PARADIGM pathway analysis of mRNASeq expression data
Bladder Urothelial Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1QN6637
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1QN6637
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 63 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
FOXM1 transcription factor network 154
Glypican 2 network 116
Aurora B signaling 104
Signaling events regulated by Ret tyrosine kinase 85
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 84
Signaling events mediated by the Hedgehog family 72
Nongenotropic Androgen signaling 71
Endothelins 69
IL4-mediated signaling events 66
Reelin signaling pathway 59
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 408 . 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 ( 408 ).

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
FOXM1 transcription factor network 0.3775 154 7898 51 -0.87 0.016 1000 -1000 -0.14 -1000
Glypican 2 network 0.2843 116 465 4 -0.16 -0.13 1000 -1000 -0.016 -1000
Aurora B signaling 0.2549 104 6986 67 -0.51 0.016 1000 -1000 -0.056 -1000
Signaling events regulated by Ret tyrosine kinase 0.2083 85 7038 82 -0.31 0.016 1000 -1000 -0.074 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2059 84 5733 68 -0.73 0.36 1000 -1000 -0.087 -1000
Signaling events mediated by the Hedgehog family 0.1765 72 3772 52 -0.18 0.18 1000 -1000 -0.043 -1000
Nongenotropic Androgen signaling 0.1740 71 3723 52 -0.26 0.14 1000 -1000 -0.047 -1000
Endothelins 0.1691 69 6640 96 -0.34 0.04 1000 -1000 -0.064 -1000
IL4-mediated signaling events 0.1618 66 6020 91 -0.78 0.55 1000 -1000 -0.11 -1000
Reelin signaling pathway 0.1446 59 3310 56 -0.24 0.041 1000 -1000 -0.074 -1000
IGF1 pathway 0.1422 58 3313 57 -0.25 0.047 1000 -1000 -0.079 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1422 58 4562 78 -0.26 0.088 1000 -1000 -0.049 -1000
Thromboxane A2 receptor signaling 0.1373 56 5937 105 -0.21 0.038 1000 -1000 -0.056 -1000
Aurora C signaling 0.1373 56 392 7 -0.22 0 1000 -1000 -0.026 -1000
PLK1 signaling events 0.1373 56 4771 85 -0.37 0.051 1000 -1000 -0.031 -1000
TCGA08_retinoblastoma 0.1324 54 432 8 -0.26 0.069 1000 -1000 -0.014 -1000
p75(NTR)-mediated signaling 0.1250 51 6479 125 -0.17 0.047 1000 -1000 -0.087 -1000
Signaling mediated by p38-alpha and p38-beta 0.1250 51 2278 44 -0.25 0.016 1000 -1000 -0.056 -1000
Ephrin A reverse signaling 0.1225 50 350 7 -0.071 0 1000 -1000 -0.017 -1000
Plasma membrane estrogen receptor signaling 0.1225 50 4311 86 -0.26 0.13 1000 -1000 -0.073 -1000
Ras signaling in the CD4+ TCR pathway 0.1201 49 842 17 -0.16 0.021 1000 -1000 -0.023 -1000
Fc-epsilon receptor I signaling in mast cells 0.1176 48 4739 97 -0.2 0.041 1000 -1000 -0.072 -1000
Rapid glucocorticoid signaling 0.1152 47 957 20 -0.24 0.037 1000 -1000 -0.014 -1000
Syndecan-1-mediated signaling events 0.1127 46 1568 34 -0.28 0.016 1000 -1000 -0.035 -1000
Integrins in angiogenesis 0.1127 46 3875 84 -0.28 0.033 1000 -1000 -0.081 -1000
HIF-1-alpha transcription factor network 0.1078 44 3408 76 -0.35 0.035 1000 -1000 -0.058 -1000
Glypican 1 network 0.1078 44 2117 48 -0.25 0.036 1000 -1000 -0.027 -1000
Glucocorticoid receptor regulatory network 0.1078 44 5048 114 -0.6 0.27 1000 -1000 -0.071 -1000
IL23-mediated signaling events 0.1054 43 2624 60 -0.61 0.016 1000 -1000 -0.13 -1000
amb2 Integrin signaling 0.1029 42 3501 82 -0.33 0.021 1000 -1000 -0.07 -1000
IL6-mediated signaling events 0.1029 42 3177 75 -0.24 0.069 1000 -1000 -0.055 -1000
BMP receptor signaling 0.1005 41 3382 81 -0.32 0.053 1000 -1000 -0.076 -1000
TCR signaling in naïve CD8+ T cells 0.1005 41 3839 93 -0.14 0.063 1000 -1000 -0.059 -1000
Calcium signaling in the CD4+ TCR pathway 0.1005 41 1298 31 -0.29 0.016 1000 -1000 -0.071 -1000
LPA receptor mediated events 0.0980 40 4174 102 -0.24 0.029 1000 -1000 -0.071 -1000
PDGFR-alpha signaling pathway 0.0956 39 1752 44 -0.34 0.033 1000 -1000 -0.054 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0931 38 4584 120 -0.32 0.18 1000 -1000 -0.062 -1000
S1P5 pathway 0.0907 37 633 17 -0.17 0.11 1000 -1000 -0.025 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0907 37 1958 52 -0.31 0.028 1000 -1000 -0.032 -1000
S1P1 pathway 0.0882 36 1319 36 -0.31 0.016 1000 -1000 -0.051 -1000
JNK signaling in the CD4+ TCR pathway 0.0858 35 598 17 -0.15 0.022 1000 -1000 -0.019 -1000
LPA4-mediated signaling events 0.0784 32 393 12 -0.16 0.022 1000 -1000 -0.018 -1000
Visual signal transduction: Cones 0.0784 32 1250 38 -0.12 0.019 1000 -1000 -0.056 -1000
Osteopontin-mediated events 0.0784 32 1237 38 -0.19 0.017 1000 -1000 -0.079 -1000
S1P4 pathway 0.0784 32 822 25 -0.17 0.032 1000 -1000 -0.032 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0760 31 1678 54 -0.2 0.031 1000 -1000 -0.086 -1000
TCGA08_p53 0.0760 31 222 7 -0.18 0.081 1000 -1000 -0.015 -1000
BCR signaling pathway 0.0760 31 3099 99 -0.18 0.038 1000 -1000 -0.076 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0760 31 2779 88 -0.23 0.041 1000 -1000 -0.097 -1000
Coregulation of Androgen receptor activity 0.0735 30 2339 76 -0.24 0.032 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.0735 30 2628 87 -0.42 0.037 1000 -1000 -0.1 -1000
Syndecan-2-mediated signaling events 0.0735 30 2134 69 -0.091 0.03 1000 -1000 -0.029 -1000
S1P3 pathway 0.0711 29 1242 42 -0.17 0.032 1000 -1000 -0.026 -1000
Arf6 signaling events 0.0662 27 1726 62 -0.24 0.03 1000 -1000 -0.045 -1000
Aurora A signaling 0.0662 27 1658 60 -0.36 0.031 1000 -1000 -0.044 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0637 26 897 34 -0.053 0.016 1000 -1000 -0.05 -1000
Class IB PI3K non-lipid kinase events 0.0637 26 78 3 -0.022 -1000 1000 -1000 -0.015 -1000
Wnt signaling 0.0613 25 178 7 -0.06 0.016 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0588 24 1490 61 -0.19 0.045 1000 -1000 -0.054 -1000
Syndecan-4-mediated signaling events 0.0588 24 1638 67 -0.19 0.017 1000 -1000 -0.076 -1000
FAS signaling pathway (CD95) 0.0564 23 1120 47 -0.56 0.02 1000 -1000 -0.034 -1000
Canonical Wnt signaling pathway 0.0539 22 1165 51 -0.19 0.081 1000 -1000 -0.05 -1000
Visual signal transduction: Rods 0.0539 22 1182 52 -0.21 0.016 1000 -1000 -0.073 -1000
ErbB2/ErbB3 signaling events 0.0490 20 1336 65 -0.23 0.027 1000 -1000 -0.057 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0490 20 577 28 -0.17 0.029 1000 -1000 -0.022 -1000
Noncanonical Wnt signaling pathway 0.0490 20 531 26 -0.092 0.016 1000 -1000 -0.043 -1000
ErbB4 signaling events 0.0466 19 1344 69 -0.23 0.039 1000 -1000 -0.067 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0466 19 643 33 -0.28 0.047 1000 -1000 -0.034 -1000
Effects of Botulinum toxin 0.0441 18 476 26 -0.076 0.016 1000 -1000 -0.054 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0417 17 1501 85 -0.22 0.024 1000 -1000 -0.06 -1000
FOXA2 and FOXA3 transcription factor networks 0.0417 17 818 46 -0.19 0.096 1000 -1000 -0.037 -1000
Caspase cascade in apoptosis 0.0392 16 1212 74 -0.055 0.044 1000 -1000 -0.029 -1000
Regulation of Androgen receptor activity 0.0392 16 1148 70 -0.21 0.03 1000 -1000 -0.059 -1000
Cellular roles of Anthrax toxin 0.0368 15 592 39 -0.1 0.017 1000 -1000 -0.018 -1000
Hedgehog signaling events mediated by Gli proteins 0.0368 15 1014 65 -0.17 0.066 1000 -1000 -0.047 -1000
Nectin adhesion pathway 0.0368 15 956 63 -0.05 0.03 1000 -1000 -0.063 -1000
EGFR-dependent Endothelin signaling events 0.0368 15 334 21 -0.069 0.023 1000 -1000 -0.062 -1000
IL2 signaling events mediated by STAT5 0.0343 14 318 22 -0.12 0.069 1000 -1000 -0.022 -1000
Regulation of nuclear SMAD2/3 signaling 0.0319 13 1803 136 -0.2 0.069 1000 -1000 -0.06 -1000
IL27-mediated signaling events 0.0319 13 712 51 -0.24 0.027 1000 -1000 -0.076 -1000
Signaling events mediated by PTP1B 0.0294 12 938 76 -0.14 0.035 1000 -1000 -0.062 -1000
IL2 signaling events mediated by PI3K 0.0294 12 710 58 -0.21 0.058 1000 -1000 -0.065 -1000
Signaling events mediated by HDAC Class III 0.0270 11 455 40 -0.23 0.026 1000 -1000 -0.032 -1000
IL1-mediated signaling events 0.0270 11 711 62 -0.094 0.075 1000 -1000 -0.081 -1000
Regulation of p38-alpha and p38-beta 0.0270 11 606 54 -0.16 0.042 1000 -1000 -0.05 -1000
Ephrin B reverse signaling 0.0245 10 491 48 -0.053 0.02 1000 -1000 -0.059 -1000
Syndecan-3-mediated signaling events 0.0245 10 376 35 -0.13 0.047 1000 -1000 -0.032 -1000
Regulation of Telomerase 0.0245 10 1078 102 -0.17 0.039 1000 -1000 -0.085 -1000
a4b1 and a4b7 Integrin signaling 0.0221 9 49 5 -0.003 0.01 1000 -1000 -0.015 -1000
Class I PI3K signaling events mediated by Akt 0.0221 9 643 68 -0.21 0.061 1000 -1000 -0.049 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0221 9 821 83 -0.28 0.043 1000 -1000 -0.064 -1000
EPHB forward signaling 0.0221 9 835 85 -0.047 0.04 1000 -1000 -0.076 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0221 9 715 74 -0.24 0.077 1000 -1000 -0.074 -1000
Signaling events mediated by PRL 0.0221 9 319 34 -0.099 0.026 1000 -1000 -0.02 -1000
E-cadherin signaling events 0.0221 9 45 5 -0.004 0.018 1000 -1000 -0.007 -1000
BARD1 signaling events 0.0196 8 504 57 -0.17 0.045 1000 -1000 -0.055 -1000
EPO signaling pathway 0.0196 8 452 55 -0.046 0.059 1000 -1000 -0.072 -1000
IFN-gamma pathway 0.0196 8 553 68 -0.17 0.054 1000 -1000 -0.079 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0196 8 308 37 -0.027 0.036 1000 -1000 -0.042 -1000
Signaling mediated by p38-gamma and p38-delta 0.0196 8 127 15 0 0.032 1000 -1000 -0.016 -1000
PDGFR-beta signaling pathway 0.0196 8 847 97 -0.062 0.054 1000 -1000 -0.073 -1000
PLK2 and PLK4 events 0.0172 7 22 3 0.003 0.016 1000 -1000 -0.013 -1000
Retinoic acid receptors-mediated signaling 0.0172 7 413 58 -0.079 0.033 1000 -1000 -0.069 -1000
Arf6 trafficking events 0.0172 7 518 71 -0.41 0.05 1000 -1000 -0.061 -1000
TRAIL signaling pathway 0.0147 6 328 48 -0.01 0.051 1000 -1000 -0.052 -1000
Insulin Pathway 0.0147 6 475 74 -0.26 0.042 1000 -1000 -0.078 -1000
Ceramide signaling pathway 0.0123 5 425 76 -0.24 0.046 1000 -1000 -0.031 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0123 5 267 45 -0.03 0.068 1000 -1000 -0.077 -1000
TCGA08_rtk_signaling 0.0123 5 155 26 -0.065 0.048 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 0.0123 5 403 76 -0.02 0.058 1000 -1000 -0.067 -1000
Signaling events mediated by HDAC Class II 0.0098 4 339 75 -0.089 0.039 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0098 4 192 43 -0.16 0.16 1000 -1000 -0.053 -1000
Paxillin-dependent events mediated by a4b1 0.0098 4 152 36 -0.036 0.037 1000 -1000 -0.058 -1000
p38 MAPK signaling pathway 0.0098 4 176 44 -0.04 0.046 1000 -1000 -0.057 -1000
FoxO family signaling 0.0074 3 200 64 -0.06 0.097 1000 -1000 -0.044 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0074 3 411 125 -0.05 0.097 1000 -1000 -0.085 -1000
Class I PI3K signaling events 0.0074 3 290 73 -0.06 0.042 1000 -1000 -0.056 -1000
E-cadherin signaling in keratinocytes 0.0074 3 143 43 -0.046 0.048 1000 -1000 -0.05 -1000
Canonical NF-kappaB pathway 0.0049 2 105 39 -0.019 0.091 1000 -1000 -0.07 -1000
Circadian rhythm pathway 0.0049 2 54 22 -0.016 0.053 1000 -1000 -0.032 -1000
Insulin-mediated glucose transport 0.0049 2 68 32 -0.14 0.042 1000 -1000 -0.046 -1000
ceramide signaling pathway 0.0049 2 113 49 -0.02 0.051 1000 -1000 -0.03 -1000
VEGFR1 specific signals 0.0049 2 138 56 -0.05 0.072 1000 -1000 -0.029 -1000
mTOR signaling pathway 0.0025 1 99 53 -0.008 0.04 1000 -1000 -0.056 -1000
Signaling events mediated by HDAC Class I 0.0025 1 116 104 -0.032 0.066 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 0.0025 1 31 31 0 0.055 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 14 23 0.008 0.054 1000 -1000 -0.042 -1000
Arf6 downstream pathway 0.0000 0 24 43 -0.038 0.039 1000 -1000 -0.032 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 13 27 -0.001 0.039 1000 -1000 -0.043 -1000
Arf1 pathway 0.0000 0 6 54 0 0.04 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.047 1000 -1000 -0.016 -1000
Total NA 3491 203346 7203 -24 -990 131000 -131000 -6.8 -131000
FOXM1 transcription factor network

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
NFATC3 -0.65 0.53 -9999 0 -1.1 209 209
PLK1 -0.13 0.18 -9999 0 -10000 0 0
BIRC5 -0.25 0.19 -9999 0 -1.5 1 1
HSPA1B -0.65 0.53 -9999 0 -1.1 208 208
MAP2K1 -0.007 0.032 -9999 0 -10000 0 0
BRCA2 -0.66 0.54 -9999 0 -1.1 215 215
FOXM1 -0.87 0.76 -9999 0 -1.4 229 229
XRCC1 -0.65 0.53 -9999 0 -1.1 207 207
FOXM1B/p19 -0.77 0.52 -9999 0 -1.1 253 253
Cyclin D1/CDK4 -0.6 0.48 -9999 0 -0.98 213 213
CDC2 -0.7 0.56 -9999 0 -1.1 228 228
TGFA -0.57 0.46 -9999 0 -0.94 206 206
SKP2 -0.66 0.53 -9999 0 -1.1 210 210
CCNE1 -0.073 0.19 -9999 0 -0.52 64 64
CKS1B -0.66 0.53 -9999 0 -1.1 215 215
RB1 -0.26 0.16 -9999 0 -0.44 58 58
FOXM1C/SP1 -0.76 0.63 -9999 0 -1.2 229 229
AURKB -0.16 0.19 -9999 0 -10000 0 0
CENPF -0.74 0.57 -9999 0 -1.1 234 234
CDK4 0.005 0.029 -9999 0 -0.51 1 1
MYC -0.57 0.47 -9999 0 -0.94 219 219
CHEK2 -0.008 0.042 -9999 0 -0.56 1 1
ONECUT1 -0.63 0.51 -9999 0 -1 223 223
CDKN2A -0.25 0.26 -9999 0 -0.5 205 205
LAMA4 -0.66 0.54 -9999 0 -1.1 212 212
FOXM1B/HNF6 -0.76 0.63 -9999 0 -1.2 223 223
FOS -0.78 0.62 -9999 0 -1.2 233 233
SP1 0.016 0.001 -9999 0 -10000 0 0
CDC25B -0.66 0.53 -9999 0 -1.1 213 213
response to radiation -0.023 0.03 -9999 0 -10000 0 0
CENPB -0.65 0.53 -9999 0 -1.1 209 209
CENPA -0.74 0.57 -9999 0 -1.2 229 229
NEK2 -0.74 0.57 -9999 0 -1.2 226 226
HIST1H2BA -0.66 0.53 -9999 0 -1.1 210 210
CCNA2 -0.13 0.23 -9999 0 -0.52 106 106
EP300 0.016 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.79 0.65 -9999 0 -1.3 226 226
CCNB2 -0.74 0.57 -9999 0 -1.2 240 240
CCNB1 -0.72 0.59 -9999 0 -1.2 223 223
ETV5 -0.66 0.53 -9999 0 -1.1 210 210
ESR1 -0.73 0.58 -9999 0 -1.2 226 226
CCND1 -0.61 0.5 -9999 0 -1 214 214
GSK3A 0.003 0.026 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.12 0.2 -9999 0 -0.37 144 144
CDK2 0.01 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.029 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.75 0.52 -9999 0 -1.1 240 240
GAS1 -0.78 0.57 -9999 0 -1.2 251 251
MMP2 -0.68 0.56 -9999 0 -1.1 217 217
RB1/FOXM1C -0.65 0.53 -9999 0 -1.1 218 218
CREBBP 0.016 0 -9999 0 -10000 0 0
Glypican 2 network

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
MDK -0.014 0.12 -9999 0 -0.51 23 23
GPC2 -0.16 0.25 -9999 0 -0.51 140 140
GPC2/Midkine -0.13 0.2 -9999 0 -0.38 151 151
neuron projection morphogenesis -0.13 0.2 -9999 0 -0.38 151 151
Aurora B signaling

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
Condensin I complex -0.16 0.15 -9999 0 -0.3 191 191
STMN1 -0.18 0.23 -9999 0 -0.4 195 195
Aurora B/RasGAP/Survivin -0.32 0.24 -9999 0 -0.45 297 297
Chromosomal passenger complex/Cul3 protein complex -0.18 0.16 -9999 0 -0.36 144 144
BIRC5 -0.36 0.24 -9999 0 -0.51 293 293
DES -0.51 0.37 -9999 0 -0.77 265 265
Aurora C/Aurora B/INCENP -0.11 0.15 -9999 0 -0.27 194 194
Aurora B/TACC1 -0.12 0.16 -9999 0 -0.3 185 185
Aurora B/PP2A -0.14 0.19 -9999 0 -0.35 184 184
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.021 0.045 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.004 -9999 0 -10000 0 0
NDC80 -0.25 0.29 -9999 0 -0.51 212 212
Cul3 protein complex -0.061 0.17 -9999 0 -0.36 98 98
KIF2C -0.12 0.1 -9999 0 -0.22 191 191
PEBP1 0.006 0.007 -9999 0 -10000 0 0
KIF20A -0.37 0.23 -9999 0 -0.51 300 300
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.14 0.19 -9999 0 -0.35 184 184
SEPT1 0.01 0.053 -9999 0 -0.52 4 4
SMC2 0.014 0.026 -9999 0 -0.51 1 1
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.058 0.071 -9999 0 -10000 0 0
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.068 0.1 -9999 0 -10000 0 0
AURKB -0.22 0.27 -9999 0 -0.51 184 184
AURKC -0.001 0.092 -9999 0 -0.51 13 13
CDCA8 -0.13 0.23 -9999 0 -0.52 109 109
cytokinesis -0.26 0.19 -9999 0 -0.42 209 209
Aurora B/Septin1 -0.24 0.19 -9999 0 -0.42 173 173
AURKA -0.14 0.24 -9999 0 -0.51 124 124
INCENP 0.005 0.027 -9999 0 -0.53 1 1
KLHL13 -0.11 0.24 -9999 0 -0.57 88 88
BUB1 -0.088 0.21 -9999 0 -0.51 80 80
hSgo1/Aurora B/Survivin -0.41 0.3 -9999 0 -0.53 317 317
EVI5 0.014 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.27 0.22 -9999 0 -0.46 206 206
SGOL1 -0.2 0.26 -9999 0 -0.51 172 172
CENPA -0.18 0.15 -9999 0 -0.31 195 195
NCAPG -0.22 0.26 -9999 0 -0.51 181 181
Aurora B/HC8 Proteasome -0.14 0.19 -9999 0 -0.35 184 184
NCAPD2 0.014 0.026 -9999 0 -0.51 1 1
Aurora B/PP1-gamma -0.14 0.19 -9999 0 -0.35 184 184
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.31 0.25 -9999 0 -0.51 253 253
NPM1 -0.067 0.085 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
KLHL9 -0.006 0.11 -9999 0 -0.57 15 15
mitotic prometaphase -0.009 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.19 -9999 0 -0.35 184 184
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.3 0.24 -9999 0 -0.49 224 224
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
NSUN2 -0.067 0.085 -9999 0 -10000 0 0
MYLK -0.19 0.2 -9999 0 -0.43 138 138
KIF23 -0.25 0.26 -9999 0 -0.51 202 202
VIM -0.15 0.2 -9999 0 -0.36 188 188
RACGAP1 0.006 0.052 -9999 0 -0.52 4 4
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.067 0.085 -9999 0 -10000 0 0
Chromosomal passenger complex -0.2 0.17 -9999 0 -0.34 215 215
Chromosomal passenger complex/EVI5 -0.32 0.29 -9999 0 -0.57 201 201
TACC1 0.011 0.05 -9999 0 -0.57 3 3
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.047 0.043 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.15 0.13 -9999 0 -0.39 33 33
JUN -0.11 0.15 -9999 0 -0.44 24 24
HRAS 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.19 -9999 0 -0.33 231 231
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.007 0.068 -9999 0 -0.51 7 7
RAP1A/GDP 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.18 -9999 0 -0.32 229 229
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.17 0.17 -9999 0 -0.32 228 228
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.16 0.15 -9999 0 -0.52 15 15
GRB7 -0.012 0.12 -9999 0 -0.53 21 21
RET51/GFRalpha1/GDNF -0.17 0.18 -9999 0 -0.32 229 229
MAPKKK cascade -0.15 0.14 -9999 0 -0.5 14 14
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.17 0.18 -9999 0 -0.33 230 230
lamellipodium assembly -0.15 0.13 -9999 0 -0.37 33 33
RET51/GFRalpha1/GDNF/SHC -0.17 0.18 -9999 0 -0.32 229 229
PIK3CA 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.17 0.17 -9999 0 -0.32 228 228
RET9/GFRalpha1/GDNF/Shank3 -0.17 0.17 -9999 0 -0.32 228 228
MAPK3 -0.13 0.16 -9999 0 -0.51 14 14
DOK1 0.014 0.026 -9999 0 -0.51 1 1
DOK6 -0.2 0.28 -9999 0 -0.57 148 148
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.16 0.18 -9999 0 -0.38 113 113
DOK5 -0.042 0.17 -9999 0 -0.56 40 40
GFRA1 -0.31 0.29 -9999 0 -0.57 228 228
MAPK8 -0.11 0.14 -9999 0 -0.42 17 17
HRAS/GTP -0.17 0.16 -9999 0 -0.57 14 14
tube development -0.15 0.16 -9999 0 -0.29 228 228
MAPK1 -0.13 0.16 -9999 0 -0.51 14 14
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.13 0.14 -9999 0 -0.25 228 228
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.26 0.25 -9999 0 -0.6 114 114
SHC1 0.014 0.026 -9999 0 -0.51 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.18 -9999 0 -0.32 229 229
RET51/GFRalpha1/GDNF/Dok5 -0.2 0.21 -9999 0 -0.36 239 239
PRKCA 0.008 0.064 -9999 0 -0.57 5 5
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
CREB1 -0.15 0.17 -9999 0 -0.29 228 228
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.13 0.14 -9999 0 -0.25 228 228
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.2 -9999 0 -0.34 232 232
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.009 0.12 -9999 0 -0.55 18 18
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade -0.11 0.14 -9999 0 -0.43 24 24
RET9/GFRalpha1/GDNF/FRS2 -0.17 0.17 -9999 0 -0.32 232 232
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.13 0.14 -9999 0 -0.25 228 228
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.13 0.15 -9999 0 -0.27 144 144
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.13 0.15 -9999 0 -0.27 141 141
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.13 0.16 -9999 0 -0.26 229 229
PI3K -0.19 0.23 -9999 0 -0.58 34 34
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.16 -9999 0 -0.29 228 228
GRB10 0.008 0.064 -9999 0 -0.57 5 5
activation of MAPKK activity -0.12 0.14 -9999 0 -0.4 17 17
RET51/GFRalpha1/GDNF/FRS2 -0.18 0.19 -9999 0 -0.33 230 230
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.001 0.09 -9999 0 -0.57 10 10
IRS2 -0.007 0.11 -9999 0 -0.57 16 16
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.13 0.16 -9999 0 -0.26 229 229
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.19 -9999 0 -0.33 229 229
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.004 0.045 -9999 0 -0.51 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.18 0.19 -9999 0 -0.33 231 231
Rac1/GTP -0.17 0.15 -9999 0 -0.45 33 33
RET9/GFRalpha1/GDNF -0.19 0.19 -9999 0 -0.36 228 228
GFRalpha1/GDNF -0.23 0.22 -9999 0 -0.42 228 228
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.001 0.11 -10000 0 -0.62 12 12
NFATC2 -0.12 0.28 -10000 0 -0.67 65 65
NFATC3 -0.093 0.13 -10000 0 -0.31 37 37
CD40LG -0.55 0.55 -10000 0 -1 194 194
ITCH 0.024 0.089 -10000 0 -0.41 1 1
CBLB 0.025 0.086 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.38 0.44 -10000 0 -1.1 91 91
JUNB 0.008 0.064 -10000 0 -0.57 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.031 0.087 -10000 0 -10000 0 0
T cell anergy -0.015 0.14 -10000 0 -0.4 42 42
TLE4 -0.073 0.25 -10000 0 -0.62 52 52
Jun/NFAT1-c-4/p21SNFT -0.46 0.56 -10000 0 -0.99 182 182
AP-1/NFAT1-c-4 -0.65 0.7 -10000 0 -1.2 199 199
IKZF1 -0.069 0.25 -10000 0 -0.64 43 43
T-helper 2 cell differentiation -0.24 0.35 -10000 0 -0.86 79 79
AP-1/NFAT1 -0.2 0.28 -10000 0 -0.52 142 142
CALM1 0.013 0.056 -10000 0 -10000 0 0
EGR2 -0.51 0.73 -10000 0 -1.6 110 110
EGR3 -0.73 0.83 -10000 0 -1.5 199 199
NFAT1/FOXP3 -0.086 0.23 -10000 0 -0.54 62 62
EGR1 -0.13 0.25 -10000 0 -0.57 100 100
JUN -0.013 0.12 -10000 0 -0.57 16 16
EGR4 -0.012 0.12 -10000 0 -0.55 19 19
mol:Ca2+ -0.004 0.061 -10000 0 -10000 0 0
GBP3 -0.062 0.22 -10000 0 -0.65 29 29
FOSL1 -0.024 0.15 -10000 0 -0.57 28 28
NFAT1-c-4/MAF/IRF4 -0.45 0.56 -10000 0 -0.94 203 203
DGKA -0.057 0.21 -10000 0 -0.55 40 40
CREM 0.015 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.48 0.55 -10000 0 -0.96 202 202
CTLA4 -0.075 0.24 -10000 0 -0.7 35 35
NFAT1-c-4 (dimer)/EGR1 -0.51 0.62 -10000 0 -1.1 203 203
NFAT1-c-4 (dimer)/EGR4 -0.46 0.56 -10000 0 -0.95 204 204
FOS -0.18 0.28 -10000 0 -0.58 129 129
IFNG -0.26 0.31 -10000 0 -0.84 65 65
T cell activation -0.26 0.32 -10000 0 -0.76 76 76
MAF 0 0.095 -10000 0 -0.57 11 11
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.36 0.5 0.78 201 -10000 0 201
TNF -0.44 0.52 -10000 0 -0.95 184 184
FASLG -0.69 0.8 -10000 0 -1.4 209 209
TBX21 -0.024 0.14 -10000 0 -0.57 24 24
BATF3 0.003 0.082 -10000 0 -0.54 9 9
PRKCQ -0.04 0.17 -10000 0 -0.56 39 39
PTPN1 -0.057 0.21 -10000 0 -0.52 48 48
NFAT1-c-4/ICER1 -0.46 0.54 -10000 0 -0.94 202 202
GATA3 -0.025 0.15 -10000 0 -0.56 29 29
T-helper 1 cell differentiation -0.23 0.32 -10000 0 -0.82 66 66
IL2RA -0.38 0.42 -10000 0 -0.95 108 108
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.057 0.21 -10000 0 -0.55 40 40
E2F1 -0.1 0.22 -10000 0 -0.5 97 97
PPARG -0.024 0.15 -10000 0 -0.56 28 28
SLC3A2 -0.057 0.21 -10000 0 -0.54 45 45
IRF4 -0.03 0.16 -10000 0 -0.56 32 32
PTGS2 -0.58 0.57 -10000 0 -1.1 199 199
CSF2 -0.57 0.53 -10000 0 -1 203 203
JunB/Fra1/NFAT1-c-4 -0.44 0.54 -10000 0 -0.93 202 202
IL4 -0.25 0.38 -10000 0 -0.93 76 76
IL5 -0.53 0.52 -10000 0 -1 191 191
IL2 -0.26 0.33 -10000 0 -0.78 74 74
IL3 -0.083 0.062 -10000 0 -10000 0 0
RNF128 -0.021 0.22 -10000 0 -0.62 46 46
NFATC1 -0.36 0.5 -10000 0 -0.78 201 201
CDK4 0.18 0.27 0.59 70 -10000 0 70
PTPRK -0.057 0.22 -10000 0 -0.56 39 39
IL8 -0.56 0.55 -10000 0 -1.1 196 196
POU2F1 0.016 0.002 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.059 0.24 -10000 0 -0.61 53 53
IHH -0.058 0.18 -10000 0 -0.52 52 52
SHH Np/Cholesterol/GAS1 -0.18 0.2 -10000 0 -0.34 221 221
LRPAP1 0.014 0.026 -10000 0 -0.51 1 1
dorsoventral neural tube patterning 0.18 0.2 0.34 221 -10000 0 221
SMO/beta Arrestin2 -0.05 0.17 -10000 0 -0.51 29 29
SMO -0.061 0.18 -10000 0 -0.5 37 37
AKT1 -0.005 0.086 -10000 0 -0.32 7 7
ARRB2 0.016 0 -10000 0 -10000 0 0
BOC -0.039 0.17 -10000 0 -0.57 38 38
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.06 0.18 -10000 0 -0.5 37 37
STIL -0.15 0.22 -10000 0 -0.47 89 89
DHH N/PTCH2 -0.019 0.13 -10000 0 -0.42 38 38
DHH N/PTCH1 -0.037 0.16 -10000 0 -0.5 26 26
PIK3CA 0.016 0 -10000 0 -10000 0 0
DHH -0.013 0.12 -10000 0 -0.57 19 19
PTHLH -0.11 0.36 -10000 0 -1 49 49
determination of left/right symmetry -0.06 0.18 -10000 0 -0.5 37 37
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
skeletal system development -0.11 0.36 -10000 0 -1 49 49
IHH N/Hhip -0.14 0.23 -10000 0 -0.44 144 144
DHH N/Hhip -0.11 0.21 -10000 0 -0.42 121 121
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.06 0.18 -10000 0 -0.5 37 37
pancreas development -0.14 0.26 -10000 0 -0.57 107 107
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K 0.022 0.021 -10000 0 -0.41 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.12 0.25 -10000 0 -0.57 98 98
somite specification -0.06 0.18 -10000 0 -0.5 37 37
SHH Np/Cholesterol/PTCH1 -0.12 0.19 -10000 0 -0.45 62 62
SHH Np/Cholesterol/PTCH2 -0.11 0.17 -10000 0 -0.32 163 163
SHH Np/Cholesterol/Megalin -0.16 0.2 -10000 0 -0.35 198 198
SHH -0.14 0.21 -10000 0 -0.41 150 150
catabolic process -0.032 0.16 -10000 0 -0.47 27 27
SMO/Vitamin D3 -0.12 0.2 -10000 0 -0.48 56 56
SHH Np/Cholesterol/Hhip -0.18 0.22 -10000 0 -0.38 212 212
LRP2 -0.094 0.21 -10000 0 -0.51 84 84
receptor-mediated endocytosis -0.15 0.21 -10000 0 -0.47 83 83
SHH Np/Cholesterol/BOC -0.13 0.18 -10000 0 -0.33 176 176
SHH Np/Cholesterol/CDO -0.14 0.18 -10000 0 -0.33 194 194
mesenchymal cell differentiation 0.18 0.22 0.37 212 -10000 0 212
mol:Vitamin D3 -0.12 0.19 -10000 0 -0.45 62 62
IHH N/PTCH2 -0.043 0.15 -10000 0 -0.34 71 71
CDON -0.066 0.2 -10000 0 -0.57 57 57
IHH N/PTCH1 -0.032 0.16 -10000 0 -0.47 27 27
Megalin/LRPAP1 -0.057 0.15 -10000 0 -0.36 85 85
PTCH2 -0.013 0.13 -10000 0 -0.57 20 20
SHH Np/Cholesterol -0.11 0.16 -10000 0 -0.32 150 150
PTCH1 -0.033 0.16 -10000 0 -0.47 27 27
HHIP -0.14 0.26 -10000 0 -0.57 107 107
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.099 0.17 -10000 0 -0.31 152 152
regulation of S phase of mitotic cell cycle -0.069 0.13 -10000 0 -0.25 149 149
GNAO1 -0.17 0.27 -10000 0 -0.57 129 129
HRAS 0.015 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.002 -10000 0 -10000 0 0
PELP1 0.015 0.002 -10000 0 -10000 0 0
AKT1 0.013 0.001 -10000 0 -10000 0 0
MAP2K1 -0.086 0.15 -10000 0 -0.35 55 55
T-DHT/AR -0.15 0.21 -10000 0 -0.42 148 148
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 129 129
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.011 0.05 -10000 0 -0.57 3 3
mol:GDP -0.16 0.21 -10000 0 -0.44 148 148
cell proliferation -0.16 0.23 -10000 0 -0.45 130 130
PIK3CA 0.016 0 -10000 0 -10000 0 0
FOS -0.26 0.4 -10000 0 -0.84 129 129
mol:Ca2+ -0.046 0.044 -10000 0 -0.085 193 193
MAPK3 -0.13 0.19 -10000 0 -0.48 55 55
MAPK1 -0.071 0.12 -10000 0 -0.27 54 54
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
mol:IP3 -0.001 0.002 -10000 0 -0.004 129 129
cAMP biosynthetic process 0.039 0.037 -10000 0 -10000 0 0
GNG2 0.007 0.07 -10000 0 -0.57 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 129 129
HRAS/GTP -0.11 0.14 -10000 0 -0.29 148 148
actin cytoskeleton reorganization -0.001 0.013 -10000 0 -0.27 1 1
SRC 0.015 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 129 129
PI3K 0.02 0.018 -10000 0 -0.35 1 1
apoptosis 0.14 0.22 0.45 129 -10000 0 129
T-DHT/AR/PELP1 -0.12 0.18 -10000 0 -0.35 148 148
HRAS/GDP -0.15 0.2 -10000 0 -0.41 148 148
CREB1 -0.16 0.24 -10000 0 -0.48 129 129
RAC1-CDC42/GTP -0.001 0.014 -10000 0 -0.27 1 1
AR -0.2 0.28 -10000 0 -0.57 148 148
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 -0.088 0.15 -10000 0 -0.34 55 55
RAC1-CDC42/GDP -0.14 0.19 -10000 0 -0.39 148 148
T-DHT/AR/PELP1/Src -0.099 0.16 -10000 0 -0.32 148 148
MAP2K2 -0.086 0.15 -10000 0 -0.35 55 55
T-DHT/AR/PELP1/Src/PI3K -0.07 0.14 -10000 0 -0.25 149 149
GNAZ -0.11 0.24 -10000 0 -0.57 89 89
SHBG 0.015 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.16 0.25 -10000 0 -0.46 147 147
mol:T-DHT 0 0.001 -10000 0 -0.003 74 74
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 0.013 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.16 0.21 -10000 0 -0.41 137 137
CDC42 0.016 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.009 0.23 -10000 0 -0.53 49 49
PTK2B 0.014 0.029 -10000 0 -0.57 1 1
mol:Ca2+ -0.013 0.22 -10000 0 -0.67 27 27
EDN1 0.04 0.12 -10000 0 -0.43 12 12
EDN3 -0.004 0.067 -10000 0 -0.51 7 7
EDN2 -0.055 0.18 -10000 0 -0.53 52 52
HRAS/GDP -0.072 0.24 -10000 0 -0.49 73 73
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.028 0.19 -10000 0 -0.41 55 55
ADCY4 -0.15 0.26 -10000 0 -0.59 70 70
ADCY5 -0.3 0.33 -10000 0 -0.64 163 163
ADCY6 -0.15 0.26 -10000 0 -0.6 69 69
ADCY7 -0.15 0.26 -10000 0 -0.57 75 75
ADCY1 -0.16 0.26 -10000 0 -0.6 76 76
ADCY2 -0.26 0.31 -10000 0 -0.64 134 134
ADCY3 -0.15 0.26 -10000 0 -0.6 69 69
ADCY8 -0.16 0.26 -10000 0 -0.6 70 70
ADCY9 -0.15 0.27 -10000 0 -0.61 70 70
arachidonic acid secretion -0.13 0.29 -10000 0 -0.49 120 120
ETB receptor/Endothelin-1/Gq/GTP -0.041 0.19 -10000 0 -0.43 56 56
GNAO1 -0.17 0.27 -10000 0 -0.57 129 129
HRAS 0.013 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.039 0.26 0.25 181 -0.51 46 227
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.32 0.24 92 -0.6 77 169
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.021 0.27 -10000 0 -0.64 47 47
EDNRB -0.052 0.19 -10000 0 -0.57 47 47
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.014 0.24 -10000 0 -0.52 54 54
CYSLTR1 -0.03 0.28 -10000 0 -0.63 57 57
SLC9A1 -0.003 0.13 -10000 0 -0.33 26 26
mol:GDP -0.085 0.25 -10000 0 -0.51 79 79
SLC9A3 -0.029 0.23 -10000 0 -0.56 50 50
RAF1 -0.13 0.28 -10000 0 -0.51 108 108
JUN -0.035 0.29 -10000 0 -0.9 32 32
JAK2 -0.01 0.24 -10000 0 -0.5 59 59
mol:IP3 -0.05 0.21 -10000 0 -0.47 59 59
ETA receptor/Endothelin-1 0.029 0.31 0.29 181 -0.55 66 247
PLCB1 -0.004 0.099 -10000 0 -0.57 12 12
PLCB2 0.009 0.042 -10000 0 -0.57 2 2
ETA receptor/Endothelin-3 -0.04 0.2 -10000 0 -0.47 65 65
FOS -0.28 0.48 -10000 0 -0.93 138 138
Gai/GDP -0.26 0.41 -10000 0 -0.84 129 129
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.076 0.28 -10000 0 -0.58 77 77
BCAR1 0.016 0.001 -10000 0 -10000 0 0
PRKCB1 -0.051 0.2 -10000 0 -0.46 59 59
GNAQ 0.014 0.009 -10000 0 -10000 0 0
GNAZ -0.11 0.24 -10000 0 -0.57 89 89
GNAL -0.24 0.29 -10000 0 -0.57 178 178
Gs family/GDP -0.22 0.25 -10000 0 -0.51 146 146
ETA receptor/Endothelin-1/Gq/GTP -0.031 0.22 -10000 0 -0.48 52 52
MAPK14 -0.026 0.16 -10000 0 -0.48 34 34
TRPC6 -0.016 0.23 -10000 0 -0.71 27 27
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.05 -10000 0 -0.57 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.035 0.17 -10000 0 -0.43 49 49
ETB receptor/Endothelin-2 -0.076 0.19 -10000 0 -0.43 90 90
ETB receptor/Endothelin-3 -0.04 0.14 -10000 0 -0.41 54 54
ETB receptor/Endothelin-1 -0.011 0.17 -10000 0 -0.39 59 59
MAPK3 -0.24 0.42 -10000 0 -0.78 141 141
MAPK1 -0.24 0.42 -10000 0 -0.78 141 141
Rac1/GDP -0.071 0.24 -10000 0 -0.48 73 73
cAMP biosynthetic process -0.24 0.29 -10000 0 -0.53 174 174
MAPK8 -0.031 0.26 -10000 0 -0.67 40 40
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.11 0.22 -10000 0 -0.43 99 99
p130Cas/CRK/Src/PYK2 -0.064 0.24 -10000 0 -0.54 61 61
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.071 0.24 -10000 0 -0.48 73 73
COL1A2 -0.062 0.35 -10000 0 -0.96 43 43
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.081 0.22 -10000 0 -0.43 107 107
mol:DAG -0.05 0.21 -10000 0 -0.47 59 59
MAP2K2 -0.18 0.33 -10000 0 -0.57 150 150
MAP2K1 -0.18 0.33 -10000 0 -0.58 146 146
EDNRA -0.037 0.26 -10000 0 -0.63 60 60
positive regulation of muscle contraction 0 0.21 -10000 0 -0.48 44 44
Gq family/GDP -0.13 0.2 -10000 0 -0.52 70 70
HRAS/GTP -0.1 0.24 -10000 0 -0.49 85 85
PRKCH -0.043 0.2 -10000 0 -0.48 52 52
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.046 0.2 -10000 0 -0.48 56 56
PRKCB -0.13 0.26 -10000 0 -0.5 113 113
PRKCE -0.042 0.2 -10000 0 -0.48 52 52
PRKCD -0.044 0.2 -10000 0 -0.48 53 53
PRKCG -0.057 0.2 -10000 0 -0.46 61 61
regulation of vascular smooth muscle contraction -0.34 0.56 -10000 0 -1.1 138 138
PRKCQ -0.072 0.23 -10000 0 -0.5 70 70
PLA2G4A -0.14 0.31 -10000 0 -0.54 121 121
GNA14 -0.069 0.2 -10000 0 -0.57 58 58
GNA15 0.011 0.05 -10000 0 -0.57 3 3
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.03 -10000 0 -0.57 1 1
Rac1/GTP 0.039 0.26 0.25 148 -0.51 45 193
MMP1 -0.19 0.23 0.32 4 -0.4 198 202
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.48 0.56 -10000 0 -1.2 126 126
STAT6 (cleaved dimer) -0.55 0.54 -10000 0 -1.2 153 153
IGHG1 -0.15 0.19 -10000 0 -0.37 75 75
IGHG3 -0.47 0.53 -10000 0 -1.1 141 141
AKT1 -0.21 0.31 -10000 0 -0.76 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.28 -10000 0 -0.81 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.32 -10000 0 -0.75 53 53
THY1 -0.48 0.56 -10000 0 -1.2 122 122
MYB -0.058 0.18 -10000 0 -0.51 57 57
HMGA1 0.005 0.072 -10000 0 -0.51 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.39 -10000 0 -0.78 110 110
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.32 -10000 0 -0.78 46 46
SP1 0.023 0.009 -10000 0 -10000 0 0
INPP5D 0.006 0.076 -10000 0 -0.57 7 7
SOCS5 0.029 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.49 0.57 -10000 0 -1.2 137 137
SOCS1 -0.29 0.35 -10000 0 -0.75 104 104
SOCS3 -0.31 0.46 -10000 0 -1.3 58 58
FCER2 -0.72 0.73 -10000 0 -1.4 192 192
PARP14 0.01 0.014 -10000 0 -10000 0 0
CCL17 -0.51 0.55 -10000 0 -1.2 128 128
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.24 -10000 0 -0.72 24 24
T cell proliferation -0.49 0.58 -10000 0 -1.2 133 133
IL4R/JAK1 -0.49 0.56 -10000 0 -1.2 128 128
EGR2 -0.67 0.72 -10000 0 -1.4 161 161
JAK2 -0.006 0.044 -10000 0 -0.61 1 1
JAK3 0.015 0.038 -10000 0 -0.52 2 2
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
JAK1 0.008 0.016 -10000 0 -10000 0 0
COL1A2 -0.2 0.4 -10000 0 -1.5 28 28
CCL26 -0.49 0.57 -10000 0 -1.2 128 128
IL4R -0.52 0.6 -10000 0 -1.3 129 129
PTPN6 0.025 0.029 -10000 0 -0.5 1 1
IL13RA2 -0.51 0.58 -10000 0 -1.2 130 130
IL13RA1 -0.006 0.044 -10000 0 -0.61 1 1
IRF4 -0.24 0.47 -10000 0 -1.2 64 64
ARG1 -0.12 0.19 -10000 0 -0.67 20 20
CBL -0.28 0.36 -10000 0 -0.76 97 97
GTF3A 0.024 0.005 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.01 0.057 -10000 0 -0.45 2 2
IRF4/BCL6 -0.19 0.43 -10000 0 -1.1 59 59
CD40LG -0.051 0.18 -10000 0 -0.57 45 45
MAPK14 -0.29 0.41 -10000 0 -0.89 84 84
mitosis -0.2 0.29 -10000 0 -0.71 49 49
STAT6 -0.58 0.7 -10000 0 -1.4 140 140
SPI1 0.002 0.092 -10000 0 -0.54 11 11
RPS6KB1 -0.19 0.28 -10000 0 -0.69 45 45
STAT6 (dimer) -0.58 0.7 -10000 0 -1.4 140 140
STAT6 (dimer)/PARP14 -0.56 0.63 -10000 0 -1.2 157 157
mast cell activation 0.011 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.33 -10000 0 -0.82 48 48
FRAP1 -0.21 0.31 -10000 0 -0.76 49 49
LTA -0.5 0.58 -10000 0 -1.2 131 131
FES 0.014 0.029 -10000 0 -0.57 1 1
T-helper 1 cell differentiation 0.55 0.65 1.3 140 -10000 0 140
CCL11 -0.51 0.59 -10000 0 -1.2 130 130
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.32 -10000 0 -0.8 45 45
IL2RG -0.008 0.12 -10000 0 -0.54 19 19
IL10 -0.51 0.59 -10000 0 -1.3 127 127
IRS1 0.001 0.09 -10000 0 -0.57 10 10
IRS2 -0.007 0.11 -10000 0 -0.57 16 16
IL4 -0.1 0.13 -10000 0 -10000 0 0
IL5 -0.49 0.56 -10000 0 -1.2 125 125
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.42 -10000 0 -0.87 130 130
COL1A1 -0.17 0.32 -10000 0 -1.7 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.58 -10000 0 -1.2 122 122
IL2R gamma/JAK3 0 0.096 -10000 0 -0.42 19 19
TFF3 -0.65 0.7 -10000 0 -1.4 160 160
ALOX15 -0.53 0.57 -10000 0 -1.2 135 135
MYBL1 0.011 0.051 -10000 0 -0.51 4 4
T-helper 2 cell differentiation -0.41 0.46 -10000 0 -0.95 135 135
SHC1 0.014 0.026 -10000 0 -0.51 1 1
CEBPB 0.016 0.032 -10000 0 -0.57 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.31 -10000 0 -0.72 53 53
mol:PI-3-4-5-P3 -0.21 0.31 -10000 0 -0.76 49 49
PI3K -0.22 0.33 -10000 0 -0.83 49 49
DOK2 -0.006 0.11 -10000 0 -0.56 15 15
ETS1 0.027 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.23 -10000 0 -0.74 19 19
ITGB3 -0.54 0.64 -10000 0 -1.3 136 136
PIGR -0.78 0.72 -10000 0 -1.4 208 208
IGHE 0.033 0.048 -10000 0 -0.22 1 1
MAPKKK cascade -0.15 0.23 -10000 0 -0.72 19 19
BCL6 0.021 0.01 -10000 0 -10000 0 0
OPRM1 -0.49 0.55 -10000 0 -1.2 129 129
RETNLB -0.49 0.56 -10000 0 -1.2 123 123
SELP -0.62 0.7 -10000 0 -1.4 155 155
AICDA -0.47 0.53 -10000 0 -1.1 126 126
Reelin signaling pathway

