PARADIGM pathway analysis of mRNASeq expression and copy number data
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 35 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
IL4-mediated signaling events 111
HIF-1-alpha transcription factor network 97
Syndecan-1-mediated signaling events 93
Glypican 2 network 75
TCGA08_retinoblastoma 74
Endothelins 59
Syndecan-2-mediated signaling events 58
amb2 Integrin signaling 54
Signaling events regulated by Ret tyrosine kinase 53
Syndecan-4-mediated signaling events 51
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 520 . 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 ( 520 ).

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
IL4-mediated signaling events 0.2135 111 10120 91 -1.2 0.99 1000 -1000 -0.18 -1000
HIF-1-alpha transcription factor network 0.1865 97 7387 76 -0.69 0.038 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 0.1788 93 3187 34 -0.32 0.028 1000 -1000 -0.054 -1000
Glypican 2 network 0.1442 75 300 4 -0.045 -0.027 1000 -1000 -0.001 -1000
TCGA08_retinoblastoma 0.1423 74 599 8 -0.13 0.083 1000 -1000 -0.007 -1000
Endothelins 0.1135 59 5674 96 -0.23 0.027 1000 -1000 -0.059 -1000
Syndecan-2-mediated signaling events 0.1115 58 4042 69 -0.2 0.037 1000 -1000 -0.034 -1000
amb2 Integrin signaling 0.1038 54 4478 82 -0.26 0.035 1000 -1000 -0.043 -1000
Signaling events regulated by Ret tyrosine kinase 0.1019 53 4388 82 -0.092 0.028 1000 -1000 -0.064 -1000
Syndecan-4-mediated signaling events 0.0981 51 3468 67 -0.28 0.04 1000 -1000 -0.054 -1000
Osteopontin-mediated events 0.0885 46 1779 38 -0.2 0.032 1000 -1000 -0.059 -1000
IL23-mediated signaling events 0.0885 46 2818 60 -0.53 0.028 1000 -1000 -0.13 -1000
Nongenotropic Androgen signaling 0.0808 42 2234 52 -0.11 0.07 1000 -1000 -0.035 -1000
Effects of Botulinum toxin 0.0769 40 1049 26 -0.14 0.028 1000 -1000 -0.018 -1000
Coregulation of Androgen receptor activity 0.0750 39 3027 76 -0.43 0.067 1000 -1000 -0.027 -1000
TCGA08_p53 0.0750 39 274 7 -0.096 0.058 1000 -1000 -0.009 -1000
Calcium signaling in the CD4+ TCR pathway 0.0750 39 1226 31 -0.29 0.028 1000 -1000 -0.053 -1000
IGF1 pathway 0.0750 39 2224 57 -0.052 0.054 1000 -1000 -0.048 -1000
BMP receptor signaling 0.0731 38 3081 81 -0.22 0.048 1000 -1000 -0.062 -1000
Visual signal transduction: Rods 0.0731 38 1980 52 -0.21 0.041 1000 -1000 -0.044 -1000
TCR signaling in naïve CD8+ T cells 0.0692 36 3426 93 -0.19 0.099 1000 -1000 -0.058 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0692 36 2844 78 -0.13 0.039 1000 -1000 -0.088 -1000
Glypican 1 network 0.0673 35 1687 48 -0.28 0.046 1000 -1000 -0.038 -1000
p75(NTR)-mediated signaling 0.0654 34 4342 125 -0.24 0.075 1000 -1000 -0.071 -1000
FOXA2 and FOXA3 transcription factor networks 0.0635 33 1557 46 -0.45 0.033 1000 -1000 -0.14 -1000
Canonical Wnt signaling pathway 0.0635 33 1727 51 -0.2 0.14 1000 -1000 -0.056 -1000
Fc-epsilon receptor I signaling in mast cells 0.0596 31 3024 97 -0.15 0.034 1000 -1000 -0.064 -1000
Reelin signaling pathway 0.0596 31 1782 56 -0.19 0.068 1000 -1000 -0.052 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0596 31 3755 120 -0.16 0.073 1000 -1000 -0.053 -1000
Thromboxane A2 receptor signaling 0.0577 30 3242 105 -0.077 0.032 1000 -1000 -0.05 -1000
EGFR-dependent Endothelin signaling events 0.0577 30 642 21 -0.067 0.04 1000 -1000 -0.045 -1000
LPA4-mediated signaling events 0.0558 29 353 12 -0.087 0.007 1000 -1000 -0.027 -1000
IL12-mediated signaling events 0.0519 27 2409 87 -0.16 0.037 1000 -1000 -0.11 -1000
Presenilin action in Notch and Wnt signaling 0.0519 27 1696 61 -0.2 0.075 1000 -1000 -0.063 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0519 27 1838 68 -0.31 0.04 1000 -1000 -0.11 -1000
Visual signal transduction: Cones 0.0500 26 988 38 -0.059 0.052 1000 -1000 -0.018 -1000
Signaling mediated by p38-gamma and p38-delta 0.0500 26 399 15 -0.14 0.027 1000 -1000 -0.035 -1000
Signaling mediated by p38-alpha and p38-beta 0.0481 25 1135 44 -0.13 0.028 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 0.0462 24 1577 65 -0.24 0.039 1000 -1000 -0.068 -1000
Ephrin B reverse signaling 0.0462 24 1177 48 -0.083 0.034 1000 -1000 -0.036 -1000
LPA receptor mediated events 0.0462 24 2468 102 -0.26 0.028 1000 -1000 -0.059 -1000
Arf6 signaling events 0.0442 23 1457 62 -0.11 0.053 1000 -1000 -0.043 -1000
Signaling events mediated by PTP1B 0.0442 23 1806 76 -0.086 0.045 1000 -1000 -0.05 -1000
Integrins in angiogenesis 0.0442 23 1965 84 -0.2 0.054 1000 -1000 -0.051 -1000
Regulation of Androgen receptor activity 0.0442 23 1643 70 -0.46 0.034 1000 -1000 -0.057 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0423 22 1231 54 -0.13 0.039 1000 -1000 -0.061 -1000
Signaling events mediated by the Hedgehog family 0.0423 22 1191 52 -0.21 0.03 1000 -1000 -0.05 -1000
BCR signaling pathway 0.0423 22 2220 99 -0.062 0.047 1000 -1000 -0.064 -1000
Plasma membrane estrogen receptor signaling 0.0423 22 1953 86 -0.12 0.046 1000 -1000 -0.06 -1000
PDGFR-beta signaling pathway 0.0423 22 2187 97 -0.058 0.058 1000 -1000 -0.058 -1000
IL1-mediated signaling events 0.0404 21 1303 62 -0.11 0.046 1000 -1000 -0.042 -1000
EPHB forward signaling 0.0404 21 1804 85 -0.17 0.092 1000 -1000 -0.073 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0404 21 1857 88 -0.15 0.046 1000 -1000 -0.073 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0385 20 701 34 -0.026 0.032 1000 -1000 -0.036 -1000
Ephrin A reverse signaling 0.0385 20 144 7 -0.008 0.015 1000 -1000 -0.018 -1000
Caspase cascade in apoptosis 0.0365 19 1430 74 -0.093 0.054 1000 -1000 -0.057 -1000
Wnt signaling 0.0365 19 139 7 -0.019 0.023 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0346 18 1258 69 -0.24 0.04 1000 -1000 -0.056 -1000
Signaling events mediated by HDAC Class III 0.0346 18 737 40 -0.13 0.051 1000 -1000 -0.021 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0346 18 597 33 -0.13 0.063 1000 -1000 -0.046 -1000
Glucocorticoid receptor regulatory network 0.0327 17 2008 114 -0.34 0.17 1000 -1000 -0.077 -1000
Syndecan-3-mediated signaling events 0.0327 17 612 35 -0.15 0.075 1000 -1000 -0.034 -1000
IL27-mediated signaling events 0.0327 17 869 51 -0.12 0.054 1000 -1000 -0.062 -1000
Noncanonical Wnt signaling pathway 0.0308 16 430 26 -0.052 0.027 1000 -1000 -0.049 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0308 16 844 52 -0.13 0.041 1000 -1000 -0.053 -1000
Regulation of nuclear SMAD2/3 signaling 0.0288 15 2116 136 -0.37 0.16 1000 -1000 -0.053 -1000
PDGFR-alpha signaling pathway 0.0288 15 674 44 -0.11 0.06 1000 -1000 -0.046 -1000
mTOR signaling pathway 0.0288 15 807 53 -0.027 0.066 1000 -1000 -0.045 -1000
Ceramide signaling pathway 0.0288 15 1209 76 -0.067 0.07 1000 -1000 -0.051 -1000
S1P1 pathway 0.0250 13 484 36 -0.043 0.026 1000 -1000 -0.047 -1000
Cellular roles of Anthrax toxin 0.0231 12 484 39 -0.028 0.03 1000 -1000 -0.027 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0231 12 1076 85 -0.086 0.07 1000 -1000 -0.05 -1000
IFN-gamma pathway 0.0231 12 851 68 -0.13 0.041 1000 -1000 -0.069 -1000
FAS signaling pathway (CD95) 0.0231 12 574 47 -0.07 0.042 1000 -1000 -0.046 -1000
IL6-mediated signaling events 0.0231 12 940 75 -0.11 0.05 1000 -1000 -0.08 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0231 12 936 74 -0.27 0.058 1000 -1000 -0.069 -1000
Signaling events mediated by PRL 0.0231 12 438 34 -0.066 0.04 1000 -1000 -0.054 -1000
p38 MAPK signaling pathway 0.0231 12 530 44 -0.11 0.057 1000 -1000 -0.038 -1000
BARD1 signaling events 0.0212 11 631 57 -0.034 0.052 1000 -1000 -0.05 -1000
EPO signaling pathway 0.0212 11 611 55 -0.014 0.05 1000 -1000 -0.062 -1000
ceramide signaling pathway 0.0212 11 566 49 0 0.064 1000 -1000 -0.052 -1000
Retinoic acid receptors-mediated signaling 0.0212 11 680 58 -0.048 0.051 1000 -1000 -0.042 -1000
S1P3 pathway 0.0212 11 475 42 -0.042 0.045 1000 -1000 -0.049 -1000
Rapid glucocorticoid signaling 0.0212 11 239 20 -0.03 0.035 1000 -1000 -0.01 -1000
PLK1 signaling events 0.0192 10 855 85 -0.042 0.067 1000 -1000 -0.038 -1000
Nectin adhesion pathway 0.0192 10 657 63 -0.042 0.062 1000 -1000 -0.068 -1000
IL2 signaling events mediated by PI3K 0.0192 10 603 58 -0.078 0.081 1000 -1000 -0.062 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0192 10 456 45 -0.022 0.052 1000 -1000 -0.06 -1000
Ras signaling in the CD4+ TCR pathway 0.0192 10 171 17 -0.001 0.044 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0173 9 653 68 -0.096 0.062 1000 -1000 -0.047 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0173 9 359 37 -0.021 0.063 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 0.0173 9 514 54 -0.035 0.061 1000 -1000 -0.058 -1000
Aurora B signaling 0.0173 9 615 67 -0.31 0.088 1000 -1000 -0.044 -1000
Circadian rhythm pathway 0.0154 8 193 22 -0.054 0.056 1000 -1000 -0.043 -1000
JNK signaling in the CD4+ TCR pathway 0.0154 8 149 17 0.01 0.052 1000 -1000 -0.045 -1000
Regulation of Telomerase 0.0154 8 908 102 -0.07 0.06 1000 -1000 -0.065 -1000
FOXM1 transcription factor network 0.0154 8 435 51 -0.13 0.14 1000 -1000 -0.16 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0135 7 196 28 -0.041 0.051 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 0.0135 7 193 26 -0.067 0.088 1000 -1000 -0.023 -1000
Insulin Pathway 0.0135 7 584 74 -0.084 0.072 1000 -1000 -0.05 -1000
VEGFR1 specific signals 0.0135 7 430 56 -0.041 0.051 1000 -1000 -0.051 -1000
S1P4 pathway 0.0135 7 176 25 0 0.037 1000 -1000 -0.032 -1000
IL2 signaling events mediated by STAT5 0.0115 6 150 22 -0.016 0.043 1000 -1000 -0.061 -1000
Arf6 trafficking events 0.0115 6 457 71 -0.18 0.049 1000 -1000 -0.036 -1000
E-cadherin signaling in keratinocytes 0.0115 6 263 43 -0.041 0.062 1000 -1000 -0.044 -1000
Class IB PI3K non-lipid kinase events 0.0115 6 18 3 -0.022 0.022 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 0.0096 5 28 5 0.021 0.034 1000 -1000 0.001 -1000
HIF-2-alpha transcription factor network 0.0096 5 219 43 -0.098 0.045 1000 -1000 -0.087 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0096 5 688 125 -0.037 0.072 1000 -1000 -0.061 -1000
Class I PI3K signaling events 0.0096 5 390 73 -0.035 0.049 1000 -1000 -0.067 -1000
Hedgehog signaling events mediated by Gli proteins 0.0077 4 291 65 -0.023 0.065 1000 -1000 -0.056 -1000
Aurora A signaling 0.0077 4 256 60 -0.04 0.056 1000 -1000 -0.031 -1000
Aurora C signaling 0.0077 4 29 7 0 0.042 1000 -1000 -0.015 -1000
TRAIL signaling pathway 0.0077 4 218 48 0 0.07 1000 -1000 -0.043 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0077 4 400 83 -0.031 0.054 1000 -1000 -0.051 -1000
E-cadherin signaling in the nascent adherens junction 0.0077 4 364 76 -0.021 0.068 1000 -1000 -0.067 -1000
E-cadherin signaling events 0.0077 4 20 5 0.021 0.043 1000 -1000 0 -1000
Canonical NF-kappaB pathway 0.0058 3 147 39 0 0.06 1000 -1000 -0.046 -1000
Arf6 downstream pathway 0.0058 3 129 43 -0.041 0.042 1000 -1000 -0.04 -1000
Insulin-mediated glucose transport 0.0058 3 107 32 -0.07 0.053 1000 -1000 -0.041 -1000
S1P5 pathway 0.0058 3 60 17 -0.023 0.032 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class I 0.0058 3 331 104 -0.074 0.067 1000 -1000 -0.045 -1000
FoxO family signaling 0.0058 3 254 64 -0.016 0.086 1000 -1000 -0.079 -1000
Paxillin-dependent events mediated by a4b1 0.0058 3 115 36 -0.052 0.054 1000 -1000 -0.045 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0038 2 61 23 0.003 0.049 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 0.0038 2 67 31 0 0.033 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0019 1 143 75 -0.033 0.067 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 0.0019 1 4 3 0.013 0.027 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0.0019 1 16 13 0 0.074 1000 -1000 -0.003 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 10 27 0 0.061 1000 -1000 -0.036 -1000
Arf1 pathway 0.0000 0 41 54 -0.001 0.038 1000 -1000 -0.026 -1000
Total NA 2718 163533 7203 -16 7.8 131000 -131000 -6.6 -131000
IL4-mediated signaling events

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
BCL2L1 -0.87 0.46 -10000 0 -1.3 238 238
STAT6 (cleaved dimer) -0.88 0.48 -10000 0 -1.2 291 291
IGHG1 -0.31 0.16 -10000 0 -0.51 75 75
IGHG3 -0.85 0.44 -10000 0 -1.2 294 294
AKT1 -0.37 0.2 -10000 0 -0.82 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.17 -10000 0 -0.77 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.38 0.2 -10000 0 -0.86 32 32
THY1 -0.91 0.48 -10000 0 -1.3 272 272
MYB -0.018 0.14 -10000 0 -0.45 48 48
HMGA1 0.027 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.45 0.21 -10000 0 -0.74 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.38 0.21 -10000 0 -0.85 33 33
SP1 0.003 0.04 -10000 0 -10000 0 0
INPP5D 0.025 0.031 -10000 0 -0.46 2 2
SOCS5 0.048 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.87 0.47 -10000 0 -1.2 279 279
SOCS1 -0.57 0.26 -10000 0 -0.8 202 202
SOCS3 -0.38 0.18 -10000 0 -0.78 19 19
FCER2 -0.69 0.36 -10000 0 -1.1 148 148
PARP14 0.024 0.021 -10000 0 -0.39 1 1
CCL17 -0.9 0.47 -10000 0 -1.3 251 251
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.31 0.17 -10000 0 -0.7 36 36
T cell proliferation -0.88 0.48 -10000 0 -1.3 255 255
IL4R/JAK1 -0.88 0.46 -10000 0 -1.3 257 257
EGR2 -0.89 0.47 -10000 0 -1.3 259 259
JAK2 -0.048 0.03 -10000 0 -10000 0 0
JAK3 0.016 0.086 -10000 0 -0.39 22 22
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
JAK1 -0.011 0.017 -10000 0 -10000 0 0
COL1A2 -0.34 0.2 -10000 0 -0.64 64 64
CCL26 -0.9 0.47 -10000 0 -1.3 262 262
IL4R -0.93 0.5 -10000 0 -1.4 253 253
PTPN6 0.045 0.014 -10000 0 -10000 0 0
IL13RA2 -0.9 0.47 -10000 0 -1.3 261 261
IL13RA1 -0.052 0.028 -10000 0 -10000 0 0
IRF4 -0.25 0.32 -10000 0 -0.9 78 78
ARG1 -0.55 0.57 -10000 0 -1.5 139 139
CBL -0.43 0.2 -10000 0 -0.71 61 61
GTF3A -0.017 0.04 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.06 0.041 -10000 0 -10000 0 0
IRF4/BCL6 -0.2 0.29 -10000 0 -0.83 71 71
CD40LG -0.034 0.16 -10000 0 -0.46 64 64
MAPK14 -0.42 0.2 -10000 0 -0.72 57 57
mitosis -0.35 0.19 -10000 0 -0.76 37 37
STAT6 -1 0.58 -10000 0 -1.4 281 281
SPI1 -0.019 0.075 -10000 0 -0.43 3 3
RPS6KB1 -0.34 0.18 -10000 0 -0.74 34 34
STAT6 (dimer) -1 0.58 -10000 0 -1.4 281 281
STAT6 (dimer)/PARP14 -0.93 0.53 -10000 0 -1.3 271 271
mast cell activation 0.02 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.36 0.21 -10000 0 -0.87 37 37
FRAP1 -0.37 0.2 -10000 0 -0.82 37 37
LTA -0.89 0.46 -10000 0 -1.3 256 256
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.99 0.54 1.4 283 -10000 0 283
CCL11 -0.92 0.44 -10000 0 -1.2 288 288
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.35 0.19 -10000 0 -0.78 33 33
IL2RG 0.02 0.078 -10000 0 -0.4 17 17
IL10 -0.88 0.46 -10000 0 -1.3 260 260
IRS1 0.024 0.038 -10000 0 -0.46 3 3
IRS2 0.025 0.031 -10000 0 -0.46 2 2
IL4 -0.23 0.24 -10000 0 -1.1 30 30
IL5 -0.88 0.46 -10000 0 -1.3 254 254
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.69 0.34 -10000 0 -0.94 260 260
COL1A1 -0.45 0.25 -10000 0 -1 27 27
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.9 0.49 -10000 0 -1.3 236 236
IL2R gamma/JAK3 0.018 0.092 -10000 0 -0.31 35 35
TFF3 -1.1 0.6 -10000 0 -1.5 309 309
ALOX15 -0.96 0.52 -10000 0 -1.4 262 262
MYBL1 0.021 0.041 -10000 0 -0.39 5 5
T-helper 2 cell differentiation -0.78 0.39 -10000 0 -1.1 284 284
SHC1 0.028 0.004 -10000 0 -10000 0 0
CEBPB -0.014 0.066 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.36 0.19 -10000 0 -0.82 26 26
mol:PI-3-4-5-P3 -0.37 0.2 -10000 0 -0.82 37 37
PI3K -0.38 0.22 -10000 0 -0.88 37 37
DOK2 0.022 0.039 -10000 0 -0.41 4 4
ETS1 0.041 0.036 -10000 0 -0.38 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.29 0.16 -10000 0 -0.63 31 31
ITGB3 -0.89 0.47 -10000 0 -1.3 255 255
PIGR -1.2 0.62 -10000 0 -1.6 361 361
IGHE 0.045 0.054 0.19 14 -10000 0 14
MAPKKK cascade -0.29 0.15 -10000 0 -0.62 31 31
BCL6 0.02 0.013 -10000 0 -10000 0 0
OPRM1 -0.88 0.46 -10000 0 -1.3 254 254
RETNLB -0.87 0.47 -10000 0 -1.3 263 263
SELP -0.95 0.53 -10000 0 -1.4 266 266
AICDA -0.85 0.44 -10000 0 -1.2 262 262
HIF-1-alpha transcription factor 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
PKM2 -0.57 0.38 -10000 0 -0.98 177 177
HDAC7 0.028 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.42 0.28 -10000 0 -0.82 73 73
SMAD4 0.026 0.009 -10000 0 -10000 0 0
ID2 -0.57 0.38 -10000 0 -1 142 142
AP1 -0.006 0.12 -10000 0 -0.33 63 63
ABCG2 -0.57 0.39 -10000 0 -1 146 146
HIF1A -0.09 0.066 -10000 0 -0.6 1 1
TFF3 -0.66 0.44 -10000 0 -1.1 218 218
GATA2 0.023 0.03 -10000 0 -0.42 2 2
AKT1 -0.092 0.068 -10000 0 -0.41 2 2
response to hypoxia -0.1 0.076 -10000 0 -0.33 22 22
MCL1 -0.56 0.38 -10000 0 -1 142 142
NDRG1 -0.54 0.38 -10000 0 -1 136 136
SERPINE1 -0.64 0.41 -10000 0 -1.1 197 197
FECH -0.56 0.38 -10000 0 -1 143 143
FURIN -0.56 0.38 -10000 0 -1 143 143
NCOA2 -0.011 0.12 -10000 0 -0.46 36 36
EP300 -0.089 0.082 -10000 0 -0.36 12 12
HMOX1 -0.57 0.38 -10000 0 -1 143 143
BHLHE40 -0.56 0.38 -10000 0 -1 141 141
BHLHE41 -0.56 0.39 -10000 0 -1 145 145
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.083 0.092 -10000 0 -0.38 2 2
ENG -0.078 0.084 0.33 5 -0.38 1 6
JUN 0.028 0.006 -10000 0 -10000 0 0
RORA -0.57 0.39 -10000 0 -1 146 146
ABCB1 -0.18 0.3 -10000 0 -1.2 36 36
TFRC -0.53 0.38 -10000 0 -1 132 132
CXCR4 -0.57 0.39 -10000 0 -1 147 147
TF -0.68 0.44 -10000 0 -1.1 226 226
CITED2 -0.56 0.38 -10000 0 -1 144 144
HIF1A/ARNT -0.62 0.45 -10000 0 -1.2 149 149
LDHA -0.081 0.16 -10000 0 -0.79 22 22
ETS1 -0.56 0.38 -10000 0 -1 145 145
PGK1 -0.56 0.38 -10000 0 -1 144 144
NOS2 -0.59 0.39 -10000 0 -1 158 158
ITGB2 -0.57 0.38 -10000 0 -1 147 147
ALDOA -0.56 0.38 -10000 0 -1 145 145
Cbp/p300/CITED2 -0.56 0.39 -10000 0 -1 132 132
FOS -0.033 0.16 -10000 0 -0.46 63 63
HK2 -0.56 0.38 -10000 0 -1 144 144
SP1 0.027 0.029 -10000 0 -10000 0 0
GCK -0.15 0.14 -10000 0 -0.71 9 9
HK1 -0.56 0.38 -10000 0 -1 143 143
NPM1 -0.56 0.38 -10000 0 -1 142 142
EGLN1 -0.56 0.38 -10000 0 -1 143 143
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.56 0.38 -10000 0 -1 144 144
SMAD3 0.028 0.005 -10000 0 -10000 0 0
EDN1 -0.089 0.16 -10000 0 -1 8 8
IGFBP1 -0.57 0.38 -10000 0 -1 153 153
VEGFA -0.37 0.25 -10000 0 -0.76 48 48
HIF1A/JAB1 -0.049 0.049 -10000 0 -10000 0 0
CP -0.61 0.43 -10000 0 -1 196 196
CXCL12 -0.58 0.4 -10000 0 -1.1 148 148
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.014 -10000 0 -10000 0 0
BNIP3 -0.56 0.38 -10000 0 -1 144 144
EGLN3 -0.57 0.39 -10000 0 -1 148 148
CA9 -0.69 0.4 -10000 0 -1 229 229
TERT -0.58 0.4 -10000 0 -1 163 163
ENO1 -0.56 0.38 -10000 0 -1 141 141
PFKL -0.56 0.38 -10000 0 -1 141 141
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.57 0.39 -10000 0 -1 140 140
ARNT -0.098 0.069 -10000 0 -0.36 8 8
HNF4A -0.019 0.12 -10000 0 -0.39 49 49
ADFP -0.57 0.38 -10000 0 -0.98 177 177
SLC2A1 -0.37 0.25 -10000 0 -0.77 47 47
LEP -0.59 0.4 -10000 0 -1 166 166
HIF1A/ARNT/Cbp/p300 -0.43 0.29 -10000 0 -0.83 80 80
EPO -0.34 0.25 -10000 0 -0.83 52 52
CREBBP -0.089 0.081 -10000 0 -0.34 13 13
HIF1A/ARNT/Cbp/p300/HDAC7 -0.41 0.29 -10000 0 -0.83 69 69
PFKFB3 -0.56 0.38 -10000 0 -1 147 147
NT5E -0.59 0.4 -10000 0 -1 167 167
Syndecan-1-mediated signaling events

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
TGFB1 0.025 0.032 -10000 0 -0.39 3 3
CCL5 -0.034 0.15 -10000 0 -0.39 76 76
SDCBP 0.025 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.18 0.14 0.27 10 -0.33 155 165
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.18 0.13 -10000 0 -0.32 153 153
Syndecan-1/Syntenin -0.17 0.13 0.32 3 -0.32 140 143
MAPK3 -0.16 0.12 0.3 4 -0.4 34 38
HGF/MET 0.02 0.079 -10000 0 -0.31 28 28
TGFB1/TGF beta receptor Type II 0.025 0.032 -10000 0 -0.39 3 3
BSG 0.027 0.005 -10000 0 -10000 0 0
keratinocyte migration -0.18 0.13 -10000 0 -0.31 153 153
Syndecan-1/RANTES -0.2 0.15 0.32 4 -0.35 184 188
Syndecan-1/CD147 -0.17 0.13 0.31 4 -0.42 36 40
Syndecan-1/Syntenin/PIP2 -0.16 0.13 0.3 3 -0.31 140 143
LAMA5 0.027 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.16 0.12 0.29 3 -0.3 140 143
MMP7 -0.11 0.19 -10000 0 -0.39 160 160
HGF 0.006 0.095 -10000 0 -0.44 22 22
Syndecan-1/CASK -0.18 0.12 -10000 0 -0.32 157 157
Syndecan-1/HGF/MET -0.18 0.13 0.31 3 -0.4 54 57
regulation of cell adhesion -0.16 0.12 0.28 4 -0.4 31 35
HPSE 0.023 0.043 -10000 0 -0.46 4 4
positive regulation of cell migration -0.18 0.14 0.27 10 -0.33 155 165
SDC1 -0.19 0.13 0.22 1 -0.33 153 154
Syndecan-1/Collagen -0.18 0.14 0.27 10 -0.33 155 165
PPIB 0.028 0.004 -10000 0 -10000 0 0
MET 0.022 0.048 -10000 0 -0.41 6 6
PRKACA 0.028 0.004 -10000 0 -10000 0 0
MMP9 -0.26 0.19 -10000 0 -0.39 355 355
MAPK1 -0.16 0.12 0.3 4 -0.4 33 37
homophilic cell adhesion -0.18 0.14 0.27 10 -0.33 157 167
MMP1 -0.32 0.15 -10000 0 -0.39 427 427
Glypican 2 network

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
MDK 0.009 0.085 -9999 0 -0.39 22 22
GPC2 -0.045 0.16 -9999 0 -0.39 88 88
GPC2/Midkine -0.027 0.14 -9999 0 -0.3 95 95
neuron projection morphogenesis -0.027 0.14 -9999 0 -0.3 95 95
TCGA08_retinoblastoma

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
CDKN2B 0.01 0.07 -10000 0 -0.43 12 12
CDKN2C 0.016 0.077 -10000 0 -0.35 19 19
CDKN2A -0.13 0.19 -10000 0 -0.39 187 187
CCND2 0.04 0.063 0.18 51 -10000 0 51
RB1 -0.079 0.098 0.3 1 -0.23 115 116
CDK4 0.047 0.073 0.2 55 -10000 0 55
CDK6 0.044 0.07 0.22 39 -10000 0 39
G1/S progression 0.083 0.098 0.23 119 -0.3 1 120
Endothelins

