0.018 -9999 0 -10000 0 0
DOK1 0.034 0.015 -9999 0 -10000 0 0
HRAS/GTP 0.014 0 -9999 0 -10000 0 0
PDGFB 0.019 0 -9999 0 -10000 0 0
RAC1 -0.031 0.1 -9999 0 -0.4 5 5
PRKCD 0.033 0.016 -9999 0 -10000 0 0
FER 0.033 0.016 -9999 0 -10000 0 0
MAPKKK cascade -0.001 0.01 -9999 0 -10000 0 0
RASA1 0.032 0.023 -9999 0 -0.29 1 1
NCK1 0.019 0 -9999 0 -10000 0 0
NCK2 0.019 0 -9999 0 -10000 0 0
p62DOK/Csk 0.045 0.015 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.016 0.056 -9999 0 -0.39 4 4
chemotaxis -0.064 0.11 -9999 0 -0.3 39 39
STAT1-3-5/STAT1-3-5 0.033 0.035 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.011 0.021 -9999 0 -0.16 5 5
PTPRJ 0.019 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.021 -9999 0 -0.38 1 1
SMARCC1 0.019 0.017 -9999 0 -10000 0 0
REL 0.019 0.001 -9999 0 -10000 0 0
HDAC7 0.036 0.072 -9999 0 -10000 0 0
JUN -0.008 0.079 -9999 0 -0.24 37 37
EP300 0.019 0 -9999 0 -10000 0 0
KAT2B 0.016 0.041 -9999 0 -0.54 2 2
KAT5 0.019 0 -9999 0 -10000 0 0
MAPK14 0.018 0.057 -9999 0 -0.38 7 7
FOXO1 0.019 0 -9999 0 -10000 0 0
T-DHT/AR 0.041 0.08 -9999 0 -0.27 2 2
MAP2K6 0.008 0.076 -9999 0 -0.54 7 7
BRM/BAF57 0.027 0.021 -9999 0 -0.38 1 1
MAP2K4 0.019 0.005 -9999 0 -10000 0 0
SMARCA2 0.017 0.029 -9999 0 -0.54 1 1
PDE9A 0.007 0.14 -9999 0 -1.1 3 3
NCOA2 0.018 0.014 -9999 0 -0.24 1 1
CEBPA -0.028 0.16 -9999 0 -0.54 31 31
EHMT2 0.019 0 -9999 0 -10000 0 0
cell proliferation 0.056 0.078 -9999 0 -10000 0 0
NR0B1 0 0 -9999 0 -10000 0 0
EGR1 -0.003 0.073 -9999 0 -0.24 31 31
RXRs/9cRA -0.036 0.14 -9999 0 -0.29 82 82
AR/RACK1/Src 0.027 0.062 -9999 0 -0.29 4 4
AR/GR 0.006 0.052 -9999 0 -0.24 2 2
GNB2L1 0.019 0.002 -9999 0 -10000 0 0
PKN1 0.017 0.029 -9999 0 -0.54 1 1
RCHY1 0.019 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.025 0.011 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.034 0.061 -9999 0 -0.29 4 4
SRC 0.031 0.046 -9999 0 -0.25 7 7
NR3C1 0.019 0 -9999 0 -10000 0 0
KLK3 -0.03 0.043 -9999 0 -10000 0 0
APPBP2 0.019 0.005 -9999 0 -10000 0 0
TRIM24 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.025 0.055 -9999 0 -0.28 7 7
TMPRSS2 -0.01 0.23 -9999 0 -1.1 15 15
RXRG -0.1 0.23 -9999 0 -0.54 82 82
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.019 0 -9999 0 -10000 0 0
RXRB 0.019 0 -9999 0 -10000 0 0
CARM1 0.018 0.002 -9999 0 -10000 0 0
NR2C2 0.019 0 -9999 0 -10000 0 0
KLK2 0.011 0.11 -9999 0 -0.41 2 2
AR -0.003 0.058 -9999 0 -0.27 2 2
SENP1 0.019 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
MDM2 0.015 0.033 -9999 0 -0.24 6 6
SRY -0.001 0.026 -9999 0 -0.24 4 4
GATA2 0.014 0.036 -9999 0 -0.24 7 7
MYST2 0.019 0 -9999 0 -10000 0 0
HOXB13 -0.14 0.13 -9999 0 -0.24 219 219
T-DHT/AR/RACK1/Src 0.029 0.057 -9999 0 -0.28 4 4
positive regulation of transcription 0.014 0.036 -9999 0 -0.24 7 7
DNAJA1 0.019 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.019 -9999 0 -0.22 1 1
NCOA1 0.024 0.002 -9999 0 -10000 0 0
SPDEF -0.029 0.098 -9999 0 -0.24 63 63
T-DHT/AR/TIF2 0.041 0.04 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.025 0.056 -9999 0 -0.28 7 7
GSK3B 0.019 0.002 -9999 0 -10000 0 0
NR2C1 0.019 0 -9999 0 -10000 0 0
mol:T-DHT 0.027 0.048 -9999 0 -0.28 7 7
SIRT1 0.019 0 -9999 0 -10000 0 0
ZMIZ2 0.019 0 -9999 0 -10000 0 0
POU2F1 0.026 0.027 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 0.013 0.053 -9999 0 -0.28 7 7
CREBBP 0.019 0 -9999 0 -10000 0 0
SMARCE1 0.019 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.034 0.12 -9999 0 -0.29 62 62
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.017 0.029 -9999 0 -0.54 1 1
TCEB1 0.019 0 -9999 0 -10000 0 0
HIF1A/p53 0.036 0.026 -9999 0 -0.44 1 1
HIF1A 0.025 0.027 -9999 0 -0.48 1 1
COPS5 0.019 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.016 -9999 0 -0.26 1 1
FIH (dimer) 0.017 0.029 -9999 0 -0.54 1 1
CDKN2A -0.11 0.14 -9999 0 -0.25 172 172
ARNT/IPAS -0.009 0.088 -9999 0 -0.38 10 10
HIF1AN 0.017 0.029 -9999 0 -0.54 1 1
GNB2L1 0.019 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.036 0.026 -9999 0 -0.44 1 1
CUL2 0.019 0 -9999 0 -10000 0 0
OS9 0.018 0.014 -9999 0 -0.24 1 1
RACK1/Elongin B/Elongin C 0.037 0.019 -9999 0 -0.32 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.035 0.03 -9999 0 -0.34 2 2
PHD1-3/OS9 0.046 0.027 -9999 0 -0.28 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.051 0.029 -9999 0 -0.41 1 1
VHL 0.019 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
HIF1A/JAB1 0.036 0.026 -9999 0 -0.44 1 1
EGLN3 0.014 0.045 -9999 0 -0.39 4 4
EGLN2 0.019 0 -9999 0 -10000 0 0
EGLN1 0.019 0 -9999 0 -10000 0 0
TP53 0.019 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.047 0.014 -9999 0 -10000 0 0
ARNT 0.019 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.019 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.018 0.066 -9999 0 -0.3 5 5
Rapid glucocorticoid signaling

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.009 0.065 -10000 0 -0.27 11 11
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.02 0.044 -10000 0 -0.32 6 6
GNB1 0.019 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 0.01 0 -10000 0 -10000 0 0
Gs family/GTP -0.008 0.055 -10000 0 -0.14 49 49
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 0.005 0.014 0.04 49 -10000 0 49
GNAL -0.02 0.1 -10000 0 -0.28 49 49
GNG2 0.01 0.07 -10000 0 -0.54 6 6
CRH 0 0 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.01 0.001 -10000 0 -10000 0 0
MAPK11 0.01 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.008 -10000 0 -10000 0 0
HSPA8 0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.055 0.072 -10000 0 -0.35 7 7
AKT1 0.019 0.013 -10000 0 -10000 0 0
GSC -0.025 0.12 -10000 0 -10000 0 0
NKX2-5 -0.11 0.22 -10000 0 -0.49 87 87
muscle cell differentiation -0.001 0.062 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.072 0.061 -10000 0 -10000 0 0
SMAD4 0.027 0.029 -10000 0 -10000 0 0
CBFB 0.019 0 -10000 0 -10000 0 0
SAP18 0.019 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.018 0.081 -10000 0 -0.32 16 16
SMAD3/SMAD4/VDR 0.073 0.037 -10000 0 -0.26 2 2
MYC 0.017 0.027 -10000 0 -0.25 3 3
CDKN2B 0 0.18 -10000 0 -1.4 5 5
AP1 0.037 0.091 -10000 0 -0.31 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.069 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.042 0.055 -10000 0 -0.28 5 5
SP3 0.022 0 -10000 0 -10000 0 0
CREB1 0.019 0 -10000 0 -10000 0 0
FOXH1 0.012 0.03 -10000 0 -0.25 3 3
SMAD3/SMAD4/GR 0.053 0.034 -10000 0 -10000 0 0
GATA3 -0.11 0.24 -10000 0 -0.56 80 80
SKI/SIN3/HDAC complex/NCoR1 0.053 0.012 -10000 0 -10000 0 0
MEF2C/TIF2 -0.01 0.12 -10000 0 -0.31 16 16
endothelial cell migration -0.002 0.1 1.4 1 -10000 0 1
MAX 0.018 0.006 -10000 0 -10000 0 0
RBBP7 0.019 0.001 -10000 0 -10000 0 0
RBBP4 0.019 0.001 -10000 0 -10000 0 0
RUNX2 0.015 0.043 -10000 0 -0.44 3 3
RUNX3 -0.017 0.14 -10000 0 -0.54 24 24
RUNX1 0.014 0.05 -10000 0 -0.54 3 3
CTBP1 0.019 0 -10000 0 -10000 0 0
NR3C1 0.018 0.006 -10000 0 -10000 0 0
VDR 0.016 0.041 -10000 0 -0.54 2 2
CDKN1A 0.057 0.047 -10000 0 -10000 0 0
KAT2B 0.017 0.041 -10000 0 -0.53 2 2
SMAD2/SMAD2/SMAD4/FOXH1 0.041 0.052 -10000 0 -0.2 1 1
DCP1A 0.019 0 -10000 0 -10000 0 0
SKI 0.019 0.001 -10000 0 -10000 0 0
SERPINE1 -0.003 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 0.054 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.051 0.041 -10000 0 -10000 0 0
SAP30 0.019 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.044 0.02 -10000 0 -10000 0 0
JUN 0.031 0.089 -10000 0 -0.31 7 7
SMAD3/SMAD4/IRF7 0.05 0.057 -10000 0 -0.34 5 5
TFE3 0.025 0.007 -10000 0 -10000 0 0
COL1A2 -0.043 0.1 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.051 0.045 0.35 2 -10000 0 2
DLX1 -0.035 0.14 -10000 0 -0.35 54 54
TCF3 0.019 0 -10000 0 -10000 0 0
FOS 0.012 0.053 -10000 0 -0.26 12 12
SMAD3/SMAD4/Max 0.053 0.034 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.04 0.007 -10000 0 -10000 0 0
ZBTB17 0.019 0.01 -10000 0 -10000 0 0
LAMC1 0.056 0.031 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.054 0.033 -10000 0 -10000 0 0
IRF7 0.012 0.065 -10000 0 -0.54 5 5
ESR1 0.011 0.077 -10000 0 -0.54 7 7
HNF4A -0.015 0.074 -10000 0 -0.24 34 34
MEF2C -0.021 0.13 -10000 0 -0.33 15 15
SMAD2-3/SMAD4 0.055 0.044 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.042 0.012 -10000 0 -10000 0 0
IGHV3OR16-13 -0.002 0.019 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.019 0 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
SKIL 0.019 0 -10000 0 -10000 0 0
HDAC1 0.017 0.029 -10000 0 -0.54 1 1
HDAC2 0.019 0.001 -10000 0 -10000 0 0
SNIP1 0.018 0.002 -10000 0 -10000 0 0
GCN5L2 0.002 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.068 0.038 -10000 0 -10000 0 0
MSG1/HSC70 -0.001 0.091 -10000 0 -0.38 16 16
SMAD2 0.016 0.02 -10000 0 -10000 0 0
SMAD3 0.029 0.025 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.049 0.045 -10000 0 -0.24 5 5
SMAD2/SMAD2/SMAD4 0.015 0.029 -10000 0 -0.32 2 2
NCOR1 0.019 0.001 -10000 0 -10000 0 0
NCOA2 0.018 0.014 -10000 0 -0.24 1 1
NCOA1 0.019 0 -10000 0 -10000 0 0
MYOD/E2A 0.019 0.023 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.082 0.059 -10000 0 -10000 0 0
IFNB1 0.035 0.051 -10000 0 -0.29 5 5
SMAD3/SMAD4/MEF2C 0.005 0.13 -10000 0 -0.4 5 5
CITED1 -0.02 0.13 -10000 0 -0.38 36 36
SMAD2-3/SMAD4/ARC105 0.065 0.04 -10000 0 -10000 0 0
RBL1 0.019 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.053 0.076 -10000 0 -0.47 5 5
RUNX1-3/PEBPB2 0.013 0.098 -10000 0 -0.34 25 25
SMAD7 0.074 0.072 -10000 0 -10000 0 0
MYC/MIZ-1 0.026 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.062 -10000 0 -0.39 1 1
IL10 -0.051 0.23 -10000 0 -0.57 41 41
PIASy/HDAC complex 0.017 0.006 -10000 0 -10000 0 0
PIAS3 0.02 0.003 -10000 0 -10000 0 0
CDK2 0.02 0.005 -10000 0 -10000 0 0
IL5 -0.043 0.17 -10000 0 -0.38 50 50
CDK4 0.019 0.021 -10000 0 -0.25 2 2
PIAS4 0.017 0.006 -10000 0 -10000 0 0
ATF3 0.015 0.031 -10000 0 -0.24 5 5
SMAD3/SMAD4/SP1 0.059 0.053 -10000 0 -10000 0 0
FOXG1 -0.022 0.086 -10000 0 -0.25 46 46
FOXO3 0.027 0.017 -10000 0 -10000 0 0
FOXO1 0.027 0.017 -10000 0 -10000 0 0
FOXO4 0.027 0.017 -10000 0 -10000 0 0
heart looping -0.02 0.12 -10000 0 -0.33 15 15
CEBPB 0.019 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.017 0.1 -10000 0 -0.33 19 19
MYOD1 0.006 0.034 -10000 0 -0.24 6 6
SMAD3/SMAD4/HNF4 0.032 0.061 -10000 0 -0.23 3 3
SMAD3/SMAD4/GATA3 -0.037 0.2 -10000 0 -0.37 87 87
SnoN/SIN3/HDAC complex/NCoR1 0.019 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.049 0.095 -10000 0 -0.28 25 25
SMAD3/SMAD4/SP1-3 0.077 0.048 -10000 0 -10000 0 0
MED15 0.019 0 -10000 0 -10000 0 0
SP1 0.017 0.027 -10000 0 -10000 0 0
SIN3B 0.019 0.001 -10000 0 -10000 0 0
SIN3A 0.019 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.019 0.14 -10000 0 -0.27 76 76
ITGB5 0.058 0.038 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.054 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.015 0.088 -10000 0 -0.23 3 3
AR -0.086 0.13 -10000 0 -0.24 144 144
negative regulation of cell growth 0.058 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.045 0.041 -10000 0 -10000 0 0