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
CDK5R1/CDK5 0.003 0.086 -9999 0 -0.36 22 22
VLDLR 0.001 0.09 -9999 0 -0.57 10 10
CRKL 0.013 0.036 -9999 0 -0.51 2 2
LRPAP1 0.014 0.026 -9999 0 -0.51 1 1
FYN 0.011 0.05 -9999 0 -0.57 3 3
ITGA3 0.007 0.068 -9999 0 -0.51 7 7
RELN/VLDLR/Fyn -0.11 0.18 -9999 0 -0.34 157 157
MAPK8IP1/MKK7/MAP3K11/JNK1 0.041 0.041 -9999 0 -10000 0 0
AKT1 -0.092 0.15 -9999 0 -0.44 27 27
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.07 0.2 -9999 0 -0.54 59 59
RELN/LRP8/DAB1 -0.19 0.23 -9999 0 -0.38 218 218
LRPAP1/LRP8 -0.048 0.15 -9999 0 -0.36 77 77
RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.38 171 171
DAB1/alpha3/beta1 Integrin -0.17 0.19 -9999 0 -0.51 70 70
long-term memory -0.23 0.27 -9999 0 -0.61 106 106
DAB1/LIS1 -0.18 0.19 -9999 0 -0.53 66 66
DAB1/CRLK/C3G -0.17 0.19 -9999 0 -0.51 67 67
PIK3CA 0.016 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.18 0.2 -9999 0 -0.54 66 66
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.12 0.24 -9999 0 -0.57 92 92
CDK5R1 -0.013 0.12 -9999 0 -0.51 22 22
RELN -0.2 0.28 -9999 0 -0.57 147 147
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
RELN/LRP8/Fyn -0.16 0.22 -9999 0 -0.38 191 191
GRIN2A/RELN/LRP8/DAB1/Fyn -0.24 0.27 -9999 0 -0.59 115 115
MAPK8 0.011 0.05 -9999 0 -0.57 3 3
RELN/VLDLR/DAB1 -0.15 0.2 -9999 0 -0.35 189 189
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.2 0.24 -9999 0 -0.42 183 183
RELN/LRP8 -0.16 0.22 -9999 0 -0.38 189 189
GRIN2B/RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.57 63 63
PI3K 0.022 0.021 -9999 0 -0.41 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.017 0.049 -9999 0 -0.36 7 7
RAP1A -0.13 0.2 -9999 0 -0.48 67 67
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.01 0.056 -9999 0 -0.55 4 4
CRLK/C3G 0.021 0.026 -9999 0 -0.36 2 2
GRIN2B -0.011 0.09 -9999 0 -0.51 13 13
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.077 0.14 -9999 0 -0.32 58 58
neuron adhesion -0.12 0.2 -9999 0 -0.44 71 71
LRP8 -0.082 0.2 -9999 0 -0.51 76 76
GSK3B -0.079 0.15 -9999 0 -0.41 27 27
RELN/VLDLR/DAB1/Fyn -0.13 0.19 -9999 0 -0.33 173 173
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.11 0.16 -9999 0 -0.28 171 171
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT -0.022 0.16 -9999 0 -0.51 36 36
neuron migration -0.13 0.21 -9999 0 -0.46 69 69
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.078 0.14 -9999 0 -0.32 58 58
RELN/VLDLR -0.14 0.21 -9999 0 -0.37 153 153
IGF1 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
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL -0.11 0.16 -10000 0 -0.29 185 185
GRB2/SOS1/SHC 0.031 0.016 -10000 0 -0.29 1 1
HRAS 0.016 0 -10000 0 -10000 0 0
IRS1/Crk -0.11 0.16 -10000 0 -0.29 183 183
IGF-1R heterotetramer/IGF1/PTP1B -0.14 0.16 -10000 0 -0.32 183 183
AKT1 -0.074 0.14 -10000 0 -0.45 10 10
BAD -0.062 0.14 -10000 0 -0.42 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.11 0.16 -10000 0 -0.29 183 183
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.16 -10000 0 -0.29 183 183
RAF1 -0.054 0.13 -10000 0 -0.39 10 10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.098 0.16 -10000 0 -0.51 9 9
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.18 -10000 0 -0.32 183 183
PIK3CA 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.074 0.14 -10000 0 -0.45 10 10
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.05 0.12 -10000 0 -0.34 10 10
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.12 -10000 0 -0.46 10 10
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.084 0.14 -10000 0 -0.37 10 10
IGF-1R heterotetramer -0.022 0.064 -10000 0 -0.63 3 3
IGF-1R heterotetramer/IGF1/IRS/Nck -0.11 0.16 -10000 0 -0.29 183 183
Crk/p130 Cas/Paxillin -0.087 0.15 -10000 0 -0.49 9 9
IGF1R -0.022 0.064 -10000 0 -0.63 3 3
IGF1 -0.25 0.3 -10000 0 -0.58 182 182
IRS2/Crk -0.11 0.18 -10000 0 -0.53 24 24
PI3K -0.098 0.16 -10000 0 -0.51 10 10
apoptosis 0.047 0.12 0.36 10 -10000 0 10
HRAS/GDP 0.012 0 -10000 0 -10000 0 0
PRKCD -0.14 0.21 -10000 0 -0.37 182 182
RAF1/14-3-3 E -0.04 0.12 -10000 0 -0.34 11 11
BAD/14-3-3 -0.05 0.13 -10000 0 -0.38 10 10
PRKCZ -0.076 0.14 -10000 0 -0.46 12 12
Crk/p130 Cas/Paxillin/FAK1 -0.08 0.093 -10000 0 -0.38 10 10
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.16 0.22 -10000 0 -0.4 183 183
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.16 -10000 0 -0.28 185 185
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.11 0.16 -10000 0 -0.29 183 183
GRB10 0.008 0.064 -10000 0 -0.57 5 5
PTPN11 -0.11 0.16 -10000 0 -0.29 183 183
IRS1 -0.13 0.18 -10000 0 -0.32 183 183
IRS2 -0.12 0.18 -10000 0 -0.31 184 184
IGF-1R heterotetramer/IGF1 -0.18 0.23 -10000 0 -0.43 183 183
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 -0.086 0.15 -10000 0 -0.48 10 10
YWHAE 0.014 0.029 -10000 0 -0.57 1 1
PRKD1 -0.15 0.23 -10000 0 -0.4 182 182
SHC1 0.014 0.026 -10000 0 -0.51 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.056 0.2 -10000 0 -0.4 91 91
CRKL -0.059 0.2 -10000 0 -0.42 90 90
HRAS -0.054 0.21 -10000 0 -0.46 47 47
mol:PIP3 -0.07 0.18 -10000 0 -0.4 90 90
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 -0.07 0.2 -10000 0 -0.44 91 91
FOXO3 -0.048 0.18 -10000 0 -0.38 90 90
AKT1 -0.061 0.2 -10000 0 -0.41 90 90
BAD -0.048 0.18 -10000 0 -0.38 90 90
megakaryocyte differentiation -0.075 0.21 -10000 0 -0.44 95 95
GSK3B -0.048 0.18 -10000 0 -0.38 90 90
RAF1 -0.032 0.17 -10000 0 -0.41 32 32
SHC1 0.014 0.026 -10000 0 -0.51 1 1
STAT3 -0.07 0.2 -10000 0 -0.44 90 90
STAT1 -0.19 0.47 -10000 0 -1 98 98
HRAS/SPRED1 -0.034 0.17 -10000 0 -0.41 32 32
cell proliferation -0.07 0.21 -10000 0 -0.44 91 91
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.069 0.2 -10000 0 -0.44 91 91
HRAS/SPRED2 -0.034 0.17 -10000 0 -0.41 32 32
LYN/TEC/p62DOK -0.084 0.18 -10000 0 -0.41 90 90
MAPK3 -0.007 0.13 -10000 0 -0.28 30 30
STAP1 -0.087 0.22 -10000 0 -0.46 92 92
GRAP2 -0.049 0.18 -10000 0 -0.57 45 45
JAK2 -0.2 0.37 -10000 0 -0.87 92 92
STAT1 (dimer) -0.18 0.46 -10000 0 -0.98 98 98
mol:Gleevec 0.001 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.095 0.19 -10000 0 -0.42 93 93
actin filament polymerization -0.071 0.2 -10000 0 -0.44 91 91
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.29 -10000 0 -0.62 92 92
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
CBL/CRKL/GRB2 -0.038 0.18 -10000 0 -0.37 90 90
PI3K -0.053 0.2 -10000 0 -0.41 90 90
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.24 0.56 -10000 0 -1.3 91 91
MAPK8 -0.072 0.21 -10000 0 -0.45 91 91
STAT3 (dimer) -0.068 0.2 -10000 0 -0.43 90 90
positive regulation of transcription -0.001 0.11 -10000 0 -0.24 20 20
mol:GDP -0.063 0.21 -10000 0 -0.4 100 100
PIK3C2B -0.07 0.2 -10000 0 -0.44 90 90
CBL/CRKL -0.047 0.19 -10000 0 -0.39 90 90
FER -0.072 0.21 -10000 0 -0.45 91 91
SH2B3 -0.07 0.2 -10000 0 -0.44 90 90
PDPK1 -0.057 0.17 -10000 0 -0.37 90 90
SNAI2 -0.076 0.21 -10000 0 -0.45 92 92
positive regulation of cell proliferation -0.13 0.34 -10000 0 -0.73 98 98
KITLG 0.009 0.068 -10000 0 -0.59 5 5
cell motility -0.13 0.34 -10000 0 -0.73 98 98
PTPN6 0.017 0.029 -10000 0 -0.52 1 1
EPOR -0.02 0.15 -10000 0 -0.56 2 2
STAT5A (dimer) -0.1 0.29 -10000 0 -0.62 92 92
SOCS1 0.014 0.026 -10000 0 -0.51 1 1
cell migration 0.088 0.22 0.46 96 -10000 0 96
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.028 0.14 -10000 0 -0.51 31 31
VAV1 -0.01 0.12 -10000 0 -0.56 18 18
GRB10 -0.073 0.21 -10000 0 -0.45 90 90
PTPN11 0.017 0.008 -10000 0 -10000 0 0
SCF/KIT -0.082 0.22 -10000 0 -0.47 91 91
GO:0007205 0.003 0.011 -10000 0 -10000 0 0
MAP2K1 -0.014 0.14 -10000 0 -0.31 30 30
CBL 0.016 0 -10000 0 -10000 0 0
KIT -0.26 0.59 -10000 0 -1.4 90 90
MAP2K2 -0.014 0.14 -10000 0 -0.31 30 30
SHC/Grb2/SOS1 -0.084 0.18 -10000 0 -0.41 90 90
STAT5A -0.1 0.3 -10000 0 -0.64 92 92
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation -0.074 0.21 -10000 0 -0.44 92 92
SHC/GRAP2 -0.025 0.14 -10000 0 -0.41 46 46
PTPRO -0.077 0.21 -10000 0 -0.44 95 95
SH2B2 -0.073 0.21 -10000 0 -0.44 91 91
DOK1 0.014 0.026 -10000 0 -0.51 1 1
MATK -0.09 0.22 -10000 0 -0.46 96 96
CREBBP 0.034 0.02 -10000 0 -10000 0 0
BCL2 -0.058 0.31 -10000 0 -1.4 16 16
Thromboxane A2 receptor signaling

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.013 0.12 -10000 0 -0.55 20 20
GNB1/GNG2 -0.08 0.089 -10000 0 -0.18 168 168
AKT1 -0.043 0.13 -10000 0 -0.2 84 84
EGF -0.018 0.12 -10000 0 -0.51 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.036 0.056 -10000 0 -0.37 1 1
mol:Ca2+ -0.087 0.18 -10000 0 -0.3 166 166
LYN 0.037 0.053 -10000 0 -0.37 1 1
RhoA/GTP -0.052 0.059 -10000 0 -0.14 20 20
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.1 0.21 -10000 0 -0.34 166 166
GNG2 0.007 0.07 -10000 0 -0.57 6 6
ARRB2 0.016 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.015 0.074 -10000 0 -0.38 5 5
G beta5/gamma2 -0.1 0.12 -10000 0 -0.24 168 168
PRKCH -0.1 0.21 -10000 0 -0.34 166 166
DNM1 0 0.095 -10000 0 -0.57 11 11
TXA2/TP beta/beta Arrestin3 -0.008 0.04 -10000 0 -0.25 10 10
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.013 0.12 -10000 0 -0.57 19 19
G12 family/GTP -0.13 0.14 -10000 0 -0.3 166 166
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.013 0.039 -10000 0 -0.54 2 2
RhoA/GTP/ROCK1 0.012 0.011 -10000 0 -10000 0 0
mol:GDP 0.038 0.12 0.3 14 -10000 0 14
mol:NADP 0.014 0.026 -10000 0 -0.51 1 1
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.12 0.25 -10000 0 -0.57 94 94
mol:IP3 -0.12 0.22 -10000 0 -0.37 166 166
cell morphogenesis 0.011 0.011 -10000 0 -10000 0 0
PLCB2 -0.17 0.29 -10000 0 -0.5 166 166
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.002 0.098 -10000 0 -0.39 3 3
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.027 0.08 -10000 0 -0.4 6 6
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.014 0.029 -10000 0 -0.57 1 1
PRKCB1 -0.12 0.22 -10000 0 -0.37 166 166
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.014 0.026 -10000 0 -0.51 1 1
TXA2/TXA2-R family -0.18 0.3 -10000 0 -0.53 166 166
LCK 0.034 0.063 -10000 0 -0.39 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.047 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.032 0.03 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.046 -10000 0 -10000 0 0
MAPK14 -0.055 0.15 -10000 0 -0.22 166 166
TGM2/GTP -0.14 0.25 -10000 0 -0.42 166 166
MAPK11 -0.055 0.15 -10000 0 -0.22 166 166
ARHGEF1 -0.042 0.11 -10000 0 -0.18 82 82
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade -0.12 0.23 -10000 0 -0.39 166 166
RAB11/GDP 0.016 0.002 -10000 0 -10000 0 0
ICAM1 -0.08 0.17 -10000 0 -0.28 169 169
cAMP biosynthetic process -0.11 0.21 -10000 0 -0.35 166 166
Gq family/GTP/EBP50 -0.005 0.088 -10000 0 -0.3 13 13
actin cytoskeleton reorganization 0.011 0.011 -10000 0 -10000 0 0
SRC 0.037 0.053 -10000 0 -0.37 1 1
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR 0.035 0.075 -10000 0 -0.31 3 3
VCAM1 -0.09 0.19 -10000 0 -0.3 166 166
TP beta/Gq family/GDP/G beta5/gamma2 0.015 0.074 -10000 0 -0.38 5 5
platelet activation -0.075 0.2 -10000 0 -0.3 166 166
PGI2/IP 0.01 0.021 -10000 0 -0.42 1 1
PRKACA 0.009 0.064 -10000 0 -0.27 20 20
Gq family/GDP/G beta5/gamma2 0.013 0.074 -10000 0 -0.36 5 5
TXA2/TP beta/beta Arrestin2 -0.015 0.087 -10000 0 -0.54 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.016 0.063 -10000 0 -0.25 21 21
mol:DAG -0.13 0.24 -10000 0 -0.42 166 166
EGFR -0.008 0.11 -10000 0 -0.54 17 17
TXA2/TP alpha -0.16 0.28 -10000 0 -0.48 166 166
Gq family/GTP -0.033 0.084 -10000 0 -0.23 61 61
YES1 0.037 0.053 -10000 0 -0.37 1 1
GNAI2/GTP -0.011 0.047 -10000 0 -0.43 1 1
PGD2/DP -0.01 0.09 -10000 0 -0.42 19 19
SLC9A3R1 -0.011 0.12 -10000 0 -0.51 21 21
FYN 0.036 0.059 -10000 0 -0.39 2 2
mol:NO 0.014 0.026 -10000 0 -0.51 1 1
GNA15 0.011 0.05 -10000 0 -0.57 3 3
PGK/cGMP -0.066 0.16 -10000 0 -0.35 95 95
RhoA/GDP 0.016 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.022 0.1 -10000 0 -0.54 6 6
NOS3 0.014 0.026 -10000 0 -0.51 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.1 0.21 -10000 0 -0.34 168 168
PRKCB -0.15 0.24 -10000 0 -0.42 168 168
PRKCE -0.098 0.21 -10000 0 -0.34 166 166
PRKCD -0.12 0.22 -10000 0 -0.38 166 166
PRKCG -0.12 0.23 -10000 0 -0.38 166 166
muscle contraction -0.16 0.28 -10000 0 -0.49 166 166
PRKCZ -0.099 0.21 -10000 0 -0.34 166 166
ARR3 0.003 0.006 -10000 0 -10000 0 0
TXA2/TP beta 0.012 0.063 -10000 0 -0.48 1 1
PRKCQ -0.12 0.22 -10000 0 -0.36 167 167
MAPKKK cascade -0.15 0.27 -10000 0 -0.46 166 166
SELE -0.13 0.24 -10000 0 -0.41 168 168
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.067 -10000 0 -0.47 1 1
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.068 0.2 -10000 0 -0.57 58 58
chemotaxis -0.21 0.35 -10000 0 -0.62 166 166
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.029 -10000 0 -0.57 1 1
Rac1/GTP 0.007 0.006 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.014 0.026 -9999 0 -0.51 1 1
Aurora C/Aurora B/INCENP -0.11 0.15 -9999 0 -0.27 194 194
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.035 0.037 -9999 0 -10000 0 0
AURKB -0.22 0.26 -9999 0 -0.51 184 184
AURKC -0.001 0.092 -9999 0 -0.51 13 13
PLK1 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
regulation of centriole-centriole cohesion 0.051 0.067 0.13 172 -10000 0 172
BUB1B -0.082 0.12 -10000 0 -0.23 135 135
PLK1 -0.021 0.051 -10000 0 -0.11 82 82
PLK1S1 -0.004 0.027 -10000 0 -0.097 1 1
KIF2A -0.009 0.046 -10000 0 -0.18 1 1
regulation of mitotic centrosome separation -0.021 0.051 -10000 0 -0.11 82 82
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.24 -10000 0 -0.41 195 195
WEE1 -0.017 0.055 -10000 0 -10000 0 0
cytokinesis -0.14 0.11 -10000 0 -0.25 153 153
PP2A-alpha B56 0.017 0.04 -10000 0 -10000 0 0
AURKA -0.02 0.049 -10000 0 -0.1 44 44
PICH/PLK1 -0.11 0.19 -10000 0 -0.38 107 107
CENPE -0.068 0.14 -10000 0 -0.33 86 86
RhoA/GTP 0.012 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.009 0.046 -10000 0 -0.18 1 1
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.016 0 -10000 0 -10000 0 0
TPX2 -0.038 0.052 -10000 0 -0.1 107 107
PAK1 0.013 0.029 -10000 0 -0.58 1 1
SPC24 -0.18 0.25 -10000 0 -0.51 153 153
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.034 0.058 -10000 0 -0.12 85 85
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.002 0.004 -10000 0 -0.011 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.01 0.026 -10000 0 -0.054 79 79
G2 phase of mitotic cell cycle -0.002 0.003 -10000 0 -0.009 5 5
STAG2 0.013 0.041 -10000 0 -0.57 2 2
GRASP65/GM130/RAB1/GTP 0.006 0.011 -10000 0 -10000 0 0
spindle elongation -0.021 0.051 -10000 0 -0.11 82 82
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.017 0.036 -10000 0 -10000 0 0
TPT1 -0.004 0.027 -10000 0 -0.097 1 1
CDC25C -0.058 0.061 -10000 0 -0.14 77 77
CDC25B 0.006 0.063 -10000 0 -0.51 6 6
SGOL1 -0.051 0.067 -10000 0 -0.13 172 172
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.077 0.11 -10000 0 -0.24 91 91
CDC14B 0.011 0.022 -10000 0 -0.43 1 1
CDC20 -0.28 0.26 -10000 0 -0.51 231 231
PLK1/PBIP1 -0.033 0.063 -10000 0 -0.29 16 16
mitosis -0.002 0.01 0.019 45 -0.017 80 125
FBXO5 -0.012 0.048 -10000 0 -0.23 3 3
CDC2 -0.003 0.006 -10000 0 -0.011 95 95
NDC80 -0.16 0.25 -10000 0 -0.51 135 135
metaphase plate congression -0.008 0.033 -10000 0 -10000 0 0
ERCC6L -0.096 0.18 -10000 0 -0.45 59 59
NLP/gamma Tubulin -0.006 0.027 -10000 0 -0.097 2 2
microtubule cytoskeleton organization -0.004 0.026 -10000 0 -0.097 1 1
G2/M transition DNA damage checkpoint -0.001 0.002 -10000 0 -10000 0 0
PPP1R12A 0.015 0.001 -10000 0 -10000 0 0
interphase -0.001 0.002 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.25 0.2 -10000 0 -0.34 302 302
GRASP65/GM130/RAB1/GTP/PLK1 0.009 0.04 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.014 0.049 -10000 0 -0.22 2 2
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.051 -10000 0 -0.3 1 1
microtubule-based process -0.22 0.15 -10000 0 -0.3 300 300
Golgi organization -0.021 0.051 -10000 0 -0.11 82 82
Cohesin/SA2 -0.026 0.039 -10000 0 -0.25 3 3
PPP1CB/MYPT1 0.018 0.009 -10000 0 -10000 0 0
KIF20A -0.37 0.23 -10000 0 -0.51 300 300
APC/C/CDC20 -0.17 0.17 -10000 0 -0.32 231 231
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.032 0.062 -10000 0 -0.29 16 16
PRC1 -0.086 0.21 -10000 0 -0.51 79 79
ECT2 -0.038 0.11 -10000 0 -0.34 43 43
C13orf34 -0.011 0.046 -10000 0 -0.22 2 2
NUDC -0.008 0.033 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.081 0.12 -10000 0 -0.23 135 135
spindle assembly -0.012 0.04 -10000 0 -0.085 45 45
spindle stabilization -0.004 0.026 -10000 0 -0.097 1 1
APC/C/HCDH1 0.019 0.019 -10000 0 -0.35 1 1
MKLP2/PLK1 -0.22 0.15 -10000 0 -0.3 300 300
CCNB1 -0.17 0.25 -10000 0 -0.5 145 145
PPP1CB 0.015 0.001 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 -0.007 0.065 -10000 0 -0.43 7 7
TUBG1 -0.004 0.027 -10000 0 -0.097 1 1
G2/M transition of mitotic cell cycle -0.078 0.1 -10000 0 -0.24 91 91
MLF1IP -0.006 0.073 -10000 0 -0.38 15 15
INCENP 0.014 0.026 -10000 0 -0.51 1 1
TCGA08_retinoblastoma

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
CDKN2B -0.029 0.15 -10000 0 -0.54 33 33
CDKN2C 0.039 0.045 -10000 0 -0.46 2 2
CDKN2A -0.26 0.27 -10000 0 -0.52 205 205
CCND2 0.053 0.079 0.23 34 -0.15 9 43
RB1 -0.052 0.086 0.16 2 -0.24 34 36
CDK4 0.069 0.08 0.24 36 -10000 0 36
CDK6 0.06 0.086 0.25 34 -0.18 7 41
G1/S progression 0.052 0.086 0.24 34 -0.16 2 36
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.023 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.12 0.21 -10000 0 -0.41 130 130
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.071 0.19 -10000 0 -0.58 25 25
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.24 -10000 0 -0.42 148 148
NT-4/5 (dimer)/p75(NTR) -0.1 0.21 -10000 0 -0.44 112 112
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.069 0.18 -10000 0 -0.56 23 23
IKBKG 0.016 0 -10000 0 -10000 0 0
BDNF -0.096 0.23 -10000 0 -0.57 78 78
MGDIs/NGR/p75(NTR)/LINGO1 -0.12 0.2 -10000 0 -0.35 156 156
FURIN 0.014 0.026 -10000 0 -0.51 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.21 -10000 0 -0.39 150 150
LINGO1 -0.009 0.11 -10000 0 -0.51 19 19
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.096 0.23 -10000 0 -0.57 78 78
NTRK1 0.005 0.068 -10000 0 -0.51 7 7
RTN4R -0.064 0.19 -10000 0 -0.51 62 62
neuron apoptosis -0.11 0.22 -10000 0 -0.52 61 61
IRAK1 0.016 0 -10000 0 -10000 0 0
SHC1 -0.1 0.21 -10000 0 -0.4 126 126
ARHGDIA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP 0.012 0 -10000 0 -10000 0 0
Gamma Secretase 0.047 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.083 0.2 -10000 0 -0.36 121 121
MAGEH1 0.013 0.041 -10000 0 -0.57 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.12 0.24 -10000 0 -0.41 144 144
Mammalian IAPs/DIABLO 0.017 0.09 -10000 0 -0.32 23 23
proNGF (dimer) -0.062 0.2 -10000 0 -0.57 54 54
MAGED1 0.016 0 -10000 0 -10000 0 0
APP 0.013 0.041 -10000 0 -0.57 2 2
NT-4/5 (dimer) -0.023 0.14 -10000 0 -0.57 27 27
ZNF274 0.016 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.077 0.18 -10000 0 -0.34 121 121
NGF -0.062 0.2 -10000 0 -0.57 54 54
cell cycle arrest -0.083 0.17 -10000 0 -0.51 27 27
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.057 0.16 -10000 0 -0.5 23 23
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.077 0.18 -10000 0 -0.36 112 112
NCSTN 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.1 0.21 -10000 0 -0.39 128 128
PSENEN 0.016 0 -10000 0 -10000 0 0
mol:ceramide -0.082 0.19 -10000 0 -0.35 121 121
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.037 0.14 -10000 0 -0.42 24 24
p75(NTR)/beta APP -0.078 0.18 -10000 0 -0.41 96 96
BEX1 -0.042 0.17 -10000 0 -0.56 39 39
mol:GDP -0.11 0.21 -10000 0 -0.4 126 126
NGF (dimer) -0.09 0.17 -10000 0 -0.31 132 132
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.095 0.18 -10000 0 -0.32 156 156
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
RAC1/GTP -0.087 0.18 -10000 0 -0.34 126 126
MYD88 0.016 0 -10000 0 -10000 0 0
CHUK 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.1 0.21 -10000 0 -0.4 128 128
RHOB 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.067 0.16 -10000 0 -0.36 97 97
NT3 (dimer) -0.095 0.23 -10000 0 -0.57 77 77
TP53 -0.075 0.18 -10000 0 -0.54 23 23
PRDM4 -0.082 0.19 -10000 0 -0.36 121 121
BDNF (dimer) -0.17 0.22 -10000 0 -0.36 213 213
PIK3CA 0.016 0 -10000 0 -10000 0 0
SORT1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.1 0.17 -10000 0 -0.57 25 25
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.082 0.19 -10000 0 -0.36 121 121
RHOC 0.016 0 -10000 0 -10000 0 0
XIAP 0.013 0.039 -10000 0 -0.54 2 2
MAPK10 -0.1 0.22 -10000 0 -0.53 58 58
DIABLO 0.016 0 -10000 0 -10000 0 0
SMPD2 -0.082 0.19 -10000 0 -0.36 121 121
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.1 0.21 -10000 0 -0.4 126 126
PSEN1 0.016 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.15 0.24 -10000 0 -0.46 149 149
MAPK8 -0.082 0.21 -10000 0 -0.52 48 48
MAPK9 -0.08 0.21 -10000 0 -0.52 48 48
APAF1 0.016 0 -10000 0 -10000 0 0
NTF3 -0.095 0.23 -10000 0 -0.57 77 77
NTF4 -0.023 0.14 -10000 0 -0.57 27 27
NDN -0.055 0.19 -10000 0 -0.57 49 49
RAC1/GDP 0.012 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.093 0.15 -10000 0 -0.53 23 23
p75 CTF/Sortilin/TRAF6/NRIF 0.04 0.015 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.1 0.21 -10000 0 -0.39 128 128
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.087 0.19 -10000 0 -0.57 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.2 -10000 0 -0.35 145 145
PRKACB 0.013 0.041 -10000 0 -0.57 2 2
proBDNF (dimer)/p75 ECD -0.06 0.17 -10000 0 -0.41 78 78
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.02 0.14 -10000 0 -0.56 25 25
BIRC2 0.013 0.036 -10000 0 -0.51 2 2
neuron projection morphogenesis -0.12 0.2 0.2 15 -0.4 113 128
BAD -0.082 0.21 -10000 0 -0.49 55 55
RIPK2 0.016 0 -10000 0 -10000 0 0
NGFR -0.12 0.25 -10000 0 -0.57 95 95
CYCS -0.069 0.18 -10000 0 -0.57 23 23
ADAM17 0.014 0.026 -10000 0 -0.51 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.082 0.19 -10000 0 -0.36 121 121
BCL2L11 -0.082 0.21 -10000 0 -0.49 55 55
BDNF (dimer)/p75(NTR) -0.15 0.24 -10000 0 -0.46 150 150
PI3K -0.082 0.19 -10000 0 -0.36 122 122
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.082 0.19 -10000 0 -0.36 121 121
NDNL2 0.016 0 -10000 0 -10000 0 0
YWHAE 0.014 0.029 -10000 0 -0.57 1 1
PRKCI 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.13 0.24 -10000 0 -0.47 126 126
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.082 0.19 -10000 0 -0.36 121 121
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.05 -10000 0 -0.57 3 3
PLG -0.003 0.056 -10000 0 -0.51 5 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.14 0.24 -10000 0 -0.48 102 102
SQSTM1 0.016 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0.041 -10000 0 -0.57 2 2
CASP3 -0.074 0.2 -10000 0 -0.45 55 55
E2F1 -0.11 0.22 -10000 0 -0.51 97 97
CASP9 0.016 0 -10000 0 -10000 0 0
IKK complex -0.076 0.13 -10000 0 -0.48 25 25
NGF (dimer)/TRKA -0.042 0.15 -10000 0 -0.4 61 61
MMP7 -0.11 0.23 -10000 0 -0.52 99 99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.069 0.18 -10000 0 -0.57 23 23
MMP3 -0.1 0.23 -10000 0 -0.55 84 84
APAF-1/Caspase 9 -0.082 0.13 -10000 0 -0.43 33 33
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.25 0.51 -9999 0 -1.1 100 100
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.058 0.15 -9999 0 -0.38 21 21
ATF2/c-Jun -0.049 0.2 -9999 0 -0.83 18 18
MAPK11 -0.058 0.15 -9999 0 -0.38 21 21
MITF -0.087 0.22 -9999 0 -0.4 109 109
MAPKAPK5 -0.059 0.18 -9999 0 -0.35 105 105
KRT8 -0.071 0.2 -9999 0 -0.38 106 106
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.088 0.22 -9999 0 -0.44 105 105
CEBPB -0.06 0.18 -9999 0 -0.36 105 105
SLC9A1 -0.059 0.18 -9999 0 -0.46 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.055 0.19 -9999 0 -0.51 23 23
p38alpha-beta/MNK1 -0.056 0.18 -9999 0 -0.49 21 21
JUN -0.048 0.2 -9999 0 -0.82 18 18
PPARGC1A -0.22 0.28 -9999 0 -0.53 122 122
USF1 -0.059 0.18 -9999 0 -0.35 105 105
RAB5/GDP/GDI1 -0.068 0.11 -9999 0 -0.35 21 21
NOS2 -0.089 0.25 -9999 0 -0.91 17 17
DDIT3 -0.059 0.18 -9999 0 -0.46 23 23
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.039 0.15 -9999 0 -0.4 21 21
p38alpha-beta/HBP1 -0.056 0.18 -9999 0 -0.49 21 21
CREB1 -0.063 0.2 -9999 0 -0.38 105 105
RAB5/GDP 0.012 0 -9999 0 -10000 0 0
EIF4E -0.043 0.16 -9999 0 -0.43 21 21
RPS6KA4 -0.059 0.18 -9999 0 -0.35 105 105
PLA2G4A -0.065 0.2 -9999 0 -0.53 35 35
GDI1 -0.059 0.18 -9999 0 -0.47 21 21
TP53 -0.079 0.22 -9999 0 -0.44 105 105
RPS6KA5 -0.069 0.2 -9999 0 -0.54 27 27
ESR1 -0.13 0.26 -9999 0 -0.67 45 45
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.073 0.2 -9999 0 -0.37 110 110
MEF2A -0.059 0.18 -9999 0 -0.35 105 105
EIF4EBP1 -0.065 0.2 -9999 0 -0.38 105 105
KRT19 -0.077 0.21 -9999 0 -0.56 32 32
ELK4 -0.059 0.18 -9999 0 -0.35 105 105
ATF6 -0.059 0.18 -9999 0 -0.35 105 105
ATF1 -0.063 0.2 -9999 0 -0.38 105 105
p38alpha-beta/MAPKAPK2 -0.056 0.18 -9999 0 -0.49 21 21
p38alpha-beta/MAPKAPK3 -0.056 0.18 -9999 0 -0.49 21 21
Ephrin A reverse signaling

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
MAPKKK cascade -0.047 0.14 -9999 0 -0.36 69 69
EFNA5 -0.006 0.11 -9999 0 -0.56 15 15
FYN -0.035 0.13 -9999 0 -0.31 72 72
neuron projection morphogenesis -0.047 0.14 -9999 0 -0.36 69 69
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.047 0.14 -9999 0 -0.36 69 69
EPHA5 -0.071 0.2 -9999 0 -0.57 56 56
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.026 0.13 -10000 0 -0.29 77 77
ER alpha/Gai/GDP/Gbeta gamma -0.19 0.34 -10000 0 -0.65 111 111
AKT1 -0.14 0.36 -10000 0 -0.89 73 73
PIK3CA 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.15 0.36 -10000 0 -0.92 73 73
mol:Ca2+ -0.042 0.18 -10000 0 -0.43 63 63
IGF1R 0.011 0.05 -10000 0 -0.57 3 3
E2/ER alpha (dimer)/Striatin -0.045 0.14 -10000 0 -0.35 73 73
SHC1 0.014 0.026 -10000 0 -0.51 1 1
apoptosis 0.13 0.34 0.84 73 -10000 0 73
RhoA/GTP -0.043 0.093 -10000 0 -0.47 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.17 0.25 -10000 0 -0.53 111 111
regulation of stress fiber formation -0.01 0.1 0.39 4 -10000 0 4
E2/ERA-ERB (dimer) -0.046 0.14 -10000 0 -0.35 75 75
KRAS 0.014 0.026 -10000 0 -0.51 1 1
G13/GTP -0.04 0.13 -10000 0 -0.32 73 73
pseudopodium formation 0.01 0.1 -10000 0 -0.39 4 4
E2/ER alpha (dimer)/PELP1 -0.045 0.14 -10000 0 -0.35 73 73
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.007 0.07 -10000 0 -0.57 6 6
GNAO1 -0.17 0.27 -10000 0 -0.57 129 129
HRAS 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.29 -10000 0 -0.68 74 74
E2/ER beta (dimer) 0.01 0.026 -10000 0 -0.37 2 2
mol:GDP -0.071 0.15 -10000 0 -0.39 73 73
mol:NADP -0.12 0.29 -10000 0 -0.68 74 74
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
mol:IP3 -0.045 0.19 -10000 0 -0.44 63 63
IGF-1R heterotetramer 0.011 0.05 -10000 0 -0.57 3 3
PLCB1 -0.053 0.19 -10000 0 -0.46 63 63
PLCB2 -0.046 0.18 -10000 0 -0.45 60 60
IGF1 -0.24 0.29 -10000 0 -0.57 182 182
mol:L-citrulline -0.12 0.29 -10000 0 -0.68 74 74
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.26 0.41 -10000 0 -0.83 129 129
JNK cascade 0.01 0.026 -10000 0 -0.36 2 2
BCAR1 0.016 0 -10000 0 -10000 0 0
ESR2 0.013 0.036 -10000 0 -0.51 2 2
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 -0.089 0.22 -10000 0 -0.57 73 73
Gq family/GDP/Gbeta gamma -0.002 0.11 -10000 0 -0.55 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.029 0.12 -10000 0 -0.3 47 47
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.17 0.25 -10000 0 -0.53 112 112
GNAZ -0.11 0.24 -10000 0 -0.57 89 89
E2/ER alpha (dimer) -0.065 0.16 -10000 0 -0.42 73 73
STRN 0.016 0 -10000 0 -10000 0 0
GNAL -0.24 0.29 -10000 0 -0.57 178 178
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.02 0.022 -10000 0 -0.3 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.05 -10000 0 -0.57 3 3
HBEGF -0.2 0.29 -10000 0 -0.6 113 113
cAMP biosynthetic process -0.17 0.18 -10000 0 -0.33 208 208
SRC -0.17 0.31 -10000 0 -0.61 111 111
PI3K 0.022 0.021 -10000 0 -0.41 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.064 0.13 -10000 0 -0.34 73 73
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.22 0.24 -10000 0 -0.49 153 153
Gs family/GTP -0.17 0.19 -10000 0 -0.34 208 208
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.015 -10000 0 -0.26 1 1
vasodilation -0.12 0.27 -10000 0 -0.64 74 74
mol:DAG -0.045 0.19 -10000 0 -0.44 63 63
Gs family/GDP/Gbeta gamma -0.15 0.18 -10000 0 -0.45 76 76
MSN 0.009 0.11 -10000 0 -0.43 4 4
Gq family/GTP -0.056 0.19 -10000 0 -0.48 60 60
mol:PI-3-4-5-P3 -0.14 0.35 -10000 0 -0.87 73 73
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.27 0.64 74 -10000 0 74
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
RhoA/GDP -0.066 0.14 -10000 0 -0.36 73 73
NOS3 -0.14 0.31 -10000 0 -0.73 74 74
GNA11 0.014 0.029 -10000 0 -0.57 1 1
MAPKKK cascade -0.11 0.29 -10000 0 -0.7 73 73
E2/ER alpha (dimer)/PELP1/Src -0.18 0.27 -10000 0 -0.57 111 111
ruffle organization 0.01 0.1 -10000 0 -0.39 4 4
ROCK2 0.001 0.11 -10000 0 -0.47 3 3
GNA14 -0.068 0.2 -10000 0 -0.57 58 58
GNA15 0.011 0.05 -10000 0 -0.57 3 3
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.22 0.29 -10000 0 -0.61 110 110
MMP2 -0.17 0.31 -10000 0 -0.64 101 101
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.13 0.24 -9999 0 -0.42 135 135
MAP3K8 0.008 0.05 -9999 0 -0.57 3 3
FOS -0.094 0.18 -9999 0 -0.44 57 57
PRKCA 0.004 0.065 -9999 0 -0.57 5 5
PTPN7 -0.004 0.096 -9999 0 -0.55 12 12
HRAS 0.015 0.002 -9999 0 -10000 0 0
PRKCB -0.16 0.26 -9999 0 -0.57 118 118
NRAS 0.015 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.021 0.021 -9999 0 -0.28 1 1
MAPK3 -0.049 0.13 -9999 0 -0.49 12 12
MAP2K1 -0.12 0.23 -9999 0 -0.45 120 120
ELK1 0.01 0.01 -9999 0 -10000 0 0
BRAF -0.11 0.22 -9999 0 -0.44 120 120
mol:GTP -0.002 0.003 -9999 0 -0.005 128 128
MAPK1 -0.049 0.13 -9999 0 -0.54 10 10
RAF1 -0.11 0.22 -9999 0 -0.44 120 120
KRAS 0.014 0.026 -9999 0 -0.51 1 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.041 -9999 0 -0.57 2 2
LAT2 -0.1 0.2 -9999 0 -0.46 66 66
AP1 -0.2 0.23 -9999 0 -0.52 112 112
mol:PIP3 -0.12 0.24 -9999 0 -0.51 76 76
IKBKB -0.076 0.15 -9999 0 -0.29 109 109
AKT1 -0.077 0.19 -9999 0 -0.44 59 59
IKBKG -0.076 0.15 -9999 0 -0.28 111 111
MS4A2 -0.15 0.26 -9999 0 -0.57 115 115
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.002 -9999 0 -10000 0 0
MAP3K1 -0.071 0.19 -9999 0 -0.41 68 68
mol:Ca2+ -0.082 0.18 -9999 0 -0.37 76 76
LYN 0.014 0.006 -9999 0 -10000 0 0
CBLB -0.099 0.19 -9999 0 -0.46 63 63
SHC1 0.014 0.026 -9999 0 -0.51 1 1
RasGAP/p62DOK -0.069 0.16 -9999 0 -0.31 119 119
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.006 0.076 -9999 0 -0.57 7 7
PLD2 -0.12 0.21 -9999 0 -0.52 62 62
PTPN13 -0.098 0.2 -9999 0 -0.48 62 62
PTPN11 0.012 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.048 0.16 -9999 0 -0.34 56 56
SYK 0.008 0.06 -9999 0 -0.59 4 4
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.16 0.21 -9999 0 -0.53 77 77
LAT -0.1 0.2 -9999 0 -0.45 66 66
PAK2 -0.089 0.21 -9999 0 -0.46 71 71
NFATC2 -0.16 0.26 -9999 0 -0.69 73 73
HRAS -0.11 0.23 -9999 0 -0.51 71 71
GAB2 0.014 0.029 -9999 0 -0.57 1 1
PLA2G1B 0.041 0.023 -9999 0 -10000 0 0
Fc epsilon R1 -0.19 0.24 -9999 0 -0.44 178 178
Antigen/IgE/Fc epsilon R1 -0.17 0.22 -9999 0 -0.4 178 178
mol:GDP -0.12 0.24 -9999 0 -0.54 74 74
JUN -0.007 0.11 -9999 0 -0.57 16 16
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.029 -9999 0 -0.57 1 1
FOS -0.17 0.27 -9999 0 -0.57 129 129
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.2 -9999 0 -0.38 123 123
CHUK -0.076 0.15 -9999 0 -0.28 110 110
KLRG1 -0.097 0.18 -9999 0 -0.44 63 63
VAV1 -0.11 0.21 -9999 0 -0.49 69 69
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.099 0.19 -9999 0 -0.46 63 63
negative regulation of mast cell degranulation -0.087 0.18 -9999 0 -0.42 64 64
BTK -0.13 0.26 -9999 0 -0.58 72 72
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.15 0.27 -9999 0 -0.66 71 71
GAB2/PI3K/SHP2 -0.13 0.17 -9999 0 -0.48 59 59
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.22 -9999 0 -0.56 63 63
RAF1 0.03 0.027 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.18 0.24 -9999 0 -0.62 70 70
FCER1G -0.004 0.11 -9999 0 -0.53 18 18
FCER1A -0.14 0.26 -9999 0 -0.58 105 105
Antigen/IgE/Fc epsilon R1/Fyn -0.16 0.21 -9999 0 -0.43 114 114
MAPK3 0.04 0.023 -9999 0 -10000 0 0
MAPK1 0.04 0.023 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.009 0.081 -9999 0 -0.59 3 3
DUSP1 -0.16 0.27 -9999 0 -0.57 119 119
NF-kappa-B/RelA -0.062 0.071 -9999 0 -0.22 7 7
actin cytoskeleton reorganization -0.1 0.2 -9999 0 -0.49 57 57
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.13 0.18 -9999 0 -0.46 68 68
FER -0.1 0.2 -9999 0 -0.46 66 66
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.082 0.16 -9999 0 -0.52 46 46
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.12 0.24 -9999 0 -0.55 72 72
cytokine secretion -0.045 0.051 -9999 0 -10000 0 0
SPHK1 -0.14 0.21 -9999 0 -0.47 83 83
PTK2 -0.11 0.21 -9999 0 -0.51 57 57
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.17 0.22 -9999 0 -0.55 78 78
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.11 0.23 -9999 0 -0.5 77 77
MAP2K2 0.036 0.024 -9999 0 -10000 0 0
MAP2K1 0.036 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.15 -9999 0 -0.4 63 63
MAP2K4 0.019 0.012 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.19 0.24 -9999 0 -0.49 125 125
mol:Choline -0.12 0.21 -9999 0 -0.51 62 62
SHC/Grb2/SOS1 -0.11 0.16 -9999 0 -0.44 58 58
FYN 0.011 0.05 -9999 0 -0.57 3 3
DOK1 0.014 0.026 -9999 0 -0.51 1 1
PXN -0.092 0.2 -9999 0 -0.47 57 57
HCLS1 -0.1 0.2 -9999 0 -0.46 64 64
PRKCB -0.12 0.21 -9999 0 -0.41 116 116
FCGR2B -0.027 0.15 -9999 0 -0.56 30 30
IGHE -0.003 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.088 0.19 -9999 0 -0.43 64 64
LCP2 0.011 0.05 -9999 0 -0.57 3 3
PLA2G4A -0.12 0.22 -9999 0 -0.5 73 73
RASA1 0.016 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.12 0.21 -9999 0 -0.51 62 62
IKK complex -0.042 0.12 -9999 0 -0.24 46 46
WIPF1 -0.002 0.099 -9999 0 -0.57 12 12
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.12 0.16 -10000 0 -0.3 180 180
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.098 0.17 -10000 0 -0.37 114 114
GNB1/GNG2 0.016 0.044 -10000 0 -0.35 6 6
GNB1 0.016 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 -0.14 0.17 -10000 0 -0.32 178 178
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 0.037 0.042 0.084 178 -10000 0 178
GNAL -0.24 0.29 -10000 0 -0.57 178 178
GNG2 0.007 0.07 -10000 0 -0.57 6 6
CRH -0.14 0.23 -10000 0 -0.51 114 114
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.031 -10000 0 -0.36 3 3
MAPK11 0.01 0 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.016 0 -9999 0 -10000 0 0
CCL5 -0.03 0.15 -9999 0 -0.55 33 33
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.12 0.14 -9999 0 -0.35 59 59
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 -0.11 0.13 -9999 0 -0.33 59 59
Syndecan-1/Syntenin -0.11 0.13 -9999 0 -0.33 59 59
MAPK3 -0.083 0.12 -9999 0 -0.4 13 13
HGF/MET -0.077 0.18 -9999 0 -0.4 96 96
TGFB1/TGF beta receptor Type II 0.016 0 -9999 0 -10000 0 0
BSG 0.016 0 -9999 0 -10000 0 0
keratinocyte migration -0.11 0.13 -9999 0 -0.32 59 59
Syndecan-1/RANTES -0.13 0.16 -9999 0 -0.38 73 73
Syndecan-1/CD147 -0.095 0.12 -9999 0 -0.36 24 24
Syndecan-1/Syntenin/PIP2 -0.1 0.12 -9999 0 -0.32 59 59
LAMA5 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.12 0.11 -9999 0 -0.31 59 59
MMP7 -0.11 0.23 -9999 0 -0.52 99 99
HGF -0.12 0.24 -9999 0 -0.56 94 94
Syndecan-1/CASK -0.12 0.13 -9999 0 -0.34 59 59
Syndecan-1/HGF/MET -0.16 0.18 -9999 0 -0.44 78 78
regulation of cell adhesion -0.073 0.12 -9999 0 -0.38 13 13
HPSE -0.036 0.16 -9999 0 -0.51 40 40
positive regulation of cell migration -0.12 0.14 -9999 0 -0.35 59 59
SDC1 -0.12 0.14 -9999 0 -0.36 59 59
Syndecan-1/Collagen -0.12 0.14 -9999 0 -0.35 59 59
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.013 0.036 -9999 0 -0.51 2 2
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.13 0.23 -9999 0 -0.51 110 110
MAPK1 -0.083 0.12 -9999 0 -0.4 13 13
homophilic cell adhesion -0.12 0.14 -9999 0 -0.35 59 59
MMP1 -0.28 0.26 -9999 0 -0.51 231 231
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.021 0.03 -9999 0 -0.41 2 2
alphaV beta3 Integrin -0.13 0.23 -9999 0 -0.42 146 146
PTK2 -0.1 0.23 -9999 0 -0.54 68 68
IGF1R 0.011 0.05 -9999 0 -0.57 3 3
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.013 0.041 -9999 0 -0.57 2 2
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.13 0.28 -9999 0 -0.7 67 67
VEGFA 0.016 0 -9999 0 -10000 0 0
ILK -0.13 0.28 -9999 0 -0.7 67 67
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.12 0.26 -9999 0 -0.65 67 67
PTK2B 0.007 0.11 -9999 0 -0.57 2 2
alphaV/beta3 Integrin/JAM-A -0.15 0.26 -9999 0 -0.63 68 68
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.017 0.13 -9999 0 -0.35 50 50
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.18 -9999 0 -0.31 186 186
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.019 0.13 -9999 0 -0.43 18 18
alphaV/beta3 Integrin/Syndecan-1 -0.017 0.13 -9999 0 -0.34 53 53
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.26 0.29 -9999 0 -0.62 134 134
PI4 Kinase 0.023 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.14 0.18 -9999 0 -0.31 206 206
RPS6KB1 -0.21 0.29 -9999 0 -0.58 134 134
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.28 0.4 -9999 0 -0.78 146 146
GPR124 -0.05 0.18 -9999 0 -0.57 46 46
MAPK1 -0.28 0.4 -9999 0 -0.78 146 146
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
alphaV/beta3 Integrin/Tumstatin -0.11 0.21 -9999 0 -0.38 144 144
cell adhesion -0.032 0.12 -9999 0 -0.34 47 47
ANGPTL3 0.005 0.057 -9999 0 -0.51 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.026 -9999 0 -0.34 2 2
IGF-1R heterotetramer 0.011 0.05 -9999 0 -0.57 3 3
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.05 -9999 0 -0.57 3 3
ITGB3 -0.05 0.18 -9999 0 -0.57 46 46
IGF1 -0.24 0.29 -9999 0 -0.57 182 182
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.05 0.19 -9999 0 -0.45 69 69
apoptosis 0.014 0.029 -9999 0 -0.57 1 1
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.011 0.12 -9999 0 -0.34 46 46
VCL 0.014 0.029 -9999 0 -0.57 1 1
alphaV/beta3 Integrin/Del1 -0.06 0.2 -9999 0 -0.44 80 80
CSF1 -0.006 0.11 -9999 0 -0.57 15 15
PIK3C2A -0.13 0.28 -9999 0 -0.7 67 67
PI4 Kinase/Pyk2 -0.14 0.2 -9999 0 -0.54 68 68
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0 0.11 -9999 0 -0.31 47 47
FAK1/Vinculin -0.075 0.18 -9999 0 -0.41 69 69
alphaV beta3/Integrin/ppsTEM5 -0.05 0.19 -9999 0 -0.45 69 69
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.088 0.22 -9999 0 -0.56 73 73
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.18 0.28 -9999 0 -0.57 136 136
F11R -0.12 0.21 -9999 0 -0.41 136 136
alphaV/beta3 Integrin/Lactadherin -0.012 0.12 -9999 0 -0.35 47 47
alphaV/beta3 Integrin/TGFBR2 -0.013 0.13 -9999 0 -0.35 48 48
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.027 0.066 -9999 0 -0.3 16 16
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.009 0.11 -9999 0 -0.31 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.035 0.16 -9999 0 -0.53 38 38
alphaV/beta3 Integrin/Pyk2 0.008 0.11 -9999 0 -0.57 2 2
SDC1 0.006 0.076 -9999 0 -0.57 7 7
VAV3 0.027 0.073 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.001 0.09 -9999 0 -0.57 10 10
FAK1/Paxillin -0.074 0.18 -9999 0 -0.41 68 68
cell migration -0.059 0.17 -9999 0 -0.37 65 65
ITGAV 0.014 0.029 -9999 0 -0.57 1 1
PI3K -0.16 0.21 -9999 0 -0.57 68 68
SPP1 -0.2 0.26 -9999 0 -0.51 165 165
KDR 0.013 0.041 -9999 0 -0.57 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.029 -9999 0 -0.57 1 1
COL4A3 -0.15 0.26 -9999 0 -0.57 116 116
angiogenesis -0.27 0.4 -9999 0 -0.75 149 149
Rac1/GTP 0.033 0.067 -9999 0 -10000 0 0
EDIL3 -0.066 0.2 -9999 0 -0.57 57 57
cell proliferation -0.013 0.12 -9999 0 -0.35 48 48
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.18 0.44 -9999 0 -0.96 57 57
HDAC7 0.018 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.12 0.36 -9999 0 -0.78 50 50
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.19 0.45 -9999 0 -1 52 52
AP1 -0.12 0.23 -9999 0 -0.45 130 130
ABCG2 -0.2 0.46 -9999 0 -0.99 57 57
HIF1A -0.012 0.084 -9999 0 -0.65 1 1
TFF3 -0.26 0.5 -9999 0 -1 86 86
GATA2 -0.009 0.12 -9999 0 -0.53 20 20
AKT1 -0.013 0.092 -9999 0 -10000 0 0
response to hypoxia -0.036 0.098 -9999 0 -0.23 17 17
MCL1 -0.18 0.44 -9999 0 -0.98 53 53
NDRG1 -0.19 0.45 -9999 0 -0.99 54 54
SERPINE1 -0.19 0.45 -9999 0 -0.98 57 57
FECH -0.18 0.44 -9999 0 -0.96 57 57
FURIN -0.18 0.44 -9999 0 -0.94 60 60
NCOA2 -0.018 0.14 -9999 0 -0.57 24 24
EP300 -0.003 0.14 -9999 0 -0.34 25 25
HMOX1 -0.19 0.45 -9999 0 -0.96 59 59
BHLHE40 -0.19 0.45 -9999 0 -0.96 60 60
BHLHE41 -0.19 0.46 -9999 0 -0.98 59 59
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.012 0.092 -9999 0 -0.41 1 1
ENG 0.035 0.1 -9999 0 -0.37 1 1
JUN -0.006 0.11 -9999 0 -0.57 16 16
RORA -0.19 0.45 -9999 0 -0.97 59 59
ABCB1 -0.2 0.4 -9999 0 -1.2 53 53
TFRC -0.19 0.45 -9999 0 -0.99 54 54
CXCR4 -0.19 0.45 -9999 0 -0.97 60 60
TF -0.22 0.47 -9999 0 -0.98 68 68
CITED2 -0.18 0.44 -9999 0 -0.95 59 59
HIF1A/ARNT -0.19 0.52 -9999 0 -1 73 73
LDHA -0.024 0.044 -9999 0 -10000 0 0
ETS1 -0.18 0.44 -9999 0 -0.95 59 59
PGK1 -0.18 0.44 -9999 0 -0.95 59 59
NOS2 -0.21 0.47 -9999 0 -1 62 62
ITGB2 -0.19 0.45 -9999 0 -1 54 54
ALDOA -0.18 0.44 -9999 0 -0.98 53 53
Cbp/p300/CITED2 -0.17 0.47 -9999 0 -1 53 53
FOS -0.17 0.27 -9999 0 -0.57 129 129
HK2 -0.18 0.45 -9999 0 -0.96 59 59
SP1 0.017 0.029 -9999 0 -10000 0 0
GCK -0.079 0.4 -9999 0 -1.5 27 27
HK1 -0.18 0.44 -9999 0 -1 48 48
NPM1 -0.18 0.44 -9999 0 -0.98 53 53
EGLN1 -0.18 0.44 -9999 0 -0.98 53 53
CREB1 0.025 0 -9999 0 -10000 0 0
PGM1 -0.18 0.44 -9999 0 -0.98 52 52
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.055 0.23 -9999 0 -0.78 13 13
IGFBP1 -0.21 0.46 -9999 0 -0.98 62 62
VEGFA -0.077 0.34 -9999 0 -0.74 28 28
HIF1A/JAB1 -0.007 0.042 -9999 0 -0.48 1 1
CP -0.28 0.51 -9999 0 -0.98 96 96
CXCL12 -0.27 0.52 -9999 0 -1 88 88
COPS5 0.016 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 0.026 0.001 -9999 0 -10000 0 0
BNIP3 -0.19 0.45 -9999 0 -0.98 54 54
EGLN3 -0.19 0.45 -9999 0 -0.98 56 56
CA9 -0.35 0.5 -9999 0 -1 89 89
TERT -0.28 0.49 -9999 0 -1 78 78
ENO1 -0.18 0.44 -9999 0 -0.95 59 59
PFKL -0.18 0.44 -9999 0 -0.98 53 53
NCOA1 0.016 0.002 -9999 0 -10000 0 0
ADM -0.19 0.45 -9999 0 -0.95 60 60
ARNT -0.01 0.078 -9999 0 -10000 0 0
HNF4A -0.041 0.16 -9999 0 -0.51 41 41
ADFP -0.2 0.44 -9999 0 -0.92 67 67
SLC2A1 -0.08 0.35 -9999 0 -0.77 28 28
LEP -0.22 0.48 -9999 0 -0.98 74 74
HIF1A/ARNT/Cbp/p300 -0.14 0.38 -9999 0 -0.8 54 54
EPO -0.086 0.31 -9999 0 -0.74 19 19
CREBBP -0.003 0.14 -9999 0 -0.33 26 26
HIF1A/ARNT/Cbp/p300/HDAC7 -0.12 0.36 -9999 0 -0.79 48 48
PFKFB3 -0.18 0.45 -9999 0 -0.95 59 59
NT5E -0.21 0.48 -9999 0 -0.98 72 72
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.17 0.27 -10000 0 -0.49 157 157
fibroblast growth factor receptor signaling pathway -0.17 0.27 -10000 0 -0.49 157 157
LAMA1 -0.091 0.21 -10000 0 -0.52 81 81
PRNP 0.001 0.09 -10000 0 -0.57 10 10
GPC1/SLIT2 -0.17 0.22 -10000 0 -0.41 185 185
SMAD2 0.036 0.032 -10000 0 -0.3 3 3
GPC1/PrPc/Cu2+ 0.011 0.059 -10000 0 -0.34 11 11
GPC1/Laminin alpha1 -0.055 0.16 -10000 0 -0.37 81 81
TDGF1 0.005 0.045 -10000 0 -0.51 3 3
CRIPTO/GPC1 0.014 0.038 -10000 0 -0.36 4 4
APP/GPC1 0.02 0.035 -10000 0 -0.39 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.025 0.032 -10000 0 -0.29 4 4
FLT1 0.016 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.028 0.035 -10000 0 -0.33 4 4
SERPINC1 -0.026 0.14 -10000 0 -0.51 30 30
FYN 0.022 0.045 -10000 0 -0.32 7 7
FGR 0.023 0.041 -10000 0 -0.31 6 6
positive regulation of MAPKKK cascade 0.021 0.078 -10000 0 -0.43 3 3
SLIT2 -0.25 0.29 -10000 0 -0.57 185 185
GPC1/NRG -0.072 0.18 -10000 0 -0.4 92 92
NRG1 -0.11 0.24 -10000 0 -0.56 91 91
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.031 0.016 -10000 0 -0.29 1 1
LYN 0.025 0.032 -10000 0 -0.29 4 4
mol:Spermine 0.012 0.019 -10000 0 -0.37 1 1
cell growth -0.17 0.27 -10000 0 -0.49 157 157
BMP signaling pathway -0.014 0.026 0.51 1 -10000 0 1
SRC 0.025 0.032 -10000 0 -0.29 4 4
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.29 -10000 0 -0.57 185 185
GPC1 0.014 0.026 -10000 0 -0.51 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA 0.016 0 -10000 0 -10000 0 0
BLK -0.024 0.12 -10000 0 -0.33 57 57
HCK 0.01 0.078 -10000 0 -0.32 21 21
FGF2 -0.18 0.28 -10000 0 -0.57 136 136
FGFR1 -0.12 0.24 -10000 0 -0.57 93 93
VEGFR1 homodimer 0.016 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.05 -10000 0 -0.57 3 3
cell death 0.02 0.035 -10000 0 -0.39 3 3
ATIII/GPC1 -0.008 0.1 -10000 0 -0.36 31 31
PLA2G2A/GPC1 -0.17 0.22 -10000 0 -0.41 185 185
LCK 0.019 0.053 -10000 0 -0.31 10 10
neuron differentiation -0.072 0.18 -10000 0 -0.4 92 92
PrPc/Cu2+ 0.001 0.066 -10000 0 -0.42 10 10
APP 0.013 0.041 -10000 0 -0.57 2 2
TGFBR2 (dimer) 0.011 0.05 -10000 0 -0.57 3 3
Glucocorticoid receptor regulatory network