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
AKT1 -0.11 0.19 0.25 2 -0.41 73 75
PTK2B 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.042 0.17 -10000 0 -0.54 22 22
EDN1 -0.069 0.15 -10000 0 -0.3 59 59
EDN3 -0.18 0.22 -10000 0 -0.46 197 197
EDN2 -0.04 0.16 -10000 0 -0.44 75 75
HRAS/GDP -0.063 0.16 0.31 4 -0.42 38 42
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.055 0.13 -10000 0 -0.35 48 48
ADCY4 -0.11 0.16 0.27 5 -0.38 82 87
ADCY5 -0.16 0.18 0.24 2 -0.41 120 122
ADCY6 -0.12 0.17 0.27 5 -0.39 88 93
ADCY7 -0.12 0.17 0.26 7 -0.38 85 92
ADCY1 -0.12 0.17 0.26 7 -0.39 85 92
ADCY2 -0.18 0.18 0.26 2 -0.42 137 139
ADCY3 -0.12 0.17 0.28 4 -0.39 82 86
ADCY8 -0.11 0.16 0.27 4 -0.39 79 83
ADCY9 -0.12 0.17 0.26 6 -0.38 84 90
arachidonic acid secretion -0.089 0.19 0.27 3 -0.46 74 77
ETB receptor/Endothelin-1/Gq/GTP -0.051 0.12 -10000 0 -0.33 48 48
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
HRAS 0.026 0.02 -10000 0 -0.4 1 1
ETA receptor/Endothelin-1/G12/GTP -0.037 0.22 0.32 9 -0.4 61 70
ETA receptor/Endothelin-1/Gs/GTP -0.072 0.22 0.32 5 -0.4 87 92
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.21 0.26 -10000 0 -0.47 208 208
EDNRB -0.009 0.062 -10000 0 -0.46 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.13 0.22 -10000 0 -0.51 77 77
CYSLTR1 -0.15 0.25 0.25 2 -0.53 106 108
SLC9A1 -0.047 0.11 -10000 0 -0.29 34 34
mol:GDP -0.072 0.16 0.31 4 -0.44 41 45
SLC9A3 -0.15 0.3 -10000 0 -0.68 97 97
RAF1 -0.093 0.18 0.27 5 -0.44 67 72
JUN -0.048 0.17 -10000 0 -0.67 10 10
JAK2 -0.11 0.18 0.26 4 -0.42 68 72
mol:IP3 -0.067 0.14 -10000 0 -0.38 54 54
ETA receptor/Endothelin-1 -0.071 0.28 0.34 14 -0.46 85 99
PLCB1 0.025 0.023 -10000 0 -0.46 1 1
PLCB2 0.023 0.039 -10000 0 -0.41 4 4
ETA receptor/Endothelin-3 -0.16 0.19 -10000 0 -0.38 200 200
FOS -0.14 0.32 0.31 1 -0.9 70 71
Gai/GDP -0.073 0.26 -10000 0 -0.71 71 71
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.19 0.24 1 -0.42 85 86
BCAR1 0.027 0.006 -10000 0 -10000 0 0
PRKCB1 -0.066 0.14 0.25 2 -0.37 53 55
GNAQ 0.027 0.009 -10000 0 -10000 0 0
GNAZ 0.012 0.079 -10000 0 -0.41 17 17
GNAL -0.03 0.16 -10000 0 -0.46 59 59
Gs family/GDP -0.084 0.16 0.25 1 -0.44 46 47
ETA receptor/Endothelin-1/Gq/GTP -0.065 0.15 -10000 0 -0.37 57 57
MAPK14 -0.038 0.11 0.24 1 -0.4 18 19
TRPC6 -0.044 0.18 -10000 0 -0.57 20 20
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.46 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.042 0.12 -10000 0 -0.39 26 26
ETB receptor/Endothelin-2 -0.041 0.12 -10000 0 -0.32 79 79
ETB receptor/Endothelin-3 -0.13 0.17 -10000 0 -0.34 195 195
ETB receptor/Endothelin-1 -0.049 0.14 -10000 0 -0.34 21 21
MAPK3 -0.13 0.28 0.3 2 -0.75 74 76
MAPK1 -0.13 0.28 0.3 2 -0.75 73 75
Rac1/GDP -0.063 0.15 0.32 3 -0.42 34 37
cAMP biosynthetic process -0.14 0.16 0.28 6 -0.41 79 85
MAPK8 -0.057 0.19 0.34 1 -0.59 33 34
SRC 0.026 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.019 0.087 -10000 0 -0.34 18 18
p130Cas/CRK/Src/PYK2 -0.069 0.16 0.31 5 -0.49 29 34
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.063 0.15 0.32 3 -0.42 34 37
COL1A2 -0.15 0.24 -10000 0 -0.44 165 165
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.079 0.16 -10000 0 -0.36 79 79
mol:DAG -0.067 0.14 -10000 0 -0.38 54 54
MAP2K2 -0.11 0.22 0.29 4 -0.55 80 84
MAP2K1 -0.11 0.22 0.28 3 -0.54 81 84
EDNRA -0.063 0.14 -10000 0 -0.29 57 57
positive regulation of muscle contraction -0.084 0.16 0.27 10 -0.39 55 65
Gq family/GDP -0.051 0.17 -10000 0 -0.42 45 45
HRAS/GTP -0.082 0.16 0.28 4 -0.42 51 55
PRKCH -0.059 0.14 0.24 7 -0.39 41 48
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.067 0.14 0.25 3 -0.4 38 41
PRKCB -0.068 0.14 0.24 4 -0.4 42 46
PRKCE -0.065 0.14 0.24 3 -0.4 36 39
PRKCD -0.06 0.13 -10000 0 -0.4 33 33
PRKCG -0.087 0.15 0.25 2 -0.38 62 64
regulation of vascular smooth muscle contraction -0.17 0.37 -10000 0 -1.1 70 70
PRKCQ -0.071 0.15 0.29 3 -0.4 51 54
PLA2G4A -0.096 0.21 0.29 2 -0.5 75 77
GNA14 -0.041 0.17 -10000 0 -0.46 71 71
GNA15 0.025 0.032 -10000 0 -0.46 2 2
GNA12 0.025 0.02 -10000 0 -0.39 1 1
GNA11 0.024 0.038 -10000 0 -0.46 3 3
Rac1/GTP -0.038 0.22 0.3 14 -0.38 67 81
MMP1 -0.23 0.19 0.48 19 -0.32 338 357
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.076 0.13 -10000 0 -0.24 197 197
EPHB2 -0.084 0.18 -10000 0 -0.39 137 137
Syndecan-2/TACI -0.008 0.086 -10000 0 -0.22 68 68
LAMA1 -0.14 0.2 -10000 0 -0.39 207 207
Syndecan-2/alpha2 ITGB1 -0.013 0.11 -10000 0 -0.36 7 7
HRAS 0.026 0.02 -10000 0 -0.4 1 1
Syndecan-2/CASK 0 0.044 -10000 0 -0.22 20 20
ITGA5 -0.1 0.19 -10000 0 -0.39 161 161
BAX 0 0.046 -10000 0 -0.42 1 1
EPB41 0.027 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.016 0.043 -10000 0 -0.2 19 19
LAMA3 -0.083 0.18 -10000 0 -0.39 135 135
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 0.031 -10000 0 -0.46 2 2
Syndecan-2/MMP2 -0.012 0.1 -10000 0 -0.26 67 67
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.037 0.026 -10000 0 -0.33 2 2
dendrite morphogenesis -0.038 0.11 -10000 0 -0.23 127 127
Syndecan-2/GM-CSF -0.1 0.13 -10000 0 -0.23 248 248
determination of left/right symmetry 0.001 0.053 -10000 0 -0.26 20 20
Syndecan-2/PKC delta 0.014 0.049 -10000 0 -0.22 20 20
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.084 0.13 0.19 27 -0.21 242 269
MAPK1 -0.081 0.13 0.19 26 -0.21 237 263
Syndecan-2/RACK1 0.027 0.048 -10000 0 -0.19 20 20
NF1 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.001 0.053 -10000 0 -0.26 20 20
ITGA2 0.024 0.038 -10000 0 -0.46 3 3
MAPK8 0.002 0.049 -10000 0 -0.23 21 21
Syndecan-2/alpha2/beta1 Integrin -0.046 0.12 -10000 0 -0.35 14 14
Syndecan-2/Kininogen 0.005 0.056 -10000 0 -0.24 23 23
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.027 0.067 0.27 2 -10000 0 2
Syndecan-2/CASK/Protein 4.1 0.016 0.044 -10000 0 -0.2 20 20
extracellular matrix organization 0.016 0.053 -10000 0 -0.23 21 21
actin cytoskeleton reorganization -0.076 0.13 -10000 0 -0.24 197 197
Syndecan-2/Caveolin-2/Ras 0.028 0.054 -10000 0 -0.22 20 20
Syndecan-2/Laminin alpha3 -0.039 0.11 -10000 0 -0.23 129 129
Syndecan-2/RasGAP 0.037 0.054 -10000 0 -0.4 1 1
alpha5/beta1 Integrin -0.058 0.14 -10000 0 -0.27 161 161
PRKCD 0.024 0.009 -10000 0 -10000 0 0
Syndecan-2 dimer -0.038 0.12 -10000 0 -0.23 127 127
GO:0007205 0.003 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.026 0.05 -10000 0 -0.39 1 1
RHOA 0.025 0.009 -10000 0 -10000 0 0
SDCBP 0.025 0.009 -10000 0 -10000 0 0
TNFRSF13B -0.022 0.12 -10000 0 -0.39 53 53
RASA1 0.024 0.031 -10000 0 -0.46 2 2
alpha2/beta1 Integrin 0.037 0.026 -10000 0 -0.33 2 2
Syndecan-2/Synbindin 0.015 0.049 -10000 0 -0.22 20 20
TGFB1 0.025 0.032 -10000 0 -0.39 3 3
CASP3 0.024 0.069 0.19 50 -0.2 16 66
FN1 -0.15 0.2 -10000 0 -0.39 222 222
Syndecan-2/IL8 -0.03 0.11 -10000 0 -0.23 109 109
SDC2 0.001 0.053 -10000 0 -0.26 20 20
KNG1 -0.013 0.067 -10000 0 -0.39 15 15
Syndecan-2/Neurofibromin 0.017 0.049 -10000 0 -0.22 20 20
TRAPPC4 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.2 0.21 -10000 0 -0.39 276 276
Syndecan-2/TGFB1 0.016 0.053 -10000 0 -0.23 21 21
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.043 -10000 0 -0.2 19 19
Syndecan-2/Ezrin 0.027 0.049 -10000 0 -0.2 19 19
PRKACA 0.029 0.073 0.19 60 -0.2 19 79
angiogenesis -0.029 0.11 -10000 0 -0.23 109 109
MMP2 -0.024 0.14 -10000 0 -0.39 62 62
IL8 -0.059 0.17 -10000 0 -0.39 106 106
calcineurin-NFAT signaling pathway -0.008 0.085 -10000 0 -0.22 68 68
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.014 0.13 -10000 0 -0.27 84 84
alphaM/beta2 Integrin/GPIbA 0.007 0.11 -10000 0 -0.3 47 47
alphaM/beta2 Integrin/proMMP-9 -0.17 0.15 -10000 0 -0.26 345 345
PLAUR 0.005 0.094 -10000 0 -0.39 28 28
HMGB1 0.019 0.026 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.014 0.094 -10000 0 -0.29 34 34
AGER 0.014 0.054 -10000 0 -0.39 7 7
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.028 0.002 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.017 0.12 -10000 0 -0.38 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.26 0.19 -10000 0 -0.39 355 355
CYR61 0.022 0.046 -10000 0 -0.4 6 6
TLN1 0.024 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.075 0.12 -10000 0 -0.35 36 36
RHOA 0.025 0.009 -10000 0 -10000 0 0
P-selectin oligomer -0.054 0.18 -10000 0 -0.46 85 85
MYH2 -0.22 0.19 -10000 0 -0.4 216 216
MST1R 0.02 0.049 -10000 0 -0.46 5 5
leukocyte activation during inflammatory response 0.009 0.1 -10000 0 -0.3 25 25
APOB 0.003 0.078 -10000 0 -0.39 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.024 0.14 -10000 0 -0.39 62 62
JAM3 0.025 0.02 -10000 0 -0.39 1 1
GP1BA 0.007 0.081 -10000 0 -0.41 18 18
alphaM/beta2 Integrin/CTGF 0.013 0.1 -10000 0 -0.3 42 42
alphaM/beta2 Integrin -0.095 0.13 -10000 0 -0.3 92 92
JAM3 homodimer 0.025 0.02 -10000 0 -0.39 1 1
ICAM2 0.026 0.031 -10000 0 -0.46 2 2
ICAM1 0.007 0.089 -10000 0 -0.39 25 25
phagocytosis triggered by activation of immune response cell surface activating receptor -0.094 0.13 -10000 0 -0.3 90 90
cell adhesion 0.007 0.11 -10000 0 -0.3 47 47
NFKB1 -0.029 0.14 -10000 0 -0.38 50 50
THY1 -0.09 0.18 -10000 0 -0.39 143 143
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
Lipoprotein(a) 0.018 0.059 -10000 0 -0.23 27 27
alphaM/beta2 Integrin/LRP/tPA 0.024 0.1 -10000 0 -0.34 20 20
IL6 -0.061 0.21 -10000 0 -0.66 46 46
ITGB2 0.008 0.072 -10000 0 -0.4 14 14
elevation of cytosolic calcium ion concentration -0.092 0.16 -10000 0 -0.37 64 64
alphaM/beta2 Integrin/JAM2/JAM3 0.024 0.11 -10000 0 -0.32 27 27
JAM2 0.016 0.074 -10000 0 -0.46 12 12
alphaM/beta2 Integrin/ICAM1 0.024 0.12 -10000 0 -0.38 20 20
alphaM/beta2 Integrin/uPA/Plg -0.089 0.15 -10000 0 -0.33 49 49
RhoA/GTP -0.13 0.15 -10000 0 -0.36 108 108
positive regulation of phagocytosis -0.063 0.11 -10000 0 -0.35 28 28
Ron/MSP 0.03 0.05 -10000 0 -0.31 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.092 0.17 -10000 0 -0.37 64 64
alphaM/beta2 Integrin/uPAR 0.004 0.12 -10000 0 -0.29 56 56
PLAU -0.15 0.21 -10000 0 -0.39 225 225
PLAT 0.014 0.069 -10000 0 -0.39 14 14
actin filament polymerization -0.21 0.18 0.23 1 -0.39 215 216
MST1 0.02 0.043 -10000 0 -0.4 5 5
alphaM/beta2 Integrin/lipoprotein(a) 0.013 0.1 -10000 0 -0.3 25 25
TNF -0.04 0.14 -10000 0 -0.55 15 15
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.099 0.16 -10000 0 -0.25 237 237
fibrinolysis -0.089 0.15 -10000 0 -0.33 49 49
HCK 0.024 0.029 -10000 0 -0.42 2 2
dendritic cell antigen processing and presentation -0.094 0.13 -10000 0 -0.3 90 90
VTN 0.001 0.1 -10000 0 -0.39 32 32
alphaM/beta2 Integrin/CYR61 0.015 0.1 -10000 0 -0.3 39 39
LPA 0.001 0.059 -10000 0 -0.39 10 10
LRP1 0.027 0.022 -10000 0 -0.46 1 1
cell migration -0.17 0.16 -10000 0 -0.38 112 112
FN1 -0.15 0.2 -10000 0 -0.39 222 222
alphaM/beta2 Integrin/Thy1 -0.056 0.16 -10000 0 -0.27 148 148
MPO -0.002 0.11 -10000 0 -0.46 29 29
KNG1 -0.013 0.067 -10000 0 -0.39 15 15
RAP1/GDP 0.035 0.01 -10000 0 -10000 0 0
ROCK1 -0.11 0.15 -10000 0 -0.36 87 87
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.015 0.041 -10000 0 -0.39 5 5
CTGF 0.02 0.059 -10000 0 -0.44 8 8
alphaM/beta2 Integrin/Hck 0.016 0.095 -10000 0 -0.3 33 33
ITGAM -0.006 0.1 -10000 0 -0.39 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.015 0.14 -10000 0 -0.28 98 98
HP -0.15 0.23 -10000 0 -0.46 178 178
leukocyte adhesion -0.049 0.14 -10000 0 -0.38 38 38
SELP -0.054 0.18 -10000 0 -0.46 85 85
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.034 0.12 -10000 0 -0.42 41 41
Crk/p130 Cas/Paxillin -0.067 0.12 -10000 0 -0.34 31 31
JUN -0.043 0.12 -10000 0 -0.35 28 28
HRAS 0.026 0.02 -10000 0 -0.4 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.048 0.16 -10000 0 -0.31 108 108
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.052 0.16 -10000 0 -0.28 160 160
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.042 0.14 -10000 0 -0.27 134 134
RHOA 0.025 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.045 0.15 -10000 0 -0.28 113 113
GRB7 0.025 0.038 -10000 0 -0.46 3 3
RET51/GFRalpha1/GDNF -0.052 0.16 -10000 0 -0.31 118 118
MAPKKK cascade -0.05 0.13 -10000 0 -0.37 30 30
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.042 0.14 -10000 0 -0.27 133 133
lamellipodium assembly -0.046 0.12 -10000 0 -0.27 75 75
RET51/GFRalpha1/GDNF/SHC -0.052 0.16 -10000 0 -0.28 160 160
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.04 0.14 -10000 0 -0.27 132 132
RET9/GFRalpha1/GDNF/Shank3 -0.039 0.14 -10000 0 -0.27 131 131
MAPK3 -0.059 0.14 0.34 4 -0.38 30 34
DOK1 0.027 0.018 -10000 0 -0.39 1 1
DOK6 0.016 0.063 -10000 0 -0.43 10 10
PXN 0.028 0.002 -10000 0 -10000 0 0
neurite development -0.054 0.13 0.33 4 -0.36 28 32
DOK5 0.003 0.1 -10000 0 -0.45 25 25
GFRA1 -0.092 0.21 -10000 0 -0.46 125 125
MAPK8 -0.054 0.11 -10000 0 -0.34 36 36
HRAS/GTP -0.049 0.15 -10000 0 -0.31 92 92
tube development -0.036 0.13 -10000 0 -0.27 107 107
MAPK1 -0.059 0.14 0.34 4 -0.38 27 31
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.042 0.11 -10000 0 -0.24 104 104
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
PDLIM7 0.022 0.041 -10000 0 -0.39 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.045 0.16 -10000 0 -0.3 101 101
SHC1 0.028 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.051 0.16 -10000 0 -0.31 117 117
RET51/GFRalpha1/GDNF/Dok5 -0.062 0.18 -10000 0 -0.33 123 123
PRKCA 0.026 0.029 -10000 0 -0.42 2 2
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
CREB1 -0.056 0.14 -10000 0 -0.29 109 109
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.045 0.11 -10000 0 -0.24 109 109
RET51/GFRalpha1/GDNF/Grb7 -0.051 0.17 -10000 0 -0.31 117 117
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.018 0.13 -10000 0 -0.4 55 55
DOK4 0.027 0.006 -10000 0 -10000 0 0
JNK cascade -0.042 0.12 -10000 0 -0.34 28 28
RET9/GFRalpha1/GDNF/FRS2 -0.04 0.14 -10000 0 -0.27 128 128
SHANK3 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.024 0.031 -10000 0 -0.46 2 2
NCK1 0.023 0.011 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.043 0.11 -10000 0 -0.24 106 106
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.049 0.12 -10000 0 -0.25 107 107
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.051 0.12 -10000 0 -0.29 59 59
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.12 -10000 0 -0.26 113 113
PI3K -0.064 0.18 -10000 0 -0.39 81 81
SOS1 0.028 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.027 0.14 -10000 0 -0.27 107 107
GRB10 0.026 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.04 0.12 -10000 0 -0.33 30 30
RET51/GFRalpha1/GDNF/FRS2 -0.051 0.16 -10000 0 -0.31 116 116
GAB1 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.024 0.038 -10000 0 -0.46 3 3
IRS2 0.025 0.031 -10000 0 -0.46 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.053 0.13 -10000 0 -0.26 115 115
RET51/GFRalpha1/GDNF/PKC alpha -0.052 0.16 -10000 0 -0.28 159 159
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GDNF -0.015 0.11 -10000 0 -0.39 38 38
RAC1 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.054 0.16 -10000 0 -0.31 119 119
Rac1/GTP -0.048 0.14 -10000 0 -0.32 75 75
RET9/GFRalpha1/GDNF -0.056 0.15 -10000 0 -0.3 132 132
GFRalpha1/GDNF -0.066 0.17 -10000 0 -0.35 132 132
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.097 0.16 -10000 0 -0.54 34 34
Syndecan-4/Syndesmos -0.16 0.15 -10000 0 -0.67 15 15
positive regulation of JNK cascade -0.17 0.15 -10000 0 -0.53 30 30
Syndecan-4/ADAM12 -0.28 0.18 -10000 0 -0.44 208 208
CCL5 -0.034 0.15 -10000 0 -0.39 76 76
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.028 0.004 -10000 0 -10000 0 0
ITGA5 -0.1 0.19 -10000 0 -0.39 161 161
SDCBP 0.025 0.009 -10000 0 -10000 0 0
PLG 0.014 0.045 -10000 0 -0.38 5 5
ADAM12 -0.27 0.19 -10000 0 -0.39 370 370
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.078 0.043 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.22 0.18 -10000 0 -0.45 122 122
Syndecan-4/CXCL12/CXCR4 -0.17 0.16 -10000 0 -0.57 30 30
Syndecan-4/Laminin alpha3 -0.2 0.17 -10000 0 -0.45 90 90
MDK 0.009 0.085 -10000 0 -0.39 22 22
Syndecan-4/FZD7 -0.16 0.16 -10000 0 -0.65 17 17
Syndecan-4/Midkine -0.16 0.16 -10000 0 -0.61 19 19
FZD7 0.022 0.046 -10000 0 -0.4 6 6
Syndecan-4/FGFR1/FGF -0.14 0.15 -10000 0 -0.64 14 14
THBS1 0.014 0.076 -10000 0 -0.41 16 16
integrin-mediated signaling pathway -0.18 0.16 -10000 0 -0.45 73 73
positive regulation of MAPKKK cascade -0.17 0.15 -10000 0 -0.53 30 30
Syndecan-4/TACI -0.17 0.16 -10000 0 -0.53 33 33
CXCR4 0.013 0.076 -10000 0 -0.39 18 18
cell adhesion -0.069 0.098 0.2 5 -0.21 102 107
Syndecan-4/Dynamin -0.15 0.15 -10000 0 -0.66 16 16
Syndecan-4/TSP1 -0.16 0.16 -10000 0 -0.56 25 25
Syndecan-4/GIPC -0.15 0.15 -10000 0 -0.67 15 15
Syndecan-4/RANTES -0.18 0.16 -10000 0 -0.49 46 46
ITGB1 0.027 0.005 -10000 0 -10000 0 0
LAMA1 -0.14 0.2 -10000 0 -0.39 207 207
LAMA3 -0.083 0.18 -10000 0 -0.39 135 135
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.04 0.098 0.86 6 -0.4 2 8
Syndecan-4/alpha-Actinin -0.15 0.15 -10000 0 -0.66 16 16
TFPI 0.023 0.044 -10000 0 -0.42 5 5
F2 -0.035 0.12 -10000 0 -0.39 52 52
alpha5/beta1 Integrin -0.058 0.14 -10000 0 -0.27 161 161
positive regulation of cell adhesion -0.25 0.19 -10000 0 -0.48 147 147
ACTN1 0.027 0.006 -10000 0 -10000 0 0
TNC -0.049 0.16 -10000 0 -0.39 94 94
Syndecan-4/CXCL12 -0.17 0.16 -10000 0 -0.6 27 27
FGF6 -0.009 0.018 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
CXCL12 -0.021 0.15 -10000 0 -0.46 51 51
TNFRSF13B -0.022 0.12 -10000 0 -0.39 53 53
FGF2 0.011 0.085 -10000 0 -0.44 17 17
FGFR1 0.019 0.047 -10000 0 -0.4 6 6
Syndecan-4/PI-4-5-P2 -0.16 0.14 -10000 0 -0.53 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.15 0.2 -10000 0 -0.38 222 222
cell migration -0.031 0.017 -10000 0 -10000 0 0
PRKCD 0.029 0.015 -10000 0 -10000 0 0
vasculogenesis -0.16 0.15 -10000 0 -0.54 25 25
SDC4 -0.16 0.15 -10000 0 -0.51 33 33
Syndecan-4/Tenascin C -0.18 0.17 -10000 0 -0.47 73 73
Syndecan-4/PI-4-5-P2/PKC alpha -0.062 0.034 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.15 0.15 -10000 0 -0.65 16 16
MMP9 -0.26 0.19 -10000 0 -0.38 355 355
Rac1/GTP -0.07 0.1 0.21 5 -0.22 101 106
cytoskeleton organization -0.15 0.15 -10000 0 -0.62 16 16
GIPC1 0.028 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.15 0.16 -10000 0 -0.64 17 17
Osteopontin-mediated events

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.12 0.13 -10000 0 -0.3 47 47
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.13 0.32 1 -0.4 10 11
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.15 -10000 0 -0.28 267 267
AP1 -0.16 0.17 -10000 0 -0.44 85 85
ILK -0.12 0.12 -10000 0 -0.37 18 18
bone resorption -0.095 0.12 0.33 1 -0.38 16 17
PTK2B 0.026 0.008 -10000 0 -10000 0 0
PYK2/p130Cas -0.083 0.14 -10000 0 -0.39 13 13
ITGAV 0.022 0.029 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.032 0.049 -10000 0 -0.33 9 9
alphaV/beta3 Integrin/Osteopontin -0.12 0.15 -10000 0 -0.28 160 160
MAP3K1 -0.12 0.13 -10000 0 -0.31 50 50
JUN 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.14 0.13 -10000 0 -0.3 139 139
MAPK1 -0.14 0.13 -10000 0 -0.3 133 133
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.12 0.12 -10000 0 -0.32 45 45
ITGB3 0.006 0.089 -10000 0 -0.42 21 21
NFKBIA -0.13 0.13 -10000 0 -0.33 47 47
FOS -0.034 0.16 -10000 0 -0.46 63 63
CD44 0.025 0.023 -10000 0 -0.46 1 1
CHUK 0.027 0.005 -10000 0 -10000 0 0
PLAU -0.2 0.19 -10000 0 -0.58 8 8
NF kappa B1 p50/RelA -0.12 0.15 -10000 0 -0.44 8 8
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.011 0.074 -10000 0 -0.3 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.12 0.13 -10000 0 -0.31 44 44
VAV3 -0.13 0.13 0.19 3 -0.4 35 38
MAP3K14 -0.13 0.13 -10000 0 -0.28 140 140
ROCK2 0.019 0.064 -10000 0 -0.46 9 9
SPP1 -0.2 0.21 -10000 0 -0.39 279 279
RAC1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.11 0.12 -10000 0 -0.38 33 33
MMP2 -0.15 0.17 -10000 0 -0.48 69 69
IL23-mediated signaling events

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
CCL2 -0.42 0.4 -10000 0 -1.2 78 78
IL23A -0.4 0.37 -10000 0 -1.1 63 63
NF kappa B1 p50/RelA/I kappa B alpha -0.38 0.38 -10000 0 -1.1 73 73
positive regulation of T cell mediated cytotoxicity -0.44 0.41 -10000 0 -1.2 86 86
ITGA3 -0.4 0.36 -10000 0 -1.1 68 68
IL17F -0.26 0.26 -10000 0 -0.69 64 64
IL12B -0.06 0.11 -10000 0 -0.42 44 44
STAT1 (dimer) -0.43 0.4 -10000 0 -1.1 89 89
CD4 -0.39 0.36 -10000 0 -1.1 65 65
IL23 -0.39 0.36 -10000 0 -1.1 64 64
IL23R -0.065 0.12 -10000 0 -0.92 7 7
IL1B -0.41 0.38 -10000 0 -1.1 72 72
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.48 0.35 -10000 0 -1.1 74 74
TYK2 -0.02 0.033 -10000 0 -0.42 1 1
STAT4 0.016 0.066 -10000 0 -0.39 13 13
STAT3 0.028 0.003 -10000 0 -10000 0 0
IL18RAP 0.007 0.084 -10000 0 -0.42 18 18
IL12RB1 -0.047 0.11 -10000 0 -0.42 37 37
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.039 0.086 -10000 0 -0.31 38 38
IL23R/JAK2 -0.075 0.12 -10000 0 -0.88 6 6
positive regulation of chronic inflammatory response -0.44 0.41 -10000 0 -1.2 86 86
natural killer cell activation 0.007 0.006 0.041 4 -10000 0 4
JAK2 -0.022 0.03 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
NFKB1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.024 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.38 0.34 -10000 0 -1 64 64
ALOX12B -0.46 0.43 -10000 0 -1.2 93 93
CXCL1 -0.42 0.39 -10000 0 -1.1 77 77
T cell proliferation -0.44 0.41 -10000 0 -1.2 86 86
NFKBIA 0.024 0.007 -10000 0 -10000 0 0
IL17A -0.2 0.2 -10000 0 -0.56 44 44
PI3K -0.38 0.37 -10000 0 -1.1 76 76
IFNG -0.023 0.035 0.094 5 -0.11 9 14
STAT3 (dimer) -0.36 0.36 -10000 0 -1 68 68
IL18R1 0.021 0.032 -10000 0 -0.42 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.25 0.22 -10000 0 -0.76 30 30
IL18/IL18R 0.021 0.086 -10000 0 -0.28 30 30
macrophage activation -0.023 0.015 -10000 0 -0.045 30 30
TNF -0.41 0.38 -10000 0 -1.1 70 70
STAT3/STAT4 -0.4 0.38 -10000 0 -1.1 83 83
STAT4 (dimer) -0.42 0.4 -10000 0 -1.1 85 85
IL18 0.009 0.074 -10000 0 -0.46 12 12
IL19 -0.53 0.5 -10000 0 -1.3 137 137
STAT5A (dimer) -0.42 0.4 -10000 0 -1.1 86 86
STAT1 0.009 0.084 -10000 0 -0.39 22 22
SOCS3 0.027 0.022 -10000 0 -0.46 1 1
CXCL9 -0.46 0.38 -10000 0 -1.1 83 83
MPO -0.43 0.4 -10000 0 -1.2 85 85
positive regulation of humoral immune response -0.44 0.41 -10000 0 -1.2 86 86
IL23/IL23R/JAK2/TYK2 -0.45 0.45 -10000 0 -1.2 86 86
IL6 -0.43 0.42 -10000 0 -1.2 84 84
STAT5A 0.028 0.003 -10000 0 -10000 0 0
IL2 0.014 0.028 -10000 0 -0.38 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.006 0.041 4 -10000 0 4
CD3E -0.4 0.36 -10000 0 -1.1 67 67
keratinocyte proliferation -0.44 0.41 -10000 0 -1.2 86 86
NOS2 -0.42 0.38 -10000 0 -1.1 74 74
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.13 -10000 0 -0.25 133 133
regulation of S phase of mitotic cell cycle -0.028 0.096 -10000 0 -0.23 88 88
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
HRAS 0.026 0.02 -10000 0 -0.4 1 1
SHBG/T-DHT 0.018 0.004 -10000 0 -10000 0 0
PELP1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.055 0.11 0.32 1 -0.31 15 16
T-DHT/AR -0.076 0.16 -10000 0 -0.33 139 139
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 66 66
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.46 1 1
mol:GDP -0.088 0.16 -10000 0 -0.35 130 130
cell proliferation -0.088 0.17 0.28 3 -0.43 72 75
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
FOS -0.11 0.27 0.28 3 -0.77 69 72
mol:Ca2+ -0.01 0.022 -10000 0 -0.064 40 40
MAPK3 -0.077 0.14 0.29 2 -0.4 33 35
MAPK1 -0.034 0.096 -10000 0 -0.32 19 19
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
mol:IP3 0 0.002 -10000 0 -0.004 66 66
cAMP biosynthetic process 0.006 0.022 0.21 2 -10000 0 2
GNG2 0.026 0.007 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 66 66
HRAS/GTP -0.033 0.12 -10000 0 -0.23 127 127
actin cytoskeleton reorganization 0.027 0.027 -10000 0 -0.23 2 2
SRC 0.026 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 66 66
PI3K 0.024 0.026 -10000 0 -0.28 2 2
apoptosis 0.07 0.16 0.41 77 -0.25 2 79
T-DHT/AR/PELP1 -0.052 0.14 -10000 0 -0.28 139 139
HRAS/GDP -0.075 0.15 -10000 0 -0.33 130 130
CREB1 -0.075 0.17 0.25 2 -0.44 76 78
RAC1-CDC42/GTP 0.034 0.031 -10000 0 -0.23 2 2
AR -0.11 0.22 -10000 0 -0.46 139 139
GNB1 0.027 0.006 -10000 0 -10000 0 0
RAF1 -0.048 0.11 0.33 1 -0.29 16 17
RAC1-CDC42/GDP -0.043 0.17 -10000 0 -0.32 120 120
T-DHT/AR/PELP1/Src -0.033 0.13 -10000 0 -0.26 129 129
MAP2K2 -0.054 0.11 0.32 1 -0.31 16 17
T-DHT/AR/PELP1/Src/PI3K -0.029 0.097 -10000 0 -0.24 88 88
GNAZ 0.012 0.079 -10000 0 -0.41 17 17
SHBG 0.024 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.029 0.14 -10000 0 -0.46 33 33
mol:T-DHT 0 0.001 0.002 3 -0.002 42 45
RAC1 0.026 0.007 -10000 0 -10000 0 0
GNRH1 -0.004 0.054 -10000 0 -0.27 20 20
Gi family/GTP -0.032 0.084 -10000 0 -0.28 29 29
CDC42 0.027 0.005 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.004 0.056 -10000 0 -0.27 22 22
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.003 0.11 -10000 0 -0.33 50 50
STXBP1 0.027 0.004 -10000 0 -10000 0 0
ACh/CHRNA1 -0.086 0.14 -10000 0 -0.28 178 178
RAB3GAP2/RIMS1/UNC13B 0.013 0.098 -10000 0 -0.28 49 49
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.032 0.14 -10000 0 -0.46 49 49
mol:ACh 0 0.033 0.094 19 -0.11 7 26
RAB3GAP2 0.028 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0 0.088 -10000 0 -0.31 5 5
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.086 0.14 -10000 0 -0.28 178 178
UNC13B 0.021 0.038 -10000 0 -0.46 3 3
CHRNA1 -0.14 0.22 -10000 0 -0.44 178 178
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.045 0.11 -10000 0 -0.24 125 125
SNAP25 -0.004 0.034 -10000 0 -0.13 34 34
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.074 0.18 -10000 0 -0.39 125 125
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.014 0.051 -10000 0 -0.23 22 22
STX1A/SNAP25 fragment 1/VAMP2 0 0.088 -10000 0 -0.31 5 5
Coregulation of Androgen receptor activity