E2F5 0.007 0.081 -10000 0 -0.54 8 8
E2F4 0.019 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.06 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.054 0.057 -10000 0 -0.31 5 5
TFDP1 0.019 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.05 0.097 -10000 0 -0.31 7 7
SMAD3/SMAD4/RUNX2 0.051 0.045 -10000 0 -0.35 2 2
TGIF2 0.019 0 -10000 0 -10000 0 0
TGIF1 0.019 0 -10000 0 -10000 0 0
ATF2 0.019 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.02 0.14 -9999 0 -0.31 75 75
Ran/GTP/Exportin 1/HDAC1 -0.001 0.012 -9999 0 -0.23 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.14 -9999 0 -0.28 75 75
SUMO1 0.019 0 -9999 0 -10000 0 0
ZFPM1 0.017 0.032 -9999 0 -0.39 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -10000 0 0
FKBP3 0.019 0 -9999 0 -10000 0 0
Histones 0.02 0.078 -9999 0 -0.23 1 1
YY1/LSF 0.03 0.053 -9999 0 -0.28 10 10
SMG5 0.019 0 -9999 0 -10000 0 0
RAN 0.019 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.017 0.11 -9999 0 -0.24 75 75
I kappa B alpha/HDAC1 -0.001 0.083 -9999 0 -0.27 1 1
SAP18 0.019 0 -9999 0 -10000 0 0
RELA -0.01 0.11 -9999 0 -0.22 75 75
HDAC1/Smad7 0.037 0.019 -9999 0 -0.32 1 1
RANGAP1 0.019 0 -9999 0 -10000 0 0
HDAC3/TR2 0 0.082 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.054 0.018 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0 0.099 -9999 0 -0.2 75 75
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.014 0.036 -9999 0 -0.24 7 7
GATA1 0 0 -9999 0 -10000 0 0
Mad/Max 0.028 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.06 0.027 -9999 0 -0.35 1 1
RBBP7 0.019 0 -9999 0 -10000 0 0
NPC 0.011 0 -9999 0 -10000 0 0
RBBP4 0.019 0 -9999 0 -10000 0 0
MAX 0.019 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.019 0 -9999 0 -10000 0 0
NFKBIA -0.011 0.09 -9999 0 -10000 0 0
KAT2B 0.016 0.041 -9999 0 -0.54 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.05 0.012 -9999 0 -10000 0 0
SIN3 complex 0.049 0 -9999 0 -10000 0 0
SMURF1 0.019 0 -9999 0 -10000 0 0
CHD3 0.019 0 -9999 0 -10000 0 0
SAP30 0.019 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.019 0 -9999 0 -10000 0 0
YY1/HDAC3 0.013 0.077 -9999 0 -0.35 1 1
YY1/HDAC2 0.037 0.019 -9999 0 -0.22 2 2
YY1/HDAC1 0.037 0.026 -9999 0 -0.25 3 3
NuRD/MBD2 Complex (MeCP1) 0.055 0.01 -9999 0 -10000 0 0
PPARG -0.03 0.14 -9999 0 -0.3 79 79
HDAC8/hEST1B 0.038 0 -9999 0 -10000 0 0
UBE2I 0.019 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -10000 0 0
TNFRSF1A 0.019 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0 0.082 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.018 -9999 0 -0.32 1 1
CREBBP 0.019 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.058 0.019 -9999 0 -10000 0 0
HDAC1 0.017 0.029 -9999 0 -0.54 1 1
HDAC3 -0.011 0.09 -9999 0 -10000 0 0
HDAC2 0.019 0 -9999 0 -10000 0 0
YY1 0.034 0.022 -9999 0 -0.27 2 2
HDAC8 0.019 0 -9999 0 -10000 0 0
SMAD7 0.019 0 -9999 0 -10000 0 0
NCOR2 0.019 0 -9999 0 -10000 0 0
MXD1 0.019 0 -9999 0 -10000 0 0
STAT3 0.031 0 -9999 0 -10000 0 0
NFKB1 0.019 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.019 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.039 0.052 -9999 0 -0.25 11 11
YY1/SAP30/HDAC1 0.046 0.024 -9999 0 -0.22 3 3
EP300 0.019 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.031 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.089 -9999 0 -10000 0 0
histone deacetylation 0.055 0.01 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.011 0.075 -9999 0 -10000 0 0
nuclear export -0.038 0 -9999 0 -10000 0 0
PRKACA 0.019 0 -9999 0 -10000 0 0
GATAD2B 0.019 0 -9999 0 -10000 0 0
GATAD2A 0.019 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.003 0.084 -9999 0 -0.28 2 2
GATA1/HDAC1 0.013 0.021 -9999 0 -0.39 1 1
GATA1/HDAC3 -0.013 0.079 -9999 0 -10000 0 0
CHD4 0.019 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.056 0.16 -9999 0 -0.38 75 75
SIN3/HDAC complex/Mad/Max 0.055 0.01 -9999 0 -10000 0 0
NuRD Complex 0.063 0.019 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.019 0.076 -9999 0 -0.23 1 1
SIN3B 0.019 0 -9999 0 -10000 0 0
MTA2 0.019 0 -9999 0 -10000 0 0
SIN3A 0.019 0 -9999 0 -10000 0 0
XPO1 0.019 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.039 0.015 -9999 0 -0.25 1 1
HDAC complex 0.048 0.017 -9999 0 -0.28 1 1
GATA1/Fog1 0.012 0.023 -9999 0 -0.39 1 1
FKBP25/HDAC1/HDAC2 0.037 0.019 -9999 0 -0.32 1 1
TNF -0.095 0.22 -9999 0 -0.54 75 75
negative regulation of cell growth 0.055 0.01 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.055 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.022 0.14 -9999 0 -0.3 75 75
SIN3/HDAC complex/NCoR1 0.052 0.01 -9999 0 -10000 0 0
TFCP2 0.006 0.082 -9999 0 -0.5 9 9
NR2C1 0.019 0 -9999 0 -10000 0 0
MBD3 0.016 0.041 -9999 0 -0.54 2 2
MBD2 0.019 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.018 0.13 -9999 0 -1.2 2 2
RAD9A 0.019 0 -9999 0 -10000 0 0
AP1 0.006 0.069 -9999 0 -0.3 7 7
IFNAR2 0.02 0.004 -9999 0 -10000 0 0
AKT1 0.019 0.034 -9999 0 -0.23 3 3
ER alpha/Oestrogen 0.007 0.056 -9999 0 -0.39 7 7
NFX1/SIN3/HDAC complex 0.055 0.013 -9999 0 -10000 0 0
EGF -0.031 0.15 -9999 0 -0.42 41 41
SMG5 0.019 0 -9999 0 -10000 0 0
SMG6 0.019 0 -9999 0 -10000 0 0
SP3/HDAC2 0.031 0.008 -9999 0 -10000 0 0
TERT/c-Abl 0.027 0.12 -9999 0 -1.1 2 2
SAP18 0.019 0.001 -9999 0 -10000 0 0
MRN complex 0.037 0.026 -9999 0 -0.32 2 2
WT1 0.002 0.004 -9999 0 -10000 0 0
WRN 0.019 0 -9999 0 -10000 0 0
SP1 0.021 0.006 -9999 0 -10000 0 0
SP3 0.02 0.002 -9999 0 -10000 0 0
TERF2IP 0.019 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.008 0.092 -9999 0 -0.94 2 2
Mad/Max 0.03 0.005 -9999 0 -10000 0 0
TERT 0.015 0.13 -9999 0 -1.3 2 2
CCND1 0.024 0.12 -9999 0 -0.99 2 2
MAX 0.02 0.002 -9999 0 -10000 0 0
RBBP7 0.019 0.001 -9999 0 -10000 0 0
RBBP4 0.019 0.001 -9999 0 -10000 0 0
TERF2 0.017 0 -9999 0 -10000 0 0
PTGES3 0.019 0 -9999 0 -10000 0 0
SIN3A 0.019 0.001 -9999 0 -10000 0 0
Telomerase/911 0.051 0.023 -9999 0 -10000 0 0
CDKN1B -0.12 0.2 -9999 0 -0.34 155 155
RAD1 0.019 0 -9999 0 -10000 0 0
XRCC5 0.019 0 -9999 0 -10000 0 0
XRCC6 0.019 0 -9999 0 -10000 0 0
SAP30 0.019 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.028 0 -9999 0 -10000 0 0
UBE3A 0.019 0.002 -9999 0 -10000 0 0
JUN -0.007 0.08 -9999 0 -0.24 37 37
E6 0.001 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.016 0.005 -9999 0 -10000 0 0
FOS 0.011 0.047 -9999 0 -0.24 12 12
IFN-gamma/IRF1 -0.15 0.23 -9999 0 -0.4 155 155
PARP2 0.019 0 -9999 0 -10000 0 0
BLM 0.019 0 -9999 0 -10000 0 0
Telomerase 0.069 0.069 -9999 0 -0.34 4 4
IRF1 -0.041 0.18 -9999 0 -0.53 43 43
ESR1 0.009 0.076 -9999 0 -0.54 7 7
KU/TER 0.028 0 -9999 0 -10000 0 0
ATM/TRF2 0.029 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.061 0.013 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.061 0.013 -9999 0 -10000 0 0
HDAC1 0.018 0.029 -9999 0 -0.54 1 1
HDAC2 0.021 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.023 0.03 -9999 0 -0.38 2 2
ABL1 0.019 0 -9999 0 -10000 0 0
MXD1 0.02 0.002 -9999 0 -10000 0 0
MRE11A 0.019 0 -9999 0 -10000 0 0
HUS1 0.019 0 -9999 0 -10000 0 0
RPS6KB1 0.019 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.044 0.12 -9999 0 -1 2 2
NR2F2 0.017 0.004 -9999 0 -10000 0 0
MAPK3 0.018 0.011 -9999 0 -10000 0 0
MAPK1 0.018 0.011 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.015 0.041 -9999 0 -0.54 2 2
NFKB1 0.019 0 -9999 0 -10000 0 0
HNRNPC 0.019 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.019 0 -9999 0 -10000 0 0
EGFR -0.007 0.087 -9999 0 -0.27 33 33
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.025 0.12 -9999 0 -0.36 34 34
MYC 0.018 0.024 -9999 0 -0.25 3 3
IL2 0.007 0.017 -9999 0 -0.24 1 1
KU 0.028 0 -9999 0 -10000 0 0
RAD50 0.016 0.041 -9999 0 -0.54 2 2
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
TGFB1 0.015 0.041 -9999 0 -0.54 2 2
TRF2/BLM 0.028 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT 0.037 0.12 -9999 0 -1.1 2 2
SP1/HDAC2 0.033 0.011 -9999 0 -10000 0 0
PINX1 0.018 0.014 -9999 0 -0.24 1 1
Telomerase/EST1A -0.008 0.092 -9999 0 -0.94 2 2
Smad3/Myc 0.029 0.029 -9999 0 -0.32 2 2
911 complex 0.038 0 -9999 0 -10000 0 0
IFNG -0.17 0.26 -9999 0 -0.53 129 129
Telomerase/PinX1 -0.008 0.092 -9999 0 -0.94 2 2
Telomerase/AKT1/mTOR/p70S6K 0.043 0.04 -9999 0 -0.29 1 1
SIN3B 0.019 0.001 -9999 0 -10000 0 0
YWHAE 0.019 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.008 0.092 -9999 0 -0.94 2 2
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.053 0.022 -9999 0 -0.25 2 2
TRF2/WRN 0.028 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.008 0.092 -9999 0 -0.94 2 2
E2F1 0.02 0.004 -9999 0 -10000 0 0
ZNFX1 0.019 0.001 -9999 0 -10000 0 0
PIF1 0.014 0.05 -9999 0 -0.54 3 3
NCL 0.019 0 -9999 0 -10000 0 0
DKC1 0.019 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.017 0.029 -10000 0 -0.54 1 1
HDAC2 0.019 0 -10000 0 -10000 0 0
GNB1/GNG2 0.024 0.073 -10000 0 -0.32 16 16
forebrain development 0.033 0.061 -10000 0 -0.38 4 4
GNAO1 -0.093 0.13 -10000 0 -0.25 155 155
SMO/beta Arrestin2 0.019 0.067 -10000 0 -0.38 10 10
SMO 0.005 0.091 -10000 0 -0.54 10 10
ARRB2 0.02 0.001 -10000 0 -10000 0 0
GLI3/SPOP 0.059 0.035 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.019 0 -10000 0 -10000 0 0
GNAI2 0.019 0.001 -10000 0 -10000 0 0
SIN3/HDAC complex 0.048 0.001 -10000 0 -10000 0 0
GNAI1 0.005 0.06 -10000 0 -0.24 20 20
XPO1 0.021 0.002 -10000 0 -10000 0 0
GLI1/Su(fu) 0.039 0.069 -10000 0 -0.32 9 9
SAP30 0.019 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.09 -10000 0 -0.54 10 10
MIM/GLI2A 0.014 0.05 -10000 0 -0.54 3 3
IFT88 0.017 0.029 -10000 0 -0.54 1 1
GNAI3 0.019 0.001 -10000 0 -10000 0 0
GLI2 0.048 0.018 -10000 0 -10000 0 0
GLI3 0.051 0.037 0.2 8 -0.23 3 11
CSNK1D 0.019 0 -10000 0 -10000 0 0
CSNK1E 0.019 0 -10000 0 -10000 0 0
SAP18 0.019 0 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.017 0.029 -10000 0 -0.54 1 1
GNG2 0.01 0.07 -10000 0 -0.54 6 6
Gi family/GTP -0.017 0.082 -10000 0 -0.31 13 13
SIN3B 0.019 0 -10000 0 -10000 0 0
SIN3A 0.019 0 -10000 0 -10000 0 0
GLI3/Su(fu) 0.071 0.026 -10000 0 -10000 0 0
GLI2/Su(fu) 0.064 0.034 -10000 0 -0.27 1 1
FOXA2 -0.006 0.065 -10000 0 -0.72 3 3
neural tube patterning 0.033 0.061 -10000 0 -0.38 4 4
SPOP 0.019 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.037 0.033 -10000 0 -10000 0 0
GNB1 0.019 0 -10000 0 -10000 0 0
CSNK1G2 0.019 0 -10000 0 -10000 0 0
CSNK1G3 0.019 0 -10000 0 -10000 0 0
MTSS1 0.014 0.05 -10000 0 -0.54 3 3
embryonic limb morphogenesis 0.033 0.061 -10000 0 -0.38 4 4
SUFU 0.03 0.036 -10000 0 -0.19 10 10
LGALS3 -0.005 0.11 -10000 0 -0.54 16 16
catabolic process 0.085 0.034 -10000 0 -10000 0 0
GLI3A/CBP 0.027 0.031 -10000 0 -0.34 2 2
KIF3A 0.019 0 -10000 0 -10000 0 0
GLI1 0.033 0.062 -10000 0 -0.39 4 4
RAB23 0.019 0 -10000 0 -10000 0 0
CSNK1A1 0.019 0 -10000 0 -10000 0 0
IFT172 0.013 0.058 -10000 0 -0.54 4 4
RBBP7 0.019 0 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.023 0.071 -10000 0 -0.27 16 16
GNAZ -0.015 0.093 -10000 0 -0.26 45 45
RBBP4 0.019 0 -10000 0 -10000 0 0
CSNK1G1 0.019 0 -10000 0 -10000 0 0
PIAS1 0.019 0 -10000 0 -10000 0 0