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
PCK2 0.014 0.061 -10000 0 -10000 0 0
SMARCC2 0.015 0.015 -10000 0 -10000 0 0
SMARCC1 0.015 0.015 -10000 0 -10000 0 0
TBX21 -0.085 0.22 -10000 0 -0.8 29 29
SUMO2 0.012 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.021 0.051 -10000 0 -0.49 4 4
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 -0.009 0.12 -10000 0 -0.57 17 17
GR alpha/HSP90/FKBP51/HSP90 0.086 0.12 0.27 29 -0.38 3 32
PRL -0.062 0.12 -10000 0 -0.58 3 3
cortisol/GR alpha (dimer)/TIF2 0.22 0.22 0.46 124 -0.41 2 126
RELA -0.098 0.12 -10000 0 -0.28 32 32
FGG 0.16 0.22 0.44 58 -0.5 7 65
GR beta/TIF2 0.083 0.14 0.28 32 -0.35 20 52
IFNG -0.33 0.26 -10000 0 -0.69 87 87
apoptosis -0.067 0.18 0.42 4 -0.54 13 17
CREB1 0.014 0.031 -10000 0 -10000 0 0
histone acetylation -0.011 0.14 0.38 2 -0.37 25 27
BGLAP -0.042 0.11 -10000 0 -0.44 4 4
GR/PKAc 0.1 0.089 0.29 13 -10000 0 13
NF kappa B1 p50/RelA -0.18 0.23 -10000 0 -0.45 139 139
SMARCD1 0.015 0.015 -10000 0 -10000 0 0
MDM2 0.09 0.087 0.24 35 -0.24 3 38
GATA3 -0.02 0.15 -10000 0 -0.56 29 29
AKT1 0.002 0.006 -10000 0 -10000 0 0
CSF2 -0.081 0.13 -10000 0 -0.51 2 2
GSK3B 0.012 0.007 -10000 0 -10000 0 0
NR1I3 -0.025 0.18 0.46 1 -0.53 3 4
CSN2 0.16 0.14 0.38 43 -10000 0 43
BRG1/BAF155/BAF170/BAF60A 0.039 0.052 -10000 0 -0.32 2 2
NFATC1 -0.01 0.12 -10000 0 -0.57 19 19
POU2F1 0.017 0.012 -10000 0 -10000 0 0
CDKN1A 0.034 0.1 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.031 0.15 -10000 0 -0.51 36 36
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.076 0.13 0.28 18 -0.48 1 19
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.16 0.39 0.42 2 -0.83 100 102
JUN -0.17 0.17 -10000 0 -0.47 60 60
IL4 -0.087 0.15 -10000 0 -0.53 21 21
CDK5R1 -0.014 0.12 -10000 0 -0.51 22 22
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.24 0.28 0.21 1 -0.57 134 135
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.11 0.28 21 -0.48 1 22
cortisol/GR alpha (monomer) 0.27 0.24 0.53 136 -10000 0 136
NCOA2 -0.019 0.14 -10000 0 -0.57 24 24
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.23 0.27 -10000 0 -0.62 129 129
AP-1/NFAT1-c-4 -0.41 0.32 -10000 0 -0.71 172 172
AFP -0.14 0.15 -10000 0 -0.59 10 10
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.16 0.12 0.35 53 -10000 0 53
TP53 0.039 0.038 -10000 0 -0.5 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.36 0.38 -10000 0 -0.8 122 122
KRT14 -0.23 0.24 -10000 0 -0.52 109 109
TBP 0.026 0.011 -10000 0 -10000 0 0
CREBBP 0.07 0.089 0.3 3 -10000 0 3
HDAC1 0.014 0.007 -10000 0 -10000 0 0
HDAC2 0.02 0.014 -10000 0 -10000 0 0
AP-1 -0.41 0.32 -10000 0 -0.72 173 173
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.042 0.17 -10000 0 -0.57 37 37
MAPK11 0.012 0.007 -10000 0 -10000 0 0
KRT5 -0.57 0.54 -10000 0 -1.1 189 189
interleukin-1 receptor activity 0.004 0.014 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.021 0.051 -10000 0 -0.49 4 4
CGA -0.073 0.14 -10000 0 -0.55 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.16 0.34 81 -0.47 5 86
MAPK3 0.011 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.24 0.26 -10000 0 -0.57 102 102
NFKB1 -0.098 0.12 -10000 0 -0.29 21 21
MAPK8 -0.13 0.14 -10000 0 -0.39 51 51
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.079 0.18 0.43 4 -0.56 13 17
BAX 0.04 0.034 -10000 0 -10000 0 0
POMC -0.3 0.29 -10000 0 -0.6 126 126
EP300 0.07 0.089 0.32 2 -10000 0 2
cortisol/GR alpha (dimer)/p53 0.26 0.2 0.48 135 -10000 0 135
proteasomal ubiquitin-dependent protein catabolic process 0.062 0.069 0.22 7 -0.23 2 9
SGK1 0.084 0.3 -10000 0 -1.3 16 16
IL13 -0.24 0.22 -10000 0 -0.76 36 36
IL6 -0.6 0.6 -10000 0 -1.2 197 197
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.22 0.19 -10000 0 -0.66 31 31
IL2 -0.29 0.22 -10000 0 -0.63 69 69
CDK5 0.014 0.003 -10000 0 -10000 0 0
PRKACB 0.013 0.041 -10000 0 -0.57 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.35 0.45 -10000 0 -0.78 162 162
CDK5R1/CDK5 -0.004 0.085 -10000 0 -0.36 22 22
NF kappa B1 p50/RelA/PKAc -0.11 0.18 -10000 0 -0.42 32 32
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.19 0.44 135 -10000 0 135
SMARCA4 0.015 0.015 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.15 0.33 80 -0.44 7 87
NF kappa B1 p50/RelA/Cbp -0.077 0.24 0.33 5 -0.43 61 66
JUN (dimer) -0.17 0.17 -10000 0 -0.47 60 60
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.073 0.2 -10000 0 -0.64 33 33
NR3C1 0.15 0.15 0.37 64 -0.42 3 67
NR4A1 -0.31 0.3 -10000 0 -0.57 231 231
TIF2/SUV420H1 -0.002 0.1 -10000 0 -0.41 24 24
MAPKKK cascade -0.067 0.18 0.42 4 -0.54 13 17
cortisol/GR alpha (dimer)/Src-1 0.25 0.2 0.47 136 -10000 0 136
PBX1 -0.009 0.12 -10000 0 -0.57 18 18
POU1F1 0.002 0.046 -10000 0 -0.5 3 3
SELE -0.56 0.59 -10000 0 -1.2 177 177
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.15 0.33 79 -0.44 7 86
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.19 0.44 135 -10000 0 135
mol:cortisol 0.15 0.14 0.29 147 -10000 0 147
MMP1 -0.26 0.19 -10000 0 -0.46 136 136
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.33 0.54 -10000 0 -1.3 70 70
IL23A -0.29 0.46 -10000 0 -1.1 64 64
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.39 -10000 0 -1 77 77
positive regulation of T cell mediated cytotoxicity -0.31 0.5 -10000 0 -1.1 76 76
ITGA3 -0.27 0.44 -10000 0 -1.1 56 56
IL17F -0.18 0.31 -10000 0 -0.7 57 57
IL12B -0.014 0.1 -10000 0 -0.52 14 14
STAT1 (dimer) -0.3 0.47 -10000 0 -1.1 76 76
CD4 -0.27 0.44 -10000 0 -1.1 61 61
IL23 -0.29 0.44 -10000 0 -1.1 65 65
IL23R -0.029 0.089 -10000 0 -10000 0 0
IL1B -0.3 0.49 -10000 0 -1.2 65 65
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.29 0.44 -10000 0 -1.1 62 62
TYK2 0.008 0.021 -10000 0 -10000 0 0
STAT4 -0.013 0.13 -10000 0 -0.57 20 20
STAT3 0.016 0 -10000 0 -10000 0 0
IL18RAP -0.017 0.13 -10000 0 -0.57 21 21
IL12RB1 -0.032 0.15 -10000 0 -0.54 30 30
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.022 0.11 -10000 0 -0.4 30 30
IL23R/JAK2 -0.034 0.11 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.31 0.5 -10000 0 -1.1 76 76
natural killer cell activation 0.003 0.008 -10000 0 -10000 0 0
JAK2 0.013 0.04 -10000 0 -0.6 1 1
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
NFKB1 0.014 0.004 -10000 0 -10000 0 0
RELA 0.014 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.27 0.42 -10000 0 -1 65 65
ALOX12B -0.28 0.44 -10000 0 -1.1 61 61
CXCL1 -0.33 0.52 -10000 0 -1.2 77 77
T cell proliferation -0.31 0.5 -10000 0 -1.1 76 76
NFKBIA 0.014 0.004 -10000 0 -10000 0 0
IL17A -0.12 0.25 -10000 0 -0.55 44 44
PI3K -0.32 0.41 -10000 0 -1 76 76
IFNG -0.017 0.035 0.1 1 -0.11 1 2
STAT3 (dimer) -0.31 0.38 -10000 0 -0.99 75 75
IL18R1 0.009 0.05 -10000 0 -0.57 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.31 -10000 0 -0.81 41 41
IL18/IL18R 0.003 0.11 -10000 0 -0.37 27 27
macrophage activation -0.018 0.017 -10000 0 -0.043 64 64
TNF -0.29 0.46 -10000 0 -1.1 64 64
STAT3/STAT4 -0.33 0.42 -10000 0 -1.1 78 78
STAT4 (dimer) -0.31 0.49 -10000 0 -1.1 77 77
IL18 0.005 0.07 -10000 0 -0.57 6 6
IL19 -0.28 0.44 -10000 0 -1 64 64
STAT5A (dimer) -0.3 0.47 -10000 0 -1.1 75 75
STAT1 0.011 0.051 -10000 0 -0.51 4 4
SOCS3 -0.046 0.18 -10000 0 -0.57 43 43
CXCL9 -0.32 0.46 -10000 0 -1.1 64 64
MPO -0.27 0.43 -10000 0 -1.1 57 57
positive regulation of humoral immune response -0.31 0.5 -10000 0 -1.1 76 76
IL23/IL23R/JAK2/TYK2 -0.33 0.53 -10000 0 -1.2 75 75
IL6 -0.61 0.68 -10000 0 -1.3 194 194
STAT5A 0.014 0.029 -10000 0 -0.57 1 1
IL2 0.004 0.013 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.008 -10000 0 -10000 0 0
CD3E -0.32 0.52 -10000 0 -1.3 73 73
keratinocyte proliferation -0.31 0.5 -10000 0 -1.1 76 76
NOS2 -0.29 0.45 -10000 0 -1.1 64 64
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.076 0.17 -9999 0 -0.46 58 58
alphaM/beta2 Integrin/GPIbA -0.053 0.12 -9999 0 -0.41 39 39
alphaM/beta2 Integrin/proMMP-9 -0.13 0.18 -9999 0 -0.37 127 127
PLAUR 0.016 0 -9999 0 -10000 0 0
HMGB1 -0.003 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.046 0.12 -9999 0 -0.43 31 31
AGER -0.011 0.069 -9999 0 -0.54 6 6
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG 0.003 0.084 -9999 0 -0.56 9 9
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.11 0.14 -9999 0 -0.5 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.23 -9999 0 -0.51 110 110
CYR61 -0.15 0.26 -9999 0 -0.57 116 116
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.057 0.13 -9999 0 -0.48 24 24
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -9999 0 -0.57 84 84
MYH2 -0.051 0.15 -9999 0 -0.43 29 29
MST1R -0.02 0.14 -9999 0 -0.55 26 26
leukocyte activation during inflammatory response -0.11 0.17 -9999 0 -0.36 114 114
APOB -0.081 0.21 -9999 0 -0.56 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.036 0.17 -9999 0 -0.57 36 36
JAM3 -0.025 0.15 -9999 0 -0.57 28 28
GP1BA 0.002 0.078 -9999 0 -0.51 9 9
alphaM/beta2 Integrin/CTGF -0.12 0.2 -9999 0 -0.44 100 100
alphaM/beta2 Integrin -0.054 0.17 -9999 0 -0.53 29 29
JAM3 homodimer -0.024 0.15 -9999 0 -0.57 28 28
ICAM2 0.014 0.029 -9999 0 -0.57 1 1
ICAM1 0.003 0.082 -9999 0 -0.51 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.053 0.16 -9999 0 -0.52 29 29
cell adhesion -0.053 0.12 -9999 0 -0.41 39 39
NFKB1 -0.14 0.22 -9999 0 -0.61 26 26
THY1 0.012 0.045 -9999 0 -0.51 3 3
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.076 0.17 -9999 0 -0.37 96 96
alphaM/beta2 Integrin/LRP/tPA -0.033 0.16 -9999 0 -0.45 40 40
IL6 -0.33 0.42 -9999 0 -0.77 189 189
ITGB2 -0.025 0.11 -9999 0 -0.55 16 16
elevation of cytosolic calcium ion concentration -0.071 0.13 -9999 0 -0.36 49 49
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.24 -9999 0 -0.44 126 126
JAM2 -0.14 0.26 -9999 0 -0.57 109 109
alphaM/beta2 Integrin/ICAM1 -0.046 0.16 -9999 0 -0.46 30 30
alphaM/beta2 Integrin/uPA/Plg -0.065 0.15 -9999 0 -0.33 81 81
RhoA/GTP -0.045 0.15 -9999 0 -0.47 26 26
positive regulation of phagocytosis -0.066 0.16 -9999 0 -0.53 32 32
Ron/MSP -0.024 0.13 -9999 0 -0.39 47 47
alphaM/beta2 Integrin/uPAR/uPA -0.053 0.14 -9999 0 -0.37 49 49
alphaM/beta2 Integrin/uPAR -0.046 0.12 -9999 0 -0.43 31 31
PLAU -0.054 0.18 -9999 0 -0.51 54 54
PLAT -0.013 0.12 -9999 0 -0.56 20 20
actin filament polymerization -0.048 0.14 -9999 0 -0.41 29 29
MST1 -0.014 0.12 -9999 0 -0.51 23 23
alphaM/beta2 Integrin/lipoprotein(a) -0.11 0.17 -9999 0 -0.36 114 114
TNF -0.13 0.21 -9999 0 -0.56 26 26
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.085 0.15 -9999 0 -0.36 84 84
fibrinolysis -0.079 0.14 -9999 0 -0.33 78 78
HCK -0.008 0.11 -9999 0 -0.55 17 17
dendritic cell antigen processing and presentation -0.053 0.16 -9999 0 -0.52 29 29
VTN -0.088 0.22 -9999 0 -0.56 73 73
alphaM/beta2 Integrin/CYR61 -0.14 0.22 -9999 0 -0.46 124 124
LPA -0.043 0.17 -9999 0 -0.56 38 38
LRP1 0.01 0.058 -9999 0 -0.57 4 4
cell migration -0.12 0.21 -9999 0 -0.43 88 88
FN1 -0.035 0.16 -9999 0 -0.53 38 38
alphaM/beta2 Integrin/Thy1 -0.048 0.12 -9999 0 -0.42 34 34
MPO 0.011 0.037 -9999 0 -0.51 2 2
KNG1 0 0 -9999 0 -10000 0 0
RAP1/GDP 0.021 0 -9999 0 -10000 0 0
ROCK1 -0.034 0.14 -9999 0 -0.49 19 19
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.003 0.056 -9999 0 -0.51 5 5
CTGF -0.1 0.24 -9999 0 -0.57 84 84
alphaM/beta2 Integrin/Hck -0.059 0.16 -9999 0 -0.51 37 37
ITGAM -0.035 0.13 -9999 0 -0.59 22 22
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.089 0.2 -9999 0 -0.4 101 101
HP -0.049 0.17 -9999 0 -0.51 48 48
leukocyte adhesion -0.17 0.21 -9999 0 -0.5 100 100
SELP -0.1 0.24 -9999 0 -0.57 84 84
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.056 0.23 -10000 0 -0.65 24 24
CRP -0.067 0.24 -10000 0 -0.7 24 24
cell cycle arrest -0.066 0.27 -10000 0 -0.66 46 46
TIMP1 -0.049 0.21 -10000 0 -0.6 16 16
IL6ST -0.068 0.21 -10000 0 -0.57 61 61
Rac1/GDP -0.13 0.26 -10000 0 -0.54 89 89
AP1 -0.057 0.18 -10000 0 -0.44 31 31
GAB2 0.017 0.03 -10000 0 -0.57 1 1
TNFSF11 -0.07 0.26 -10000 0 -0.72 28 28
HSP90B1 0.024 0.055 -10000 0 -0.56 1 1
GAB1 0.018 0.004 -10000 0 -10000 0 0
MAPK14 -0.17 0.31 -10000 0 -0.71 79 79
AKT1 0.063 0.022 -10000 0 -10000 0 0
FOXO1 0.068 0.025 -10000 0 -10000 0 0
MAP2K6 -0.16 0.28 -10000 0 -0.6 90 90
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.095 0.26 -10000 0 -0.57 66 66
MITF -0.16 0.28 -10000 0 -0.55 103 103
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0 -10000 0 -10000 0 0
A2M -0.1 0.42 -10000 0 -1.4 37 37
CEBPB 0.023 0.029 -10000 0 -0.57 1 1
GRB2/SOS1/GAB family/SHP2 -0.015 0.1 0.25 5 -0.45 3 8
STAT3 -0.078 0.28 -10000 0 -0.7 48 48
STAT1 -0.006 0.019 -10000 0 -10000 0 0
CEBPD -0.058 0.24 -10000 0 -0.66 27 27
PIK3CA 0.018 0 -10000 0 -10000 0 0
PI3K 0.026 0.022 -10000 0 -0.41 1 1
JUN -0.007 0.11 -10000 0 -0.57 16 16
PIAS3/MITF -0.14 0.27 -10000 0 -0.53 97 97
MAPK11 -0.17 0.31 -10000 0 -0.71 79 79
STAT3 (dimer)/FOXO1 -0.032 0.25 -10000 0 -0.57 40 40
GRB2/SOS1/GAB family -0.14 0.21 0.21 5 -0.56 58 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.27 -10000 0 -0.49 114 114
GRB2 0.018 0.004 -10000 0 -10000 0 0
JAK2 0.014 0.029 -10000 0 -0.57 1 1
LBP -0.066 0.22 -10000 0 -0.57 21 21
PIK3R1 0.016 0.029 -10000 0 -0.57 1 1
JAK1 0.017 0.007 -10000 0 -10000 0 0
MYC -0.08 0.3 -10000 0 -0.86 36 36
FGG -0.081 0.25 -10000 0 -0.74 22 22
macrophage differentiation -0.066 0.27 -10000 0 -0.66 46 46
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.19 0.23 -10000 0 -0.46 113 113
JUNB -0.061 0.24 -10000 0 -0.64 35 35
FOS -0.17 0.27 -10000 0 -0.57 129 129
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.27 -10000 0 -0.51 108 108
STAT1/PIAS1 -0.12 0.24 -10000 0 -0.53 69 69
GRB2/SOS1/GAB family/SHP2/PI3K 0.051 0.025 -10000 0 -0.27 1 1
STAT3 (dimer) -0.074 0.28 -10000 0 -0.69 46 46
PRKCD -0.068 0.25 -10000 0 -0.56 60 60
IL6R -0.033 0.16 -10000 0 -0.57 35 35
SOCS3 -0.21 0.42 -10000 0 -1 68 68
gp130 (dimer)/JAK1/JAK1/LMO4 -0.013 0.14 -10000 0 -0.34 62 62
Rac1/GTP -0.12 0.26 -10000 0 -0.54 88 88
HCK -0.008 0.11 -10000 0 -0.55 17 17
MAPKKK cascade 0.023 0.085 -10000 0 -0.85 1 1
bone resorption -0.065 0.24 -10000 0 -0.65 31 31
IRF1 -0.056 0.23 -10000 0 -0.58 39 39
mol:GDP -0.15 0.27 -10000 0 -0.55 94 94
SOS1 0.018 0.007 -10000 0 -10000 0 0
VAV1 -0.15 0.28 -10000 0 -0.56 94 94
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.2 0.34 -10000 0 -0.77 83 83
PTPN11 -0.004 0.018 -10000 0 -10000 0 0
IL6/IL6RA -0.2 0.25 -10000 0 -0.45 194 194
gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.14 -10000 0 -0.34 62 62
gp130 (dimer)/JAK2/JAK2/LMO4 -0.02 0.14 -10000 0 -0.34 62 62
IL6 -0.24 0.29 -10000 0 -0.57 184 184
PIAS3 0.016 0 -10000 0 -10000 0 0
PTPRE 0.005 0.046 -10000 0 -0.52 3 3
PIAS1 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.25 -10000 0 -0.44 130 130
LMO4 0.018 0.031 -10000 0 -0.57 1 1
STAT3 (dimer)/PIAS3 -0.14 0.23 -10000 0 -0.67 51 51
MCL1 0.069 0.021 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.21 -9999 0 -0.57 40 40
SMAD6-7/SMURF1 0.028 0.038 -9999 0 -0.31 5 5
NOG -0.026 0.14 -9999 0 -0.51 31 31
SMAD9 -0.15 0.25 -9999 0 -0.55 106 106
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.033 0.1 -9999 0 -0.39 6 6
BMP7/USAG1 -0.27 0.27 -9999 0 -0.48 234 234
SMAD5/SKI -0.023 0.1 -9999 0 -0.36 6 6
SMAD1 0.046 0.021 -9999 0 -10000 0 0
BMP2 -0.046 0.18 -9999 0 -0.57 43 43
SMAD1/SMAD1/SMAD4 -0.002 0.019 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.063 0.19 -9999 0 -0.51 60 60
BMPR1A-1B/BAMBI -0.051 0.16 -9999 0 -0.35 89 89
AHSG -0.053 0.16 -9999 0 -0.51 46 46
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.034 0.14 -9999 0 -0.35 64 64
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.066 0.15 -9999 0 -0.38 34 34
BMP2-4 (homodimer) -0.045 0.16 -9999 0 -0.41 64 64
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.007 0.11 -9999 0 -0.3 7 7
RGMA -0.16 0.27 -9999 0 -0.57 119 119
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.068 0.14 -9999 0 -0.36 40 40
BMP2-4/USAG1 -0.15 0.22 -9999 0 -0.38 178 178
SMAD6/SMURF1/SMAD5 -0.023 0.1 -9999 0 -0.36 6 6
SOSTDC1 -0.18 0.27 -9999 0 -0.57 137 137
BMP7/BMPR2/BMPR1A-1B -0.12 0.2 -9999 0 -0.34 152 152
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.012 0.046 -9999 0 -0.53 3 3
HFE2 0.002 0.051 -9999 0 -0.51 4 4
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.061 0.18 -9999 0 -0.37 94 94
SMAD5/SMAD5/SMAD4 -0.023 0.1 -9999 0 -0.36 6 6
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.071 0.096 -9999 0 -0.36 24 24
BMP7 (homodimer) -0.2 0.28 -9999 0 -0.57 147 147
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.029 0.12 -9999 0 -0.36 49 49
SMAD1/SKI 0.053 0.02 -9999 0 -10000 0 0
SMAD6 0.01 0.053 -9999 0 -0.52 4 4
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.068 0.17 -9999 0 -0.35 101 101
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.15 0.25 -9999 0 -0.54 121 121
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.032 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.034 0.14 -9999 0 -0.36 60 60
CHRDL1 -0.32 0.29 -9999 0 -0.57 235 235
ENDOFIN/SMAD1 0.053 0.02 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.001 0.024 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.041 0.17 -9999 0 -0.56 40 40
SMURF2 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.24 0.22 -9999 0 -0.39 259 259
BMP2-4/GREM1 -0.13 0.19 -9999 0 -0.33 179 179
SMAD7 0.014 0.029 -9999 0 -0.57 1 1
SMAD8A/SMAD8A/SMAD4 -0.13 0.24 -9999 0 -0.51 106 106
SMAD1/SMAD6 0.053 0.02 -9999 0 -10000 0 0
TAK1/SMAD6 0.023 0 -9999 0 -10000 0 0
BMP7 -0.2 0.28 -9999 0 -0.57 147 147
BMP6 0.012 0.046 -9999 0 -0.53 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.059 0.13 -9999 0 -0.34 37 37
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.053 0.02 -9999 0 -10000 0 0
SMAD7/SMURF1 0.022 0.021 -9999 0 -0.41 1 1
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.013 0.039 -9999 0 -0.54 2 2
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.097 0.18 -9999 0 -0.45 51 51
CHRD -0.042 0.17 -9999 0 -0.57 40 40
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.083 0.15 -9999 0 -0.41 39 39
BMP4 -0.015 0.13 -9999 0 -0.56 22 22
FST -0.029 0.15 -9999 0 -0.55 32 32
BMP2-4/NOG -0.051 0.17 -9999 0 -0.38 82 82
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.11 0.18 -9999 0 -0.53 26 26
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.09 0.2 -10000 0 -0.55 59 59
FYN -0.073 0.32 -10000 0 -0.74 66 66
LAT/GRAP2/SLP76 -0.099 0.24 -10000 0 -0.6 67 67
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.026 0.2 -10000 0 -0.46 61 61
B2M 0.016 0.005 -10000 0 -10000 0 0
IKBKG -0.022 0.043 -10000 0 -0.13 31 31
MAP3K8 0.011 0.05 -10000 0 -0.57 3 3
mol:Ca2+ -0.022 0.038 -10000 0 -0.11 42 42
integrin-mediated signaling pathway 0.017 0.036 -10000 0 -0.35 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.063 0.3 -10000 0 -0.68 66 66
TRPV6 -0.11 0.22 -10000 0 -0.56 81 81
CD28 -0.01 0.12 -10000 0 -0.57 18 18
SHC1 -0.066 0.3 -10000 0 -0.69 65 65
receptor internalization -0.077 0.31 -10000 0 -0.73 64 64
PRF1 -0.08 0.34 -10000 0 -0.94 43 43
KRAS 0.014 0.026 -10000 0 -0.51 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.009 0.16 -10000 0 -0.37 59 59
LAT -0.066 0.3 -10000 0 -0.69 65 65
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.04 0.17 -10000 0 -0.57 39 39
CD3E -0.045 0.18 -10000 0 -0.58 42 42
CD3G -0.051 0.19 -10000 0 -0.57 46 46
RASGRP2 -0.039 0.081 -10000 0 -0.17 106 106
RASGRP1 -0.02 0.2 -10000 0 -0.45 63 63
HLA-A 0.014 0.03 -10000 0 -0.58 1 1
RASSF5 0.01 0.058 -10000 0 -0.57 4 4
RAP1A/GTP/RAPL 0.018 0.036 -10000 0 -0.35 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.069 -10000 0 -0.13 57 57
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.04 0.076 -10000 0 -0.22 53 53
PRKCA -0.041 0.11 -10000 0 -0.28 59 59
GRAP2 -0.049 0.18 -10000 0 -0.57 45 45
mol:IP3 -0.042 0.2 0.23 69 -0.45 60 129
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.081 0.31 -10000 0 -0.73 61 61
ORAI1 0.063 0.12 0.31 81 -0.37 1 82
CSK -0.069 0.3 -10000 0 -0.72 63 63
B7 family/CD28 -0.14 0.27 -10000 0 -0.69 64 64
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.092 0.35 -10000 0 -0.81 67 67
PTPN6 -0.073 0.3 -10000 0 -0.69 67 67
VAV1 -0.074 0.31 -10000 0 -0.72 67 67
Monovalent TCR/CD3 -0.07 0.26 -10000 0 -0.54 74 74
CBL 0.016 0 -10000 0 -10000 0 0
LCK -0.079 0.32 -10000 0 -0.76 65 65
PAG1 -0.069 0.3 -10000 0 -0.7 65 65
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.093 0.35 -10000 0 -0.8 67 67
CD80 -0.054 0.18 -10000 0 -0.51 54 54
CD86 0.008 0.063 -10000 0 -0.56 5 5
PDK1/CARD11/BCL10/MALT1 -0.049 0.093 -10000 0 -0.26 57 57
HRAS 0.016 0 -10000 0 -10000 0 0
GO:0035030 -0.063 0.24 -10000 0 -0.56 64 64
CD8A -0.041 0.18 -10000 0 -0.57 40 40
CD8B -0.046 0.18 -10000 0 -0.57 44 44
PTPRC -0.056 0.19 -10000 0 -0.57 50 50
PDK1/PKC theta -0.037 0.25 -10000 0 -0.57 64 64
CSK/PAG1 -0.06 0.29 -10000 0 -0.71 60 60
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I 0.021 0.025 -10000 0 -0.42 1 1
GRAP2/SLP76 -0.12 0.29 -10000 0 -0.69 71 71
STIM1 0.034 0.061 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.086 -10000 0 -0.17 45 45
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.087 0.34 -10000 0 -0.8 64 64
mol:DAG -0.058 0.16 -10000 0 -0.4 61 61
RAP1A/GDP 0.005 0.03 -10000 0 -0.062 26 26
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 0.004 0.081 -10000 0 -0.57 8 8
cytotoxic T cell degranulation -0.073 0.31 -10000 0 -0.85 45 45
RAP1A/GTP -0.017 0.027 -10000 0 -0.068 41 41
mol:PI-3-4-5-P3 -0.042 0.24 -10000 0 -0.55 64 64
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.065 0.26 0.25 63 -0.6 61 124
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.007 0.11 -10000 0 -0.57 16 16
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.096 0.23 -10000 0 -0.57 68 68
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.06 0.21 -10000 0 -0.53 62 62
CARD11 -0.001 0.095 -10000 0 -0.55 12 12
PRKCB -0.085 0.15 -10000 0 -0.35 81 81
PRKCE -0.039 0.11 -10000 0 -0.28 58 58
PRKCQ -0.058 0.29 -10000 0 -0.66 66 66
LCP2 0.011 0.05 -10000 0 -0.57 3 3
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.016 0.17 -10000 0 -0.39 61 61
IKK complex 0.014 0.069 -10000 0 -0.12 51 51
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 0.005 0.13 -10000 0 -0.27 57 57
PDPK1 -0.02 0.19 -10000 0 -0.44 61 61
TCR/CD3/MHC I/CD8/Fyn -0.11 0.38 -10000 0 -0.86 70 70
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.084 -9999 0 -0.37 19 19
NFATC2 -0.059 0.14 -9999 0 -0.37 71 71
NFATC3 0.008 0.027 -9999 0 -10000 0 0
CD40LG -0.26 0.33 -9999 0 -0.71 107 107
PTGS2 -0.29 0.36 -9999 0 -0.72 134 134
JUNB 0.008 0.064 -9999 0 -0.57 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.011 -9999 0 -10000 0 0
CALM1 0.012 0.008 -9999 0 -10000 0 0
JUN -0.011 0.12 -9999 0 -0.58 16 16
mol:Ca2+ -0.008 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.003 0.004 -9999 0 -10000 0 0
FOSL1 -0.025 0.15 -9999 0 -0.57 28 28
CREM 0.015 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.13 0.17 -9999 0 -0.48 57 57
FOS -0.18 0.28 -9999 0 -0.58 129 129
IFNG -0.28 0.33 -9999 0 -0.71 107 107
AP-1/NFAT1-c-4 -0.29 0.37 -9999 0 -0.72 131 131
FASLG -0.25 0.32 -9999 0 -0.71 94 94
NFAT1-c-4/ICER1 -0.071 0.16 -9999 0 -0.4 55 55
IL2RA -0.25 0.33 -9999 0 -0.76 85 85
FKBP12/FK506 0.012 0 -9999 0 -10000 0 0
CSF2 -0.27 0.33 -9999 0 -0.72 104 104
JunB/Fra1/NFAT1-c-4 -0.1 0.16 -9999 0 -0.43 55 55
IL4 -0.24 0.3 -9999 0 -0.66 92 92
IL2 -0.009 0.019 -9999 0 -10000 0 0
IL3 -0.024 0.023 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 0.003 0.082 -9999 0 -0.54 9 9
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.002 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.015 0.13 -9999 0 -0.37 36 36
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.11 -9999 0 -0.33 11 11
AP1 -0.15 0.21 -9999 0 -0.58 57 57
mol:PIP3 -0.063 0.13 -9999 0 -0.46 26 26
AKT1 0.029 0.1 -9999 0 -0.39 10 10
PTK2B -0.007 0.1 -9999 0 -0.25 45 45
RHOA 0.017 0.05 -9999 0 -0.26 1 1
PIK3CB 0.015 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.097 -9999 0 -0.26 36 36
MAGI3 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.04 0.15 -9999 0 -0.36 59 59
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.014 0.12 -9999 0 -0.33 26 26
NF kappa B1 p50/RelA -0.053 0.12 -9999 0 -0.43 20 20
endothelial cell migration -0.054 0.22 -9999 0 -0.56 60 60
ADCY4 -0.12 0.23 -9999 0 -0.48 92 92
ADCY5 -0.24 0.31 -9999 0 -0.58 159 159
ADCY6 -0.11 0.23 -9999 0 -0.47 92 92
ADCY7 -0.11 0.23 -9999 0 -0.47 92 92
ADCY1 -0.12 0.23 -9999 0 -0.47 96 96
ADCY2 -0.21 0.3 -9999 0 -0.55 142 142
ADCY3 -0.11 0.23 -9999 0 -0.47 92 92
ADCY8 -0.12 0.23 -9999 0 -0.48 92 92
ADCY9 -0.12 0.24 -9999 0 -0.49 93 93
GSK3B 0.002 0.096 -9999 0 -0.3 17 17
arachidonic acid secretion -0.12 0.23 -9999 0 -0.48 94 94
GNG2 0.007 0.07 -9999 0 -0.57 6 6
TRIP6 0.024 0.022 -9999 0 -10000 0 0
GNAO1 -0.13 0.23 -9999 0 -0.41 154 154
HRAS 0.016 0 -9999 0 -10000 0 0
NFKBIA 0 0.12 -9999 0 -0.35 16 16
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.08 -9999 0 -0.92 3 3
JUN -0.007 0.11 -9999 0 -0.57 16 16
LPA/LPA2/NHERF2 -0.007 0.035 -9999 0 -0.33 3 3
TIAM1 -0.005 0.094 -9999 0 -1.1 3 3
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
mol:IP3 0.001 0.098 -9999 0 -0.26 36 36
PLCB3 0.024 0.036 -9999 0 -0.29 3 3
FOS -0.17 0.27 -9999 0 -0.57 129 129
positive regulation of mitosis -0.12 0.23 -9999 0 -0.48 94 94
LPA/LPA1-2-3 -0.045 0.16 -9999 0 -0.36 66 66
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation -0.008 0.12 -9999 0 -0.35 24 24
GNAZ -0.099 0.2 -9999 0 -0.38 130 130
EGFR/PI3K-beta/Gab1 -0.065 0.13 -9999 0 -0.48 26 26
positive regulation of dendritic cell cytokine production -0.072 0.15 -9999 0 -0.36 66 66
LPA/LPA2/MAGI-3 -0.006 0.035 -9999 0 -0.33 3 3
ARHGEF1 0 0.12 -9999 0 -0.53 7 7
GNAI2 -0.02 0.14 -9999 0 -0.33 60 60
GNAI3 -0.02 0.14 -9999 0 -0.33 60 60
GNAI1 -0.023 0.14 -9999 0 -0.33 63 63
LPA/LPA3 -0.036 0.13 -9999 0 -0.41 38 38
LPA/LPA2 -0.004 0.046 -9999 0 -0.4 3 3
LPA/LPA1 -0.058 0.15 -9999 0 -0.4 60 60
HB-EGF/EGFR -0.083 0.18 -9999 0 -0.33 126 126
HBEGF -0.091 0.19 -9999 0 -0.38 119 119
mol:DAG 0.001 0.098 -9999 0 -0.26 36 36
cAMP biosynthetic process -0.16 0.27 -9999 0 -0.48 142 142
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0.001 -9999 0 -10000 0 0
LYN 0 0.12 -9999 0 -0.34 18 18
GNAQ -0.009 0.094 -9999 0 -0.29 35 35
LPAR2 0.012 0.045 -9999 0 -0.51 3 3
LPAR3 -0.039 0.17 -9999 0 -0.56 38 38
LPAR1 -0.039 0.17 -9999 0 -0.6 31 31
IL8 -0.12 0.23 -9999 0 -0.49 93 93
PTK2 -0.031 0.15 -9999 0 -0.34 60 60
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
CASP3 -0.04 0.15 -9999 0 -0.36 59 59
EGFR -0.008 0.11 -9999 0 -0.54 17 17
PLCG1 -0.019 0.11 -9999 0 -0.29 48 48
PLD2 -0.031 0.15 -9999 0 -0.34 60 60
G12/G13 -0.009 0.12 -9999 0 -0.36 31 31
PI3K-beta -0.034 0.09 -9999 0 -0.45 10 10
cell migration -0.019 0.054 -9999 0 -0.22 9 9
SLC9A3R2 0.016 0 -9999 0 -10000 0 0
PXN -0.009 0.12 -9999 0 -0.36 24 24
HRAS/GTP -0.12 0.24 -9999 0 -0.49 94 94
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.13 0.23 -9999 0 -0.51 110 110
PRKCE 0.016 0 -9999 0 -10000 0 0
PRKCD 0.009 0.094 -9999 0 -0.33 7 7
Gi(beta/gamma) -0.11 0.23 -9999 0 -0.46 94 94
mol:LPA -0.01 0.051 -9999 0 -0.19 29 29
TRIP6/p130 Cas/FAK1/Paxillin -0.051 0.12 -9999 0 -0.48 17 17
MAPKKK cascade -0.12 0.23 -9999 0 -0.48 94 94
contractile ring contraction involved in cytokinesis 0.017 0.049 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.054 0.15 -9999 0 -0.32 90 90
GNA15 -0.011 0.098 -9999 0 -0.3 38 38
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT -0.015 0.12 -9999 0 -0.34 25 25
GNA11 -0.01 0.099 -9999 0 -0.31 35 35
Rac1/GTP 0.023 0.087 -9999 0 -0.99 3 3
MMP2 -0.054 0.22 -9999 0 -0.56 60 60
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.075 0.2 -9999 0 -0.59 56 56
PDGF/PDGFRA/CRKL -0.042 0.15 -9999 0 -0.42 57 57
positive regulation of JUN kinase activity -0.011 0.11 -9999 0 -0.29 56 56
CRKL 0.013 0.036 -9999 0 -0.51 2 2
PDGF/PDGFRA/Caveolin-3 -0.052 0.15 -9999 0 -0.42 58 58
AP1 -0.34 0.46 -9999 0 -1 129 129
mol:IP3 -0.05 0.16 -9999 0 -0.43 56 56
PLCG1 -0.05 0.16 -9999 0 -0.43 56 56
PDGF/PDGFRA/alphaV Integrin -0.041 0.15 -9999 0 -0.42 56 56
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.05 0.16 -9999 0 -0.43 56 56
CAV3 0 0.044 -9999 0 -0.51 3 3
CAV1 -0.012 0.12 -9999 0 -0.57 19 19
SHC/Grb2/SOS1 -0.01 0.12 -9999 0 -0.3 56 56
PDGF/PDGFRA/Shf -0.047 0.16 -9999 0 -0.43 60 60
FOS -0.3 0.48 -9999 0 -0.99 129 129
JUN -0.038 0.094 -9999 0 -0.48 16 16
oligodendrocyte development -0.041 0.15 -9999 0 -0.42 56 56
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
mol:DAG -0.05 0.16 -9999 0 -0.43 56 56
PDGF/PDGFRA -0.075 0.2 -9999 0 -0.59 56 56
actin cytoskeleton reorganization -0.04 0.15 -9999 0 -0.41 56 56
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.014 0.026 -9999 0 -0.51 1 1
PI3K -0.023 0.13 -9999 0 -0.34 57 57
PDGF/PDGFRA/Crk/C3G -0.023 0.13 -9999 0 -0.34 56 56
JAK1 -0.038 0.15 -9999 0 -0.41 56 56
ELK1/SRF -0.009 0.12 -9999 0 -0.35 24 24
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.006 0.076 -9999 0 -0.57 7 7
CSNK2A1 0.022 0.028 -9999 0 -10000 0 0
GO:0007205 -0.054 0.16 -9999 0 -0.46 56 56
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.011 0.11 -9999 0 -0.29 56 56
PDGF/PDGFRA/SHB -0.04 0.15 -9999 0 -0.41 56 56
PDGF/PDGFRA/Caveolin-1 -0.059 0.19 -9999 0 -0.47 64 64
ITGAV 0.014 0.029 -9999 0 -0.57 1 1
ELK1 -0.049 0.15 -9999 0 -0.41 56 56
PIK3CA 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.04 0.15 -9999 0 -0.41 56 56
JAK-STAT cascade -0.038 0.15 -9999 0 -0.41 56 56
cell proliferation -0.047 0.16 -9999 0 -0.43 60 60
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0.036 -10000 0 -0.51 2 2
RAS family/GTP/Tiam1 -0.083 0.12 -10000 0 -0.27 49 49
NT3 (dimer)/TRKC -0.26 0.27 -10000 0 -0.48 226 226
NT3 (dimer)/TRKB -0.26 0.3 -10000 0 -0.48 230 230
SHC/Grb2/SOS1/GAB1/PI3K 0.043 0.016 -10000 0 -0.24 1 1
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.096 0.23 -10000 0 -0.57 78 78
PIK3CA 0.016 0 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 0.005 0.068 -10000 0 -0.51 7 7
NTRK2 -0.22 0.28 -10000 0 -0.57 164 164
NTRK3 -0.27 0.29 -10000 0 -0.57 196 196
NT-4/5 (dimer)/TRKB -0.22 0.27 -10000 0 -0.44 214 214
neuron apoptosis 0.18 0.25 0.52 121 -10000 0 121
SHC 2-3/Grb2 -0.2 0.28 -10000 0 -0.57 121 121
SHC1 0.014 0.026 -10000 0 -0.51 1 1
SHC2 -0.21 0.28 -10000 0 -0.63 103 103
SHC3 -0.21 0.26 -10000 0 -0.58 113 113
STAT3 (dimer) 0.011 0.061 -10000 0 -0.34 7 7
NT3 (dimer)/TRKA -0.13 0.22 -10000 0 -0.39 154 154
RIN/GDP -0.063 0.1 -10000 0 -0.24 32 32
GIPC1 0.016 0 -10000 0 -10000 0 0
KRAS 0.014 0.026 -10000 0 -0.51 1 1
DNAJA3 -0.1 0.16 -10000 0 -0.37 92 92
RIN/GTP 0 0.018 -10000 0 -0.37 1 1
CCND1 0.007 0.13 -10000 0 -0.52 21 21
MAGED1 0.016 0 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.023 0.14 -10000 0 -0.57 27 27
SHC/GRB2/SOS1 0.031 0.016 -10000 0 -0.29 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.049 0.17 -10000 0 -0.37 81 81
TRKA/NEDD4-2 0.015 0.049 -10000 0 -0.36 7 7
ELMO1 0.011 0.05 -10000 0 -0.57 3 3
RhoG/GTP/ELMO1/DOCK1 0.017 0.046 -10000 0 -0.43 4 4
NGF -0.062 0.2 -10000 0 -0.57 54 54
HRAS 0.016 0 -10000 0 -10000 0 0
DOCK1 0.013 0.041 -10000 0 -0.57 2 2
GAB2 0.014 0.029 -10000 0 -0.57 1 1
RIT2 0 0.025 -10000 0 -0.51 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.007 0.068 -10000 0 -0.51 7 7
DNM1 0 0.095 -10000 0 -0.57 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.1 0.16 -10000 0 -0.36 94 94
mol:GDP -0.094 0.15 -10000 0 -0.35 44 44
NGF (dimer) -0.062 0.2 -10000 0 -0.57 54 54
RhoG/GDP 0.008 0.037 -10000 0 -0.42 3 3
RIT1/GDP -0.057 0.1 -10000 0 -0.24 29 29
TIAM1 0.011 0.05 -10000 0 -0.57 3 3
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
BDNF (dimer)/TRKB -0.18 0.24 -10000 0 -0.4 201 201
KIDINS220/CRKL/C3G 0.021 0.026 -10000 0 -0.36 2 2
SHC/RasGAP 0.022 0.019 -10000 0 -0.36 1 1
FRS2 family/SHP2 0.026 0.042 -10000 0 -0.29 7 7
SHC/GRB2/SOS1/GAB1 0.04 0.015 -10000 0 -10000 0 0
RIT1/GTP 0.012 0 -10000 0 -10000 0 0
NT3 (dimer) -0.095 0.23 -10000 0 -0.57 77 77
RAP1/GDP -0.066 0.067 -10000 0 -0.22 9 9
KIDINS220/CRKL 0.013 0.036 -10000 0 -0.51 2 2
BDNF (dimer) -0.096 0.23 -10000 0 -0.57 78 78
ubiquitin-dependent protein catabolic process -0.024 0.13 -10000 0 -0.33 61 61
Schwann cell development -0.054 0.037 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.035 0.038 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.044 0.022 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.32 0.28 -10000 0 -0.61 168 168
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
Rap1/GTP -0.063 0.072 -10000 0 -10000 0 0
STAT3 0.011 0.061 -10000 0 -0.34 7 7
axon guidance -0.31 0.26 -10000 0 -0.58 168 168
MAPK3 -0.035 0.15 -10000 0 -0.34 69 69
MAPK1 -0.035 0.15 -10000 0 -0.34 69 69
CDC42/GDP -0.057 0.1 -10000 0 -0.24 32 32
NTF3 -0.095 0.23 -10000 0 -0.57 77 77
NTF4 -0.023 0.14 -10000 0 -0.57 27 27
NGF (dimer)/TRKA/FAIM -0.024 0.13 -10000 0 -0.34 61 61
PI3K 0.022 0.021 -10000 0 -0.41 1 1
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.14 0.17 -10000 0 -0.38 96 96
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.22 0.25 -10000 0 -0.43 228 228
RGS19 0.014 0.026 -10000 0 -0.51 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.01 0.073 -10000 0 -10000 0 0
Rac1/GDP -0.057 0.1 -10000 0 -0.24 30 30
NGF (dimer)/TRKA/GRIT -0.035 0.13 -10000 0 -0.34 61 61
neuron projection morphogenesis -0.072 0.18 -10000 0 -0.52 26 26
NGF (dimer)/TRKA/NEDD4-2 -0.024 0.13 -10000 0 -0.34 61 61
MAP2K1 0.045 0.014 -10000 0 -10000 0 0
NGFR -0.12 0.25 -10000 0 -0.57 95 95
NGF (dimer)/TRKA/GIPC/GAIP -0.005 0.11 -10000 0 -0.42 9 9
RAS family/GTP/PI3K 0.035 0.016 -10000 0 -0.24 1 1
FRS2 family/SHP2/GRB2/SOS1 0.042 0.036 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.05 -10000 0 -0.57 3 3
MAPKKK cascade -0.13 0.24 -10000 0 -0.73 54 54
RASA1 0.016 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.015 0.049 -10000 0 -0.36 7 7
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.36 194 194
NGF (dimer)/TRKA/p62/Atypical PKCs -0.004 0.12 -10000 0 -0.55 2 2
MATK -0.025 0.15 -10000 0 -0.56 29 29
NEDD4L 0.016 0 -10000 0 -10000 0 0
RAS family/GDP -0.062 0.063 -10000 0 -0.23 3 3
NGF (dimer)/TRKA -0.11 0.18 -10000 0 -0.36 123 123
Rac1/GTP -0.11 0.11 -10000 0 -0.29 83 83
FRS2 family/SHP2/CRK family 0.041 0.041 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.11 0.15 0.42 59 -10000 0 59
GNAI2 0.016 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.008 0.064 -10000 0 -0.31 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.17 0.27 -10000 0 -0.57 129 129
RhoA/GTP -0.09 0.18 -10000 0 -0.43 59 59
negative regulation of cAMP metabolic process -0.11 0.19 -10000 0 -0.34 131 131
GNAZ -0.11 0.24 -10000 0 -0.57 89 89
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -10000 0 -10000 0 0
S1PR5 -0.005 0.1 -10000 0 -0.52 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.11 0.19 -10000 0 -0.35 131 131
RhoA/GDP 0.012 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.05 -10000 0 -0.57 3 3
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.019 0.028 -9999 0 -10000 0 0
VDR 0.011 0.048 -9999 0 -0.55 3 3
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.011 0.13 -9999 0 -0.39 7 7
RXRs/LXRs/DNA/Oxysterols 0.007 0.12 -9999 0 -0.38 7 7
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.006 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.004 0.11 -9999 0 -0.27 51 51
RXRs/NUR77 -0.23 0.22 -9999 0 -0.37 273 273
RXRs/PPAR -0.045 0.14 -9999 0 -0.37 17 17
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0.035 -9999 0 -0.4 3 3
RARs/VDR/DNA/Vit D3 0.009 0.094 -9999 0 -0.29 36 36
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.048 -9999 0 -0.55 3 3
RARs/RARs/DNA/9cRA 0.004 0.088 -9999 0 -0.29 34 34
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.043 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.004 0.11 -9999 0 -0.27 51 51
THRA 0.016 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0.035 -9999 0 -0.4 3 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.044 0.15 -9999 0 -0.3 106 106
NR1H4 -0.12 0.23 -9999 0 -0.56 89 89
RXRs/LXRs/DNA -0.014 0.15 -9999 0 -0.38 7 7
NR1H2 0.022 0.005 -9999 0 -10000 0 0
NR1H3 0.022 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.04 0.14 -9999 0 -0.28 108 108
NR4A1 -0.31 0.29 -9999 0 -0.57 230 230
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.079 0.16 -9999 0 -0.28 113 113
RXRG -0.14 0.25 -9999 0 -0.56 107 107
RXR alpha/CCPG 0.026 0.022 -9999 0 -0.4 1 1
RXRA 0.02 0.029 -9999 0 -0.56 1 1
RXRB 0.022 0.005 -9999 0 -10000 0 0
THRB -0.019 0.14 -9999 0 -0.57 24 24
PPARG -0.024 0.15 -9999 0 -0.56 28 28
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.009 0.13 -9999 0 -0.48 5 5
mol:Oxysterols 0.006 0.007 -9999 0 -10000 0 0
cholesterol transport 0.007 0.12 -9999 0 -0.38 7 7
PPARA 0.013 0.041 -9999 0 -0.57 2 2
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.033 0.16 -9999 0 -0.57 34 34
RXRs/NUR77/BCL2 -0.2 0.2 -9999 0 -0.32 275 275
SREBF1 0.016 0.11 -9999 0 -0.47 2 2
RXRs/RXRs/DNA/9cRA -0.044 0.15 -9999 0 -0.3 106 106
ABCA1 0.017 0.11 -9999 0 -0.46 1 1
RARs/THRs 0.002 0.12 -9999 0 -0.31 51 51
RXRs/FXR -0.11 0.21 -9999 0 -0.35 157 157
BCL2 -0.007 0.11 -9999 0 -0.57 16 16
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.032 -9999 0 -0.41 2 2
PDGFRB -0.002 0.091 -9999 0 -0.58 10 10
SPHK1 -0.035 0.061 -9999 0 -1.1 1 1
mol:S1P -0.04 0.063 -9999 0 -0.66 2 2
S1P1/S1P/Gi -0.19 0.27 -9999 0 -0.49 147 147
GNAO1 -0.17 0.27 -9999 0 -0.57 129 129
PDGFB-D/PDGFRB/PLCgamma1 -0.16 0.25 -9999 0 -0.51 99 99
PLCG1 -0.17 0.25 -9999 0 -0.54 98 98
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.091 -9999 0 -0.58 10 10
GNAI2 0.012 0.007 -9999 0 -10000 0 0
GNAI3 0.012 0.007 -9999 0 -10000 0 0
GNAI1 0.008 0.051 -9999 0 -0.58 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.015 0.028 -9999 0 -0.34 2 2
S1P1/S1P -0.042 0.07 -9999 0 -0.42 4 4
negative regulation of cAMP metabolic process -0.18 0.26 -9999 0 -0.48 147 147
MAPK3 -0.22 0.32 -9999 0 -0.6 145 145
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
KDR 0.012 0.041 -9999 0 -0.57 2 2
PLCB2 -0.014 0.081 -9999 0 -0.35 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.034 0.058 -9999 0 -0.35 4 4
receptor internalization -0.04 0.066 -9999 0 -0.39 4 4
PTGS2 -0.31 0.47 -9999 0 -1.1 106 106
Rac1/GTP -0.034 0.058 -9999 0 -0.35 4 4
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA 0.015 0.003 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.18 0.26 -9999 0 -0.48 147 147
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.12 0.24 -9999 0 -0.57 89 89
MAPK1 -0.22 0.32 -9999 0 -0.6 145 145
S1P1/S1P/PDGFB-D/PDGFRB -0.032 0.11 -9999 0 -0.43 11 11
ABCC1 0.011 0.037 -9999 0 -0.51 2 2
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.01 0.14 -9999 0 -0.34 54 54
MAP4K1 -0.003 0.1 -9999 0 -0.56 13 13
MAP3K8 0.011 0.05 -9999 0 -0.57 3 3
PRKCB -0.15 0.26 -9999 0 -0.57 118 118
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.013 0.036 -9999 0 -0.51 2 2
MAP3K1 0.015 0.11 -9999 0 -0.56 6 6
JUN -0.15 0.29 -9999 0 -0.57 123 123
MAP3K7 0.015 0.11 -9999 0 -0.56 6 6
GRAP2 -0.049 0.18 -9999 0 -0.57 45 45
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 0.022 0.11 -9999 0 -0.52 7 7
LAT 0.014 0.026 -9999 0 -0.51 1 1
LCP2 0.011 0.05 -9999 0 -0.57 3 3
MAPK8 -0.15 0.3 -9999 0 -0.6 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.12 -9999 0 -0.28 46 46
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.001 0.13 -9999 0 -0.32 50 50
LPA4-mediated signaling events