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
NRIP1 0.008 0.046 -10000 0 -0.46 1 1
SVIL 0.009 0.044 -10000 0 -0.46 1 1
ZNF318 0.052 0.06 0.2 36 -10000 0 36
JMJD2C 0.006 0.016 0.049 1 -0.067 14 15
T-DHT/AR/Ubc9 -0.095 0.15 -10000 0 -0.32 139 139
CARM1 0.023 0.014 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.031 0.012 -10000 0 -10000 0 0
CTNNB1 0.011 0.032 -10000 0 -10000 0 0
AKT1 0.033 0.019 -10000 0 -10000 0 0
PTK2B 0.012 0.031 -10000 0 -10000 0 0
MED1 0.036 0.019 -10000 0 -10000 0 0
MAK 0.042 0.083 0.2 17 -0.39 9 26
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 0.009 0.043 -10000 0 -0.46 1 1
GSN 0.008 0.042 -10000 0 -10000 0 0
NCOA2 -0.013 0.12 -10000 0 -0.46 36 36
NCOA6 0.01 0.037 -10000 0 -10000 0 0
DNA-PK 0.067 0.058 0.27 1 -10000 0 1
NCOA4 0.026 0.006 -10000 0 -10000 0 0
PIAS3 0.012 0.033 -10000 0 -10000 0 0
cell proliferation -0.01 0.12 -10000 0 -0.53 16 16
XRCC5 0.033 0.015 -10000 0 -10000 0 0
UBE3A 0.004 0.052 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.16 -10000 0 -0.34 153 153
FHL2 -0.016 0.096 -10000 0 -0.52 6 6
RANBP9 0.011 0.037 -10000 0 -10000 0 0
JMJD1A -0.059 0.068 -10000 0 -0.13 234 234
CDK6 0.025 0.03 -10000 0 -0.42 2 2
TGFB1I1 -0.001 0.076 -10000 0 -0.4 14 14
T-DHT/AR/CyclinD1 -0.083 0.14 -10000 0 -0.3 121 121
XRCC6 0.033 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.12 0.17 -10000 0 -0.35 140 140
CTDSP1 0.018 0.022 -10000 0 -10000 0 0
CTDSP2 0.045 0.04 -10000 0 -10000 0 0
BRCA1 0.01 0.039 -10000 0 -10000 0 0
TCF4 0.037 0.031 -10000 0 -10000 0 0
CDKN2A -0.12 0.19 -10000 0 -0.38 187 187
SRF 0.04 0.021 -10000 0 -10000 0 0
NKX3-1 -0.13 0.13 -10000 0 -0.25 252 252
KLK3 -0.22 0.51 -10000 0 -1.4 87 87
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.038 0.023 -10000 0 -10000 0 0
AOF2 -0.012 0.026 -10000 0 -0.07 86 86
APPL1 0.025 0.035 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.087 0.15 -10000 0 -0.32 137 137
AR -0.14 0.22 -10000 0 -0.49 139 139
UBA3 0.016 0.022 -10000 0 -10000 0 0
PATZ1 0.037 0.023 -10000 0 -10000 0 0
PAWR 0.021 0.017 -10000 0 -10000 0 0
PRKDC 0.03 0.017 -10000 0 -10000 0 0
PA2G4 0.039 0.026 -10000 0 -10000 0 0
UBE2I 0.028 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.08 0.14 -10000 0 -0.29 136 136
RPS6KA3 0.006 0.052 -10000 0 -0.46 2 2
T-DHT/AR/ARA70 -0.098 0.15 -10000 0 -0.32 136 136
LATS2 0.036 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.072 0.14 0.17 2 -0.29 138 140
Cyclin D3/CDK11 p58 0.021 0.006 -10000 0 -10000 0 0
VAV3 -0.017 0.12 -10000 0 -0.47 32 32
KLK2 -0.055 0.095 -10000 0 -0.41 18 18
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.098 0.15 -10000 0 -0.32 146 146
TMPRSS2 -0.43 0.46 -10000 0 -0.92 241 241
CCND1 0.01 0.043 -10000 0 -0.47 3 3
PIAS1 0.004 0.052 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.03 0.038 1 -0.062 167 168
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.005 0.073 -10000 0 -0.2 5 5
T-DHT/AR/CDK6 -0.09 0.15 -10000 0 -0.32 133 133
CMTM2 0.016 0.068 -10000 0 -0.38 14 14
SNURF -0.001 0.1 -10000 0 -0.46 23 23
ZMIZ1 -0.01 0.045 -10000 0 -10000 0 0
CCND3 0.028 0.007 -10000 0 -10000 0 0
TGIF1 0.033 0.025 -10000 0 -10000 0 0
FKBP4 0.01 0.037 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.096 0.13 -10000 0 -0.27 187 187
TP53 -0.031 0.065 -10000 0 -0.3 20 20
Senescence -0.031 0.064 -10000 0 -0.3 20 20
Apoptosis -0.031 0.064 -10000 0 -0.3 20 20
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.058 0.093 0.3 27 -10000 0 27
MDM4 0.028 0.004 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.021 0.033 -10000 0 -10000 0 0
NFATC2 -0.053 0.095 -10000 0 -0.31 55 55
NFATC3 -0.023 0.033 -10000 0 -10000 0 0
CD40LG -0.23 0.26 0.35 6 -0.61 116 122
PTGS2 -0.23 0.25 0.35 5 -0.6 108 113
JUNB 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.012 0.026 -10000 0 -10000 0 0
CaM/Ca2+ -0.012 0.026 -10000 0 -10000 0 0
CALM1 0.007 0.025 -10000 0 -10000 0 0
JUN 0.007 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.014 -10000 0 -10000 0 0
FOSL1 0.018 0.059 -10000 0 -0.4 10 10
CREM 0.027 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.14 -10000 0 -0.39 48 48
FOS -0.053 0.16 -10000 0 -0.47 63 63
IFNG -0.23 0.25 0.35 4 -0.59 115 119
AP-1/NFAT1-c-4 -0.24 0.26 -10000 0 -0.62 111 111
FASLG -0.22 0.24 0.34 4 -0.62 89 93
NFAT1-c-4/ICER1 -0.076 0.1 -10000 0 -0.32 40 40
IL2RA -0.22 0.24 0.35 6 -0.6 97 103
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.29 0.27 0.35 5 -0.59 173 178
JunB/Fra1/NFAT1-c-4 -0.072 0.11 -10000 0 -0.32 39 39
IL4 -0.21 0.22 0.35 4 -0.58 81 85
IL2 -0.014 0.16 -10000 0 -0.91 15 15
IL3 -0.037 0.17 -10000 0 -0.73 28 28
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
BATF3 0.024 0.037 -10000 0 -0.39 4 4
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.004 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.011 -10000 0 -10000 0 0
CRKL -0.022 0.092 -10000 0 -0.24 74 74
GRB2/SOS1/SHC 0.054 0.013 -10000 0 -10000 0 0
HRAS 0.026 0.02 -10000 0 -0.4 1 1
IRS1/Crk -0.016 0.097 -10000 0 -0.24 78 78
IGF-1R heterotetramer/IGF1/PTP1B 0.003 0.12 -10000 0 -0.27 77 77
AKT1 0.008 0.11 0.18 105 -0.4 2 107
BAD 0.005 0.1 0.17 100 -0.38 2 102
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.024 0.094 -10000 0 -0.24 78 78
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.011 0.1 0.21 1 -0.24 78 79
RAF1 -0.008 0.16 0.28 10 -0.44 38 48
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.018 0.11 -10000 0 -0.23 73 73
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.012 0.11 -10000 0 -0.26 82 82
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
RPS6KB1 0.012 0.12 0.18 118 -0.4 2 120
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.006 0.13 0.26 14 -0.37 27 41
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.005 0.087 -10000 0 -0.38 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.033 0.11 -10000 0 -0.22 68 68
IGF-1R heterotetramer 0.013 0.039 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.005 0.11 -10000 0 -0.24 76 76
Crk/p130 Cas/Paxillin 0.015 0.1 -10000 0 -0.36 1 1
IGF1R 0.013 0.039 -10000 0 -10000 0 0
IGF1 -0.052 0.19 -10000 0 -0.47 85 85
IRS2/Crk -0.014 0.094 -10000 0 -0.23 73 73
PI3K 0.009 0.094 -10000 0 -0.24 55 55
apoptosis -0.027 0.096 0.32 1 -0.26 16 17
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
PRKCD -0.035 0.13 -10000 0 -0.33 77 77
RAF1/14-3-3 E 0.002 0.15 0.28 13 -0.39 35 48
BAD/14-3-3 0.027 0.1 0.27 16 -0.34 1 17
PRKCZ 0.007 0.11 0.18 106 -0.4 2 108
Crk/p130 Cas/Paxillin/FAK1 0.021 0.084 -10000 0 -0.31 1 1
PTPN1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.037 0.14 -10000 0 -0.35 79 79
BCAR1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.017 0.11 -10000 0 -0.23 74 74
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.008 0.1 -10000 0 -0.24 76 76
GRB10 0.026 0.007 -10000 0 -10000 0 0
PTPN11 -0.023 0.095 -10000 0 -0.24 78 78
IRS1 -0.025 0.1 -10000 0 -0.26 79 79
IRS2 -0.023 0.095 -10000 0 -0.24 75 75
IGF-1R heterotetramer/IGF1 -0.02 0.14 -10000 0 -0.35 80 80
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 0.021 0.12 0.26 12 -0.32 4 16
YWHAE 0.027 0.006 -10000 0 -10000 0 0
PRKD1 -0.039 0.13 -10000 0 -0.34 76 76
SHC1 0.028 0.004 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.054 0.16 -10000 0 -0.34 56 56
SMAD6-7/SMURF1 0.048 0.021 -10000 0 -10000 0 0
NOG -0.019 0.13 -10000 0 -0.42 48 48
SMAD9 -0.072 0.2 -10000 0 -0.55 66 66
SMAD4 0.025 0.009 -10000 0 -10000 0 0
SMAD5 -0.049 0.12 -10000 0 -0.41 30 30
BMP7/USAG1 -0.067 0.18 -10000 0 -0.36 133 133
SMAD5/SKI -0.045 0.14 0.25 1 -0.42 33 34
SMAD1 0.024 0.041 -10000 0 -10000 0 0
BMP2 0.012 0.077 -10000 0 -0.39 18 18
SMAD1/SMAD1/SMAD4 0.026 0.052 -10000 0 -10000 0 0
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.015 0.13 -10000 0 -0.4 50 50
BMPR1A-1B/BAMBI 0.014 0.1 -10000 0 -0.25 65 65
AHSG -0.003 0.071 -10000 0 -0.39 16 16
CER1 -0.009 0.042 -10000 0 -0.39 5 5
BMP2-4/CER1 0.023 0.074 -10000 0 -0.25 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.082 0.17 -10000 0 -0.46 47 47
BMP2-4 (homodimer) 0.019 0.078 -10000 0 -0.3 27 27
RGMB 0.026 0.007 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.034 0.09 -10000 0 -0.26 14 14
RGMA -0.029 0.16 -10000 0 -0.46 59 59
SMURF1 0.026 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.077 0.15 -10000 0 -0.39 58 58
BMP2-4/USAG1 -0.041 0.14 -10000 0 -0.28 135 135
SMAD6/SMURF1/SMAD5 -0.046 0.13 0.25 1 -0.42 32 33
SOSTDC1 -0.091 0.2 -10000 0 -0.45 124 124
BMP7/BMPR2/BMPR1A-1B 0.014 0.12 -10000 0 -0.28 44 44
SKI 0.027 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.046 -10000 0 -0.4 6 6
HFE2 -0.14 0.21 -10000 0 -0.46 152 152
ZFYVE16 0.026 0.007 -10000 0 -10000 0 0
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.018 0.077 -10000 0 -0.26 32 32
SMAD5/SMAD5/SMAD4 -0.043 0.14 0.25 1 -0.42 32 33
MAPK1 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.059 0.14 -10000 0 -0.39 38 38
BMP7 (homodimer) -0.007 0.12 -10000 0 -0.46 35 35
NUP214 0.027 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.015 0.06 -10000 0 -0.27 20 20
SMAD1/SKI 0.025 0.068 -10000 0 -0.37 1 1
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.015 0.077 -10000 0 -0.25 35 35
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.15 0.2 -10000 0 -0.39 216 216
BMPR2 (homodimer) 0.027 0.006 -10000 0 -10000 0 0
GADD34/PP1CA 0.048 0.021 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.008 0.097 -10000 0 -0.28 50 50
CHRDL1 -0.22 0.24 -10000 0 -0.46 259 259
ENDOFIN/SMAD1 0.028 0.067 -10000 0 -0.35 1 1
SMAD6-7/SMURF1/SMAD1 0.044 0.067 -10000 0 -10000 0 0
SMAD6/SMURF1 0.026 0.008 -10000 0 -10000 0 0
BAMBI 0.012 0.083 -10000 0 -0.44 17 17
SMURF2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.12 0.18 -10000 0 -0.3 246 246
BMP2-4/GREM1 -0.072 0.15 -10000 0 -0.24 209 209
SMAD7 0.026 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.066 0.2 -10000 0 -0.51 74 74
SMAD1/SMAD6 0.023 0.068 -10000 0 -0.35 1 1
TAK1/SMAD6 0.037 0.013 -10000 0 -10000 0 0
BMP7 -0.007 0.12 -10000 0 -0.46 35 35
BMP6 0.021 0.046 -10000 0 -0.4 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.065 0.15 -10000 0 -0.39 54 54
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.026 0.069 -10000 0 -0.37 1 1
SMAD7/SMURF1 0.035 0.015 -10000 0 -10000 0 0
CTDSPL 0.024 0.009 -10000 0 -10000 0 0
PPP1CA 0.025 0.008 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
CTDSP1 0.027 0.006 -10000 0 -10000 0 0
PPP1R15A 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.16 -10000 0 -0.36 105 105
CHRD 0.01 0.064 -10000 0 -0.39 12 12
BMPR2 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.085 0.16 -10000 0 -0.4 63 63
BMP4 0.017 0.067 -10000 0 -0.46 10 10
FST -0.11 0.19 -10000 0 -0.39 166 166
BMP2-4/NOG 0.007 0.11 -10000 0 -0.26 71 71
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.021 0.11 -10000 0 -0.26 40 40
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.023 -10000 0 -0.27 3 3
Metarhodopsin II/Arrestin 0.021 0.022 -10000 0 -0.23 3 3
PDE6G/GNAT1/GTP 0.021 0.048 -10000 0 -0.23 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.003 0.037 -10000 0 -0.39 3 3
GRK1 -0.01 0.03 -10000 0 -0.39 2 2
CNG Channel -0.21 0.17 -10000 0 -0.41 162 162
mol:Na + -0.11 0.14 -10000 0 -0.38 48 48
mol:ADP -0.01 0.03 -10000 0 -0.39 2 2
RGS9-1/Gbeta5/R9AP 0.041 0.062 -10000 0 -0.26 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.11 0.14 -10000 0 -0.39 48 48
CNGB1 -0.18 0.21 -10000 0 -0.39 260 260
RDH5 0.026 0.028 -10000 0 -0.42 2 2
SAG -0.012 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.11 0.15 0.38 7 -0.37 48 55
Na + (4 Units) -0.11 0.13 -10000 0 -0.36 48 48
RGS9 0.017 0.065 -10000 0 -0.4 12 12
GNB1/GNGT1 -0.003 0.1 -10000 0 -0.27 64 64
GNAT1/GDP 0.041 0.062 -10000 0 -0.26 13 13
GUCY2D 0.006 0.088 -10000 0 -0.39 24 24
GNGT1 -0.031 0.14 -10000 0 -0.39 64 64
GUCY2F -0.009 0.026 -10000 0 -0.39 1 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.11 0.14 -10000 0 -0.26 218 218
mol:11-cis-retinal 0.026 0.028 -10000 0 -0.42 2 2
mol:cGMP 0.007 0.09 -10000 0 -0.33 5 5
GNB1 0.027 0.006 -10000 0 -10000 0 0
Rhodopsin 0.028 0.034 -10000 0 -0.29 5 5
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 -0.006 0.12 -10000 0 -0.46 34 34
Metarhodopsin II 0.02 0.023 -10000 0 -0.21 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.015 0.097 -10000 0 -0.22 67 67
RGS9BP 0.017 0.065 -10000 0 -0.46 9 9
Metarhodopsin II/Transducin -0.007 0.054 -10000 0 -0.27 10 10
GCAP Family/Ca ++ 0.012 0.08 -10000 0 -0.21 55 55
PDE6A/B -0.14 0.2 -10000 0 -0.34 238 238
mol:Pi 0.04 0.062 -10000 0 -0.26 20 20
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.007 0.084 -10000 0 -0.21 55 55
PDE6B -0.009 0.12 -10000 0 -0.43 39 39
PDE6A -0.18 0.24 -10000 0 -0.46 215 215
PDE6G 0.016 0.068 -10000 0 -0.39 14 14
RHO -0.005 0.036 -10000 0 -0.39 3 3
PDE6 -0.091 0.17 -10000 0 -0.4 36 36
GUCA1A -0.018 0.13 -10000 0 -0.39 54 54
GC2/GCAP Family 0.02 0.087 -10000 0 -0.22 42 42
GUCA1C -0.016 0.006 -10000 0 -10000 0 0
GUCA1B 0.023 0.042 -10000 0 -0.44 4 4
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.008 0.16 0.27 14 -0.4 43 57
FYN -0.024 0.18 0.27 19 -0.47 43 62
LAT/GRAP2/SLP76 -0.015 0.17 0.26 5 -0.45 43 48
IKBKB 0.026 0.008 -10000 0 -10000 0 0
AKT1 -0.02 0.14 0.24 14 -0.36 45 59
B2M 0.026 0.012 -10000 0 -10000 0 0
IKBKG -0.002 0.048 0.096 20 -0.14 12 32
MAP3K8 0.024 0.038 -10000 0 -0.46 3 3
mol:Ca2+ -0.035 0.031 -10000 0 -0.088 56 56
integrin-mediated signaling pathway 0.035 0.021 -10000 0 -0.28 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.034 0.19 0.26 14 -0.48 49 63
TRPV6 -0.19 0.26 1.1 5 -0.46 222 227
CD28 0.013 0.077 -10000 0 -0.4 17 17
SHC1 -0.031 0.18 0.28 15 -0.48 48 63
receptor internalization -0.038 0.18 0.18 3 -0.45 69 72
PRF1 -0.044 0.21 -10000 0 -0.76 24 24
KRAS 0.026 0.007 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.007 0.12 0.22 12 -0.31 37 49
LAT -0.036 0.18 0.22 14 -0.5 49 63
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.011 0.077 -10000 0 -0.43 15 15
CD3E 0.013 0.071 -10000 0 -0.42 13 13
CD3G -0.001 0.11 -10000 0 -0.44 28 28
RASGRP2 0.006 0.02 0.071 1 -0.13 2 3
RASGRP1 -0.022 0.15 0.26 14 -0.41 38 52
HLA-A 0 0.005 -10000 0 -10000 0 0
RASSF5 0.026 0.031 -10000 0 -0.46 2 2
RAP1A/GTP/RAPL 0.035 0.021 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.059 0.14 32 -0.12 10 42
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.063 -10000 0 -0.22 27 27
PRKCA -0.006 0.089 0.15 15 -0.26 23 38
GRAP2 0.017 0.066 -10000 0 -0.43 11 11
mol:IP3 0.036 0.16 0.21 173 -0.37 30 203
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.028 0.15 -10000 0 -0.45 47 47
ORAI1 0.099 0.16 0.6 2 -0.94 5 7
CSK -0.031 0.18 0.22 15 -0.46 51 66
B7 family/CD28 -0.049 0.19 -10000 0 -0.5 48 48
CHUK 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.047 0.19 0.21 6 -0.48 60 66
PTPN6 -0.032 0.17 0.22 13 -0.45 51 64
VAV1 -0.036 0.18 0.22 11 -0.49 49 60
Monovalent TCR/CD3 -0.008 0.12 -10000 0 -0.37 35 35
CBL 0.025 0.008 -10000 0 -10000 0 0
LCK -0.027 0.18 0.26 17 -0.48 44 61
PAG1 -0.026 0.18 0.22 30 -0.48 46 76
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.046 0.18 0.22 8 -0.46 61 69
CD80 -0.073 0.18 -10000 0 -0.39 121 121
CD86 0.024 0.02 -10000 0 -0.39 1 1
PDK1/CARD11/BCL10/MALT1 -0.021 0.081 -10000 0 -0.26 28 28
HRAS 0.026 0.02 -10000 0 -0.4 1 1
GO:0035030 -0.059 0.15 0.19 3 -0.42 50 53
CD8A -0.007 0.12 -10000 0 -0.43 39 39
CD8B -0.02 0.14 -10000 0 -0.42 54 54
PTPRC 0.017 0.069 -10000 0 -0.43 12 12
PDK1/PKC theta -0.029 0.16 0.29 13 -0.44 42 55
CSK/PAG1 -0.022 0.17 0.25 19 -0.47 43 62
SOS1 0.028 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.016 0.18 0.25 5 -0.48 46 51
STIM1 0.056 0.12 1.2 4 -10000 0 4
RAS family/GTP 0.014 0.073 0.18 19 -0.18 11 30
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.04 0.2 0.2 1 -0.48 67 68
mol:DAG -0.015 0.12 0.12 11 -0.33 35 46
RAP1A/GDP 0.012 0.029 0.085 17 -10000 0 17
PLCG1 0.027 0.006 -10000 0 -10000 0 0
CD247 0.009 0.086 -10000 0 -0.41 21 21
cytotoxic T cell degranulation -0.042 0.2 -10000 0 -0.73 24 24
RAP1A/GTP 0.002 0.008 -10000 0 -0.053 1 1
mol:PI-3-4-5-P3 -0.025 0.16 0.25 16 -0.4 48 64
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.032 0.2 0.23 157 -0.48 32 189
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0.007 0.092 -10000 0 -0.4 25 25
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.023 0.16 0.28 3 -0.46 38 41
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.016 0.15 -10000 0 -0.39 68 68
CARD11 0.001 0.099 -10000 0 -0.4 30 30
PRKCB -0.007 0.093 0.15 15 -0.29 23 38
PRKCE -0.005 0.088 0.15 14 -0.26 23 37
PRKCQ -0.034 0.18 0.28 14 -0.48 45 59
LCP2 0.024 0.032 -10000 0 -0.39 3 3
BCL10 0.027 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.015 0.12 0.22 15 -0.31 43 58
IKK complex 0.015 0.06 0.14 40 -0.12 6 46
RAS family/GDP -0.002 0.01 -10000 0 -10000 0 0
MAP3K14 -0.007 0.095 0.18 12 -0.26 24 36
PDPK1 -0.018 0.13 0.24 15 -0.35 39 54
TCR/CD3/MHC I/CD8/Fyn -0.052 0.21 -10000 0 -0.53 58 58
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.031 0.14 0.3 4 -0.38 55 59
CRKL -0.035 0.14 -10000 0 -0.4 55 55
HRAS -0.022 0.14 -10000 0 -0.41 17 17
mol:PIP3 -0.015 0.14 0.31 1 -0.37 51 52
SPRED1 0.028 0.003 -10000 0 -10000 0 0
SPRED2 0.026 0.031 -10000 0 -0.46 2 2
GAB1 -0.035 0.15 -10000 0 -0.42 60 60
FOXO3 -0.022 0.14 0.36 1 -0.38 46 47
AKT1 -0.025 0.16 -10000 0 -0.39 61 61
BAD -0.02 0.15 0.31 1 -0.38 47 48
megakaryocyte differentiation -0.038 0.15 -10000 0 -0.41 61 61
GSK3B -0.004 0.15 0.32 2 -0.37 41 43
RAF1 -0.014 0.11 0.35 1 -0.36 10 11
SHC1 0.028 0.004 -10000 0 -10000 0 0
STAT3 -0.036 0.15 -10000 0 -0.42 60 60
STAT1 -0.11 0.34 -10000 0 -1 62 62
HRAS/SPRED1 -0.004 0.12 0.3 2 -0.38 9 11
cell proliferation -0.037 0.15 -10000 0 -0.42 60 60
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
TEC 0.006 0.097 -10000 0 -0.46 21 21
RPS6KB1 -0.026 0.15 -10000 0 -0.4 61 61
HRAS/SPRED2 -0.006 0.12 -10000 0 -0.37 13 13
LYN/TEC/p62DOK -0.013 0.16 -10000 0 -0.42 48 48
MAPK3 -0.008 0.092 0.3 3 -0.3 8 11
STAP1 -0.047 0.15 0.25 1 -0.42 63 64
GRAP2 0.017 0.066 -10000 0 -0.43 11 11
JAK2 -0.089 0.3 -10000 0 -0.86 62 62
STAT1 (dimer) -0.1 0.34 -10000 0 -0.98 62 62
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.016 0.16 -10000 0 -0.4 58 58
actin filament polymerization -0.038 0.14 -10000 0 -0.41 60 60
LYN 0.024 0.02 -10000 0 -0.39 1 1
STAP1/STAT5A (dimer) -0.065 0.21 -10000 0 -0.59 62 62
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
CBL/CRKL/GRB2 -0.005 0.14 0.28 1 -0.37 52 53
PI3K -0.013 0.14 -10000 0 -0.4 43 43
PTEN 0.027 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.4 -10000 0 -1.2 61 61
MAPK8 -0.038 0.15 -10000 0 -0.43 60 60
STAT3 (dimer) -0.035 0.14 -10000 0 -0.41 60 60
positive regulation of transcription -0.004 0.079 0.28 3 -0.25 6 9
mol:GDP -0.021 0.15 -10000 0 -0.38 52 52
PIK3C2B -0.036 0.15 -10000 0 -0.42 61 61
CBL/CRKL -0.016 0.14 0.28 1 -0.38 55 56
FER -0.035 0.15 -10000 0 -0.42 61 61
SH2B3 -0.035 0.15 -10000 0 -0.42 61 61
PDPK1 -0.013 0.13 0.3 1 -0.36 42 43
SNAI2 -0.034 0.14 -10000 0 -0.41 50 50
positive regulation of cell proliferation -0.073 0.26 -10000 0 -0.72 63 63
KITLG 0.019 0.045 -10000 0 -0.48 3 3
cell motility -0.073 0.26 -10000 0 -0.72 63 63
PTPN6 0.027 0.011 -10000 0 -10000 0 0
EPOR -0.013 0.17 -10000 0 -0.89 8 8
STAT5A (dimer) -0.054 0.22 -10000 0 -0.6 62 62
SOCS1 0.003 0.097 -10000 0 -0.39 30 30
cell migration 0.039 0.15 0.42 61 -10000 0 61
SOS1 0.028 0.004 -10000 0 -10000 0 0
EPO -0.021 0.12 -10000 0 -0.39 51 51
VAV1 0.02 0.06 -10000 0 -0.45 8 8
GRB10 -0.034 0.14 -10000 0 -0.42 55 55
PTPN11 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT -0.035 0.16 -10000 0 -0.44 61 61
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.01 0.094 0.35 2 -0.34 4 6
CBL 0.025 0.008 -10000 0 -10000 0 0
KIT -0.13 0.43 -10000 0 -1.2 66 66
MAP2K2 -0.009 0.094 0.29 4 -0.34 4 8
SHC/Grb2/SOS1 -0.001 0.15 -10000 0 -0.4 55 55
STAT5A -0.053 0.22 -10000 0 -0.61 62 62
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.033 0.14 -10000 0 -0.4 50 50
SHC/GRAP2 0.032 0.051 -10000 0 -0.3 11 11
PTPRO -0.039 0.15 -10000 0 -0.42 61 61
SH2B2 -0.039 0.14 -10000 0 -0.42 60 60
DOK1 0.027 0.018 -10000 0 -0.39 1 1
MATK -0.04 0.15 -10000 0 -0.43 61 61
CREBBP 0.025 0.05 -10000 0 -10000 0 0
BCL2 -0.064 0.28 -10000 0 -1.1 23 23
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.034 0.066 -10000 0 -0.27 19 19
fibroblast growth factor receptor signaling pathway 0.034 0.065 -10000 0 -0.27 19 19
LAMA1 -0.14 0.2 -10000 0 -0.39 207 207
PRNP 0.026 0.007 -10000 0 -10000 0 0
GPC1/SLIT2 -0.008 0.12 -10000 0 -0.33 63 63
SMAD2 0.016 0.028 -10000 0 -0.26 1 1
GPC1/PrPc/Cu2+ 0.034 0.017 -10000 0 -0.23 1 1
GPC1/Laminin alpha1 -0.09 0.15 -10000 0 -0.27 207 207
TDGF1 0.003 0.048 -10000 0 -0.39 6 6
CRIPTO/GPC1 0.029 0.038 -10000 0 -0.27 7 7
APP/GPC1 0.037 0.022 -10000 0 -0.27 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.003 0.024 -10000 0 -0.23 2 2
FLT1 0.026 0.019 -10000 0 -0.39 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.031 -10000 0 -0.25 3 3
SERPINC1 0.014 0.061 -10000 0 -0.39 11 11
FYN 0.001 0.032 -10000 0 -0.23 5 5
FGR 0.001 0.031 -10000 0 -0.23 7 7
positive regulation of MAPKKK cascade 0.003 0.095 0.3 8 -0.35 9 17
SLIT2 -0.033 0.16 -10000 0 -0.46 62 62
GPC1/NRG -0.01 0.11 -10000 0 -0.28 75 75
NRG1 -0.035 0.15 -10000 0 -0.39 74 74
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.038 -10000 0 -0.23 7 7
LYN 0.001 0.032 -10000 0 -0.23 8 8
mol:Spermine 0.007 0.012 -10000 0 -0.27 1 1
cell growth 0.034 0.065 -10000 0 -0.27 19 19
BMP signaling pathway -0.026 0.019 0.39 1 -10000 0 1
SRC 0.001 0.03 -10000 0 -0.23 6 6
TGFBR1 0.027 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.28 0.24 -10000 0 -0.46 320 320
GPC1 0.026 0.019 -10000 0 -0.39 1 1
TGFBR1 (dimer) 0.027 0.005 -10000 0 -10000 0 0
VEGFA 0.022 0.045 -10000 0 -0.39 6 6
BLK -0.031 0.084 -10000 0 -0.24 66 66
HCK 0.001 0.034 -10000 0 -0.27 6 6
FGF2 0.011 0.085 -10000 0 -0.44 17 17
FGFR1 0.019 0.047 -10000 0 -0.4 6 6
VEGFR1 homodimer 0.026 0.019 -10000 0 -0.39 1 1
TGFBR2 0.022 0.032 -10000 0 -0.46 2 2
cell death 0.037 0.022 -10000 0 -0.27 2 2
ATIII/GPC1 0.031 0.048 -10000 0 -0.27 12 12
PLA2G2A/GPC1 -0.19 0.18 -10000 0 -0.33 321 321
LCK -0.004 0.045 -10000 0 -0.23 18 18
neuron differentiation -0.01 0.11 -10000 0 -0.28 75 75
PrPc/Cu2+ 0.02 0.005 -10000 0 -10000 0 0
APP 0.026 0.019 -10000 0 -0.39 1 1
TGFBR2 (dimer) 0.022 0.032 -10000 0 -0.46 2 2
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.028 0.063 -10000 0 -0.33 15 15
Necdin/E2F1 0.02 0.079 -10000 0 -0.31 26 26
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0 0.13 -10000 0 -0.28 32 32
NGF (dimer)/p75(NTR)/BEX1 -0.034 0.14 -10000 0 -0.24 149 149
NT-4/5 (dimer)/p75(NTR) 0.022 0.08 -10000 0 -0.32 26 26
IKBKB 0.026 0.008 -10000 0 -10000 0 0
AKT1 0.004 0.12 -10000 0 -0.37 1 1
IKBKG 0.027 0.006 -10000 0 -10000 0 0
BDNF -0.004 0.12 -10000 0 -0.43 35 35
MGDIs/NGR/p75(NTR)/LINGO1 0.011 0.11 -10000 0 -0.26 68 68
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.007 0.12 -10000 0 -0.27 71 71
LINGO1 -0.006 0.11 -10000 0 -0.39 41 41
Sortilin/TRAF6/NRIF 0.026 0.045 -10000 0 -10000 0 0
proBDNF (dimer) -0.004 0.12 -10000 0 -0.43 35 35
NTRK1 -0.007 0.12 -10000 0 -0.39 43 43
RTN4R 0.015 0.07 -10000 0 -0.39 15 15
neuron apoptosis -0.039 0.13 0.46 1 -0.46 21 22
IRAK1 0.027 0.006 -10000 0 -10000 0 0
SHC1 -0.042 0.11 -10000 0 -0.24 119 119
ARHGDIA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.075 0.026 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.01 0.13 -10000 0 -0.29 35 35
MAGEH1 0.027 0.019 -10000 0 -0.39 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.014 0.14 -10000 0 -0.31 42 42
Mammalian IAPs/DIABLO 0.054 0.05 -10000 0 -10000 0 0
proNGF (dimer) -0.054 0.16 -10000 0 -0.39 98 98
MAGED1 0.024 0.04 -10000 0 -0.42 4 4
APP 0.026 0.019 -10000 0 -0.39 1 1
NT-4/5 (dimer) 0.025 0.034 -10000 0 -0.41 3 3
ZNF274 0.027 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.019 0.1 -10000 0 -0.25 17 17
NGF -0.054 0.16 -10000 0 -0.39 98 98
cell cycle arrest -0.065 0.1 -10000 0 -0.32 18 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.005 0.066 -10000 0 -0.25 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.037 0.071 -10000 0 -0.27 24 24
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.016 0.12 -10000 0 -0.24 123 123
PSENEN 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide -0.047 0.11 -10000 0 -0.29 33 33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.001 0.048 -10000 0 -0.28 2 2
p75(NTR)/beta APP 0.022 0.076 -10000 0 -0.3 27 27
BEX1 -0.01 0.1 -10000 0 -0.39 35 35
mol:GDP -0.052 0.1 -10000 0 -0.24 122 122
NGF (dimer) -0.077 0.15 -10000 0 -0.34 49 49
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.025 0.11 -10000 0 -0.32 17 17
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
RAC1/GTP -0.01 0.1 -10000 0 -0.2 109 109
MYD88 0.024 0.009 -10000 0 -10000 0 0
CHUK 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.016 0.13 -10000 0 -0.24 123 123
RHOB 0.028 0.003 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.025 0.061 -10000 0 -0.27 20 20
NT3 (dimer) -0.11 0.22 -10000 0 -0.46 144 144
TP53 -0.015 0.095 0.53 1 -0.45 5 6
PRDM4 -0.048 0.11 -10000 0 -0.29 34 34
BDNF (dimer) -0.2 0.17 -10000 0 -0.28 367 367
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
SORT1 0.011 0.088 -10000 0 -0.46 17 17
activation of caspase activity -0.005 0.13 -10000 0 -0.28 32 32
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.008 0.13 -10000 0 -0.29 31 31
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
MAPK10 -0.044 0.12 0.31 3 -0.38 20 23
DIABLO 0.028 0.002 -10000 0 -10000 0 0
SMPD2 -0.047 0.11 -10000 0 -0.29 33 33
APH1B 0.028 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.026 0.14 -10000 0 -0.25 134 134
PSEN1 0.027 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.081 0.18 -10000 0 -0.34 161 161
MAPK8 -0.036 0.1 0.35 2 -0.38 10 12
MAPK9 -0.035 0.11 0.34 3 -0.38 10 13
APAF1 0.028 0.002 -10000 0 -10000 0 0
NTF3 -0.11 0.22 -10000 0 -0.46 144 144
NTF4 0.025 0.034 -10000 0 -0.41 3 3
NDN 0.019 0.064 -10000 0 -0.46 9 9
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.004 0.11 -10000 0 -0.35 1 1
p75 CTF/Sortilin/TRAF6/NRIF 0.054 0.061 -10000 0 -0.26 16 16
RhoA-B-C/GTP -0.017 0.12 -10000 0 -0.24 123 123
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.033 0.11 -10000 0 -0.27 37 37
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.023 0.11 -10000 0 -0.28 38 38
PRKACB 0.026 0.022 -10000 0 -0.46 1 1
proBDNF (dimer)/p75 ECD 0.015 0.089 -10000 0 -0.31 36 36
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.39 15 15
BIRC2 0.024 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.049 0.1 0.21 1 -0.31 27 28
BAD -0.039 0.11 0.38 2 -0.38 11 13
RIPK2 0.025 0.009 -10000 0 -10000 0 0
NGFR 0.005 0.098 -10000 0 -0.42 26 26
CYCS -0.043 0.1 -10000 0 -0.42 7 7
ADAM17 0.026 0.031 -10000 0 -0.46 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.003 0.11 -10000 0 -0.27 15 15
BCL2L11 -0.04 0.11 0.38 2 -0.38 11 13
BDNF (dimer)/p75(NTR) 0 0.11 -10000 0 -0.3 60 60
PI3K -0.01 0.11 -10000 0 -0.26 17 17
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.01 0.13 -10000 0 -0.23 131 131
NDNL2 0.028 0.004 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.013 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.037 0.14 -10000 0 -0.28 122 122
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.012 0.14 -10000 0 -0.3 38 38
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.46 1 1
PLG -0.015 0.041 -10000 0 -0.39 5 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.049 0.12 -10000 0 -0.34 38 38
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
NGFRAP1 0.026 0.026 -10000 0 -0.39 2 2
CASP3 -0.037 0.1 0.37 2 -0.35 15 17
E2F1 0.01 0.08 -10000 0 -0.39 20 20
CASP9 0.027 0.006 -10000 0 -10000 0 0
IKK complex 0.008 0.11 -10000 0 -0.36 1 1
NGF (dimer)/TRKA -0.045 0.14 -10000 0 -0.29 132 132
MMP7 -0.11 0.19 -10000 0 -0.39 160 160
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.002 0.13 -10000 0 -0.28 29 29
MMP3 -0.24 0.2 -10000 0 -0.39 322 322
APAF-1/Caspase 9 -0.032 0.088 -10000 0 -0.35 6 6
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.27 -10000 0 -0.85 31 31
PCK1 -0.45 0.58 -10000 0 -1.2 171 171
HNF4A -0.2 0.3 -10000 0 -0.98 30 30
KCNJ11 -0.27 0.4 -10000 0 -1 85 85
AKT1 -0.091 0.15 -10000 0 -0.49 11 11
response to starvation -0.003 0.017 -10000 0 -0.2 1 1
DLK1 -0.34 0.46 -10000 0 -0.99 152 152
NKX2-1 -0.015 0.18 0.32 47 -0.38 17 64
ACADM -0.18 0.28 -10000 0 -0.86 34 34
TAT -0.13 0.19 -10000 0 -0.7 14 14
CEBPB 0.027 0.008 -10000 0 -10000 0 0
CEBPA 0.025 0.038 -10000 0 -0.46 3 3
TTR -0.26 0.29 -10000 0 -0.84 64 64
PKLR -0.2 0.29 -10000 0 -0.85 39 39
APOA1 -0.21 0.32 -10000 0 -1 28 28
CPT1C -0.18 0.27 -10000 0 -0.85 32 32
ALAS1 -0.085 0.16 -10000 0 -0.8 2 2
TFRC -0.16 0.22 -10000 0 -0.74 14 14
FOXF1 0.021 0.05 -10000 0 -0.4 7 7
NF1 0.033 0.005 -10000 0 -10000 0 0
HNF1A (dimer) 0.018 0.062 -10000 0 -0.38 10 10
CPT1A -0.16 0.27 -10000 0 -0.87 24 24
HMGCS1 -0.16 0.27 -10000 0 -0.83 30 30
NR3C1 0.028 0.024 -10000 0 -10000 0 0
CPT1B -0.19 0.28 -10000 0 -0.92 31 31
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0.023 -10000 0 -10000 0 0
GCK -0.19 0.28 -10000 0 -0.84 35 35
CREB1 -0.037 0.099 -10000 0 -0.22 58 58
IGFBP1 -0.082 0.15 -10000 0 -0.57 11 11
PDX1 -0.094 0.17 -10000 0 -0.77 3 3
UCP2 -0.17 0.27 -10000 0 -0.87 29 29
ALDOB -0.2 0.3 -10000 0 -0.88 36 36
AFP -0.15 0.17 -10000 0 -0.5 38 38
BDH1 -0.15 0.27 -10000 0 -0.88 24 24
HADH -0.19 0.29 -10000 0 -0.9 28 28
F2 -0.22 0.32 -10000 0 -1 26 26
HNF1A 0.018 0.062 -10000 0 -0.38 10 10
G6PC -0.054 0.1 -10000 0 -0.49 1 1
SLC2A2 -0.1 0.17 -10000 0 -0.85 2 2
INS -0.023 0.032 -10000 0 -0.4 2 2
FOXA1 -0.16 0.24 -10000 0 -0.47 191 191
FOXA3 -0.094 0.17 -10000 0 -0.42 70 70
FOXA2 -0.22 0.33 -10000 0 -0.93 43 43
ABCC8 -0.19 0.29 -10000 0 -0.89 30 30
ALB -0.16 0.18 -10000 0 -0.58 43 43
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.017 0.22 2 -10000 0 2
AES 0.026 0.015 0.21 1 -10000 0 1
FBXW11 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.03 -10000 0 -0.31 3 3
SMAD4 0.025 0.009 -10000 0 -10000 0 0
DKK2 0.015 0.074 -10000 0 -0.42 14 14
TLE1 0.026 0.015 0.21 1 -10000 0 1
MACF1 0.028 0.005 -10000 0 -10000 0 0
CTNNB1 0.037 0.12 0.26 19 -0.39 11 30
WIF1 -0.2 0.23 -10000 0 -0.46 221 221
beta catenin/RanBP3 -0.006 0.1 0.37 16 -0.4 5 21
KREMEN2 -0.12 0.2 -10000 0 -0.39 178 178
DKK1 -0.13 0.2 -10000 0 -0.39 191 191
beta catenin/beta TrCP1 0.049 0.12 0.26 19 -0.39 6 25
FZD1 0.025 0.029 -10000 0 -0.42 2 2
AXIN2 -0.015 0.2 0.68 4 -1.3 10 14
AXIN1 0.028 0.004 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.027 0.092 -10000 0 -0.58 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.14 0.33 2 -0.55 14 16
Axin1/APC/GSK3 0.042 0.07 0.25 5 -0.38 3 8
Axin1/APC/GSK3/beta catenin/Macf1 0.04 0.098 0.3 8 -0.39 7 15
HNF1A 0.019 0.06 0.22 1 -0.39 10 11
CTBP1 0.025 0.017 0.22 1 -10000 0 1
MYC 0.12 0.24 0.57 101 -0.51 2 103
RANBP3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.05 0.14 -10000 0 -0.23 180 180
NKD1 0.012 0.077 -10000 0 -0.39 18 18
TCF4 0.024 0.017 0.22 1 -10000 0 1
TCF3 0.026 0.015 0.22 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.056 0.044 -10000 0 -0.26 2 2
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.002 0.11 0.42 17 -0.45 7 24
LEF1 0.022 0.044 0.22 1 -0.39 5 6
DVL1 0.048 0.066 0.23 1 -0.47 3 4
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.059 0.11 0.26 4 -0.52 9 13
DKK1/LRP6/Kremen 2 -0.13 0.18 -10000 0 -0.28 282 282
LRP6 0.026 0.023 -10000 0 -0.46 1 1
CSNK1A1 0.026 0.018 0.25 1 -10000 0 1
NLK 0.027 0.008 -10000 0 -10000 0 0
CCND1 0.14 0.28 0.58 126 -1.2 4 130
WNT1 0.016 0.05 -10000 0 -0.39 7 7
GSK3A 0.028 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.009 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
PPP2R5D 0.036 0.078 0.24 9 -0.4 7 16
APC 0.026 0.067 0.31 7 -10000 0 7
WNT1/LRP6/FZD1 0.079 0.096 0.21 167 -10000 0 167
CREBBP 0.026 0.016 0.22 1 -10000 0 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.006 -10000 0 -10000 0 0
LAT2 -0.047 0.11 -10000 0 -0.35 25 25
AP1 -0.021 0.14 0.3 1 -0.42 12 13
mol:PIP3 -0.062 0.15 0.35 9 -0.42 24 33
IKBKB -0.024 0.1 0.22 26 -0.26 13 39
AKT1 -0.029 0.15 0.39 18 -0.38 12 30
IKBKG -0.025 0.1 0.24 19 -0.26 13 32
MS4A2 0.008 0.091 -10000 0 -0.46 18 18
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
MAP3K1 0.019 0.14 0.26 71 -0.37 8 79
mol:Ca2+ -0.046 0.13 0.32 9 -0.31 24 33
LYN 0.024 0.022 -10000 0 -0.4 1 1
CBLB -0.043 0.11 -10000 0 -0.34 23 23
SHC1 0.028 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.034 0.069 -10000 0 -0.26 25 25
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.025 0.031 -10000 0 -0.46 2 2
PLD2 -0.076 0.14 0.34 9 -0.4 21 30
PTPN13 -0.035 0.13 0.36 1 -0.54 7 8
PTPN11 0.014 0.026 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.004 0.14 0.32 25 -0.33 8 33
SYK 0.024 0.04 -10000 0 -0.48 3 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.068 0.14 -10000 0 -0.42 24 24
LAT -0.051 0.12 -10000 0 -0.34 29 29
PAK2 0.015 0.15 0.26 76 -0.39 10 86
NFATC2 -0.088 0.19 -10000 0 -0.59 60 60
HRAS -0.027 0.12 0.26 5 -0.38 19 24
GAB2 0.022 0.038 -10000 0 -0.46 3 3
PLA2G1B -0.065 0.28 -10000 0 -0.82 60 60
Fc epsilon R1 -0.082 0.18 -10000 0 -0.31 192 192
Antigen/IgE/Fc epsilon R1 -0.072 0.16 -10000 0 -0.28 192 192
mol:GDP -0.027 0.12 0.28 1 -0.41 15 16
JUN 0.028 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
FOS -0.034 0.16 -10000 0 -0.46 63 63
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.047 0.12 -10000 0 -0.34 31 31
CHUK -0.032 0.098 0.26 11 -0.26 13 24
KLRG1 -0.051 0.11 -10000 0 -0.35 27 27
VAV1 -0.049 0.12 -10000 0 -0.35 30 30
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.045 0.11 -10000 0 -0.35 24 24
negative regulation of mast cell degranulation -0.034 0.12 0.24 2 -0.34 25 27
BTK -0.03 0.11 -10000 0 -0.42 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.083 0.16 -10000 0 -0.41 48 48
GAB2/PI3K/SHP2 -0.062 0.11 -10000 0 -0.41 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.056 0.12 -10000 0 -0.36 27 27
RAF1 -0.074 0.3 -10000 0 -0.9 60 60
Fc epsilon R1/FcgammaRIIB/SHIP -0.054 0.17 -10000 0 -0.28 162 162
FCER1G 0.017 0.064 -10000 0 -0.39 12 12
FCER1A -0.15 0.24 -10000 0 -0.47 180 180
Antigen/IgE/Fc epsilon R1/Fyn -0.059 0.16 -10000 0 -0.26 180 180
MAPK3 -0.067 0.28 -10000 0 -0.83 60 60
MAPK1 -0.067 0.28 -10000 0 -0.83 60 60
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.008 0.14 0.33 1 -0.55 21 22
DUSP1 0.005 0.1 -10000 0 -0.46 23 23
NF-kappa-B/RelA -0.013 0.061 0.13 2 -0.19 1 3
actin cytoskeleton reorganization -0.032 0.12 0.37 1 -0.53 7 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.023 0.11 -10000 0 -0.38 12 12
FER -0.046 0.11 -10000 0 -0.34 27 27
RELA 0.027 0.006 -10000 0 -10000 0 0
ITK -0.021 0.073 -10000 0 -0.27 29 29
SOS1 0.028 0.004 -10000 0 -10000 0 0
PLCG1 -0.028 0.13 0.31 6 -0.41 16 22
cytokine secretion -0.013 0.042 -10000 0 -10000 0 0
SPHK1 -0.05 0.12 -10000 0 -0.34 33 33
PTK2 -0.033 0.13 0.38 1 -0.56 7 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.063 0.15 -10000 0 -0.42 25 25
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.059 0.15 0.34 9 -0.41 22 31
MAP2K2 -0.073 0.28 -10000 0 -0.84 60 60
MAP2K1 -0.072 0.28 -10000 0 -0.84 60 60
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.039 0.12 0.21 13 -0.34 26 39
MAP2K4 0.003 0.18 -10000 0 -0.82 23 23
Fc epsilon R1/FcgammaRIIB -0.065 0.18 -10000 0 -0.29 186 186
mol:Choline -0.075 0.14 0.33 9 -0.39 21 30
SHC/Grb2/SOS1 -0.013 0.13 0.25 1 -0.4 13 14
FYN 0.027 0.019 -10000 0 -0.39 1 1
DOK1 0.027 0.018 -10000 0 -0.39 1 1
PXN -0.031 0.12 0.36 1 -0.53 6 7
HCLS1 -0.044 0.11 0.18 1 -0.35 24 25
PRKCB -0.044 0.12 0.29 11 -0.34 16 27
FCGR2B 0.021 0.057 -10000 0 -0.46 7 7
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.034 0.12 0.24 2 -0.35 25 27
LCP2 0.024 0.032 -10000 0 -0.39 3 3
PLA2G4A -0.056 0.13 -10000 0 -0.35 43 43
RASA1 0.024 0.031 -10000 0 -0.46 2 2
mol:Phosphatidic acid -0.075 0.14 0.33 9 -0.39 21 30
IKK complex -0.012 0.092 0.2 34 -0.21 4 38
WIPF1 0.023 0.037 -10000 0 -0.39 4 4
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.022 -10000 0 -0.27 2 2
VLDLR 0.02 0.049 -10000 0 -0.46 5 5
CRKL 0.026 0.019 -10000 0 -0.39 1 1
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
ITGA3 0.012 0.079 -10000 0 -0.39 19 19
RELN/VLDLR/Fyn -0.021 0.13 -10000 0 -0.28 102 102
MAPK8IP1/MKK7/MAP3K11/JNK1 0.068 0.044 -10000 0 -0.24 3 3
AKT1 -0.023 0.081 -10000 0 -0.23 61 61
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 -0.001 0.073 -10000 0 -0.39 16 16
RELN/LRP8/DAB1 -0.026 0.13 -10000 0 -0.26 120 120
LRPAP1/LRP8 0.033 0.044 -10000 0 -0.27 10 10
RELN/LRP8/DAB1/Fyn -0.015 0.13 -10000 0 -0.25 100 100
DAB1/alpha3/beta1 Integrin -0.023 0.12 -10000 0 -0.4 6 6
long-term memory -0.059 0.16 -10000 0 -0.44 30 30
DAB1/LIS1 -0.009 0.13 -10000 0 -0.39 6 6
DAB1/CRLK/C3G -0.017 0.12 -10000 0 -0.39 7 7
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DAB1/NCK2 -0.008 0.13 -10000 0 -0.4 6 6
ARHGEF2 0.028 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.069 0.18 -10000 0 -0.43 105 105
CDK5R1 0.026 0.026 -10000 0 -0.39 2 2
RELN -0.073 0.2 -10000 0 -0.46 103 103
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
RELN/LRP8/Fyn -0.022 0.14 -10000 0 -0.28 111 111
GRIN2A/RELN/LRP8/DAB1/Fyn -0.058 0.17 -10000 0 -0.45 30 30
MAPK8 0.022 0.053 -10000 0 -0.46 6 6
RELN/VLDLR/DAB1 -0.026 0.12 -10000 0 -0.26 113 113
ITGB1 0.027 0.005 -10000 0 -10000 0 0
MAP1B -0.038 0.13 0.2 1 -0.27 88 89
RELN/LRP8 -0.022 0.14 -10000 0 -0.28 109 109
GRIN2B/RELN/LRP8/DAB1/Fyn -0.01 0.13 -10000 0 -0.42 6 6
PI3K 0.027 0.03 -10000 0 -0.33 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.06 -10000 0 -0.28 19 19
RAP1A -0.029 0.13 0.34 10 -0.39 6 16
PAFAH1B1 0.027 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.034 -10000 0 -0.41 3 3
CRLK/C3G 0.038 0.018 -10000 0 -0.27 1 1
GRIN2B -0.009 0.043 -10000 0 -0.39 5 5
NCK2 0.028 0.003 -10000 0 -10000 0 0
neuron differentiation -0.014 0.089 -10000 0 -0.34 8 8
neuron adhesion -0.034 0.12 0.34 9 -0.37 7 16
LRP8 0.02 0.057 -10000 0 -0.39 10 10
GSK3B -0.013 0.088 -10000 0 -0.32 8 8
RELN/VLDLR/DAB1/Fyn -0.016 0.12 -10000 0 -0.25 99 99
MAP3K11 0.027 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.09 -10000 0 -0.24 68 68
CDK5 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.19 0.22 0.8 1 -0.43 227 228
neuron migration -0.023 0.14 0.32 7 -0.37 6 13
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.015 0.09 -10000 0 -0.34 8 8
RELN/VLDLR -0.012 0.13 -10000 0 -0.26 107 107
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.026 0.019 -10000 0 -0.39 1 1
RAS family/GTP/Tiam1 -0.06 0.1 -10000 0 -0.24 56 56
NT3 (dimer)/TRKC -0.14 0.22 -10000 0 -0.39 215 215
NT3 (dimer)/TRKB -0.13 0.21 -10000 0 -0.35 227 227
SHC/Grb2/SOS1/GAB1/PI3K 0.021 0.022 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.004 0.12 -10000 0 -0.43 35 35
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DYNLT1 0.027 0.005 -10000 0 -10000 0 0
NTRK1 -0.007 0.12 -10000 0 -0.39 43 43
NTRK2 -0.097 0.21 -10000 0 -0.45 134 134
NTRK3 -0.098 0.21 -10000 0 -0.46 127 127
NT-4/5 (dimer)/TRKB -0.046 0.16 -10000 0 -0.28 151 151
neuron apoptosis 0.041 0.12 0.37 19 -10000 0 19
SHC 2-3/Grb2 -0.044 0.13 -10000 0 -0.4 19 19
SHC1 0.028 0.004 -10000 0 -10000 0 0
SHC2 -0.046 0.12 -10000 0 -0.38 27 27
SHC3 -0.041 0.12 -10000 0 -0.43 18 18
STAT3 (dimer) 0.025 0.058 -10000 0 -0.34 13 13
NT3 (dimer)/TRKA -0.075 0.17 -10000 0 -0.29 187 187
RIN/GDP -0.028 0.097 0.21 12 -0.24 11 23
GIPC1 0.028 0.004 -10000 0 -10000 0 0
KRAS 0.026 0.007 -10000 0 -10000 0 0
DNAJA3 -0.012 0.086 0.21 2 -0.28 11 13
RIN/GTP 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.011 0.057 -10000 0 -0.72 3 3
MAGED1 0.024 0.04 -10000 0 -0.42 4 4
PTPN11 0.028 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.025 0.034 -10000 0 -0.41 3 3
SHC/GRB2/SOS1 0.054 0.013 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.031 0.14 -10000 0 -0.25 140 140
TRKA/NEDD4-2 0.012 0.084 -10000 0 -0.27 41 41
ELMO1 0.025 0.029 -10000 0 -0.42 2 2
RhoG/GTP/ELMO1/DOCK1 0.033 0.025 -10000 0 -0.26 3 3
NGF -0.054 0.16 -10000 0 -0.39 98 98
HRAS 0.026 0.02 -10000 0 -0.4 1 1
DOCK1 0.027 0.022 -10000 0 -0.46 1 1
GAB2 0.022 0.038 -10000 0 -0.46 3 3
RIT2 -0.015 0.011 -10000 0 -10000 0 0
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
DNM1 0 0.1 -10000 0 -0.39 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.002 0.089 0.22 1 -0.28 13 14
mol:GDP -0.044 0.13 0.25 13 -0.34 15 28
NGF (dimer) -0.054 0.16 -10000 0 -0.39 98 98
RhoG/GDP 0.018 0.021 -10000 0 -0.3 2 2
RIT1/GDP -0.026 0.097 0.19 12 -0.24 10 22
TIAM1 0.021 0.053 -10000 0 -0.46 6 6
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
BDNF (dimer)/TRKB -0.051 0.16 -10000 0 -0.28 158 158
KIDINS220/CRKL/C3G 0.038 0.018 -10000 0 -0.27 1 1
SHC/RasGAP 0.038 0.02 -10000 0 -0.33 1 1
FRS2 family/SHP2 0.052 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.066 0.02 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.003 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.22 -10000 0 -0.46 144 144
RAP1/GDP -0.027 0.078 0.13 1 -0.21 5 6
KIDINS220/CRKL 0.026 0.019 -10000 0 -0.39 1 1
BDNF (dimer) -0.004 0.12 -10000 0 -0.43 35 35
ubiquitin-dependent protein catabolic process -0.025 0.13 -10000 0 -0.24 130 130
Schwann cell development -0.036 0.032 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.045 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.22 -10000 0 -0.48 128 128
ABL1 0.027 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.082 -10000 0 -0.39 7 7
STAT3 0.025 0.058 -10000 0 -0.34 13 13
axon guidance -0.16 0.2 -10000 0 -0.46 128 128
MAPK3 -0.047 0.12 -10000 0 -0.35 17 17
MAPK1 -0.045 0.11 -10000 0 -0.35 17 17
CDC42/GDP -0.023 0.1 0.2 16 -0.24 10 26
NTF3 -0.11 0.22 -10000 0 -0.46 144 144
NTF4 0.025 0.034 -10000 0 -0.41 3 3
NGF (dimer)/TRKA/FAIM -0.027 0.12 -10000 0 -0.24 122 122
PI3K 0.027 0.03 -10000 0 -0.33 2 2
FRS3 0.027 0.006 -10000 0 -10000 0 0
FAIM 0.023 0.011 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
RASGRF1 -0.047 0.12 0.21 2 -0.3 49 51
SOS1 0.028 0.004 -10000 0 -10000 0 0
MCF2L -0.14 0.2 -10000 0 -0.36 217 217
RGS19 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.07 -10000 0 -0.43 1 1
Rac1/GDP -0.024 0.095 0.19 11 -0.24 10 21
NGF (dimer)/TRKA/GRIT -0.036 0.12 -10000 0 -0.24 132 132
neuron projection morphogenesis 0.005 0.12 -10000 0 -0.7 6 6
NGF (dimer)/TRKA/NEDD4-2 -0.024 0.13 -10000 0 -0.24 130 130
MAP2K1 0.022 0.037 0.36 1 -10000 0 1
NGFR 0.005 0.098 -10000 0 -0.42 26 26
NGF (dimer)/TRKA/GIPC/GAIP -0.014 0.072 -10000 0 -0.29 1 1
RAS family/GTP/PI3K 0.017 0.02 -10000 0 -0.22 2 2
FRS2 family/SHP2/GRB2/SOS1 0.073 0.028 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
PRKCI 0.02 0.013 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.46 1 1
MAPKKK cascade -0.027 0.11 -10000 0 -0.46 18 18
RASA1 0.024 0.031 -10000 0 -0.46 2 2
TRKA/c-Abl 0.014 0.086 -10000 0 -0.27 42 42
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.033 0.15 -10000 0 -0.27 122 122
NGF (dimer)/TRKA/p62/Atypical PKCs -0.009 0.11 -10000 0 -0.32 12 12
MATK 0.017 0.065 -10000 0 -0.4 12 12
NEDD4L 0.025 0.009 -10000 0 -10000 0 0
RAS family/GDP -0.046 0.059 -10000 0 -0.21 5 5
NGF (dimer)/TRKA -0.027 0.075 0.23 2 -0.25 24 26
Rac1/GTP -0.069 0.082 -10000 0 -0.25 31 31
FRS2 family/SHP2/CRK family 0.069 0.033 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 0.006 0.089 -10000 0 -0.39 25 25
GNB1/GNG2 -0.042 0.067 -10000 0 -0.18 69 69
AKT1 -0.015 0.11 0.2 11 -0.27 22 33
EGF -0.067 0.19 -10000 0 -0.46 98 98
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.017 0.078 0.27 9 -10000 0 9
mol:Ca2+ -0.028 0.14 0.24 4 -0.3 70 74
LYN 0.013 0.074 0.27 7 -0.33 1 8
RhoA/GTP -0.013 0.057 0.11 1 -0.14 1 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.035 0.15 0.25 10 -0.34 71 81
GNG2 0.026 0.007 -10000 0 -10000 0 0
ARRB2 0.027 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.012 0.12 0.27 1 -0.54 18 19
G beta5/gamma2 -0.053 0.088 -10000 0 -0.24 62 62
PRKCH -0.034 0.15 0.29 11 -0.34 70 81
DNM1 0 0.1 -10000 0 -0.39 34 34
TXA2/TP beta/beta Arrestin3 0.006 0.041 -10000 0 -0.47 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.018 0.059 -10000 0 -0.42 9 9
G12 family/GTP -0.043 0.12 -10000 0 -0.3 66 66
ADRBK1 0.026 0.008 -10000 0 -10000 0 0
ADRBK2 0.026 0.019 -10000 0 -0.39 1 1
RhoA/GTP/ROCK1 0.032 0.014 -10000 0 -10000 0 0
mol:GDP 0.01 0.099 0.33 15 -0.21 2 17
mol:NADP 0.021 0.045 -10000 0 -0.39 6 6
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 0.001 0.11 -10000 0 -0.44 28 28
mol:IP3 -0.04 0.16 0.3 1 -0.37 71 72
cell morphogenesis 0.031 0.014 -10000 0 -10000 0 0
PLCB2 -0.063 0.21 0.33 1 -0.5 71 72
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.008 0.098 0.27 8 -0.36 3 11
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.014 0.075 0.27 9 -10000 0 9
RHOA 0.025 0.009 -10000 0 -10000 0 0
PTGIR 0.011 0.08 -10000 0 -0.39 20 20
PRKCB1 -0.041 0.16 0.28 1 -0.36 76 77
GNAQ 0.027 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.021 0.045 -10000 0 -0.39 6 6
TXA2/TXA2-R family -0.064 0.22 0.33 1 -0.51 77 78
LCK 0.013 0.082 0.27 9 -10000 0 9
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.014 0.072 -10000 0 -0.29 12 12
TXA2-R family/G12 family/GDP/G beta/gamma 0.014 0.089 0.26 1 -0.43 17 18
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.019 0.072 -10000 0 -0.28 12 12
MAPK14 -0.018 0.11 0.19 18 -0.23 64 82
TGM2/GTP -0.056 0.17 -10000 0 -0.41 67 67
MAPK11 -0.018 0.11 0.22 18 -0.23 60 78
ARHGEF1 -0.016 0.081 0.16 6 -0.18 29 35
GNAI2 0.024 0.009 -10000 0 -10000 0 0
JNK cascade -0.042 0.17 0.27 3 -0.37 77 80
RAB11/GDP 0.027 0.004 -10000 0 -10000 0 0
ICAM1 -0.028 0.13 0.22 4 -0.28 82 86
cAMP biosynthetic process -0.039 0.15 0.26 3 -0.34 69 72
Gq family/GTP/EBP50 -0.008 0.088 0.24 7 -0.36 9 16
actin cytoskeleton reorganization 0.031 0.014 -10000 0 -10000 0 0
SRC 0.015 0.075 0.27 9 -10000 0 9
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
EGF/EGFR 0.007 0.098 0.23 32 -0.28 3 35
VCAM1 -0.035 0.14 0.22 4 -0.3 89 93
TP beta/Gq family/GDP/G beta5/gamma2 -0.012 0.12 0.27 1 -0.54 18 19
platelet activation -0.023 0.14 0.27 16 -0.3 67 83
PGI2/IP 0.009 0.056 -10000 0 -0.27 20 20
PRKACA 0.011 0.039 -10000 0 -0.24 5 5
Gq family/GDP/G beta5/gamma2 -0.007 0.1 0.28 1 -0.45 18 19
TXA2/TP beta/beta Arrestin2 0.002 0.048 -10000 0 -0.32 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.066 -10000 0 -0.29 16 16
mol:DAG -0.047 0.18 0.31 1 -0.41 76 77
EGFR 0.021 0.044 -10000 0 -0.46 4 4
TXA2/TP alpha -0.057 0.2 0.35 1 -0.46 70 71
Gq family/GTP -0.024 0.089 0.28 2 -0.22 84 86
YES1 0.015 0.071 0.27 7 -10000 0 7
GNAI2/GTP 0.006 0.06 -10000 0 -0.26 11 11
PGD2/DP 0.014 0.042 -10000 0 -0.3 9 9
SLC9A3R1 0.024 0.043 -10000 0 -0.46 4 4
FYN 0.016 0.076 0.27 7 -0.29 1 8
mol:NO 0.021 0.045 -10000 0 -0.39 6 6
GNA15 0.025 0.031 -10000 0 -0.46 2 2
PGK/cGMP 0.015 0.074 -10000 0 -0.26 34 34
RhoA/GDP 0.024 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.021 0.091 -10000 0 -0.34 16 16
NOS3 0.021 0.045 -10000 0 -0.39 6 6
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.037 0.15 0.27 2 -0.34 72 74
PRKCB -0.039 0.16 0.28 5 -0.35 78 83
PRKCE -0.036 0.16 0.28 2 -0.35 72 74
PRKCD -0.045 0.16 0.27 1 -0.37 78 79
PRKCG -0.05 0.17 0.27 2 -0.38 83 85
muscle contraction -0.057 0.2 0.31 2 -0.47 77 79
PRKCZ -0.037 0.15 0.25 4 -0.34 73 77
ARR3 -0.012 0.017 -10000 0 -10000 0 0
TXA2/TP beta 0.018 0.072 -10000 0 -0.28 11 11
PRKCQ -0.042 0.16 0.28 1 -0.36 77 78
MAPKKK cascade -0.053 0.19 0.32 1 -0.44 74 75
SELE -0.042 0.16 0.22 4 -0.38 77 81
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.075 -10000 0 -0.29 12 12
ROCK1 0.026 0.007 -10000 0 -10000 0 0
GNA14 -0.041 0.17 -10000 0 -0.46 71 71
chemotaxis -0.077 0.25 -10000 0 -0.58 82 82
GNA12 0.025 0.02 -10000 0 -0.39 1 1
GNA13 0.028 0.003 -10000 0 -10000 0 0
GNA11 0.024 0.038 -10000 0 -0.46 3 3
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.026 0.02 -9999 0 -0.4 1 1
EGFR 0.021 0.044 -9999 0 -0.46 4 4
EGF/EGFR -0.009 0.11 -9999 0 -0.24 90 90
EGF/EGFR dimer/SHC/GRB2/SOS1 0.011 0.12 -9999 0 -0.24 85 85
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.032 -9999 0 -0.39 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.067 0.19 -9999 0 -0.46 98 98
EGF/EGFR dimer/SHC -0.012 0.13 -9999 0 -0.28 87 87
mol:GDP 0.006 0.12 -9999 0 -0.24 85 85
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.022 0.048 -9999 0 -0.46 5 5
GRB2/SOS1 0.04 0.008 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.1 -9999 0 -0.33 2 2
SHC1 0.028 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.006 0.11 -9999 0 -0.44 1 1
FRAP1 -0.046 0.084 -9999 0 -0.23 85 85
EGF/EGFR dimer -0.029 0.14 -9999 0 -0.33 88 88
SOS1 0.028 0.004 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.033 0.045 -9999 0 -0.31 8 8
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.005 0.012 -10000 0 -0.28 1 1
ADCY5 -0.063 0.11 -10000 0 -0.28 111 111
ADCY6 -0.01 0.04 -10000 0 -0.28 11 11
ADCY7 -0.005 0.012 -10000 0 -0.28 1 1
ADCY1 -0.013 0.044 -10000 0 -0.23 20 20
ADCY2 -0.087 0.13 -10000 0 -0.28 155 155
ADCY3 -0.005 0.012 -10000 0 -0.28 1 1
ADCY8 -0.013 0.034 -10000 0 -0.23 12 12
PRKCE 0.007 0.015 -10000 0 -0.33 1 1
ADCY9 -0.006 0.021 -10000 0 -0.28 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.008 0.11 0.23 32 -0.27 5 37
IL12-mediated signaling events