PRKACA 0.019 0 -10000 0 -10000 0 0
GLI2/SPOP 0.055 0.017 -10000 0 -10000 0 0
STK36 0.021 0.002 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.006 0.081 -10000 0 -0.32 12 12
PTCH1 0.037 0.099 -10000 0 -1.1 2 2
MIM/GLI1 0.041 0.064 -10000 0 -0.37 4 4
CREBBP 0.027 0.031 -10000 0 -0.34 2 2
Su(fu)/SIN3/HDAC complex 0.055 0.019 -10000 0 -0.26 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.02 0.059 -9999 0 -0.32 11 11
SNTA1 0.014 0.036 -9999 0 -0.24 7 7
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.019 0.062 -9999 0 -0.32 12 12
MAPK12 0.02 0.06 -9999 0 -0.3 12 12
CCND1 0.017 0.031 -9999 0 -0.19 1 1
p38 gamma/SNTA1 0.027 0.059 -9999 0 -0.27 12 12
MAP2K3 0.019 0 -9999 0 -10000 0 0
PKN1 0.017 0.029 -9999 0 -0.54 1 1
G2/M transition checkpoint 0.02 0.06 -9999 0 -0.3 12 12
MAP2K6 0.018 0.049 -9999 0 -0.31 8 8
MAPT -0.03 0.072 -9999 0 -0.27 15 15
MAPK13 0.014 0.07 -9999 0 -0.38 11 11
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.019 0.019 -9999 0 -0.33 1 1
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.008 0.15 -9999 0 -0.93 4 4
MKNK1 0.019 0 -9999 0 -10000 0 0
MAPK14 0.008 0.067 -9999 0 -0.29 4 4
ATF2/c-Jun 0.006 0.097 -9999 0 -0.32 11 11
MAPK11 0.008 0.067 -9999 0 -0.28 5 5
MITF 0.006 0.11 -9999 0 -0.38 20 20
MAPKAPK5 0.02 0.074 -9999 0 -0.32 5 5
KRT8 -0.035 0.14 -9999 0 -0.32 60 60
MAPKAPK3 0.019 0 -9999 0 -10000 0 0
MAPKAPK2 0.019 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.012 0.093 -9999 0 -0.41 5 5
CEBPB 0.02 0.074 -9999 0 -0.32 5 5
SLC9A1 0.02 0.074 -9999 0 -0.32 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.02 0.082 -9999 0 -0.33 5 5
p38alpha-beta/MNK1 0.028 0.075 -9999 0 -0.32 5 5
JUN 0.005 0.096 -9999 0 -0.32 11 11
PPARGC1A -0.039 0.11 -9999 0 -0.38 14 14
USF1 0.02 0.074 -9999 0 -0.34 4 4
RAB5/GDP/GDI1 0.021 0.05 -9999 0 -0.24 4 4
NOS2 0.012 0.11 -9999 0 -0.75 2 2
DDIT3 0.02 0.074 -9999 0 -0.34 4 4
RAB5A 0.019 0 -9999 0 -10000 0 0
HSPB1 0.025 0.059 -9999 0 -0.27 4 4
p38alpha-beta/HBP1 0.028 0.075 -9999 0 -0.32 5 5
CREB1 0.025 0.076 -9999 0 -0.35 4 4
RAB5/GDP 0.014 0 -9999 0 -10000 0 0
EIF4E 0.025 0.061 -9999 0 -0.28 4 4
RPS6KA4 0.02 0.074 -9999 0 -0.34 4 4
PLA2G4A 0.02 0.074 -9999 0 -0.3 10 10
GDI1 0.02 0.074 -9999 0 -0.34 4 4
TP53 0.017 0.086 -9999 0 -0.4 5 5
RPS6KA5 0.019 0.079 -9999 0 -0.34 6 6
ESR1 0.014 0.096 -9999 0 -0.39 12 12
HBP1 0.019 0 -9999 0 -10000 0 0
MEF2C 0.019 0.077 -9999 0 -0.32 6 6
MEF2A 0.02 0.074 -9999 0 -0.34 4 4
EIF4EBP1 0.024 0.077 -9999 0 -0.34 5 5
KRT19 0 0.087 -9999 0 -0.32 8 8
ELK4 0.02 0.074 -9999 0 -0.32 5 5
ATF6 0.02 0.074 -9999 0 -0.32 5 5
ATF1 0.025 0.076 -9999 0 -0.35 4 4
p38alpha-beta/MAPKAPK2 0.028 0.075 -9999 0 -0.32 5 5
p38alpha-beta/MAPKAPK3 0.028 0.075 -9999 0 -0.32 5 5
Insulin 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
CBL/APS/CAP -0.013 0.045 -9999 0 -0.24 11 11
TC10/GTP -0.007 0.039 -9999 0 -0.23 11 11
Insulin Receptor/Insulin/IRS1/Shp2 0.028 0.039 -9999 0 -10000 0 0
HRAS 0.019 0 -9999 0 -10000 0 0
APS homodimer 0.008 0.076 -9999 0 -0.54 7 7
GRB14 -0.027 0.096 -9999 0 -0.24 59 59
FOXO3 0.028 0.012 -9999 0 -10000 0 0
AKT1 0.026 0.05 -9999 0 -10000 0 0
INSR 0.02 0.014 -9999 0 -0.24 1 1
Insulin Receptor/Insulin 0.046 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.017 0.019 -9999 0 -0.24 2 2
SORBS1 0.012 0.059 -9999 0 -0.48 5 5
CRK 0.019 0 -9999 0 -10000 0 0
PTPN1 0.035 0.005 -9999 0 -10000 0 0
CAV1 0.02 0.034 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.047 0.054 -9999 0 -0.26 11 11
Insulin Receptor/Insulin/IRS1/NCK2 0.028 0.039 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.024 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.023 -9999 0 -10000 0 0
RPS6KB1 0.031 0.047 -9999 0 -10000 0 0
PARD6A 0.019 0 -9999 0 -10000 0 0
CBL 0.019 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.004 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.024 -9999 0 -10000 0 0
HRAS/GTP -0.04 0.079 -9999 0 -0.3 4 4
Insulin Receptor 0.02 0.014 -9999 0 -0.24 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.038 0.037 -9999 0 -10000 0 0
PRKCI 0.009 0.017 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.017 0.034 -9999 0 -10000 0 0
SHC1 0.019 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.036 0.016 -9999 0 -0.27 1 1
PI3K 0.031 0.034 -9999 0 -10000 0 0
NCK2 0.019 0 -9999 0 -10000 0 0
RHOQ 0.019 0 -9999 0 -10000 0 0
mol:H2O2 0 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.014 0 -9999 0 -10000 0 0
AKT2 0.026 0.05 -9999 0 -10000 0 0
PRKCZ 0.006 0.042 -9999 0 -0.52 2 2
SH2B2 0.008 0.076 -9999 0 -0.54 7 7
SHC/SHIP -0.018 0.11 -9999 0 -0.26 62 62
F2RL2 -0.061 0.18 -9999 0 -0.43 66 66
TRIP10 0.018 0.014 -9999 0 -0.24 1 1
Insulin Receptor/Insulin/Shc 0.027 0.006 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.025 0.008 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.048 0.006 -9999 0 -10000 0 0
RAPGEF1 0.019 0 -9999 0 -10000 0 0
RASA1 0.017 0.029 -9999 0 -0.54 1 1
NCK1 0.019 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.038 0.057 -9999 0 -0.28 11 11
TC10/GDP 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.039 0.012 -9999 0 -10000 0 0
INPP5D -0.031 0.12 -9999 0 -0.28 62 62
SOS1 0.019 0 -9999 0 -10000 0 0
SGK1 0.002 0.003 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.019 0 -9999 0 -10000 0 0
IRS1 -0.002 0.071 -9999 0 -0.24 29 29
p62DOK/RasGAP 0.036 0.016 -9999 0 -0.27 1 1
INS 0.003 0.001 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.031 0.12 -9999 0 -0.28 62 62
GRB2 0.019 0 -9999 0 -10000 0 0
EIF4EBP1 0.03 0.047 -9999 0 -10000 0 0
PTPRA 0.021 0 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
TC10/GTP/CIP4 0.025 0.008 -9999 0 -10000 0 0
PDPK1 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.026 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.016 0.038 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.018 0.009 -9999 0 -10000 0 0
Par3/Par6 0.001 0.1 -9999 0 -0.27 41 41
Signaling events mediated by PRL

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
CCNE1 0.019 0 -10000 0 -10000 0 0
mol:Halofuginone 0.005 0.013 -10000 0 -10000 0 0
ITGA1 0.009 0.051 -10000 0 -0.24 14 14
CDKN1A 0.031 0.025 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.026 0.025 -10000 0 -0.38 1 1
mol:Ca2+ -0.075 0.14 -10000 0 -0.32 87 87
AGT -0.089 0.2 -10000 0 -0.43 88 88
CCNA2 0.029 0.048 -10000 0 -0.32 1 1
TUBA1B 0.019 0 -10000 0 -10000 0 0
EGR1 0.011 0.054 -10000 0 -0.32 1 1
CDK2/Cyclin E1 0.049 0.022 -10000 0 -10000 0 0
MAPK3 0.024 0.025 -10000 0 -0.38 1 1
PRL-2 /Rab GGTase beta 0.028 0 -10000 0 -10000 0 0
MAPK1 0.024 0.025 -10000 0 -0.38 1 1
PTP4A1 0.024 0.049 -10000 0 -0.35 1 1
PTP4A3 0.016 0.035 -10000 0 -0.34 3 3
PTP4A2 0.019 0 -10000 0 -10000 0 0
ITGB1 0.023 0.028 -10000 0 -0.2 5 5
SRC 0.019 0 -10000 0 -10000 0 0
RAC1 0.031 0.033 -10000 0 -0.38 1 1
Rab GGTase beta/Rab GGTase alpha 0.028 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.033 0.046 -10000 0 -0.32 1 1
RABGGTA 0.019 0 -10000 0 -10000 0 0
BCAR1 0.002 0.023 0.23 3 -10000 0 3
RHOC 0.031 0.033 -10000 0 -0.38 1 1
RHOA 0.031 0.033 -10000 0 -0.38 1 1
cell motility 0.036 0.034 -10000 0 -0.38 1 1
PRL-1/alpha Tubulin 0.033 0.046 -10000 0 -0.32 1 1
PRL-3/alpha1 Integrin 0.019 0.042 -10000 0 -0.38 1 1
ROCK1 0.036 0.034 -10000 0 -0.38 1 1
RABGGTB 0.019 0 -10000 0 -10000 0 0
CDK2 0.019 0 -10000 0 -10000 0 0
mitosis 0.024 0.049 -10000 0 -0.35 1 1
ATF5 0.019 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.01 0.07 0.54 6 -10000 0 6
PI3K Class IB/PDE3B 0.01 0.07 -10000 0 -0.54 6 6
PDE3B 0.01 0.07 -10000 0 -0.54 6 6
Aurora B 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
Condensin I complex 0.038 0.033 -9999 0 -0.44 1 1
STMN1 0.025 0.03 -9999 0 -0.38 2 2
Aurora B/RasGAP/Survivin 0.038 0.027 -9999 0 -0.32 2 2
Chromosomal passenger complex/Cul3 protein complex 0.019 0.054 -9999 0 -0.22 4 4
BIRC5 0.02 0.001 -9999 0 -10000 0 0
DES -0.057 0.16 -9999 0 -0.56 32 32
Aurora C/Aurora B/INCENP -0.032 0.13 -9999 0 -0.29 78 78
Aurora B/TACC1 0.025 0.018 -9999 0 -0.31 1 1
Aurora B/PP2A 0.028 0.021 -9999 0 -0.37 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.018 0.009 -9999 0 -0.15 1 1
mitotic metaphase/anaphase transition 0 0.001 -9999 0 -10000 0 0
NDC80 0.022 0.043 -9999 0 -0.38 4 4
Cul3 protein complex -0.002 0.091 -9999 0 -0.34 16 16
KIF2C 0.03 0.011 -9999 0 -0.15 1 1
PEBP1 0.02 0.001 -9999 0 -10000 0 0
KIF20A 0.017 0.029 -9999 0 -0.54 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.027 0.03 -9999 0 -0.38 2 2
SEPT1 -0.15 0.26 -9999 0 -0.54 110 110
SMC2 0.017 0.029 -9999 0 -0.54 1 1
SMC4 0.019 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.041 0.038 -9999 0 -0.68 1 1
PSMA3 0.019 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
H3F3B 0.02 0.018 -9999 0 -0.33 1 1
AURKB 0.019 0.029 -9999 0 -0.54 1 1
AURKC -0.098 0.23 -9999 0 -0.54 77 77
CDCA8 0.02 0.001 -9999 0 -10000 0 0
cytokinesis 0.047 0.035 -9999 0 -0.36 2 2
Aurora B/Septin1 -0.02 0.13 -9999 0 -0.32 3 3
AURKA 0.019 0.001 -9999 0 -10000 0 0
INCENP 0.02 0.001 -9999 0 -10000 0 0
KLHL13 -0.039 0.13 -9999 0 -0.29 69 69
BUB1 0.019 0.001 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.037 0.018 -9999 0 -0.28 1 1
EVI5 0.02 0.001 -9999 0 -10000 0 0
RhoA/GTP 0.057 0.025 -9999 0 -0.27 2 2
SGOL1 0.019 0 -9999 0 -10000 0 0
CENPA 0.033 0.037 -9999 0 -0.42 2 2
NCAPG 0.016 0.041 -9999 0 -0.54 2 2
Aurora B/HC8 Proteasome 0.028 0.021 -9999 0 -0.37 1 1
NCAPD2 0.019 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.027 0.03 -9999 0 -0.38 2 2
RHOA 0.019 0 -9999 0 -10000 0 0
NCAPH 0.017 0.029 -9999 0 -0.54 1 1
NPM1 0.026 0.029 -9999 0 -0.54 1 1
RASA1 0.017 0.029 -9999 0 -0.54 1 1
KLHL9 0.01 0.07 -9999 0 -0.54 6 6
mitotic prometaphase 0.001 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.021 -9999 0 -0.37 1 1
PPP1CC 0.017 0.029 -9999 0 -0.54 1 1
Centraspindlin 0.054 0.027 -9999 0 -0.3 2 2
RhoA/GDP 0.014 0 -9999 0 -10000 0 0
NSUN2 0.026 0.029 -9999 0 -0.54 1 1
MYLK 0.017 0.036 -9999 0 -0.33 4 4
KIF23 0.019 0.029 -9999 0 -0.54 1 1
VIM 0.026 0.021 -9999 0 -0.37 1 1
RACGAP1 0.02 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.026 0.029 -9999 0 -0.54 1 1
Chromosomal passenger complex 0.042 0.022 -9999 0 -0.34 1 1
Chromosomal passenger complex/EVI5 0.057 0.025 -9999 0 -0.27 1 1
TACC1 0.019 0 -9999 0 -10000 0 0
PPP2R5D 0.019 0 -9999 0 -10000 0 0
CUL3 0.019 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.022 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.085 0.042 -9999 0 -10000 0 0
ERC1 0.019 0 -9999 0 -10000 0 0
RIP2/NOD2 0.005 0.095 -9999 0 -0.38 21 21
NFKBIA 0.048 0 -9999 0 -10000 0 0
BIRC2 0.014 0.052 -9999 0 -0.46 4 4
IKBKB 0.019 0 -9999 0 -10000 0 0
RIPK2 0.019 0 -9999 0 -10000 0 0
IKBKG 0.038 0.062 -9999 0 -0.48 1 1
IKK complex/A20 0.007 0.14 -9999 0 -0.41 18 18
NEMO/A20/RIP2 0.019 0 -9999 0 -10000 0 0
XPO1 0.019 0 -9999 0 -10000 0 0
NEMO/ATM 0.046 0.06 -9999 0 -0.45 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.019 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.026 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.009 0.039 -9999 0 -0.4 1 1