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
ADCY4 0.021 0.026 -9999 0 -0.35 2 2
ADCY5 -0.16 0.18 -9999 0 -0.35 206 206
ADCY6 0.022 0 -9999 0 -10000 0 0
ADCY7 0.022 0 -9999 0 -10000 0 0
ADCY1 0.013 0.056 -9999 0 -0.31 12 12
ADCY2 -0.12 0.18 -9999 0 -0.35 153 153
ADCY3 0.022 0 -9999 0 -10000 0 0
ADCY8 0.011 0.031 -9999 0 -0.3 4 4
PRKCE 0.013 0 -9999 0 -10000 0 0
ADCY9 0.016 0.048 -9999 0 -0.35 7 7
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.062 0.094 -9999 0 -0.28 9 9
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.017 0.051 -9999 0 -0.27 12 12
RGS9BP -0.009 0.12 -9999 0 -0.56 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0.025 -9999 0 -0.51 1 1
mol:Na + -0.1 0.18 -9999 0 -0.34 136 136
mol:ADP 0.01 0.027 -9999 0 -0.36 2 2
GNAT2 0.007 0.052 -9999 0 -0.51 4 4
RGS9-1/Gbeta5/R9AP -0.062 0.17 -9999 0 -0.35 100 100
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.006 0.038 -9999 0 -0.3 6 6
GRK7 0.011 0.026 -9999 0 -0.51 1 1
CNGB3 -0.12 0.23 -9999 0 -0.51 108 108
Cone Metarhodopsin II/X-Arrestin 0.002 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.18 -9999 0 -0.32 147 147
Cone PDE6 -0.051 0.14 -9999 0 -0.42 11 11
Cone Metarhodopsin II 0.008 0.021 -9999 0 -0.28 2 2
Na + (4 Units) -0.1 0.18 -9999 0 -0.32 147 147
GNAT2/GDP -0.048 0.14 -9999 0 -0.29 97 97
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.007 0.035 -9999 0 -0.28 6 6
Cone Transducin 0.019 0.054 -9999 0 -0.29 12 12
SLC24A2 -0.017 0.12 -9999 0 -0.51 22 22
GNB3/GNGT2 0.015 0.059 -9999 0 -0.4 8 8
GNB3 0.01 0.056 -9999 0 -0.55 4 4
GNAT2/GTP 0.006 0.037 -9999 0 -0.37 4 4
CNGA3 -0.047 0.17 -9999 0 -0.57 40 40
ARR3 0.003 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.1 0.18 -9999 0 -0.34 136 136
mol:Pi -0.062 0.17 -9999 0 -0.35 100 100
Cone CNG Channel -0.094 0.14 -9999 0 -0.52 12 12
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.017 0.12 -9999 0 -0.51 22 22
RGS9 -0.11 0.24 -9999 0 -0.57 87 87
PDE6C 0.003 0.006 -9999 0 -10000 0 0
GNGT2 0.01 0.058 -9999 0 -0.57 4 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0.036 -9999 0 -0.51 2 2
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.09 0.15 -9999 0 -0.54 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.053 0.14 -9999 0 -0.47 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.17 -9999 0 -0.35 166 166
AP1 -0.17 0.25 -9999 0 -0.52 102 102
ILK -0.1 0.16 -9999 0 -0.46 11 11
bone resorption -0.075 0.15 -9999 0 -0.48 18 18
PTK2B 0.014 0.029 -9999 0 -0.57 1 1
PYK2/p130Cas -0.083 0.15 -9999 0 -0.51 6 6
ITGAV 0.017 0.03 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0 0.097 -9999 0 -0.4 22 22
alphaV/beta3 Integrin/Osteopontin -0.15 0.16 -9999 0 -0.34 85 85
MAP3K1 -0.1 0.16 -9999 0 -0.32 52 52
JUN -0.007 0.11 -9999 0 -0.57 16 16
MAPK3 -0.09 0.16 -9999 0 -0.34 41 41
MAPK1 -0.09 0.16 -9999 0 -0.34 41 41
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.092 0.16 -9999 0 -0.46 12 12
ITGB3 -0.047 0.18 -9999 0 -0.56 46 46
NFKBIA -0.073 0.15 -9999 0 -0.52 6 6
FOS -0.17 0.27 -9999 0 -0.57 129 129
CD44 -0.006 0.11 -9999 0 -0.56 15 15
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU -0.09 0.18 -9999 0 -0.48 41 41
NF kappa B1 p50/RelA -0.095 0.1 -9999 0 -0.45 6 6
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.035 0.13 -9999 0 -0.4 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.11 0.16 -9999 0 -0.32 49 49
VAV3 -0.097 0.16 -9999 0 -0.52 10 10
MAP3K14 -0.1 0.16 -9999 0 -0.34 49 49
ROCK2 0.006 0.076 -9999 0 -0.57 7 7
SPP1 -0.19 0.26 -9999 0 -0.5 165 165
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.082 0.14 -9999 0 -0.48 10 10
MMP2 -0.16 0.24 -9999 0 -0.55 72 72
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.17 0.27 -9999 0 -0.57 129 129
CDC42/GTP -0.088 0.18 -9999 0 -0.44 58 58
PLCG1 -0.091 0.18 -9999 0 -0.45 58 58
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0.023 0 -9999 0 -10000 0 0
cell migration -0.11 0.16 -9999 0 -0.43 58 58
S1PR5 -0.005 0.1 -9999 0 -0.52 16 16
S1PR4 0.006 0.073 -9999 0 -0.54 7 7
MAPK3 -0.091 0.18 -9999 0 -0.45 58 58
MAPK1 -0.091 0.18 -9999 0 -0.45 58 58
S1P/S1P5/Gi -0.11 0.19 -9999 0 -0.35 131 131
GNAI1 0.011 0.05 -9999 0 -0.57 3 3
CDC42/GDP 0.012 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.008 0.064 -9999 0 -0.31 16 16
RHOA 0.032 0.039 -9999 0 -0.28 4 4
S1P/S1P4/Gi -0.1 0.2 -9999 0 -0.35 130 130
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.57 89 89
S1P/S1P4/G12/G13 0.025 0.042 -9999 0 -0.29 7 7
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.001 0.09 -9999 0 -0.57 10 10
LRPAP1 0.014 0.026 -9999 0 -0.51 1 1
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.22 -9999 0 -0.38 189 189
CaM/Ca2+ 0.012 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.14 0.2 -9999 0 -0.36 146 146
IQGAP1/CaM 0.023 0 -9999 0 -10000 0 0
DAB1 -0.07 0.2 -9999 0 -0.54 59 59
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.051 0.17 -9999 0 -0.51 52 52
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.048 0.15 -9999 0 -0.36 77 77
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 -0.013 0.12 -9999 0 -0.51 22 22
LIS1/Poliovirus Protein 3A 0.02 0 -9999 0 -10000 0 0
CDK5R2 -0.023 0.13 -9999 0 -0.51 27 27
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.38 189 189
YWHAE 0.014 0.029 -9999 0 -0.57 1 1
NDEL1/14-3-3 E -0.094 0.18 -9999 0 -0.44 44 44
MAP1B -0.034 0.096 -9999 0 -0.31 45 45
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.2 -9999 0 -0.51 45 45
RELN -0.2 0.28 -9999 0 -0.57 147 147
PAFAH/LIS1 -0.01 0.11 -9999 0 -0.29 52 52
LIS1/CLIP170 0.031 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.092 0.11 -9999 0 -0.35 34 34
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.18 -9999 0 -0.46 41 41
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.11 0.18 -9999 0 -0.44 55 55
LIS1/IQGAP1 0.031 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.026 0 -9999 0 -10000 0 0
PAFAH1B3 -0.014 0.12 -9999 0 -0.51 23 23
PAFAH1B2 0.016 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.006 0.067 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.083 0.17 -9999 0 -0.43 37 37
LRP8 -0.082 0.2 -9999 0 -0.51 76 76
NDEL1/Katanin 60 -0.093 0.18 -9999 0 -0.44 44 44
P39/CDK5 -0.12 0.2 -9999 0 -0.51 47 47
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0 -9999 0 -10000 0 0
CDK5 -0.12 0.19 -9999 0 -0.52 35 35
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.12 0.19 -9999 0 -0.56 27 27
RELN/VLDLR -0.14 0.21 -9999 0 -0.37 153 153
CDC42 0 0 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.18 0.19 -10000 0 -0.37 205 205
TP53 -0.043 0.06 -10000 0 -10000 0 0
Senescence -0.043 0.06 -10000 0 -10000 0 0
Apoptosis -0.043 0.06 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.081 0.12 0.26 4 -0.32 13 17
MDM4 0.016 0 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.048 0.17 -10000 0 -0.41 53 53
IKBKB -0.004 0.075 -10000 0 -0.26 7 7
AKT1 -0.043 0.12 -10000 0 -0.24 76 76
IKBKG -0.002 0.078 -10000 0 -0.27 9 9
CALM1 -0.042 0.14 -10000 0 -0.42 32 32
PIK3CA 0.016 0 -10000 0 -10000 0 0
MAP3K1 -0.08 0.23 -10000 0 -0.53 67 67
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.14 -10000 0 -0.45 32 32
DOK1 0.014 0.026 -10000 0 -0.51 1 1
AP-1 -0.049 0.11 -10000 0 -0.25 57 57
LYN 0.016 0 -10000 0 -10000 0 0
BLNK -0.003 0.1 -10000 0 -0.57 13 13
SHC1 0.014 0.026 -10000 0 -0.51 1 1
BCR complex -0.087 0.21 -10000 0 -0.46 92 92
CD22 -0.18 0.3 -10000 0 -0.7 80 80
CAMK2G -0.031 0.13 -10000 0 -0.41 26 26
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.006 0.076 -10000 0 -0.57 7 7
SHC/GRB2/SOS1 -0.07 0.14 -10000 0 -0.48 25 25
GO:0007205 -0.054 0.15 -10000 0 -0.46 32 32
SYK 0.01 0.058 -10000 0 -0.57 4 4
ELK1 -0.043 0.14 -10000 0 -0.43 32 32
NFATC1 -0.092 0.23 -10000 0 -0.52 71 71
B-cell antigen/BCR complex -0.087 0.21 -10000 0 -0.46 92 92
PAG1/CSK 0.023 0 -10000 0 -10000 0 0
NFKBIB 0.011 0.029 -10000 0 -10000 0 0
HRAS -0.037 0.14 -10000 0 -0.41 31 31
NFKBIA 0.011 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.017 0.024 -10000 0 -10000 0 0
RasGAP/Csk -0.058 0.2 -10000 0 -0.58 36 36
mol:GDP -0.051 0.14 -10000 0 -0.44 32 32
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B -0.016 0.13 -10000 0 -0.55 23 23
NF-kappa-B/RelA/I kappa B alpha 0.017 0.024 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.11 0.24 -10000 0 -0.51 87 87
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
mol:IP3 -0.054 0.15 -10000 0 -0.47 32 32
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.12 0.19 -10000 0 -0.47 55 55
CHUK -0.002 0.078 -10000 0 -0.27 9 9
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.053 0.12 -10000 0 -0.48 18 18
PTPN6 -0.13 0.3 -10000 0 -0.65 80 80
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 0.013 0.032 -10000 0 -0.1 18 18
VAV2 -0.14 0.28 -10000 0 -0.63 78 78
ubiquitin-dependent protein catabolic process 0.016 0.028 -10000 0 -10000 0 0
BTK -0.059 0.26 0.35 5 -1.2 21 26
CD19 -0.18 0.28 -10000 0 -0.6 94 94
MAP4K1 -0.003 0.1 -10000 0 -0.56 13 13
CD72 -0.002 0.096 -10000 0 -0.51 14 14
PAG1 0.016 0 -10000 0 -10000 0 0
MAPK14 -0.057 0.2 -10000 0 -0.44 65 65
SH3BP5 0.014 0.029 -10000 0 -0.57 1 1
PIK3AP1 -0.05 0.17 -10000 0 -0.51 37 37
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.064 0.21 -10000 0 -0.44 83 83
RAF1 -0.027 0.13 -10000 0 -0.45 19 19
RasGAP/p62DOK/SHIP -0.093 0.19 -10000 0 -0.59 37 37
CD79A -0.11 0.24 -10000 0 -0.56 87 87
re-entry into mitotic cell cycle -0.049 0.11 -10000 0 -0.25 57 57
RASA1 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.006 0.11 -10000 0 -0.41 14 14
MAPK1 -0.006 0.11 -10000 0 -0.41 14 14
CD72/SHP1 -0.12 0.28 -10000 0 -0.64 75 75
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.059 0.2 -10000 0 -0.44 68 68
actin cytoskeleton organization -0.1 0.24 -10000 0 -0.54 71 71
NF-kappa-B/RelA 0.038 0.046 -10000 0 -10000 0 0
Calcineurin -0.045 0.1 -10000 0 -0.47 14 14
PI3K -0.15 0.21 -10000 0 -0.5 91 91
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.052 0.16 -10000 0 -0.46 36 36
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.1 0.28 -10000 0 -0.78 50 50
DAPP1 -0.14 0.3 -10000 0 -0.89 46 46
cytokine secretion -0.083 0.21 -10000 0 -0.47 71 71
mol:DAG -0.054 0.15 -10000 0 -0.47 32 32
PLCG2 0.009 0.06 -10000 0 -0.53 5 5
MAP2K1 -0.016 0.12 -10000 0 -0.46 14 14
B-cell antigen/BCR complex/FcgammaRIIB -0.088 0.23 -10000 0 -0.46 100 100
mol:PI-3-4-5-P3 -0.11 0.14 -10000 0 -0.34 90 90
ETS1 -0.02 0.12 -10000 0 -0.47 14 14
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.05 0.18 -10000 0 -0.56 25 25
B-cell antigen/BCR complex/LYN -0.12 0.26 -10000 0 -0.52 90 90
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.11 0.26 -10000 0 -0.59 71 71
B-cell antigen/BCR complex/LYN/SYK -0.16 0.27 -10000 0 -0.65 77 77
CARD11 -0.051 0.15 -10000 0 -0.43 38 38
FCGR2B -0.027 0.15 -10000 0 -0.56 30 30
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.008 0.038 -10000 0 -0.096 1 1
PTPRC -0.056 0.19 -10000 0 -0.57 50 50
PDPK1 -0.044 0.12 -10000 0 -0.25 61 61
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0.016 0.027 -10000 0 -0.1 9 9
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.016 0.29 -10000 0 -0.82 42 42
NCK1/PAK1/Dok-R -0.045 0.12 -10000 0 -0.41 42 42
NCK1/Dok-R -0.028 0.34 -10000 0 -1 42 42
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.009 0.071 0.24 34 -10000 0 34
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.015 0.026 -10000 0 -0.5 1 1
Rac/GDP 0.012 0 -10000 0 -10000 0 0
F2 -0.019 0.15 0.25 33 -0.53 26 59
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.095 0.28 -10000 0 -0.93 42 42
FN1 -0.035 0.16 -10000 0 -0.53 38 38
PLD2 -0.026 0.34 -10000 0 -1 42 42
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.056 0.18 -10000 0 -0.51 56 56
ELK1 -0.008 0.31 -10000 0 -0.93 42 42
GRB7 -0.012 0.12 -10000 0 -0.53 21 21
PAK1 0.014 0.029 -10000 0 -0.57 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.32 -10000 0 -1 42 42
CDKN1A 0.022 0.21 -10000 0 -0.59 31 31
ITGA5 -0.007 0.11 -10000 0 -0.57 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.028 0.34 -10000 0 -1 42 42
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO 0.037 0.22 -10000 0 -0.61 42 42
PLG -0.035 0.34 -10000 0 -1 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.004 0.28 -10000 0 -0.81 42 42
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.015 0.029 -10000 0 -0.57 1 1
ANGPT2 -0.046 0.2 -10000 0 -0.59 29 29
BMX -0.11 0.37 -10000 0 -1.1 42 42
ANGPT1 -0.06 0.37 -10000 0 -1.3 34 34
tube development 0.014 0.22 -10000 0 -0.63 35 35
ANGPT4 0.001 0.072 -10000 0 -0.5 8 8
response to hypoxia -0.001 0.022 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.066 0.36 -10000 0 -1.1 42 42
alpha5/beta1 Integrin 0.006 0.084 -10000 0 -0.41 16 16
FGF2 -0.18 0.28 -10000 0 -0.57 136 136
STAT5A (dimer) 0.014 0.25 -10000 0 -0.71 34 34
mol:L-citrulline 0.037 0.22 -10000 0 -0.61 42 42
AGTR1 -0.23 0.29 -10000 0 -0.57 175 175
MAPK14 -0.024 0.34 -10000 0 -1 42 42
Tie2/SHP2 -0.039 0.17 -10000 0 -1.1 9 9
TEK 0.01 0.2 -10000 0 -1.2 9 9
RPS6KB1 0.014 0.28 -10000 0 -0.79 42 42
Angiotensin II/AT1 -0.17 0.21 -10000 0 -0.42 175 175
Tie2/Ang1/GRB2 -0.03 0.35 -10000 0 -1.1 42 42
MAPK3 -0.013 0.32 -10000 0 -0.95 42 42
MAPK1 -0.013 0.32 -10000 0 -0.95 42 42
Tie2/Ang1/GRB7 -0.045 0.36 -10000 0 -1.1 42 42
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.028 0.34 -10000 0 -1 42 42
PI3K -0.004 0.32 -10000 0 -0.94 42 42
FES -0.025 0.34 -10000 0 -1 42 42
Crk/Dok-R -0.028 0.34 -10000 0 -1 42 42
Tie2/Ang1/ABIN2 -0.03 0.35 -10000 0 -1.1 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.023 0.26 -10000 0 -0.73 42 42
STAT5A 0.015 0.029 -10000 0 -0.57 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.014 0.28 -10000 0 -0.79 42 42
Tie2/Ang2 -0.007 0.28 -10000 0 -0.85 32 32
Tie2/Ang1 -0.037 0.37 -10000 0 -1.1 42 42
FOXO1 0.031 0.26 -10000 0 -0.73 42 42
ELF1 0.024 0.016 -10000 0 -10000 0 0
ELF2 -0.028 0.34 -10000 0 -1 42 42
mol:Choline -0.022 0.33 -10000 0 -0.99 42 42
cell migration -0.029 0.072 -10000 0 -0.23 43 43
FYN 0.007 0.25 -10000 0 -0.72 34 34
DOK2 -0.006 0.11 -10000 0 -0.56 15 15
negative regulation of cell cycle 0.026 0.2 -10000 0 -0.54 31 31
ETS1 0.007 0.068 -10000 0 -0.24 4 4
PXN 0.031 0.24 -10000 0 -0.66 42 42
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 0.031 0.25 -10000 0 -0.69 42 42
RAC1 0.016 0 -10000 0 -10000 0 0
TNF -0.019 0.13 -10000 0 -0.5 21 21
MAPKKK cascade -0.022 0.33 -10000 0 -0.99 42 42
RASA1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.029 0.35 -10000 0 -1.1 42 42
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.041 0.2 -10000 0 -0.55 42 42
mol:Phosphatidic acid -0.022 0.33 -10000 0 -0.99 42 42
mol:Angiotensin II 0.002 0.001 -10000 0 -10000 0 0
mol:NADP 0.037 0.22 -10000 0 -0.61 42 42
Rac1/GTP -0.078 0.23 -10000 0 -0.74 42 42
MMP2 -0.051 0.36 -10000 0 -1.1 42 42
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.029 -10000 0 -0.5 1 1
SVIL 0.007 0.059 -10000 0 -0.57 4 4
ZNF318 0.023 0.033 -10000 0 -10000 0 0
JMJD2C -0.002 0.025 -10000 0 -0.073 41 41
T-DHT/AR/Ubc9 -0.12 0.19 -10000 0 -0.37 148 148
CARM1 0.015 0.002 -10000 0 -10000 0 0
PRDX1 0.016 0.002 -10000 0 -10000 0 0
PELP1 0.017 0.005 -10000 0 -10000 0 0
CTNNB1 0.013 0.01 -10000 0 -10000 0 0
AKT1 0.018 0.009 -10000 0 -10000 0 0
PTK2B 0.012 0.03 -10000 0 -0.57 1 1
MED1 0.018 0.01 -10000 0 -10000 0 0
MAK 0.012 0.083 0.19 4 -0.5 9 13
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.01 0.043 -10000 0 -0.57 2 2
GSN 0.003 0.077 -10000 0 -0.57 7 7
NCOA2 -0.019 0.14 -10000 0 -0.57 24 24
NCOA6 0.012 0.029 -10000 0 -0.51 1 1
DNA-PK 0.032 0.036 -10000 0 -10000 0 0
NCOA4 0.015 0.001 -10000 0 -10000 0 0
PIAS3 0.013 0.01 -10000 0 -10000 0 0
cell proliferation -0.02 0.051 0.16 1 -0.21 5 6
XRCC5 0.017 0.007 -10000 0 -10000 0 0
UBE3A 0.011 0.02 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.15 0.22 -10000 0 -0.4 160 160
FHL2 -0.023 0.13 -10000 0 -1.1 3 3
RANBP9 0.013 0.012 -10000 0 -10000 0 0
JMJD1A -0.011 0.056 -10000 0 -0.12 83 83
CDK6 0 0.095 -10000 0 -0.57 11 11
TGFB1I1 -0.006 0.1 -10000 0 -0.57 13 13
T-DHT/AR/CyclinD1 -0.14 0.2 -10000 0 -0.38 160 160
XRCC6 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.12 0.21 -10000 0 -0.38 151 151
CTDSP1 0.015 0.003 -10000 0 -10000 0 0
CTDSP2 0.021 0.022 -10000 0 -10000 0 0
BRCA1 0.012 0.03 -10000 0 -0.53 1 1
TCF4 0.011 0.073 -10000 0 -0.57 6 6
CDKN2A -0.24 0.26 -10000 0 -0.5 205 205
SRF 0.026 0.015 -10000 0 -10000 0 0
NKX3-1 -0.073 0.18 -10000 0 -0.99 7 7
KLK3 -0.052 0.3 -10000 0 -1.5 16 16
TMF1 0.015 0.003 -10000 0 -10000 0 0
HNRNPA1 0.018 0.012 -10000 0 -10000 0 0
AOF2 -0.003 0.015 -10000 0 -0.071 16 16
APPL1 0.031 0.02 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.12 0.19 -10000 0 -0.37 148 148
AR -0.2 0.29 -10000 0 -0.58 148 148
UBA3 0.015 0.003 -10000 0 -10000 0 0
PATZ1 0.018 0.012 -10000 0 -10000 0 0
PAWR 0.013 0.029 -10000 0 -0.57 1 1
PRKDC 0.017 0.007 -10000 0 -10000 0 0
PA2G4 0.019 0.015 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.11 0.18 -10000 0 -0.34 148 148
RPS6KA3 0.013 0.014 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.12 0.19 -10000 0 -0.37 148 148
LATS2 0.017 0.031 -10000 0 -0.57 1 1
T-DHT/AR/PRX1 -0.11 0.18 -10000 0 -0.33 148 148
Cyclin D3/CDK11 p58 0.012 0.003 -10000 0 -10000 0 0
VAV3 0.003 0.078 -10000 0 -0.54 8 8
KLK2 -0.088 0.12 -10000 0 -0.46 21 21
CASP8 0.016 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.2 -10000 0 -0.35 159 159
TMPRSS2 -0.21 0.42 -10000 0 -1 81 81
CCND1 -0.013 0.12 -10000 0 -0.53 21 21
PIAS1 0.011 0.02 -10000 0 -10000 0 0
mol:T-DHT -0.007 0.026 -10000 0 -0.07 38 38
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.009 0.031 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.2 -10000 0 -0.38 154 154
CMTM2 0.01 0.058 -10000 0 -0.51 5 5
SNURF -0.029 0.15 -10000 0 -0.57 30 30
ZMIZ1 0.011 0.022 -10000 0 -10000 0 0
CCND3 0.016 0.001 -10000 0 -10000 0 0
TGIF1 0.018 0.012 -10000 0 -10000 0 0
FKBP4 0.013 0.012 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.01 0.13 -10000 0 -0.35 22 22
TBX21 -0.13 0.49 -10000 0 -1.2 54 54
B2M 0.016 0.008 -10000 0 -10000 0 0
TYK2 0.018 0.022 -10000 0 -10000 0 0
IL12RB1 -0.023 0.15 -10000 0 -0.55 30 30
GADD45B -0.07 0.38 -10000 0 -0.96 45 45
IL12RB2 -0.07 0.2 -10000 0 -0.51 68 68
GADD45G -0.063 0.36 -10000 0 -0.93 41 41
natural killer cell activation 0.002 0.025 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.011 0.072 -10000 0 -0.57 6 6
IL2RA -0.035 0.16 -10000 0 -0.54 37 37
IFNG -0.091 0.21 -10000 0 -0.51 81 81
STAT3 (dimer) -0.066 0.34 -10000 0 -0.78 59 59
HLA-DRB5 -0.025 0.14 -10000 0 -0.55 27 27
FASLG -0.14 0.49 -10000 0 -1.2 64 64
NF kappa B2 p52/RelB -0.19 0.38 -10000 0 -0.98 64 64
CD4 0.009 0.041 -10000 0 -0.57 2 2
SOCS1 0.014 0.026 -10000 0 -0.51 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.044 0.17 -10000 0 -0.57 39 39
CD3E -0.049 0.18 -10000 0 -0.57 42 42
CD3G -0.055 0.19 -10000 0 -0.57 46 46
IL12Rbeta2/JAK2 -0.039 0.15 -10000 0 -0.36 69 69
CCL3 -0.13 0.48 -10000 0 -1.1 61 61
CCL4 -0.16 0.53 -10000 0 -1.3 63 63
HLA-A 0.014 0.03 -10000 0 -0.57 1 1
IL18/IL18R 0.037 0.12 -10000 0 -0.38 27 27
NOS2 -0.1 0.41 -10000 0 -1 48 48
IL12/IL12R/TYK2/JAK2/SPHK2 -0.01 0.12 -10000 0 -0.35 22 22
IL1R1 -0.11 0.43 -10000 0 -1 55 55
IL4 0.001 0.025 -10000 0 -10000 0 0
JAK2 0.016 0.037 -10000 0 -0.58 1 1
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.38 -10000 0 -0.87 66 66
RAB7A -0.021 0.3 -10000 0 -0.74 37 37
lysosomal transport -0.016 0.29 -10000 0 -0.69 38 38
FOS -0.42 0.66 -10000 0 -1.2 154 154
STAT4 (dimer) -0.062 0.39 -10000 0 -0.9 54 54
STAT5A (dimer) -0.22 0.39 -10000 0 -0.93 75 75
GZMA -0.16 0.53 -10000 0 -1.3 62 62
GZMB -0.14 0.49 -10000 0 -1.3 53 53
HLX 0.014 0.026 -10000 0 -0.51 1 1
LCK -0.13 0.48 -10000 0 -1.1 62 62
TCR/CD3/MHC II/CD4 -0.12 0.29 -10000 0 -0.63 69 69
IL2/IL2R -0.015 0.14 -10000 0 -0.42 30 30
MAPK14 -0.05 0.36 -10000 0 -0.86 50 50
CCR5 -0.085 0.41 -10000 0 -1 46 46
IL1B -0.031 0.16 -10000 0 -0.55 35 35
STAT6 -0.01 0.15 -10000 0 -0.76 5 5
STAT4 -0.013 0.13 -10000 0 -0.57 20 20
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.011 0.051 -10000 0 -0.51 4 4
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.005 0.096 -10000 0 -0.5 14 14
CD8A -0.041 0.18 -10000 0 -0.57 40 40
CD8B -0.046 0.18 -10000 0 -0.56 44 44
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.01 0.12 0.35 22 -10000 0 22
IL2RB 0.006 0.074 -10000 0 -0.55 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.049 0.35 -10000 0 -0.81 53 53
IL2RG -0.01 0.12 -10000 0 -0.54 19 19
IL12 0.003 0.095 -10000 0 -0.36 21 21
STAT5A 0.014 0.029 -10000 0 -0.57 1 1
CD247 0 0.081 -10000 0 -0.56 8 8
IL2 0.004 0.007 -10000 0 -10000 0 0
SPHK2 0.014 0.026 -10000 0 -0.51 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.076 -10000 0 -0.5 8 8
IL12/IL12R/TYK2/JAK2 -0.15 0.55 -10000 0 -1.2 64 64
MAP2K3 -0.055 0.36 -10000 0 -0.87 49 49
RIPK2 0.016 0 -10000 0 -10000 0 0
MAP2K6 -0.058 0.37 -10000 0 -0.87 50 50
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.008 0.11 -10000 0 -0.57 14 14
IL18RAP -0.011 0.13 -10000 0 -0.57 21 21
IL12Rbeta1/TYK2 -0.007 0.12 -10000 0 -0.4 30 30
EOMES -0.063 0.3 -10000 0 -1.4 19 19
STAT1 (dimer) -0.076 0.34 -10000 0 -0.77 57 57
T cell proliferation -0.031 0.29 -10000 0 -0.64 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.015 0.052 -10000 0 -0.58 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.13 0.24 -10000 0 -0.7 48 48
ATF2 -0.035 0.34 -10000 0 -0.79 47 47
Syndecan-2-mediated signaling events

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.028 0.14 -9999 0 -0.33 64 64
EPHB2 -0.02 0.13 -9999 0 -0.51 28 28
Syndecan-2/TACI -0.034 0.14 -9999 0 -0.35 66 66
LAMA1 -0.091 0.21 -9999 0 -0.52 81 81
Syndecan-2/alpha2 ITGB1 -0.034 0.15 -9999 0 -0.32 62 62
HRAS 0.016 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.008 0.093 -9999 0 -0.35 29 29
ITGA5 -0.007 0.11 -9999 0 -0.57 16 16
BAX 0.02 0.089 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.003 0.085 -9999 0 -0.3 29 29
LAMA3 -0.082 0.21 -9999 0 -0.54 72 72
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.058 -9999 0 -0.57 4 4
Syndecan-2/MMP2 -0.028 0.16 -9999 0 -0.42 52 52
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.018 0.047 -9999 0 -0.36 6 6
dendrite morphogenesis -0.019 0.12 -9999 0 -0.32 56 56
Syndecan-2/GM-CSF -0.057 0.15 -9999 0 -0.32 100 100
determination of left/right symmetry -0.007 0.11 -9999 0 -0.41 29 29
Syndecan-2/PKC delta 0.003 0.094 -9999 0 -0.34 29 29
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.041 0.14 -9999 0 -0.28 100 100
MAPK1 -0.041 0.14 -9999 0 -0.28 100 100
Syndecan-2/RACK1 0.013 0.081 -9999 0 -0.28 29 29
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.007 0.11 -9999 0 -0.41 29 29
ITGA2 0.008 0.064 -9999 0 -0.52 6 6
MAPK8 0.011 0.099 -9999 0 -0.33 32 32
Syndecan-2/alpha2/beta1 Integrin -0.038 0.14 -9999 0 -0.32 45 45
Syndecan-2/Kininogen -0.008 0.093 -9999 0 -0.35 29 29
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.021 0.077 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.003 0.085 -9999 0 -0.31 29 29
extracellular matrix organization 0.003 0.094 -9999 0 -0.34 29 29
actin cytoskeleton reorganization -0.028 0.14 -9999 0 -0.33 64 64
Syndecan-2/Caveolin-2/Ras 0.01 0.094 -9999 0 -0.31 32 32
Syndecan-2/Laminin alpha3 -0.057 0.16 -9999 0 -0.35 94 94
Syndecan-2/RasGAP 0.02 0.078 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.006 0.084 -9999 0 -0.41 16 16
PRKCD 0.016 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.019 0.12 -9999 0 -0.32 56 56
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.03 0.076 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.044 0.17 -9999 0 -0.56 40 40
RASA1 0.016 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.018 0.047 -9999 0 -0.36 6 6
Syndecan-2/Synbindin 0.003 0.094 -9999 0 -0.34 29 29
TGFB1 0.016 0 -9999 0 -10000 0 0
CASP3 0.014 0.086 -9999 0 -0.3 29 29
FN1 -0.035 0.16 -9999 0 -0.53 38 38
Syndecan-2/IL8 -0.051 0.16 -9999 0 -0.36 84 84
SDC2 -0.007 0.11 -9999 0 -0.41 29 29
KNG1 0 0 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.003 0.094 -9999 0 -0.34 29 29
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.082 0.2 -9999 0 -0.51 75 75
Syndecan-2/TGFB1 0.003 0.094 -9999 0 -0.34 29 29
Syndecan-2/Syntenin/PI-4-5-P2 0.003 0.085 -9999 0 -0.31 29 29
Syndecan-2/Ezrin 0.013 0.086 -9999 0 -0.3 29 29
PRKACA 0.014 0.086 -9999 0 -0.3 29 29
angiogenesis -0.05 0.16 -9999 0 -0.36 84 84
MMP2 -0.036 0.17 -9999 0 -0.57 36 36
IL8 -0.07 0.21 -9999 0 -0.57 60 60
calcineurin-NFAT signaling pathway -0.034 0.14 -9999 0 -0.35 66 66
S1P3 pathway