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.023 0.12 -10000 0 -0.35 23 23
TBX21 -0.081 0.32 -10000 0 -1.1 33 33
B2M 0.021 0.019 -10000 0 -10000 0 0
TYK2 0.019 0.037 -10000 0 -0.41 1 1
IL12RB1 -0.009 0.12 -10000 0 -0.42 37 37
GADD45B -0.036 0.23 -10000 0 -0.78 14 14
IL12RB2 -0.07 0.17 -10000 0 -0.39 113 113
GADD45G -0.038 0.24 -10000 0 -0.76 22 22
natural killer cell activation 0.002 0.019 0.04 4 -0.043 23 27
RELB 0.024 0.037 -10000 0 -0.39 4 4
RELA 0.027 0.006 -10000 0 -10000 0 0
IL18 0.013 0.075 -10000 0 -0.46 12 12
IL2RA -0.011 0.12 -10000 0 -0.39 47 47
IFNG -0.055 0.16 -10000 0 -0.39 97 97
STAT3 (dimer) -0.044 0.24 -10000 0 -0.7 33 33
HLA-DRB5 -0.002 0.007 -10000 0 -0.022 46 46
FASLG -0.086 0.34 0.55 1 -1 42 43
NF kappa B2 p52/RelB -0.055 0.28 -10000 0 -0.86 32 32
CD4 0.019 0.033 -10000 0 -0.43 2 2
SOCS1 0.003 0.097 -10000 0 -0.39 30 30
EntrezGene:6955 -0.004 0.012 -10000 0 -0.026 92 92
CD3D 0.002 0.079 -10000 0 -0.43 15 15
CD3E 0.005 0.073 -10000 0 -0.42 13 13
CD3G -0.009 0.11 -10000 0 -0.44 28 28
IL12Rbeta2/JAK2 -0.035 0.13 -10000 0 -0.28 102 102
CCL3 -0.072 0.29 -10000 0 -0.94 32 32
CCL4 -0.069 0.29 -10000 0 -0.93 31 31
HLA-A -0.002 0.008 -10000 0 -0.024 42 42
IL18/IL18R 0.037 0.095 -10000 0 -0.28 29 29
NOS2 -0.073 0.3 -10000 0 -0.93 32 32
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.12 -10000 0 -0.34 18 18
IL1R1 -0.063 0.28 0.52 2 -0.88 31 33
IL4 -0.004 0.035 -10000 0 -10000 0 0
JAK2 0.017 0.03 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.011 -10000 0 -0.024 93 93
TCR/CD3/MHC I/CD8 -0.063 0.23 -10000 0 -0.61 52 52
RAB7A -0.005 0.22 0.48 3 -0.66 13 16
lysosomal transport -0.002 0.22 0.44 6 -0.63 13 19
FOS -0.16 0.46 -10000 0 -1.2 76 76
STAT4 (dimer) -0.035 0.26 0.45 2 -0.78 26 28
STAT5A (dimer) -0.086 0.3 -10000 0 -0.87 42 42
GZMA -0.086 0.33 -10000 0 -1.1 35 35
GZMB -0.081 0.31 -10000 0 -0.98 31 31
HLX 0.024 0.037 -10000 0 -0.39 4 4
LCK -0.075 0.3 -10000 0 -0.93 35 35
TCR/CD3/MHC II/CD4 -0.027 0.13 -10000 0 -0.31 59 59
IL2/IL2R 0.024 0.1 -10000 0 -0.27 33 33
MAPK14 -0.034 0.24 -10000 0 -0.71 27 27
CCR5 -0.07 0.28 -10000 0 -0.89 28 28
IL1B -0.021 0.13 -10000 0 -0.4 52 52
STAT6 -0.003 0.1 -10000 0 -0.9 2 2
STAT4 0.016 0.066 -10000 0 -0.39 13 13
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.009 0.084 -10000 0 -0.39 22 22
NFKB1 0.027 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B -0.016 0.12 -10000 0 -0.39 44 44
CD8A -0.011 0.12 -10000 0 -0.43 39 39
CD8B -0.024 0.14 -10000 0 -0.42 54 54
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.023 0.12 0.35 23 -10000 0 23
IL2RB 0.021 0.053 -10000 0 -0.4 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.029 0.24 0.44 2 -0.71 26 28
IL2RG 0.014 0.076 -10000 0 -0.4 17 17
IL12 -0.011 0.1 -10000 0 -0.29 53 53
STAT5A 0.028 0.003 -10000 0 -10000 0 0
CD247 0 0.088 -10000 0 -0.41 21 21
IL2 -0.003 0.028 -10000 0 -0.39 1 1
SPHK2 0.027 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0 0.084 -10000 0 -0.46 15 15
IL12/IL12R/TYK2/JAK2 -0.075 0.31 -10000 0 -0.96 35 35
MAP2K3 -0.035 0.24 -10000 0 -0.69 26 26
RIPK2 0.025 0.009 -10000 0 -10000 0 0
MAP2K6 -0.041 0.25 -10000 0 -0.74 26 26
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.008 -10000 0 -0.025 52 52
IL18RAP 0.011 0.084 -10000 0 -0.42 18 18
IL12Rbeta1/TYK2 0.009 0.097 -10000 0 -0.3 38 38
EOMES -0.11 0.28 -10000 0 -0.78 52 52
STAT1 (dimer) -0.059 0.25 -10000 0 -0.73 35 35
T cell proliferation -0.008 0.2 0.44 1 -0.56 24 25
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.025 0.032 -10000 0 -0.44 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.047 0.21 -10000 0 -0.64 21 21
ATF2 -0.026 0.23 -10000 0 -0.67 26 26
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.029 0.089 -10000 0 -0.46 5 5
HDAC1 0.025 0.005 -10000 0 -10000 0 0
AES 0.027 0.005 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
DTX1 0.025 0.036 -10000 0 -0.44 3 3
LRP6/FZD1 0.034 0.03 -10000 0 -0.31 3 3
TLE1 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.019 0.095 -10000 0 -0.26 60 60
NCSTN 0.027 0.004 -10000 0 -10000 0 0
ADAM10 0.025 0.031 -10000 0 -0.46 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.018 0.12 -10000 0 -0.71 11 11
NICD/RBPSUH 0.029 0.086 -10000 0 -0.48 4 4
WIF1 -0.2 0.23 -10000 0 -0.46 221 221
NOTCH1 0.014 0.081 -10000 0 -0.43 12 12
PSENEN 0.027 0.005 -10000 0 -10000 0 0
KREMEN2 -0.12 0.2 -10000 0 -0.39 178 178
DKK1 -0.13 0.2 -10000 0 -0.39 191 191
beta catenin/beta TrCP1 -0.006 0.11 -10000 0 -0.39 17 17
APH1B 0.028 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 0.006 0.059 -10000 0 -0.4 5 5
CtBP/CBP/TCF1/TLE1/AES 0.016 0.036 -10000 0 -0.32 2 2
PSEN1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.034 0.16 -10000 0 -0.46 63 63
JUN 0.028 0.004 -10000 0 -10000 0 0
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 -0.018 0.11 -10000 0 -0.38 23 23
MAPK3 0.028 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.05 0.14 -10000 0 -0.23 180 180
HNF1A 0.019 0.057 -10000 0 -0.39 10 10
CTBP1 0.025 0.007 -10000 0 -10000 0 0
MYC 0.022 0.041 -10000 0 -0.77 1 1
NKD1 0.012 0.077 -10000 0 -0.39 18 18
FZD1 0.024 0.029 -10000 0 -0.42 2 2
NOTCH1 precursor/Deltex homolog 1 0.03 0.09 -10000 0 -0.58 3 3
apoptosis -0.019 0.094 -10000 0 -0.26 60 60
Delta 1/NOTCHprecursor 0.028 0.089 -10000 0 -0.48 4 4
DLL1 0.021 0.053 -10000 0 -0.46 6 6
PPARD 0.005 0.15 -10000 0 -0.83 15 15
Gamma Secretase 0.075 0.026 -10000 0 -10000 0 0
APC -0.009 0.098 -10000 0 -0.39 25 25
DVL1 -0.015 0.079 -10000 0 -0.35 18 18
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.13 0.18 -10000 0 -0.28 281 281
LRP6 0.025 0.023 -10000 0 -0.46 1 1
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.013 0.005 -10000 0 -10000 0 0
CCND1 -0.001 0.15 -10000 0 -0.99 9 9
WNT1 0.011 0.051 -10000 0 -0.39 7 7
Axin1/APC/beta catenin -0.004 0.12 0.26 4 -0.48 17 21
DKK2 0.015 0.074 -10000 0 -0.42 14 14
NOTCH1 precursor/DVL1 -0.004 0.11 -10000 0 -0.54 10 10
GSK3B 0.024 0.009 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.032 0.09 -10000 0 -0.59 3 3
PPP2R5D 0.005 0.079 0.23 4 -0.37 14 18
MAPK1 0.027 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.075 0.15 -10000 0 -0.26 190 190
RBPJ 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.042 0.16 -10000 0 -0.45 66 66
NFATC2 -0.027 0.19 -10000 0 -0.59 31 31
NFATC3 -0.003 0.068 -10000 0 -0.27 5 5
CD40LG -0.25 0.31 -10000 0 -0.84 61 61
ITCH 0.007 0.074 -10000 0 -10000 0 0
CBLB 0.004 0.076 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.31 -10000 0 -0.83 70 70
JUNB 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.094 -10000 0 -10000 0 0
T cell anergy -0.008 0.14 0.32 4 -0.41 33 37
TLE4 -0.017 0.14 -10000 0 -0.55 12 12
Jun/NFAT1-c-4/p21SNFT -0.092 0.23 -10000 0 -0.86 19 19
AP-1/NFAT1-c-4 -0.24 0.32 -10000 0 -0.93 47 47
IKZF1 -0.02 0.15 -10000 0 -0.62 15 15
T-helper 2 cell differentiation -0.067 0.21 -10000 0 -0.68 32 32
AP-1/NFAT1 -0.086 0.17 -10000 0 -0.48 42 42
CALM1 0.016 0.06 -10000 0 -10000 0 0
EGR2 -0.064 0.26 -10000 0 -1.3 17 17
EGR3 -0.056 0.23 -10000 0 -1.2 12 12
NFAT1/FOXP3 -0.054 0.21 -10000 0 -0.51 57 57
EGR1 0.004 0.1 -10000 0 -0.46 22 22
JUN -0.02 0.042 -10000 0 -10000 0 0
EGR4 -0.021 0.13 -10000 0 -0.4 57 57
mol:Ca2+ -0.009 0.054 -10000 0 -0.24 2 2
GBP3 -0.031 0.17 -10000 0 -0.6 28 28
FOSL1 0.018 0.059 -10000 0 -0.4 10 10
NFAT1-c-4/MAF/IRF4 -0.051 0.22 -10000 0 -0.84 20 20
DGKA -0.016 0.13 -10000 0 -0.5 13 13
CREM 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.25 -10000 0 -0.92 20 20
CTLA4 -0.081 0.22 -10000 0 -0.55 66 66
NFAT1-c-4 (dimer)/EGR1 -0.061 0.23 -10000 0 -0.93 18 18
NFAT1-c-4 (dimer)/EGR4 -0.073 0.23 -10000 0 -0.87 18 18
FOS -0.079 0.16 -10000 0 -0.48 63 63
IFNG -0.11 0.23 -10000 0 -0.71 31 31
T cell activation -0.091 0.16 -10000 0 -0.71 5 5
MAF 0.022 0.048 -10000 0 -0.46 5 5
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.04 0.15 0.68 14 -10000 0 14
TNF -0.095 0.22 -10000 0 -0.8 26 26
FASLG -0.12 0.35 -10000 0 -1.3 30 30
TBX21 -0.012 0.11 -10000 0 -0.44 29 29
BATF3 0.025 0.037 -10000 0 -0.39 4 4
PRKCQ 0.014 0.072 -10000 0 -0.45 11 11
PTPN1 -0.016 0.13 -10000 0 -0.5 13 13
NFAT1-c-4/ICER1 -0.052 0.21 -10000 0 -0.89 16 16
GATA3 0.011 0.083 -10000 0 -0.4 20 20
T-helper 1 cell differentiation -0.11 0.22 -10000 0 -0.7 32 32
IL2RA -0.18 0.28 -10000 0 -0.72 78 78
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.13 -10000 0 -0.51 11 11
E2F1 0.014 0.08 -10000 0 -0.38 20 20
PPARG -0.13 0.23 -10000 0 -0.46 166 166
SLC3A2 -0.016 0.13 -10000 0 -0.48 15 15
IRF4 -0.001 0.11 -10000 0 -0.4 33 33
PTGS2 -0.25 0.3 -10000 0 -0.84 64 64
CSF2 -0.31 0.32 -10000 0 -0.82 85 85
JunB/Fra1/NFAT1-c-4 -0.038 0.21 -10000 0 -0.85 16 16
IL4 -0.07 0.22 -10000 0 -0.73 29 29
IL5 -0.23 0.28 -10000 0 -0.83 45 45
IL2 -0.092 0.16 -10000 0 -0.75 4 4
IL3 -0.054 0.15 -10000 0 -0.69 22 22
RNF128 -0.032 0.18 -10000 0 -0.53 58 58
NFATC1 -0.04 0.15 -10000 0 -0.69 13 13
CDK4 0.039 0.12 0.63 3 -10000 0 3
PTPRK -0.015 0.13 -10000 0 -0.48 14 14
IL8 -0.26 0.3 -10000 0 -0.82 66 66
POU2F1 0.028 0.004 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.048 -10000 0 -0.2 18 18
RGS9BP 0.017 0.065 -10000 0 -0.46 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.01 0.03 -10000 0 -0.39 2 2
mol:Na + -0.007 0.09 -10000 0 -0.23 72 72
mol:ADP -0.022 0.062 -10000 0 -0.28 28 28
GNAT2 0.02 0.017 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.041 0.062 -10000 0 -0.26 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.009 -10000 0 -10000 0 0
GRK7 -0.003 0.093 -10000 0 -0.39 28 28
CNGB3 -0.04 0.14 -10000 0 -0.39 73 73
Cone Metarhodopsin II/X-Arrestin 0.014 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.13 0.18 39 -0.23 135 174
Cone PDE6 0.052 0.06 -10000 0 -0.25 9 9
Cone Metarhodopsin II 0.01 0.054 -10000 0 -0.21 28 28
Na + (4 Units) -0.038 0.12 -10000 0 -0.23 141 141
GNAT2/GDP 0.049 0.057 -10000 0 -0.24 11 11
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.039 0.18 22 -10000 0 22
Cone Transducin 0.039 0.051 -10000 0 -0.22 18 18
SLC24A2 -0.059 0.16 -10000 0 -0.39 97 97
GNB3/GNGT2 0.028 0.061 -10000 0 -0.28 18 18
GNB3 0.013 0.074 -10000 0 -0.4 16 16
GNAT2/GTP 0.019 0.004 -10000 0 -10000 0 0
CNGA3 0.009 0.028 -10000 0 -0.39 1 1
ARR3 -0.012 0.017 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.007 0.09 -10000 0 -0.23 72 72
mol:Pi 0.04 0.062 -10000 0 -0.26 20 20
Cone CNG Channel 0.012 0.085 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.059 0.16 -10000 0 -0.39 97 97
RGS9 0.017 0.065 -10000 0 -0.4 12 12
PDE6C -0.011 0.017 -10000 0 -10000 0 0
GNGT2 0.026 0.031 -10000 0 -0.46 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.011 0.016 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.021 -10000 0 -0.28 3 3
SNTA1 0.026 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.009 0.027 -10000 0 -0.25 6 6
MAPK12 -0.017 0.066 0.18 2 -0.24 38 40
CCND1 -0.001 0.061 -10000 0 -0.45 7 7
p38 gamma/SNTA1 0.006 0.074 0.23 9 -0.25 24 33
MAP2K3 0.027 0.006 -10000 0 -10000 0 0
PKN1 0.026 0.026 -10000 0 -0.39 2 2
G2/M transition checkpoint -0.016 0.065 0.18 2 -0.24 38 40
MAP2K6 -0.01 0.059 -10000 0 -0.27 25 25
MAPT -0.14 0.16 0.2 2 -0.3 236 238
MAPK13 0.012 0.027 -10000 0 -0.33 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.011 -10000 0 -0.16 2 2
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.049 0.17 -10000 0 -0.61 23 23
MKNK1 0.028 0.003 -10000 0 -10000 0 0
MAPK14 -0.013 0.095 -10000 0 -0.3 22 22
ATF2/c-Jun -0.009 0.069 -10000 0 -0.34 4 4
MAPK11 -0.016 0.097 -10000 0 -0.3 23 23
MITF -0.029 0.12 -10000 0 -0.34 37 37
MAPKAPK5 -0.019 0.1 -10000 0 -0.33 23 23
KRT8 -0.067 0.15 -10000 0 -0.34 88 88
MAPKAPK3 0.024 0.009 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.022 0.14 -10000 0 -0.42 24 24
CEBPB -0.02 0.1 -10000 0 -0.34 23 23
SLC9A1 -0.021 0.1 -10000 0 -0.33 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.018 0.1 0.24 1 -0.36 15 16
p38alpha-beta/MNK1 0 0.12 -10000 0 -0.35 22 22
JUN -0.006 0.072 -10000 0 -0.33 4 4
PPARGC1A -0.12 0.19 -10000 0 -0.35 176 176
USF1 -0.018 0.1 -10000 0 -0.33 23 23
RAB5/GDP/GDI1 -0.004 0.074 -10000 0 -0.28 12 12
NOS2 -0.057 0.19 -10000 0 -0.62 28 28
DDIT3 -0.023 0.1 -10000 0 -0.33 27 27
RAB5A 0.025 0.009 -10000 0 -10000 0 0
HSPB1 -0.014 0.09 0.29 11 -0.31 14 25
p38alpha-beta/HBP1 0 0.12 -10000 0 -0.35 22 22
CREB1 -0.016 0.097 -10000 0 -0.36 14 14
RAB5/GDP 0.018 0.007 -10000 0 -10000 0 0
EIF4E -0.016 0.093 0.24 1 -0.34 13 14
RPS6KA4 -0.02 0.1 -10000 0 -0.32 24 24
PLA2G4A -0.03 0.11 -10000 0 -0.36 18 18
GDI1 -0.017 0.097 -10000 0 -0.38 13 13
TP53 -0.032 0.11 -10000 0 -0.41 24 24
RPS6KA5 -0.023 0.1 -10000 0 -0.31 25 25
ESR1 -0.031 0.12 -10000 0 -0.35 33 33
HBP1 0.026 0.007 -10000 0 -10000 0 0
MEF2C -0.026 0.11 -10000 0 -0.38 20 20
MEF2A -0.019 0.1 -10000 0 -0.38 13 13
EIF4EBP1 -0.016 0.096 -10000 0 -0.33 21 21
KRT19 -0.13 0.17 -10000 0 -0.32 177 177
ELK4 -0.018 0.1 -10000 0 -0.37 14 14
ATF6 -0.018 0.1 -10000 0 -0.33 23 23
ATF1 -0.016 0.096 -10000 0 -0.37 12 12
p38alpha-beta/MAPKAPK2 0.001 0.12 -10000 0 -0.35 22 22
p38alpha-beta/MAPKAPK3 -0.002 0.11 -10000 0 -0.35 22 22
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.004 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.009 0.085 -10000 0 -0.3 3 3
NFATC4 -0.024 0.071 0.27 6 -0.34 3 9
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.017 0.075 -10000 0 -0.26 4 4
JUN -0.008 0.075 0.2 7 -0.38 3 10
HRAS 0.025 0.02 -10000 0 -0.4 1 1
DOCK7 -0.028 0.073 0.29 2 -10000 0 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.005 0.093 -10000 0 -0.27 11 11
AKT1 0.005 0.006 -10000 0 -10000 0 0
BAD -0.004 0.004 -10000 0 -10000 0 0
MAPK10 -0.017 0.066 0.2 12 -0.25 3 15
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.017 0.08 -10000 0 -0.28 3 3
RAF1 -0.022 0.094 0.26 6 -0.32 3 9
ErbB2/ErbB3/neuregulin 2 -0.13 0.15 -10000 0 -0.27 265 265
STAT3 0.015 0.12 -10000 0 -0.81 10 10
cell migration -0.009 0.066 0.23 12 -0.22 1 13
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.18 0.29 0.32 1 -0.6 136 137
FOS -0.12 0.22 0.31 7 -0.39 173 180
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.075 -10000 0 -0.26 4 4
MAPK3 -0.14 0.24 0.3 2 -0.5 124 126
MAPK1 -0.14 0.24 0.3 2 -0.5 123 125
JAK2 -0.027 0.068 -10000 0 -10000 0 0
NF2 0.008 0.041 -10000 0 -0.63 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.062 -10000 0 -0.26 11 11
NRG1 -0.036 0.15 -10000 0 -0.39 74 74
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
MAPK8 -0.01 0.078 0.22 6 -0.29 11 17
MAPK9 -0.011 0.057 0.2 12 -10000 0 12
ERBB2 -0.019 0.007 -10000 0 -10000 0 0
ERBB3 0.019 0.061 -10000 0 -0.46 8 8
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
apoptosis 0.009 0.032 -10000 0 -0.17 13 13
STAT3 (dimer) 0.016 0.12 -10000 0 -0.8 10 10
RNF41 -0.007 0.007 -10000 0 -10000 0 0
FRAP1 -0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.021 0.05 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0 0.02 -10000 0 -10000 0 0
CHRNA1 -0.18 0.29 0.28 2 -0.62 134 136
myelination -0.014 0.086 0.3 15 -0.31 3 18
PPP3CB -0.026 0.07 0.28 2 -10000 0 2
KRAS 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.069 -10000 0 -10000 0 0
NRG2 -0.24 0.24 -10000 0 -0.46 274 274
mol:GDP -0.006 0.062 -10000 0 -0.26 11 11
SOS1 0.027 0.004 -10000 0 -10000 0 0
MAP2K2 -0.038 0.11 0.26 6 -0.36 2 8
SRC 0.026 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.027 0.074 0.29 2 -10000 0 2
MAP2K1 -0.12 0.23 -10000 0 -0.62 35 35
heart morphogenesis -0.017 0.075 -10000 0 -0.26 4 4
RAS family/GDP 0.009 0.081 -10000 0 -0.34 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.011 0.043 -10000 0 -0.66 2 2
CHRNE 0.004 0.022 0.09 1 -0.14 5 6
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.005 0.006 -10000 0 -10000 0 0
nervous system development -0.017 0.075 -10000 0 -0.26 4 4
CDC42 0.027 0.005 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.026 0.022 -10000 0 -0.46 1 1
EPHB2 -0.083 0.18 -10000 0 -0.39 137 137
EFNB1 -0.004 0.069 -10000 0 -0.27 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.024 0.12 -10000 0 -0.36 14 14
Ephrin B2/EPHB1-2 -0.025 0.11 -10000 0 -0.21 131 131
neuron projection morphogenesis -0.033 0.11 -10000 0 -0.35 14 14
Ephrin B1/EPHB1-2/Tiam1 -0.031 0.12 -10000 0 -0.33 23 23
DNM1 0 0.1 -10000 0 -0.38 34 34
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.018 0.11 0.42 1 -0.44 29 30
YES1 -0.025 0.16 -10000 0 -0.69 29 29
Ephrin B1/EPHB1-2/NCK2 -0.027 0.12 -10000 0 -0.33 19 19
PI3K 0.007 0.11 -10000 0 -0.44 23 23
mol:GDP -0.032 0.12 -10000 0 -0.33 23 23
ITGA2B -0.013 0.12 -10000 0 -0.39 51 51
endothelial cell proliferation 0.033 0.018 -10000 0 -0.28 1 1
FYN -0.025 0.16 -10000 0 -0.69 29 29
MAP3K7 -0.021 0.11 0.24 1 -0.48 27 28
FGR -0.021 0.16 -10000 0 -0.67 30 30
TIAM1 0.021 0.053 -10000 0 -0.46 6 6
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
RGS3 0.027 0.005 -10000 0 -10000 0 0
cell adhesion -0.019 0.12 -10000 0 -0.45 27 27
LYN -0.024 0.16 -10000 0 -0.68 29 29
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.15 -10000 0 -0.62 30 30
Ephrin B1/EPHB1-2 -0.02 0.12 -10000 0 -0.53 25 25
SRC -0.021 0.16 -10000 0 -0.66 30 30
ITGB3 0.01 0.087 -10000 0 -0.41 21 21
EPHB1 0.004 0.09 -10000 0 -0.42 22 22
EPHB4 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.018 -10000 0 -0.28 1 1
alphaIIb/beta3 Integrin -0.003 0.11 -10000 0 -0.29 69 69
BLK -0.031 0.16 -10000 0 -0.68 29 29
HCK -0.02 0.16 -10000 0 -0.67 29 29
regulation of stress fiber formation 0.027 0.12 0.33 19 -10000 0 19
MAPK8 -0.018 0.11 -10000 0 -0.45 27 27
Ephrin B1/EPHB1-2/RGS3 -0.027 0.12 -10000 0 -0.34 18 18
endothelial cell migration -0.004 0.1 0.3 2 -0.4 24 26
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTPN13 0.016 0.079 -10000 0 -0.57 9 9
regulation of focal adhesion formation 0.027 0.12 0.33 19 -10000 0 19
chemotaxis 0.028 0.12 0.33 18 -10000 0 18
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.028 0.11 -10000 0 -0.36 14 14
angiogenesis -0.023 0.12 -10000 0 -0.52 28 28
LCK -0.022 0.16 -10000 0 -0.67 30 30
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.021 0.08 -10000 0 -0.26 13 13
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.079 0.28 2 -0.34 1 3
AP1 -0.027 0.11 -10000 0 -0.38 14 14
mol:PIP3 -0.012 0.068 -10000 0 -0.42 5 5
AKT1 0.014 0.098 0.27 11 -0.32 2 13
PTK2B -0.014 0.079 0.19 2 -0.3 15 17
RHOA -0.022 0.091 0.19 2 -0.3 39 41
PIK3CB 0.023 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.06 0.22 1 -0.32 2 3
MAGI3 0.026 0.022 -10000 0 -0.46 1 1
RELA 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.011 0.081 -10000 0 -0.28 26 26
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.092 0.14 0.26 5 -0.33 45 50
NF kappa B1 p50/RelA -0.014 0.085 -10000 0 -0.37 5 5
endothelial cell migration -0.032 0.13 -10000 0 -0.35 70 70
ADCY4 -0.006 0.081 -10000 0 -0.35 14 14
ADCY5 -0.041 0.11 -10000 0 -0.4 20 20
ADCY6 -0.009 0.09 -10000 0 -0.4 15 15
ADCY7 -0.004 0.078 -10000 0 -0.36 12 12
ADCY1 -0.008 0.082 0.22 2 -0.36 13 15
ADCY2 -0.058 0.11 0.22 1 -0.38 23 24
ADCY3 -0.006 0.08 -10000 0 -0.36 13 13
ADCY8 -0.012 0.078 -10000 0 -0.35 13 13
ADCY9 -0.006 0.082 -10000 0 -0.37 13 13
GSK3B 0.006 0.097 0.21 41 -0.31 10 51
arachidonic acid secretion -0.004 0.082 -10000 0 -0.38 12 12
GNG2 0.026 0.007 -10000 0 -10000 0 0
TRIP6 0.016 0.017 -10000 0 -10000 0 0
GNAO1 -0.011 0.077 -10000 0 -0.28 16 16
HRAS 0.026 0.02 -10000 0 -0.4 1 1
NFKBIA -0.007 0.079 0.28 3 -0.34 4 7
GAB1 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.001 0.2 -10000 0 -0.81 29 29
JUN 0.027 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.024 0.038 -10000 0 -0.22 1 1
TIAM1 -0.023 0.23 -10000 0 -0.95 29 29
PIK3R1 0.024 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.011 0.059 0.2 3 -0.32 2 5
PLCB3 0.01 0.034 0.19 5 -0.2 1 6
FOS -0.034 0.16 -10000 0 -0.46 63 63
positive regulation of mitosis -0.004 0.082 -10000 0 -0.38 12 12
LPA/LPA1-2-3 0.015 0.096 -10000 0 -0.28 25 25
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.027 0.006 -10000 0 -10000 0 0
stress fiber formation 0.004 0.074 0.23 2 -0.32 5 7
GNAZ -0.018 0.09 -10000 0 -0.28 32 32
EGFR/PI3K-beta/Gab1 -0.005 0.074 -10000 0 -0.44 5 5
positive regulation of dendritic cell cytokine production 0.013 0.095 -10000 0 -0.28 25 25
LPA/LPA2/MAGI-3 0.023 0.039 -10000 0 -0.28 1 1
ARHGEF1 0.007 0.088 0.36 3 -0.27 7 10
GNAI2 -0.012 0.077 -10000 0 -0.28 16 16
GNAI3 -0.011 0.078 -10000 0 -0.29 16 16
GNAI1 -0.011 0.079 -10000 0 -0.29 17 17
LPA/LPA3 0.001 0.063 -10000 0 -0.33 12 12
LPA/LPA2 0.009 0.036 -10000 0 -0.13 4 4
LPA/LPA1 -0.011 0.094 -10000 0 -0.23 75 75
HB-EGF/EGFR -0.14 0.12 -10000 0 -0.23 315 315
HBEGF -0.18 0.13 -10000 0 -0.27 353 353
mol:DAG -0.011 0.059 0.2 3 -0.32 2 5
cAMP biosynthetic process -0.015 0.084 0.22 2 -0.36 13 15
NFKB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
LYN 0.001 0.083 0.28 6 -0.32 5 11
GNAQ 0.004 0.046 -10000 0 -0.25 11 11
LPAR2 0.027 0.003 -10000 0 -10000 0 0
LPAR3 0.016 0.074 -10000 0 -0.46 12 12
LPAR1 -0.001 0.089 -10000 0 -0.4 16 16
IL8 -0.11 0.13 0.36 2 -0.4 32 34
PTK2 -0.011 0.078 -10000 0 -0.34 7 7
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.011 0.082 -10000 0 -0.28 26 26
EGFR 0.02 0.044 -10000 0 -0.46 4 4
PLCG1 -0.012 0.062 0.16 1 -0.26 15 16
PLD2 -0.009 0.083 -10000 0 -0.34 8 8
G12/G13 0.02 0.083 -10000 0 -0.27 15 15
PI3K-beta -0.015 0.075 -10000 0 -0.32 4 4
cell migration 0.008 0.071 -10000 0 -0.24 24 24
SLC9A3R2 0.027 0.019 -10000 0 -0.39 1 1
PXN 0.003 0.075 0.23 2 -0.33 5 7
HRAS/GTP -0.006 0.081 -10000 0 -0.38 12 12
RAC1 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.26 0.19 -10000 0 -0.39 355 355
PRKCE 0.026 0.022 -10000 0 -0.46 1 1
PRKCD -0.01 0.055 -10000 0 -0.34 1 1
Gi(beta/gamma) -0.001 0.077 -10000 0 -0.34 11 11
mol:LPA -0.014 0.044 -10000 0 -0.2 6 6
TRIP6/p130 Cas/FAK1/Paxillin 0.014 0.08 -10000 0 -0.39 3 3
MAPKKK cascade -0.004 0.082 -10000 0 -0.38 12 12
contractile ring contraction involved in cytokinesis -0.028 0.1 0.19 2 -0.3 44 46
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.033 0.1 -10000 0 -0.26 81 81
GNA15 0.002 0.052 -10000 0 -0.28 12 12
GNA12 0.025 0.02 -10000 0 -0.39 1 1
GNA13 0.028 0.003 -10000 0 -10000 0 0
MAPT -0.094 0.14 0.26 5 -0.34 45 50
GNA11 0.002 0.051 -10000 0 -0.26 14 14
Rac1/GTP -0.002 0.21 -10000 0 -0.86 29 29
MMP2 -0.032 0.13 -10000 0 -0.35 70 70
Arf6 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
CENTA1/KIF3B 0.029 0.034 -10000 0 -0.28 5 5
ARNO/beta Arrestin1-2 0.01 0.12 -10000 0 -0.76 9 9
EGFR 0.02 0.044 -10000 0 -0.46 4 4
EPHA2 0.021 0.053 -10000 0 -0.46 6 6
USP6 0.026 0.019 -10000 0 -0.39 1 1
IQSEC1 0.025 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.029 0.14 -10000 0 -0.34 88 88
ARRB2 0.01 0.003 -10000 0 -10000 0 0
mol:GTP 0.035 0.051 0.14 27 -0.16 2 29
ARRB1 0.024 0.032 -10000 0 -0.46 2 2
FBXO8 0.027 0.006 -10000 0 -10000 0 0
TSHR 0.01 0.064 -10000 0 -0.39 12 12
EGF -0.067 0.19 -10000 0 -0.46 98 98
somatostatin receptor activity 0 0 0.001 26 -0.001 19 45
ARAP2 0.022 0.048 -10000 0 -0.46 5 5
mol:GDP -0.006 0.094 0.18 12 -0.29 24 36
mol:PI-3-4-5-P3 0 0 0.001 17 -0.001 13 30
ITGA2B -0.013 0.12 -10000 0 -0.39 51 51
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.041 -10000 0 -0.26 4 4
ADAP1 0.025 0.023 -10000 0 -0.46 1 1
KIF13B 0.022 0.044 -10000 0 -0.46 4 4
HGF/MET 0.02 0.079 -10000 0 -0.31 28 28
PXN 0.028 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.11 0.21 22 -0.29 19 41
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.016 0.12 -10000 0 -0.28 88 88
ADRB2 -0.009 0.13 -10000 0 -0.46 37 37
receptor agonist activity 0 0 0 23 0 11 34
actin filament binding 0 0 0 25 -0.001 18 43
SRC 0.026 0.007 -10000 0 -10000 0 0
ITGB3 0.01 0.088 -10000 0 -0.41 21 21
GNAQ 0.027 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 47 -0.001 15 62
ARF6/GDP 0.034 0.13 0.23 39 -0.47 15 54
ARF6/GDP/GULP/ACAP1 -0.044 0.16 0.25 1 -0.36 47 48
alphaIIb/beta3 Integrin/paxillin/GIT1 0.032 0.1 -10000 0 -0.3 10 10
ACAP1 0.017 0.063 -10000 0 -0.39 12 12
ACAP2 0.02 0.013 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.016 0.015 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
HGF 0.006 0.095 -10000 0 -0.44 22 22
CYTH3 0.007 0.002 -10000 0 -10000 0 0
CYTH2 0.003 0.13 -10000 0 -0.98 9 9
NCK1 0.023 0.011 -10000 0 -10000 0 0
fibronectin binding 0 0 0 18 0 17 35
endosomal lumen acidification 0 0 0 42 0 19 61
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.11 0.22 -10000 0 -0.46 145 145
GNAQ/ARNO 0.019 0.12 -10000 0 -0.91 9 9
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 13 0 1 14
MET 0.022 0.048 -10000 0 -0.41 6 6
GNA14 -0.041 0.17 -10000 0 -0.46 71 71
GNA15 0.025 0.031 -10000 0 -0.46 2 2
GIT1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 33 -0.001 17 50
GNA11 0.024 0.038 -10000 0 -0.46 3 3
LHCGR -0.011 0.016 -10000 0 -10000 0 0
AGTR1 -0.022 0.13 -10000 0 -0.46 41 41
desensitization of G-protein coupled receptor protein signaling pathway 0.016 0.015 -10000 0 -10000 0 0
IPCEF1/ARNO -0.015 0.14 -10000 0 -0.8 9 9
alphaIIb/beta3 Integrin -0.003 0.11 -10000 0 -0.29 69 69
Signaling events mediated by PTP1B