BCL10/MALT1/TRAF6 0.037 0.02 -9999 0 -0.32 1 1
NOD2 -0.013 0.13 -9999 0 -0.54 21 21
NFKB1 0.022 0 -9999 0 -10000 0 0
RELA 0.022 0 -9999 0 -10000 0 0
MALT1 0.017 0.029 -9999 0 -0.54 1 1
cIAP1/UbcH5C 0.024 0.038 -9999 0 -0.38 3 3
ATM 0.019 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.056 0.16 -9999 0 -0.38 75 75
TRAF6 0.019 0 -9999 0 -10000 0 0
PRKCA 0.013 0.044 -9999 0 -0.29 7 7
CHUK 0.019 0 -9999 0 -10000 0 0
UBE2D3 0.019 0 -9999 0 -10000 0 0
TNF -0.095 0.22 -9999 0 -0.54 75 75
NF kappa B1 p50/RelA 0.052 0 -9999 0 -10000 0 0
BCL10 0.018 0.014 -9999 0 -0.24 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.048 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0 -9999 0 -10000 0 0
TNFRSF1A 0.019 0 -9999 0 -10000 0 0
IKK complex 0.055 0.059 -9999 0 -0.44 1 1
CYLD 0.019 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.061 -9999 0 -0.42 1 1
Signaling events mediated by HDAC Class III

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
EP300 0.019 0 -10000 0 -10000 0 0
HDAC4 0.019 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.066 0.38 10 -10000 0 10
CDKN1A 0.008 0.018 -10000 0 -10000 0 0
KAT2B 0.016 0.041 -10000 0 -0.54 2 2
BAX 0.019 0 -10000 0 -10000 0 0
FOXO3 -0.007 0.001 -10000 0 -10000 0 0
FOXO1 0.019 0 -10000 0 -10000 0 0
FOXO4 0.026 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.019 0 -10000 0 -10000 0 0
TAT 0 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.015 0.041 -10000 0 -0.24 7 7
PPARGC1A -0.094 0.15 -10000 0 -0.26 146 146
FHL2 0.01 0.07 -10000 0 -0.54 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.024 0.004 -10000 0 -10000 0 0
HIST2H4A 0.012 0.066 -10000 0 -0.38 10 10
SIRT1/FOXO3a 0.003 0.004 -10000 0 -10000 0 0
SIRT1 0.013 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.035 0.004 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.028 0.005 -10000 0 -10000 0 0
apoptosis -0.034 0.004 -10000 0 -10000 0 0
SIRT1/PGC1A -0.042 0.085 -10000 0 -0.32 10 10
p53/SIRT1 0.001 0.016 -10000 0 -10000 0 0
SIRT1/FOXO4 0.029 0.004 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.028 0.041 -10000 0 -0.29 6 6
HIST1H1E 0.026 0.002 -10000 0 -10000 0 0
SIRT1/p300 0.024 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.023 0.035 0.38 2 -10000 0 2
TP53 0.013 0.006 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.035 0.004 -10000 0 -10000 0 0
CREBBP 0.019 0 -10000 0 -10000 0 0
MEF2D 0.019 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.01 0.004 -10000 0 -10000 0 0
ACSS2 0.021 0.019 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.023 0.035 -10000 0 -0.38 2 2
TCGA08_rtk_signaling

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
PDGFRA 0.003 0.076 -10000 0 -0.31 18 18
HRAS 0.019 0 -10000 0 -10000 0 0
EGFR -0.007 0.087 -10000 0 -0.27 33 33
AKT 0.039 0.026 -10000 0 -10000 0 0
FOXO3 0.019 0 -10000 0 -10000 0 0
AKT1 0.019 0 -10000 0 -10000 0 0
FOXO1 0.019 0 -10000 0 -10000 0 0
AKT3 0.019 0 -10000 0 -10000 0 0
FOXO4 0.019 0 -10000 0 -10000 0 0
MET -0.024 0.14 -10000 0 -0.43 35 35
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
PIK3CB 0.019 0 -10000 0 -10000 0 0
NRAS 0.019 0 -10000 0 -10000 0 0
PIK3CG -0.055 0.19 -10000 0 -0.54 49 49
PIK3R3 0.019 0 -10000 0 -10000 0 0
PIK3R2 0.019 0 -10000 0 -10000 0 0
NF1 0.019 0 -10000 0 -10000 0 0
RAS 0.009 0.049 -10000 0 -0.14 1 1
ERBB2 0.019 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.03 0.039 0.15 4 -10000 0 4
PI3K 0.008 0.063 -10000 0 -0.23 8 8
PIK3R1 0.019 0 -10000 0 -10000 0 0
KRAS 0.018 0.014 -10000 0 -0.24 1 1
FOXO 0.05 0.03 -10000 0 -10000 0 0
AKT2 0.019 0 -10000 0 -10000 0 0
PTEN 0.017 0.029 -10000 0 -0.54 1 1
FOXM1 transcription factor network

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
NFATC3 0.28 0.18 -9999 0 -0.98 2 2
PLK1 0.09 0.036 -9999 0 -10000 0 0
BIRC5 0.09 0.036 -9999 0 -10000 0 0
HSPA1B 0.27 0.19 -9999 0 -0.98 2 2
MAP2K1 0.065 0.026 -9999 0 -10000 0 0
BRCA2 0.27 0.23 -9999 0 -1.1 6 6
FOXM1 0.29 0.2 -9999 0 -1.2 2 2
XRCC1 0.28 0.18 -9999 0 -0.98 2 2
FOXM1B/p19 -0.022 0.1 -9999 0 -1 2 2
Cyclin D1/CDK4 0.22 0.2 -9999 0 -0.89 2 2
CDC2 0.28 0.19 -9999 0 -1 2 2
TGFA 0.21 0.23 -9999 0 -0.78 6 6
SKP2 0.28 0.18 -9999 0 -0.98 2 2
CCNE1 0.028 0.006 -9999 0 -10000 0 0
CKS1B 0.28 0.18 -9999 0 -0.98 2 2
RB1 -0.004 0.081 -9999 0 -0.96 2 2
FOXM1C/SP1 0.27 0.18 -9999 0 -1.1 2 2
AURKB 0.086 0.09 -9999 0 -1.5 1 1
CENPF 0.28 0.19 -9999 0 -1.2 2 2
CDK4 0.032 0.024 -9999 0 -0.24 2 2
MYC 0.27 0.17 -9999 0 -0.85 2 2
CHEK2 0.065 0.026 -9999 0 -10000 0 0
ONECUT1 0.18 0.24 -9999 0 -0.83 3 3
CDKN2A -0.12 0.14 -9999 0 -0.26 172 172
LAMA4 0.27 0.19 -9999 0 -0.98 2 2
FOXM1B/HNF6 0.18 0.24 -9999 0 -0.95 3 3
FOS 0.27 0.19 -9999 0 -0.98 2 2
SP1 0.021 0.002 -9999 0 -10000 0 0
CDC25B 0.28 0.18 -9999 0 -0.98 2 2
response to radiation 0.039 0.024 -9999 0 -10000 0 0
CENPB 0.28 0.18 -9999 0 -0.98 2 2
CENPA 0.28 0.2 -9999 0 -1.4 2 2
NEK2 0.27 0.21 -9999 0 -1.3 3 3
HIST1H2BA 0.27 0.18 -9999 0 -0.98 2 2
CCNA2 0.027 0.031 -9999 0 -0.55 1 1
EP300 0.019 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.28 0.2 -9999 0 -1.1 2 2
CCNB2 0.27 0.22 -9999 0 -0.96 6 6
CCNB1 0.28 0.19 -9999 0 -1 2 2
ETV5 0.28 0.2 -9999 0 -1.1 3 3
ESR1 0.26 0.25 -9999 0 -1 9 9
CCND1 0.22 0.21 -9999 0 -0.9 2 2
GSK3A 0.057 0.024 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.079 0.035 -9999 0 -0.35 1 1
CDK2 0.028 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.048 0.026 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 0.1 0.16 -9999 0 -1.1 2 2
GAS1 0.27 0.22 -9999 0 -1 5 5
MMP2 0.26 0.22 -9999 0 -0.99 4 4
RB1/FOXM1C 0.24 0.2 -9999 0 -0.93 3 3
CREBBP 0.019 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.017 0.029 -10000 0 -0.54 1 1
HDAC3 0.019 0 -10000 0 -10000 0 0
VDR 0.016 0.041 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.037 0.026 -10000 0 -0.32 2 2
EP300 0.019 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.044 0.043 -10000 0 -0.22 1 1
KAT2B 0.016 0.041 -10000 0 -0.54 2 2
MAPK14 0.019 0 -10000 0 -10000 0 0
AKT1 0.025 0.059 0.22 7 -0.24 13 20
RAR alpha/9cRA/Cyclin H 0.057 0.022 -10000 0 -0.26 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.04 0.049 -10000 0 -0.18 16 16
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.028 0.017 -10000 0 -0.18 1 1
NCOR2 0.019 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.012 0.03 -10000 0 -0.39 2 2
RXRs/RARs/NRIP1/9cRA 0.036 0.072 -10000 0 -0.58 1 1
NCOA2 0.018 0.014 -10000 0 -0.24 1 1
NCOA3 0.019 0 -10000 0 -10000 0 0
NCOA1 0.019 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.016 0.041 -10000 0 -0.54 2 2
RARG 0.02 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.026 0 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
MAPK1 0.019 0 -10000 0 -10000 0 0
MAPK8 0.02 0.001 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.029 0.063 -10000 0 -0.64 1 1
RARA 0.031 0.021 -10000 0 -0.23 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.04 0.049 -10000 0 -0.18 16 16
PRKCA 0.017 0.044 -10000 0 -0.28 7 7
RXRs/RARs/NRIP1/9cRA/HDAC1 0.026 0.076 -10000 0 -0.62 1 1
RXRG -0.05 0.15 -10000 0 -0.32 83 83
RXRA 0.037 0.021 -10000 0 -0.23 1 1
RXRB 0.028 0.028 -10000 0 -0.27 2 2
VDR/Vit D3/DNA 0.012 0.03 -10000 0 -0.39 2 2
RBP1 0 0.09 -10000 0 -0.38 17 17
CRBP1/9-cic-RA 0.001 0.065 -10000 0 -0.27 17 17
RARB 0 0.11 -10000 0 -0.52 15 15
PRKCG 0.014 0.025 -10000 0 -0.24 3 3
MNAT1 0.019 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.033 0.074 -10000 0 -0.63 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.038 0.065 -10000 0 -0.31 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.043 -10000 0 -0.21 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 0.026 0.076 -10000 0 -0.62 1 1
positive regulation of DNA binding -0.001 0.015 -10000 0 -0.25 1 1
NRIP1 0.027 0.072 -10000 0 -0.56 1 1
RXRs/RARs 0.019 0.077 -10000 0 -0.36 5 5
RXRs/RXRs/DNA/9cRA 0.021 0.061 -10000 0 -0.66 1 1
PRKACA 0.019 0 -10000 0 -10000 0 0
CDK7 0.019 0 -10000 0 -10000 0 0
TFIIH 0.038 0 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.014 -10000 0 -10000 0 0
CCNH 0.019 0 -10000 0 -10000 0 0
CREBBP 0.019 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.05 0.038 0.22 1 -0.31 2 3
CaM/Ca2+ 0.014 0 -10000 0 -10000 0 0
AKT1 0.019 0 -10000 0 -10000 0 0
AKT2 0.019 0 -10000 0 -10000 0 0
STXBP4 0.019 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.048 0.046 0.23 1 -0.35 2 3
YWHAZ 0.019 0 -10000 0 -10000 0 0
CALM1 0.019 0 -10000 0 -10000 0 0
YWHAQ 0.019 0 -10000 0 -10000 0 0
TBC1D4 0.023 0.028 -10000 0 -0.38 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.019 0 -10000 0 -10000 0 0
YWHAB 0.019 0 -10000 0 -10000 0 0
SNARE/Synip 0.038 0 -10000 0 -10000 0 0
YWHAG 0.019 0 -10000 0 -10000 0 0
ASIP -0.007 0.073 -10000 0 -0.24 31 31
PRKCI 0.019 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.014 0 -10000 0 -10000 0 0
RHOQ 0.019 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.016 0.041 -10000 0 -0.54 2 2
TRIP10 0.018 0.014 -10000 0 -0.24 1 1
TC10/GTP/CIP4/Exocyst 0.025 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.036 0.032 -10000 0 -10000 0 0
VAMP2 0.019 0 -10000 0 -10000 0 0
SLC2A4 0.049 0.048 0.23 1 -0.38 2 3
STX4 0.019 0 -10000 0 -10000 0 0
GSK3B 0.031 0 -10000 0 -10000 0 0
SFN -0.035 0.11 -10000 0 -0.24 74 74
LNPEP 0.019 0 -10000 0 -10000 0 0
YWHAE 0.019 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA 0.004 0.076 -9999 0 -0.31 18 18
PDGF/PDGFRA/CRKL 0.017 0.054 -9999 0 -0.37 4 4
positive regulation of JUN kinase activity 0.039 0.041 -9999 0 -0.26 4 4
CRKL 0.018 0.014 -9999 0 -0.24 1 1
PDGF/PDGFRA/Caveolin-3 0.004 0.052 -9999 0 -0.34 5 5
AP1 0.019 0.077 -9999 0 -0.44 1 1
mol:IP3 0.016 0.055 -9999 0 -0.38 4 4
PLCG1 0.016 0.055 -9999 0 -0.38 4 4
PDGF/PDGFRA/alphaV Integrin 0.017 0.054 -9999 0 -0.33 5 5
RAPGEF1 0.019 0 -9999 0 -10000 0 0
CRK 0.019 0 -9999 0 -10000 0 0
mol:Ca2+ 0.016 0.055 -9999 0 -0.38 4 4
CAV3 0 0 -9999 0 -10000 0 0
CAV1 0.019 0 -9999 0 -10000 0 0
SHC/Grb2/SOS1 0.041 0.042 -9999 0 -0.27 4 4
PDGF/PDGFRA/Shf 0.017 0.054 -9999 0 -0.37 4 4
FOS 0.019 0.076 -9999 0 -0.44 1 1
JUN -0.013 0.054 -9999 0 -0.2 10 10
oligodendrocyte development 0.017 0.053 -9999 0 -0.33 5 5
GRB2 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
mol:DAG 0.016 0.055 -9999 0 -0.38 4 4
PDGF/PDGFRA 0.004 0.076 -9999 0 -0.31 18 18
actin cytoskeleton reorganization 0.008 0.073 -9999 0 -0.38 8 8
SRF 0.024 0.003 -9999 0 -10000 0 0
SHC1 0.019 0 -9999 0 -10000 0 0
PI3K 0.029 0.046 -9999 0 -0.3 4 4
PDGF/PDGFRA/Crk/C3G 0.03 0.045 -9999 0 -0.3 4 4
JAK1 0.016 0.052 -9999 0 -0.37 4 4
ELK1/SRF 0.034 0.04 -9999 0 -0.27 4 4
SHB 0.006 0.071 -9999 0 -0.33 14 14
SHF 0.017 0.019 -9999 0 -0.24 2 2
CSNK2A1 0.016 0.007 -9999 0 -10000 0 0
GO:0007205 0.016 0.056 -9999 0 -0.41 4 4
SOS1 0.019 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.039 0.041 -9999 0 -0.26 4 4
PDGF/PDGFRA/SHB 0.008 0.073 -9999 0 -0.38 8 8
PDGF/PDGFRA/Caveolin-1 0.018 0.053 -9999 0 -0.37 4 4
ITGAV 0.018 0.014 -9999 0 -0.24 1 1
ELK1 0.022 0.049 -9999 0 -0.34 4 4