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 0.001 0.09 -9999 0 -0.57 10 10
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.1 0.19 -9999 0 -0.39 95 95
GNAO1 -0.17 0.27 -9999 0 -0.57 129 129
S1P/S1P3/G12/G13 0.025 0.05 -9999 0 -0.3 9 9
AKT1 -0.035 0.16 -9999 0 -0.87 10 10
AKT3 -0.061 0.26 -9999 0 -1.3 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.001 0.09 -9999 0 -0.57 10 10
GNAI2 0.017 0.004 -9999 0 -10000 0 0
GNAI3 0.017 0.004 -9999 0 -10000 0 0
GNAI1 0.012 0.05 -9999 0 -0.57 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.004 0.085 -9999 0 -0.56 9 9
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.22 -9999 0 -0.51 67 67
MAPK3 -0.091 0.21 -9999 0 -0.48 67 67
MAPK1 -0.091 0.21 -9999 0 -0.48 67 67
JAK2 -0.092 0.22 -9999 0 -0.49 68 68
CXCR4 -0.097 0.22 -9999 0 -0.5 68 68
FLT1 0.019 0.003 -9999 0 -10000 0 0
RhoA/GDP 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
SRC -0.091 0.21 -9999 0 -0.48 67 67
S1P/S1P3/Gi -0.1 0.22 -9999 0 -0.52 67 67
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.089 0.2 -9999 0 -0.47 67 67
VEGFA 0.019 0.003 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.097 0.19 -9999 0 -0.34 131 131
VEGFR1 homodimer/VEGFA homodimer 0.032 0.008 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.012 0.11 -9999 0 -0.26 66 66
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.57 89 89
G12/G13 0.023 0 -9999 0 -10000 0 0
GNA14 -0.068 0.2 -9999 0 -0.57 58 58
GNA15 0.011 0.05 -9999 0 -0.57 3 3
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.014 0.029 -9999 0 -0.57 1 1
Rac1/GTP -0.089 0.2 -9999 0 -0.47 67 67
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.036 -9999 0 -0.35 4 4
ARNO/beta Arrestin1-2 -0.034 0.085 -9999 0 -0.37 1 1
EGFR -0.008 0.11 -9999 0 -0.54 17 17
EPHA2 0.008 0.064 -9999 0 -0.57 5 5
USP6 0.016 0 -9999 0 -10000 0 0
IQSEC1 0.014 0.026 -9999 0 -0.51 1 1
EGFR/EGFR/EGF/EGF -0.018 0.12 -9999 0 -0.37 42 42
ARRB2 0.012 0.014 -9999 0 -0.18 2 2
mol:GTP 0.016 0.031 -9999 0 -0.21 4 4
ARRB1 0.01 0.058 -9999 0 -0.57 4 4
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR 0.002 0.068 -9999 0 -0.51 7 7
EGF -0.018 0.12 -9999 0 -0.51 25 25
somatostatin receptor activity 0 0 -9999 0 -0.001 71 71
ARAP2 0.013 0.041 -9999 0 -0.57 2 2
mol:GDP -0.071 0.12 -9999 0 -0.25 85 85
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 52 52
ITGA2B -0.025 0.14 -9999 0 -0.51 31 31
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.057 -9999 0 -0.3 5 5
ADAP1 0.01 0.058 -9999 0 -0.57 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.077 0.18 -9999 0 -0.4 96 96
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.065 0.12 -9999 0 -0.26 71 71
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.004 0.1 -9999 0 -0.3 43 43
ADRB2 -0.059 0.2 -9999 0 -0.57 52 52
receptor agonist activity 0 0 -9999 0 0 81 81
actin filament binding 0 0 -9999 0 0 71 71
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 -0.05 0.18 -9999 0 -0.57 46 46
GNAQ 0.015 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 63 63
ARF6/GDP 0.009 0.096 -9999 0 -0.37 17 17
ARF6/GDP/GULP/ACAP1 -0.1 0.18 -9999 0 -0.42 74 74
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.02 0.13 -9999 0 -0.33 46 46
ACAP1 -0.014 0.13 -9999 0 -0.56 21 21
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.004 0.021 -9999 0 -0.27 2 2
EFNA1 0.004 0.077 -9999 0 -0.51 9 9
HGF -0.12 0.24 -9999 0 -0.56 94 94
CYTH3 0.013 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 52 52
endosomal lumen acidification 0 0 0 5 0 70 75
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.075 0.21 -9999 0 -0.57 63 63
GNAQ/ARNO 0.018 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 7 7
MET 0.013 0.036 -9999 0 -0.51 2 2
GNA14 -0.068 0.2 -9999 0 -0.57 58 58
GNA15 0.011 0.05 -9999 0 -0.57 3 3
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 66 66
GNA11 0.014 0.029 -9999 0 -0.57 1 1
LHCGR 0.001 0.036 -9999 0 -0.51 2 2
AGTR1 -0.24 0.29 -9999 0 -0.57 175 175
desensitization of G-protein coupled receptor protein signaling pathway 0.004 0.021 -9999 0 -0.27 2 2
IPCEF1/ARNO -0.002 0.077 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.054 0.17 -9999 0 -0.41 72 72
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.015 0.077 -9999 0 -10000 0 0
BIRC5 -0.36 0.24 -9999 0 -0.51 293 293
NFKBIA -0.014 0.078 -9999 0 -10000 0 0
CPEB1 -0.26 0.29 -9999 0 -0.57 192 192
AKT1 -0.014 0.078 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.022 0.068 -9999 0 -0.4 1 1
NDEL1/TACC3 -0.023 0.1 -9999 0 -0.37 14 14
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.018 0.004 -9999 0 -10000 0 0
PAK1/Aurora A -0.016 0.08 -9999 0 -0.47 1 1
MDM2 -0.001 0.092 -9999 0 -0.51 13 13
JUB 0.012 0.045 -9999 0 -0.51 3 3
TPX2 -0.18 0.19 -9999 0 -0.36 219 219
TP53 0 0.056 -9999 0 -10000 0 0
DLG7 -0.025 0.077 -9999 0 -10000 0 0
AURKAIP1 0.014 0.026 -9999 0 -0.51 1 1
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.025 0.11 -9999 0 -0.39 14 14
G2/M transition of mitotic cell cycle -0.022 0.067 -9999 0 -0.4 1 1
AURKA -0.029 0.096 -9999 0 -10000 0 0
AURKB -0.049 0.06 -9999 0 -10000 0 0
CDC25B -0.007 0.07 -9999 0 -10000 0 0
G2/M transition checkpoint -0.023 0.071 -9999 0 -0.35 3 3
mRNA polyadenylation -0.18 0.18 -9999 0 -0.36 192 192
Aurora A/CPEB -0.18 0.18 -9999 0 -0.36 192 192
Aurora A/TACC1/TRAP/chTOG 0.005 0.072 -9999 0 -0.4 2 2
BRCA1 0.014 0.026 -9999 0 -0.51 1 1
centrosome duplication -0.016 0.08 -9999 0 -0.47 1 1
regulation of centrosome cycle -0.033 0.096 -9999 0 -0.36 14 14
spindle assembly 0.004 0.071 -9999 0 -0.4 2 2
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.18 0.15 -9999 0 -0.35 121 121
CENPA -0.049 0.062 -9999 0 -10000 0 0
Aurora A/PP2A -0.015 0.077 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.004 0.06 -9999 0 -10000 0 0
negative regulation of DNA binding 0 0.055 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.023 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.023 0.071 -9999 0 -0.35 3 3
mitotic prometaphase 0.012 0.015 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.029 0.096 -9999 0 -10000 0 0
TACC1 0.011 0.05 -9999 0 -0.57 3 3
TACC3 -0.024 0.14 -9999 0 -0.51 31 31
Aurora A/Antizyme1 -0.004 0.07 -9999 0 -10000 0 0
Aurora A/RasGAP -0.015 0.077 -9999 0 -10000 0 0
OAZ1 0.016 0 -9999 0 -10000 0 0
RAN 0.016 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 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.031 0.018 -9999 0 -0.34 1 1
Importin alpha/Importin beta/TPX2 -0.18 0.19 -9999 0 -0.36 219 219
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.16 0.19 -9999 0 -0.39 120 120
PAK1 0.014 0.029 -9999 0 -0.57 1 1
CKAP5 0.016 0 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.041 0.14 0.42 52 -10000 0 52
KIRREL -0.053 0.19 -10000 0 -0.58 46 46
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.041 0.15 -10000 0 -0.42 52 52
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.016 0 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.044 0.12 -10000 0 -0.33 46 46
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.007 0.1 -10000 0 -0.3 25 25
FYN -0.029 0.12 -10000 0 -0.32 47 47
mol:Ca2+ -0.048 0.11 -10000 0 -0.33 46 46
mol:DAG -0.049 0.12 -10000 0 -0.33 46 46
NPHS2 -0.023 0.11 -10000 0 -0.52 19 19
mol:IP3 -0.049 0.12 -10000 0 -0.33 46 46
regulation of endocytosis -0.018 0.11 -10000 0 -0.33 25 25
Nephrin/NEPH1/podocin/Cholesterol -0.04 0.12 -10000 0 -0.31 66 66
establishment of cell polarity -0.041 0.14 -10000 0 -0.42 52 52
Nephrin/NEPH1/podocin/NCK1-2 -0.013 0.12 -10000 0 -0.46 7 7
Nephrin/NEPH1/beta Arrestin2 -0.017 0.12 -10000 0 -0.34 25 25
NPHS1 -0.008 0.064 -10000 0 -0.5 6 6
Nephrin/NEPH1/podocin -0.029 0.12 -10000 0 -0.32 47 47
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.044 0.12 -10000 0 -0.33 46 46
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.044 0.12 -10000 0 -0.33 46 46
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.025 0.12 -10000 0 -0.31 47 47
cytoskeleton organization -0.007 0.12 -10000 0 -0.47 7 7
Nephrin/NEPH1 -0.027 0.1 -10000 0 -0.3 52 52
Nephrin/NEPH1/ZO-1 -0.042 0.11 -10000 0 -0.34 46 46
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.022 0.14 0.57 26 -10000 0 26
PI3K Class IB/PDE3B -0.022 0.14 -10000 0 -0.57 26 26
PDE3B -0.022 0.14 -10000 0 -0.57 26 26
Wnt signaling

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
Noncanonical Wnts/FZD -0.038 0.14 -9999 0 -0.43 21 21
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.053 0.18 -9999 0 -0.52 52 52
WNT4 -0.025 0.15 -9999 0 -0.56 29 29
FZD3 0.011 0.05 -9999 0 -0.57 3 3
WNT5A -0.007 0.11 -9999 0 -0.53 17 17
WNT11 -0.06 0.19 -9999 0 -0.53 56 56
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.004 0.031 -10000 0 -10000 0 0
HDAC1 0.014 0.011 -10000 0 -10000 0 0
AES 0.015 0.004 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.011 0.12 -10000 0 -0.55 19 19
LRP6/FZD1 0.021 0.028 -10000 0 -0.38 2 2
TLE1 0.011 0.05 -10000 0 -0.57 3 3
AP1 -0.097 0.19 -10000 0 -0.32 145 145
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.016 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.034 0.072 -10000 0 -10000 0 0
NICD/RBPSUH 0.04 0.001 -10000 0 -10000 0 0
WIF1 -0.12 0.24 -10000 0 -0.56 90 90
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.19 0.25 -10000 0 -0.51 158 158
DKK1 -0.085 0.22 -10000 0 -0.56 72 72
beta catenin/beta TrCP1 0.035 0.048 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 0.004 0.016 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.031 0.05 0.28 4 -0.26 3 7
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.17 0.27 -10000 0 -0.57 129 129
JUN -0.007 0.11 -10000 0 -0.57 16 16
MAP3K7 0.015 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.051 0.2 18 -10000 0 18
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.16 0.21 -10000 0 -0.35 208 208
HNF1A 0.009 0.058 -10000 0 -0.51 5 5
CTBP1 0.014 0.026 -10000 0 -0.5 1 1
MYC -0.037 0.3 -10000 0 -1.4 18 18
NKD1 -0.028 0.15 -10000 0 -0.56 31 31
FZD1 0.013 0.039 -10000 0 -0.54 2 2
NOTCH1 precursor/Deltex homolog 1 0.026 0.062 -10000 0 -10000 0 0
apoptosis -0.097 0.18 -10000 0 -0.32 145 145
Delta 1/NOTCHprecursor 0.036 0.035 -10000 0 -10000 0 0
DLL1 0.007 0.068 -10000 0 -0.55 6 6
PPARD 0.023 0.026 -10000 0 -10000 0 0
Gamma Secretase 0.045 0.011 -10000 0 -10000 0 0
APC 0.004 0.016 -10000 0 -10000 0 0
DVL1 0.011 0.032 -10000 0 -10000 0 0
CSNK2A1 0.016 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.15 0.21 -10000 0 -0.35 199 199
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.016 0.002 -10000 0 -10000 0 0
NLK 0.018 0.012 -10000 0 -10000 0 0
CCND1 -0.011 0.2 -10000 0 -1.5 7 7
WNT1 0.008 0.045 -10000 0 -0.51 3 3
Axin1/APC/beta catenin 0.045 0.034 -10000 0 -10000 0 0
DKK2 -0.1 0.22 -10000 0 -0.51 94 94
NOTCH1 precursor/DVL1 0.002 0.009 -10000 0 -10000 0 0
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.012 0.054 -10000 0 -10000 0 0
PPP2R5D 0.017 0.076 0.28 31 -10000 0 31
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.045 0.14 -10000 0 -0.31 81 81
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.018 0.006 -10000 0 -10000 0 0
Syndecan-4-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
PTK2 -0.003 0.11 -9999 0 -0.54 12 12
Syndecan-4/Syndesmos -0.028 0.13 -9999 0 -0.55 10 10
positive regulation of JNK cascade -0.098 0.18 -9999 0 -0.48 39 39
Syndecan-4/ADAM12 -0.052 0.15 -9999 0 -0.49 21 21
CCL5 -0.03 0.15 -9999 0 -0.55 33 33
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.007 0.11 -9999 0 -0.57 16 16
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.003 0.057 -9999 0 -0.51 5 5
ADAM12 -0.036 0.16 -9999 0 -0.51 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.037 0.051 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.18 -9999 0 -0.45 47 47
Syndecan-4/CXCL12/CXCR4 -0.1 0.19 -9999 0 -0.52 39 39
Syndecan-4/Laminin alpha3 -0.075 0.17 -9999 0 -0.43 50 50
MDK -0.014 0.12 -9999 0 -0.51 23 23
Syndecan-4/FZD7 -0.041 0.14 -9999 0 -0.48 17 17
Syndecan-4/Midkine -0.042 0.14 -9999 0 -0.5 15 15
FZD7 -0.012 0.12 -9999 0 -0.57 19 19
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.56 81 81
THBS1 -0.003 0.1 -9999 0 -0.57 13 13
integrin-mediated signaling pathway -0.054 0.16 -9999 0 -0.49 30 30
positive regulation of MAPKKK cascade -0.098 0.18 -9999 0 -0.48 39 39
Syndecan-4/TACI -0.058 0.15 -9999 0 -0.5 18 18
CXCR4 0.004 0.081 -9999 0 -0.57 8 8
cell adhesion 0.003 0.1 -9999 0 -0.4 16 16
Syndecan-4/Dynamin -0.028 0.13 -9999 0 -0.55 10 10
Syndecan-4/TSP1 -0.037 0.14 -9999 0 -0.57 12 12
Syndecan-4/GIPC -0.028 0.13 -9999 0 -0.55 10 10
Syndecan-4/RANTES -0.05 0.16 -9999 0 -0.53 20 20
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.091 0.21 -9999 0 -0.52 81 81
LAMA3 -0.082 0.21 -9999 0 -0.54 72 72
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.017 0.069 -9999 0 -0.53 5 5
Syndecan-4/alpha-Actinin -0.028 0.13 -9999 0 -0.55 10 10
TFPI 0.003 0.086 -9999 0 -0.57 9 9
F2 -0.031 0.14 -9999 0 -0.51 30 30
alpha5/beta1 Integrin 0.006 0.084 -9999 0 -0.41 16 16
positive regulation of cell adhesion -0.11 0.2 -9999 0 -0.51 51 51
ACTN1 0.016 0 -9999 0 -10000 0 0
TNC -0.043 0.17 -9999 0 -0.56 42 42
Syndecan-4/CXCL12 -0.11 0.18 -9999 0 -0.52 37 37
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.15 0.26 -9999 0 -0.57 114 114
TNFRSF13B -0.044 0.17 -9999 0 -0.56 40 40
FGF2 -0.18 0.28 -9999 0 -0.57 136 136
FGFR1 -0.12 0.24 -9999 0 -0.57 93 93
Syndecan-4/PI-4-5-P2 -0.037 0.13 -9999 0 -0.56 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.034 0.16 -9999 0 -0.53 38 38
cell migration -0.014 0.022 -9999 0 -10000 0 0
PRKCD 0.016 0.008 -9999 0 -10000 0 0
vasculogenesis -0.036 0.13 -9999 0 -0.54 12 12
SDC4 -0.039 0.13 -9999 0 -0.59 10 10
Syndecan-4/Tenascin C -0.056 0.17 -9999 0 -0.51 30 30
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.04 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.028 0.13 -9999 0 -0.55 10 10
MMP9 -0.13 0.23 -9999 0 -0.51 110 110
Rac1/GTP 0.003 0.11 -9999 0 -0.42 16 16
cytoskeleton organization -0.027 0.12 -9999 0 -0.53 10 10
GIPC1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.034 0.14 -9999 0 -0.59 13 13
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.05 0.23 20 -10000 0 20
RFC1 0.012 0.05 0.24 16 -10000 0 16
PRKDC 0.012 0.05 0.24 16 -10000 0 16
RIPK1 0.02 0.005 -10000 0 -10000 0 0
CASP7 -0.028 0.044 0.25 2 -10000 0 2
FASLG/FAS/FADD/FAF1 -0.035 0.081 0.22 6 -0.3 22 28
MAP2K4 -0.084 0.17 -10000 0 -0.44 21 21
mol:ceramide -0.052 0.13 -10000 0 -0.38 28 28
GSN 0.006 0.063 0.24 18 -0.34 5 23
FASLG/FAS/FADD/FAF1/Caspase 8 -0.031 0.1 -10000 0 -0.35 24 24
FAS 0.001 0.071 -10000 0 -0.58 6 6
BID 0.003 0.038 0.3 4 -0.31 2 6
MAP3K1 -0.035 0.1 -10000 0 -0.26 12 12
MAP3K7 0.009 0.008 -10000 0 -10000 0 0
RB1 0.011 0.053 0.23 19 -0.34 1 20
CFLAR 0.02 0.005 -10000 0 -10000 0 0
HGF/MET -0.061 0.16 -10000 0 -0.34 102 102
ARHGDIB 0.012 0.05 0.23 19 -10000 0 19
FADD 0.002 0.064 -10000 0 -0.52 6 6
actin filament polymerization -0.006 0.063 0.33 5 -0.24 18 23
NFKB1 -0.095 0.1 -10000 0 -10000 0 0
MAPK8 -0.16 0.25 -10000 0 -0.42 184 184
DFFA 0.012 0.05 0.24 16 -10000 0 16
DNA fragmentation during apoptosis 0.012 0.05 0.23 20 -10000 0 20
FAS/FADD/MET 0.007 0.064 -10000 0 -0.32 14 14
CFLAR/RIP1 0.012 0.011 -10000 0 -10000 0 0
FAIM3 0.007 0.077 -10000 0 -0.54 8 8
FAF1 0.01 0.009 -10000 0 -10000 0 0
PARP1 0.012 0.05 0.23 20 -10000 0 20
DFFB 0.012 0.05 0.23 20 -10000 0 20
CHUK -0.082 0.089 -10000 0 -10000 0 0
FASLG -0.031 0.14 -10000 0 -0.56 28 28
FAS/FADD 0.002 0.07 -10000 0 -0.39 12 12
HGF -0.12 0.24 -10000 0 -0.56 94 94
LMNA 0.011 0.047 0.22 16 -10000 0 16
CASP6 0.012 0.05 0.24 16 -10000 0 16
CASP10 0.009 0.008 -10000 0 -10000 0 0
CASP3 0.014 0.059 0.27 20 -10000 0 20
PTPN13 0.004 0.081 -10000 0 -0.57 8 8
CASP8 0.006 0.043 0.39 4 -10000 0 4
IL6 -0.56 0.67 -10000 0 -1.3 184 184
MET 0.013 0.036 -10000 0 -0.51 2 2
ICAD/CAD 0.011 0.047 0.22 16 -10000 0 16
FASLG/FAS/FADD/FAF1/Caspase 10 -0.053 0.13 -10000 0 -0.39 28 28
activation of caspase activity by cytochrome c 0.003 0.038 0.3 4 -0.31 2 6
PAK2 0.012 0.05 0.24 16 -10000 0 16
BCL2 -0.006 0.11 -10000 0 -0.57 16 16
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.033 -10000 0 -10000 0 0
AES 0.019 0.025 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.029 -10000 0 -0.38 2 2
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.1 0.22 -10000 0 -0.51 94 94
TLE1 0.015 0.056 -10000 0 -0.57 3 3
MACF1 0.016 0 -10000 0 -10000 0 0
CTNNB1 0.039 0.078 0.27 5 -10000 0 5
WIF1 -0.12 0.24 -10000 0 -0.56 90 90
beta catenin/RanBP3 0.037 0.13 0.37 49 -10000 0 49
KREMEN2 -0.19 0.25 -10000 0 -0.51 158 158
DKK1 -0.085 0.22 -10000 0 -0.56 72 72
beta catenin/beta TrCP1 0.047 0.074 0.26 5 -10000 0 5
FZD1 0.013 0.039 -10000 0 -0.54 2 2
AXIN2 -0.092 0.37 -10000 0 -1.4 29 29
AXIN1 0.016 0.001 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.035 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.081 0.058 0.25 3 -0.31 2 5
Axin1/APC/GSK3 0.019 0.048 0.23 5 -10000 0 5
Axin1/APC/GSK3/beta catenin/Macf1 0.062 0.036 -10000 0 -10000 0 0
HNF1A 0.013 0.064 -10000 0 -0.51 5 5
CTBP1 0.018 0.036 -10000 0 -0.48 1 1
MYC -0.064 0.32 -10000 0 -1.5 18 18
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.17 0.21 -10000 0 -0.35 208 208
NKD1 -0.028 0.15 -10000 0 -0.56 31 31
TCF4 0.011 0.073 -10000 0 -0.55 6 6
TCF3 0.019 0.026 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.03 0.035 -10000 0 -0.3 1 1
Ran/GTP 0.012 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.056 0.16 0.48 45 -10000 0 45
LEF1 0.011 0.072 -10000 0 -0.5 7 7
DVL1 0.059 0.038 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.065 0.089 -10000 0 -0.34 3 3
DKK1/LRP6/Kremen 2 -0.15 0.21 -10000 0 -0.35 199 199
LRP6 0.016 0.001 -10000 0 -10000 0 0
CSNK1A1 0.018 0.031 -10000 0 -10000 0 0
NLK 0.015 0.005 -10000 0 -10000 0 0
CCND1 -0.038 0.22 -10000 0 -1.3 9 9
WNT1 0.008 0.045 -10000 0 -0.51 3 3
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0 -10000 0 -10000 0 0
PPP2R5D 0.051 0.075 0.3 31 -10000 0 31
APC 0.041 0.031 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.07 0.089 0.24 79 -10000 0 79
CREBBP 0.019 0.026 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP 0.004 0.037 -9999 0 -0.37 4 4
Metarhodopsin II/Arrestin 0.002 0.004 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.002 0.068 -9999 0 -0.3 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.005 0.051 -9999 0 -0.51 4 4
GRK1 0 0.025 -9999 0 -0.51 1 1
CNG Channel -0.14 0.16 -9999 0 -0.48 45 45
mol:Na + -0.16 0.16 -9999 0 -0.48 47 47
mol:ADP 0 0.025 -9999 0 -0.51 1 1
RGS9-1/Gbeta5/R9AP -0.062 0.17 -9999 0 -0.35 100 100
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.16 -9999 0 -0.5 47 47
CNGB1 -0.21 0.26 -9999 0 -0.51 174 174
RDH5 0.014 0.029 -9999 0 -0.57 1 1
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.17 -9999 0 -0.46 47 47
Na + (4 Units) -0.14 0.14 -9999 0 -0.45 47 47
RGS9 -0.11 0.24 -9999 0 -0.57 87 87
GNB1/GNGT1 0.003 0.081 -9999 0 -0.36 20 20
GNAT1/GDP -0.05 0.14 -9999 0 -0.3 97 97
GUCY2D -0.045 0.16 -9999 0 -0.51 45 45
GNGT1 -0.012 0.11 -9999 0 -0.51 20 20
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.094 -9999 0 -0.29 29 29
mol:11-cis-retinal 0.014 0.029 -9999 0 -0.57 1 1
mol:cGMP -0.021 0.11 -9999 0 -0.45 4 4
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin 0.013 0.022 -9999 0 -0.42 1 1
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.052 0.18 -9999 0 -0.54 50 50
Metarhodopsin II 0.002 0.015 -9999 0 -0.28 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.024 0.12 -9999 0 -0.31 20 20
RGS9BP -0.009 0.12 -9999 0 -0.56 17 17
Metarhodopsin II/Transducin 0.011 0.035 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.001 0.073 -9999 0 -0.28 24 24
PDE6A/B -0.002 0.1 -9999 0 -0.41 23 23
mol:Pi -0.062 0.17 -9999 0 -0.35 100 100
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.008 0.069 -9999 0 -0.26 24 24
PDE6B -0.01 0.12 -9999 0 -0.57 18 18
PDE6A 0.007 0.063 -9999 0 -0.51 6 6
PDE6G -0.004 0.098 -9999 0 -0.51 15 15
RHO 0.003 0.007 -9999 0 -10000 0 0
PDE6 -0.088 0.15 -9999 0 -0.56 16 16
GUCA1A -0.015 0.12 -9999 0 -0.51 21 21
GC2/GCAP Family 0.002 0.073 -9999 0 -0.43 2 2
GUCA1C 0 0.025 -9999 0 -0.51 1 1
GUCA1B 0.012 0.046 -9999 0 -0.53 3 3
ErbB2/ErbB3 signaling events

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.021 0.12 -9999 0 -0.5 6 6
NFATC4 -0.024 0.11 -9999 0 -0.37 11 11
ERBB2IP 0.016 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.016 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.043 0.13 -9999 0 -0.46 8 8
JUN 0.002 0.085 -9999 0 -0.27 3 3
HRAS 0.015 0.001 -9999 0 -10000 0 0
DOCK7 -0.036 0.12 -9999 0 -0.43 8 8
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.062 0.15 -9999 0 -0.31 87 87
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.022 0.003 -9999 0 -10000 0 0
MAPK10 -0.016 0.095 -9999 0 -0.26 17 17
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.046 0.14 -9999 0 -0.5 8 8
RAF1 -0.013 0.12 -9999 0 -0.48 6 6
ErbB2/ErbB3/neuregulin 2 -0.15 0.18 -9999 0 -0.33 185 185
STAT3 0.003 0.005 -9999 0 -10000 0 0
cell migration -0.003 0.088 -9999 0 -0.22 18 18
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.093 0.24 -9999 0 -0.52 64 64
FOS -0.13 0.27 -9999 0 -0.51 131 131
NRAS 0.015 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.043 0.13 -9999 0 -0.46 8 8
MAPK3 -0.058 0.19 -9999 0 -0.51 23 23
MAPK1 -0.058 0.19 -9999 0 -0.51 23 23
JAK2 -0.036 0.12 -9999 0 -0.43 8 8
NF2 -0.001 0.004 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.039 0.13 -9999 0 -0.28 81 81
NRG1 -0.11 0.24 -9999 0 -0.56 91 91
GRB2/SOS1 0.023 0.001 -9999 0 -10000 0 0
MAPK8 -0.032 0.12 -9999 0 -0.26 84 84
MAPK9 0.003 0.074 -9999 0 -0.21 8 8
ERBB2 -0.012 0.066 -9999 0 -0.37 13 13
ERBB3 -0.003 0.097 -9999 0 -0.56 12 12
SHC1 0.014 0.026 -9999 0 -0.51 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.004 0.013 -9999 0 -10000 0 0
STAT3 (dimer) 0.022 0.006 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.076 -9999 0 -0.3 8 8
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.054 -9999 0 -0.31 13 13
CHRNA1 -0.054 0.18 -9999 0 -0.38 53 53
myelination -0.015 0.11 -9999 0 -0.35 11 11
PPP3CB -0.033 0.12 -9999 0 -0.4 8 8
KRAS 0.014 0.026 -9999 0 -0.51 1 1
RAC1-CDC42/GDP -0.017 0.12 -9999 0 -0.42 8 8
NRG2 -0.23 0.29 -9999 0 -0.57 172 172
mol:GDP -0.039 0.13 -9999 0 -0.28 81 81
SOS1 0.015 0.001 -9999 0 -10000 0 0
MAP2K2 -0.009 0.12 -9999 0 -0.45 7 7
SRC 0.016 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.033 0.12 -9999 0 -0.43 8 8
MAP2K1 -0.071 0.19 -9999 0 -0.45 37 37
heart morphogenesis -0.043 0.13 -9999 0 -0.46 8 8
RAS family/GDP -0.021 0.12 -9999 0 -0.5 6 6
GRB2 0.015 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.007 -9999 0 -10000 0 0
CHRNE 0.012 0.026 -9999 0 -0.18 3 3
HSP90AA1 0.016 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.043 0.13 -9999 0 -0.46 8 8
CDC42 0.016 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.014 0.026 -9999 0 -0.51 1 1
SPHK1 -0.058 0.18 -9999 0 -0.51 57 57
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.058 -9999 0 -0.29 1 1
GNAO1 -0.17 0.27 -9999 0 -0.57 129 129
mol:Sphinganine-1-P -0.028 0.13 -9999 0 -0.36 58 58
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.029 0.042 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0.023 0 -9999 0 -10000 0 0
S1PR3 0.003 0.085 -9999 0 -0.56 9 9
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.017 0.041 -9999 0 -0.25 1 1
S1PR5 -0.005 0.1 -9999 0 -0.52 16 16
S1PR4 0.006 0.073 -9999 0 -0.54 7 7
GNAI1 0.011 0.05 -9999 0 -0.57 3 3
S1P/S1P5/G12 0.009 0.072 -9999 0 -0.28 16 16
S1P/S1P3/Gq -0.013 0.12 -9999 0 -0.27 59 59
S1P/S1P4/Gi -0.1 0.19 -9999 0 -0.45 67 67
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ -0.11 0.24 -9999 0 -0.57 89 89
GNA14 -0.068 0.2 -9999 0 -0.57 58 58
GNA15 0.011 0.05 -9999 0 -0.57 3 3
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.014 0.029 -9999 0 -0.57 1 1
ABCC1 0.013 0.036 -9999 0 -0.51 2 2
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.087 0.22 -9999 0 -0.57 71 71
GNB1/GNG2 -0.022 0.13 -9999 0 -0.5 13 13
mol:DAG -0.011 0.12 -9999 0 -0.45 13 13
PLCG1 -0.012 0.13 -9999 0 -0.46 13 13
YES1 -0.027 0.13 -9999 0 -0.5 13 13
FZD3 0.011 0.05 -9999 0 -0.57 3 3
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.012 0.13 -9999 0 -0.5 11 11
MAP3K7 -0.078 0.17 -9999 0 -0.38 60 60
mol:Ca2+ -0.011 0.12 -9999 0 -0.43 13 13
mol:IP3 -0.011 0.12 -9999 0 -0.45 13 13
NLK -0.003 0.008 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.092 0.18 -9999 0 -0.42 61 61
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.038 0.14 -9999 0 -0.43 21 21
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.027 0.13 -9999 0 -0.5 13 13
GO:0007205 -0.011 0.12 -9999 0 -0.47 11 11
WNT6 -0.053 0.18 -9999 0 -0.52 52 52
WNT4 -0.025 0.15 -9999 0 -0.56 29 29
NFAT1/CK1 alpha -0.052 0.16 -9999 0 -0.44 29 29
GNG2 0.007 0.07 -9999 0 -0.57 6 6
WNT5A -0.007 0.11 -9999 0 -0.53 17 17
WNT11 -0.06 0.19 -9999 0 -0.53 56 56
CDC42 -0.017 0.13 -9999 0 -0.47 13 13
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.068 -9999 0 -0.31 13 13
epithelial cell differentiation -0.042 0.087 -9999 0 -0.39 8 8
ITCH 0.017 0.027 -9999 0 -0.51 1 1
WWP1 0.034 0.029 -9999 0 -10000 0 0
FYN 0.011 0.05 -9999 0 -0.57 3 3
EGFR -0.008 0.11 -9999 0 -0.54 17 17
PRL -0.004 0.067 -9999 0 -0.51 7 7
neuron projection morphogenesis 0.01 0.12 -9999 0 -0.46 1 1
PTPRZ1 -0.17 0.26 -9999 0 -0.55 133 133
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.007 0.13 -9999 0 -0.52 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.036 0.14 -9999 0 -0.3 75 75
ADAM17 0.017 0.027 -9999 0 -0.51 1 1
ErbB4/ErbB4 0.033 0.036 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.004 0.06 -9999 0 -0.33 1 1
NCOR1 0.016 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.028 0.14 -9999 0 -0.34 15 15
GRIN2B -0.031 0.14 -9999 0 -0.45 9 9
ErbB4/ErbB2/betacellulin -0.006 0.12 -9999 0 -0.39 5 5
STAT1 0.011 0.051 -9999 0 -0.51 4 4
HBEGF -0.003 0.1 -9999 0 -0.57 13 13
PRLR -0.048 0.18 -9999 0 -0.53 47 47
E4ICDs/ETO2 0.023 0.067 -9999 0 -0.31 13 13
axon guidance 0.034 0.1 -9999 0 -0.33 1 1
NEDD4 0.017 0.03 -9999 0 -0.56 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.037 0.13 -9999 0 -0.38 54 54
CBFA2T3 -0.003 0.1 -9999 0 -0.57 13 13
ErbB4/ErbB2/HBEGF 0.025 0.079 -9999 0 -0.4 3 3
MAPK3 0.002 0.12 -9999 0 -0.48 1 1
STAT1 (dimer) 0.031 0.042 -9999 0 -10000 0 0
MAPK1 0.002 0.12 -9999 0 -0.48 1 1
JAK2 0.014 0.029 -9999 0 -0.57 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.034 0.14 -9999 0 -0.35 16 16
NRG1 -0.069 0.18 -9999 0 -0.4 92 92
NRG3 -0.01 0.094 -9999 0 -0.51 14 14
NRG2 -0.23 0.29 -9999 0 -0.57 172 172
NRG4 -0.041 0.17 -9999 0 -0.57 39 39
heart development 0.034 0.1 -9999 0 -0.33 1 1
neural crest cell migration -0.034 0.14 -9999 0 -0.35 16 16
ERBB2 0.015 0.071 -9999 0 -0.36 14 14
WWOX/E4ICDs 0.034 0.034 -9999 0 -0.31 1 1
SHC1 0.014 0.026 -9999 0 -0.51 1 1
ErbB4/EGFR/neuregulin 4 -0.003 0.12 -9999 0 -0.43 9 9
apoptosis 0.017 0.044 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.17 -9999 0 -0.32 172 172
ErbB4/ErbB2/epiregulin -0.047 0.14 -9999 0 -0.39 15 15
ErbB4/ErbB4/betacellulin/betacellulin -0.01 0.12 -9999 0 -0.32 50 50
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.037 0.095 -9999 0 -0.44 5 5
MDM2 0.029 0.063 -9999 0 -0.33 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.056 0.12 -9999 0 -0.33 13 13
STAT5A 0.039 0.1 -9999 0 -0.39 1 1
ErbB4/EGFR/neuregulin 1 beta -0.038 0.14 -9999 0 -0.37 17 17
DLG4 0.014 0.029 -9999 0 -0.57 1 1
GRB2/SHC 0.022 0.019 -9999 0 -0.36 1 1
E4ICDs/TAB2/NCoR1 -0.004 0.017 -9999 0 -10000 0 0
STAT5A (dimer) -0.043 0.093 -9999 0 -0.43 7 7
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.037 0.094 -9999 0 -10000 0 0
LRIG1 -0.039 0.17 -9999 0 -0.57 38 38
EREG -0.14 0.25 -9999 0 -0.54 111 111
BTC -0.057 0.19 -9999 0 -0.57 50 50
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.032 0.1 -9999 0 -0.34 1 1
ERBB4 0.033 0.036 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
YAP1 -0.003 0.036 -9999 0 -0.69 1 1
GRB2 0.016 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.004 0.12 -9999 0 -0.44 10 10
glial cell differentiation 0.004 0.017 -9999 0 -10000 0 0
WWOX 0.014 0.029 -9999 0 -0.57 1 1
cell proliferation -0.053 0.17 -9999 0 -0.44 31 31
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.28 0.29 -9999 0 -0.57 206 206
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0.026 -9999 0 -0.51 1 1
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 0.036 0.015 -9999 0 -10000 0 0
HIF1A 0.027 0.016 -9999 0 -10000 0 0
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.046 0.014 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.25 0.26 -9999 0 -0.51 205 205
ARNT/IPAS -0.2 0.22 -9999 0 -0.41 206 206
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.016 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.036 0.015 -9999 0 -10000 0 0
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.031 0.016 -9999 0 -0.29 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.036 0.015 -9999 0 -10000 0 0
PHD1-3/OS9 0.034 0.047 -9999 0 -0.3 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.047 0.018 -9999 0 -10000 0 0
VHL 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.036 0.015 -9999 0 -10000 0 0
EGLN3 0.004 0.081 -9999 0 -0.57 8 8
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.008 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.092 0.13 -9999 0 -0.28 8 8
Effects of Botulinum toxin

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
STX1A 0.009 0.037 -9999 0 -0.37 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.003 0.08 -9999 0 -0.4 15 15
STXBP1 -0.007 0.11 -9999 0 -0.57 16 16
ACh/CHRNA1 -0.05 0.13 -9999 0 -0.33 71 71
RAB3GAP2/RIMS1/UNC13B 0.014 0.069 -9999 0 -0.34 15 15
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 -0.012 0.11 -9999 0 -0.56 15 15
mol:ACh -0.001 0.037 -9999 0 -0.12 31 31
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.03 0.084 -9999 0 -0.38 12 12
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.05 0.13 -9999 0 -0.33 71 71
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.076 0.2 -9999 0 -0.51 71 71
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.029 0.12 -9999 0 -0.38 42 42
SNAP25 -0.017 0.082 -9999 0 -0.26 39 39
VAMP2 0.008 0 -9999 0 -10000 0 0
SYT1 -0.043 0.17 -9999 0 -0.56 42 42
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.004 0.078 -9999 0 -0.34 20 20
STX1A/SNAP25 fragment 1/VAMP2 -0.03 0.084 -9999 0 -0.38 12 12
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.021 0.026 -9999 0 -0.36 2 2
CRKL -0.008 0.1 -9999 0 -0.36 3 3
mol:PIP3 -0.021 0.006 -9999 0 -10000 0 0
AKT1 0.002 0.004 -9999 0 -10000 0 0
PTK2B 0.014 0.029 -9999 0 -0.57 1 1
RAPGEF1 0.001 0.097 -9999 0 -0.37 2 2
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.054 0.16 -9999 0 -0.33 96 96
MAP3K5 0.006 0.1 -9999 0 -0.38 6 6
HGF/MET/CIN85/CBL/ENDOPHILINS -0.039 0.14 -9999 0 -0.3 87 87
AP1 -0.11 0.2 -9999 0 -0.4 130 130
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.026 -9999 0 -0.51 1 1
apoptosis -0.22 0.36 -9999 0 -0.75 130 130
STAT3 (dimer) -0.013 0.12 -9999 0 -0.48 1 1
GAB1/CRKL/SHP2/PI3K -0.035 0.068 -9999 0 -0.37 3 3
INPP5D 0.006 0.076 -9999 0 -0.57 7 7
CBL/CRK 0.003 0.095 -9999 0 -0.33 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 -0.004 0.016 -9999 0 -0.2 2 2
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.03 0.059 -9999 0 -0.39 1 1
PAK1 0.009 0.015 -9999 0 -0.29 1 1
HGF/MET/RANBP10 -0.054 0.16 -9999 0 -0.33 96 96
HRAS -0.027 0.13 -9999 0 -0.38 1 1
DOCK1 -0.001 0.1 -9999 0 -0.4 3 3
GAB1 -0.016 0.1 -9999 0 -0.34 2 2
CRK -0.007 0.098 -9999 0 -0.31 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.1 0.19 -9999 0 -0.47 87 87
JUN -0.007 0.11 -9999 0 -0.57 16 16
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.032 0.092 -9999 0 -0.2 87 87
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
cell morphogenesis 0.014 0.12 -9999 0 -0.42 3 3
GRB2/SHC -0.01 0.083 -9999 0 -0.41 1 1
FOS -0.17 0.27 -9999 0 -0.57 129 129
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.004 0.016 -9999 0 -0.2 2 2
HGF/MET/MUC20 -0.065 0.16 -9999 0 -0.34 96 96
cell migration -0.01 0.082 -9999 0 -0.4 1 1
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
MET/RANBP10 0.021 0.026 -9999 0 -0.36 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.12 -9999 0 -0.24 87 87
MET/MUC20 0.01 0.026 -9999 0 -0.37 2 2
RAP1B 0.009 0.092 -9999 0 -0.34 2 2
RAP1A 0.009 0.092 -9999 0 -0.34 2 2
HGF/MET/RANBP9 -0.054 0.16 -9999 0 -0.33 96 96
RAF1 -0.017 0.13 -9999 0 -10000 0 0
STAT3 -0.013 0.12 -9999 0 -0.49 1 1
cell proliferation -0.021 0.16 -9999 0 -0.32 87 87
RPS6KB1 -0.002 0.035 -9999 0 -10000 0 0
MAPK3 -0.009 0.014 -9999 0 -10000 0 0
MAPK1 -0.009 0.014 -9999 0 -10000 0 0
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.024 0.096 -9999 0 -0.34 7 7
SRC -0.01 0.11 -9999 0 -0.46 1 1
PI3K -0.01 0.085 -9999 0 -0.43 2 2
MET/Glomulin 0.013 0.023 -9999 0 -0.32 2 2
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 -0.008 0.12 -9999 0 -10000 0 0
MET 0.013 0.036 -9999 0 -0.51 2 2
MAP4K1 -0.002 0.11 -9999 0 -0.4 5 5
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 -0.008 0.12 -9999 0 -10000 0 0
BAD 0.01 0.005 -9999 0 -10000 0 0
MAP2K4 0.014 0.096 -9999 0 -0.35 5 5
SHP2/GRB2/SOS1/GAB1 -0.036 0.066 -9999 0 -0.29 1 1
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.02 0.085 -9999 0 -0.44 1 1
PLCgamma1/PKC 0.012 0 -9999 0 -10000 0 0
HGF -0.12 0.24 -9999 0 -0.56 94 94
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
PTPRJ 0.014 0.029 -9999 0 -0.57 1 1
NCK/PLCgamma1 -0.012 0.092 -9999 0 -0.43 1 1
PDPK1 -0.008 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.06 0.17 -9999 0 -0.35 99 99
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.015 0.25 -10000 0 -0.79 16 16
PCK1 -0.024 0.18 -10000 0 -0.67 11 11
HNF4A -0.046 0.3 -10000 0 -0.99 18 18
KCNJ11 -0.04 0.32 -10000 0 -0.92 30 30
AKT1 0.018 0.11 -10000 0 -0.4 3 3
response to starvation -0.004 0.019 -10000 0 -10000 0 0
DLK1 -0.053 0.33 -10000 0 -0.93 34 34
NKX2-1 0.096 0.23 0.66 12 -0.62 1 13
ACADM -0.018 0.26 -10000 0 -0.85 15 15
TAT -0.026 0.19 -10000 0 -0.66 15 15
CEBPB 0.012 0.031 -10000 0 -0.58 1 1
CEBPA -0.002 0.093 -10000 0 -0.53 12 12
TTR -0.094 0.24 -10000 0 -0.69 27 27
PKLR -0.037 0.27 -10000 0 -0.84 18 18
APOA1 -0.026 0.3 -10000 0 -0.95 17 17
CPT1C -0.02 0.26 -10000 0 -0.82 15 15
ALAS1 0.032 0.14 -10000 0 -10000 0 0
TFRC -0.008 0.19 -10000 0 -0.64 5 5
FOXF1 -0.19 0.28 -10000 0 -0.56 148 148
NF1 0.024 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.022 0.075 -10000 0 -0.55 5 5
CPT1A -0.017 0.25 -10000 0 -0.86 14 14
HMGCS1 -0.015 0.25 -10000 0 -0.83 13 13
NR3C1 -0.001 0.1 -10000 0 -0.57 12 12
CPT1B -0.018 0.26 -10000 0 -0.82 17 17
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.014 0.042 -10000 0 -10000 0 0
GCK -0.064 0.34 -10000 0 -0.93 37 37
CREB1 0.014 0.023 -10000 0 -10000 0 0
IGFBP1 -0.008 0.17 -10000 0 -0.59 11 11
PDX1 -0.075 0.22 -10000 0 -0.66 10 10
UCP2 -0.017 0.25 -10000 0 -0.85 12 12
ALDOB -0.026 0.29 -10000 0 -0.87 20 20
AFP -0.07 0.14 -10000 0 -0.47 22 22
BDH1 -0.015 0.25 -10000 0 -0.83 13 13
HADH -0.006 0.26 -10000 0 -0.83 14 14
F2 -0.025 0.29 -10000 0 -0.97 15 15
HNF1A -0.022 0.075 -10000 0 -0.55 5 5
G6PC -0.031 0.12 -10000 0 -0.56 5 5
SLC2A2 -0.017 0.19 -10000 0 -0.73 7 7
INS -0.006 0.028 -10000 0 -10000 0 0
FOXA1 -0.057 0.19 -10000 0 -0.57 45 45
FOXA3 -0.099 0.22 -10000 0 -0.5 85 85
FOXA2 -0.014 0.3 -10000 0 -0.89 18 18
ABCC8 -0.014 0.26 -10000 0 -0.86 14 14
ALB -0.085 0.16 -10000 0 -0.46 26 26
Caspase cascade in apoptosis

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
TOP1 -0.005 0.12 -10000 0 -0.36 33 33
ACTA1 -0.026 0.16 -10000 0 -0.48 35 35
NUMA1 -0.005 0.12 -10000 0 -0.36 33 33
SPTAN1 -0.021 0.16 -10000 0 -0.48 33 33
LIMK1 -0.021 0.16 -10000 0 -0.48 33 33
BIRC3 -0.02 0.14 -10000 0 -0.56 25 25
BIRC2 0.013 0.036 -10000 0 -0.51 2 2
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.036 0.17 -10000 0 -0.4 65 65
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0.039 -10000 0 -0.54 2 2
PTK2 -0.005 0.12 -10000 0 -0.36 33 33
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.16 -10000 0 -0.47 33 33
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.026 0.17 -10000 0 -0.48 38 38
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A 0.017 0.048 -10000 0 -0.48 2 2
BID -0.008 0.087 -10000 0 -0.24 40 40
MAP3K1 0.002 0.056 -10000 0 -0.21 7 7
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.021 0.16 -10000 0 -0.48 33 33
CASP9 0.016 0 -10000 0 -10000 0 0
DNA repair -0.006 0.052 0.15 7 -0.2 12 19
neuron apoptosis 0.021 0.058 -10000 0 -0.77 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.01 0.15 -10000 0 -0.45 33 33
APAF1 0.016 0 -10000 0 -10000 0 0
CASP6 0.018 0.076 -10000 0 -0.35 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.012 0.15 -10000 0 -0.46 33 33
CASP7 0.009 0.078 0.31 22 -10000 0 22
KRT18 0.013 0.041 -10000 0 -0.64 1 1
apoptosis -0.004 0.15 0.27 1 -0.43 33 34
DFFA -0.021 0.16 -10000 0 -0.48 33 33
DFFB -0.021 0.16 -10000 0 -0.48 33 33
PARP1 0.006 0.052 0.2 12 -0.15 7 19
actin filament polymerization 0.012 0.15 0.44 33 -10000 0 33
TNF -0.011 0.12 -10000 0 -0.51 21 21
CYCS -0.001 0.066 -10000 0 -0.2 24 24
SATB1 0.016 0.09 -10000 0 -0.38 2 2
SLK -0.021 0.16 -10000 0 -0.48 33 33
p15 BID/BAX 0.001 0.078 -10000 0 -0.25 19 19
CASP2 0.042 0.05 -10000 0 -10000 0 0
JNK cascade -0.002 0.055 0.21 7 -10000 0 7
CASP3 -0.031 0.17 -10000 0 -0.51 33 33
LMNB2 0.04 0.045 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.014 0.026 -10000 0 -0.51 1 1
Mammalian IAPs/DIABLO 0.017 0.09 -10000 0 -0.32 23 23
negative regulation of DNA binding 0.017 0.048 -10000 0 -0.48 2 2
stress fiber formation -0.02 0.16 -10000 0 -0.47 33 33
GZMB -0.054 0.19 -10000 0 -0.48 65 65
CASP1 0.012 0.054 -10000 0 -0.33 10 10
LMNB1 0.039 0.046 -10000 0 -10000 0 0
APP 0.021 0.059 -10000 0 -0.78 2 2
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.013 0 -10000 0 -10000 0 0
VIM -0.009 0.14 0.28 1 -0.43 33 34
LMNA 0.04 0.045 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.035 0.053 -10000 0 -10000 0 0
LRDD 0.016 0 -10000 0 -10000 0 0
SREBF1 -0.022 0.16 -10000 0 -0.48 33 33
APAF-1/Caspase 9 0.002 0.044 0.32 2 -10000 0 2
nuclear fragmentation during apoptosis -0.005 0.12 -10000 0 -0.36 33 33
CFL2 -0.013 0.15 -10000 0 -0.45 33 33
GAS2 -0.055 0.19 -10000 0 -0.42 63 63
positive regulation of apoptosis 0.044 0.045 -10000 0 -10000 0 0
PRF1 -0.021 0.14 -10000 0 -0.54 27 27
Regulation of Androgen receptor activity