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
PDGFRB -0.042 0.15 -10000 0 -0.39 85 85
Jak2/Leptin Receptor -0.06 0.17 -10000 0 -0.47 49 49
PTP1B/AKT1 -0.021 0.099 0.19 1 -0.32 22 23
FYN 0.027 0.019 -10000 0 -0.39 1 1
p210 bcr-abl/PTP1B -0.031 0.1 0.23 3 -0.31 34 37
EGFR 0.012 0.047 -10000 0 -0.47 4 4
EGF/EGFR -0.051 0.13 -10000 0 -0.3 85 85
CSF1 0.022 0.053 -10000 0 -0.46 6 6
AKT1 0.026 0.007 -10000 0 -10000 0 0
INSR 0.027 0.022 -10000 0 -0.46 1 1
PTP1B/N-cadherin -0.043 0.12 0.22 2 -0.33 33 35
Insulin Receptor/Insulin -0.008 0.099 -10000 0 -0.36 10 10
HCK 0.024 0.029 -10000 0 -0.42 2 2
CRK 0.027 0.006 -10000 0 -10000 0 0
TYK2 -0.029 0.099 0.22 2 -0.32 24 26
EGF -0.067 0.19 -10000 0 -0.47 98 98
YES1 0.025 0.009 -10000 0 -10000 0 0
CAV1 -0.037 0.12 0.21 12 -0.34 33 45
TXN 0.026 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.012 0.11 0.24 2 -0.36 15 17
cell migration 0.031 0.1 0.31 34 -0.23 3 37
STAT3 0.027 0.003 -10000 0 -10000 0 0
PRLR -0.062 0.18 -10000 0 -0.46 90 90
ITGA2B -0.014 0.12 -10000 0 -0.39 51 51
CSF1R 0.025 0.031 -10000 0 -0.46 2 2
Prolactin Receptor/Prolactin -0.035 0.14 -10000 0 -0.34 91 91
FGR 0.027 0.019 -10000 0 -0.39 1 1
PTP1B/p130 Cas -0.02 0.1 0.23 2 -0.32 23 25
Crk/p130 Cas -0.009 0.1 0.24 2 -0.36 13 15
DOK1 -0.039 0.11 0.24 3 -0.34 27 30
JAK2 -0.071 0.18 -10000 0 -0.47 57 57
Jak2/Leptin Receptor/Leptin -0.047 0.14 0.23 1 -0.44 20 21
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
PTPN1 -0.031 0.1 0.23 3 -0.31 34 37
LYN 0.024 0.02 -10000 0 -0.39 1 1
CDH2 -0.03 0.14 -10000 0 -0.4 66 66
SRC 0.002 0.11 -10000 0 -0.56 15 15
ITGB3 0.009 0.088 -10000 0 -0.41 21 21
CAT1/PTP1B -0.086 0.15 0.21 9 -0.4 44 53
CAPN1 0.026 0.007 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.011 0.083 -10000 0 -0.35 5 5
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.038 0.13 -10000 0 -0.39 20 20
negative regulation of transcription -0.07 0.17 -10000 0 -0.46 57 57
FCGR2A 0.007 0.091 -10000 0 -0.39 26 26
FER 0.023 0.032 -10000 0 -0.47 2 2
alphaIIb/beta3 Integrin -0.004 0.11 -10000 0 -0.29 69 69
BLK -0.035 0.14 -10000 0 -0.4 70 70
Insulin Receptor/Insulin/Shc 0.045 0.027 -10000 0 -0.25 3 3
RHOA 0.024 0.009 -10000 0 -10000 0 0
LEPR 0.026 0.031 -10000 0 -0.46 2 2
BCAR1 0.027 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.075 0.14 0.24 3 -0.43 33 36
PRL -0.002 0.044 -10000 0 -0.39 5 5
SOCS3 0.025 0.1 -10000 0 -1.1 4 4
SPRY2 0.02 0.058 -10000 0 -0.47 7 7
Insulin Receptor/Insulin/IRS1 0.042 0.037 -10000 0 -0.27 6 6
CSF1/CSF1R -0.013 0.11 0.24 2 -0.33 22 24
Ras protein signal transduction 0.013 0.075 0.56 8 -10000 0 8
IRS1 0.024 0.038 -10000 0 -0.46 3 3
INS -0.001 0.031 -10000 0 -0.39 2 2
LEP -0.049 0.16 -10000 0 -0.43 75 75
STAT5B -0.039 0.12 0.21 3 -0.37 37 40
STAT5A -0.039 0.12 0.21 3 -0.37 36 39
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.049 0.13 0.22 3 -0.3 50 53
CSN2 -0.013 0.094 -10000 0 -0.5 6 6
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
LAT 0.002 0.08 -10000 0 -0.56 6 6
YBX1 0.033 0.006 -10000 0 -10000 0 0
LCK 0.018 0.063 -10000 0 -0.39 12 12
SHC1 0.028 0.004 -10000 0 -10000 0 0
NOX4 -0.045 0.16 -10000 0 -0.39 87 87
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.04 -10000 0 -0.29 7 7
alphaV beta3 Integrin 0.029 0.086 -10000 0 -0.27 37 37
PTK2 0.002 0.11 0.33 8 -0.5 4 12
IGF1R 0.027 0.005 -10000 0 -10000 0 0
PI4KB 0.027 0.004 -10000 0 -10000 0 0
MFGE8 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
CDKN1B 0.005 0.051 -10000 0 -0.23 4 4
VEGFA 0.022 0.045 -10000 0 -0.39 6 6
ILK 0.005 0.055 -10000 0 -0.35 2 2
ROCK1 0.026 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.048 -10000 0 -0.41 1 1
PTK2B 0.009 0.064 0.36 1 -0.28 7 8
alphaV/beta3 Integrin/JAM-A 0.02 0.099 -10000 0 -0.29 21 21
CBL 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.034 0.066 -10000 0 -0.25 25 25
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.014 0.12 -10000 0 -0.26 79 79
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.011 0.048 -10000 0 -0.32 3 3
alphaV/beta3 Integrin/Syndecan-1 0.039 0.064 -10000 0 -0.25 23 23
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.1 0.16 -10000 0 -0.42 47 47
PI4 Kinase 0.039 0.011 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.11 0.15 -10000 0 -0.24 278 278
RPS6KB1 -0.12 0.13 0.22 1 -0.4 47 48
TLN1 0.024 0.01 -10000 0 -10000 0 0
MAPK3 -0.058 0.13 -10000 0 -0.49 32 32
GPR124 0.022 0.033 -10000 0 -0.39 3 3
MAPK1 -0.057 0.13 -10000 0 -0.49 31 31
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
alphaV/beta3 Integrin/Tumstatin 0.004 0.11 -10000 0 -0.26 75 75
cell adhesion 0.028 0.06 -10000 0 -0.29 7 7
ANGPTL3 -0.003 0.037 -10000 0 -0.39 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.039 -10000 0 -0.24 7 7
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
TGFBR2 0.022 0.032 -10000 0 -0.46 2 2
ITGB3 0.01 0.087 -10000 0 -0.41 21 21
IGF1 -0.053 0.18 -10000 0 -0.46 85 85
RAC1 0.026 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.033 0.066 -10000 0 -0.25 23 23
apoptosis 0.025 0.026 -10000 0 -0.39 2 2
CD47 0.025 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.034 0.065 -10000 0 -0.25 23 23
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.003 0.12 -10000 0 -0.27 85 85
CSF1 0.022 0.053 -10000 0 -0.46 6 6
PIK3C2A 0.006 0.055 -10000 0 -0.35 2 2
PI4 Kinase/Pyk2 0.006 0.084 -10000 0 -0.42 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.07 -10000 0 -0.23 24 24
FAK1/Vinculin 0.014 0.098 0.3 9 -0.39 4 13
alphaV beta3/Integrin/ppsTEM5 0.034 0.067 -10000 0 -0.26 23 23
RHOA 0.025 0.009 -10000 0 -10000 0 0
VTN 0.001 0.1 -10000 0 -0.39 32 32
BCAR1 0.027 0.006 -10000 0 -10000 0 0
FGF2 0.011 0.085 -10000 0 -0.44 17 17
F11R 0.003 0.062 -10000 0 -0.32 18 18
alphaV/beta3 Integrin/Lactadherin 0.039 0.064 -10000 0 -0.25 23 23
alphaV/beta3 Integrin/TGFBR2 0.032 0.067 -10000 0 -0.25 25 25
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.054 0.045 -10000 0 -0.26 5 5
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.032 0.059 -10000 0 -0.22 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.15 0.2 -10000 0 -0.39 222 222
alphaV/beta3 Integrin/Pyk2 0.033 0.065 -10000 0 -0.28 7 7
SDC1 0.028 0.003 -10000 0 -10000 0 0
VAV3 0 0.077 -10000 0 -0.46 3 3
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.024 0.038 -10000 0 -0.46 3 3
FAK1/Paxillin 0.013 0.099 0.31 8 -0.39 4 12
cell migration 0.01 0.092 0.27 12 -0.36 4 16
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
PI3K 0.014 0.095 -10000 0 -0.4 7 7
SPP1 -0.2 0.21 -10000 0 -0.39 279 279
KDR 0.025 0.031 -10000 0 -0.46 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.025 0.027 -10000 0 -0.39 2 2
COL4A3 -0.025 0.14 -10000 0 -0.41 59 59
angiogenesis -0.051 0.14 -10000 0 -0.5 32 32
Rac1/GTP 0.014 0.073 -10000 0 -0.43 3 3
EDIL3 -0.038 0.16 -10000 0 -0.42 73 73
cell proliferation 0.032 0.067 -10000 0 -0.25 25 25
Regulation of Androgen receptor activity