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
PDGF/PDGFRA/Crk 0.018 0.053 -9999 0 -0.37 4 4
JAK-STAT cascade 0.016 0.052 -9999 0 -0.37 4 4
cell proliferation 0.017 0.054 -9999 0 -0.37 4 4
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.031 0.009 -9999 0 -10000 0 0
PLK1 0.059 0.14 -9999 0 -10000 0 0
CDKN1B 0.18 0.024 -9999 0 -10000 0 0
FOXO3 0.053 0.15 -9999 0 -10000 0 0
KAT2B 0.019 0.044 -9999 0 -0.52 2 2
FOXO1/SIRT1 0.057 0.024 -9999 0 -10000 0 0
CAT 0.059 0.14 -9999 0 -10000 0 0
CTNNB1 0.019 0 -9999 0 -10000 0 0
AKT1 0.025 0.019 -9999 0 -10000 0 0
FOXO1 0.035 0.011 -9999 0 -10000 0 0
MAPK10 0.019 0.05 -9999 0 -10000 0 0
mol:GTP 0.003 0 -9999 0 -10000 0 0
FOXO4 0.1 0.03 -9999 0 -10000 0 0
response to oxidative stress 0.007 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.15 0.042 -9999 0 -10000 0 0
XPO1 0.02 0 -9999 0 -10000 0 0
EP300 0.02 0 -9999 0 -10000 0 0
BCL2L11 0.018 0.088 -9999 0 -1.4 1 1
FOXO1/SKP2 0.042 0.009 -9999 0 -10000 0 0
mol:GDP 0.007 0.02 -9999 0 -10000 0 0
RAN 0.021 0 -9999 0 -10000 0 0
GADD45A 0.14 0.031 -9999 0 -10000 0 0
YWHAQ 0.019 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.074 0.023 -9999 0 -10000 0 0
MST1 0.019 0.041 -9999 0 -0.36 3 3
CSNK1D 0.019 0 -9999 0 -10000 0 0
CSNK1E 0.019 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.052 0.034 -9999 0 -10000 0 0
YWHAB 0.019 0 -9999 0 -10000 0 0
MAPK8 0.044 0.009 -9999 0 -10000 0 0
MAPK9 0.043 0.009 -9999 0 -10000 0 0
YWHAG 0.019 0 -9999 0 -10000 0 0
YWHAE 0.019 0 -9999 0 -10000 0 0
YWHAZ 0.019 0 -9999 0 -10000 0 0
SIRT1 0.036 0.034 -9999 0 -10000 0 0
SOD2 0.15 0.051 -9999 0 -10000 0 0
RBL2 0.079 0.11 -9999 0 -10000 0 0
RAL/GDP 0.037 0.014 -9999 0 -10000 0 0
CHUK 0.022 0.019 -9999 0 -10000 0 0
Ran/GTP 0.019 0.001 -9999 0 -10000 0 0
CSNK1G2 0.019 0 -9999 0 -10000 0 0
RAL/GTP 0.045 0.014 -9999 0 -10000 0 0
CSNK1G1 0.019 0 -9999 0 -10000 0 0
FASLG -0.43 0.69 -9999 0 -1.4 120 120
SKP2 0.019 0 -9999 0 -10000 0 0
USP7 0.021 0 -9999 0 -10000 0 0
IKBKB 0.022 0.019 -9999 0 -10000 0 0
CCNB1 0.059 0.14 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.12 0.11 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.009 -9999 0 -10000 0 0
CSNK1A1 0.019 0 -9999 0 -10000 0 0
SGK1 0.022 0.019 -9999 0 -10000 0 0
CSNK1G3 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.001 -9999 0 -10000 0 0
ZFAND5 0.1 0.028 -9999 0 -10000 0 0
SFN -0.035 0.11 -9999 0 -0.24 74 74
CDK2 0.018 0 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.056 0.046 -9999 0 -10000 0 0
CREBBP 0.018 0 -9999 0 -10000 0 0
FBXO32 0.056 0.15 -9999 0 -1.2 1 1
BCL6 0.079 0.11 -9999 0 -10000 0 0
RALB 0.02 0 -9999 0 -10000 0 0
RALA 0.02 0 -9999 0 -10000 0 0
YWHAH 0.019 0 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.009 0.1 -9999 0 -0.38 20 20
AKT1 0.077 0.053 -9999 0 -10000 0 0
PTK2B 0.02 0.087 -9999 0 -0.33 1 1
VEGFR2 homodimer/Frs2 0.039 0.035 -9999 0 -10000 0 0
CAV1 0.019 0 -9999 0 -10000 0 0
CALM1 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.044 0.046 -9999 0 -10000 0 0
endothelial cell proliferation 0.009 0.13 -9999 0 -0.36 4 4
mol:Ca2+ 0.049 0.041 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.055 0.043 -9999 0 -10000 0 0
RP11-342D11.1 0.038 0.04 -9999 0 -10000 0 0
CDH5 0.018 0.014 -9999 0 -0.24 1 1
VEGFA homodimer 0.042 0.033 -9999 0 -10000 0 0
SHC1 0.019 0 -9999 0 -10000 0 0
SHC2 -0.063 0.12 -9999 0 -0.25 111 111
HRAS/GDP -0.004 0.018 -9999 0 -10000 0 0
SH2D2A -0.03 0.16 -9999 0 -0.54 32 32
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.02 0.12 -9999 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.017 0.1 -9999 0 -0.36 4 4
VEGFR1 homodimer 0.018 0.014 -9999 0 -0.24 1 1
SHC/GRB2/SOS1 0.064 0.04 -9999 0 -10000 0 0
GRB10 0.049 0.044 -9999 0 -10000 0 0
PTPN11 0.019 0 -9999 0 -10000 0 0
GRB2 0.019 0 -9999 0 -10000 0 0
PAK1 0.018 0.014 -9999 0 -0.24 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.062 0.042 -9999 0 -10000 0 0
HRAS 0.019 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.034 0.06 -9999 0 -10000 0 0
HIF1A 0.019 0 -9999 0 -10000 0 0
FRS2 0.017 0.024 -9999 0 -0.24 3 3
oxygen and reactive oxygen species metabolic process 0.053 0.042 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.014 0.036 -9999 0 -0.24 7 7
Nck/Pak 0.028 0.009 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.046 0.045 -9999 0 -10000 0 0
mol:GDP -0.005 0.02 -9999 0 -10000 0 0
mol:NADP 0.071 0.042 -9999 0 -0.33 1 1
eNOS/Hsp90 0.076 0.043 -9999 0 -0.31 1 1
PIK3R1 0.019 0 -9999 0 -10000 0 0
mol:IP3 0.05 0.042 -9999 0 -10000 0 0
HIF1A/ARNT 0.028 0 -9999 0 -10000 0 0
SHB 0.006 0.071 -9999 0 -0.33 14 14
VEGFA 0.006 0.061 -9999 0 -0.24 21 21
VEGFC 0.018 0.014 -9999 0 -0.24 1 1
FAK1/Vinculin 0.05 0.071 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.087 -9999 0 -10000 0 0
PTPN6 -0.12 0.24 -9999 0 -0.54 92 92
EPAS1 0.029 0.022 -9999 0 -10000 0 0
mol:L-citrulline 0.071 0.042 -9999 0 -0.33 1 1
ITGAV 0.018 0.014 -9999 0 -0.24 1 1
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.054 0.044 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.052 0.047 -9999 0 -10000 0 0
VEGFR2/3 heterodimer 0.038 0.04 -9999 0 -0.32 1 1
VEGFB 0.019 0 -9999 0 -10000 0 0
MAPK11 0.051 0.041 -9999 0 -10000 0 0
VEGFR2 homodimer 0.036 0.038 -9999 0 -10000 0 0
FLT1 0.018 0.014 -9999 0 -0.24 1 1
NEDD4 0.02 0.02 -9999 0 -0.24 2 2
MAPK3 0.014 0.073 -9999 0 -10000 0 0
MAPK1 0.014 0.073 -9999 0 -10000 0 0
VEGFA145/NRP2 0.019 0.046 -9999 0 -0.38 1 1
VEGFR1/2 heterodimer 0.04 0.035 -9999 0 -0.32 1 1
KDR 0.036 0.039 -9999 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.056 0.045 -9999 0 -10000 0 0
SRC 0.019 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.019 0.07 -9999 0 -10000 0 0
PI3K 0.069 0.058 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.046 0.045 -9999 0 -0.28 1 1
FES 0.043 0.059 -9999 0 -10000 0 0
GAB1 0.064 0.04 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.045 -9999 0 -10000 0 0
CTNNB1 0.019 0 -9999 0 -10000 0 0
SOS1 0.019 0 -9999 0 -10000 0 0
ARNT 0.019 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.077 0.041 -9999 0 -0.31 1 1
VEGFR2 homodimer/VEGFA homodimer/Yes 0.046 0.045 -9999 0 -10000 0 0
PI3K/GAB1 0.083 0.053 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.061 0.043 -9999 0 -10000 0 0
PRKACA 0.019 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.047 0.037 -9999 0 -0.28 1 1
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
CDC42 0.05 0.042 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.017 0.1 -9999 0 -0.35 4 4
PTK2 0.041 0.072 -9999 0 -10000 0 0
EDG1 0.038 0.04 -9999 0 -10000 0 0
mol:DAG 0.05 0.042 -9999 0 -10000 0 0
CaM/Ca2+ 0.055 0.039 -9999 0 -10000 0 0
MAP2K3 0.052 0.042 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.059 0.048 -9999 0 -10000 0 0
PLCG1 0.05 0.042 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.048 0.056 -9999 0 -10000 0 0
IQGAP1 0.019 0 -9999 0 -10000 0 0
YES1 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.045 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.035 0.15 -9999 0 -0.38 12 12
cell migration 0.073 0.064 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.067 0.055 -9999 0 -10000 0 0
FYN 0.019 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.047 0.039 -9999 0 -10000 0 0
mol:NO 0.071 0.042 -9999 0 -0.33 1 1
PXN 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.004 0.018 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.056 0.047 -9999 0 -10000 0 0
VHL 0.019 0 -9999 0 -10000 0 0
ITGB3 -0.032 0.14 -9999 0 -0.36 50 50
NOS3 0.073 0.045 -9999 0 -0.37 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck 0.003 0.079 -9999 0 -0.28 3 3
RAC1 0.019 0 -9999 0 -10000 0 0
PRKCA 0.05 0.048 -9999 0 -0.33 1 1
PRKCB -0.033 0.14 -9999 0 -0.34 16 16
VCL 0.019 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.043 0.042 -9999 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.047 -9999 0 -0.39 1 1
VEGFA165/NRP2 0.019 0.046 -9999 0 -0.38 1 1
MAPKKK cascade 0.075 0.041 -9999 0 -10000 0 0
NRP2 0.017 0.029 -9999 0 -0.54 1 1
VEGFC homodimer 0.018 0.014 -9999 0 -0.24 1 1
NCK1 0.019 0 -9999 0 -10000 0 0
ROCK1 0.019 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.05 0.071 -9999 0 -10000 0 0
MAP3K13 0.049 0.045 -9999 0 -10000 0 0
PDPK1 0.068 0.052 -9999 0 -10000 0 0
p38 MAPK signaling pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.022 -9999 0 -0.28 2 2
TRAF2/ASK1 0.024 0.026 -9999 0 -0.32 2 2
ATM 0.019 0 -9999 0 -10000 0 0
MAP2K3 0.042 0.02 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.042 0.05 -9999 0 -0.44 2 2
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.046 0.18 -9999 0 -0.53 43 43
TXN 0.01 0 -9999 0 -10000 0 0
CALM1 0.019 0 -9999 0 -10000 0 0
GADD45A 0.017 0.024 -9999 0 -0.24 3 3
GADD45B 0.019 0 -9999 0 -10000 0 0
MAP3K1 0.019 0 -9999 0 -10000 0 0
MAP3K6 0.018 0.014 -9999 0 -0.24 1 1
MAP3K7 0.019 0 -9999 0 -10000 0 0
MAP3K4 0.019 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.025 0.032 -9999 0 -0.38 2 2
TAK1/TAB family -0.002 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0.037 0 -9999 0 -10000 0 0
TRAF2 0.019 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.011 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.019 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.011 0.1 -9999 0 -0.33 31 31
CCM2 0.019 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.008 0.064 -9999 0 -0.32 9 9
MAPK11 0.019 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.018 0.063 -9999 0 -0.29 11 11
OSM/MEKK3 0.028 0 -9999 0 -10000 0 0
TAOK1 0.02 0 -9999 0 -10000 0 0
TAOK2 0.02 0 -9999 0 -10000 0 0
TAOK3 0.02 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.019 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.016 0.041 -9999 0 -0.54 2 2
MAP3K10 0.019 0 -9999 0 -10000 0 0
MAP3K3 0.019 0 -9999 0 -10000 0 0
TRX/ASK1 0.02 0.025 -9999 0 -0.32 2 2
GADD45/MTK1/MTK1 0.008 0.099 -9999 0 -0.26 42 42
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.043 0.042 -9999 0 -0.28 6 6
HDAC3 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.014 0 -9999 0 -10000 0 0
GATA1/HDAC5 0.014 0 -9999 0 -10000 0 0
GATA2/HDAC5 0.025 0.025 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.038 0 -9999 0 -10000 0 0
HDAC9 -0.008 0.12 -9999 0 -0.54 18 18
Glucocorticoid receptor/Hsp90/HDAC6 0.037 0.019 -9999 0 -0.32 1 1
HDAC4/ANKRA2 0.027 0.021 -9999 0 -0.38 1 1
HDAC5/YWHAB 0.028 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -10000 0 0
GATA2 0.014 0.036 -9999 0 -0.24 7 7
HDAC4/RFXANK 0.028 0 -9999 0 -10000 0 0
BCOR 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.019 0 -9999 0 -10000 0 0
HDAC5 0.019 0 -9999 0 -10000 0 0
GNB1/GNG2 0.021 0.052 -9999 0 -0.38 6 6
Histones 0.036 0.051 -9999 0 -10000 0 0
ADRBK1 0.019 0 -9999 0 -10000 0 0
HDAC4 0.019 0 -9999 0 -10000 0 0
XPO1 0.019 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.027 0.021 -9999 0 -0.38 1 1
HDAC4/Ubc9 0.028 0 -9999 0 -10000 0 0
HDAC7 0.019 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0 -9999 0 -10000 0 0
TUBA1B 0.019 0 -9999 0 -10000 0 0