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
HDAC1 0.026 0.002 -9999 0 -10000 0 0
SMARCC1 0.012 0.014 -9999 0 -10000 0 0
REL 0.01 0.061 -9999 0 -0.54 5 5
HDAC7 -0.013 0.13 -9999 0 -0.38 4 4
JUN -0.008 0.11 -9999 0 -0.57 16 16
EP300 0.016 0 -9999 0 -10000 0 0
KAT2B 0.014 0.029 -9999 0 -0.57 1 1
KAT5 0.016 0.001 -9999 0 -10000 0 0
MAPK14 0.016 0.053 -9999 0 -0.4 6 6
FOXO1 0.014 0.029 -9999 0 -0.57 1 1
T-DHT/AR -0.019 0.14 -9999 0 -0.36 25 25
MAP2K6 0.005 0.07 -9999 0 -0.56 6 6
BRM/BAF57 0.022 0.007 -9999 0 -10000 0 0
MAP2K4 0.014 0.007 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.16 0.4 -9999 0 -1.2 49 49
NCOA2 -0.019 0.14 -9999 0 -0.57 24 24
CEBPA 0 0.09 -9999 0 -0.52 12 12
EHMT2 0.015 0.004 -9999 0 -10000 0 0
cell proliferation 0 0.15 -9999 0 -0.45 12 12
NR0B1 -0.035 0.14 -9999 0 -0.51 32 32
EGR1 -0.13 0.25 -9999 0 -0.57 100 100
RXRs/9cRA -0.065 0.15 -9999 0 -0.31 107 107
AR/RACK1/Src -0.015 0.087 -9999 0 -0.37 6 6
AR/GR -0.074 0.15 -9999 0 -0.32 68 68
GNB2L1 0.016 0.001 -9999 0 -10000 0 0
PKN1 0.014 0.029 -9999 0 -0.57 1 1
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.019 0.04 -9999 0 -0.41 3 3
T-DHT/AR/TIF2/CARM1 -0.018 0.12 -9999 0 -0.39 18 18
SRC 0.028 0.056 -9999 0 -0.32 2 2
NR3C1 -0.002 0.099 -9999 0 -0.57 12 12
KLK3 -0.12 0.26 -9999 0 -0.93 28 28
APPBP2 0.013 0.008 -9999 0 -10000 0 0
TRIM24 0.011 0.045 -9999 0 -0.51 3 3
T-DHT/AR/TIP60 -0.009 0.091 -9999 0 -0.39 6 6
TMPRSS2 -0.21 0.45 -9999 0 -1.1 73 73
RXRG -0.14 0.25 -9999 0 -0.57 107 107
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.014 0.029 -9999 0 -0.57 1 1
RXRB 0.015 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.002 -9999 0 -10000 0 0
NR2C2 0.013 0.039 -9999 0 -0.54 2 2
KLK2 -0.024 0.14 -9999 0 -0.42 21 21
AR -0.08 0.16 -9999 0 -0.28 148 148
SENP1 0.015 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0 0.092 -9999 0 -0.5 13 13
SRY 0 0.063 -9999 0 -0.51 6 6
GATA2 -0.011 0.12 -9999 0 -0.53 20 20
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.078 0.21 -9999 0 -0.56 65 65
T-DHT/AR/RACK1/Src -0.002 0.09 -9999 0 -0.38 6 6
positive regulation of transcription -0.011 0.12 -9999 0 -0.53 20 20
DNAJA1 0.013 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.024 -9999 0 -10000 0 0
NCOA1 0.02 0.006 -9999 0 -10000 0 0
SPDEF -0.096 0.22 -9999 0 -0.54 81 81
T-DHT/AR/TIF2 0.004 0.091 -9999 0 -0.33 11 11
T-DHT/AR/Hsp90 -0.009 0.091 -9999 0 -0.39 6 6
GSK3B 0.015 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.002 -9999 0 -10000 0 0
mol:T-DHT 0.021 0.06 -9999 0 -0.31 8 8
SIRT1 0.016 0 -9999 0 -10000 0 0
ZMIZ2 0.017 0.007 -9999 0 -10000 0 0
POU2F1 0.018 0.041 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.049 0.11 -9999 0 -0.39 13 13
CREBBP 0.016 0.001 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.01 0.058 -10000 0 -0.57 4 4
ANTXR2 -0.02 0.14 -10000 0 -0.57 25 25
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.019 -10000 0 -0.075 28 28
monocyte activation -0.005 0.087 -10000 0 -0.41 17 17
MAP2K2 -0.002 0.007 -10000 0 -10000 0 0
MAP2K1 -0.004 0.015 -10000 0 -10000 0 0
MAP2K7 -0.004 0.015 -10000 0 -10000 0 0
MAP2K6 -0.009 0.04 -10000 0 -0.31 6 6
CYAA -0.005 0.083 -10000 0 -0.31 28 28
MAP2K4 -0.004 0.015 -10000 0 -10000 0 0
IL1B -0.014 0.091 -10000 0 -0.29 37 37
Channel -0.004 0.089 -10000 0 -0.33 28 28
NLRP1 -0.009 0.043 -10000 0 -0.31 7 7
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.006 0.021 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.019 0.075 28 -10000 0 28
MAPK3 -0.004 0.015 -10000 0 -10000 0 0
MAPK1 -0.004 0.015 -10000 0 -10000 0 0
PGR -0.1 0.15 -10000 0 -0.31 129 129
PA/Cellular Receptors -0.005 0.097 -10000 0 -0.36 28 28
apoptosis -0.005 0.019 -10000 0 -0.075 28 28
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.003 0.084 -10000 0 -0.31 28 28
macrophage activation 0.017 0.018 -10000 0 -10000 0 0
TNF -0.011 0.12 -10000 0 -0.51 21 21
VCAM1 -0.005 0.088 -10000 0 -0.41 17 17
platelet activation -0.006 0.021 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.022 0.12 2 -10000 0 2
IL18 0.006 0.057 -10000 0 -0.35 8 8
negative regulation of macrophage activation -0.005 0.019 -10000 0 -0.075 28 28
LEF -0.005 0.019 -10000 0 -0.076 28 28
CASP1 -0.009 0.037 -10000 0 -0.19 11 11
mol:cAMP -0.006 0.021 -10000 0 -10000 0 0
necrosis -0.005 0.019 -10000 0 -0.075 28 28
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.003 0.084 -10000 0 -0.31 28 28
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.016 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.004 0.095 -9999 0 -0.35 26 26
forebrain development -0.09 0.25 -9999 0 -0.58 64 64
GNAO1 -0.17 0.27 -9999 0 -0.57 129 129
SMO/beta Arrestin2 0.001 0.096 -9999 0 -0.41 21 21
SMO -0.015 0.13 -9999 0 -0.57 21 21
ARRB2 0.015 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.054 0.057 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.04 0.002 -9999 0 -10000 0 0
GNAI1 0.011 0.05 -9999 0 -0.57 3 3
XPO1 0.016 0.007 -9999 0 -10000 0 0
GLI1/Su(fu) -0.094 0.2 -9999 0 -0.68 29 29
SAP30 0.016 0.001 -9999 0 -10000 0 0
mol:GDP -0.015 0.13 -9999 0 -0.57 21 21
MIM/GLI2A 0.017 0.008 -9999 0 -10000 0 0
IFT88 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0.002 -9999 0 -10000 0 0
GLI2 0.022 0.075 -9999 0 -10000 0 0
GLI3 0.047 0.061 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.016 0 -9999 0 -10000 0 0
GNG2 0.007 0.07 -9999 0 -0.57 6 6
Gi family/GTP -0.12 0.22 -9999 0 -0.38 138 138
SIN3B 0.016 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.066 0.042 -9999 0 -10000 0 0
GLI2/Su(fu) 0.027 0.088 -9999 0 -10000 0 0
FOXA2 -0.056 0.12 -9999 0 -10000 0 0
neural tube patterning -0.09 0.25 -9999 0 -0.58 64 64
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.046 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.017 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.09 0.25 -9999 0 -0.58 64 64
SUFU 0.019 0.052 -9999 0 -10000 0 0
LGALS3 0.014 0.029 -9999 0 -0.57 1 1
catabolic process 0.059 0.076 -9999 0 -10000 0 0
GLI3A/CBP -0.029 0.13 -9999 0 -0.34 61 61
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 -0.092 0.26 -9999 0 -0.6 64 64
RAB23 0.014 0.029 -9999 0 -0.57 1 1
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.016 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.027 0.049 -9999 0 -0.29 1 1
GNAZ -0.11 0.24 -9999 0 -0.57 89 89
RBBP4 0.016 0.001 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.028 0.07 -9999 0 -10000 0 0
STK36 0.016 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.097 0.21 -9999 0 -0.48 67 67
PTCH1 -0.072 0.22 -9999 0 -0.68 31 31
MIM/GLI1 -0.093 0.25 -9999 0 -0.63 52 52
CREBBP -0.029 0.13 -9999 0 -0.34 61 61
Su(fu)/SIN3/HDAC complex 0.055 0.015 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.001 0.09 -9999 0 -0.57 10 10
alphaV beta3 Integrin -0.026 0.14 -9999 0 -0.42 46 46
PTK2 -0.046 0.12 -9999 0 -0.44 29 29
positive regulation of JNK cascade -0.023 0.078 -9999 0 -0.3 29 29
CDC42/GDP 0.028 0.12 -9999 0 -0.41 29 29
Rac1/GDP 0.03 0.12 -9999 0 -0.4 29 29
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.028 0.096 -9999 0 -0.37 29 29
nectin-3/I-afadin -0.009 0.11 -9999 0 -0.4 31 31
RAPGEF1 0.02 0.14 -9999 0 -0.45 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0.15 -9999 0 -0.52 29 29
PDGFB-D/PDGFRB 0.001 0.09 -9999 0 -0.57 10 10
TLN1 0.018 0.066 -9999 0 -0.32 6 6
Rap1/GTP -0.023 0.082 -9999 0 -0.32 29 29
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.03 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.009 0.11 -9999 0 -0.4 31 31
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.021 0.15 -9999 0 -0.5 29 29
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0.014 0.099 -9999 0 -0.57 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.022 0.021 -9999 0 -0.41 1 1
positive regulation of lamellipodium assembly -0.025 0.084 -9999 0 -0.32 31 31
PVRL1 0.014 0.029 -9999 0 -0.57 1 1
PVRL3 -0.028 0.15 -9999 0 -0.56 31 31
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
CDH1 -0.004 0.11 -9999 0 -0.57 14 14
CLDN1 -0.019 0.14 -9999 0 -0.55 25 25
JAM-A/CLDN1 -0.006 0.12 -9999 0 -0.32 46 46
SRC -0.047 0.15 -9999 0 -0.59 29 29
ITGB3 -0.05 0.18 -9999 0 -0.57 46 46
nectin-1(dimer)/I-afadin/I-afadin 0.022 0.021 -9999 0 -0.41 1 1
FARP2 0.016 0.14 -9999 0 -0.49 29 29
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.004 0.097 -9999 0 -0.34 31 31
nectin-1/I-afadin 0.022 0.021 -9999 0 -0.41 1 1
nectin-2/I-afadin 0.023 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.021 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.003 0.099 -9999 0 -0.34 32 32
CDC42/GTP/IQGAP1/filamentous actin 0.021 0 -9999 0 -10000 0 0
F11R 0.014 0.029 -9999 0 -0.57 1 1
positive regulation of filopodium formation -0.023 0.078 -9999 0 -0.3 29 29
alphaV/beta3 Integrin/Talin 0.001 0.12 -9999 0 -0.43 15 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.023 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.023 0 -9999 0 -10000 0 0
PIP5K1C 0.01 0.07 -9999 0 -0.35 6 6
VAV2 0.012 0.15 -9999 0 -0.5 31 31
RAP1/GDP -0.027 0.097 -9999 0 -0.37 29 29
ITGAV 0.014 0.029 -9999 0 -0.57 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.004 0.097 -9999 0 -0.34 31 31
nectin-3(dimer)/I-afadin/I-afadin -0.009 0.11 -9999 0 -0.4 31 31
Rac1/GTP -0.03 0.1 -9999 0 -0.38 31 31
PTPRM 0 0.077 -9999 0 -0.24 35 35
E-cadherin/beta catenin/alpha catenin -0.009 0.052 -9999 0 -0.54 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.016 0 -9999 0 -10000 0 0
EGFR -0.008 0.11 -9999 0 -0.54 17 17
EGF/EGFR -0.069 0.12 -9999 0 -0.29 69 69
EGF/EGFR dimer/SHC/GRB2/SOS1 0.016 0.09 -9999 0 -0.49 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.069 0.21 -9999 0 -0.57 59 59
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.018 0.12 -9999 0 -0.51 25 25
EGF/EGFR dimer/SHC -0.004 0.1 -9999 0 -0.31 42 42
mol:GDP -0.025 0.075 -9999 0 -0.48 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.076 -9999 0 -0.53 8 8
GRB2/SOS1 0.023 0 -9999 0 -10000 0 0
HRAS/GTP -0.022 0.067 -9999 0 -0.45 1 1
SHC1 0.014 0.026 -9999 0 -0.51 1 1
HRAS/GDP -0.023 0.069 -9999 0 -0.45 1 1
FRAP1 0.012 0.084 -9999 0 -0.47 1 1
EGF/EGFR dimer -0.018 0.12 -9999 0 -0.37 42 42
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.047 0.16 -9999 0 -0.41 66 66
IL2 signaling events mediated by STAT5

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
GAB2 0.015 0.029 -9999 0 -0.57 1 1
ELF1 -0.001 0.086 -9999 0 -0.34 18 18
CCNA2 -0.12 0.23 -9999 0 -0.51 106 106
PIK3CA 0.017 0 -9999 0 -10000 0 0
JAK3 0.014 0.037 -9999 0 -0.51 2 2
PIK3R1 0.015 0.029 -9999 0 -0.57 1 1
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.062 0.098 -9999 0 -0.62 4 4
SHC1 0.015 0.026 -9999 0 -0.51 1 1
SP1 -0.003 0.098 -9999 0 -0.34 32 32
IL2RA -0.019 0.19 -9999 0 -0.58 37 37
IL2RB 0.007 0.074 -9999 0 -0.55 7 7
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.009 0.12 -9999 0 -0.54 19 19
G1/S transition of mitotic cell cycle -0.059 0.24 -9999 0 -0.76 37 37
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 -0.03 0.23 -9999 0 -0.8 32 32
LCK 0.008 0.068 -9999 0 -0.55 6 6
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 0.005 0.007 -9999 0 -10000 0 0
CDK6 0 0.095 -9999 0 -0.57 11 11
CCND3 0.069 0.086 -9999 0 -0.51 4 4
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.007 -10000 0 -10000 0 0
HSPA8 0.015 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.065 0.15 0.22 6 -0.38 69 75
AKT1 0.016 0.014 -10000 0 -10000 0 0
GSC -0.005 0.085 -10000 0 -10000 0 0
NKX2-5 -0.076 0.19 -10000 0 -0.5 65 65
muscle cell differentiation 0.051 0.088 0.4 11 -10000 0 11
SMAD2-3/SMAD4/SP1 0.049 0.096 -10000 0 -0.37 6 6
SMAD4 0.01 0.05 -10000 0 -0.24 1 1
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.027 0.046 -10000 0 -0.29 8 8
SMAD3/SMAD4/VDR -0.001 0.042 -10000 0 -0.43 2 2
MYC -0.01 0.12 -10000 0 -0.57 18 18
CDKN2B -0.009 0.25 -10000 0 -1.4 11 11
AP1 -0.054 0.21 -10000 0 -0.66 24 24
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.069 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.027 0.076 -10000 0 -0.31 10 10
SP3 0.019 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.1 0.22 -10000 0 -0.5 92 92
SMAD3/SMAD4/GR -0.019 0.083 -10000 0 -0.43 12 12
GATA3 -0.028 0.15 -10000 0 -0.57 29 29
SKI/SIN3/HDAC complex/NCoR1 0.055 0.008 -10000 0 -10000 0 0
MEF2C/TIF2 -0.073 0.2 -10000 0 -0.55 40 40
endothelial cell migration 0.005 0.16 1.4 5 -10000 0 5
MAX 0.014 0.006 -10000 0 -10000 0 0
RBBP7 0.016 0.001 -10000 0 -10000 0 0
RBBP4 0.016 0.001 -10000 0 -10000 0 0
RUNX2 0.008 0.064 -10000 0 -0.52 6 6
RUNX3 -0.004 0.11 -10000 0 -0.57 14 14
RUNX1 0.016 0 -10000 0 -10000 0 0
CTBP1 0.014 0.026 -10000 0 -0.51 1 1
NR3C1 -0.003 0.099 -10000 0 -0.57 12 12
VDR 0.011 0.048 -10000 0 -0.55 3 3
CDKN1A 0.052 0.12 -10000 0 -1.4 2 2
KAT2B 0.014 0.029 -10000 0 -0.57 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.039 0.15 -10000 0 -0.37 29 29
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.016 0.001 -10000 0 -10000 0 0
SERPINE1 -0.007 0.17 -10000 0 -1.4 5 5
SMAD3/SMAD4/ATF2 -0.005 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.07 0.15 -10000 0 -0.39 72 72
SAP30 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.019 0.025 -10000 0 -10000 0 0
JUN -0.054 0.21 -10000 0 -0.67 23 23
SMAD3/SMAD4/IRF7 -0.02 0.08 -10000 0 -0.37 9 9
TFE3 0.022 0.012 -10000 0 -10000 0 0
COL1A2 -0.042 0.26 -10000 0 -0.96 29 29
mesenchymal cell differentiation 0.01 0.058 0.31 7 -10000 0 7
DLX1 -0.04 0.16 -10000 0 -0.51 42 42
TCF3 0.016 0 -10000 0 -10000 0 0
FOS -0.16 0.28 -10000 0 -0.57 129 129
SMAD3/SMAD4/Max -0.008 0.042 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.032 0.007 -10000 0 -10000 0 0
ZBTB17 0.016 0.012 -10000 0 -10000 0 0
LAMC1 0.046 0.06 -10000 0 -0.62 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.005 0.045 -10000 0 -0.27 1 1
IRF7 -0.005 0.1 -10000 0 -0.52 15 15
ESR1 -0.087 0.22 -10000 0 -0.56 73 73
HNF4A -0.04 0.16 -10000 0 -0.51 41 41
MEF2C -0.068 0.19 -10000 0 -0.57 27 27
SMAD2-3/SMAD4 0.012 0.064 -10000 0 -0.32 1 1
Cbp/p300/Src-1 0.033 0.01 -10000 0 -10000 0 0
IGHV3OR16-13 -0.003 0.016 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0.005 -10000 0 -10000 0 0
SKIL 0.014 0.026 -10000 0 -0.51 1 1
HDAC1 0.016 0.001 -10000 0 -10000 0 0
HDAC2 0.016 0.001 -10000 0 -10000 0 0
SNIP1 0.016 0.001 -10000 0 -10000 0 0
GCN5L2 0 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.036 0.065 -10000 0 -0.33 1 1
MSG1/HSC70 0.014 0.053 -10000 0 -0.36 8 8
SMAD2 0.018 0.021 -10000 0 -10000 0 0
SMAD3 0.01 0.046 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.041 0.043 -10000 0 -0.25 1 1
SMAD2/SMAD2/SMAD4 0.01 0.029 -10000 0 -0.34 1 1
NCOR1 0.016 0.001 -10000 0 -10000 0 0
NCOA2 -0.019 0.14 -10000 0 -0.57 24 24
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A 0.012 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.061 0.091 -10000 0 -0.39 3 3
IFNB1 0.012 0.1 -10000 0 -0.47 10 10
SMAD3/SMAD4/MEF2C -0.067 0.19 -10000 0 -0.56 29 29
CITED1 0.005 0.072 -10000 0 -0.51 8 8
SMAD2-3/SMAD4/ARC105 0.034 0.064 -10000 0 -10000 0 0
RBL1 0.013 0.036 -10000 0 -0.51 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.043 0.1 -10000 0 -0.49 11 11
RUNX1-3/PEBPB2 0.019 0.067 -10000 0 -0.34 14 14
SMAD7 -0.004 0.18 -10000 0 -0.55 16 16
MYC/MIZ-1 -0.007 0.093 -10000 0 -0.42 18 18
SMAD3/SMAD4 0.005 0.067 0.24 3 -0.4 5 8
IL10 -0.007 0.18 -10000 0 -0.6 25 25
PIASy/HDAC complex 0.015 0.006 -10000 0 -10000 0 0
PIAS3 0.016 0.003 -10000 0 -10000 0 0
CDK2 0.016 0.004 -10000 0 -10000 0 0
IL5 -0.001 0.12 -10000 0 -0.47 10 10
CDK4 0.015 0.026 -10000 0 -0.51 1 1
PIAS4 0.015 0.006 -10000 0 -10000 0 0
ATF3 -0.088 0.22 -10000 0 -0.57 72 72
SMAD3/SMAD4/SP1 0.028 0.093 -10000 0 -0.35 9 9
FOXG1 -0.067 0.18 -10000 0 -0.51 55 55
FOXO3 0.027 0.019 -10000 0 -10000 0 0
FOXO1 0.026 0.029 -10000 0 -0.42 1 1
FOXO4 0.026 0.027 -10000 0 -0.35 1 1
heart looping -0.067 0.19 -10000 0 -0.57 27 27
CEBPB 0.014 0.03 -10000 0 -0.57 1 1
SMAD3/SMAD4/DLX1 -0.037 0.1 -10000 0 -0.31 43 43
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.036 0.1 -10000 0 -0.36 17 17
SMAD3/SMAD4/GATA3 -0.04 0.12 -10000 0 -0.38 34 34
SnoN/SIN3/HDAC complex/NCoR1 0.014 0.026 -10000 0 -0.51 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.026 0.085 -10000 0 -0.39 8 8
SMAD3/SMAD4/SP1-3 0.041 0.085 -10000 0 -0.34 3 3
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.017 0.037 -10000 0 -10000 0 0
SIN3B 0.016 0.001 -10000 0 -10000 0 0
SIN3A 0.016 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.073 0.18 -10000 0 -0.45 31 31
ITGB5 0.054 0.072 -10000 0 -0.33 1 1
TGIF/SIN3/HDAC complex/CtBP 0.055 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.14 0.18 -10000 0 -0.36 149 149
AR -0.2 0.28 -10000 0 -0.57 148 148
negative regulation of cell growth 0.009 0.098 -10000 0 -0.4 5 5
SMAD3/SMAD4/MYOD -0.006 0.048 -10000 0 -0.28 1 1
E2F5 0.012 0.046 -10000 0 -0.53 3 3
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.011 0.13 -10000 0 -0.4 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.045 0.078 -10000 0 -0.34 12 12
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.054 0.21 -10000 0 -0.69 23 23
SMAD3/SMAD4/RUNX2 -0.01 0.058 -10000 0 -0.31 7 7
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.016 0 -10000 0 -10000 0 0
IL27-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
TGFB1 0.019 0.005 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.027 0.13 0.55 5 -10000 0 5
IL27/IL27R/JAK1 -0.054 0.16 -10000 0 -0.75 4 4
TBX21 -0.042 0.2 -10000 0 -0.57 23 23
IL12B -0.009 0.095 -10000 0 -0.51 14 14
IL12A 0.005 0.053 -10000 0 -0.37 8 8
IL6ST -0.074 0.21 -10000 0 -0.58 61 61
IL27RA/JAK1 0.016 0.037 -10000 0 -10000 0 0
IL27 -0.019 0.12 -10000 0 -0.51 23 23
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.15 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.027 0.13 0.55 5 -10000 0 5
T cell proliferation during immune response 0.027 0.13 0.55 5 -10000 0 5
MAPKKK cascade -0.027 0.13 -10000 0 -0.55 5 5
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.01 0.051 -10000 0 -0.5 4 4
IL12RB1 -0.025 0.14 -10000 0 -0.53 30 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.065 0.22 -10000 0 -0.54 34 34
IL27/IL27R/JAK2/TYK2 -0.027 0.13 -10000 0 -0.56 5 5
positive regulation of T cell mediated cytotoxicity -0.027 0.13 -10000 0 -0.55 5 5
STAT1 (dimer) -0.082 0.21 0.5 13 -0.71 13 26
JAK2 0.012 0.03 -10000 0 -0.57 1 1
JAK1 0.016 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.019 0.12 -10000 0 -0.52 5 5
T cell proliferation -0.15 0.19 -10000 0 -0.51 40 40
IL12/IL12R/TYK2/JAK2 -0.001 0.086 -10000 0 -10000 0 0
IL17A -0.12 0.15 -10000 0 -10000 0 0
mast cell activation 0.027 0.13 0.55 5 -10000 0 5
IFNG -0.008 0.035 -10000 0 -0.095 6 6
T cell differentiation -0.005 0.006 -10000 0 -0.019 30 30
STAT3 (dimer) -0.019 0.12 -10000 0 -0.52 5 5
STAT5A (dimer) -0.019 0.12 -10000 0 -0.52 5 5
STAT4 (dimer) -0.034 0.14 -10000 0 -0.51 10 10
STAT4 -0.013 0.13 -10000 0 -0.57 20 20
T cell activation -0.01 0.008 0.051 4 -10000 0 4
IL27R/JAK2/TYK2 -0.026 0.13 -10000 0 -0.61 2 2
GATA3 -0.071 0.35 -10000 0 -1.4 27 27
IL18 0.007 0.052 -10000 0 -0.42 6 6
positive regulation of mast cell cytokine production -0.018 0.12 -10000 0 -0.51 5 5
IL27/EBI3 -0.014 0.11 -10000 0 -0.39 32 32
IL27RA 0.006 0.038 -10000 0 -10000 0 0
IL6 -0.24 0.29 -10000 0 -0.57 184 184
STAT5A 0.014 0.029 -10000 0 -0.57 1 1
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.004 0.022 -10000 0 -10000 0 0
IL1B -0.022 0.12 -10000 0 -0.4 35 35
EBI3 -0.002 0.089 -10000 0 -0.53 11 11
TNF -0.007 0.084 -10000 0 -0.37 21 21
Signaling events mediated by PTP1B

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
PDGFRB 0.001 0.09 -10000 0 -0.57 10 10
Jak2/Leptin Receptor -0.007 0.092 0.2 16 -0.32 12 28
PTP1B/AKT1 0.026 0.048 -10000 0 -0.25 1 1
FYN 0.011 0.05 -10000 0 -0.57 3 3
p210 bcr-abl/PTP1B 0.02 0.053 -10000 0 -0.24 4 4
EGFR -0.007 0.11 -10000 0 -0.54 17 17
EGF/EGFR -0.026 0.074 -10000 0 -0.28 18 18
CSF1 -0.006 0.11 -10000 0 -0.57 15 15
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.003 0.1 -10000 0 -0.28 31 31
Insulin Receptor/Insulin -0.004 0.025 -10000 0 -10000 0 0
HCK -0.008 0.11 -10000 0 -0.55 17 17
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 0.027 0.05 -10000 0 -0.25 2 2
EGF -0.017 0.12 -10000 0 -0.5 25 25
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 0.023 0.068 -10000 0 -0.26 4 4
TXN 0.013 0.037 -10000 0 -0.51 2 2
PTP1B/IRS1/GRB2 0.028 0.071 -10000 0 -0.35 6 6
cell migration -0.02 0.053 0.24 4 -10000 0 4
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.046 0.18 -10000 0 -0.53 47 47
ITGA2B -0.025 0.14 -10000 0 -0.51 31 31
CSF1R -0.016 0.13 -10000 0 -0.56 22 22
Prolactin Receptor/Prolactin -0.044 0.13 -10000 0 -0.38 54 54
FGR 0.013 0.041 -10000 0 -0.57 2 2
PTP1B/p130 Cas 0.027 0.05 -10000 0 -0.25 2 2
Crk/p130 Cas 0.035 0.049 -10000 0 -10000 0 0
DOK1 0.029 0.062 -10000 0 -0.26 6 6
JAK2 0.011 0.072 -10000 0 -0.32 6 6
Jak2/Leptin Receptor/Leptin -0.072 0.15 -10000 0 -0.43 44 44
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
PTPN1 0.02 0.054 -10000 0 -0.24 4 4
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.043 0.16 -10000 0 -0.51 45 45
SRC 0.028 0.023 -10000 0 -10000 0 0
ITGB3 -0.051 0.18 -10000 0 -0.57 46 46
CAT1/PTP1B -0.001 0.11 -10000 0 -0.41 9 9
CAPN1 0.016 0.002 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K -0.001 0.024 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.071 0.15 -10000 0 -0.46 44 44
negative regulation of transcription 0.015 0.073 -10000 0 -0.3 7 7
FCGR2A -0.001 0.093 -10000 0 -0.51 13 13
FER 0.012 0.05 -10000 0 -0.57 3 3
alphaIIb/beta3 Integrin -0.056 0.17 -10000 0 -0.41 72 72
BLK -0.06 0.19 -10000 0 -0.55 53 53
Insulin Receptor/Insulin/Shc 0.021 0.016 -10000 0 -0.3 1 1
RHOA 0.016 0.002 -10000 0 -10000 0 0
LEPR -0.009 0.12 -10000 0 -0.56 18 18
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.022 0.13 -10000 0 -0.46 14 14
PRL -0.002 0.067 -10000 0 -0.51 7 7
SOCS3 -0.14 0.43 -10000 0 -1.4 43 43
SPRY2 0.004 0.082 -10000 0 -0.57 8 8
Insulin Receptor/Insulin/IRS1 0.013 0.058 -10000 0 -0.35 10 10
CSF1/CSF1R 0.009 0.11 -10000 0 -0.38 20 20
Ras protein signal transduction 0.011 0.018 -10000 0 -10000 0 0
IRS1 0.001 0.09 -10000 0 -0.57 10 10
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.06 0.19 -10000 0 -0.55 52 52
STAT5B 0.022 0.055 -10000 0 -0.23 4 4
STAT5A 0.022 0.055 -10000 0 -0.23 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.071 -10000 0 -0.31 10 10
CSN2 -0.013 0.047 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
LAT 0.024 0.034 -10000 0 -0.39 1 1
YBX1 0.024 0.025 -10000 0 -0.49 1 1
LCK 0.007 0.068 -10000 0 -0.55 6 6
SHC1 0.014 0.026 -10000 0 -0.51 1 1
NOX4 -0.023 0.14 -10000 0 -0.5 30 30
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.054 0.079 -10000 0 -0.57 2 2
UGCG -0.014 0.16 -10000 0 -0.66 23 23
AKT1/mTOR/p70S6K/Hsp90/TERT 0.024 0.12 -10000 0 -0.36 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.011 0.16 -10000 0 -0.65 23 23
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.12 -10000 0 -0.4 33 33
FRAP1 0.046 0.17 -10000 0 -0.46 34 34
FOXO3 0.058 0.14 -10000 0 -0.45 21 21
AKT1 0.05 0.15 -10000 0 -0.46 26 26
GAB2 0.014 0.029 -10000 0 -0.57 1 1
SMPD1 0.023 0.028 -10000 0 -10000 0 0
SGMS1 0.023 0.028 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.019 -10000 0 -0.34 1 1
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation 0.017 0.13 -10000 0 -0.32 39 39
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K 0.027 0.023 -10000 0 -0.4 1 1
RPS6KB1 0.018 0.038 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.013 6 6
JAK3 0.016 0.037 -10000 0 -0.5 2 2
PIK3R1 0.017 0.029 -10000 0 -0.57 1 1
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC 0.032 0.24 -10000 0 -0.94 21 21
MYB -0.022 0.14 -10000 0 -1.3 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.052 0.12 -10000 0 -0.6 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.035 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.12 -10000 0 -0.58 7 7
Rac1/GDP 0.031 0.019 -10000 0 -0.3 1 1
T cell proliferation 0.056 0.11 -10000 0 -0.58 6 6
SHC1 0.014 0.026 -10000 0 -0.5 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.013 -10000 0 -0.031 57 57
PRKCZ 0.056 0.12 -10000 0 -0.61 6 6
NF kappa B1 p50/RelA -0.024 0.12 -10000 0 -0.44 22 22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.047 0.084 -10000 0 -0.49 7 7
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.035 0.16 -10000 0 -0.54 37 37
IL2RB 0.009 0.074 -10000 0 -0.55 7 7
TERT -0.21 0.26 -10000 0 -0.51 176 176
E2F1 -0.01 0.088 -10000 0 -0.3 7 7
SOS1 0.016 0.004 -10000 0 -10000 0 0
RPS6 0.016 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.015 57 -10000 0 57
PTPN11 0.016 0.004 -10000 0 -10000 0 0
IL2RG -0.007 0.12 -10000 0 -0.54 19 19
actin cytoskeleton organization 0.056 0.11 -10000 0 -0.58 6 6
GRB2 0.016 0.004 -10000 0 -10000 0 0
IL2 0.007 0.008 -10000 0 -10000 0 0
PIK3CA 0.018 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.02 -10000 0 -0.28 1 1
LCK 0.01 0.068 -10000 0 -0.55 6 6
BCL2 0.037 0.22 -10000 0 -0.8 21 21
Signaling events mediated by HDAC Class III