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
HDAC1 0.01 0.011 -10000 0 -10000 0 0
SMARCC1 0.004 0.035 -10000 0 -0.6 1 1
REL 0.022 0.065 -10000 0 -0.46 9 9
HDAC7 -0.091 0.14 0.23 2 -0.47 26 28
JUN 0.026 0.005 -10000 0 -10000 0 0
EP300 0.026 0.022 -10000 0 -0.46 1 1
KAT2B 0.006 0.092 -10000 0 -0.46 19 19
KAT5 0.027 0.007 -10000 0 -10000 0 0
MAPK14 -0.023 0.079 -10000 0 -0.35 25 25
FOXO1 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.085 0.16 -10000 0 -0.47 29 29
MAP2K6 -0.017 0.11 -10000 0 -0.48 25 25
BRM/BAF57 0.023 0.034 -10000 0 -0.33 1 1
MAP2K4 0.006 0.026 -10000 0 -10000 0 0
SMARCA2 0.015 0.029 -10000 0 -0.46 1 1
PDE9A -0.079 0.22 -10000 0 -0.96 22 22
NCOA2 -0.009 0.12 -10000 0 -0.46 36 36
CEBPA 0.025 0.038 -10000 0 -0.46 3 3
EHMT2 0.025 0.007 -10000 0 -10000 0 0
cell proliferation -0.077 0.16 0.28 12 -0.44 29 41
NR0B1 -0.02 0.084 -10000 0 -0.39 24 24
EGR1 -0.001 0.099 -10000 0 -0.46 22 22
RXRs/9cRA 0.004 0.099 -10000 0 -0.26 60 60
AR/RACK1/Src -0.042 0.11 0.25 3 -0.39 22 25
AR/GR -0.062 0.14 -10000 0 -0.31 76 76
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.026 0.026 -10000 0 -0.39 2 2
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.009 0.04 -10000 0 -0.35 4 4
T-DHT/AR/TIF2/CARM1 -0.05 0.13 -10000 0 -0.37 37 37
SRC -0.036 0.078 0.2 13 -0.31 23 36
NR3C1 0.027 0.006 -10000 0 -10000 0 0
KLK3 -0.24 0.43 0.37 1 -1.2 87 88
APPBP2 0.006 0.026 -10000 0 -10000 0 0
TRIM24 0.018 0.029 -10000 0 -0.46 1 1
T-DHT/AR/TIP60 -0.046 0.11 0.23 1 -0.4 21 22
TMPRSS2 -0.46 0.53 -10000 0 -1 240 240
RXRG -0.037 0.16 -10000 0 -0.46 63 63
mol:9cRA -0.001 0.003 -10000 0 -10000 0 0
RXRA 0.027 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.006 -10000 0 -10000 0 0
CARM1 0.028 0.004 -10000 0 -10000 0 0
NR2C2 0.018 0.053 -10000 0 -0.46 6 6
KLK2 -0.043 0.12 -10000 0 -0.39 18 18
AR -0.076 0.14 0.16 1 -0.3 118 119
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.013 -10000 0 -10000 0 0
SRY 0.005 0.011 0.029 90 -10000 0 90
GATA2 0.023 0.03 -10000 0 -0.42 2 2
MYST2 0.001 0.001 -10000 0 -10000 0 0
HOXB13 -0.14 0.19 -10000 0 -0.39 193 193
T-DHT/AR/RACK1/Src -0.039 0.11 0.24 5 -0.4 22 27
positive regulation of transcription 0.023 0.03 -10000 0 -0.42 2 2
DNAJA1 0.005 0.025 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.008 -10000 0 -10000 0 0
NCOA1 0.034 0.028 -10000 0 -10000 0 0
SPDEF -0.1 0.2 -10000 0 -0.45 128 128
T-DHT/AR/TIF2 -0.05 0.13 0.2 2 -0.41 31 33
T-DHT/AR/Hsp90 -0.049 0.11 0.22 1 -0.4 23 24
GSK3B 0.022 0.009 -10000 0 -10000 0 0
NR2C1 0.029 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.043 0.074 -10000 0 -0.32 26 26
SIRT1 0.026 0.022 -10000 0 -0.46 1 1
ZMIZ2 0.031 0.014 -10000 0 -10000 0 0
POU2F1 -0.024 0.07 -10000 0 -0.17 6 6
T-DHT/AR/DAX-1 -0.063 0.12 -10000 0 -0.4 27 27
CREBBP 0.027 0.004 -10000 0 -10000 0 0
SMARCE1 0.019 0.02 -10000 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 0.026 0.007 -10000 0 -10000 0 0
VLDLR 0.02 0.049 -10000 0 -0.46 5 5
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.022 0.14 -10000 0 -0.28 109 109
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.032 0.12 -10000 0 -0.26 96 96
IQGAP1/CaM 0.039 0.011 -10000 0 -10000 0 0
DAB1 -0.001 0.073 -10000 0 -0.39 16 16
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.13 0.2 -10000 0 -0.39 198 198
CALM1 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.033 0.044 -10000 0 -0.27 10 10
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.022 -10000 0 -0.46 1 1
CDK5R1 0.026 0.026 -10000 0 -0.39 2 2
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.044 0.14 -10000 0 -0.39 74 74
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.03 0.14 -10000 0 -0.28 113 113
YWHAE 0.027 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.03 0.12 0.3 5 -0.39 3 8
MAP1B 0.003 0.027 -10000 0 -0.33 2 2
RAC1 0.014 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.023 0.11 -10000 0 -0.4 4 4
RELN -0.073 0.2 -10000 0 -0.46 103 103
PAFAH/LIS1 -0.067 0.12 -10000 0 -0.23 189 189
LIS1/CLIP170 0.029 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.022 0.097 -10000 0 -0.38 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.036 0.12 -10000 0 -0.37 25 25
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.041 0.12 0.33 3 -0.35 10 13
LIS1/IQGAP1 0.028 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.014 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.026 0.026 -10000 0 -0.39 2 2
PAFAH1B2 0.023 0.032 -10000 0 -0.46 2 2
MAP1B/LIS1/Dynein heavy chain 0.019 0.035 -10000 0 -0.26 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.021 0.12 0.3 4 -0.38 3 7
LRP8 0.02 0.057 -10000 0 -0.39 10 10
NDEL1/Katanin 60 -0.031 0.12 0.3 5 -0.39 3 8
P39/CDK5 -0.052 0.13 -10000 0 -0.4 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.011 -10000 0 -10000 0 0
CDK5 -0.046 0.11 0.18 25 -0.42 3 28
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.01 -10000 0 -10000 0 0
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.018 0.12 -10000 0 -0.25 83 83
RELN/VLDLR -0.012 0.13 -10000 0 -0.26 107 107
CDC42 0.014 0.006 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.15 0.14 -10000 0 -0.54 15 15
IHH -0.038 0.058 -10000 0 -0.37 3 3
SHH Np/Cholesterol/GAS1 0.004 0.066 -10000 0 -0.21 44 44
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.004 0.065 0.21 44 -10000 0 44
SMO/beta Arrestin2 -0.084 0.12 -10000 0 -0.45 26 26
SMO -0.09 0.12 -10000 0 -0.47 27 27
AKT1 -0.038 0.1 -10000 0 -0.51 14 14
ARRB2 0.027 0.006 -10000 0 -10000 0 0
BOC -0.017 0.14 -10000 0 -0.46 44 44
ADRBK1 0.026 0.008 -10000 0 -10000 0 0
heart looping -0.088 0.12 -10000 0 -0.46 27 27
STIL -0.085 0.096 -10000 0 -0.41 13 13
DHH N/PTCH2 0.03 0.059 -10000 0 -0.3 15 15
DHH N/PTCH1 -0.084 0.099 -10000 0 -0.49 8 8
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DHH 0.021 0.029 -10000 0 -0.39 2 2
PTHLH -0.21 0.18 -10000 0 -0.59 27 27
determination of left/right symmetry -0.088 0.12 -10000 0 -0.46 27 27
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
skeletal system development -0.21 0.18 -10000 0 -0.59 27 27
IHH N/Hhip -0.032 0.084 -10000 0 -0.33 30 30
DHH N/Hhip 0.018 0.076 -10000 0 -0.28 32 32
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.088 0.12 -10000 0 -0.46 27 27
pancreas development -0.006 0.097 -10000 0 -0.39 30 30
HHAT 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.33 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.051 -10000 0 -0.41 7 7
somite specification -0.088 0.12 -10000 0 -0.46 27 27
SHH Np/Cholesterol/PTCH1 -0.089 0.096 -10000 0 -0.35 31 31
SHH Np/Cholesterol/PTCH2 0.001 0.075 -10000 0 -0.23 48 48
SHH Np/Cholesterol/Megalin -0.007 0.081 -10000 0 -0.23 54 54
SHH -0.018 0.073 -10000 0 -0.27 38 38
catabolic process -0.099 0.1 -10000 0 -0.43 14 14
SMO/Vitamin D3 -0.085 0.11 -10000 0 -0.46 14 14
SHH Np/Cholesterol/Hhip -0.01 0.084 -10000 0 -0.23 60 60
LRP2 -0.001 0.091 -10000 0 -0.39 26 26
receptor-mediated endocytosis -0.087 0.11 -10000 0 -0.47 15 15
SHH Np/Cholesterol/BOC -0.015 0.092 -10000 0 -0.24 73 73
SHH Np/Cholesterol/CDO 0 0.07 -10000 0 -0.22 48 48
mesenchymal cell differentiation 0.01 0.084 0.23 60 -10000 0 60
mol:Vitamin D3 -0.086 0.1 0.37 1 -0.35 31 32
IHH N/PTCH2 -0.02 0.069 -10000 0 -0.36 13 13
CDON 0.016 0.068 -10000 0 -0.46 10 10
IHH N/PTCH1 -0.097 0.11 -10000 0 -0.44 14 14
Megalin/LRPAP1 0.022 0.068 -10000 0 -0.27 26 26
PTCH2 0.016 0.073 -10000 0 -0.43 13 13
SHH Np/Cholesterol -0.001 0.058 -10000 0 -0.2 38 38
PTCH1 -0.099 0.1 -10000 0 -0.44 14 14
HHIP -0.006 0.098 -10000 0 -0.39 30 30
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 -0.02 0.12 0.25 6 -0.38 20 26
IKBKB 0.006 0.1 0.26 13 -0.34 12 25
AKT1 0.005 0.11 0.28 32 -0.23 17 49
IKBKG 0.016 0.083 0.25 11 -0.29 6 17
CALM1 -0.006 0.098 0.28 9 -0.39 9 18
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
MAP3K1 -0.029 0.15 0.31 5 -0.52 22 27
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.099 0.27 3 -0.4 11 14
DOK1 0.027 0.018 -10000 0 -0.39 1 1
AP-1 -0.013 0.091 0.22 15 -0.24 13 28
LYN 0.024 0.02 -10000 0 -0.39 1 1
BLNK -0.017 0.14 -10000 0 -0.46 47 47
SHC1 0.028 0.004 -10000 0 -10000 0 0
BCR complex -0.038 0.16 -10000 0 -0.34 106 106
CD22 -0.05 0.15 -10000 0 -0.43 50 50
CAMK2G -0.004 0.094 0.27 9 -0.39 7 16
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
INPP5D 0.025 0.031 -10000 0 -0.46 2 2
SHC/GRB2/SOS1 -0.039 0.12 -10000 0 -0.38 28 28
GO:0007205 -0.011 0.1 0.27 3 -0.4 11 14
SYK 0.024 0.038 -10000 0 -0.46 3 3
ELK1 -0.01 0.097 0.26 4 -0.38 11 15
NFATC1 -0.045 0.13 0.26 6 -0.41 26 32
B-cell antigen/BCR complex -0.038 0.16 -10000 0 -0.34 106 106
PAG1/CSK 0.036 0.02 -10000 0 -0.27 1 1
NFKBIB 0.018 0.046 0.13 17 -0.13 16 33
HRAS -0.014 0.1 0.26 5 -0.4 10 15
NFKBIA 0.018 0.046 0.13 17 -0.12 15 32
NF-kappa-B/RelA/I kappa B beta 0.022 0.041 0.13 17 -10000 0 17
RasGAP/Csk 0.004 0.14 -10000 0 -0.33 47 47
mol:GDP -0.008 0.097 0.26 3 -0.38 12 15
PTEN 0.027 0.006 -10000 0 -10000 0 0
CD79B 0.004 0.099 -10000 0 -0.41 27 27
NF-kappa-B/RelA/I kappa B alpha 0.022 0.04 0.13 17 -10000 0 17
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.047 0.16 0.29 2 -0.49 25 27
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.012 0.099 0.27 2 -0.41 11 13
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.031 0.12 0.27 11 -0.38 21 32
CHUK 0.008 0.094 0.25 10 -0.32 14 24
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.005 0.11 0.24 2 -0.36 14 16
PTPN6 -0.049 0.14 -10000 0 -0.49 29 29
RELA 0.027 0.006 -10000 0 -10000 0 0
BCL2A1 0.015 0.033 0.11 7 -0.11 1 8
VAV2 -0.059 0.16 -10000 0 -0.5 32 32
ubiquitin-dependent protein catabolic process 0.021 0.046 0.13 18 -0.13 16 34
BTK 0.018 0.05 -10000 0 -1 1 1
CD19 -0.062 0.16 -10000 0 -0.39 74 74
MAP4K1 0.015 0.07 -10000 0 -0.4 14 14
CD72 -0.014 0.12 -10000 0 -0.39 47 47
PAG1 0.024 0.02 -10000 0 -0.39 1 1
MAPK14 -0.021 0.13 0.28 7 -0.44 21 28
SH3BP5 0.022 0.038 -10000 0 -0.46 3 3
PIK3AP1 -0.017 0.11 -10000 0 -0.37 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.036 0.13 -10000 0 -0.49 20 20
RAF1 -0.013 0.096 0.27 4 -0.38 9 13
RasGAP/p62DOK/SHIP 0.003 0.14 -10000 0 -0.41 26 26
CD79A -0.06 0.17 -10000 0 -0.41 103 103
re-entry into mitotic cell cycle -0.013 0.091 0.23 14 -0.24 12 26
RASA1 0.024 0.031 -10000 0 -0.46 2 2
MAPK3 -0.009 0.087 0.26 5 -0.33 9 14
MAPK1 -0.006 0.09 0.25 9 -0.32 8 17
CD72/SHP1 -0.041 0.16 0.32 6 -0.52 32 38
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.025 0.13 0.29 6 -0.43 23 29
actin cytoskeleton organization -0.044 0.14 0.33 2 -0.44 30 32
NF-kappa-B/RelA 0.047 0.078 0.25 17 -0.21 3 20
Calcineurin 0.016 0.096 0.27 6 -0.36 7 13
PI3K -0.052 0.13 -10000 0 -0.4 43 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.011 0.1 0.22 3 -0.4 16 19
SOS1 0.028 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.032 0.2 -10000 0 -0.7 33 33
DAPP1 -0.046 0.21 -10000 0 -0.77 33 33
cytokine secretion -0.042 0.12 0.26 6 -0.38 26 32
mol:DAG -0.012 0.099 0.27 2 -0.41 11 13
PLCG2 0.025 0.023 -10000 0 -0.46 1 1
MAP2K1 -0.01 0.093 0.26 5 -0.36 9 14
B-cell antigen/BCR complex/FcgammaRIIB -0.02 0.15 -10000 0 -0.3 107 107
mol:PI-3-4-5-P3 -0.033 0.1 -10000 0 -0.29 39 39
ETS1 -0.006 0.088 0.26 10 -0.36 7 17
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.021 0.15 -10000 0 -0.41 31 31
B-cell antigen/BCR complex/LYN -0.032 0.14 -10000 0 -0.43 33 33
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 -0.049 0.15 0.33 1 -0.47 30 31
B-cell antigen/BCR complex/LYN/SYK -0.021 0.16 0.36 1 -0.44 45 46
CARD11 -0.011 0.12 0.28 11 -0.39 18 29
FCGR2B 0.021 0.057 -10000 0 -0.46 7 7
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.017 0.054 0.15 31 -0.12 8 39
PTPRC 0.017 0.069 -10000 0 -0.42 12 12
PDPK1 -0.005 0.1 0.25 29 -0.23 17 46
PPP3CB 0.028 0.004 -10000 0 -10000 0 0
PPP3CC 0.026 0.008 -10000 0 -10000 0 0
POU2F2 0.016 0.035 0.13 7 -10000 0 7
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.04 0.073 -10000 0 -0.25 12 12
ER alpha/Gai/GDP/Gbeta gamma -0.024 0.16 -10000 0 -0.5 39 39
AKT1 -0.006 0.16 -10000 0 -0.72 24 24
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.001 0.17 -10000 0 -0.74 24 24
mol:Ca2+ -0.032 0.13 -10000 0 -0.36 62 62
IGF1R 0.027 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.084 -10000 0 -0.26 43 43
SHC1 0.028 0.004 -10000 0 -10000 0 0
apoptosis 0.005 0.16 0.69 24 -10000 0 24
RhoA/GTP 0.014 0.044 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.014 0.14 -10000 0 -0.45 26 26
regulation of stress fiber formation 0.005 0.057 0.31 1 -0.18 1 2
E2/ERA-ERB (dimer) 0.015 0.074 -10000 0 -0.25 35 35
KRAS 0.026 0.007 -10000 0 -10000 0 0
G13/GTP 0.022 0.056 -10000 0 -0.22 24 24
pseudopodium formation -0.005 0.057 0.18 1 -0.31 1 2
E2/ER alpha (dimer)/PELP1 0.023 0.059 -10000 0 -0.24 23 23
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.026 0.007 -10000 0 -10000 0 0
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
HRAS 0.026 0.02 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.008 0.16 0.25 9 -0.5 34 43
E2/ER beta (dimer) 0.012 0.047 -10000 0 -0.28 13 13
mol:GDP 0.003 0.071 -10000 0 -0.36 12 12
mol:NADP -0.008 0.16 0.25 9 -0.5 34 43
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
mol:IP3 -0.039 0.13 -10000 0 -0.37 62 62
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
PLCB1 -0.035 0.14 -10000 0 -0.38 63 63
PLCB2 -0.037 0.14 -10000 0 -0.37 68 68
IGF1 -0.053 0.18 -10000 0 -0.46 85 85
mol:L-citrulline -0.008 0.16 0.25 9 -0.5 34 43
RHOA 0.025 0.009 -10000 0 -10000 0 0
Gai/GDP -0.05 0.23 -10000 0 -0.6 72 72
JNK cascade 0.012 0.046 -10000 0 -0.28 13 13
BCAR1 0.027 0.006 -10000 0 -10000 0 0
ESR2 0.016 0.066 -10000 0 -0.39 13 13
GNAQ 0.027 0.005 -10000 0 -10000 0 0
ESR1 0.006 0.095 -10000 0 -0.42 24 24
Gq family/GDP/Gbeta gamma -0.025 0.16 -10000 0 -0.68 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.03 0.087 -10000 0 -0.86 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.013 0.14 -10000 0 -0.44 28 28
GNAZ 0.012 0.079 -10000 0 -0.41 17 17
E2/ER alpha (dimer) 0.005 0.067 -10000 0 -0.3 24 24
STRN 0.008 0.097 -10000 0 -0.46 21 21
GNAL -0.03 0.16 -10000 0 -0.46 59 59
PELP1 0.027 0.006 -10000 0 -10000 0 0
MAPK11 0.008 0.039 -10000 0 -0.23 13 13
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.46 1 1
HBEGF -0.083 0.17 0.32 14 -0.49 45 59
cAMP biosynthetic process -0.015 0.097 -10000 0 -0.23 83 83
SRC -0.018 0.16 0.21 17 -0.49 35 52
PI3K 0.027 0.03 -10000 0 -0.33 2 2
GNB1 0.027 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.031 0.075 -10000 0 -0.33 10 10
SOS1 0.028 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.039 0.12 -10000 0 -0.4 30 30
Gs family/GTP -0.01 0.1 -10000 0 -0.23 83 83
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.022 -10000 0 -0.21 1 1
vasodilation -0.006 0.15 0.25 9 -0.47 34 43
mol:DAG -0.039 0.13 -10000 0 -0.37 62 62
Gs family/GDP/Gbeta gamma -0.012 0.092 -10000 0 -0.36 12 12
MSN -0.005 0.06 0.19 1 -0.33 1 2
Gq family/GTP -0.035 0.15 -10000 0 -0.39 69 69
mol:PI-3-4-5-P3 -0.001 0.16 -10000 0 -0.71 24 24
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.006 0.15 0.47 34 -0.25 9 43
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.072 -10000 0 -0.35 10 10
NOS3 -0.01 0.17 0.26 7 -0.53 33 40
GNA11 0.024 0.038 -10000 0 -0.46 3 3
MAPKKK cascade 0.002 0.16 -10000 0 -0.54 27 27
E2/ER alpha (dimer)/PELP1/Src 0.012 0.14 0.28 4 -0.46 28 32
ruffle organization -0.005 0.057 0.18 1 -0.31 1 2
ROCK2 -0.004 0.065 0.2 1 -0.36 1 2
GNA14 -0.041 0.17 -10000 0 -0.46 71 71
GNA15 0.025 0.031 -10000 0 -0.46 2 2
GNA13 0.028 0.003 -10000 0 -10000 0 0
MMP9 -0.12 0.17 0.36 16 -0.5 46 62
MMP2 -0.026 0.16 0.27 9 -0.49 29 38
PDGFR-beta signaling pathway

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0 0.093 -10000 0 -0.35 10 10
PDGFB-D/PDGFRB/SLAP -0.015 0.11 -10000 0 -0.27 81 81
PDGFB-D/PDGFRB/APS/CBL 0.005 0.1 -10000 0 -0.22 80 80
AKT1 0.026 0.12 0.36 16 -0.32 2 18
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.009 0.11 0.27 14 -0.4 11 25
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
FGR -0.015 0.11 0.34 1 -0.46 14 15
mol:Ca2+ 0.002 0.12 0.27 14 -0.38 22 36
MYC 0.058 0.13 0.38 32 -10000 0 32
SHC1 0.028 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.007 0.089 -10000 0 -0.23 2 2
LRP1/PDGFRB/PDGFB 0.005 0.11 -10000 0 -0.24 85 85
GRB10 0.026 0.007 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0.001 0.12 0.27 14 -0.39 22 36
PTEN 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.038 -10000 0 -0.46 3 3
PDGFB-D/PDGFRB/SHP2 -0.011 0.11 -10000 0 -0.27 85 85
PDGFB-D/PDGFRB/GRB10 -0.01 0.11 -10000 0 -0.27 80 80
cell cycle arrest -0.015 0.11 -10000 0 -0.27 81 81
HRAS 0.026 0.02 -10000 0 -0.4 1 1
HIF1A 0.021 0.11 0.34 14 -0.31 1 15
GAB1 0.006 0.11 0.29 7 -0.38 11 18
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.007 0.1 0.26 14 -0.38 5 19
PDGFB-D/PDGFRB 0.006 0.1 -10000 0 -0.22 79 79
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.011 0.11 -10000 0 -0.27 85 85
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0 0.079 -10000 0 -0.38 2 2
positive regulation of MAPKKK cascade -0.011 0.11 -10000 0 -0.27 85 85
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
mol:IP3 0.002 0.12 0.27 14 -0.39 22 36
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.027 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.012 0.12 -10000 0 -0.27 85 85
SHB 0.025 0.009 -10000 0 -10000 0 0
BLK -0.058 0.15 -10000 0 -0.48 43 43
PTPN2 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.011 0.11 -10000 0 -0.27 83 83
BCAR1 0.027 0.006 -10000 0 -10000 0 0
VAV2 0.012 0.11 0.31 12 -0.4 9 21
CBL 0.025 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.01 0.11 -10000 0 -0.27 83 83
LCK -0.016 0.1 0.34 1 -0.48 12 13
PDGFRB -0.04 0.15 -10000 0 -0.38 85 85
ACP1 0.028 0.003 -10000 0 -10000 0 0
HCK -0.007 0.09 -10000 0 -0.76 3 3
ABL1 0.004 0.11 0.27 14 -0.38 10 24
PDGFB-D/PDGFRB/CBL 0.004 0.12 0.32 3 -0.42 19 22
PTPN1 0.027 0.007 -10000 0 -10000 0 0
SNX15 0.027 0.006 -10000 0 -10000 0 0
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.009 0.084 -10000 0 -0.39 22 22
cell proliferation 0.057 0.12 0.36 37 -10000 0 37
SLA 0.021 0.033 -10000 0 -0.39 3 3
actin cytoskeleton reorganization 0.032 0.11 0.34 10 -10000 0 10
SRC -0.01 0.1 -10000 0 -0.66 6 6
PI3K -0.015 0.064 -10000 0 -0.35 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.006 0.11 -10000 0 -0.23 84 84
SH2B2 0.025 0.02 -10000 0 -0.39 1 1
PLCgamma1/SPHK1 0.009 0.12 0.27 14 -0.42 10 24
LYN -0.006 0.071 -10000 0 -10000 0 0
LRP1 0.027 0.022 -10000 0 -0.46 1 1
SOS1 0.028 0.004 -10000 0 -10000 0 0
STAT5B 0.028 0.003 -10000 0 -10000 0 0
STAT5A 0.028 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.024 0.089 -10000 0 -10000 0 0
SPHK1 0.017 0.067 -10000 0 -0.38 14 14
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.002 0.12 0.27 14 -0.39 22 36
PLCG1 0.001 0.12 0.27 14 -0.4 22 36
NHERF/PDGFRB 0.006 0.11 -10000 0 -0.23 85 85
YES1 -0.017 0.094 0.35 1 -0.57 7 8
cell migration 0.005 0.11 -10000 0 -0.23 85 85
SHC/Grb2/SOS1 0.032 0.095 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.019 -10000 0 -0.39 1 1
SLC9A3R1 0.024 0.043 -10000 0 -0.46 4 4
NHERF1-2/PDGFRB/PTEN 0.018 0.1 -10000 0 -0.32 6 6
FYN -0.012 0.091 -10000 0 -0.43 4 4
DOK1 -0.006 0.093 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.014 -10000 0 -0.28 1 1
PDGFB 0.022 0.048 -10000 0 -0.39 7 7
RAC1 0.025 0.11 0.34 15 -0.41 5 20
PRKCD -0.007 0.09 0.19 10 -10000 0 10
FER -0.005 0.093 -10000 0 -10000 0 0
MAPKKK cascade -0.014 0.094 0.36 7 -10000 0 7
RASA1 -0.005 0.095 0.19 1 -0.26 2 3
NCK1 0.023 0.011 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.007 0.091 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.012 0.11 -10000 0 -0.26 82 82
chemotaxis 0.004 0.1 0.27 14 -0.38 10 24
STAT1-3-5/STAT1-3-5 0.011 0.1 -10000 0 -0.35 6 6
Bovine Papilomavirus E5/PDGFRB -0.027 0.11 -10000 0 -0.26 85 85
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
IL1-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
UBC13/UEV1A 0.021 0.002 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.46 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.067 -10000 0 -0.43 3 3
IRAK/TOLLIP 0.03 0.01 -10000 0 -10000 0 0
IKBKB 0.026 0.008 -10000 0 -10000 0 0
IKBKG 0.027 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.11 0.18 -10000 0 -0.31 213 213
IL1A -0.079 0.18 -10000 0 -0.39 131 131
IL1B -0.015 0.087 -10000 0 -0.28 51 51
IRAK/TRAF6/p62/Atypical PKCs 0.046 0.035 -10000 0 -10000 0 0
IL1R2 -0.064 0.19 -10000 0 -0.46 97 97
IL1R1 0.027 0.022 -10000 0 -0.46 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.015 0.057 0.25 1 -0.62 1 2
TOLLIP 0.027 0.006 -10000 0 -10000 0 0
TICAM2 0.026 0.008 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.04 0.053 0.24 1 -0.33 1 2
JUN -0.013 0.053 0.16 13 -0.4 1 14
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.027 0.08 -10000 0 -0.66 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.011 0.11 -10000 0 -0.41 3 3
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.11 -10000 0 -0.39 3 3
IL1 beta fragment/IL1R1/IL1RAP 0.01 0.075 -10000 0 -0.71 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.013 0.056 0.17 13 -0.42 1 14
IRAK1 0.015 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.051 0.16 -10000 0 -0.33 126 126
IRAK4 0.027 0.022 -10000 0 -0.46 1 1
PRKCI 0.02 0.013 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.33 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.064 -10000 0 -0.44 3 3
CHUK 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.01 0.075 -10000 0 -0.71 1 1
IL1 beta/IL1R2 -0.048 0.14 0.22 2 -0.27 139 141
IRAK/TRAF6/TAK1/TAB1/TAB2 0.037 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.015 0.07 -10000 0 -0.61 1 1
IRAK3 0.022 0.044 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.028 0.081 -10000 0 -0.66 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.069 -10000 0 -0.3 11 11
IL1 alpha/IL1R1/IL1RAP -0.02 0.12 -10000 0 -0.24 106 106
RELA 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
MYD88 0.024 0.009 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.016 -10000 0 -10000 0 0
IL1RAP 0.018 0.031 -10000 0 -0.42 2 2
UBE2N 0.028 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.008 0.061 -10000 0 -0.57 1 1
CASP1 0.024 0.023 -10000 0 -0.46 1 1
IL1RN/IL1R2 -0.11 0.22 -10000 0 -0.39 182 182
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.017 0.077 -10000 0 -0.68 1 1
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.088 -10000 0 -0.3 14 14
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL1RN -0.093 0.21 -10000 0 -0.46 126 126
TRAF6/TAK1/TAB1/TAB2 0.038 0.011 -10000 0 -10000 0 0
MAP2K6 0.008 0.06 0.19 15 -0.22 24 39
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.047 0.13 -10000 0 -0.25 148 148
cell-cell adhesion 0.044 0.088 0.43 5 -10000 0 5
Ephrin B/EPHB2/RasGAP -0.017 0.14 -10000 0 -0.43 5 5
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.021 0.044 -10000 0 -0.28 9 9
Ephrin B1/EPHB1 0.02 0.058 -10000 0 -0.25 21 21
HRAS/GDP -0.011 0.1 -10000 0 -0.32 13 13
Ephrin B/EPHB1/GRB7 0.039 0.09 -10000 0 -0.26 27 27
Endophilin/SYNJ1 -0.048 0.1 0.21 1 -0.39 4 5
KRAS 0.026 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.04 0.085 -10000 0 -0.26 22 22
endothelial cell migration 0.037 0.034 -10000 0 -0.24 2 2
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.038 -10000 0 -0.46 3 3
PAK1 -0.043 0.12 0.36 3 -0.46 9 12
HRAS 0.026 0.02 -10000 0 -0.4 1 1
RRAS -0.048 0.11 0.21 1 -0.39 5 6
DNM1 0 0.1 -10000 0 -0.39 34 34
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.019 0.092 0.35 3 -0.44 2 5
lamellipodium assembly -0.044 0.088 -10000 0 -0.43 5 5
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.066 -10000 0 -0.36 4 4
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
EPHB2 -0.084 0.18 -10000 0 -0.39 137 137
EPHB3 0.011 0.068 -10000 0 -0.46 10 10
EPHB1 0.004 0.09 -10000 0 -0.42 22 22
EPHB4 0.026 0.008 -10000 0 -10000 0 0
mol:GDP -0.037 0.092 0.29 1 -0.32 19 20
Ephrin B/EPHB2 -0.024 0.13 -10000 0 -0.26 29 29
Ephrin B/EPHB3 0.028 0.07 -10000 0 -0.24 25 25
JNK cascade 0.002 0.16 0.36 51 -0.4 3 54
Ephrin B/EPHB1 0.03 0.081 -10000 0 -0.26 24 24
RAP1/GDP -0.018 0.1 0.3 2 -0.35 5 7
EFNB2 0.026 0.022 -10000 0 -0.46 1 1
EFNB3 -0.001 0.11 -10000 0 -0.46 29 29
EFNB1 0.028 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.026 0.11 -10000 0 -0.21 133 133
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.02 0.11 -10000 0 -0.47 5 5
Rap1/GTP -0.036 0.097 -10000 0 -0.44 5 5
axon guidance -0.047 0.13 -10000 0 -0.25 148 148
MAPK3 0.004 0.061 0.19 4 -0.33 4 8
MAPK1 0.007 0.066 0.2 12 -0.33 4 16
Rac1/GDP -0.029 0.097 0.27 2 -0.32 12 14
actin cytoskeleton reorganization -0.049 0.081 -10000 0 -0.35 6 6
CDC42/GDP -0.025 0.1 0.26 5 -0.32 11 16
PI3K 0.041 0.037 -10000 0 -0.24 2 2
EFNA5 0.005 0.099 -10000 0 -0.46 22 22
Ephrin B2/EPHB4 0.033 0.018 -10000 0 -0.28 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.024 0.086 -10000 0 -0.31 14 14
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.038 0.094 -10000 0 -0.43 5 5
PTK2 0.092 0.21 0.6 75 -10000 0 75
MAP4K4 0.002 0.16 0.36 51 -0.4 3 54
SRC 0.026 0.007 -10000 0 -10000 0 0
KALRN -0.009 0.12 -10000 0 -0.46 35 35
Intersectin/N-WASP 0.038 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.007 0.13 0.31 36 -0.39 8 44
MAP2K1 0.005 0.062 -10000 0 -0.34 4 4
WASL 0.027 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.016 0.12 -10000 0 -0.3 11 11
cell migration 0.01 0.093 0.29 3 -0.38 5 8
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 -0.049 0.1 0.21 1 -0.4 4 5
PXN 0.028 0.002 -10000 0 -10000 0 0
TF -0.17 0.15 0.21 1 -0.4 103 104
HRAS/GTP -0.024 0.11 -10000 0 -0.46 5 5
Ephrin B1/EPHB1-2 -0.026 0.11 -10000 0 -0.21 133 133
cell adhesion mediated by integrin 0 0.066 0.24 15 -0.27 7 22
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.023 0.12 -10000 0 -0.48 5 5
RAC1-CDC42/GTP -0.042 0.092 -10000 0 -0.43 6 6
RASA1 0.024 0.031 -10000 0 -0.46 2 2
RAC1-CDC42/GDP -0.02 0.099 0.29 2 -0.35 5 7
ruffle organization -0.021 0.13 0.36 15 -0.44 5 20
NCK1 0.023 0.011 -10000 0 -10000 0 0
receptor internalization -0.069 0.1 0.2 3 -0.36 21 24
Ephrin B/EPHB2/KALRN -0.029 0.14 -10000 0 -0.46 10 10
ROCK1 0.055 0.078 0.18 127 -0.25 4 131
RAS family/GDP -0.053 0.081 -10000 0 -0.35 6 6
Rac1/GTP -0.041 0.095 -10000 0 -0.46 5 5
Ephrin B/EPHB1/Src/Paxillin 0.008 0.068 -10000 0 -0.33 6 6
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.018 0.2 -10000 0 -0.84 21 21
NCK1/PAK1/Dok-R -0.024 0.079 -10000 0 -0.39 18 18
NCK1/Dok-R 0.01 0.22 -10000 0 -1 20 20
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.04 0.24 13 -10000 0 13
RELA 0.027 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
F2 -0.041 0.13 0.27 13 -0.4 52 65
TNIP2 0.026 0.007 -10000 0 -10000 0 0
NF kappa B/RelA 0.031 0.21 -10000 0 -0.95 20 20
FN1 -0.15 0.2 -10000 0 -0.39 222 222
PLD2 -0.005 0.22 -10000 0 -1 21 21
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB14 -0.017 0.14 -10000 0 -0.45 46 46
ELK1 0.003 0.21 -10000 0 -0.94 21 21
GRB7 0.025 0.038 -10000 0 -0.46 3 3
PAK1 0.025 0.008 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.25 -10000 0 -1.1 20 20
CDKN1A 0.031 0.16 0.44 1 -0.61 15 16
ITGA5 -0.1 0.19 -10000 0 -0.39 161 161
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.015 0.23 -10000 0 -1 20 20
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:NO 0.025 0.16 0.42 2 -0.62 21 23
PLG -0.01 0.22 -10000 0 -1 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.019 0.19 -10000 0 -0.8 21 21
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
ANGPT2 0.014 0.16 -10000 0 -0.59 6 6
BMX -0.029 0.24 -10000 0 -1.1 21 21
ANGPT1 -0.005 0.2 -10000 0 -1.2 13 13
tube development 0.021 0.17 0.38 1 -0.64 19 20
ANGPT4 0.018 0.016 -10000 0 -10000 0 0
response to hypoxia -0.002 0.014 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.013 0.24 -10000 0 -1.1 21 21
alpha5/beta1 Integrin -0.058 0.14 -10000 0 -0.27 161 161
FGF2 0.011 0.085 -10000 0 -0.44 17 17
STAT5A (dimer) 0.031 0.19 -10000 0 -0.75 17 17
mol:L-citrulline 0.025 0.16 0.42 2 -0.62 21 23
AGTR1 -0.02 0.13 -10000 0 -0.46 41 41
MAPK14 -0.001 0.24 -10000 0 -1 23 23
Tie2/SHP2 -0.004 0.2 -10000 0 -1.1 13 13
TEK 0 0.2 -10000 0 -1.2 13 13
RPS6KB1 0.018 0.19 -10000 0 -0.81 21 21
Angiotensin II/AT1 -0.012 0.093 -10000 0 -0.33 41 41
Tie2/Ang1/GRB2 0.007 0.24 -10000 0 -1.1 21 21
MAPK3 -0.005 0.21 -10000 0 -0.96 21 21
MAPK1 -0.002 0.21 -10000 0 -0.96 21 21
Tie2/Ang1/GRB7 0.006 0.24 -10000 0 -1.1 20 20
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.006 0.23 -10000 0 -1.1 20 20
PI3K -0.006 0.22 -10000 0 -0.97 21 21
FES 0.004 0.24 -10000 0 -1 22 22
Crk/Dok-R 0.017 0.23 -10000 0 -1 20 20
Tie2/Ang1/ABIN2 0.008 0.24 -10000 0 -1.1 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.023 0.18 0.39 1 -0.75 21 22
STAT5A 0.028 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.043 0.2 0.43 4 -0.79 20 24
Tie2/Ang2 0.011 0.21 -10000 0 -0.88 18 18
Tie2/Ang1 -0.004 0.25 -10000 0 -1.1 21 21
FOXO1 0.024 0.18 -10000 0 -0.76 20 20
ELF1 0.028 0.045 -10000 0 -0.47 3 3
ELF2 -0.002 0.22 -10000 0 -1.1 20 20
mol:Choline -0.003 0.21 -10000 0 -0.99 21 21
cell migration -0.043 0.06 -10000 0 -0.22 22 22
FYN 0.015 0.19 -10000 0 -0.74 18 18
DOK2 0.022 0.039 -10000 0 -0.41 4 4
negative regulation of cell cycle 0.032 0.15 0.39 2 -0.55 15 17
ETS1 0.023 0.054 -10000 0 -0.28 15 15
PXN 0.046 0.18 0.39 8 -0.66 20 28
ITGB1 0.027 0.005 -10000 0 -10000 0 0
NOS3 0.023 0.18 0.43 2 -0.71 21 23
RAC1 0.026 0.007 -10000 0 -10000 0 0
TNF 0.008 0.098 -10000 0 -0.34 35 35
MAPKKK cascade -0.003 0.21 -10000 0 -0.99 21 21
RASA1 0.024 0.031 -10000 0 -0.46 2 2
Tie2/Ang1/Shc 0.008 0.24 -10000 0 -1.1 21 21
NCK1 0.023 0.011 -10000 0 -10000 0 0
vasculogenesis 0.027 0.15 0.38 3 -0.56 21 24
mol:Phosphatidic acid -0.003 0.21 -10000 0 -0.99 21 21
mol:Angiotensin II 0 0.004 -10000 0 -10000 0 0
mol:NADP 0.025 0.16 0.42 2 -0.62 21 23
Rac1/GTP 0.021 0.18 -10000 0 -0.75 21 21
MMP2 -0.025 0.23 -10000 0 -1 21 21
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.001 0.11 0.32 49 -10000 0 49
KIRREL 0.002 0.1 -10000 0 -0.46 23 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.001 0.11 -10000 0 -0.32 49 49
PLCG1 0.027 0.006 -10000 0 -10000 0 0
ARRB2 0.027 0.006 -10000 0 -10000 0 0
WASL 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.024 0.097 -10000 0 -0.3 23 23
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.002 0.062 -10000 0 -0.26 16 16
FYN -0.016 0.084 0.27 9 -0.28 24 33
mol:Ca2+ 0.022 0.094 -10000 0 -0.3 22 22
mol:DAG 0.023 0.095 -10000 0 -0.3 22 22
NPHS2 -0.013 0.068 -10000 0 -0.4 13 13
mol:IP3 0.023 0.095 -10000 0 -0.3 22 22
regulation of endocytosis 0.021 0.084 -10000 0 -0.27 23 23
Nephrin/NEPH1/podocin/Cholesterol 0.011 0.092 -10000 0 -0.24 54 54
establishment of cell polarity 0.001 0.11 -10000 0 -0.32 49 49
Nephrin/NEPH1/podocin/NCK1-2 0.032 0.09 -10000 0 -0.32 12 12
Nephrin/NEPH1/beta Arrestin2 0.023 0.085 -10000 0 -0.27 22 22
NPHS1 -0.02 0.098 -10000 0 -0.4 30 30
Nephrin/NEPH1/podocin 0.015 0.085 -10000 0 -0.28 24 24
TJP1 0.028 0.004 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.024 0.096 -10000 0 -0.3 22 22
CD2AP 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.025 0.098 -10000 0 -0.3 24 24
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.026 0.092 0.28 7 -0.26 44 51
cytoskeleton organization -0.01 0.071 0.23 3 -0.3 19 22
Nephrin/NEPH1 0.006 0.076 -10000 0 -0.22 48 48
Nephrin/NEPH1/ZO-1 0.02 0.092 -10000 0 -0.25 48 48
Ephrin A reverse 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
MAPKKK cascade 0.015 0.07 -10000 0 -0.27 29 29
EFNA5 0.005 0.099 -10000 0 -0.46 22 22
FYN -0.008 0.063 0.18 5 -0.26 23 28
neuron projection morphogenesis 0.015 0.07 -10000 0 -0.27 29 29
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.015 0.071 -10000 0 -0.27 29 29
EPHA5 0.002 0.051 -10000 0 -0.39 7 7
Caspase cascade in apoptosis