HDAC6 0.019 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.028 0 -9999 0 -10000 0 0
CAMK4 -0.063 0.2 -9999 0 -0.54 54 54
Tubulin/HDAC6 0.038 0 -9999 0 -10000 0 0
SUMO1 0.019 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.019 0 -9999 0 -10000 0 0
GATA1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.019 0 -9999 0 -10000 0 0
NR3C1 0.019 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0 -9999 0 -10000 0 0
SRF 0.019 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.028 0 -9999 0 -10000 0 0
Tubulin 0.028 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.028 0 -9999 0 -10000 0 0
GNB1 0.019 0 -9999 0 -10000 0 0
RANGAP1 0.019 0 -9999 0 -10000 0 0
BCL6/BCoR 0.028 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.038 0 -9999 0 -10000 0 0
HDAC4/SRF -0.014 0.13 -9999 0 -0.32 54 54
HDAC4/ER alpha 0.02 0.056 -9999 0 -0.38 7 7
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.036 0.05 -9999 0 -10000 0 0
cell motility 0.038 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.019 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.028 0 -9999 0 -10000 0 0
BCL6 0.019 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.019 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.027 0.021 -9999 0 -0.38 1 1
ESR1 0.008 0.076 -9999 0 -0.54 7 7
HDAC6/HDAC11 0.028 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0 -9999 0 -10000 0 0
NPC 0.011 0 -9999 0 -10000 0 0
MEF2C 0.016 0.041 -9999 0 -0.54 2 2
RAN 0.019 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.055 0.023 -9999 0 -0.26 2 2
GNG2 0.01 0.07 -9999 0 -0.54 6 6
NCOR2 0.019 0 -9999 0 -10000 0 0
TUBB2A 0.019 0 -9999 0 -10000 0 0
HDAC11 0.019 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
RANBP2 0.019 0 -9999 0 -10000 0 0
ANKRA2 0.017 0.029 -9999 0 -0.54 1 1
RFXANK 0.019 0 -9999 0 -10000 0 0
nuclear import -0.037 0 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.038 0.07 -10000 0 -1.1 1 1
regulation of axonogenesis -0.031 0.013 -10000 0 -10000 0 0
myoblast fusion -0.025 0.035 0.41 1 -10000 0 1
mol:GTP 0.013 0.019 -10000 0 -0.23 1 1
regulation of calcium-dependent cell-cell adhesion -0.024 0.084 0.29 23 -10000 0 23
ARF1/GTP 0.025 0.015 -10000 0 -10000 0 0
mol:GM1 0.012 0.014 -10000 0 -0.17 1 1
mol:Choline 0.03 0.012 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.037 -10000 0 -0.44 1 1
MAPK3 0.031 0.028 -10000 0 -0.33 1 1
ARF6/GTP/NME1/Tiam1 0.025 0.084 -10000 0 -0.3 23 23
ARF1 0.019 0 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.035 -10000 0 -0.41 1 1
ARF1/GDP 0.034 0.033 -10000 0 -0.37 1 1
ARF6 0.018 0.011 -10000 0 -10000 0 0
RAB11A 0.019 0 -10000 0 -10000 0 0
TIAM1 -0.013 0.13 -10000 0 -0.54 22 22
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.031 0.028 -10000 0 -0.33 1 1
actin filament bundle formation -0.029 0.03 0.37 1 -10000 0 1
KALRN 0 0.037 -10000 0 -0.3 3 3
RAB11FIP3/RAB11A 0.028 0 -10000 0 -10000 0 0
RhoA/GDP 0.029 0.031 -10000 0 -0.38 1 1
NME1 0.02 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.031 -10000 0 -0.38 1 1
substrate adhesion-dependent cell spreading 0.013 0.019 -10000 0 -0.23 1 1
cortical actin cytoskeleton organization 0.029 0.038 -10000 0 -0.45 1 1
RAC1 0.019 0 -10000 0 -10000 0 0
liver development 0.013 0.019 -10000 0 -0.23 1 1
ARF6/GTP 0.013 0.019 -10000 0 -0.23 1 1
RhoA/GTP 0.025 0.015 -10000 0 -0.16 1 1
mol:GDP 0.026 0.037 -10000 0 -0.41 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.036 0.013 -10000 0 -10000 0 0
RHOA 0.019 0 -10000 0 -10000 0 0
PLD1 0.024 0.015 -10000 0 -10000 0 0
RAB11FIP3 0.019 0 -10000 0 -10000 0 0
tube morphogenesis 0.029 0.037 -10000 0 -0.44 1 1
ruffle organization 0.031 0.013 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.013 0.019 -10000 0 -0.23 1 1
PLD2 0.024 0.015 -10000 0 -0.16 1 1
PIP5K1A 0.031 0.013 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.03 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.038 -10000 0 -0.45 1 1
IGF1 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
NCK2 0.019 0 -9999 0 -10000 0 0
PTK2 0.019 0 -9999 0 -10000 0 0
CRKL 0.017 0.043 -9999 0 -0.26 4 4
GRB2/SOS1/SHC 0.038 0 -9999 0 -10000 0 0
HRAS 0.019 0 -9999 0 -10000 0 0
IRS1/Crk 0.019 0.043 -9999 0 -0.26 4 4
IGF-1R heterotetramer/IGF1/PTP1B 0.027 0.041 -9999 0 -0.3 4 4
AKT1 0.035 0.037 -9999 0 -10000 0 0
BAD 0.039 0.035 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.017 0.042 -9999 0 -0.26 4 4
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.02 0.043 -9999 0 -0.26 4 4
RAF1 0.047 0.033 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.034 0.043 -9999 0 -0.24 4 4
YWHAZ 0.019 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.013 0.047 -9999 0 -0.27 5 5
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
RPS6KB1 0.035 0.037 -9999 0 -10000 0 0
GNB2L1 0.019 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.038 0.03 -9999 0 -10000 0 0
PXN 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0.028 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.024 -9999 0 -0.2 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.048 0.034 -9999 0 -0.22 4 4
IGF-1R heterotetramer 0.014 0.03 -9999 0 -0.25 4 4
IGF-1R heterotetramer/IGF1/IRS/Nck 0.024 0.045 -9999 0 -0.26 4 4
Crk/p130 Cas/Paxillin 0.039 0.041 -9999 0 -0.22 4 4
IGF1R 0.014 0.03 -9999 0 -0.25 4 4
IGF1 0.007 0.067 -9999 0 -0.36 10 10
IRS2/Crk 0.027 0.041 -9999 0 -0.24 4 4
PI3K 0.033 0.044 -9999 0 -0.24 4 4
apoptosis -0.046 0.033 -9999 0 -10000 0 0
HRAS/GDP 0.014 0 -9999 0 -10000 0 0
PRKCD 0.036 0.044 -9999 0 -0.34 4 4
RAF1/14-3-3 E 0.054 0.032 -9999 0 -10000 0 0
BAD/14-3-3 0.048 0.034 -9999 0 -10000 0 0
PRKCZ 0.033 0.041 -9999 0 -0.23 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.002 0.018 -9999 0 -10000 0 0
PTPN1 0.019 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.031 0.047 -9999 0 -0.37 4 4
BCAR1 0.019 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.038 0.038 -9999 0 -0.25 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.019 0 -9999 0 -10000 0 0
IRS1/NCK2 0.02 0.043 -9999 0 -0.26 4 4
GRB10 0.017 0.019 -9999 0 -0.24 2 2
PTPN11 0.017 0.042 -9999 0 -0.26 4 4
IRS1 0.009 0.046 -9999 0 -0.27 5 5
IRS2 0.017 0.042 -9999 0 -0.26 4 4
IGF-1R heterotetramer/IGF1 0.014 0.053 -9999 0 -0.4 4 4
GRB2 0.019 0 -9999 0 -10000 0 0
PDPK1 0.03 0.039 -9999 0 -0.22 4 4
YWHAE 0.019 0 -9999 0 -10000 0 0
PRKD1 0.035 0.049 -9999 0 -0.34 5 5
SHC1 0.019 0 -9999 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A 0.032 0.014 -9999 0 -10000 0 0
BIRC5 0.019 0 -9999 0 -10000 0 0
NFKBIA 0.032 0.006 -9999 0 -10000 0 0
CPEB1 -0.023 0.15 -9999 0 -0.53 28 28
AKT1 0.032 0.006 -9999 0 -10000 0 0
NDEL1 0.019 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.03 0.005 -9999 0 -10000 0 0
NDEL1/TACC3 0.041 0.004 -9999 0 -10000 0 0
GADD45A 0.017 0.024 -9999 0 -0.24 3 3
GSK3B 0.018 0.004 -9999 0 -10000 0 0
PAK1/Aurora A 0.033 0.009 -9999 0 -10000 0 0
MDM2 0.015 0.033 -9999 0 -0.24 6 6
JUB 0.018 0.014 -9999 0 -0.24 1 1
TPX2 0.026 0 -9999 0 -10000 0 0
TP53 0.033 0.014 -9999 0 -10000 0 0
DLG7 0.022 0.006 -9999 0 -10000 0 0
AURKAIP1 0.019 0 -9999 0 -10000 0 0
ARHGEF7 0.019 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.043 0.005 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.03 0.005 -9999 0 -10000 0 0
AURKA 0.028 0.008 -9999 0 -10000 0 0
AURKB 0.017 0.025 -9999 0 -0.28 2 2
CDC25B 0.033 0.006 -9999 0 -10000 0 0
G2/M transition checkpoint 0.029 0.008 -9999 0 -10000 0 0
mRNA polyadenylation 0.006 0.082 -9999 0 -0.28 27 27
Aurora A/CPEB 0.006 0.083 -9999 0 -0.29 27 27
Aurora A/TACC1/TRAP/chTOG 0.052 0.017 -9999 0 -0.26 1 1
BRCA1 0.019 0 -9999 0 -10000 0 0
centrosome duplication 0.033 0.009 -9999 0 -10000 0 0
regulation of centrosome cycle 0.039 0.004 -9999 0 -10000 0 0
spindle assembly 0.051 0.016 -9999 0 -0.25 1 1
TDRD7 0.017 0.029 -9999 0 -0.54 1 1
Aurora A/RasGAP/Survivin 0.049 0.016 -9999 0 -0.24 1 1
CENPA 0.021 0.027 -9999 0 -0.34 2 2
Aurora A/PP2A 0.033 0.005 -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 0.033 0.014 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.028 0 -9999 0 -10000 0 0
RASA1 0.017 0.029 -9999 0 -0.54 1 1
Ajuba/Aurora A 0.03 0.008 -9999 0 -10000 0 0
mitotic prometaphase 0 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.008 -9999 0 -10000 0 0
TACC1 0.019 0 -9999 0 -10000 0 0
TACC3 0.019 0 -9999 0 -10000 0 0
Aurora A/Antizyme1 0.043 0.005 -9999 0 -10000 0 0
Aurora A/RasGAP 0.032 0.019 -9999 0 -0.32 1 1
OAZ1 0.019 0 -9999 0 -10000 0 0
RAN 0.019 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.004 -9999 0 -10000 0 0
GIT1 0.019 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.038 0.008 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.026 0 -9999 0 -10000 0 0
PPP2R5D 0.019 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.039 0.005 -9999 0 -10000 0 0
PAK1 0.018 0.014 -9999 0 -0.24 1 1
CKAP5 0.019 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.025 0.009 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.043 0.007 -9999 0 -10000 0 0
CDKN1B 0.041 0.008 -9999 0 -10000 0 0
CDKN1A 0.04 0.013 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.019 0 -9999 0 -10000 0 0
FOXO3 0.041 0.008 -9999 0 -10000 0 0
AKT1 0.035 0.008 -9999 0 -10000 0 0
BAD 0.019 0 -9999 0 -10000 0 0
AKT3 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.041 0.008 -9999 0 -10000 0 0
AKT1/ASK1 0.041 0.022 -9999 0 -10000 0 0
BAD/YWHAZ 0.038 0 -9999 0 -10000 0 0
RICTOR 0.017 0.029 -9999 0 -0.54 1 1
RAF1 0.019 0 -9999 0 -10000 0 0
JNK cascade -0.039 0.021 -9999 0 -10000 0 0
TSC1 0.041 0.008 -9999 0 -10000 0 0
YWHAZ 0.019 0 -9999 0 -10000 0 0
AKT1/RAF1 0.045 0.008 -9999 0 -10000 0 0
EP300 0.019 0 -9999 0 -10000 0 0
mol:GDP 0.035 0.008 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.041 0.008 -9999 0 -10000 0 0
YWHAQ 0.019 0 -9999 0 -10000 0 0
TBC1D4 0.024 0.023 -9999 0 -0.31 1 1
MAP3K5 0.016 0.041 -9999 0 -0.54 2 2
MAPKAP1 0.019 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.041 0.02 -9999 0 -10000 0 0
YWHAH 0.019 0 -9999 0 -10000 0 0
AKT1S1 0.041 0.008 -9999 0 -10000 0 0
CASP9 0.041 0.008 -9999 0 -10000 0 0
YWHAB 0.019 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.05 0.008 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.037 0.019 -9999 0 -0.32 1 1
YWHAE 0.019 0 -9999 0 -10000 0 0
SRC 0.019 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0.045 0.012 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0.003 -9999 0 -10000 0 0
CHUK 0.041 0.008 -9999 0 -10000 0 0
BAD/BCL-XL 0.059 0.01 -9999 0 -10000 0 0
mTORC2 0.023 0.017 -9999 0 -0.3 1 1
AKT2 0.02 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.057 0.023 -9999 0 -10000 0 0
PDPK1 0.019 0 -9999 0 -10000 0 0
MDM2 0.039 0.016 -9999 0 -10000 0 0
MAPKKK cascade -0.044 0.008 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.058 0.016 -9999 0 -10000 0 0
TSC1/TSC2 0.046 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.016 -9999 0 -10000 0 0
glucose import 0.019 0.039 -9999 0 -0.28 1 1
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.035 0.006 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.019 0.039 -9999 0 -0.28 1 1