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
EP300 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.1 0.36 31 -10000 0 31
CDKN1A -0.004 0.053 -10000 0 -0.76 2 2
KAT2B 0.014 0.029 -10000 0 -0.57 1 1
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.014 0.029 -10000 0 -0.57 1 1
FOXO4 0.026 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.013 0.11 -10000 0 -0.51 18 18
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.012 0.021 -10000 0 -0.42 1 1
PPARGC1A -0.23 0.29 -10000 0 -0.57 170 170
FHL2 0.011 0.05 -10000 0 -0.57 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.011 -10000 0 -10000 0 0
HIST2H4A -0.005 0.1 -10000 0 -0.36 31 31
SIRT1/FOXO3a 0.001 0.01 -10000 0 -10000 0 0
SIRT1 0.001 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.01 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.009 0.033 -10000 0 -10000 0 0
apoptosis -0.001 0.01 -10000 0 -10000 0 0
SIRT1/PGC1A -0.14 0.17 -10000 0 -0.35 170 170
p53/SIRT1 0.002 0.028 0.4 2 -10000 0 2
SIRT1/FOXO4 0.001 0.013 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.003 0.03 -10000 0 -0.29 4 4
HIST1H1E 0.011 0.047 -10000 0 -10000 0 0
SIRT1/p300 0.001 0.011 -10000 0 -10000 0 0
muscle cell differentiation 0 0.02 0.35 1 -10000 0 1
TP53 0.001 0.014 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.01 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.015 0.074 -10000 0 -0.36 18 18
ACSS2 0.023 0.021 -10000 0 -0.36 1 1
SIRT1/PCAF/MYOD 0.018 0.02 -10000 0 -0.35 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.018 0.006 -10000 0 -10000 0 0
PRKCZ 0.011 0.05 -10000 0 -0.57 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.017 0.048 -10000 0 -0.29 2 2
IRAK/TOLLIP 0.034 0.004 -10000 0 -10000 0 0
IKBKB 0.016 0 -10000 0 -10000 0 0
IKBKG 0.016 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.094 0.19 -10000 0 -0.39 115 115
IL1A -0.089 0.22 -10000 0 -0.54 77 77
IL1B -0.018 0.13 -10000 0 -0.4 43 43
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.021 -10000 0 -10000 0 0
IL1R2 -0.043 0.17 -10000 0 -0.52 45 45
IL1R1 0.014 0.029 -10000 0 -0.57 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.032 0.062 0.22 10 -0.4 1 11
TOLLIP 0.016 0 -10000 0 -10000 0 0
TICAM2 0.014 0.029 -10000 0 -0.57 1 1
MAP3K3 0.016 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.011 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.075 0.01 -10000 0 -10000 0 0
JUN 0.034 0.067 -10000 0 -10000 0 0
MAP3K7 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.013 0.11 -10000 0 -0.5 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.028 0.14 -10000 0 -0.32 39 39
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.018 0.13 -10000 0 -0.52 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.004 0.12 -10000 0 -0.33 30 30
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.039 0.042 -10000 0 -10000 0 0
IRAK1 0.027 0.005 -10000 0 -10000 0 0
IL1RN/IL1R1 0.008 0.08 -10000 0 -0.39 15 15
IRAK4 0.016 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
PI3K 0.022 0.021 -10000 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.023 0.067 -10000 0 -0.38 2 2
CHUK 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.004 0.12 -10000 0 -0.33 30 30
IL1 beta/IL1R2 -0.043 0.16 -10000 0 -0.35 79 79
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.029 0.079 -10000 0 -0.45 4 4
IRAK3 -0.002 0.099 -10000 0 -0.57 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.013 0.11 -10000 0 -0.5 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.001 0.093 -10000 0 -0.5 1 1
IL1 alpha/IL1R1/IL1RAP -0.043 0.15 -10000 0 -0.32 86 86
RELA 0.016 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.016 0 -10000 0 -10000 0 0
MYD88 0.016 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.043 0.004 -10000 0 -10000 0 0
IL1RAP 0.002 0.085 -10000 0 -0.51 11 11
UBE2N 0.016 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.026 0.07 -10000 0 -0.41 4 4
CASP1 0.003 0.086 -10000 0 -0.57 9 9
IL1RN/IL1R2 -0.033 0.14 -10000 0 -0.38 57 57
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.006 0.11 -10000 0 -0.53 4 4
TMEM189-UBE2V1 0.008 0.008 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.016 0.076 -10000 0 -0.51 1 1
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL1RN -0.004 0.1 -10000 0 -0.52 15 15
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.034 0.035 -10000 0 -0.26 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.021 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.007 0.069 -9999 0 -0.56 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.025 0.023 -9999 0 -0.21 1 1
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 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 0.016 0 -9999 0 -10000 0 0
FYN 0.011 0.05 -9999 0 -0.57 3 3
MAP3K12 0.014 0.029 -9999 0 -0.57 1 1
FGR 0.013 0.041 -9999 0 -0.57 2 2
p38 alpha/TAB1 -0.021 0.055 -9999 0 -0.27 12 12
PRKG1 -0.12 0.25 -9999 0 -0.57 94 94
DUSP8 -0.029 0.16 -9999 0 -0.57 31 31
PGK/cGMP/p38 alpha -0.072 0.12 -9999 0 -0.38 34 34
apoptosis -0.02 0.053 -9999 0 -0.26 12 12
RAL/GTP 0.02 0.016 -9999 0 -0.3 1 1
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 -0.16 0.27 -9999 0 -0.57 119 119
PAK1 0.014 0.029 -9999 0 -0.57 1 1
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.04 0.015 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 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 0.014 0.026 -9999 0 -0.51 1 1
RAC1-CDC42/GTP 0.021 0 -9999 0 -10000 0 0
MAPK11 0.027 0.099 -9999 0 -0.32 13 13
BLK -0.06 0.19 -9999 0 -0.55 53 53
HCK -0.008 0.11 -9999 0 -0.55 17 17
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.009 0.057 -9999 0 -0.51 5 5
TRAF6/MEKK3 0.02 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.031 0.082 -9999 0 -0.29 12 12
positive regulation of innate immune response 0.035 0.11 -9999 0 -0.36 13 13
LCK 0.007 0.068 -9999 0 -0.55 6 6
p38alpha-beta/MKP7 0.042 0.1 -9999 0 -0.38 8 8
p38alpha-beta/MKP5 0.039 0.11 -9999 0 -0.37 9 9
PGK/cGMP -0.088 0.18 -9999 0 -0.42 94 94
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.035 0.18 -9999 0 -0.41 45 45
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.014 0.026 -9999 0 -0.51 1 1
PAK3 -0.006 0.087 -9999 0 -0.51 12 12
Ephrin B reverse 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
EFNB2 0.013 0.036 -10000 0 -0.51 2 2
EPHB2 -0.02 0.13 -10000 0 -0.5 28 28
EFNB1 0.015 0.071 -10000 0 -0.41 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.035 0.1 -10000 0 -0.52 5 5
Ephrin B2/EPHB1-2 -0.016 0.12 -10000 0 -0.29 60 60
neuron projection morphogenesis -0.04 0.094 -10000 0 -0.5 5 5
Ephrin B1/EPHB1-2/Tiam1 -0.007 0.12 -10000 0 -0.56 5 5
DNM1 0 0.095 -10000 0 -0.57 11 11
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.089 -10000 0 -0.61 8 8
YES1 -0.014 0.12 -10000 0 -0.86 8 8
Ephrin B1/EPHB1-2/NCK2 -0.004 0.12 -10000 0 -0.57 3 3
PI3K 0.016 0.092 -10000 0 -0.58 9 9
mol:GDP -0.008 0.12 -10000 0 -0.55 5 5
ITGA2B -0.024 0.14 -10000 0 -0.51 31 31
endothelial cell proliferation 0.018 0.023 -10000 0 -0.3 2 2
FYN -0.015 0.12 -10000 0 -0.88 8 8
MAP3K7 -0.008 0.092 -10000 0 -0.65 8 8
FGR -0.015 0.12 -10000 0 -0.87 8 8
TIAM1 0.011 0.05 -10000 0 -0.57 3 3
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.022 0.14 -10000 0 -0.54 13 13
LYN -0.014 0.12 -10000 0 -0.86 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.11 -10000 0 -0.8 8 8
Ephrin B1/EPHB1-2 -0.015 0.099 -10000 0 -0.71 8 8
SRC -0.014 0.12 -10000 0 -0.85 8 8
ITGB3 -0.05 0.18 -10000 0 -0.57 46 46
EPHB1 -0.03 0.16 -10000 0 -0.56 32 32
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.019 0.023 -10000 0 -0.3 2 2
alphaIIb/beta3 Integrin -0.053 0.17 -10000 0 -0.41 72 72
BLK -0.031 0.13 -10000 0 -0.86 8 8
HCK -0.019 0.13 -10000 0 -0.88 8 8
regulation of stress fiber formation 0.005 0.12 0.56 3 -10000 0 3
MAPK8 0.02 0.097 -10000 0 -0.64 8 8
Ephrin B1/EPHB1-2/RGS3 -0.004 0.12 -10000 0 -0.57 3 3
endothelial cell migration -0.007 0.079 -10000 0 -0.55 8 8
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.006 0.096 -10000 0 -0.68 8 8
regulation of focal adhesion formation 0.005 0.12 0.56 3 -10000 0 3
chemotaxis 0.005 0.12 0.56 3 -10000 0 3
PIK3CA 0.016 0 -10000 0 -10000 0 0
Rac1/GTP -0.041 0.096 -10000 0 -0.51 5 5
angiogenesis -0.014 0.098 -10000 0 -0.71 8 8
LCK -0.016 0.12 -10000 0 -0.85 8 8
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.014 0.026 -9999 0 -0.51 1 1
Syndecan-3/Src/Cortactin -0.028 0.13 -9999 0 -0.8 1 1
Syndecan-3/Neurocan -0.008 0.048 -9999 0 -0.59 1 1
POMC -0.006 0.11 -9999 0 -0.53 16 16
EGFR -0.008 0.11 -9999 0 -0.54 17 17
Syndecan-3/EGFR -0.012 0.059 -9999 0 -0.59 1 1
AGRP 0.004 0.045 -9999 0 -0.51 3 3
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.005 0.084 -9999 0 -0.51 11 11
long-term memory 0.034 0.048 -9999 0 -0.8 1 1
Syndecan-3/IL8 -0.042 0.11 -9999 0 -0.29 59 59
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0.022 0.019 -9999 0 -0.36 1 1
FYN 0.011 0.05 -9999 0 -0.57 3 3
limb bud formation -0.002 0.03 -9999 0 -0.62 1 1
MC4R -0.001 0.057 -9999 0 -0.51 5 5
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.13 0.25 -9999 0 -0.56 103 103
FGFR/FGF/Syndecan-3 -0.002 0.031 -9999 0 -0.62 1 1
neuron projection morphogenesis -0.043 0.12 -9999 0 -0.6 2 2
Syndecan-3/AgRP -0.003 0.035 -9999 0 -0.59 1 1
Syndecan-3/AgRP/MC4R 0.001 0.046 -9999 0 -0.57 1 1
Fyn/Cortactin 0.019 0.041 -9999 0 -0.4 4 4
SDC3 -0.002 0.031 -9999 0 -0.63 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.042 0.1 -9999 0 -0.28 59 59
IL8 -0.07 0.21 -9999 0 -0.57 60 60
Syndecan-3/Fyn/Cortactin 0.035 0.05 -9999 0 -0.84 1 1
Syndecan-3/CASK -0.001 0.03 -9999 0 -0.6 1 1
alpha-MSH/MC4R -0.004 0.087 -9999 0 -0.38 21 21
Gamma Secretase 0.047 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.2 -9999 0 -0.54 19 19
RAD9A 0.008 0.063 -9999 0 -0.51 6 6
AP1 -0.13 0.23 -9999 0 -0.45 130 130
IFNAR2 0.01 0.009 -9999 0 -10000 0 0
AKT1 -0.029 0.092 -9999 0 -0.24 31 31
ER alpha/Oestrogen -0.069 0.16 -9999 0 -0.42 73 73
NFX1/SIN3/HDAC complex 0.032 0.029 -9999 0 -10000 0 0
EGF -0.02 0.12 -9999 0 -0.51 25 25
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0.015 0.014 -9999 0 -10000 0 0
TERT/c-Abl -0.13 0.17 -9999 0 -0.52 15 15
SAP18 0.015 0.002 -9999 0 -10000 0 0
MRN complex 0.032 0 -9999 0 -10000 0 0
WT1 -0.061 0.17 -9999 0 -0.51 52 52
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.011 0.01 -9999 0 -10000 0 0
SP3 0.013 0.004 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.14 -9999 0 -0.54 8 8
Mad/Max 0.013 0.023 -9999 0 -0.37 1 1
TERT -0.13 0.2 -9999 0 -0.56 17 17
CCND1 -0.13 0.23 -9999 0 -0.96 12 12
MAX 0.013 0.004 -9999 0 -10000 0 0
RBBP7 0.015 0.002 -9999 0 -10000 0 0
RBBP4 0.015 0.002 -9999 0 -10000 0 0
TERF2 0.015 0 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.015 0.002 -9999 0 -10000 0 0
Telomerase/911 0.024 0.038 -9999 0 -10000 0 0
CDKN1B -0.024 0.13 -9999 0 -10000 0 0
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 0.015 0.002 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.014 0.004 -9999 0 -10000 0 0
JUN -0.009 0.11 -9999 0 -0.57 16 16
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.007 -9999 0 -10000 0 0
FOS -0.17 0.27 -9999 0 -0.57 129 129
IFN-gamma/IRF1 -0.052 0.15 -9999 0 -0.34 81 81
PARP2 0.016 0 -9999 0 -10000 0 0
BLM 0 0.088 -9999 0 -0.51 12 12
Telomerase -0.007 0.063 -9999 0 -0.41 1 1
IRF1 0.019 0.005 -9999 0 -10000 0 0
ESR1 -0.09 0.22 -9999 0 -0.57 73 73
KU/TER 0.023 0 -9999 0 -10000 0 0
ATM/TRF2 0.024 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.029 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.035 0.032 -9999 0 -10000 0 0
HDAC1 0.015 0.002 -9999 0 -10000 0 0
HDAC2 0.01 0.01 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.029 0.005 -9999 0 -10000 0 0
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.012 0.027 -9999 0 -0.52 1 1
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.13 0.17 -9999 0 -0.56 11 11
NR2F2 0.019 0.03 -9999 0 -0.57 1 1
MAPK3 0.011 0.01 -9999 0 -10000 0 0
MAPK1 0.011 0.01 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.017 0.002 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
HNRNPC 0.016 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 0.016 0 -9999 0 -10000 0 0
EGFR -0.009 0.11 -9999 0 -0.54 17 17
mol:Oestrogen -0.002 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.026 0.12 -9999 0 -0.37 42 42
MYC -0.016 0.12 -9999 0 -0.57 18 18
IL2 -0.001 0.013 -9999 0 -10000 0 0
KU 0.023 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.017 0.002 -9999 0 -10000 0 0
TRF2/BLM -0.01 0.055 -9999 0 -0.33 12 12
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.19 -9999 0 -0.6 8 8
SP1/HDAC2 0.017 0.016 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.14 -9999 0 -0.58 6 6
Smad3/Myc 0.017 0.076 -9999 0 -0.34 18 18
911 complex 0.027 0.039 -9999 0 -0.29 6 6
IFNG -0.087 0.21 -9999 0 -0.5 81 81
Telomerase/PinX1 -0.12 0.14 -9999 0 -0.56 7 7
Telomerase/AKT1/mTOR/p70S6K -0.012 0.067 -9999 0 -10000 0 0
SIN3B 0.015 0.002 -9999 0 -10000 0 0
YWHAE 0.014 0.029 -9999 0 -0.57 1 1
Telomerase/EST1B -0.12 0.14 -9999 0 -0.54 8 8
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.12 0.14 -9999 0 -0.54 8 8
E2F1 -0.11 0.22 -9999 0 -0.51 97 97
ZNFX1 0.015 0.002 -9999 0 -10000 0 0
PIF1 -0.029 0.15 -9999 0 -0.51 35 35
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.008 0.064 -9999 0 -0.57 5 5
ITGA4 -0.003 0.1 -9999 0 -0.56 13 13
alpha4/beta7 Integrin 0.004 0.088 -9999 0 -0.4 18 18
alpha4/beta1 Integrin 0.01 0.075 -9999 0 -0.4 13 13
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.026 0.019 -9999 0 -0.36 1 1
BAD/BCL-XL/YWHAZ 0.039 0.015 -9999 0 -10000 0 0
CDKN1B 0.043 0 -9999 0 -10000 0 0
CDKN1A 0.042 0.021 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.043 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.016 0 -9999 0 -10000 0 0
AKT3 0.008 0.066 -9999 0 -0.34 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.042 0.013 -9999 0 -10000 0 0
AKT1/ASK1 0.041 0.014 -9999 0 -10000 0 0
BAD/YWHAZ 0.032 0 -9999 0 -10000 0 0
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.014 0.026 -9999 0 -0.51 1 1
JNK cascade 0.001 0.012 -9999 0 -10000 0 0
TSC1 0.043 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0.043 0.013 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.036 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.043 0 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.028 0 -9999 0 -10000 0 0
MAP3K5 0.014 0.029 -9999 0 -0.57 1 1
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.044 0.026 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.043 0 -9999 0 -10000 0 0
CASP9 0.043 0 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.051 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0 -9999 0 -10000 0 0
YWHAE 0.014 0.029 -9999 0 -0.57 1 1
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.017 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0 -9999 0 -10000 0 0
CHUK 0.043 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.058 0.012 -9999 0 -10000 0 0
mTORC2 0.02 0 -9999 0 -10000 0 0
AKT2 0.02 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.061 0.03 -9999 0 -10000 0 0
PDPK1 0.016 0 -9999 0 -10000 0 0
MDM2 0.035 0.046 -9999 0 -10000 0 0
MAPKKK cascade -0.042 0.013 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.05 0.043 -9999 0 -10000 0 0
TSC1/TSC2 0.05 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.041 -9999 0 -10000 0 0
glucose import -0.2 0.15 -9999 0 -0.3 294 294
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.037 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.21 0.15 -9999 0 -0.3 294 294
GSK3A 0.043 0 -9999 0 -10000 0 0
FOXO1 0.042 0.015 -9999 0 -10000 0 0
GSK3B 0.043 0 -9999 0 -10000 0 0
SFN -0.031 0.15 -9999 0 -0.51 36 36
G1/S transition of mitotic cell cycle 0.05 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.045 0.039 -9999 0 -0.3 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.014 0.026 -10000 0 -0.51 1 1
NFATC1 0.035 0.078 -10000 0 -10000 0 0
NFATC2 -0.024 0.075 -10000 0 -0.28 5 5
NFATC3 0.009 0.038 -10000 0 -0.4 3 3
YWHAE 0.014 0.029 -10000 0 -0.57 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.045 0.14 -10000 0 -0.43 32 32
Exportin 1/Ran/NUP214 0.014 0.016 -10000 0 -10000 0 0
mol:DAG -0.003 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.069 0.12 -10000 0 -0.4 35 35
BCL2/BAX 0.006 0.084 -10000 0 -0.41 16 16
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.01 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.007 0.008 -10000 0 -10000 0 0
BAD 0.016 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.039 0.14 -10000 0 -0.41 32 32
Calcineurin A alpha-beta B1/BCL2 -0.007 0.11 -10000 0 -0.57 16 16
FKBP8 0.016 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.039 0.14 0.4 32 -10000 0 32
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.011 0.051 -10000 0 -0.51 4 4
XPO1 0.015 0.001 -10000 0 -10000 0 0
SFN -0.031 0.15 -10000 0 -0.51 36 36
MAP3K8 0.003 0.05 -10000 0 -0.57 3 3
NFAT4/CK1 alpha -0.002 0.02 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.13 0.17 -10000 0 -0.38 46 46
CABIN1 -0.046 0.14 -10000 0 -0.43 32 32
CALM1 0.011 0.005 -10000 0 -10000 0 0
RAN 0.015 0.001 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 0 0.094 -10000 0 -0.56 11 11
mol:Ca2+ -0.009 0.009 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.007 0.038 -10000 0 -0.36 4 4
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.003 0.05 -10000 0 -0.57 3 3
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.028 0.082 -10000 0 -0.34 3 3
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.01 0.014 -10000 0 -10000 0 0
CASP3 0.007 0.008 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.006 -10000 0 -10000 0 0
apoptosis -0.005 0.024 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.036 -10000 0 -0.28 1 1
PRKCB -0.15 0.26 -10000 0 -0.57 118 118
PRKCE 0.016 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.023 0.034 -10000 0 -0.36 3 3
BAD/BCL-XL 0.022 0.019 -10000 0 -0.36 1 1
PRKCD 0.016 0 -10000 0 -10000 0 0
NUP214 0.015 0.001 -10000 0 -10000 0 0
PRKCZ 0.003 0.05 -10000 0 -0.57 3 3
PRKCA 0.008 0.064 -10000 0 -0.57 5 5
PRKCG -0.01 0.094 -10000 0 -0.51 14 14
PRKCQ -0.04 0.17 -10000 0 -0.56 39 39
FKBP38/BCL2 0.006 0.084 -10000 0 -0.41 16 16
EP300 0.009 0.006 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.014 0.079 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.01 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0 0.06 -10000 0 -0.35 11 11
NFATc/ERK1 0.043 0.074 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.066 0.12 -10000 0 -0.39 35 35
NR4A1 -0.28 0.3 -10000 0 -0.54 230 230
GSK3B 0.007 0.008 -10000 0 -10000 0 0
positive T cell selection 0.009 0.038 -10000 0 -0.4 3 3
NFAT1/CK1 alpha -0.034 0.049 -10000 0 -0.29 3 3
RCH1/ KPNB1 0.02 0.037 -10000 0 -0.36 4 4
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.007 0.008 -10000 0 -10000 0 0
AKAP5 0.011 0.051 -10000 0 -0.51 4 4
MEF2D 0.009 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.017 0.077 -10000 0 -10000 0 0
CREBBP 0.009 0.006 -10000 0 -10000 0 0
BCL2 -0.007 0.11 -10000 0 -0.57 16 16
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.014 0.1 -10000 0 -0.32 43 43
cell-cell adhesion 0.04 0.09 0.45 7 -10000 0 7
Ephrin B/EPHB2/RasGAP 0.01 0.1 -10000 0 -0.32 15 15
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
SHC1 0.014 0.026 -10000 0 -0.51 1 1
Ephrin B1/EPHB3 0.007 0.067 -10000 0 -0.31 18 18
Ephrin B1/EPHB1 -0.007 0.098 -10000 0 -0.34 32 32
HRAS/GDP -0.025 0.084 -10000 0 -0.46 6 6
Ephrin B/EPHB1/GRB7 -0.01 0.13 -10000 0 -0.58 6 6
Endophilin/SYNJ1 0.009 0.095 -10000 0 -0.48 3 3
KRAS 0.014 0.026 -10000 0 -0.51 1 1
Ephrin B/EPHB1/Src 0.005 0.12 -10000 0 -0.59 5 5
endothelial cell migration -0.002 0.021 -10000 0 -0.28 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 -0.012 0.12 -10000 0 -0.53 21 21
PAK1 0.012 0.1 -10000 0 -0.48 3 3
HRAS 0.016 0 -10000 0 -10000 0 0
RRAS 0.007 0.1 -10000 0 -0.46 5 5
DNM1 0 0.095 -10000 0 -0.57 11 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.004 0.11 -10000 0 -0.56 5 5
lamellipodium assembly -0.04 0.09 -10000 0 -0.45 7 7
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.092 -10000 0 -0.44 4 4
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
EPHB2 -0.02 0.13 -10000 0 -0.51 28 28
EPHB3 -0.008 0.11 -10000 0 -0.51 18 18
EPHB1 -0.03 0.16 -10000 0 -0.56 32 32
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.099 -10000 0 -0.35 14 14
Ephrin B/EPHB2 0.001 0.1 -10000 0 -0.33 15 15
Ephrin B/EPHB3 0.007 0.095 -10000 0 -0.33 16 16
JNK cascade 0.001 0.11 -10000 0 -0.56 1 1
Ephrin B/EPHB1 -0.005 0.12 -10000 0 -0.32 41 41
RAP1/GDP 0.031 0.09 -10000 0 -0.38 6 6
EFNB2 0.013 0.036 -10000 0 -0.51 2 2
EFNB3 -0.015 0.13 -10000 0 -0.55 22 22
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.017 0.12 -10000 0 -0.29 60 60
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.04 0.092 -10000 0 -0.48 7 7
Rap1/GTP -0.039 0.089 -10000 0 -0.45 7 7
axon guidance -0.014 0.1 -10000 0 -0.32 43 43
MAPK3 0.031 0.083 -10000 0 -0.38 4 4
MAPK1 0.031 0.083 -10000 0 -0.38 4 4
Rac1/GDP 0.025 0.093 -10000 0 -0.41 6 6
actin cytoskeleton reorganization -0.029 0.067 -10000 0 -0.36 6 6
CDC42/GDP 0.025 0.093 -10000 0 -0.41 6 6
PI3K 0.035 0.025 -10000 0 -0.28 1 1
EFNA5 -0.006 0.11 -10000 0 -0.56 15 15
Ephrin B2/EPHB4 0.02 0.022 -10000 0 -0.3 2 2
Ephrin B/EPHB2/Intersectin/N-WASP 0.02 0.069 -10000 0 -0.26 14 14
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.039 0.087 -10000 0 -0.44 7 7
PTK2 0.011 0.027 -10000 0 -10000 0 0
MAP4K4 0.001 0.11 -10000 0 -0.57 1 1
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.008 0.065 -10000 0 -0.53 6 6
Intersectin/N-WASP 0.023 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.037 0.1 -10000 0 -0.37 7 7
MAP2K1 0.023 0.087 -10000 0 -0.41 4 4
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.006 0.11 -10000 0 -0.3 28 28
cell migration 0.027 0.098 -10000 0 -0.45 4 4
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.009 0.097 -10000 0 -0.49 3 3
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.016 0.13 -10000 0 -0.49 10 10
HRAS/GTP -0.043 0.098 -10000 0 -0.49 7 7
Ephrin B1/EPHB1-2 -0.016 0.11 -10000 0 -0.28 60 60
cell adhesion mediated by integrin 0.014 0.074 0.29 22 -10000 0 22
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.006 0.12 -10000 0 -0.52 7 7
RAC1-CDC42/GTP -0.047 0.1 -10000 0 -0.44 13 13
RASA1 0.016 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.031 0.09 -10000 0 -0.38 6 6
ruffle organization 0.018 0.12 -10000 0 -0.45 7 7
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization 0.009 0.1 -10000 0 -0.48 4 4
Ephrin B/EPHB2/KALRN 0.006 0.11 -10000 0 -0.52 3 3
ROCK1 0.016 0.061 -10000 0 -0.27 18 18
RAS family/GDP -0.027 0.064 -10000 0 -0.37 5 5
Rac1/GTP -0.042 0.095 -10000 0 -0.48 7 7
Ephrin B/EPHB1/Src/Paxillin 0.01 0.097 -10000 0 -0.26 41 41
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.027 0.051 -10000 0 -0.24 14 14
epithelial cell differentiation -0.01 0.051 -10000 0 -0.28 14 14
CYFIP2 0 0.095 -10000 0 -0.57 11 11
ENAH 0.06 0.055 -10000 0 -0.32 1 1
EGFR -0.008 0.11 -10000 0 -0.54 17 17
EPHA2 0.008 0.064 -10000 0 -0.57 5 5
MYO6 0.033 0.055 -10000 0 -0.26 14 14
CTNNB1 0.016 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.022 0.06 -10000 0 -0.34 11 11
AQP5 -0.013 0.045 -10000 0 -0.35 1 1
CTNND1 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.054 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.017 0.086 -10000 0 -0.28 18 18
EGF -0.018 0.12 -10000 0 -0.51 25 25
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.096 0.2 -10000 0 -0.49 80 80
cortical microtubule organization -0.01 0.051 -10000 0 -0.28 14 14
GO:0000145 0.031 0.052 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.058 -10000 0 -0.28 14 14
MLLT4 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.013 0.051 -10000 0 -0.45 1 1
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.057 -10000 0 -0.3 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.045 0.055 -10000 0 -10000 0 0
PVRL2 0.016 0 -10000 0 -10000 0 0
ZYX 0.032 0.057 -10000 0 -10000 0 0
ARF6/GTP -0.008 0.044 -10000 0 -10000 0 0
CDH1 -0.004 0.11 -10000 0 -0.57 14 14
EGFR/EGFR/EGF/EGF -0.031 0.083 -10000 0 -0.5 3 3
RhoA/GDP -0.009 0.047 -10000 0 -10000 0 0
actin cytoskeleton organization 0.039 0.055 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.05 -10000 0 -0.57 3 3
GIT1 0.016 0 -10000 0 -10000 0 0
IGF1R 0.011 0.05 -10000 0 -0.57 3 3
IGF1 -0.24 0.29 -10000 0 -0.57 182 182
DIAPH1 -0.014 0.094 -10000 0 -0.58 11 11
Wnt receptor signaling pathway 0.01 0.051 0.28 14 -10000 0 14
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.051 -10000 0 -0.46 1 1
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.039 0.056 -10000 0 -10000 0 0
EFNA1 0.004 0.077 -10000 0 -0.51 9 9
LPP 0.04 0.055 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.016 0.062 -10000 0 -0.53 1 1
SEC6/SEC8 -0.007 0.039 -10000 0 -10000 0 0
MGAT3 0.017 0.088 -10000 0 -0.29 18 18
HGF/MET -0.066 0.11 -10000 0 -0.49 2 2
HGF -0.12 0.24 -10000 0 -0.56 94 94
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.027 0.051 -10000 0 -0.24 14 14
actin cable formation 0.077 0.054 -10000 0 -10000 0 0
KIAA1543 0.031 0.095 -10000 0 -0.52 9 9
KIFC3 0.033 0.055 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ACTN1 0.033 0.055 -10000 0 -0.26 14 14
NCK1/GIT1 0.023 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.051 -10000 0 -0.28 14 14
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.033 0.055 -10000 0 -10000 0 0
PIP5K1C 0.033 0.055 -10000 0 -10000 0 0
LIMA1 0.016 0 -10000 0 -10000 0 0
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 0.055 0.062 -10000 0 -0.39 1 1
adherens junction assembly 0.048 0.094 -10000 0 -0.5 9 9
IGF-1R heterotetramer/IGF1 -0.12 0.13 -10000 0 -0.53 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.023 0 -10000 0 -10000 0 0
MET 0.013 0.036 -10000 0 -0.51 2 2
PLEKHA7 0.033 0.06 -10000 0 -0.28 14 14
mol:GTP 0.028 0.056 -10000 0 -0.3 5 5
establishment of epithelial cell apical/basal polarity 0.061 0.05 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.027 0.051 -10000 0 -0.24 14 14
regulation of cell-cell adhesion 0.039 0.055 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.027 0.051 -10000 0 -0.24 14 14
Signaling events mediated by PRL

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
CCNE1 -0.066 0.19 -9999 0 -0.51 64 64
mol:Halofuginone 0.006 0.001 -9999 0 -10000 0 0
ITGA1 0.016 0 -9999 0 -10000 0 0
CDKN1A -0.001 0.08 -9999 0 -0.67 2 2
PRL-3/alpha Tubulin 0.023 0 -9999 0 -10000 0 0
mol:Ca2+ -0.056 0.14 -9999 0 -0.42 54 54
AGT -0.061 0.2 -9999 0 -0.57 54 54
CCNA2 -0.099 0.18 -9999 0 -0.52 24 24
TUBA1B 0.016 0 -9999 0 -10000 0 0
EGR1 -0.077 0.18 -9999 0 -0.4 100 100
CDK2/Cyclin E1 -0.025 0.12 -9999 0 -0.41 15 15
MAPK3 0.026 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.023 0 -9999 0 -10000 0 0
MAPK1 0.026 0 -9999 0 -10000 0 0
PTP4A1 -0.039 0.14 -9999 0 -10000 0 0
PTP4A3 0.016 0 -9999 0 -10000 0 0
PTP4A2 0.016 0 -9999 0 -10000 0 0
ITGB1 0.026 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1 0.002 0.066 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.023 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.031 0.14 -9999 0 -0.52 2 2
RABGGTA 0.016 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.002 0.066 -9999 0 -10000 0 0
RHOA 0.002 0.066 -9999 0 -10000 0 0
cell motility 0.005 0.07 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.028 0.13 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.023 0 -9999 0 -10000 0 0
ROCK1 0.005 0.071 -9999 0 -10000 0 0
RABGGTB 0.016 0 -9999 0 -10000 0 0
CDK2 0.016 0 -9999 0 -10000 0 0
mitosis -0.039 0.14 -9999 0 -10000 0 0
ATF5 0.011 0.051 -9999 0 -0.51 4 4
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.018 0.075 -9999 0 -0.36 15 15
E-cadherin/beta catenin 0.008 0.078 -9999 0 -0.41 14 14
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.013 0.041 -9999 0 -0.57 2 2
CDH1 -0.004 0.11 -9999 0 -0.57 14 14
BARD1 signaling events

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
BARD1/CSTF1 0.013 0.067 -10000 0 -0.41 10 10
ATM 0.016 0 -10000 0 -10000 0 0
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.028 0.02 -10000 0 -10000 0 0
protein ubiquitination -0.043 0.093 -10000 0 -0.52 1 1
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0.032 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0.032 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.045 0.037 -10000 0 -10000 0 0
FANCF 0.013 0.039 -10000 0 -0.54 2 2
BRCA1 0.014 0.026 -10000 0 -0.51 1 1
CCNE1 -0.066 0.19 -10000 0 -0.51 64 64
CDK2/Cyclin E1 -0.036 0.14 -10000 0 -0.36 64 64
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.012 0.069 -10000 0 -0.4 11 11
FANCE 0.014 0.026 -10000 0 -0.51 1 1
FANCC 0.014 0.026 -10000 0 -0.51 1 1
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.019 0.13 -10000 0 -0.51 27 27
DNA repair -0.025 0.13 -10000 0 -0.39 6 6
BRCA1/BARD1/ubiquitin 0.012 0.069 -10000 0 -0.4 11 11
BARD1/DNA-PK 0.032 0.052 -10000 0 -0.3 10 10
FANCL 0.014 0.026 -10000 0 -0.51 1 1
mRNA polyadenylation -0.013 0.066 0.41 10 -10000 0 10
BRCA1/BARD1/CTIP/M/R/N Complex 0.04 0.043 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.022 0.059 -10000 0 -0.33 11 11
BRCA1/BARD1/P53 0.031 0.054 -10000 0 -0.3 10 10
BARD1/CSTF1/BRCA1 0.022 0.059 -10000 0 -0.33 11 11
BRCA1/BACH1 0.014 0.026 -10000 0 -0.51 1 1
BARD1 0.001 0.09 -10000 0 -0.57 10 10
PCNA 0.014 0.026 -10000 0 -0.51 1 1
BRCA1/BARD1/UbcH5C 0.022 0.059 -10000 0 -0.33 11 11
BRCA1/BARD1/UbcH7 0.022 0.059 -10000 0 -0.33 11 11
BRCA1/BARD1/RAD51/PCNA -0.074 0.15 -10000 0 -0.38 10 10
BARD1/DNA-PK/P53 0.039 0.049 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.012 0.069 -10000 0 -0.4 11 11
BRCA1/BARD1/CTIP 0.03 0.054 -10000 0 -0.3 10 10
FA complex 0.035 0.043 -10000 0 -10000 0 0
BARD1/EWS 0.013 0.067 -10000 0 -0.41 10 10
RBBP8 0.026 0 -10000 0 -10000 0 0
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.03 0.054 0.3 10 -10000 0 10
BRCA1/BARD1 -0.005 0.11 -10000 0 -0.53 1 1
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.001 0.066 -10000 0 -0.42 10 10
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.17 0.25 -10000 0 -0.51 145 145
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.012 0.069 -10000 0 -0.4 11 11
EWSR1 0.016 0 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.063 0.089 -9999 0 -0.42 3 3
CRKL 0.029 0.075 -9999 0 -0.29 3 3
mol:DAG 0.04 0.063 -9999 0 -0.28 1 1
HRAS 0.056 0.065 -9999 0 -10000 0 0
MAPK8 0.014 0.087 -9999 0 -0.34 6 6
RAP1A 0.03 0.073 -9999 0 -0.29 3 3
GAB1 0.03 0.073 -9999 0 -0.29 3 3
MAPK14 0.016 0.08 -9999 0 -0.28 1 1
EPO -0.024 0.14 -9999 0 -0.5 31 31
PLCG1 0.041 0.064 -9999 0 -0.29 1 1
EPOR/TRPC2/IP3 Receptors 0.007 0.072 -9999 0 -0.5 8 8
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.034 0.15 -9999 0 -0.34 76 76
GAB1/SHC/GRB2/SOS1 -0.015 0.044 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.009 0.11 -9999 0 -0.35 39 39
IRS2 0.018 0.094 -9999 0 -0.34 6 6
STAT1 0.046 0.08 -9999 0 -0.38 3 3
STAT5B 0.044 0.071 -9999 0 -0.34 3 3
cell proliferation 0.022 0.081 -9999 0 -0.41 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.018 0.052 -9999 0 -0.43 2 2
TEC 0.03 0.073 -9999 0 -0.29 3 3
SOCS3 -0.046 0.18 -9999 0 -0.57 43 43
STAT1 (dimer) 0.046 0.079 -9999 0 -0.37 3 3
JAK2 0.015 0.03 -9999 0 -0.56 1 1
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
EPO/EPOR (dimer)/JAK2 0.037 0.082 -9999 0 -0.3 4 4
EPO/EPOR -0.009 0.11 -9999 0 -0.35 39 39
LYN 0.017 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.038 0.074 -9999 0 -0.28 1 1
elevation of cytosolic calcium ion concentration 0.007 0.072 -9999 0 -0.5 8 8
SHC1 0.014 0.026 -9999 0 -0.51 1 1
EPO/EPOR (dimer)/LYN 0.013 0.092 -9999 0 -0.27 39 39
mol:IP3 0.04 0.063 -9999 0 -0.28 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.027 0.099 -9999 0 -0.43 5 5
SH2B3 0.016 0.007 -9999 0 -10000 0 0
NFKB1 0.016 0.08 -9999 0 -0.28 3 3
EPO/EPOR (dimer)/JAK2/SOCS3 -0.035 0.082 -9999 0 -0.25 43 43
PTPN6 0.022 0.076 -9999 0 -0.3 4 4
TEC/VAV2/GRB2 0.045 0.072 -9999 0 -10000 0 0
EPOR 0.007 0.072 -9999 0 -0.5 8 8
INPP5D 0.006 0.076 -9999 0 -0.57 7 7
mol:GDP -0.015 0.044 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.009 0.06 -9999 0 -0.53 5 5
CRKL/CBL/C3G 0.045 0.071 -9999 0 -10000 0 0
VAV2 0.029 0.076 -9999 0 -0.29 3 3
CBL 0.03 0.073 -9999 0 -0.29 3 3
SHC/Grb2/SOS1 -0.017 0.048 -9999 0 -10000 0 0
STAT5A 0.044 0.073 -9999 0 -0.34 3 3
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.059 0.094 -9999 0 -0.47 3 3
LYN/PLCgamma2 0.019 0.044 -9999 0 -0.38 5 5
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK 0.013 0.1 -9999 0 -0.36 9 9
BCL2 0.041 0.19 -9999 0 -0.89 16 16
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.002 0.096 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.013 0.036 -9999 0 -0.51 2 2
STAT1 (dimer)/Cbp/p300 0.036 0.092 -9999 0 -0.36 4 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.019 -9999 0 -0.34 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.031 0.062 -9999 0 -0.31 7 7
CaM/Ca2+ -0.035 0.069 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.005 0.099 -9999 0 -0.42 4 4
AKT1 0.021 0.084 -9999 0 -0.41 1 1
MAP2K1 0.017 0.087 -9999 0 -10000 0 0
MAP3K11 0.006 0.091 -9999 0 -10000 0 0
IFNGR1 0.013 0.009 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.19 -9999 0 -0.41 130 130
Rap1/GTP -0.024 0.049 -9999 0 -0.32 1 1
CRKL/C3G 0.021 0.026 -9999 0 -0.36 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.005 0.1 -9999 0 -10000 0 0
CEBPB 0.054 0.087 -9999 0 -0.36 4 4
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.006 0.097 -9999 0 -10000 0 0
STAT1 0.005 0.098 -9999 0 -0.42 4 4
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.087 0.2 -9999 0 -0.5 81 81
PIK3CA 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.014 0.094 -9999 0 -0.4 4 4
CEBPB/PTGES2/Cbp/p300 -0.009 0.025 -9999 0 -10000 0 0
mol:Ca2+ -0.004 0.094 -9999 0 -10000 0 0
MAPK3 0.034 0.077 -9999 0 -10000 0 0
STAT1 (dimer) -0.039 0.084 -9999 0 -0.44 7 7
MAPK1 0.034 0.077 -9999 0 -10000 0 0
JAK2 0.012 0.03 -9999 0 -0.56 1 1
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
JAK1 0.013 0.009 -9999 0 -10000 0 0
CAMK2D 0.013 0.041 -9999 0 -0.57 2 2
DAPK1 0.053 0.091 -9999 0 -0.62 4 4
SMAD7 0.02 0.06 -9999 0 -0.35 1 1
CBL/CRKL/C3G 0.02 0.087 -9999 0 -0.39 1 1
PI3K -0.033 0.067 -9999 0 -0.44 1 1
IFNG -0.088 0.2 -9999 0 -0.5 81 81
apoptosis 0.034 0.071 -9999 0 -0.44 4 4
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.17 0.27 -9999 0 -0.57 129 129
CAMK2B -0.04 0.16 -9999 0 -0.51 43 43
FRAP1 0.02 0.08 -9999 0 -0.38 1 1
PRKCD 0.022 0.086 -9999 0 -0.41 1 1
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.031 0.062 -9999 0 -0.31 7 7
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
IRF1 0.05 0.079 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy 0.009 0.094 -9999 0 -0.4 4 4
SOCS1 0.006 0.02 -9999 0 -10000 0 0
mol:GDP -0.029 0.06 -9999 0 -0.37 1 1
CASP1 0.016 0.072 -9999 0 -0.29 10 10
PTGES2 0.016 0 -9999 0 -10000 0 0
IRF9 0.054 0.036 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.032 0.066 -9999 0 -0.43 1 1
RAP1/GDP -0.024 0.049 -9999 0 -0.32 1 1
CBL 0.005 0.09 -9999 0 -10000 0 0
MAP3K1 0.007 0.091 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.031 0.062 -9999 0 -0.31 7 7
PTPN11 -0.004 0.094 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.019 0.079 -9999 0 -0.35 17 17
CRKL 0.013 0.036 -9999 0 -0.51 2 2
Rac1/GDP 0.012 0 -9999 0 -10000 0 0
DOCK1 0.013 0.041 -9999 0 -0.57 2 2
ITGA4 -0.003 0.1 -9999 0 -0.56 13 13
alpha4/beta7 Integrin/MAdCAM1 0.014 0.091 -9999 0 -0.33 17 17
EPO -0.027 0.14 -9999 0 -0.51 31 31
alpha4/beta7 Integrin 0.004 0.088 -9999 0 -0.4 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.01 0.075 -9999 0 -0.4 13 13
EPO/EPOR (dimer) -0.015 0.11 -9999 0 -0.36 39 39
lamellipodium assembly 0.001 0.018 -9999 0 -0.28 1 1
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0.022 0.021 -9999 0 -0.41 1 1
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 0.011 0.077 -9999 0 -0.29 13 13
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
MADCAM1 -0.004 0.095 -9999 0 -0.51 14 14
cell adhesion 0.013 0.09 -9999 0 -0.33 17 17
CRKL/CBL 0.021 0.026 -9999 0 -0.36 2 2
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.013 0.1 -9999 0 -0.38 23 23
ITGB7 0.008 0.064 -9999 0 -0.57 5 5
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.004 0.11 -9999 0 -0.41 26 26
p130Cas/Crk/Dock1 0.036 0.093 -9999 0 -0.5 6 6
VCAM1 -0.011 0.12 -9999 0 -0.56 19 19
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.03 0.059 -9999 0 -0.3 13 13
BCAR1 0.022 0.098 -9999 0 -0.56 6 6
EPOR 0.005 0.072 -9999 0 -0.51 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.018 -9999 0 -0.28 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.033 0.016 -9999 0 -0.29 1 1
SNTA1 0.016 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.001 0.098 -9999 0 -0.29 41 41
MAPK12 0.025 0.054 -9999 0 -0.27 13 13
CCND1 0.011 0.067 -9999 0 -0.45 7 7
p38 gamma/SNTA1 0.032 0.05 -9999 0 -0.27 5 5
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.014 0.029 -9999 0 -0.57 1 1
G2/M transition checkpoint 0.025 0.053 -9999 0 -0.27 13 13
MAP2K6 0.021 0.048 -9999 0 -0.32 8 8
MAPT 0.004 0.1 -9999 0 -0.31 35 35
MAPK13 0.026 0.019 -9999 0 -0.36 1 1
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.018 0.025 -9999 0 -0.34 2 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0 0.11 -9999 0 -0.52 10 10
PDGFB-D/PDGFRB/SLAP -0.001 0.12 -9999 0 -0.5 19 19
PDGFB-D/PDGFRB/APS/CBL 0.018 0.067 -9999 0 -0.32 15 15
AKT1 0.049 0.067 -9999 0 -0.41 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.002 0.12 -9999 0 -0.56 10 10
PIK3CA 0.016 0 -9999 0 -10000 0 0
FGR -0.011 0.069 -9999 0 -0.39 12 12
mol:Ca2+ 0.016 0.1 -9999 0 -0.59 10 10
MYC 0.007 0.19 -9999 0 -0.72 24 24
SHC1 0.014 0.026 -9999 0 -0.51 1 1
HRAS/GDP 0.034 0.048 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.018 0.069 -9999 0 -0.34 15 15
GRB10 0.008 0.064 -9999 0 -0.57 5 5
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.015 0.1 -9999 0 -0.6 10 10
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 -0.012 0.12 -9999 0 -0.53 21 21
PDGFB-D/PDGFRB/SHP2 0.012 0.067 -9999 0 -0.41 10 10
PDGFB-D/PDGFRB/GRB10 0.007 0.081 -9999 0 -0.41 15 15
cell cycle arrest -0.001 0.12 -9999 0 -0.5 19 19
HRAS 0.016 0 -9999 0 -10000 0 0
HIF1A 0.054 0.063 -9999 0 -0.36 1 1
GAB1 0.012 0.11 -9999 0 -0.57 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0.1 -9999 0 -0.51 10 10
PDGFB-D/PDGFRB 0.02 0.06 -9999 0 -0.35 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.012 0.067 -9999 0 -0.41 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.033 0.093 -9999 0 -0.48 10 10
positive regulation of MAPKKK cascade 0.012 0.067 -9999 0 -0.41 10 10
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
mol:IP3 0.016 0.1 -9999 0 -0.6 10 10
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.008 0.11 -9999 0 -0.39 31 31
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.062 0.18 -9999 0 -0.55 44 44
PTPN2 0.015 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.012 0.067 -9999 0 -0.41 10 10
BCAR1 0.016 0 -9999 0 -10000 0 0
VAV2 0.013 0.12 -9999 0 -0.55 12 12
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.011 0.074 -9999 0 -0.44 10 10
LCK -0.014 0.091 -9999 0 -0.46 13 13
PDGFRB 0.001 0.092 -9999 0 -0.58 10 10
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.025 0.14 -9999 0 -0.62 18 18
ABL1 0.013 0.095 -9999 0 -0.51 10 10
PDGFB-D/PDGFRB/CBL 0.01 0.12 -9999 0 -0.64 10 10
PTPN1 0.015 0.004 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.011 0.051 -9999 0 -0.51 4 4
cell proliferation 0.011 0.17 -9999 0 -0.63 24 24
SLA -0.004 0.11 -9999 0 -0.56 14 14
actin cytoskeleton reorganization 0.05 0.048 -9999 0 -10000 0 0
SRC -0.007 0.059 -9999 0 -0.37 10 10
PI3K -0.015 0.056 -9999 0 -0.46 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.004 0.094 -9999 0 -0.32 32 32
SH2B2 0.009 0.057 -9999 0 -0.51 5 5
PLCgamma1/SPHK1 -0.002 0.12 -9999 0 -0.58 10 10
LYN -0.007 0.059 -9999 0 -0.37 10 10
LRP1 0.01 0.058 -9999 0 -0.57 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.014 0.029 -9999 0 -0.57 1 1
NCK1-2/p130 Cas -0.001 0.044 -9999 0 -10000 0 0
SPHK1 -0.057 0.18 -9999 0 -0.5 57 57
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.016 0.1 -9999 0 -0.6 10 10
PLCG1 0.015 0.11 -9999 0 -0.62 10 10
NHERF/PDGFRB 0.005 0.09 -9999 0 -0.31 31 31
YES1 -0.007 0.059 -9999 0 -0.37 10 10
cell migration 0.005 0.09 -9999 0 -0.31 31 31
SHC/Grb2/SOS1 -0.001 0.045 -9999 0 -10000 0 0
SLC9A3R2 0.016 0 -9999 0 -10000 0 0
SLC9A3R1 -0.011 0.12 -9999 0 -0.51 21 21
NHERF1-2/PDGFRB/PTEN 0.016 0.082 -9999 0 -0.3 10 10
FYN -0.011 0.071 -9999 0 -0.4 13 13
DOK1 0.028 0.055 -9999 0 -0.3 10 10
HRAS/GTP 0.012 0 -9999 0 -10000 0 0
PDGFB 0.014 0.026 -9999 0 -0.51 1 1
RAC1 0.018 0.14 -9999 0 -0.46 27 27
PRKCD 0.029 0.054 -9999 0 -0.31 10 10
FER 0.027 0.061 -9999 0 -0.31 13 13
MAPKKK cascade -0.007 0.04 -9999 0 -10000 0 0
RASA1 0.029 0.054 -9999 0 -0.31 10 10
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.037 0.051 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.012 0.067 -9999 0 -0.41 10 10
chemotaxis 0.013 0.093 -9999 0 -0.5 10 10
STAT1-3-5/STAT1-3-5 -0.009 0.044 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0.067 -9999 0 -0.42 10 10
PTPRJ 0.014 0.029 -9999 0 -0.57 1 1
PLK2 and PLK4 events

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
PLK2 0.014 0.026 -9999 0 -0.51 1 1
PLK4 0.003 0.081 -9999 0 -0.51 10 10
regulation of centriole replication 0.016 0.062 -9999 0 -0.36 11 11
Retinoic acid receptors-mediated signaling

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
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.011 0.048 -10000 0 -0.55 3 3
Cbp/p300/PCAF 0.031 0.018 -10000 0 -0.34 1 1
EP300 0.016 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.033 0.062 -10000 0 -0.26 3 3
KAT2B 0.014 0.029 -10000 0 -0.57 1 1
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.016 0.086 0.22 17 -0.26 27 44
RAR alpha/9cRA/Cyclin H -0.007 0.038 -10000 0 -0.35 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.027 0.071 -10000 0 -0.29 3 3
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.017 0.053 -10000 0 -0.38 5 5
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0.035 -10000 0 -0.4 3 3
RXRs/RARs/NRIP1/9cRA 0.013 0.1 -10000 0 -0.53 6 6
NCOA2 -0.019 0.14 -10000 0 -0.57 24 24
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.048 -10000 0 -0.55 3 3
RARG 0.017 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.022 0.001 -10000 0 -10000 0 0
MAPK3 0.017 0 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.013 0.05 -10000 0 -0.57 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.004 0.078 -10000 0 -0.46 6 6
RARA 0.023 0.047 -10000 0 -0.26 8 8
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.012 0.099 -10000 0 -0.44 7 7
PRKCA 0.012 0.065 -10000 0 -0.57 5 5
RXRs/RARs/NRIP1/9cRA/HDAC1 0 0.11 -10000 0 -0.45 10 10
RXRG -0.079 0.16 -10000 0 -0.34 111 111
RXRA 0.031 0.047 -10000 0 -0.26 7 7
RXRB 0.019 0.058 -10000 0 -0.38 5 5
VDR/Vit D3/DNA 0.009 0.035 -10000 0 -0.4 3 3
RBP1 -0.023 0.14 -10000 0 -0.56 27 27
CRBP1/9-cic-RA -0.016 0.1 -10000 0 -0.41 27 27
RARB -0.03 0.16 -10000 0 -0.57 34 34
PRKCG -0.006 0.094 -10000 0 -0.5 14 14
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.014 0.1 -10000 0 -0.52 6 6
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.018 0.095 -10000 0 -0.41 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.068 -10000 0 -0.32 4 4
RXRs/RARs/NRIP1/9cRA/HDAC3 0 0.11 -10000 0 -0.45 10 10
positive regulation of DNA binding -0.006 0.037 -10000 0 -0.33 2 2
NRIP1 0.002 0.1 -10000 0 -0.69 3 3
RXRs/RARs -0.008 0.11 -10000 0 -0.46 10 10
RXRs/RXRs/DNA/9cRA -0.018 0.072 -10000 0 -0.5 5 5
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0.032 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.004 0.022 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.41 0.26 -10000 0 -0.57 294 294
CLTC 0.037 0.009 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.03 0.01 -10000 0 -10000 0 0
Dynamin 2/GTP 0.028 0.014 -10000 0 -0.26 1 1
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.033 0.007 -10000 0 -10000 0 0
CPE 0.006 0.076 -10000 0 -0.35 18 18
CTNNB1 0.016 0 -10000 0 -10000 0 0
membrane fusion 0.03 0.011 -10000 0 -10000 0 0
CTNND1 0.036 0.014 -10000 0 -10000 0 0
DNM2 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.007 -10000 0 -10000 0 0
TSHR 0.013 0.042 -10000 0 -0.3 7 7
INS 0.014 0.003 -10000 0 -10000 0 0
BIN1 -0.062 0.2 -10000 0 -0.57 54 54
mol:Choline 0.03 0.011 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.016 -10000 0 -0.3 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.014 -10000 0 -0.26 1 1
JUP 0.032 0.018 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.014 0.12 -10000 0 -0.31 54 54
ARF6/GTP 0.012 0 -10000 0 -10000 0 0
CDH1 0.025 0.042 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.012 0 -10000 0 -10000 0 0
MAPK8IP3 0.009 0.059 -10000 0 -0.52 5 5
positive regulation of endocytosis 0.012 0 -10000 0 -10000 0 0
EXOC2 0.016 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.05 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.024 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.022 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.017 0.037 -10000 0 -0.31 5 5
ACAP1 0.024 0.028 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.054 0.11 -10000 0 -0.27 2 2
clathrin heavy chain/ACAP1 0.042 0.012 -10000 0 -10000 0 0
JIP4/KLC1 0.03 0 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.05 0 -10000 0 -10000 0 0
RALA/GTP 0.011 0.019 -10000 0 -0.37 1 1
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.021 0 -10000 0 -10000 0 0
receptor recycling 0.012 0 -10000 0 -10000 0 0
CTNNA1 0.036 0.014 -10000 0 -10000 0 0
NME1 0.021 0.016 -10000 0 -0.3 1 1
clathrin coat assembly 0.037 0.009 -10000 0 -10000 0 0
IL2RA 0.017 0.054 -10000 0 -10000 0 0
VAMP3 0.022 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.17 0.11 -10000 0 -0.28 16 16
EXOC6 0.016 0 -10000 0 -10000 0 0
PLD1 0.025 0.016 -10000 0 -0.28 1 1
PLD2 0.026 0.006 -10000 0 -10000 0 0
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.037 0.007 -10000 0 -10000 0 0
SDC1 0.029 0.031 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.016 -10000 0 -0.3 1 1
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.024 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.03 0.011 -10000 0 -10000 0 0
endocytosis 0.015 0.11 0.31 54 -10000 0 54
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 0.005 0.1 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0.016 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.029 0.014 -10000 0 -0.26 1 1
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 0.013 0.091 -10000 0 -10000 0 0
RALA 0.014 0.026 -10000 0 -0.51 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.02 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.009 0.11 -10000 0 -0.51 19 19
positive regulation of NF-kappaB transcription factor activity 0 0.092 -10000 0 -0.36 24 24
MAP2K4 0.047 0.031 -10000 0 -10000 0 0
IKBKB 0.016 0 -10000 0 -10000 0 0
TNFRSF10B 0.016 0 -10000 0 -10000 0 0
TNFRSF10A 0.014 0.029 -10000 0 -0.57 1 1
SMPD1 0.016 0.033 -10000 0 -10000 0 0
IKBKG 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.008 0.064 -10000 0 -0.57 5 5
TRAIL/TRAILR2 0.006 0.08 -10000 0 -0.36 19 19
TRAIL/TRAILR3 -0.003 0.098 -10000 0 -0.36 28 28
TRAIL/TRAILR1 0.005 0.082 -10000 0 -0.36 20 20
TRAIL/TRAILR4 0 0.092 -10000 0 -0.37 24 24
TRAIL/TRAILR1/DAP3/GTP 0.016 0.064 -10000 0 -0.27 20 20
IKK complex -0.005 0.02 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.012 0 -10000 0 -10000 0 0
MAPK3 0.009 0.08 -10000 0 -0.36 19 19
MAP3K1 0.04 0.033 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.008 0.064 -10000 0 -0.57 5 5
TRADD 0.016 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.029 -10000 0 -0.57 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.034 0.039 -10000 0 -10000 0 0
CFLAR 0.016 0 -10000 0 -10000 0 0
MAPK1 0.009 0.08 -10000 0 -0.36 19 19
TRAIL/TRAILR1/FADD/TRADD/RIP 0.029 0.068 -10000 0 -10000 0 0
mol:ceramide 0.016 0.033 -10000 0 -10000 0 0
FADD 0.008 0.063 -10000 0 -0.51 6 6
MAPK8 0.051 0.039 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.003 0.081 -10000 0 -0.53 9 9
CHUK 0.016 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.011 0.079 -10000 0 -0.29 26 26
DAP3 0.016 0 -10000 0 -10000 0 0
CASP10 -0.01 0.059 0.27 5 -10000 0 5
JNK cascade 0 0.092 -10000 0 -0.36 24 24
TRAIL (trimer) -0.009 0.11 -10000 0 -0.51 19 19
TNFRSF10C 0.003 0.081 -10000 0 -0.53 9 9
TRAIL/TRAILR1/DAP3/GTP/FADD 0.02 0.068 -10000 0 -0.28 1 1
TRAIL/TRAILR2/FADD 0.012 0.077 -10000 0 -0.29 25 25
cell death 0.016 0.033 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.034 0.036 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.016 0 -10000 0 -10000 0 0
CASP8 0.004 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.03 0.066 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.13 0.14 -9999 0 -0.54 6 6
TC10/GTP -0.12 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.025 0.054 -9999 0 -0.31 10 10
HRAS 0.016 0 -9999 0 -10000 0 0
APS homodimer 0.009 0.057 -9999 0 -0.51 5 5
GRB14 -0.056 0.18 -9999 0 -0.51 56 56
FOXO3 -0.026 0.11 -9999 0 -0.58 16 16
AKT1 0.018 0.094 -9999 0 -0.44 2 2
INSR 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.042 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.008 0.064 -9999 0 -0.57 5 5
SORBS1 -0.26 0.29 -9999 0 -0.57 189 189
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.04 0 -9999 0 -10000 0 0
CAV1 0.009 0.093 -9999 0 -0.34 25 25
CBL/APS/CAP/Crk-II/C3G -0.1 0.16 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.025 0.054 -9999 0 -0.31 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.043 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.039 0.038 -9999 0 -10000 0 0
RPS6KB1 0.026 0.089 -9999 0 -0.4 2 2
PARD6A 0.014 0.029 -9999 0 -0.57 1 1
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.012 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.027 0.064 -9999 0 -0.4 2 2
HRAS/GTP -0.01 0.044 -9999 0 -10000 0 0
Insulin Receptor 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.032 0.052 -9999 0 -10000 0 0
PRKCI -0.008 0.028 -9999 0 -0.46 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.034 0.08 -9999 0 -0.48 2 2
SHC1 0.014 0.026 -9999 0 -0.51 1 1
negative regulation of MAPKKK cascade 0.001 0.01 -9999 0 -10000 0 0
PI3K -0.007 0.044 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.012 0 -9999 0 -10000 0 0
AKT2 0.018 0.094 -9999 0 -0.44 2 2
PRKCZ -0.011 0.049 -9999 0 -0.48 4 4
SH2B2 0.009 0.057 -9999 0 -0.51 5 5
SHC/SHIP 0.026 0.063 -9999 0 -10000 0 0
F2RL2 -0.023 0.14 -9999 0 -0.54 28 28
TRIP10 0.014 0.029 -9999 0 -0.57 1 1
Insulin Receptor/Insulin/Shc 0.023 0.015 -9999 0 -0.28 1 1
TC10/GTP/CIP4/Exocyst 0.02 0.018 -9999 0 -0.35 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.04 0.014 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.12 0.17 -9999 0 -10000 0 0
TC10/GDP 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.029 0.041 -9999 0 -0.31 6 6
INPP5D 0.018 0.064 -9999 0 -0.29 17 17
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.036 0.17 -9999 0 -0.88 16 16
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.001 0.09 -9999 0 -0.57 10 10
p62DOK/RasGAP 0.001 0.011 -9999 0 -10000 0 0
INS 0.004 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.018 0.064 -9999 0 -0.29 17 17
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.016 0.1 -9999 0 -0.39 5 5
PTPRA 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0.02 0.018 -9999 0 -0.35 1 1
PDPK1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.044 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.015 0.053 -9999 0 -0.32 10 10
Insulin Receptor/Insulin/IRS3 0.016 0 -9999 0 -10000 0 0
Par3/Par6 0.015 0.079 -9999 0 -0.28 17 17
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.027 -10000 0 -0.36 2 2
MAP4K4 0.037 0.059 -10000 0 -10000 0 0
BAG4 0.016 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.005 0.034 -10000 0 -0.33 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.02 0.14 -10000 0 -0.56 25 25
BAX 0.002 0.009 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.022 0.007 -10000 0 -10000 0 0
BAD -0.004 0.019 0.14 2 -10000 0 2
SMPD1 0.025 0.031 -10000 0 -10000 0 0
RB1 -0.005 0.024 -10000 0 -0.31 1 1
FADD/Caspase 8 0.046 0.063 -10000 0 -10000 0 0
MAP2K4 0.004 0.018 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.003 0.023 -10000 0 -0.31 1 1
EGF -0.018 0.12 -10000 0 -0.51 25 25
mol:ceramide -0.015 0.02 0.14 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.026 0.019 -10000 0 -0.36 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.005 0.024 -10000 0 -0.31 1 1
cell proliferation -0.086 0.13 -10000 0 -0.27 9 9
BID 0.03 0.041 -10000 0 -10000 0 0
MAP3K1 -0.004 0.019 0.14 2 -10000 0 2
EIF2A 0.012 0.017 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 0.016 0.022 -10000 0 -0.28 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.022 -10000 0 -0.28 1 1
Cathepsin D/ceramide -0.003 0.019 -10000 0 -10000 0 0
FADD 0.034 0.066 -10000 0 -0.32 2 2
KSR1 -0.004 0.019 -10000 0 -10000 0 0
MAPK8 0.007 0.035 -10000 0 -0.24 6 6
PRKRA -0.004 0.019 0.14 2 -10000 0 2
PDGFA 0.014 0.026 -10000 0 -0.51 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 -0.24 0.29 -10000 0 -0.57 182 182
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.015 0.02 0.14 2 -10000 0 2
CTSD 0.016 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.023 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.091 0.14 -10000 0 -0.3 8 8
PRKCD 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.05 -10000 0 -0.57 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.026 0.019 -10000 0 -0.36 1 1
RelA/NF kappa B1 0.023 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.029 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.031 0.06 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.015 0.071 -10000 0 -0.29 21 21
mol:Sphingosine-1-phosphate 0.025 0.027 -10000 0 -0.36 2 2
MAP2K1 0.012 0.022 -10000 0 -0.29 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS 0.006 0.035 0.16 16 -10000 0 16
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.023 0 -10000 0 -10000 0 0
EIF2AK2 0.004 0.018 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.015 0.071 -10000 0 -0.29 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.041 0.036 -10000 0 -10000 0 0
MAP2K2 0.012 0.022 -10000 0 -0.29 1 1
SMPD3 0.027 0.035 -10000 0 -10000 0 0
TNF -0.011 0.12 -10000 0 -0.51 21 21
PKC zeta/PAR4 0.019 0.042 -10000 0 -0.41 4 4
mol:PHOSPHOCHOLINE -0.002 0.037 0.14 22 -10000 0 22
NF kappa B1/RelA/I kappa B alpha 0.043 0.031 -10000 0 -10000 0 0
AIFM1 0.006 0.035 0.16 16 -10000 0 16
BCL2 -0.007 0.11 -10000 0 -0.57 16 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.016 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.015 0.064 -9999 0 -0.47 3 3
NEF -0.007 0.048 -9999 0 -10000 0 0
NFKBIA 0.013 0.026 -9999 0 -10000 0 0
BIRC3 0.014 0.15 -9999 0 -0.57 25 25
CYCS 0.034 0.084 -9999 0 -0.47 3 3
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.002 0.091 -9999 0 -0.56 8 8
MAP2K7 0.04 0.072 -9999 0 -0.52 2 2
protein ubiquitination 0.066 0.046 -9999 0 -0.34 1 1
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.007 0.07 -9999 0 -0.57 6 6
BID 0.026 0.088 -9999 0 -0.5 3 3
NF-kappa-B/RelA/I kappa B alpha -0.016 0.064 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.014 0.029 -9999 0 -0.57 1 1
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.008 0.063 -9999 0 -0.51 6 6
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.016 0.064 -9999 0 -10000 0 0
MAPK8 0.045 0.072 -9999 0 -0.67 1 1
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.011 0.048 -9999 0 -0.55 3 3
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.02 0.091 -9999 0 -0.3 23 23
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.057 0.054 -9999 0 -0.45 1 1
CHUK 0.068 0.048 -9999 0 -0.37 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.037 0.057 -9999 0 -0.57 1 1
TCRz/NEF -0.027 0.092 -9999 0 -0.34 29 29
TNF -0.011 0.12 -9999 0 -0.51 21 21
FASLG -0.019 0.17 -9999 0 -0.55 35 35
NFKB1 0.013 0.026 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.015 0.071 -9999 0 -0.29 21 21
CASP6 -0.01 0.043 -9999 0 -0.54 1 1
CASP7 0.051 0.15 -9999 0 -0.51 23 23
RELA 0.013 0.026 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 0.051 0.15 -9999 0 -0.51 23 23
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.023 0 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.051 -9999 0 -0.41 1 1
APAF-1/Caspase 9 -0.03 0.093 -9999 0 -0.38 23 23
BCL2 0.041 0.086 -9999 0 -0.5 2 2
TCGA08_rtk_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
PDGFRA -0.065 0.2 -10000 0 -0.57 56 56
HRAS 0.016 0 -10000 0 -10000 0 0
EGFR -0.008 0.11 -10000 0 -0.54 17 17
AKT 0.032 0.06 -10000 0 -0.26 14 14
FOXO3 0.016 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
FOXO1 0.014 0.029 -10000 0 -0.57 1 1
AKT3 -0.004 0.11 -10000 0 -0.57 14 14
FOXO4 0.014 0.026 -10000 0 -0.51 1 1
MET 0.013 0.036 -10000 0 -0.51 2 2
PIK3CA 0.016 0 -10000 0 -10000 0 0
PIK3CB 0.016 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
PIK3CG -0.006 0.11 -10000 0 -0.56 15 15
PIK3R3 0.016 0 -10000 0 -10000 0 0
PIK3R2 0.016 0 -10000 0 -10000 0 0
NF1 0.016 0 -10000 0 -10000 0 0
RAS 0.001 0.068 -10000 0 -0.26 6 6
ERBB2 -0.001 0.092 -10000 0 -0.51 13 13
proliferation/survival/translation -0.035 0.031 0.19 2 -10000 0 2
PI3K 0.011 0.069 -10000 0 -0.22 12 12
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
KRAS 0.014 0.026 -10000 0 -0.51 1 1
FOXO 0.048 0.028 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
PTEN 0.016 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.031 0.091 -9999 0 -0.45 14 14
KLHL20 -0.013 0.039 -9999 0 -0.21 3 3
CYFIP2 0 0.095 -9999 0 -0.57 11 11
Rac1/GDP 0.058 0.059 -9999 0 -10000 0 0
ENAH 0.032 0.091 -9999 0 -0.45 14 14
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.006 0.032 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.029 -9999 0 -0.19 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.025 0.075 -9999 0 -0.32 18 18
RAPGEF1 0.046 0.08 -9999 0 -0.38 14 14
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.022 0.093 -9999 0 -0.47 14 14
CRK 0.04 0.086 -9999 0 -0.42 14 14
E-cadherin/gamma catenin/alpha catenin 0.016 0.075 -9999 0 -0.36 15 15
alphaE/beta7 Integrin 0.018 0.047 -9999 0 -0.41 5 5
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.03 0.001 -9999 0 -10000 0 0
DLG1 0.032 0.091 -9999 0 -0.45 14 14
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.024 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.027 0.032 -9999 0 -0.3 4 4
PI3K -0.006 0.03 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.007 0.087 -9999 0 -0.43 15 15
TIAM1 0.011 0.05 -9999 0 -0.57 3 3
E-cadherin(dimer)/Ca2+ 0.025 0.058 -9999 0 -0.28 14 14
AKT1 -0.003 0.017 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
CDH1 -0.004 0.11 -9999 0 -0.57 14 14
RhoA/GDP 0.058 0.059 -9999 0 -10000 0 0
actin cytoskeleton organization 0.04 0.045 -9999 0 -0.15 2 2
CDC42/GDP 0.058 0.059 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.018 0.058 -9999 0 -0.27 15 15
ITGB7 0.008 0.064 -9999 0 -0.57 5 5
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.027 0.062 -9999 0 -0.3 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.016 0.058 -9999 0 -0.29 14 14
mol:GDP 0.054 0.066 -9999 0 -0.3 13 13
CDC42/GTP/IQGAP1 0.021 0 -9999 0 -10000 0 0
JUP 0.013 0.041 -9999 0 -0.57 2 2
p120 catenin/RhoA/GDP -0.006 0.048 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.021 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.023 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.026 0.056 -9999 0 -0.19 21 21
NME1 0.014 0.026 -9999 0 -0.51 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.032 0.091 -9999 0 -0.45 14 14
regulation of cell-cell adhesion -0.005 0.029 -9999 0 -10000 0 0
WASF2 -0.005 0.015 -9999 0 -10000 0 0
Rap1/GTP -0.007 0.037 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.03 0.077 -9999 0 -0.57 2 2
CCND1 0.03 0.068 -9999 0 -0.24 21 21
VAV2 0.041 0.099 -9999 0 -0.44 16 16
RAP1/GDP 0.055 0.052 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.088 -9999 0 -0.43 14 14
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.038 0.074 -9999 0 -0.54 2 2
E-cadherin/beta catenin -0.013 0.068 -9999 0 -0.38 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.03 0.091 -9999 0 -0.45 14 14
PIK3CA 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.02 0.062 -9999 0 -0.33 3 3
E-cadherin/beta catenin/alpha catenin 0.018 0.068 -9999 0 -0.34 14 14
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.087 -9999 0 -0.48 14 14
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.035 0.041 -10000 0 -0.3 6 6
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 0.02 0.005 -10000 0 -10000 0 0
GATA1/HDAC5 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC5 0.004 0.086 -10000 0 -0.37 20 20
HDAC5/BCL6/BCoR 0.032 0 -10000 0 -10000 0 0
HDAC9 -0.025 0.15 -10000 0 -0.57 28 28
Glucocorticoid receptor/Hsp90/HDAC6 0.021 0.063 -10000 0 -0.34 12 12
HDAC4/ANKRA2 0.023 0 -10000 0 -10000 0 0
HDAC5/YWHAB 0.023 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -10000 0 -10000 0 0
GATA2 -0.011 0.12 -10000 0 -0.53 20 20
HDAC4/RFXANK 0.022 0.019 -10000 0 -0.36 1 1
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.016 0 -10000 0 -10000 0 0
HDAC5 0.016 0 -10000 0 -10000 0 0
GNB1/GNG2 0.017 0.052 -10000 0 -0.41 6 6
Histones 0.028 0.066 -10000 0 -0.23 4 4
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.023 0 -10000 0 -10000 0 0
HDAC4/Ubc9 0.023 0 -10000 0 -10000 0 0
HDAC7 0.016 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.022 0.021 -10000 0 -0.41 1 1
TUBA1B 0.016 0 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.022 0.019 -10000 0 -0.36 1 1
CAMK4 0 0.094 -10000 0 -0.56 11 11
Tubulin/HDAC6 0.03 0.026 -10000 0 -0.34 2 2
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
GATA1 0.011 0.007 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.014 0.029 -10000 0 -0.57 1 1
NR3C1 -0.002 0.099 -10000 0 -0.57 12 12
SUMO1/HDAC4 0.036 0 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.023 0 -10000 0 -10000 0 0
Tubulin 0.021 0.03 -10000 0 -0.41 2 2
HDAC4/14-3-3 E 0.022 0.021 -10000 0 -0.41 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
RANGAP1 0.016 0 -10000 0 -10000 0 0
BCL6/BCoR 0.023 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.032 0 -10000 0 -10000 0 0
HDAC4/SRF 0.022 0.059 -10000 0 -0.33 11 11
HDAC4/ER alpha -0.054 0.16 -10000 0 -0.41 73 73
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.028 0.066 -10000 0 -0.23 4 4
cell motility 0.03 0.026 -10000 0 -0.34 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.023 0 -10000 0 -10000 0 0
BCL6 0.016 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.023 0 -10000 0 -10000 0 0
ESR1 -0.089 0.22 -10000 0 -0.57 73 73
HDAC6/HDAC11 0.018 0.046 -10000 0 -0.4 5 5
Ran/GTP/Exportin 1 0.039 0 -10000 0 -10000 0 0
NPC 0.009 0 -10000 0 -10000 0 0
MEF2C -0.004 0.11 -10000 0 -0.57 14 14
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.036 0.058 -10000 0 -0.27 14 14
GNG2 0.007 0.07 -10000 0 -0.57 6 6
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.013 0.041 -10000 0 -0.57 2 2
HDAC11 0.009 0.063 -10000 0 -0.56 5 5
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RANBP2 0.016 0 -10000 0 -10000 0 0
ANKRA2 0.016 0 -10000 0 -10000 0 0
RFXANK 0.014 0.026 -10000 0 -0.51 1 1
nuclear import -0.034 0.017 0.31 1 -10000 0 1
HIF-2-alpha transcription factor network