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
TOP1 -0.02 0.12 0.26 3 -0.46 14 17
ACTA1 -0.093 0.12 0.21 2 -0.37 44 46
NUMA1 -0.029 0.13 0.25 3 -0.49 17 20
SPTAN1 -0.031 0.11 0.3 5 -0.32 38 43
LIMK1 -0.031 0.11 0.27 5 -0.31 38 43
BIRC3 0.012 0.071 -10000 0 -0.39 15 15
BIRC2 0.024 0.01 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
CASP10 -0.057 0.12 -10000 0 -0.31 87 87
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
PTK2 -0.017 0.1 0.24 3 -0.37 10 13
DIABLO 0.028 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.031 0.11 0.3 5 -0.31 38 43
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.002 -10000 0 -10000 0 0
GSN -0.031 0.11 0.27 4 -0.32 38 42
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.014 0.21 -10000 0 -0.84 26 26
BID -0.019 0.061 -10000 0 -0.2 38 38
MAP3K1 -0.021 0.1 -10000 0 -0.42 26 26
TRADD 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.027 0.12 0.37 4 -0.32 37 41
CASP9 0.027 0.006 -10000 0 -10000 0 0
DNA repair 0.003 0.05 0.2 2 -0.18 3 5
neuron apoptosis -0.001 0.14 -10000 0 -0.7 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.036 0.14 0.27 4 -0.57 10 14
APAF1 0.028 0.002 -10000 0 -10000 0 0
CASP6 -0.011 0.16 -10000 0 -0.91 13 13
TRAF2 0.023 0.041 -10000 0 -0.39 5 5
ICAD/CAD -0.034 0.11 0.26 5 -0.31 36 41
CASP7 -0.007 0.083 0.29 4 -0.33 5 9
KRT18 0.007 0.072 -10000 0 -0.5 8 8
apoptosis -0.031 0.12 0.26 3 -0.45 11 14
DFFA -0.035 0.11 0.26 4 -0.32 38 42
DFFB -0.034 0.11 0.27 5 -0.32 39 44
PARP1 -0.003 0.051 0.18 3 -0.21 2 5
actin filament polymerization 0.023 0.12 0.3 35 -0.34 13 48
TNF 0.008 0.088 -10000 0 -0.4 23 23
CYCS -0.005 0.066 0.19 4 -0.24 7 11
SATB1 -0.021 0.15 -10000 0 -0.85 13 13
SLK -0.035 0.11 0.27 3 -0.32 38 41
p15 BID/BAX 0.002 0.072 0.2 2 -0.26 2 4
CASP2 0.015 0.06 0.21 4 -0.37 4 8
JNK cascade 0.02 0.1 0.42 26 -10000 0 26
CASP3 -0.036 0.12 0.27 4 -0.33 42 46
LMNB2 0.008 0.12 0.24 2 -0.48 21 23
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CASP4 0.024 0.023 -10000 0 -0.46 1 1
Mammalian IAPs/DIABLO 0.054 0.05 -10000 0 -10000 0 0
negative regulation of DNA binding -0.012 0.2 -10000 0 -0.82 26 26
stress fiber formation -0.035 0.11 0.27 3 -0.31 38 41
GZMB -0.05 0.15 -10000 0 -0.36 88 88
CASP1 0.013 0.032 -10000 0 -0.7 1 1
LMNB1 0.002 0.13 0.24 2 -0.59 16 18
APP -0.002 0.14 -10000 0 -0.71 18 18
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.002 -10000 0 -10000 0 0
VIM -0.029 0.12 0.26 3 -0.43 14 17
LMNA 0.018 0.092 0.26 1 -0.47 11 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.019 0.059 -10000 0 -0.33 6 6
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.034 0.11 0.27 3 -0.32 38 41
APAF-1/Caspase 9 -0.006 0.11 -10000 0 -0.6 16 16
nuclear fragmentation during apoptosis -0.028 0.13 0.25 3 -0.48 17 20
CFL2 -0.024 0.12 0.35 13 -0.3 35 48
GAS2 -0.063 0.13 0.26 4 -0.34 54 58
positive regulation of apoptosis 0.012 0.12 0.23 3 -0.54 16 19
PRF1 -0.004 0.11 -10000 0 -0.39 39 39
Wnt signaling

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
Noncanonical Wnts/FZD -0.017 0.11 -9999 0 -0.45 15 15
FZD6 0.023 0.024 -9999 0 -0.46 1 1
WNT6 -0.009 0.12 -9999 0 -0.4 43 43
WNT4 0.013 0.079 -9999 0 -0.44 15 15
FZD3 0.019 0.057 -9999 0 -0.46 7 7
WNT5A 0.019 0.052 -9999 0 -0.45 6 6
WNT11 -0.019 0.13 -9999 0 -0.41 52 52
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.005 0.081 -10000 0 -10000 0 0
epithelial cell differentiation -0.028 0.1 -10000 0 -0.39 3 3
ITCH 0.038 0.02 -10000 0 -10000 0 0
WWP1 -0.004 0.077 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
EGFR 0.021 0.044 -10000 0 -0.46 4 4
PRL -0.007 0.044 -10000 0 -0.39 5 5
neuron projection morphogenesis -0.018 0.094 0.27 3 -10000 0 3
PTPRZ1 0.007 0.095 -10000 0 -0.46 20 20
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.003 0.11 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.035 0.095 -10000 0 -0.38 2 2
ADAM17 0.039 0.036 -10000 0 -0.45 2 2
ErbB4/ErbB4 -0.019 0.08 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.011 0.087 -10000 0 -0.38 1 1
NCOR1 0.027 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.023 0.099 -10000 0 -0.36 3 3
GRIN2B -0.028 0.097 0.27 3 -0.35 3 6
ErbB4/ErbB2/betacellulin -0.07 0.13 -10000 0 -0.32 36 36
STAT1 0.009 0.084 -10000 0 -0.39 22 22
HBEGF 0.027 0.006 -10000 0 -10000 0 0
PRLR -0.061 0.18 -10000 0 -0.46 90 90
E4ICDs/ETO2 -0.005 0.082 -10000 0 -10000 0 0
axon guidance -0.007 0.073 0.38 1 -10000 0 1
NEDD4 0.04 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.035 0.14 -10000 0 -0.34 91 91
CBFA2T3 0.026 0.022 -10000 0 -0.46 1 1
ErbB4/ErbB2/HBEGF 0.009 0.066 -10000 0 -10000 0 0
MAPK3 -0.015 0.098 0.27 3 -10000 0 3
STAT1 (dimer) -0.014 0.095 -10000 0 -0.33 8 8
MAPK1 -0.015 0.097 0.27 3 -10000 0 3
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.029 0.094 -10000 0 -0.36 2 2
NRG1 -0.023 0.1 -10000 0 -0.28 75 75
NRG3 0.002 0.053 -10000 0 -0.44 6 6
NRG2 -0.24 0.24 -10000 0 -0.46 274 274
NRG4 -0.004 0.12 -10000 0 -0.46 31 31
heart development -0.007 0.073 0.38 1 -10000 0 1
neural crest cell migration -0.029 0.093 -10000 0 -0.36 2 2
ERBB2 0.021 0.025 -10000 0 -0.31 2 2
WWOX/E4ICDs -0.004 0.079 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.011 0.1 -10000 0 -0.36 12 12
apoptosis 0.03 0.1 0.53 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.15 0.16 -10000 0 -0.38 85 85
ErbB4/ErbB2/epiregulin -0.052 0.13 -10000 0 -0.33 30 30
ErbB4/ErbB4/betacellulin/betacellulin -0.09 0.15 -10000 0 -0.37 47 47
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.025 0.12 -10000 0 -0.41 3 3
MDM2 -0.009 0.081 0.28 11 -10000 0 11
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.02 0.086 -10000 0 -0.33 1 1
STAT5A -0.006 0.07 0.34 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta -0.025 0.096 -10000 0 -0.35 2 2
DLG4 0.026 0.022 -10000 0 -0.46 1 1
GRB2/SHC 0.04 0.008 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.006 0.075 -10000 0 -10000 0 0
STAT5A (dimer) -0.024 0.12 -10000 0 -0.43 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.005 0.082 0.33 1 -10000 0 1
LRIG1 0.016 0.065 -10000 0 -0.46 9 9
EREG -0.097 0.21 -10000 0 -0.46 131 131
BTC -0.13 0.22 -10000 0 -0.46 159 159
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.007 0.071 0.38 1 -10000 0 1
ERBB4 -0.021 0.073 -10000 0 -10000 0 0
STAT5B 0.028 0.003 -10000 0 -10000 0 0
YAP1 -0.014 0.1 -10000 0 -0.43 28 28
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.005 0.09 -10000 0 -0.42 1 1
glial cell differentiation 0.006 0.075 -10000 0 -10000 0 0
WWOX 0.025 0.008 -10000 0 -10000 0 0
cell proliferation -0.096 0.16 0.31 1 -0.45 28 29
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.022 -10000 0 -0.46 1 1
HDAC4 0.027 0.006 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.002 0.062 0.28 25 -10000 0 25
CDKN1A -0.006 0.011 -10000 0 -10000 0 0
KAT2B 0.007 0.092 -10000 0 -0.46 19 19
BAX 0.027 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.018 0.38 1 -10000 0 1
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.015 0.021 -10000 0 -0.26 3 3
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
TAT 0.002 0.048 -10000 0 -0.39 6 6
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.057 0.13 -10000 0 -0.34 87 87
PPARGC1A -0.13 0.23 -10000 0 -0.46 166 166
FHL2 0.026 0.031 -10000 0 -0.46 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.018 -10000 0 -0.33 1 1
HIST2H4A -0.002 0.062 -10000 0 -0.28 25 25
SIRT1/FOXO3a 0.013 0.029 0.27 1 -0.21 6 7
SIRT1 0.023 0.022 -10000 0 -0.46 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.021 -10000 0 -0.28 1 1
SIRT1/Histone H1b 0.018 0.047 -10000 0 -0.23 3 3
apoptosis -0.05 0.02 0.28 1 -10000 0 1
SIRT1/PGC1A -0.071 0.15 -10000 0 -0.28 165 165
p53/SIRT1 0.026 0.036 -10000 0 -0.33 5 5
SIRT1/FOXO4 0.026 0.034 -10000 0 -0.23 4 4
FOXO1/FHL2/SIRT1 0.046 0.027 -10000 0 -0.26 3 3
HIST1H1E 0.009 0.035 -10000 0 -0.25 4 4
SIRT1/p300 0.036 0.024 -10000 0 -0.33 2 2
muscle cell differentiation 0.028 0.12 0.29 93 -0.2 3 96
TP53 0.019 0.043 -10000 0 -0.46 4 4
KU70/SIRT1/BAX 0.051 0.02 -10000 0 -0.28 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
MEF2D 0.028 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.038 -10000 0 -0.28 7 7
ACSS2 0.011 0.016 -10000 0 -0.33 1 1
SIRT1/PCAF/MYOD -0.028 0.12 0.2 3 -0.29 93 96
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.096 0.21 -10000 0 -0.46 128 128
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.026 -10000 0 -0.39 2 2
TCEB1 0.025 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.024 0.065 0.26 4 -0.3 8 12
HIF1A 0.005 0.044 -10000 0 -0.27 10 10
COPS5 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.063 0.036 -10000 0 -10000 0 0
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.13 0.19 -10000 0 -0.39 187 187
ARNT/IPAS -0.05 0.16 -10000 0 -0.33 124 124
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/ARNT 0.024 0.059 0.26 3 -0.27 10 13
CUL2 0.027 0.005 -10000 0 -10000 0 0
OS9 0.028 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.047 0.022 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.021 0.054 0.26 1 -0.27 11 12
PHD1-3/OS9 0.05 0.064 -10000 0 -0.26 5 5
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.058 0.26 1 -0.33 2 3
VHL 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.021 0.055 0.26 1 -0.27 10 11
EGLN3 0.004 0.096 -10000 0 -0.4 27 27
EGLN2 0.027 0.005 -10000 0 -10000 0 0
EGLN1 0.027 0.004 -10000 0 -10000 0 0
TP53 0.023 0.043 -10000 0 -0.46 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.013 0.17 -10000 0 -0.49 49 49
ARNT 0.027 0.004 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.054 0.1 -10000 0 -0.36 10 10
Glucocorticoid receptor regulatory network

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
PCK2 0.05 0.063 -10000 0 -10000 0 0
SMARCC2 0.029 0.009 -10000 0 -10000 0 0
SMARCC1 0.025 0.012 -10000 0 -10000 0 0
TBX21 -0.083 0.16 -10000 0 -0.67 21 21
SUMO2 0.027 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.084 -10000 0 -0.38 22 22
FKBP4 0.026 0.008 -10000 0 -10000 0 0
FKBP5 0.024 0.036 -10000 0 -0.44 3 3
GR alpha/HSP90/FKBP51/HSP90 0.087 0.08 0.33 12 -0.25 1 13
PRL -0.077 0.13 -10000 0 -0.6 5 5
cortisol/GR alpha (dimer)/TIF2 0.11 0.18 0.56 31 -10000 0 31
RELA -0.011 0.09 -10000 0 -0.26 10 10
FGG 0.074 0.17 0.5 17 -0.37 15 32
GR beta/TIF2 0.052 0.12 0.33 15 -0.29 23 38
IFNG -0.2 0.2 -10000 0 -0.61 51 51
apoptosis 0.016 0.15 0.49 9 -0.56 10 19
CREB1 0.029 0.015 -10000 0 -10000 0 0
histone acetylation -0.006 0.098 0.3 10 -0.38 7 17
BGLAP -0.041 0.094 -10000 0 -0.47 6 6
GR/PKAc 0.1 0.077 0.33 11 -0.29 1 12
NF kappa B1 p50/RelA -0.02 0.15 -10000 0 -0.41 26 26
SMARCD1 0.029 0.008 -10000 0 -10000 0 0
MDM2 0.052 0.065 0.24 23 -10000 0 23
GATA3 0.013 0.084 -10000 0 -0.4 20 20
AKT1 0.021 0.006 -10000 0 -10000 0 0
CSF2 -0.14 0.14 -10000 0 -0.52 13 13
GSK3B 0.024 0.013 -10000 0 -10000 0 0
NR1I3 0.023 0.15 0.46 9 -0.66 4 13
CSN2 0.073 0.12 0.4 16 -10000 0 16
BRG1/BAF155/BAF170/BAF60A 0.065 0.037 -10000 0 -0.4 1 1
NFATC1 0.025 0.01 -10000 0 -10000 0 0
POU2F1 0.028 0.014 -10000 0 -10000 0 0
CDKN1A 0.016 0.05 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.006 -10000 0 -10000 0 0
SFN 0.024 0.04 -10000 0 -0.42 4 4
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.081 0.34 9 -10000 0 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.002 0.21 0.45 8 -0.8 25 33
JUN -0.15 0.13 -10000 0 -0.52 26 26
IL4 -0.049 0.089 -10000 0 -0.52 3 3
CDK5R1 0.026 0.026 -10000 0 -0.39 2 2
PRKACA 0.028 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.2 0.18 4 -0.4 100 104
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.08 0.34 10 -10000 0 10
cortisol/GR alpha (monomer) 0.17 0.21 0.67 37 -10000 0 37
NCOA2 -0.009 0.12 -10000 0 -0.46 36 36
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.11 0.15 -10000 0 -0.51 63 63
AP-1/NFAT1-c-4 -0.24 0.19 -10000 0 -0.61 59 59
AFP -0.1 0.13 -10000 0 -0.64 7 7
SUV420H1 0.026 0.008 -10000 0 -10000 0 0
IRF1 0.083 0.11 0.46 8 -10000 0 8
TP53 0.038 0.044 -10000 0 -0.45 4 4
PPP5C 0.027 0.005 -10000 0 -10000 0 0
KRT17 -0.21 0.23 -10000 0 -0.76 36 36
KRT14 -0.16 0.31 -10000 0 -1.2 34 34
TBP 0.033 0.017 -10000 0 -10000 0 0
CREBBP 0.066 0.074 0.32 28 -0.34 1 29
HDAC1 0.027 0.007 -10000 0 -10000 0 0
HDAC2 0.042 0.017 -10000 0 -10000 0 0
AP-1 -0.24 0.19 -10000 0 -0.61 60 60
MAPK14 0.026 0.011 -10000 0 -10000 0 0
MAPK10 0 0.11 -10000 0 -0.45 27 27
MAPK11 0.026 0.011 -10000 0 -10000 0 0
KRT5 -0.16 0.19 -10000 0 -0.78 21 21
interleukin-1 receptor activity 0.015 0.016 -10000 0 -10000 0 0
NCOA1 0.03 0.004 -10000 0 -10000 0 0
STAT1 0.015 0.084 -10000 0 -0.38 22 22
CGA -0.048 0.093 -10000 0 -0.53 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.14 0.41 46 -0.33 1 47
MAPK3 0.027 0.011 -10000 0 -10000 0 0
MAPK1 0.026 0.011 -10000 0 -10000 0 0
ICAM1 -0.089 0.17 -10000 0 -0.56 23 23
NFKB1 -0.012 0.094 -10000 0 -0.27 13 13
MAPK8 -0.12 0.12 -10000 0 -0.51 24 24
MAPK9 0.026 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.016 0.16 0.5 9 -0.59 10 19
BAX 0.016 0.051 -10000 0 -10000 0 0
POMC -0.11 0.25 -10000 0 -1.3 14 14
EP300 0.064 0.074 0.32 27 -0.35 2 29
cortisol/GR alpha (dimer)/p53 0.16 0.18 0.58 36 -0.39 1 37
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.054 0.24 10 -10000 0 10
SGK1 0.07 0.12 0.55 2 -1.1 2 4
IL13 -0.14 0.15 -10000 0 -0.68 11 11
IL6 -0.13 0.3 -10000 0 -0.92 53 53
PRKACG -0.008 0.019 -10000 0 -10000 0 0
IL5 -0.12 0.12 -10000 0 -0.67 3 3
IL2 -0.16 0.16 -10000 0 -0.71 13 13
CDK5 0.027 0.008 -10000 0 -10000 0 0
PRKACB 0.026 0.022 -10000 0 -0.46 1 1
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
IL8 -0.12 0.21 -10000 0 -0.64 35 35
CDK5R1/CDK5 0.038 0.023 -10000 0 -0.27 2 2
NF kappa B1 p50/RelA/PKAc 0.011 0.13 -10000 0 -0.35 10 10
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.17 0.55 34 -10000 0 34
SMARCA4 0.028 0.009 -10000 0 -10000 0 0
chromatin remodeling 0.087 0.1 0.38 19 -0.48 1 20
NF kappa B1 p50/RelA/Cbp 0.054 0.16 0.39 12 -0.38 9 21
JUN (dimer) -0.15 0.13 -10000 0 -0.52 26 26
YWHAH 0.027 0.004 -10000 0 -10000 0 0
VIPR1 -0.072 0.16 -10000 0 -0.79 18 18
NR3C1 0.099 0.13 0.46 25 -10000 0 25
NR4A1 -0.004 0.11 -10000 0 -0.47 20 20
TIF2/SUV420H1 0.011 0.09 -10000 0 -0.33 32 32
MAPKKK cascade 0.016 0.15 0.49 9 -0.56 10 19
cortisol/GR alpha (dimer)/Src-1 0.16 0.18 0.56 41 -10000 0 41
PBX1 -0.059 0.19 -10000 0 -0.46 91 91
POU1F1 -0.001 0.023 -10000 0 -10000 0 0
SELE -0.17 0.35 -10000 0 -0.96 74 74
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.087 0.1 0.38 19 -0.49 1 20
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.17 0.55 34 -10000 0 34
mol:cortisol 0.082 0.12 0.38 39 -10000 0 39
MMP1 -0.34 0.16 -10000 0 -0.53 116 116
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.037 0.12 -9999 0 -0.38 7 7
Syndecan-3/Neurocan 0.012 0.074 -9999 0 -0.36 12 12
POMC -0.025 0.14 -9999 0 -0.4 63 63
EGFR 0.021 0.044 -9999 0 -0.46 4 4
Syndecan-3/EGFR 0.018 0.064 -9999 0 -0.36 11 11
AGRP -0.002 0.022 -9999 0 -10000 0 0
NCSTN 0.027 0.004 -9999 0 -10000 0 0
PSENEN 0.027 0.005 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.028 0.004 -9999 0 -10000 0 0
APH1A 0.027 0.005 -9999 0 -10000 0 0
NCAN -0.005 0.089 -9999 0 -0.39 25 25
long-term memory 0.026 0.059 -9999 0 -0.35 9 9
Syndecan-3/IL8 -0.019 0.1 -9999 0 -0.4 14 14
PSEN1 0.027 0.006 -9999 0 -10000 0 0
Src/Cortactin 0.028 0.02 -9999 0 -10000 0 0
FYN 0.027 0.019 -9999 0 -0.39 1 1
limb bud formation 0.004 0.061 -9999 0 -0.37 13 13
MC4R 0.002 0.028 -9999 0 -0.39 1 1
SRC 0.026 0.007 -9999 0 -10000 0 0
PTN -0.15 0.24 -9999 0 -0.46 186 186
FGFR/FGF/Syndecan-3 0.004 0.062 -9999 0 -0.38 13 13
neuron projection morphogenesis -0.033 0.13 -9999 0 -0.35 9 9
Syndecan-3/AgRP 0.017 0.063 -9999 0 -0.36 13 13
Syndecan-3/AgRP/MC4R 0.028 0.064 -9999 0 -0.34 13 13
Fyn/Cortactin 0.029 0.019 -9999 0 -10000 0 0
SDC3 0.004 0.062 -9999 0 -0.38 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.019 0.1 -9999 0 -0.4 14 14
IL8 -0.059 0.17 -9999 0 -0.39 106 106
Syndecan-3/Fyn/Cortactin 0.027 0.06 -9999 0 -0.35 9 9
Syndecan-3/CASK 0.003 0.059 -9999 0 -0.36 13 13
alpha-MSH/MC4R -0.006 0.11 -9999 0 -0.28 63 63
Gamma Secretase 0.075 0.026 -9999 0 -10000 0 0
IL27-mediated signaling events

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.038 -10000 0 -0.38 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.054 0.13 0.5 17 -10000 0 17
IL27/IL27R/JAK1 -0.039 0.15 -10000 0 -0.52 14 14
TBX21 -0.089 0.17 -10000 0 -0.53 29 29
IL12B -0.013 0.12 -10000 0 -0.39 44 44
IL12A -0.007 0.055 -10000 0 -0.32 15 15
IL6ST -0.039 0.16 -10000 0 -0.47 60 60
IL27RA/JAK1 -0.004 0.067 -10000 0 -10000 0 0
IL27 -0.004 0.088 -10000 0 -0.4 23 23
TYK2 0.017 0.028 -10000 0 -0.4 1 1
T-helper cell lineage commitment 0.003 0.11 0.43 1 -0.57 1 2
T-helper 2 cell differentiation 0.054 0.13 0.5 17 -10000 0 17
T cell proliferation during immune response 0.054 0.13 0.5 17 -10000 0 17
MAPKKK cascade -0.054 0.13 -10000 0 -0.5 17 17
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT2 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.008 0.085 -10000 0 -0.39 22 22
IL12RB1 -0.003 0.11 -10000 0 -0.39 37 37
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.12 0.19 -10000 0 -0.51 43 43
IL27/IL27R/JAK2/TYK2 -0.055 0.14 -10000 0 -0.5 18 18
positive regulation of T cell mediated cytotoxicity -0.054 0.13 -10000 0 -0.5 17 17
STAT1 (dimer) -0.081 0.2 0.52 1 -0.6 24 25
JAK2 0.017 0.019 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.044 0.14 -10000 0 -0.48 17 17
T cell proliferation -0.067 0.14 -10000 0 -0.5 25 25
IL12/IL12R/TYK2/JAK2 -0.05 0.19 -10000 0 -0.75 27 27
IL17A 0.003 0.11 0.43 1 -0.57 1 2
mast cell activation 0.054 0.13 0.5 17 -10000 0 17
IFNG -0.011 0.038 -10000 0 -0.1 8 8
T cell differentiation -0.005 0.007 -10000 0 -0.019 64 64
STAT3 (dimer) -0.044 0.14 -10000 0 -0.48 17 17
STAT5A (dimer) -0.044 0.14 -10000 0 -0.48 17 17
STAT4 (dimer) -0.047 0.14 -10000 0 -0.48 22 22
STAT4 0.016 0.066 -10000 0 -0.39 13 13
T cell activation -0.005 0.012 0.05 19 -10000 0 19
IL27R/JAK2/TYK2 -0.021 0.12 -10000 0 -0.54 3 3
GATA3 -0.004 0.12 0.6 4 -1.3 3 7
IL18 -0.002 0.051 -10000 0 -0.33 12 12
positive regulation of mast cell cytokine production -0.043 0.14 -10000 0 -0.48 17 17
IL27/EBI3 0.006 0.083 -10000 0 -0.3 31 31
IL27RA -0.012 0.068 -10000 0 -10000 0 0
IL6 -0.014 0.14 -10000 0 -0.45 46 46
STAT5A 0.028 0.003 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.001 0.047 -10000 0 -10000 0 0
IL1B -0.022 0.085 -10000 0 -0.28 52 52
EBI3 0.013 0.061 -10000 0 -0.42 9 9
TNF -0.006 0.059 -10000 0 -0.28 23 23
Noncanonical Wnt signaling pathway