GSK3A 0.041 0.008 -9999 0 -10000 0 0
FOXO1 0.041 0.008 -9999 0 -10000 0 0
GSK3B 0.041 0.008 -9999 0 -10000 0 0
SFN -0.035 0.11 -9999 0 -0.24 74 74
G1/S transition of mitotic cell cycle 0.046 0.007 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.042 0.029 -9999 0 -10000 0 0
PRKACA 0.019 0 -9999 0 -10000 0 0
KPNA1 0.019 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
YWHAG 0.019 0 -9999 0 -10000 0 0
RHEB 0.019 0 -9999 0 -10000 0 0
CREBBP 0.019 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.003 0.022 -10000 0 -10000 0 0
oxygen homeostasis 0.008 0.013 -10000 0 -10000 0 0
TCEB2 0.017 0.029 -10000 0 -0.54 1 1
TCEB1 0.019 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.093 0.065 -10000 0 -10000 0 0
EPO 0.14 0.15 -10000 0 -0.48 2 2
FIH (dimer) 0.026 0.032 -10000 0 -0.53 1 1
APEX1 0.028 0.014 -10000 0 -10000 0 0
SERPINE1 0.13 0.17 -10000 0 -0.54 3 3
FLT1 0.024 0.035 -10000 0 -10000 0 0
ADORA2A 0.11 0.18 -10000 0 -0.47 14 14
germ cell development 0.13 0.15 -10000 0 -0.58 2 2
SLC11A2 0.13 0.15 -10000 0 -0.56 2 2
BHLHE40 0.13 0.16 -10000 0 -0.51 3 3
HIF1AN 0.026 0.032 -10000 0 -0.53 1 1
HIF2A/ARNT/SIRT1 0.11 0.1 -10000 0 -0.29 1 1
ETS1 0.036 0.005 -10000 0 -10000 0 0
CITED2 0.021 0.027 -10000 0 -10000 0 0
KDR 0.021 0.045 -10000 0 -10000 0 0
PGK1 0.13 0.15 -10000 0 -0.56 2 2
SIRT1 0.019 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 -10000 0 -0.64 2 2
EPAS1 0.078 0.078 -10000 0 -0.28 1 1
SP1 0.028 0.002 -10000 0 -10000 0 0
ABCG2 0.11 0.21 -10000 0 -0.52 23 23
EFNA1 0.13 0.15 -10000 0 -0.56 2 2
FXN 0.13 0.15 -10000 0 -0.54 2 2
POU5F1 0.13 0.16 -10000 0 -0.61 2 2
neuron apoptosis -0.16 0.18 0.63 2 -10000 0 2
EP300 0.019 0 -10000 0 -10000 0 0
EGLN3 0.023 0.047 -10000 0 -0.38 4 4
EGLN2 0.027 0.012 -10000 0 -10000 0 0
EGLN1 0.027 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.019 -10000 0 -0.32 1 1
VHL 0.019 0 -10000 0 -10000 0 0
ARNT 0.029 0.014 -10000 0 -10000 0 0
SLC2A1 0.12 0.15 -10000 0 -0.54 2 2
TWIST1 0.075 0.18 -10000 0 -0.64 2 2
ELK1 0.028 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.12 0.1 -10000 0 -10000 0 0
VEGFA 0.13 0.16 -10000 0 -0.61 2 2
CREBBP 0.019 0 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.001 0.07 -10000 0 -0.24 28 28
CLTC 0.037 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.031 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0.03 0 -10000 0 -10000 0 0
EXOC4 0.019 0 -10000 0 -10000 0 0
CD59 0.033 0 -10000 0 -10000 0 0
CPE 0.015 0.04 -10000 0 -0.33 3 3
CTNNB1 0.019 0 -10000 0 -10000 0 0
membrane fusion 0.03 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.019 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.036 0 -10000 0 -10000 0 0
TSHR -0.008 0.097 -10000 0 -0.33 31 31
INS 0.013 0 -10000 0 -10000 0 0
BIN1 -0.005 0.11 -10000 0 -0.54 16 16
mol:Choline 0.03 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.019 0 -10000 0 -10000 0 0
mol:Ca2+ 0.03 0 -10000 0 -10000 0 0
JUP 0.03 0.013 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.022 0.066 -10000 0 -0.29 16 16
ARF6/GTP 0.014 0 -10000 0 -10000 0 0
CDH1 -0.028 0.098 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.014 0 -10000 0 -10000 0 0
MAPK8IP3 0.019 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0.014 0 -10000 0 -10000 0 0
EXOC2 0.019 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.049 0.016 -10000 0 -0.24 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.019 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.001 0.073 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.022 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.026 0 -10000 0 -10000 0 0
ACAP1 -0.016 0.064 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.027 0 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.015 -10000 0 -10000 0 0
JIP4/KLC1 0.036 0 -10000 0 -10000 0 0
EXOC1 0.019 0 -10000 0 -10000 0 0
exocyst 0.049 0.016 -10000 0 -0.24 1 1
RALA/GTP 0.014 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.026 0 -10000 0 -10000 0 0
receptor recycling 0.014 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.022 0 -10000 0 -10000 0 0
clathrin coat assembly 0.037 0 -10000 0 -10000 0 0
IL2RA -0.023 0.096 -10000 0 -10000 0 0
VAMP3 0.022 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.006 0.02 -10000 0 -10000 0 0
EXOC6 0.017 0.029 -10000 0 -0.54 1 1
PLD1 0.026 0 -10000 0 -10000 0 0
PLD2 0.026 0 -10000 0 -10000 0 0
EXOC5 0.019 0 -10000 0 -10000 0 0
PIP5K1C 0.036 0 -10000 0 -10000 0 0
SDC1 0.028 0.031 -10000 0 -10000 0 0
ARF6/GDP 0.024 0 -10000 0 -10000 0 0
EXOC7 0.019 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.002 0.075 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.03 0 -10000 0 -10000 0 0
endocytosis -0.021 0.066 0.29 16 -10000 0 16
SCAMP2 0.019 0 -10000 0 -10000 0 0
ADRB2 0.04 0.029 -10000 0 -10000 0 0
EXOC3 0.018 0.014 -10000 0 -0.24 1 1
ASAP2 0.019 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.032 0 -10000 0 -10000 0 0
KLC1 0.019 0 -10000 0 -10000 0 0
AVPR2 0.037 0.026 -10000 0 -10000 0 0
RALA 0.019 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.013 0.07 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.04 0.012 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.026 0.012 -9999 0 -10000 0 0
mol:DAG 0.033 0.057 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.029 0.035 -9999 0 -0.29 1 1
CaM/Ca2+ 0.042 0.054 -9999 0 -10000 0 0
HIF1A 0.029 0.008 -9999 0 -10000 0 0
GAB1 0.019 0 -9999 0 -10000 0 0
AKT1 0.052 0.055 -9999 0 -10000 0 0
PLCG1 0.033 0.057 -9999 0 -10000 0 0
NOS3 0.056 0.064 -9999 0 -0.59 1 1
CBL 0.019 0 -9999 0 -10000 0 0
mol:NO 0.056 0.062 -9999 0 -0.57 1 1
FLT1 0.036 0.015 -9999 0 -10000 0 0
PGF 0.001 0.099 -9999 0 -0.54 12 12
VEGFR1 homodimer/NRP2/VEGFR121 0.041 0.039 -9999 0 -0.28 1 1
CALM1 0.019 0 -9999 0 -10000 0 0
PIK3CA 0.018 0.014 -9999 0 -0.24 1 1
eNOS/Hsp90 0.064 0.062 -9999 0 -0.55 1 1
endothelial cell proliferation -0.029 0.14 -9999 0 -0.53 9 9
mol:Ca2+ 0.033 0.057 -9999 0 -10000 0 0
MAPK3 0.039 0.055 -9999 0 -10000 0 0
MAPK1 0.039 0.055 -9999 0 -10000 0 0
PIK3R1 0.019 0 -9999 0 -10000 0 0
PLGF homodimer 0.001 0.099 -9999 0 -0.54 12 12
PRKACA 0.019 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.019 0 -9999 0 -10000 0 0
VEGFA homodimer 0.004 0.061 -9999 0 -0.24 21 21
VEGFR1 homodimer/VEGFA homodimer 0.032 0.039 -9999 0 -0.32 1 1
platelet activating factor biosynthetic process 0.044 0.053 -9999 0 -10000 0 0
PI3K 0.049 0.056 -9999 0 -10000 0 0
PRKCA 0.034 0.058 -9999 0 -10000 0 0
PRKCB -0.052 0.15 -9999 0 -0.52 8 8
VEGFR1 homodimer/PLGF homodimer 0.029 0.064 -9999 0 -0.31 12 12
VEGFA 0.004 0.061 -9999 0 -0.24 21 21
VEGFB 0.019 0 -9999 0 -10000 0 0
mol:IP3 0.033 0.057 -9999 0 -10000 0 0
RASA1 0.043 0.02 -9999 0 -10000 0 0
NRP2 0.017 0.029 -9999 0 -0.54 1 1
VEGFR1 homodimer 0.036 0.015 -9999 0 -10000 0 0
VEGFB homodimer 0.019 0 -9999 0 -10000 0 0
NCK1 0.019 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.065 0.061 -9999 0 -0.55 1 1
PTPN11 0.019 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.047 0.055 -9999 0 -10000 0 0
mol:L-citrulline 0.056 0.062 -9999 0 -0.57 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.038 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.042 0.036 -9999 0 -0.28 1 1
CD2AP 0.017 0.029 -9999 0 -0.54 1 1
PI3K/GAB1 0.056 0.054 -9999 0 -10000 0 0
PDPK1 0.044 0.051 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.042 0.036 -9999 0 -10000 0 0
mol:NADP 0.056 0.062 -9999 0 -0.57 1 1
HSP90AA1 0.017 0.029 -9999 0 -0.54 1 1
ubiquitin-dependent protein catabolic process 0.049 0.037 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.039 0.022 -9999 0 -0.31 1 1
Arf1 pathway

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
coatomer protein complex 0.024 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0 -9999 0 -10000 0 0
AP2 0.028 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.027 0 -9999 0 -10000 0 0
CLTB 0.019 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.03 0 -9999 0 -10000 0 0
CD4 -0.034 0.16 -9999 0 -0.54 35 35
CLTA 0.019 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.015 0 -9999 0 -10000 0 0
ARF1/GTP 0.023 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.03 0 -9999 0 -10000 0 0
mol:Choline 0.015 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.019 0 -9999 0 -10000 0 0
DDEF1 0.015 0 -9999 0 -10000 0 0
ARF1/GDP 0.01 0 -9999 0 -10000 0 0
AP2M1 0.019 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.02 0 -9999 0 -10000 0 0
Rac/GTP 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.034 0 -9999 0 -10000 0 0
ARFIP2 0.017 0 -9999 0 -10000 0 0
COPA 0.019 0 -9999 0 -10000 0 0
RAC1 0.019 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.029 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.013 0 -9999 0 -10000 0 0
GGA3 0.019 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0 -9999 0 -10000 0 0
AP2A1 0.019 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.031 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.024 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.025 0 -9999 0 -10000 0 0
CYTH2 0.019 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.014 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 0.019 0.069 -9999 0 -0.2 35 35
PLD2 0.015 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.013 0 -9999 0 -10000 0 0
PIP5K1A 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.027 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.015 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.013 0 -9999 0 -10000 0 0
GOSR2 0.018 0 -9999 0 -10000 0 0
USO1 0.018 0 -9999 0 -10000 0 0
GBF1 0.018 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.027 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.005 0.1 -9999 0 -0.32 35 35
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0 -9999 0 -9999 0 0
SMAD2 0.015 0 -9999 0 -9999 0 0
SMAD3 0.046 0 -9999 0 -9999 0 0
SMAD3/SMAD4 0.056 0 -9999 0 -9999 0 0
SMAD4/Ubc9/PIASy 0.038 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 0.053 0 -9999 0 -9999 0 0
PPM1A 0.019 0 -9999 0 -9999 0 0
CALM1 0.019 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0.026 0 -9999 0 -9999 0 0
MAP3K1 0.019 0 -9999 0 -9999 0 0
TRAP-1/SMAD4 0.028 0 -9999 0 -9999 0 0
MAPK3 0.019 0 -9999 0 -9999 0 0
MAPK1 0.019 0 -9999 0 -9999 0 0
NUP214 0.019 0 -9999 0 -9999 0 0
CTDSP1 0.019 0 -9999 0 -9999 0 0
CTDSP2 0.019 0 -9999 0 -9999 0 0
CTDSPL 0.019 0 -9999 0 -9999 0 0
KPNB1 0.019 0 -9999 0 -9999 0 0
TGFBRAP1 0.019 0 -9999 0 -9999 0 0
UBE2I 0.019 0 -9999 0 -9999 0 0
NUP153 0.019 0 -9999 0 -9999 0 0
KPNA2 0.019 0 -9999 0 -9999 0 0
PIAS4 0.019 0 -9999 0 -9999 0 0
BARD1 signaling 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
BARD1/CSTF1 0.028 0.001 -9999 0 -10000 0 0
ATM 0.019 0 -9999 0 -10000 0 0
UBE2D3 0.019 0 -9999 0 -10000 0 0
PRKDC 0.019 0 -9999 0 -10000 0 0
ATR 0.019 0 -9999 0 -10000 0 0
UBE2L3 0.019 0 -9999 0 -10000 0 0
FANCD2 0.031 0 -9999 0 -10000 0 0
protein ubiquitination 0.051 0.001 -9999 0 -10000 0 0
XRCC5 0.019 0 -9999 0 -10000 0 0
XRCC6 0.019 0 -9999 0 -10000 0 0