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
MMP14 0.008 0.024 -10000 0 -10000 0 0
oxygen homeostasis 0.01 0.017 -10000 0 -10000 0 0
TCEB2 0.014 0.026 -10000 0 -0.51 1 1
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.001 0.04 -10000 0 -10000 0 0
EPO 0.12 0.21 -10000 0 -0.56 5 5
FIH (dimer) 0.026 0.015 -10000 0 -10000 0 0
APEX1 0.025 0.017 -10000 0 -10000 0 0
SERPINE1 0.13 0.22 -10000 0 -0.64 9 9
FLT1 0.011 0.025 -10000 0 -10000 0 0
ADORA2A 0.13 0.2 -10000 0 -0.54 6 6
germ cell development 0.093 0.26 -10000 0 -0.52 28 28
SLC11A2 0.14 0.2 -10000 0 -0.56 6 6
BHLHE40 0.14 0.21 -10000 0 -0.61 7 7
HIF1AN 0.026 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.081 0.14 -10000 0 -10000 0 0
ETS1 0.034 0.006 -10000 0 -10000 0 0
CITED2 0.008 0.019 -10000 0 -10000 0 0
KDR 0.006 0.085 -10000 0 -1.2 2 2
PGK1 0.14 0.2 -10000 0 -0.56 6 6
SIRT1 0.016 0.002 -10000 0 -10000 0 0
response to hypoxia 0 0.004 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.22 -10000 0 -0.64 6 6
EPAS1 0.089 0.1 -10000 0 -0.28 3 3
SP1 0.025 0.003 -10000 0 -10000 0 0
ABCG2 0.13 0.23 -10000 0 -0.64 8 8
EFNA1 0.13 0.21 -10000 0 -0.57 7 7
FXN 0.13 0.2 -10000 0 -0.54 6 6
POU5F1 0.092 0.26 -10000 0 -0.54 28 28
neuron apoptosis -0.16 0.22 0.63 6 -10000 0 6
EP300 0.016 0 -10000 0 -10000 0 0
EGLN3 0.015 0.083 -10000 0 -0.56 8 8
EGLN2 0.026 0.016 -10000 0 -10000 0 0
EGLN1 0.026 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.031 0.016 -10000 0 -0.29 1 1
VHL 0.016 0 -10000 0 -10000 0 0
ARNT 0.025 0.017 -10000 0 -10000 0 0
SLC2A1 0.13 0.2 -10000 0 -0.53 8 8
TWIST1 0.07 0.3 -10000 0 -0.64 35 35
ELK1 0.025 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.008 0.061 -10000 0 -10000 0 0
VEGFA 0.14 0.2 -10000 0 -0.56 6 6
CREBBP 0.016 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0.036 -9999 0 -0.51 2 2
Rac1/GDP 0.002 0.01 -9999 0 -10000 0 0
DOCK1 0.013 0.041 -9999 0 -0.57 2 2
ITGA4 -0.003 0.1 -9999 0 -0.56 13 13
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.004 0.088 -9999 0 -0.4 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.02 0.064 -9999 0 -0.34 13 13
alpha4/beta7 Integrin/Paxillin 0.024 0.069 -9999 0 -0.3 17 17
lamellipodium assembly 0 0.028 -9999 0 -0.36 1 1
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0.022 0.021 -9999 0 -0.41 1 1
ARF6 0.016 0 -9999 0 -10000 0 0
TLN1 0.016 0 -9999 0 -10000 0 0
PXN 0.026 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
ARF6/GTP -0.008 0.042 -9999 0 -10000 0 0
cell adhesion 0.036 0.055 -9999 0 -0.27 12 12
CRKL/CBL 0.021 0.026 -9999 0 -0.36 2 2
alpha4/beta1 Integrin/Paxillin 0.029 0.059 -9999 0 -0.3 13 13
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.008 0.064 -9999 0 -0.57 5 5
ARF6/GDP 0.002 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.023 0.099 -9999 0 -0.57 6 6
p130Cas/Crk/Dock1 0.03 0.026 -9999 0 -0.34 2 2
VCAM1 -0.011 0.12 -9999 0 -0.56 19 19
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.056 -9999 0 -0.27 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.037 0.056 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
mol:GDP -0.036 0.055 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.056 -9999 0 -0.27 12 12
Rac1/GTP 0 0.031 -9999 0 -0.4 1 1
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 0.016 0.015 -9999 0 -0.3 1 1
TRAF2/ASK1 0.02 0.018 -9999 0 -0.35 1 1
ATM 0.016 0 -9999 0 -10000 0 0
MAP2K3 0.041 0.023 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.046 0.037 -9999 0 -0.28 1 1
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.007 0.07 -9999 0 -0.57 6 6
TXN 0.009 0.014 -9999 0 -0.19 2 2
CALM1 0.016 0 -9999 0 -10000 0 0
GADD45A 0.016 0 -9999 0 -10000 0 0
GADD45B 0 0.095 -9999 0 -0.57 11 11
MAP3K1 0.016 0 -9999 0 -10000 0 0
MAP3K6 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
MAP3K4 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.022 0.021 -9999 0 -0.41 1 1
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0.03 0.015 -9999 0 -0.26 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.01 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.04 0.16 -9999 0 -0.51 43 43
CCM2 0.014 0.026 -9999 0 -0.51 1 1
CaM/Ca2+/CAMKIIB -0.013 0.099 -9999 0 -0.3 43 43
MAPK11 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.002 0.091 -9999 0 -0.26 44 44
OSM/MEKK3 0.022 0.019 -9999 0 -0.36 1 1
TAOK1 0.019 0.018 -9999 0 -0.34 1 1
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 0.016 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.014 0.029 -9999 0 -0.57 1 1
MAP3K10 0.014 0.026 -9999 0 -0.51 1 1
MAP3K3 0.016 0 -9999 0 -10000 0 0
TRX/ASK1 0.017 0.021 -9999 0 -0.34 1 1
GADD45/MTK1/MTK1 0.024 0.067 -9999 0 -0.3 16 16
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.023 0.076 -9999 0 -10000 0 0
PLK1 -0.057 0.23 -9999 0 -0.61 9 9
CDKN1B 0.072 0.11 -9999 0 -0.32 1 1
FOXO3 -0.016 0.18 -9999 0 -0.52 9 9
KAT2B 0.012 0.034 -9999 0 -0.55 1 1
FOXO1/SIRT1 0.021 0.046 -9999 0 -10000 0 0
CAT -0.005 0.17 -9999 0 -0.62 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.015 0.021 -9999 0 -10000 0 0
FOXO1 0.032 0.047 -9999 0 -0.29 1 1
MAPK10 0.012 0.096 -9999 0 -0.29 38 38
mol:GTP 0.003 0 -9999 0 -10000 0 0
FOXO4 0.093 0.066 -9999 0 -10000 0 0
response to oxidative stress -0.001 0.024 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.06 0.12 -9999 0 -0.49 5 5
XPO1 0.017 0 -9999 0 -10000 0 0
EP300 0.016 0.006 -9999 0 -10000 0 0
BCL2L11 0.023 0.034 -9999 0 -10000 0 0
FOXO1/SKP2 0.03 0.063 -9999 0 -0.45 2 2
mol:GDP -0.001 0.024 -9999 0 -10000 0 0
RAN 0.018 0 -9999 0 -10000 0 0
GADD45A 0.067 0.094 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.076 0.034 -9999 0 -10000 0 0
MST1 -0.016 0.12 -9999 0 -0.51 23 23
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.056 0.046 -9999 0 -0.34 1 1
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.039 0.033 -9999 0 -0.27 4 4
MAPK9 0.04 0.017 -9999 0 -0.25 1 1
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.014 0.029 -9999 0 -0.57 1 1
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.015 0.015 -9999 0 -10000 0 0
SOD2 0.077 0.12 -9999 0 -0.48 1 1
RBL2 0.031 0.14 -9999 0 -10000 0 0
RAL/GDP 0.025 0.025 -9999 0 -0.31 1 1
CHUK 0.014 0.019 -9999 0 -10000 0 0
Ran/GTP 0.017 0.001 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
RAL/GTP 0.036 0.022 -9999 0 -0.28 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.056 0.33 -9999 0 -1.4 21 21
SKP2 0.004 0.077 -9999 0 -0.51 9 9
USP7 0.018 0 -9999 0 -10000 0 0
IKBKB 0.014 0.019 -9999 0 -10000 0 0
CCNB1 -0.057 0.23 -9999 0 -0.61 8 8
FOXO1-3a-4/beta catenin 0.097 0.12 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.063 -9999 0 -0.45 2 2
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.009 0.12 -9999 0 -0.57 16 16
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.001 -9999 0 -10000 0 0
ZFAND5 0.096 0.059 -9999 0 -10000 0 0
SFN -0.031 0.15 -9999 0 -0.51 36 36
CDK2 0.015 0.009 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.043 0.064 -9999 0 -0.36 2 2
CREBBP 0.015 0.009 -9999 0 -10000 0 0
FBXO32 -0.007 0.18 -9999 0 -0.72 4 4
BCL6 0.031 0.14 -9999 0 -0.46 1 1
RALB 0.017 0 -9999 0 -10000 0 0
RALA 0.016 0.026 -9999 0 -0.5 1 1
YWHAH 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.026 0.14 -9999 0 -0.42 46 46
AKT1 0.095 0.061 -9999 0 -0.63 2 2
PTK2B 0.026 0.12 -9999 0 -0.57 5 5
VEGFR2 homodimer/Frs2 0.033 0.07 -9999 0 -0.76 2 2
CAV1 -0.012 0.12 -9999 0 -0.57 19 19
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.043 0.069 -9999 0 -0.73 2 2
endothelial cell proliferation 0.051 0.11 -9999 0 -0.56 3 3
mol:Ca2+ 0.058 0.065 -9999 0 -0.71 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.056 0.055 -9999 0 -0.69 2 2
RP11-342D11.1 0.048 0.064 -9999 0 -0.72 2 2
CDH5 0.013 0.041 -9999 0 -0.57 2 2
VEGFA homodimer 0.041 0.015 -9999 0 -10000 0 0
SHC1 0.014 0.026 -9999 0 -0.51 1 1
SHC2 -0.021 0.14 -9999 0 -0.57 26 26
HRAS/GDP -0.006 0.048 -9999 0 -0.6 2 2
SH2D2A 0.011 0.051 -9999 0 -0.51 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.005 0.045 -9999 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.064 -9999 0 -0.73 2 2
VEGFR1 homodimer 0.016 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.006 0.054 -9999 0 -0.68 2 2
GRB10 0.054 0.094 -9999 0 -0.68 6 6
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.014 0.029 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.005 0.066 -9999 0 -0.93 2 2
HRAS 0.016 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.031 0.085 -9999 0 -0.38 5 5
HIF1A 0.014 0.026 -9999 0 -0.51 1 1
FRS2 0.007 0.068 -9999 0 -0.51 7 7
oxygen and reactive oxygen species metabolic process -0.004 0.049 -9999 0 -0.68 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.014 0.029 -9999 0 -0.57 1 1
Nck/Pak 0.022 0.021 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.046 0.064 -9999 0 -0.73 2 2
mol:GDP -0.006 0.052 -9999 0 -0.65 2 2
mol:NADP 0.085 0.049 -9999 0 -0.48 2 2
eNOS/Hsp90 0.088 0.046 -9999 0 -0.45 2 2
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
mol:IP3 0.058 0.065 -9999 0 -0.73 2 2
HIF1A/ARNT 0.022 0.019 -9999 0 -0.36 1 1
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA 0.018 0.007 -9999 0 -10000 0 0
VEGFC 0.01 0.056 -9999 0 -0.55 4 4
FAK1/Vinculin 0.051 0.1 -9999 0 -0.65 3 3
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.019 0.12 -9999 0 -0.61 5 5
PTPN6 0.014 0.026 -9999 0 -0.51 1 1
EPAS1 0.025 0.027 -9999 0 -0.35 2 2
mol:L-citrulline 0.085 0.049 -9999 0 -0.48 2 2
ITGAV 0.014 0.029 -9999 0 -0.57 1 1
PIK3CA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.051 0.066 -9999 0 -0.69 2 2
VEGFR2 homodimer/VEGFA homodimer 0.052 0.07 -9999 0 -0.79 2 2
VEGFR2/3 heterodimer 0.037 0.068 -9999 0 -0.9 2 2
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 0.061 0.067 -9999 0 -0.74 2 2
VEGFR2 homodimer 0.037 0.064 -9999 0 -0.85 2 2
FLT1 0.016 0 -9999 0 -10000 0 0
NEDD4 0.016 0.03 -9999 0 -0.56 1 1
MAPK3 0.026 0.09 -9999 0 -0.75 2 2
MAPK1 0.026 0.09 -9999 0 -0.75 2 2
VEGFA145/NRP2 0.005 0.091 -9999 0 -0.41 19 19
VEGFR1/2 heterodimer 0.038 0.057 -9999 0 -0.76 2 2
KDR 0.037 0.064 -9999 0 -0.86 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.044 0.093 -9999 0 -0.66 3 3
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.03 0.089 -9999 0 -0.77 2 2
PI3K 0.083 0.072 -9999 0 -0.79 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.058 -9999 0 -0.73 2 2
FES 0.058 0.068 -9999 0 -0.74 2 2
GAB1 -0.005 0.053 -9999 0 -0.72 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.058 -9999 0 -0.73 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.076 0.071 -9999 0 -0.45 2 2
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.058 -9999 0 -0.73 2 2
PI3K/GAB1 0.097 0.063 -9999 0 -0.66 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.008 0.055 -9999 0 -0.66 2 2
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.072 -9999 0 -0.84 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 0.059 0.066 -9999 0 -0.74 2 2
actin cytoskeleton reorganization 0.045 0.064 -9999 0 -0.72 2 2
PTK2 0.045 0.11 -9999 0 -0.71 3 3
EDG1 0.048 0.064 -9999 0 -0.72 2 2
mol:DAG 0.058 0.065 -9999 0 -0.73 2 2
CaM/Ca2+ 0.061 0.06 -9999 0 -0.66 2 2
MAP2K3 0.063 0.068 -9999 0 -0.7 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.056 0.096 -9999 0 -0.69 6 6
PLCG1 0.059 0.066 -9999 0 -0.74 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.056 0.055 -9999 0 -0.69 2 2
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.048 0.058 -9999 0 -0.73 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.059 -9999 0 -0.73 2 2
cell migration 0.078 0.094 -9999 0 -0.71 2 2
mol:PI-3-4-5-P3 0.081 0.066 -9999 0 -0.7 2 2
FYN 0.011 0.05 -9999 0 -0.57 3 3
VEGFB/NRP1 0.055 0.061 -9999 0 -0.68 2 2
mol:NO 0.085 0.049 -9999 0 -0.48 2 2
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.048 -9999 0 -0.61 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.056 0.096 -9999 0 -0.69 6 6
VHL 0.016 0 -9999 0 -10000 0 0
ITGB3 -0.05 0.18 -9999 0 -0.57 46 46
NOS3 0.087 0.054 -9999 0 -0.55 2 2
VEGFR2 homodimer/VEGFA homodimer/Sck 0.027 0.11 -9999 0 -0.73 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.061 0.073 -9999 0 -0.62 3 3
PRKCB -0.024 0.16 -9999 0 -0.73 4 4
VCL 0.014 0.029 -9999 0 -0.57 1 1
VEGFA165/NRP1 0.049 0.064 -9999 0 -0.72 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.048 0.058 -9999 0 -0.73 2 2
VEGFA165/NRP2 0.005 0.091 -9999 0 -0.41 19 19
MAPKKK cascade 0.079 0.081 -9999 0 -0.55 6 6
NRP2 -0.012 0.12 -9999 0 -0.57 19 19
VEGFC homodimer 0.01 0.056 -9999 0 -0.55 4 4
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.052 0.1 -9999 0 -0.65 3 3
MAP3K13 0.056 0.072 -9999 0 -0.74 2 2
PDPK1 0.087 0.059 -9999 0 -0.6 2 2
Class I PI3K signaling events

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
ARF5/GTP 0 0.009 -9999 0 -10000 0 0
DAPP1 0.016 0.097 -9999 0 -0.45 7 7
Src family/SYK family/BLNK-LAT/BTK-ITK 0.011 0.15 -9999 0 -0.5 21 21
mol:DAG 0.034 0.085 -9999 0 -0.23 17 17
HRAS 0.017 0.001 -9999 0 -10000 0 0
RAP1A 0.016 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.042 0.044 -9999 0 -10000 0 0
PLCG2 0.009 0.06 -9999 0 -0.53 5 5
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0.01 -9999 0 -10000 0 0
ARF1/GTP 0 0.008 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP 0 0.01 -9999 0 -10000 0 0
ADAP1 -0.003 0.027 -9999 0 -10000 0 0
ARAP3 0 0.01 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.011 0.05 -9999 0 -0.57 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.011 0.05 -9999 0 -0.57 3 3
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.013 0.041 -9999 0 -0.57 2 2
mol:Ca2+ 0.029 0.048 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.011 0.05 -9999 0 -0.57 3 3
ZAP70 -0.007 0.11 -9999 0 -0.56 16 16
mol:IP3 0.034 0.064 -9999 0 -0.2 4 4
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.042 0.044 -9999 0 -10000 0 0
RhoA/GDP -0.002 0.01 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0 -9999 0 -10000 0 0
BLNK -0.003 0.1 -9999 0 -0.57 13 13
actin cytoskeleton reorganization 0.065 0.04 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.027 0.048 -9999 0 -0.34 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP 0 0.009 -9999 0 -10000 0 0
RhoA/GTP 0 0.009 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT 0.012 0.12 -9999 0 -0.46 13 13
BLK -0.06 0.19 -9999 0 -0.55 53 53
PDPK1 0.016 0 -9999 0 -10000 0 0
CYTH1 0 0.009 -9999 0 -10000 0 0
HCK -0.008 0.11 -9999 0 -0.55 17 17
CYTH3 0 0.009 -9999 0 -10000 0 0
CYTH2 0 0.009 -9999 0 -10000 0 0
KRAS 0.015 0.026 -9999 0 -0.5 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.032 0.096 -9999 0 -0.44 16 16
SGK1 -0.019 0.094 -9999 0 -0.48 16 16
INPP5D 0.006 0.076 -9999 0 -0.57 7 7
mol:GDP 0.034 0.046 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.01 0.058 -9999 0 -0.57 4 4
ARF6/GDP -0.002 0.01 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.01 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP 0 0.01 -9999 0 -10000 0 0
VAV1 -0.01 0.12 -9999 0 -0.56 18 18
mol:PI-3-4-P2 0.019 0.056 -9999 0 -0.41 7 7
RAS family/GTP/PI3K Class I 0.036 0.012 -9999 0 -10000 0 0
PLEKHA1 0.027 0.048 -9999 0 -0.34 7 7
Rac1/GDP 0.042 0.044 -9999 0 -10000 0 0
LAT 0.014 0.026 -9999 0 -0.51 1 1
Rac1/GTP 0.036 0.057 -9999 0 -0.27 6 6
ITK -0.029 0.081 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.034 0.11 -9999 0 -0.33 17 17
LCK 0.007 0.068 -9999 0 -0.55 6 6
BTK -0.015 0.059 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.05 0.04 -10000 0 -0.32 2 2
adherens junction organization 0.038 0.064 -10000 0 -0.26 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.064 -10000 0 -0.36 2 2
FMN1 0.029 0.078 -10000 0 -0.52 2 2
mol:IP3 0.042 0.039 -10000 0 -0.38 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.062 -10000 0 -0.27 15 15
CTNNB1 0.016 0.002 -10000 0 -10000 0 0
AKT1 0.048 0.044 -10000 0 -0.42 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.085 -10000 0 -0.41 14 14
CTNND1 0.017 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.04 0.058 -10000 0 -0.56 1 1
VASP 0.04 0.059 -10000 0 -0.57 1 1
ZYX 0.039 0.061 -10000 0 -0.41 2 2
JUB 0.038 0.065 -10000 0 -0.52 2 2
EGFR(dimer) 0.028 0.082 -10000 0 -0.31 10 10
E-cadherin/beta catenin-gamma catenin -0.012 0.066 -10000 0 -0.34 15 15
mol:PI-3-4-5-P3 0.04 0.046 -10000 0 -0.35 2 2
PIK3CA 0.017 0.001 -10000 0 -10000 0 0
PI3K 0.041 0.046 -10000 0 -0.36 2 2
FYN 0.046 0.056 -10000 0 -0.29 4 4
mol:Ca2+ 0.041 0.038 -10000 0 -0.37 1 1
JUP 0.013 0.041 -10000 0 -0.57 2 2
PIK3R1 0.015 0.029 -10000 0 -0.57 1 1
mol:DAG 0.042 0.039 -10000 0 -0.38 1 1
CDH1 -0.005 0.11 -10000 0 -0.57 14 14
RhoA/GDP 0.046 0.064 -10000 0 -0.36 2 2
establishment of polarity of embryonic epithelium 0.04 0.058 -10000 0 -0.56 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.008 0.11 -10000 0 -0.54 17 17
CASR 0.038 0.056 -10000 0 -0.35 1 1
RhoA/GTP -0.005 0.026 -10000 0 -0.34 1 1
AKT2 0.048 0.044 -10000 0 -0.42 1 1
actin cable formation 0.036 0.076 -10000 0 -0.5 2 2
apoptosis -0.046 0.043 0.33 2 -10000 0 2
CTNNA1 0.017 0.001 -10000 0 -10000 0 0
mol:GDP 0.039 0.068 -10000 0 -0.39 2 2
PIP5K1A 0.04 0.059 -10000 0 -0.57 1 1
PLCG1 0.042 0.04 -10000 0 -0.39 1 1
Rac1/GTP -0.017 0.062 -10000 0 -0.49 2 2
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.091 0.03 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.002 0.095 -9999 0 -0.36 27 27
NFKBIA 0.053 0 -9999 0 -10000 0 0
BIRC2 0.013 0.036 -9999 0 -0.51 2 2
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.016 0 -9999 0 -10000 0 0
IKBKG -0.005 0.02 -9999 0 -10000 0 0
IKK complex/A20 -0.013 0.046 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM 0.051 0.032 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.021 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.003 0.013 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.032 0 -9999 0 -10000 0 0
NOD2 -0.019 0.13 -9999 0 -0.51 27 27
NFKB1 0.02 0 -9999 0 -10000 0 0
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.021 0.026 -9999 0 -0.36 2 2
ATM 0.016 0 -9999 0 -10000 0 0
TNF/TNFR1A 0.004 0.084 -9999 0 -0.36 21 21
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.008 0.064 -9999 0 -0.57 5 5
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF -0.011 0.12 -9999 0 -0.51 21 21
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.053 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex 0.059 0.031 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.026 -9999 0 -10000 0 0
Circadian rhythm pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.052 0.038 -10000 0 -10000 0 0
CLOCK 0.019 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.049 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.007 0.057 -10000 0 -0.35 10 10
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 0.049 0.016 -10000 0 -10000 0 0
ARNTL 0.019 0.002 -10000 0 -10000 0 0
TIMELESS 0.048 0.029 -10000 0 -10000 0 0
NPAS2 0.017 0.041 -10000 0 -0.56 2 2
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.016 0.007 0.062 3 -10000 0 3
CHEK1 0.009 0.057 -10000 0 -0.51 5 5
mol:HEME 0.016 0.007 -10000 0 -0.062 3 3
PER1 -0.007 0.11 -10000 0 -0.57 16 16
BMAL/CLOCK/NPAS2 0.05 0.027 -10000 0 -0.33 2 2
BMAL1/CLOCK 0.051 0.039 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.052 0.038 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.053 0.039 -10000 0 -10000 0 0
mol:NADPH 0.016 0.007 -10000 0 -0.062 3 3
PER1/TIMELESS 0.036 0.07 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.01 0.079 -10000 0 -0.51 10 10
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.12 0.083 -10000 0 -0.37 5 5
CaM/Ca2+ 0.012 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.13 0.12 0.22 1 -0.37 7 8
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.026 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0.032 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP 0.005 0.051 -10000 0 -0.51 4 4
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.012 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.036 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.05 -10000 0 -0.57 3 3
TRIP10 0.014 0.029 -10000 0 -0.57 1 1
TC10/GTP/CIP4/Exocyst 0.02 0.018 -10000 0 -0.35 1 1
AS160/14-3-3 0.042 0.042 -10000 0 -0.3 1 1
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 -0.14 0.12 0.23 1 -0.41 7 8
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.03 0 -10000 0 -10000 0 0
SFN -0.031 0.15 -10000 0 -0.51 36 36
LNPEP 0.016 0 -10000 0 -10000 0 0
YWHAE 0.014 0.029 -10000 0 -0.57 1 1
ceramide signaling pathway

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.039 0.073 -10000 0 -10000 0 0
BAG4 0.016 0 -10000 0 -10000 0 0
BAD 0.032 0.025 -10000 0 -10000 0 0
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.02 0.14 -10000 0 -0.56 25 25
BAX 0.032 0.025 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.014 0.019 -10000 0 -10000 0 0
IKBKB 0.046 0.07 -10000 0 -10000 0 0
MAP2K2 0.046 0.024 -10000 0 -10000 0 0
MAP2K1 0.046 0.024 -10000 0 -10000 0 0
SMPD1 0.021 0.019 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.045 0.076 -10000 0 -10000 0 0
MAP2K4 0.04 0.023 -10000 0 -10000 0 0
protein ubiquitination 0.048 0.071 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.051 0.025 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.04 0.026 -10000 0 -0.2 1 1
CRADD 0.016 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.026 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0.021 0 -10000 0 -10000 0 0
MADD 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.025 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
RELA/p50 0.016 0 -10000 0 -10000 0 0
MAPK3 0.049 0.024 -10000 0 -10000 0 0
MAPK1 0.049 0.024 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.023 0 -10000 0 -10000 0 0
FADD 0.036 0.079 -10000 0 -10000 0 0
KSR1 0.033 0.024 -10000 0 -10000 0 0
MAPK8 0.044 0.032 -10000 0 -0.22 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.046 0.07 -10000 0 -10000 0 0
TNF R/SODD 0.023 0 -10000 0 -10000 0 0
TNF -0.011 0.12 -10000 0 -0.5 21 21
CYCS 0.037 0.031 0.15 13 -10000 0 13
IKBKG 0.046 0.07 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.033 0.075 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AIFM1 0.037 0.031 0.15 13 -10000 0 13
TNF/TNF R/SODD 0.016 0.071 -10000 0 -0.29 21 21
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.031 0.021 -10000 0 -10000 0 0
NSMAF 0.04 0.07 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.007 0.11 -10000 0 -0.57 16 16
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.038 0.015 -9999 0 -0.28 1 1
VEGFR1 homodimer/NRP1 0.026 0.015 -9999 0 -0.28 1 1
mol:DAG 0.036 0.053 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.034 0.014 -9999 0 -10000 0 0
CaM/Ca2+ 0.043 0.05 -9999 0 -10000 0 0
HIF1A 0.024 0.025 -9999 0 -0.49 1 1
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.059 0.044 -9999 0 -10000 0 0
PLCG1 0.036 0.053 -9999 0 -10000 0 0
NOS3 0.066 0.041 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
mol:NO 0.065 0.04 -9999 0 -10000 0 0
FLT1 0.035 0.019 -9999 0 -0.34 1 1
PGF -0.001 0.092 -9999 0 -0.51 13 13
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.072 -9999 0 -0.29 19 19
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.072 0.039 -9999 0 -10000 0 0
endothelial cell proliferation -0.022 0.13 -9999 0 -0.41 8 8
mol:Ca2+ 0.036 0.053 -9999 0 -10000 0 0
MAPK3 0.046 0.057 -9999 0 -10000 0 0
MAPK1 0.046 0.057 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
PLGF homodimer -0.001 0.092 -9999 0 -0.51 13 13
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.012 0.12 -9999 0 -0.57 19 19
VEGFA homodimer 0.016 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.038 0.015 -9999 0 -0.28 1 1
platelet activating factor biosynthetic process 0.052 0.055 -9999 0 -10000 0 0
PI3K 0.043 0.053 -9999 0 -10000 0 0
PRKCA 0.039 0.06 -9999 0 -10000 0 0
PRKCB -0.05 0.15 -9999 0 -0.52 5 5
VEGFR1 homodimer/PLGF homodimer 0.027 0.059 -9999 0 -0.28 14 14
VEGFA 0.016 0 -9999 0 -10000 0 0
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.036 0.053 -9999 0 -10000 0 0
RASA1 0.045 0.014 -9999 0 -10000 0 0
NRP2 -0.012 0.12 -9999 0 -0.57 19 19
VEGFR1 homodimer 0.035 0.018 -9999 0 -0.34 1 1
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.058 0.072 -9999 0 -0.41 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.052 -9999 0 -10000 0 0
mol:L-citrulline 0.065 0.04 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.053 0.013 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.014 -9999 0 -10000 0 0
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 0.049 0.05 -9999 0 -10000 0 0
PDPK1 0.048 0.049 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.045 0.014 -9999 0 -10000 0 0
mol:NADP 0.065 0.04 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.013 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.02 0.079 -9999 0 -0.33 20 20
mTOR signaling pathway

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.008 0.046 -10000 0 -0.28 11 11
FRAP1 0.016 0.01 -10000 0 -10000 0 0
AKT1 0.026 0.043 -10000 0 -0.26 1 1
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.028 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.007 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.004 0.023 -10000 0 -10000 0 0
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.011 0.057 -10000 0 -0.35 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.023 -10000 0 -10000 0 0
MAP3K5 0.011 0.019 -10000 0 -0.38 1 1
PIK3R1 0.014 0.029 -10000 0 -0.57 1 1
apoptosis 0.011 0.019 -10000 0 -0.38 1 1
mol:LY294002 0 0 -10000 0 -0.001 10 10
EIF4B 0.035 0.022 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.039 0.02 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.002 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.02 0.054 -10000 0 -0.31 11 11
mTOR/RHEB/GTP/Raptor/GBL 0.034 0.016 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
RHEB/GTP -0.004 0.023 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 10 10
FKBP12/Rapamycin 0.012 0.002 -10000 0 -10000 0 0
PDPK1 -0.007 0.041 -10000 0 -0.25 11 11
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.024 0.033 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0 -10000 0 -10000 0 0
TSC1/TSC2 0.04 0.037 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 10 -10000 0 10
RPS6 0.016 0 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.001 0.06 -10000 0 -0.38 10 10
INS 0 0 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.007 0.041 -10000 0 -0.25 11 11
EIF4EBP1 0.012 0.015 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
PPP2R5D 0.023 0.01 -10000 0 -10000 0 0
peptide biosynthetic process 0.02 0 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.02 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.02 0.013 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.009 0.039 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.047 0.036 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones 0.047 0.028 -9999 0 -10000 0 0
YY1/LSF 0.036 0.013 -9999 0 -0.23 1 1
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.04 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.031 0.031 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.037 0.034 -9999 0 -10000 0 0
HDAC1/Smad7 0.031 0.018 -9999 0 -0.34 1 1
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 0.031 0.031 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.056 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.041 0.03 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.011 0.12 -9999 0 -0.53 20 20
GATA1 0.011 0.007 -9999 0 -10000 0 0
Mad/Max 0.022 0.019 -9999 0 -0.36 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.066 0.003 -9999 0 -10000 0 0
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0.009 0 -9999 0 -10000 0 0
RBBP4 0.016 0 -9999 0 -10000 0 0
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.025 0.035 -9999 0 -10000 0 0
KAT2B 0.014 0.029 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.051 0 -9999 0 -10000 0 0
SIN3 complex 0.04 0 -9999 0 -10000 0 0
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 0.016 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 0.044 0.031 -9999 0 -10000 0 0
YY1/HDAC2 0.036 0.013 -9999 0 -10000 0 0
YY1/HDAC1 0.036 0.013 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.056 0 -9999 0 -10000 0 0
PPARG 0.015 0.099 -9999 0 -0.33 26 26
HDAC8/hEST1B 0.032 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.031 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.031 0.018 -9999 0 -0.34 1 1
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.059 0 -9999 0 -10000 0 0
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 0.025 0.035 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.035 0.015 -9999 0 -0.28 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.014 0.029 -9999 0 -0.57 1 1
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.026 -9999 0 -0.51 1 1
STAT3 0.03 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.043 0.012 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.043 0.012 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.03 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.035 -9999 0 -10000 0 0
histone deacetylation 0.055 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.042 0.029 -9999 0 -10000 0 0
nuclear export -0.032 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.016 0.072 -9999 0 -0.27 20 20
GATA1/HDAC1 0.02 0.005 -9999 0 -10000 0 0
GATA1/HDAC3 0.02 0.034 -9999 0 -10000 0 0
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.004 0.084 -9999 0 -0.36 21 21
SIN3/HDAC complex/Mad/Max 0.055 0.005 -9999 0 -10000 0 0
NuRD Complex 0.065 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.017 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.036 0 -9999 0 -10000 0 0
HDAC complex 0.04 0 -9999 0 -10000 0 0
GATA1/Fog1 0.02 0.005 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.032 0 -9999 0 -10000 0 0
TNF -0.011 0.12 -9999 0 -0.51 21 21
negative regulation of cell growth 0.055 0.005 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.056 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.041 0.038 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.053 0 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.016 0 -9999 0 -10000 0 0
MBD2 0.016 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.022 0.021 -9999 0 -0.41 1 1
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.027 0.039 -9999 0 -0.32 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.051 0.031 -9999 0 -10000 0 0
NFKBIA 0.029 0.035 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.031 0 -9999 0 -10000 0 0
ARRB2 0.02 0 -9999 0 -10000 0 0
REL 0.009 0.062 -9999 0 -0.54 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.018 -9999 0 -0.34 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.029 -9999 0 -0.57 1 1
NFKB1 0.026 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.037 0.034 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.055 0.03 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K 0.022 0.021 -9999 0 -0.41 1 1
NF kappa B1 p50/RelA 0.037 0.034 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.01 0.058 -9999 0 -0.57 4 4
I kappa B alpha/PIK3R1 0.035 0.04 -9999 0 -0.49 1 1
cell death 0.053 0.029 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.027 0.039 -9999 0 -0.32 5 5
LCK 0.007 0.068 -9999 0 -0.55 6 6
BCL3 0.014 0.029 -9999 0 -0.57 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.016 0 -9999 0 -10000 0 0
SMAD3 0.048 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.054 0.007 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.032 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.044 0.025 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.024 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.018 0.047 -9999 0 -0.41 5 5
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 0.008 0.064 -9999 0 -0.57 5 5
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.011 0.051 -9999 0 -0.51 4 4
PIAS4 0.016 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.05 0.005 -10000 0 -10000 0 0
regulation of axonogenesis -0.034 0.013 0.22 1 -10000 0 1
myoblast fusion -0.023 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.035 0.3 4 -10000 0 4
ARF1/GTP 0 0.001 -10000 0 -10000 0 0
mol:GM1 0.013 0.004 -10000 0 -10000 0 0
mol:Choline 0.033 0.019 -10000 0 -0.34 1 1
lamellipodium assembly 0 0.015 -10000 0 -10000 0 0
MAPK3 0.034 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.039 0.035 -10000 0 -0.31 4 4
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.014 -10000 0 -10000 0 0
ARF1/GDP 0.032 0.013 -10000 0 -10000 0 0
ARF6 0.015 0.002 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.014 0.05 -10000 0 -0.57 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.034 0.004 -10000 0 -10000 0 0
actin filament bundle formation -0.03 0.011 -10000 0 -10000 0 0
KALRN -0.003 0.032 -10000 0 -0.26 6 6
RAB11FIP3/RAB11A 0.023 0 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.012 -10000 0 -10000 0 0
NME1 0.017 0.026 -10000 0 -0.5 1 1
Rac1/GDP 0.031 0.012 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.003 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0 0.015 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
liver development 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0.003 -10000 0 -10000 0 0
RhoA/GTP 0 0.001 -10000 0 -10000 0 0
mol:GDP 0 0.014 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.002 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.024 0.021 -10000 0 -0.4 1 1
RAB11FIP3 0.016 0 -10000 0 -10000 0 0
tube morphogenesis 0 0.015 -10000 0 -10000 0 0
ruffle organization 0.034 0.013 -10000 0 -0.22 1 1
regulation of epithelial cell migration 0 0.003 -10000 0 -10000 0 0
PLD2 0.025 0.004 -10000 0 -10000 0 0
PIP5K1A 0.034 0.013 -10000 0 -0.22 1 1
mol:Phosphatidic acid 0.033 0.019 -10000 0 -0.34 1 1
Rac1/GTP 0 0.015 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.027 0.047 -9999 0 -10000 0 0
HDAC4 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.016 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 0.033 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.036 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.036 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.031 0.052 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.025 0 -9999 0 -10000 0 0
Ran/GTP 0.032 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.092 -9999 0 -0.51 13 13
UBE2I 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0 -9999 0 -10000 0 0
NPC 0.009 0 -9999 0 -10000 0 0
PIAS2 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 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 0.023 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.03 0 -9999 0 -10000 0 0
CD4 0.013 0.041 -9999 0 -0.57 2 2
CLTA 0.016 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 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.032 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.016 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 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.03 0 -9999 0 -10000 0 0
ARFIP2 0.014 0 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.03 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.022 0 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.032 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.022 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.012 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 0.04 0.017 -9999 0 -0.2 2 2
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.013 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.013 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.026 -9999 0 -0.34 2 2
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 0.023 0 -9999 0 -9999 0 0
FBXW11 0.016 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 0.016 0 -9999 0 -9999 0 0
CHUK 0.016 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.047 0 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
MAP3K14 0.016 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.023 0 -9999 0 -9999 0 0
RELB 0.016 0 -9999 0 -9999 0 0
NFKB2 0.016 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.021 0 -9999 0 -9999 0 0
regulation of B cell activation 0.021 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 408 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZF.AA5P TCGA.ZF.AA5N TCGA.ZF.AA5H TCGA.ZF.AA58
109_MAP3K5 0.063 -0.15 -0.045 0.063
47_PPARGC1A 0.016 -2.9e-16 -0.57 -0.57
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 0.016 -0.57 -0.57
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0.04 0.03 0.04 -0.3
30_TGFB1/TGF beta receptor Type II 0.019 0.019 0.019 0.015
84_STAT5B 0.036 -0.12 0.051 0.031
84_STAT5A 0.036 -0.12 0.051 0.031
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/BLCA-TP/22311247/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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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