M/R/N Complex 0.037 0.026 -9999 0 -0.32 2 2
MRE11A 0.019 0 -9999 0 -10000 0 0
DNA-PK 0.038 0 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.061 0 -9999 0 -10000 0 0
FANCF 0.019 0 -9999 0 -10000 0 0
BRCA1 0.019 0 -9999 0 -10000 0 0
CCNE1 0.019 0 -9999 0 -10000 0 0
CDK2/Cyclin E1 0.028 0 -9999 0 -10000 0 0
FANCG 0.019 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 0.028 0.001 -9999 0 -10000 0 0
FANCE 0.019 0 -9999 0 -10000 0 0
FANCC 0.019 0 -9999 0 -10000 0 0
NBN 0.019 0 -9999 0 -10000 0 0
FANCA 0.019 0 -9999 0 -10000 0 0
DNA repair 0.08 0 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0.028 0.001 -9999 0 -10000 0 0
BARD1/DNA-PK 0.049 0.001 -9999 0 -10000 0 0
FANCL 0.019 0 -9999 0 -10000 0 0
mRNA polyadenylation -0.028 0.001 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.045 0.02 -9999 0 -0.23 1 1
BRCA1/BACH1/BARD1/TopBP1 0.038 0.001 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.049 0.001 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.038 0.001 -9999 0 -10000 0 0
BRCA1/BACH1 0.019 0 -9999 0 -10000 0 0
BARD1 0.019 0.001 -9999 0 -10000 0 0
PCNA 0.019 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.038 0.001 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.038 0.001 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.049 0.001 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.056 0.001 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.028 0.001 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.043 0.001 -9999 0 -10000 0 0
FA complex 0.047 0 -9999 0 -10000 0 0
BARD1/EWS 0.028 0.001 -9999 0 -10000 0 0
RBBP8 0.026 0 -9999 0 -10000 0 0
TP53 0.019 0 -9999 0 -10000 0 0
TOPBP1 0.019 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.001 -9999 0 -10000 0 0
BRCA1/BARD1 0.056 0.001 -9999 0 -10000 0 0
CSTF1 0.019 0 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0.014 0.001 -9999 0 -10000 0 0
CDK2 0.019 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 0.019 0 -9999 0 -10000 0 0
RAD50 0.016 0.041 -9999 0 -0.54 2 2
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.028 0.001 -9999 0 -10000 0 0
EWSR1 0.019 0 -9999 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.019 0 -9999 0 -10000 0 0
PLK4 0.017 0.029 -9999 0 -0.54 1 1
regulation of centriole replication 0.025 0.021 -9999 0 -0.38 1 1
Circadian rhythm pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.059 0.009 -9999 0 -10000 0 0
CLOCK 0.022 0.014 -9999 0 -0.24 1 1
TIMELESS/CRY2 0.051 0.01 -9999 0 -10000 0 0
DEC1/BMAL1 0.016 0.021 -9999 0 -0.39 1 1
ATR 0.019 0 -9999 0 -10000 0 0
NR1D1 0.047 0.011 -9999 0 -10000 0 0
ARNTL 0.021 0.029 -9999 0 -0.53 1 1
TIMELESS 0.047 0.011 -9999 0 -10000 0 0
NPAS2 0.017 0.058 -9999 0 -0.53 4 4
CRY2 0.019 0 -9999 0 -10000 0 0
mol:CO -0.016 0 -9999 0 -10000 0 0
CHEK1 0.019 0 -9999 0 -10000 0 0
mol:HEME 0.016 0 -9999 0 -10000 0 0
PER1 0.019 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.053 0.043 -9999 0 -0.31 5 5
BMAL1/CLOCK 0.058 0.025 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.059 0.009 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.06 0.01 -9999 0 -10000 0 0
mol:NADPH 0.016 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.051 0.01 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.013 0.001 -9999 0 -10000 0 0
BUB1B 0.027 0.016 -9999 0 -0.27 1 1
PLK1 0.022 0.002 -9999 0 -10000 0 0
PLK1S1 0.019 0.001 -9999 0 -10000 0 0
KIF2A 0.027 0.002 -9999 0 -10000 0 0
regulation of mitotic centrosome separation 0.022 0.002 -9999 0 -10000 0 0
GOLGA2 0.019 0 -9999 0 -10000 0 0
Hec1/SPC24 0.038 0.031 -9999 0 -0.26 4 4
WEE1 0.031 0.001 -9999 0 -10000 0 0
cytokinesis 0.038 0.022 -9999 0 -0.39 1 1
PP2A-alpha B56 0.05 0 -9999 0 -10000 0 0
AURKA 0.02 0.001 -9999 0 -10000 0 0
PICH/PLK1 0.042 0.02 -9999 0 -0.22 2 2
CENPE 0.022 0.042 -9999 0 -0.28 7 7
RhoA/GTP 0.014 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.027 0.002 -9999 0 -10000 0 0
PPP2CA 0.019 0 -9999 0 -10000 0 0
FZR1 0.019 0 -9999 0 -10000 0 0
TPX2 0.019 0.001 -9999 0 -10000 0 0
PAK1 0.018 0.014 -9999 0 -0.24 1 1
SPC24 0.017 0.029 -9999 0 -0.54 1 1
FBXW11 0.019 0 -9999 0 -10000 0 0
CLSPN 0.018 0.023 -9999 0 -0.29 2 2
GORASP1 0.019 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.012 0.001 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.019 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.03 0 -9999 0 -10000 0 0
spindle elongation 0.022 0.002 -9999 0 -10000 0 0
ODF2 0.019 0 -9999 0 -10000 0 0
BUB1 0.031 0 -9999 0 -10000 0 0
TPT1 0.019 0.001 -9999 0 -10000 0 0
CDC25C 0.021 0.02 -9999 0 -0.36 1 1
CDC25B 0.02 0 -9999 0 -10000 0 0
SGOL1 0.013 0.001 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.033 0 -9999 0 -10000 0 0
CDC14B 0.013 0 -9999 0 -10000 0 0
CDC20 0.019 0 -9999 0 -10000 0 0
PLK1/PBIP1 0.02 0.033 -9999 0 -0.26 5 5
mitosis 0 0 -9999 0 -10000 0 0
FBXO5 0.026 0.001 -9999 0 -10000 0 0
CDC2 0.002 0 -9999 0 -10000 0 0
NDC80 0.014 0.05 -9999 0 -0.54 3 3
metaphase plate congression 0.02 0.001 -9999 0 -10000 0 0
ERCC6L 0.041 0.02 -9999 0 -0.23 2 2
NLP/gamma Tubulin 0.017 0.001 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.019 0.001 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0 -9999 0 -10000 0 0
PPP1R12A 0.019 0 -9999 0 -10000 0 0
interphase 0 0 -9999 0 -10000 0 0
PLK1/PRC1-2 0.041 0.016 -9999 0 -0.26 1 1
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.001 -9999 0 -10000 0 0
RAB1A 0.019 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.023 0.002 -9999 0 -10000 0 0
mitotic prometaphase 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.001 -9999 0 -10000 0 0
microtubule-based process 0.03 0.016 -9999 0 -0.28 1 1
Golgi organization 0.022 0.002 -9999 0 -10000 0 0
Cohesin/SA2 0.027 0.002 -9999 0 -10000 0 0
PPP1CB/MYPT1 0.028 0 -9999 0 -10000 0 0
KIF20A 0.017 0.029 -9999 0 -0.54 1 1
APC/C/CDC20 0.031 0.002 -9999 0 -10000 0 0
PPP2R1A 0.019 0 -9999 0 -10000 0 0
chromosome segregation 0.019 0.032 -9999 0 -0.25 5 5
PRC1 0.019 0 -9999 0 -10000 0 0
ECT2 0.027 0.002 -9999 0 -10000 0 0
C13orf34 0.024 0.002 -9999 0 -10000 0 0
NUDC 0.02 0.001 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.027 0.016 -9999 0 -0.27 1 1
spindle assembly 0.021 0.002 -9999 0 -10000 0 0
spindle stabilization 0.019 0.001 -9999 0 -10000 0 0
APC/C/HCDH1 0.024 0 -9999 0 -10000 0 0
MKLP2/PLK1 0.03 0.016 -9999 0 -0.28 1 1
CCNB1 0.02 0 -9999 0 -10000 0 0
PPP1CB 0.019 0 -9999 0 -10000 0 0
BTRC 0.019 0 -9999 0 -10000 0 0
ROCK2 0.03 0.001 -9999 0 -10000 0 0
TUBG1 0.019 0.001 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0 -9999 0 -10000 0 0
MLF1IP 0.008 0.048 -9999 0 -0.4 5 5
INCENP 0.019 0 -9999 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.019 0 -10000 0 -10000 0 0
mol:PIP3 -0.005 0.023 0.27 1 -10000 0 1
FRAP1 0.016 0.008 -10000 0 -10000 0 0
AKT1 0.023 0.024 0.23 1 -10000 0 1
INSR 0.018 0.014 -10000 0 -0.24 1 1
Insulin Receptor/Insulin 0.012 0.008 -10000 0 -10000 0 0
mol:GTP 0.036 0.02 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0 -10000 0 -10000 0 0
TSC2 0.019 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.005 -10000 0 -10000 0 0
TSC1 0.019 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.014 0.028 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.001 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.019 0 -10000 0 -10000 0 0
RPS6KB1 0.028 0.015 0.18 1 -10000 0 1
MAP3K5 0.01 0.028 -10000 0 -0.37 2 2
PIK3R1 0.019 0 -10000 0 -10000 0 0
apoptosis 0.01 0.028 -10000 0 -0.37 2 2
mol:LY294002 0 0 -10000 0 -10000 0 0
EIF4B 0.033 0.015 0.18 1 -10000 0 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.028 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.031 0.012 0.17 1 -10000 0 1
FKBP1A 0.019 0 -10000 0 -10000 0 0
RHEB/GTP 0.038 0.017 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -10000 0 0
FKBP12/Rapamycin 0.014 0.001 -10000 0 -10000 0 0
PDPK1 0.018 0.025 0.23 1 -10000 0 1
EIF4E 0.019 0 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.048 -10000 0 -0.61 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.021 0.001 -10000 0 -10000 0 0
TSC1/TSC2 0.041 0.023 0.22 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RPS6 0.019 0 -10000 0 -10000 0 0
PPP5C 0.019 0 -10000 0 -10000 0 0
EIF4G1 0.019 0 -10000 0 -10000 0 0
IRS1 0.002 0.029 -10000 0 -10000 0 0
INS 0 0 -10000 0 -10000 0 0
PTEN 0.017 0.029 -10000 0 -0.54 1 1
PDK2 0.017 0.026 0.23 1 -10000 0 1
EIF4EBP1 0.017 0.013 -10000 0 -10000 0 0
PIK3CA 0.018 0.014 -10000 0 -0.24 1 1
PPP2R5D 0.022 0.008 -10000 0 -10000 0 0
peptide biosynthetic process 0.02 0.007 -10000 0 -10000 0 0
RHEB 0.019 0 -10000 0 -10000 0 0
EIF4A1 0.019 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 1 -10000 0 1
EEF2 0.02 0.007 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.027 0.012 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.017 0.029 -9999 0 -0.54 1 1
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.038 0.015 -9999 0 -10000 0 0
HDAC4 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -0.21 1 1
SUMO1 0.019 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.031 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.019 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.019 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.039 0.015 -9999 0 -0.25 1 1
RANGAP1 0.019 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.046 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.025 0 -9999 0 -10000 0 0
Ran/GTP 0.034 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.015 0.033 -9999 0 -0.24 6 6
UBE2I 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0 -9999 0 -10000 0 0
NPC 0.011 0 -9999 0 -10000 0 0
PIAS2 0.019 0 -9999 0 -10000 0 0
PIAS1 0.019 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -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 0.028 0 -9999 0 -9999 0 0
FBXW11 0.019 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -9999 0 0
CHUK 0.019 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.056 0 -9999 0 -9999 0 0
NFKB1 0.019 0 -9999 0 -9999 0 0
MAP3K14 0.019 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.028 0 -9999 0 -9999 0 0
RELB 0.019 0 -9999 0 -9999 0 0
NFKB2 0.019 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.026 0 -9999 0 -9999 0 0
regulation of B cell activation 0.025 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 367 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z2.AA3V TCGA.Z2.AA3S TCGA.Z2.A8RT TCGA.YG.AA3P
109_MAP3K5 0.061 -0.017 0.061 -0.28
47_PPARGC1A 0.019 0.019 0.019 0.019
105_BMP4 0.019 0.019 0.019 0.019
105_BMP6 0.019 0.019 0.019 0.019
105_BMP7 -0.25 0.019 0.019 0.019
105_BMP2 0.019 0.019 0.019 0.019
131_RELN/VLDLR 0.049 0.049 0.049 0.049
30_TGFB1/TGF beta receptor Type II 0.018 0.018 0.018 0.018
84_STAT5B 0.043 0.041 -0.029 0.055
84_STAT5A 0.043 0.041 -0.029 0.055
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/SKCM-TM/14527799/SKCM-TM.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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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