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
NFATC2 -0.029 0.15 -10000 0 -0.46 57 57
GNB1/GNG2 0 0.12 -10000 0 -0.46 12 12
mol:DAG -0.014 0.1 0.19 3 -0.44 10 13
PLCG1 -0.015 0.1 0.2 3 -0.46 10 13
YES1 -0.019 0.096 -10000 0 -0.47 11 11
FZD3 0.019 0.057 -10000 0 -0.46 7 7
FZD6 0.023 0.024 -10000 0 -0.46 1 1
G protein 0.003 0.12 0.26 4 -0.47 10 14
MAP3K7 -0.051 0.12 0.28 6 -0.41 20 26
mol:Ca2+ -0.014 0.098 0.19 3 -0.43 10 13
mol:IP3 -0.014 0.1 0.19 3 -0.44 10 13
NLK 0.006 0.066 -10000 0 -0.72 4 4
GNB1 0.027 0.006 -10000 0 -10000 0 0
CAMK2A -0.052 0.14 0.29 7 -0.41 26 33
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.017 0.11 -10000 0 -0.45 15 15
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.021 0.098 -10000 0 -0.44 13 13
GO:0007205 -0.016 0.1 0.25 9 -0.45 10 19
WNT6 -0.009 0.12 -10000 0 -0.4 43 43
WNT4 0.013 0.079 -10000 0 -0.44 15 15
NFAT1/CK1 alpha -0.014 0.14 0.28 5 -0.46 15 20
GNG2 0.026 0.007 -10000 0 -10000 0 0
WNT5A 0.019 0.052 -10000 0 -0.45 6 6
WNT11 -0.019 0.13 -10000 0 -0.41 52 52
CDC42 -0.008 0.1 0.19 21 -0.48 9 30
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.01 0.058 0.63 2 -10000 0 2
VDR 0.026 0.031 -10000 0 -0.46 2 2
FAM120B 0.027 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.005 0.093 -10000 0 -0.34 9 9
RXRs/LXRs/DNA/Oxysterols 0.014 0.097 -10000 0 -0.39 11 11
MED1 0.028 0.003 -10000 0 -10000 0 0
mol:9cRA 0.003 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.008 0.092 -10000 0 -0.36 4 4
RXRs/NUR77 0.025 0.12 -10000 0 -0.26 62 62
RXRs/PPAR -0.081 0.13 -10000 0 -0.34 35 35
NCOR2 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 -10000 0 -0.33 2 2
RARs/VDR/DNA/Vit D3 0.034 0.083 -10000 0 -0.24 38 38
RARA 0.027 0.004 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.031 -10000 0 -0.46 2 2
RARs/RARs/DNA/9cRA 0.023 0.076 -10000 0 -0.24 37 37
RARG 0.027 0.022 -10000 0 -0.46 1 1
RPS6KB1 0.016 0.046 0.54 3 -10000 0 3
RARs/THRs/DNA/SMRT -0.01 0.093 -10000 0 -0.35 5 5
THRA 0.028 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.022 -10000 0 -0.33 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.02 0.1 -10000 0 -0.25 54 54
NR1H4 -0.004 0.027 -10000 0 -0.39 1 1
RXRs/LXRs/DNA 0.041 0.12 -10000 0 -0.36 4 4
NR1H2 0.029 0.015 -10000 0 -10000 0 0
NR1H3 0.024 0.047 -10000 0 -0.38 6 6
RXRs/VDR/DNA/Vit D3 0.027 0.1 -10000 0 -0.24 55 55
NR4A1 0.018 0.068 -10000 0 -0.46 10 10
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.002 0.074 -10000 0 -0.25 7 7
RXRG -0.032 0.16 -10000 0 -0.45 63 63
RXR alpha/CCPG 0.041 0.013 -10000 0 -10000 0 0
RXRA 0.028 0.015 -10000 0 -10000 0 0
RXRB 0.028 0.016 -10000 0 -10000 0 0
THRB -0.004 0.12 -10000 0 -0.46 30 30
PPARG -0.13 0.23 -10000 0 -0.46 166 166
PPARD 0.027 0.006 -10000 0 -10000 0 0
TNF 0.001 0.13 -10000 0 -0.8 6 6
mol:Oxysterols 0.003 0.007 -10000 0 -10000 0 0
cholesterol transport 0.014 0.096 -10000 0 -0.38 11 11
PPARA 0.027 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.01 0.12 -10000 0 -0.46 36 36
RXRs/NUR77/BCL2 -0.012 0.093 -10000 0 -0.24 62 62
SREBF1 0.01 0.088 -10000 0 -0.53 1 1
RXRs/RXRs/DNA/9cRA 0.02 0.1 -10000 0 -0.25 54 54
ABCA1 0.006 0.1 -10000 0 -0.85 3 3
RARs/THRs 0.028 0.11 -10000 0 -0.47 2 2
RXRs/FXR 0.026 0.11 -10000 0 -0.25 54 54
BCL2 0.022 0.039 -10000 0 -0.41 4 4
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.006 0.033 -10000 0 -0.46 1 1
HSPA8 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.055 0.099 -10000 0 -0.29 14 14
AKT1 0.005 0.047 -10000 0 -10000 0 0
GSC 0.006 0.14 -10000 0 -1.4 2 2
NKX2-5 0 0.009 -10000 0 -10000 0 0
muscle cell differentiation 0.045 0.15 0.39 44 -10000 0 44
SMAD2-3/SMAD4/SP1 -0.004 0.12 -10000 0 -0.32 2 2
SMAD4 0.009 0.047 -10000 0 -10000 0 0
CBFB 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.019 0.049 -10000 0 -0.24 6 6
SMAD3/SMAD4/VDR 0.058 0.056 -10000 0 -10000 0 0
MYC 0.028 0.023 -10000 0 -10000 0 0
CDKN2B -0.37 0.65 -10000 0 -1.5 122 122
AP1 0.007 0.094 -10000 0 -0.29 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.035 0.082 -10000 0 -0.45 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.067 0.16 -10000 0 -0.35 103 103
SP3 0.028 0.006 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 -0.023 0.12 -10000 0 -0.38 53 53
SMAD3/SMAD4/GR 0.062 0.065 -10000 0 -10000 0 0
GATA3 0.011 0.084 -10000 0 -0.39 20 20
SKI/SIN3/HDAC complex/NCoR1 0.029 0.058 -10000 0 -0.47 4 4
MEF2C/TIF2 -0.012 0.13 0.32 1 -0.42 21 22
endothelial cell migration 0.16 0.16 0.74 2 -10000 0 2
MAX 0.038 0.015 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.027 0.022 -10000 0 -0.46 1 1
RUNX2 0.025 0.029 -10000 0 -0.42 2 2
RUNX3 0.022 0.048 -10000 0 -0.39 7 7
RUNX1 0.027 0.006 -10000 0 -10000 0 0
CTBP1 0.026 0.007 -10000 0 -10000 0 0
NR3C1 0.039 0.015 -10000 0 -10000 0 0
VDR 0.026 0.031 -10000 0 -0.46 2 2
CDKN1A -0.012 0.1 -10000 0 -0.58 7 7
KAT2B 0.005 0.092 -10000 0 -0.46 19 19
SMAD2/SMAD2/SMAD4/FOXH1 -0.002 0.1 -10000 0 -0.29 20 20
DCP1A 0.024 0.009 -10000 0 -10000 0 0
SKI 0.027 0.006 -10000 0 -10000 0 0
SERPINE1 -0.16 0.17 -10000 0 -0.74 2 2
SMAD3/SMAD4/ATF2 0.034 0.061 -10000 0 -0.26 1 1
SMAD3/SMAD4/ATF3 0.03 0.073 -10000 0 -0.31 7 7
SAP30 0.026 0.019 -10000 0 -0.38 1 1
Cbp/p300/PIAS3 0.016 0.047 -10000 0 -0.28 1 1
JUN -0.001 0.091 0.29 1 -10000 0 1
SMAD3/SMAD4/IRF7 0.026 0.082 -10000 0 -0.38 4 4
TFE3 -0.001 0.03 -10000 0 -10000 0 0
COL1A2 -0.094 0.16 -10000 0 -0.32 158 158
mesenchymal cell differentiation -0.033 0.063 0.3 2 -10000 0 2
DLX1 -0.13 0.2 -10000 0 -0.39 196 196
TCF3 0.027 0.005 -10000 0 -10000 0 0
FOS -0.031 0.16 -10000 0 -0.46 63 63
SMAD3/SMAD4/Max 0.06 0.065 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.047 0.021 -10000 0 -0.28 1 1
ZBTB17 0.03 0.013 -10000 0 -10000 0 0
LAMC1 0.001 0.044 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.033 0.06 -10000 0 -10000 0 0
IRF7 0.013 0.074 -10000 0 -0.4 15 15
ESR1 0.013 0.097 -10000 0 -0.42 24 24
HNF4A -0.024 0.12 -10000 0 -0.39 49 49
MEF2C 0.006 0.12 0.43 2 -0.41 13 15
SMAD2-3/SMAD4 0.028 0.08 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.04 0.027 -10000 0 -0.28 1 1
IGHV3OR16-13 0.006 0.047 -10000 0 -0.34 9 9
TGIF2/HDAC complex 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.01 0.023 -10000 0 -10000 0 0
SKIL 0.02 0.013 -10000 0 -10000 0 0
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.005 -10000 0 -10000 0 0
SNIP1 0.029 0.004 -10000 0 -10000 0 0
GCN5L2 -0.005 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.018 0.06 -10000 0 -10000 0 0
MSG1/HSC70 0.036 0.037 -10000 0 -0.27 6 6
SMAD2 0.007 0.044 -10000 0 -10000 0 0
SMAD3 0.013 0.046 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.041 -10000 0 -0.4 1 1
SMAD2/SMAD2/SMAD4 -0.051 0.13 0.21 3 -0.4 51 54
NCOR1 0.027 0.006 -10000 0 -10000 0 0
NCOA2 -0.009 0.12 -10000 0 -0.46 36 36
NCOA1 0.028 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.022 0.13 -10000 0 -0.33 81 81
SMAD2-3/SMAD4/SP1/MIZ-1 0.01 0.12 -10000 0 -0.33 3 3
IFNB1 -0.003 0.077 -10000 0 -0.39 9 9
SMAD3/SMAD4/MEF2C 0.019 0.13 -10000 0 -0.42 11 11
CITED1 0.022 0.045 -10000 0 -0.39 6 6
SMAD2-3/SMAD4/ARC105 0.039 0.08 -10000 0 -10000 0 0
RBL1 0.025 0.023 -10000 0 -0.46 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.089 0.23 -10000 0 -0.53 107 107
RUNX1-3/PEBPB2 0.048 0.036 -10000 0 -0.22 7 7
SMAD7 -0.014 0.1 -10000 0 -0.41 2 2
MYC/MIZ-1 0.041 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.064 0.11 0.28 4 -0.4 7 11
IL10 0.001 0.079 -10000 0 -0.36 9 9
PIASy/HDAC complex 0.031 0.013 -10000 0 -10000 0 0
PIAS3 0.024 0.007 -10000 0 -10000 0 0
CDK2 0.021 0.014 -10000 0 -10000 0 0
IL5 -0.003 0.069 -10000 0 -0.37 3 3
CDK4 0.01 0.023 -10000 0 -10000 0 0
PIAS4 0.031 0.013 -10000 0 -10000 0 0
ATF3 0.02 0.057 -10000 0 -0.43 8 8
SMAD3/SMAD4/SP1 -0.01 0.099 -10000 0 -0.3 3 3
FOXG1 -0.061 0.15 -10000 0 -0.41 79 79
FOXO3 -0.008 0.049 -10000 0 -10000 0 0
FOXO1 -0.008 0.049 -10000 0 -10000 0 0
FOXO4 -0.009 0.051 -10000 0 -0.33 1 1
heart looping 0.006 0.12 0.43 2 -0.41 13 15
CEBPB 0.012 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.069 0.14 -10000 0 -0.28 76 76
MYOD1 -0.069 0.17 -10000 0 -0.46 81 81
SMAD3/SMAD4/HNF4 0.005 0.098 -10000 0 -0.29 11 11
SMAD3/SMAD4/GATA3 0.028 0.085 -10000 0 -0.32 3 3
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.057 0.068 -10000 0 -0.28 1 1
SMAD3/SMAD4/SP1-3 0.007 0.096 -10000 0 -10000 0 0
MED15 0.026 0.019 -10000 0 -0.39 1 1
SP1 -0.017 0.06 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.001 0.098 -10000 0 -0.28 18 18
ITGB5 -0.01 0.073 0.35 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.035 0.037 -10000 0 -0.32 1 1
SMAD3/SMAD4/AR -0.052 0.15 -10000 0 -0.29 134 134
AR -0.11 0.21 -10000 0 -0.46 139 139
negative regulation of cell growth 0.008 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.02 0.13 -10000 0 -0.3 77 77
E2F5 0.022 0.038 -10000 0 -0.46 3 3
E2F4 0.027 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.094 -10000 0 -0.29 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 -0.046 0.16 -10000 0 -0.36 101 101
TFDP1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.022 0.1 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.034 0.064 -10000 0 -0.3 2 2
TGIF2 0.026 0.007 -10000 0 -10000 0 0
TGIF1 0.025 0.009 -10000 0 -10000 0 0
ATF2 0.026 0.022 -10000 0 -0.46 1 1
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.01 0.07 -10000 0 -0.45 10 10
PDGF/PDGFRA/CRKL 0.023 0.055 -10000 0 -0.31 11 11
positive regulation of JUN kinase activity 0.058 0.042 -10000 0 -0.24 6 6
CRKL 0.026 0.019 -10000 0 -0.39 1 1
PDGF/PDGFRA/Caveolin-3 -0.051 0.15 -10000 0 -0.34 105 105
AP1 -0.1 0.3 0.31 2 -0.87 66 68
mol:IP3 -0.001 0.054 -10000 0 -0.32 10 10
PLCG1 -0.001 0.054 -10000 0 -0.32 10 10
PDGF/PDGFRA/alphaV Integrin 0.023 0.055 -10000 0 -0.3 11 11
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.053 -10000 0 -0.32 10 10
CAV3 -0.086 0.18 -10000 0 -0.46 99 99
CAV1 -0.004 0.11 -10000 0 -0.39 38 38
SHC/Grb2/SOS1 0.06 0.043 -10000 0 -0.25 6 6
PDGF/PDGFRA/Shf 0.019 0.074 -10000 0 -0.35 16 16
FOS -0.11 0.29 0.32 2 -0.86 66 68
JUN -0.023 0.025 -10000 0 -10000 0 0
oligodendrocyte development 0.023 0.055 -10000 0 -0.3 11 11
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
mol:DAG -0.001 0.054 -10000 0 -0.32 10 10
PDGF/PDGFRA 0.01 0.07 -10000 0 -0.45 10 10
actin cytoskeleton reorganization 0.022 0.052 -10000 0 -0.3 10 10
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.033 0.043 -10000 0 -0.27 6 6
PDGF/PDGFRA/Crk/C3G 0.044 0.046 -10000 0 -0.26 9 9
JAK1 0.003 0.047 -10000 0 -0.31 10 10
ELK1/SRF 0.004 0.046 0.17 1 -0.27 6 7
SHB 0.025 0.009 -10000 0 -10000 0 0
SHF 0.02 0.061 -10000 0 -0.46 8 8
CSNK2A1 0.029 0.02 -10000 0 -10000 0 0
GO:0007205 -0.007 0.053 -10000 0 -0.33 10 10
SOS1 0.028 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.058 0.042 -10000 0 -0.24 6 6
PDGF/PDGFRA/SHB 0.022 0.052 -10000 0 -0.3 10 10
PDGF/PDGFRA/Caveolin-1 0.001 0.096 -10000 0 -0.29 48 48
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
ELK1 -0.013 0.053 -10000 0 -0.29 10 10
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.024 0.053 -10000 0 -0.3 10 10
JAK-STAT cascade 0.003 0.047 -10000 0 -0.31 10 10
cell proliferation 0.019 0.073 -10000 0 -0.35 16 16
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.028 0.003 -10000 0 -10000 0 0
mol:PIP3 0.001 0.03 -10000 0 -0.21 3 3
FRAP1 0.029 0.068 -10000 0 -0.42 7 7
AKT1 0.034 0.074 0.16 109 -0.23 2 111
INSR 0.027 0.022 -10000 0 -0.46 1 1
Insulin Receptor/Insulin 0.028 0.022 -10000 0 -0.25 3 3
mol:GTP 0.06 0.071 0.26 6 -10000 0 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.01 0.021 -10000 0 -10000 0 0
TSC2 0.027 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.014 0.03 -10000 0 -10000 0 0
TSC1 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.017 0.051 -10000 0 -0.2 25 25
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.03 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.028 0.004 -10000 0 -10000 0 0
RPS6KB1 0.048 0.071 0.23 13 -0.26 1 14
MAP3K5 0.005 0.034 0.19 7 -0.18 10 17
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
apoptosis 0.005 0.034 0.19 7 -0.18 10 17
mol:LY294002 0 0 -10000 0 -0.001 23 23
EIF4B 0.045 0.068 0.23 14 -10000 0 14
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.057 0.061 0.22 8 -10000 0 8
eIF4E/eIF4G1/eIF4A1 0.012 0.033 -10000 0 -0.27 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.042 -10000 0 -0.2 9 9
mTOR/RHEB/GTP/Raptor/GBL 0.037 0.06 0.21 20 -0.19 1 21
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
RHEB/GTP 0.053 0.058 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 23 23
FKBP12/Rapamycin 0.021 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.072 0.16 103 -0.22 3 106
EIF4E 0.027 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.038 0.1 -10000 0 -0.5 14 14
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.005 0.099 -10000 0 -0.73 6 6
TSC1/TSC2 0.066 0.077 0.29 7 -10000 0 7
tumor necrosis factor receptor activity 0 0 0.001 23 -10000 0 23
RPS6 0.025 0.009 -10000 0 -10000 0 0
PPP5C 0.027 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.013 -10000 0 -10000 0 0
IRS1 0 0.05 -10000 0 -0.22 25 25
INS -0.017 0.025 -10000 0 -0.39 2 2
PTEN 0.026 0.006 -10000 0 -10000 0 0
PDK2 0.024 0.072 0.16 105 -0.21 2 107
EIF4EBP1 -0.027 0.22 -10000 0 -1 24 24
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PPP2R5D 0.03 0.068 0.25 6 -0.37 7 13
peptide biosynthetic process -0.009 0.024 0.18 4 -0.22 3 7
RHEB 0.027 0.007 -10000 0 -10000 0 0
EIF4A1 0.027 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 133 -10000 0 133
EEF2 -0.01 0.024 0.18 4 -0.22 3 7
eIF4E/4E-BP1 -0.012 0.21 -10000 0 -0.95 24 24
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.022 -10000 0 -0.27 3 3
MAP4K4 0.019 0.064 0.21 3 -0.39 5 8
BAG4 0.023 0.023 -10000 0 -0.46 1 1
PKC zeta/ceramide -0.009 0.068 -10000 0 -0.21 34 34
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.39 15 15
BAX -0.004 0.053 -10000 0 -0.34 10 10
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.023 0.13 0.69 19 -10000 0 19
BAD -0.019 0.068 0.2 10 -0.22 31 41
SMPD1 0.019 0.067 0.19 19 -0.24 9 28
RB1 -0.022 0.061 0.2 1 -0.22 31 32
FADD/Caspase 8 0.057 0.1 0.24 66 -0.4 3 69
MAP2K4 -0.02 0.058 0.18 4 -0.27 9 13
NSMAF 0.025 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.02 0.061 0.18 7 -0.26 11 18
EGF -0.067 0.19 -10000 0 -0.46 98 98
mol:ceramide -0.023 0.065 -10000 0 -0.22 33 33
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.011 0.022 -10000 0 -0.26 3 3
ASAH1 0.026 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.022 0.061 0.19 1 -0.21 31 32
cell proliferation -0.029 0.097 -10000 0 -0.27 22 22
BID 0.011 0.11 -10000 0 -0.61 10 10
MAP3K1 -0.022 0.061 0.19 2 -0.22 29 31
EIF2A 0.022 0.1 0.26 22 -0.27 8 30
TRADD 0.027 0.006 -10000 0 -10000 0 0
CRADD 0.028 0.002 -10000 0 -10000 0 0
MAPK3 -0.015 0.061 0.18 1 -0.27 7 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.061 0.18 2 -0.28 7 9
Cathepsin D/ceramide -0.008 0.067 -10000 0 -0.21 33 33
FADD 0.044 0.082 0.2 75 -0.37 3 78
KSR1 -0.021 0.064 0.19 5 -0.22 32 37
MAPK8 -0.018 0.07 -10000 0 -0.26 18 18
PRKRA -0.017 0.069 0.19 14 -0.22 29 43
PDGFA 0.024 0.032 -10000 0 -0.39 3 3
TRAF2 0.023 0.041 -10000 0 -0.39 5 5
IGF1 -0.053 0.18 -10000 0 -0.46 85 85
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.064 -10000 0 -0.22 33 33
CTSD 0.027 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.03 0.1 -10000 0 -0.29 22 22
PRKCD 0.024 0.009 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.46 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.011 0.022 -10000 0 -0.26 3 3
RelA/NF kappa B1 0.038 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.052 -10000 0 -0.38 5 5
TNFR1A/BAG4/TNF-alpha 0.033 0.061 -10000 0 -0.24 21 21
mol:Sphingosine-1-phosphate 0.012 0.022 -10000 0 -0.27 3 3
MAP2K1 -0.019 0.06 0.2 1 -0.27 7 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
CYCS 0.002 0.048 0.18 3 -0.19 8 11
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.023 -10000 0 -0.33 1 1
EIF2AK2 -0.017 0.068 0.2 14 -0.27 11 25
TNF-alpha/TNFR1A/FAN 0.034 0.06 -10000 0 -0.23 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.024 0.076 -10000 0 -0.42 9 9
MAP2K2 -0.019 0.059 -10000 0 -0.25 10 10
SMPD3 -0.001 0.097 0.2 4 -0.3 39 43
TNF 0.008 0.088 -10000 0 -0.4 23 23
PKC zeta/PAR4 0.039 0.019 -10000 0 -0.33 1 1
mol:PHOSPHOCHOLINE 0.032 0.087 0.21 82 -0.18 4 86
NF kappa B1/RelA/I kappa B alpha 0.07 0.033 -10000 0 -0.24 1 1
AIFM1 -0.001 0.055 0.17 4 -0.22 5 9
BCL2 0.022 0.039 -10000 0 -0.41 4 4
S1P1 pathway

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.033 0.041 -10000 0 -0.29 7 7
PDGFRB -0.042 0.15 -10000 0 -0.39 85 85
SPHK1 0.001 0.056 -10000 0 -0.64 3 3
mol:S1P -0.003 0.054 -10000 0 -0.54 3 3
S1P1/S1P/Gi -0.031 0.12 -10000 0 -0.4 33 33
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.032 0.13 0.27 1 -0.36 27 28
PLCG1 -0.034 0.11 -10000 0 -0.37 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.042 0.15 -10000 0 -0.39 85 85
GNAI2 0.023 0.011 -10000 0 -10000 0 0
GNAI3 0.026 0.008 -10000 0 -10000 0 0
GNAI1 0.025 0.023 -10000 0 -0.47 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0 0.031 -10000 0 -0.25 7 7
S1P1/S1P -0.005 0.056 -10000 0 -0.33 3 3
negative regulation of cAMP metabolic process -0.03 0.12 -10000 0 -0.39 33 33
MAPK3 -0.04 0.14 -10000 0 -0.44 32 32
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
KDR 0.025 0.031 -10000 0 -0.46 2 2
PLCB2 0 0.063 0.24 2 -0.37 1 3
RAC1 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.048 -10000 0 -0.28 3 3
receptor internalization -0.005 0.052 -10000 0 -0.31 3 3
PTGS2 -0.043 0.18 -10000 0 -0.66 19 19
Rac1/GTP -0.004 0.047 -10000 0 -0.29 3 3
RHOA 0.025 0.009 -10000 0 -10000 0 0
VEGFA 0.021 0.045 -10000 0 -0.39 6 6
negative regulation of T cell proliferation -0.03 0.12 -10000 0 -0.39 33 33
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.011 0.08 -10000 0 -0.42 17 17
MAPK1 -0.039 0.14 -10000 0 -0.44 32 32
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.087 0.23 2 -0.32 2 4
ABCC1 0.025 0.032 -10000 0 -0.39 3 3
Cellular roles of Anthrax toxin

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
ANTXR1 0.025 0.032 -10000 0 -0.39 3 3
ANTXR2 0.018 0.06 -10000 0 -0.39 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.007 -10000 0 -0.047 13 13
monocyte activation -0.016 0.1 -10000 0 -0.37 36 36
MAP2K2 0.001 0.094 -10000 0 -0.56 14 14
MAP2K1 -0.003 0.007 -10000 0 -10000 0 0
MAP2K7 -0.003 0.007 -10000 0 -10000 0 0
MAP2K6 -0.014 0.05 -10000 0 -0.24 24 24
CYAA -0.008 0.029 -10000 0 -0.19 13 13
MAP2K4 -0.003 0.007 -10000 0 -10000 0 0
IL1B -0.017 0.063 0.19 7 -0.19 52 59
Channel 0.029 0.038 -10000 0 -0.2 13 13
NLRP1 -0.003 0.011 -10000 0 -0.19 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.075 -10000 0 -0.38 19 19
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.007 0.047 13 -10000 0 13
MAPK3 -0.003 0.007 -10000 0 -10000 0 0
MAPK1 -0.003 0.009 0.15 1 -10000 0 1
PGR -0.028 0.073 0.15 1 -0.23 57 58
PA/Cellular Receptors 0.03 0.042 -10000 0 -0.23 13 13
apoptosis -0.002 0.007 -10000 0 -0.047 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.028 0.034 -10000 0 -0.18 13 13
macrophage activation -0.004 0.009 0.14 1 -10000 0 1
TNF 0.008 0.088 -10000 0 -0.4 23 23
VCAM1 -0.015 0.1 -10000 0 -0.37 34 34
platelet activation -0.003 0.075 -10000 0 -0.38 19 19
MAPKKK cascade 0.003 0.021 0.11 1 -0.1 2 3
IL18 -0.005 0.038 0.15 3 -0.24 11 14
negative regulation of macrophage activation -0.002 0.007 -10000 0 -0.047 13 13
LEF -0.002 0.007 -10000 0 -0.047 13 13
CASP1 0 0.009 -10000 0 -0.088 2 2
mol:cAMP -0.003 0.075 -10000 0 -0.38 19 19
necrosis -0.002 0.007 -10000 0 -0.047 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.028 0.036 -10000 0 -0.19 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.035 0.035 -10000 0 -0.29 5 5
CRKL 0.015 0.12 0.31 7 -0.46 21 28
mol:PIP3 0 0.035 -10000 0 -0.74 1 1
AKT1 0.004 0.051 -10000 0 -0.65 1 1
PTK2B 0.026 0.008 -10000 0 -10000 0 0
RAPGEF1 0.019 0.12 0.28 14 -0.45 19 33
RANBP10 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.031 0.068 -10000 0 -0.26 24 24
MAP3K5 0.014 0.12 0.28 7 -0.48 19 26
HGF/MET/CIN85/CBL/ENDOPHILINS 0.044 0.072 -10000 0 -0.25 17 17
AP1 -0.01 0.11 -10000 0 -0.3 63 63
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
apoptosis -0.086 0.28 -10000 0 -0.73 80 80
STAT3 (dimer) 0.018 0.068 -10000 0 -0.31 7 7
GAB1/CRKL/SHP2/PI3K 0.031 0.1 0.32 2 -0.45 9 11
INPP5D 0.025 0.031 -10000 0 -0.46 2 2
CBL/CRK 0.022 0.11 0.31 1 -0.44 19 20
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.006 -10000 0 -10000 0 0
ELK1 -0.005 0.071 0.3 16 -0.21 1 17
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.052 0.15 1 -0.25 8 9
PAK1 0.011 0.068 0.4 5 -0.62 1 6
HGF/MET/RANBP10 0.034 0.072 -10000 0 -0.26 28 28
HRAS 0 0.12 -10000 0 -0.5 20 20
DOCK1 0.014 0.12 0.28 8 -0.45 19 27
GAB1 0.008 0.12 0.25 1 -0.47 22 23
CRK 0.01 0.11 0.28 2 -0.46 21 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.12 -10000 0 -0.47 25 25
JUN 0.028 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.002 0.044 -10000 0 -0.2 19 19
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
cell morphogenesis 0.07 0.13 0.32 50 -0.41 6 56
GRB2/SHC 0.033 0.057 -10000 0 -0.23 6 6
FOS -0.034 0.16 -10000 0 -0.46 63 63
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.005 0.07 0.3 16 -0.21 1 17
HGF/MET/MUC20 0.019 0.067 -10000 0 -0.26 28 28
cell migration 0.031 0.054 -10000 0 -0.22 6 6
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.025 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.034 0.037 -10000 0 -0.29 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.052 -10000 0 -0.25 15 15
MET/MUC20 0.016 0.034 -10000 0 -0.29 6 6
RAP1B 0.025 0.12 0.3 14 -0.44 16 30
RAP1A 0.017 0.11 0.29 9 -0.43 17 26
HGF/MET/RANBP9 0.035 0.071 -10000 0 -0.26 26 26
RAF1 0.006 0.12 -10000 0 -0.48 16 16
STAT3 0.018 0.068 -10000 0 -0.31 7 7
cell proliferation 0.02 0.1 0.31 9 -0.36 16 25
RPS6KB1 0.011 0.023 -10000 0 -0.26 1 1
MAPK3 -0.008 0.098 0.68 7 -10000 0 7
MAPK1 -0.011 0.084 0.72 4 -10000 0 4
RANBP9 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.028 0.12 0.29 7 -0.44 18 25
SRC 0.007 0.047 -10000 0 -0.31 4 4
PI3K 0.023 0.051 -10000 0 -0.25 6 6
MET/Glomulin 0.016 0.037 -10000 0 -0.24 7 7
SOS1 0.028 0.004 -10000 0 -10000 0 0
MAP2K1 0.007 0.11 0.3 1 -0.47 14 15
MET 0.022 0.048 -10000 0 -0.41 6 6
MAP4K1 0.012 0.13 0.3 6 -0.51 19 25
PTK2 0.023 0.011 -10000 0 -10000 0 0
MAP2K2 0.007 0.11 -10000 0 -0.47 13 13
BAD 0.008 0.06 0.38 3 -0.62 1 4
MAP2K4 0.015 0.12 0.27 9 -0.43 19 28
SHP2/GRB2/SOS1/GAB1 0.03 0.1 -10000 0 -0.43 15 15
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PXN 0.028 0.002 -10000 0 -10000 0 0
SH3KBP1 0.026 0.026 -10000 0 -0.39 2 2
HGS 0 0.042 -10000 0 -0.23 6 6
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF 0.006 0.095 -10000 0 -0.44 22 22
RASA1 0.024 0.031 -10000 0 -0.46 2 2
NCK1 0.023 0.011 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.03 0.05 -10000 0 -0.24 4 4
PDPK1 -0.002 0.036 -10000 0 -0.68 1 1
HGF/MET/SHIP 0.033 0.077 -10000 0 -0.27 29 29
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.019 0.088 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.019 -10000 0 -0.39 1 1
STAT1 (dimer)/Cbp/p300 0.023 0.096 0.29 1 -0.3 10 11
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.032 0.044 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.07 -10000 0 -0.26 5 5
CaM/Ca2+ 0.02 0.084 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.004 0.093 -10000 0 -0.33 10 10
AKT1 0.041 0.11 0.3 20 -10000 0 20
MAP2K1 -0.005 0.077 0.27 2 -10000 0 2
MAP3K11 -0.002 0.079 0.28 1 -10000 0 1
IFNGR1 0.02 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.13 0.21 -10000 0 -0.45 122 122
Rap1/GTP -0.007 0.058 -10000 0 -10000 0 0
CRKL/C3G 0.038 0.018 -10000 0 -0.27 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.021 0.097 -10000 0 -10000 0 0
CEBPB 0.023 0.11 0.31 4 -0.49 6 10
STAT3 0.028 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.004 0.14 -10000 0 -0.7 8 8
STAT1 -0.008 0.09 0.28 1 -0.33 10 11
CALM1 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.05 0.16 -10000 0 -0.38 97 97
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.007 0.093 0.28 1 -0.32 10 11
CEBPB/PTGES2/Cbp/p300 0.017 0.068 -10000 0 -0.34 4 4
mol:Ca2+ 0.017 0.085 -10000 0 -10000 0 0
MAPK3 0.004 0.12 -10000 0 -0.65 10 10
STAT1 (dimer) -0.037 0.097 -10000 0 -0.37 4 4
MAPK1 0.007 0.1 -10000 0 -0.58 7 7
JAK2 0.017 0.023 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
JAK1 0.02 0.023 -10000 0 -10000 0 0
CAMK2D 0.027 0.005 -10000 0 -10000 0 0
DAPK1 0.024 0.095 0.28 7 -0.58 4 11
SMAD7 0.003 0.064 0.17 20 -10000 0 20
CBL/CRKL/C3G 0.019 0.084 0.28 2 -10000 0 2
PI3K 0.011 0.075 -10000 0 -10000 0 0
IFNG -0.05 0.16 -10000 0 -0.38 97 97
apoptosis 0.021 0.083 0.26 4 -0.44 5 9
CAMK2G 0.028 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.003 -10000 0 -10000 0 0
CAMK2A -0.082 0.2 -10000 0 -0.46 114 114
CAMK2B -0.11 0.22 -10000 0 -0.46 143 143
FRAP1 0.029 0.1 0.29 20 -10000 0 20
PRKCD 0.036 0.11 0.3 16 -10000 0 16
RAP1B 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.032 0.07 -10000 0 -0.26 5 5
PTPN2 0.026 0.007 -10000 0 -10000 0 0
EP300 0.027 0.022 -10000 0 -0.46 1 1
IRF1 -0.005 0.087 0.28 8 -10000 0 8
STAT1 (dimer)/PIASy 0.007 0.093 0.24 4 -0.32 10 14
SOCS1 -0.007 0.15 -10000 0 -1 8 8
mol:GDP 0.016 0.08 0.26 2 -10000 0 2
CASP1 0.004 0.065 0.18 19 -0.3 1 20
PTGES2 0.027 0.005 -10000 0 -10000 0 0
IRF9 0.026 0.046 0.16 13 -10000 0 13
mol:PI-3-4-5-P3 0.003 0.067 -10000 0 -10000 0 0
RAP1/GDP 0.01 0.069 -10000 0 -10000 0 0
CBL 0.001 0.078 0.27 2 -10000 0 2
MAP3K1 0 0.08 0.28 2 -10000 0 2
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.027 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.07 -10000 0 -0.26 5 5
PTPN11 0.002 0.086 0.29 2 -10000 0 2
CREBBP 0.028 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0 0.038 0.21 10 -10000 0 10
RFC1 -0.002 0.028 0.21 3 -10000 0 3
PRKDC 0.016 0.069 0.22 45 -10000 0 45
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 0.012 0.084 -10000 0 -0.55 9 9
FASLG/FAS/FADD/FAF1 0 0.059 0.22 7 -0.25 13 20
MAP2K4 0.026 0.12 0.3 7 -0.44 11 18
mol:ceramide 0.009 0.086 -10000 0 -0.33 12 12
GSN 0.001 0.037 0.21 10 -10000 0 10
FASLG/FAS/FADD/FAF1/Caspase 8 0.017 0.081 0.25 2 -0.32 9 11
FAS 0.023 0.026 -10000 0 -0.46 1 1
BID -0.015 0.024 0.26 1 -0.24 2 3
MAP3K1 0.042 0.098 0.32 6 -0.39 7 13
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
RB1 -0.003 0.026 0.2 1 -10000 0 1
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET 0.028 0.084 -10000 0 -0.27 36 36
ARHGDIB 0.003 0.044 0.22 15 -10000 0 15
FADD 0.017 0.017 -10000 0 -10000 0 0
actin filament polymerization 0.003 0.046 -10000 0 -0.21 10 10
NFKB1 0.005 0.1 -10000 0 -0.54 10 10
MAPK8 0.01 0.16 0.3 6 -0.46 37 43
DFFA -0.003 0.024 0.2 1 -0.19 2 3
DNA fragmentation during apoptosis -0.006 0.041 0.21 4 -0.31 2 6
FAS/FADD/MET 0.031 0.042 -10000 0 -0.26 5 5
CFLAR/RIP1 0.039 0.013 -10000 0 -10000 0 0
FAIM3 0.021 0.056 -10000 0 -0.4 9 9
FAF1 0.023 0.017 -10000 0 -10000 0 0
PARP1 -0.003 0.03 0.21 3 -10000 0 3
DFFB -0.003 0.035 0.21 4 -0.31 2 6
CHUK 0.003 0.092 -10000 0 -0.54 8 8
FASLG -0.01 0.12 -10000 0 -0.42 39 39
FAS/FADD 0.024 0.029 -10000 0 -0.33 1 1
HGF 0.006 0.095 -10000 0 -0.44 22 22
LMNA -0.005 0.033 0.19 2 -10000 0 2
CASP6 -0.003 0.024 0.2 1 -10000 0 1
CASP10 0.024 0.015 -10000 0 -10000 0 0
CASP3 0 0.023 0.23 2 -0.18 1 3
PTPN13 0.018 0.064 -10000 0 -0.46 9 9
CASP8 -0.016 0.029 0.19 9 -10000 0 9
IL6 -0.07 0.36 -10000 0 -1.2 45 45
MET 0.022 0.048 -10000 0 -0.41 6 6
ICAD/CAD -0.003 0.03 0.19 3 -0.29 2 5
FASLG/FAS/FADD/FAF1/Caspase 10 0.009 0.086 -10000 0 -0.33 12 12
activation of caspase activity by cytochrome c -0.015 0.024 0.26 1 -0.24 2 3
PAK2 0.04 0.093 0.22 100 -0.19 3 103
BCL2 0.022 0.039 -10000 0 -0.41 4 4
IL6-mediated signaling events

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
BCL2L1 -0.016 0.16 -10000 0 -10000 0 0
CRP -0.034 0.16 0.49 2 -0.66 1 3
cell cycle arrest -0.035 0.16 -10000 0 -0.58 2 2
TIMP1 -0.016 0.16 -10000 0 -0.63 2 2
IL6ST -0.03 0.16 -10000 0 -0.46 60 60
Rac1/GDP -0.024 0.12 -10000 0 -0.46 15 15
AP1 0.007 0.14 -10000 0 -0.55 8 8
GAB2 0.022 0.038 -10000 0 -0.46 3 3
TNFSF11 -0.057 0.18 -10000 0 -0.62 1 1
HSP90B1 0.023 0.092 -10000 0 -0.66 6 6
GAB1 0.027 0.006 -10000 0 -10000 0 0
MAPK14 -0.029 0.12 -10000 0 -0.45 17 17
AKT1 0.047 0.064 0.3 8 -0.58 1 9
FOXO1 0.046 0.06 0.28 10 -0.55 1 11
MAP2K6 -0.036 0.12 -10000 0 -0.46 19 19
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.025 0.12 -10000 0 -0.46 13 13
MITF -0.033 0.12 -10000 0 -0.4 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.019 -10000 0 -0.39 1 1
A2M 0.019 0.1 -10000 0 -1.1 4 4
CEBPB 0.028 0.014 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.005 0.11 -10000 0 -0.5 13 13
STAT3 -0.04 0.16 -10000 0 -0.61 2 2
STAT1 0.005 0.085 -10000 0 -0.78 5 5
CEBPD -0.012 0.16 -10000 0 -10000 0 0
PIK3CA 0.021 0.013 -10000 0 -10000 0 0
PI3K 0.028 0.03 -10000 0 -0.33 2 2
JUN 0.027 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.022 0.12 -10000 0 -0.42 20 20
MAPK11 -0.029 0.12 -10000 0 -0.47 17 17
STAT3 (dimer)/FOXO1 0.009 0.15 0.37 4 -10000 0 4
GRB2/SOS1/GAB family 0.017 0.12 -10000 0 -0.42 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.021 0.12 -10000 0 -0.41 20 20
GRB2 0.028 0.004 -10000 0 -10000 0 0
JAK2 0.024 0.01 -10000 0 -10000 0 0
LBP -0.11 0.33 -10000 0 -0.88 70 70
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
JAK1 0.029 0.006 -10000 0 -10000 0 0
MYC 0.004 0.16 0.49 2 -10000 0 2
FGG -0.045 0.17 -10000 0 -0.62 1 1
macrophage differentiation -0.035 0.16 -10000 0 -0.58 2 2
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.008 0.13 -10000 0 -0.37 20 20
JUNB -0.027 0.14 -10000 0 -10000 0 0
FOS -0.034 0.16 -10000 0 -0.46 63 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.026 0.12 -10000 0 -0.41 24 24
STAT1/PIAS1 -0.016 0.12 -10000 0 -0.4 15 15
GRB2/SOS1/GAB family/SHP2/PI3K 0.044 0.056 -10000 0 -0.48 2 2
STAT3 (dimer) -0.038 0.16 -10000 0 -0.6 2 2
PRKCD -0.016 0.14 0.35 8 -0.52 4 12
IL6R 0.022 0.057 -10000 0 -0.46 7 7
SOCS3 -0.025 0.13 -10000 0 -0.6 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 0.017 0.11 -10000 0 -0.28 59 59
Rac1/GTP -0.025 0.13 -10000 0 -0.46 15 15
HCK 0.024 0.029 -10000 0 -0.42 2 2
MAPKKK cascade 0.022 0.11 -10000 0 -0.53 10 10
bone resorption -0.053 0.17 -10000 0 -0.59 1 1
IRF1 -0.028 0.15 -10000 0 -10000 0 0
mol:GDP -0.033 0.12 -10000 0 -0.41 23 23
SOS1 0.028 0.004 -10000 0 -10000 0 0
VAV1 -0.033 0.12 -10000 0 -0.42 23 23
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.021 0.13 -10000 0 -0.52 17 17
PTPN11 0.016 0.049 -10000 0 -0.7 2 2
IL6/IL6RA 0.004 0.11 -10000 0 -0.32 51 51
gp130 (dimer)/TYK2/TYK2/LMO4 0.014 0.11 -10000 0 -0.28 60 60
gp130 (dimer)/JAK2/JAK2/LMO4 0.012 0.1 -10000 0 -0.28 55 55
IL6 -0.016 0.14 -10000 0 -0.45 46 46
PIAS3 0.027 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.011 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.028 0.12 -10000 0 -0.32 46 46
LMO4 0.028 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.03 0.17 -10000 0 -0.6 2 2
MCL1 0.05 0.073 0.54 2 -0.52 1 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.02 0.032 -10000 0 -0.25 6 6
epithelial cell differentiation 0.048 0.037 -10000 0 -0.24 5 5
CYFIP2 0.025 0.029 -10000 0 -0.42 2 2
ENAH 0.019 0.07 0.23 11 -0.46 1 12
EGFR 0.021 0.044 -10000 0 -0.46 4 4
EPHA2 0.021 0.053 -10000 0 -0.46 6 6
MYO6 0.017 0.036 0.21 2 -10000 0 2
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.026 -10000 0 -0.26 2 2
AQP5 -0.27 0.22 -10000 0 -0.46 272 272
CTNND1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.017 0.037 0.2 3 -10000 0 3
regulation of calcium-dependent cell-cell adhesion 0.001 0.062 0.19 1 -10000 0 1
EGF -0.067 0.19 -10000 0 -0.46 98 98
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.092 0.19 -10000 0 -0.43 117 117
cortical microtubule organization 0.048 0.037 -10000 0 -0.24 5 5
GO:0000145 -0.002 0.037 0.17 14 -10000 0 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.052 0.039 -10000 0 -0.24 5 5
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.012 0.028 -10000 0 -0.4 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.041 -10000 0 -0.26 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.007 0.03 0.21 1 -10000 0 1
PVRL2 0.027 0.005 -10000 0 -10000 0 0
ZYX 0.016 0.036 0.21 2 -10000 0 2
ARF6/GTP 0.057 0.044 -10000 0 -0.24 4 4
CDH1 0.021 0.053 -10000 0 -0.46 6 6
EGFR/EGFR/EGF/EGF -0.01 0.11 -10000 0 -0.39 4 4
RhoA/GDP 0.049 0.036 -10000 0 -0.23 4 4
actin cytoskeleton organization -0.002 0.036 0.17 13 -10000 0 13
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
IGF1R 0.027 0.005 -10000 0 -10000 0 0
IGF1 -0.053 0.18 -10000 0 -0.46 85 85
DIAPH1 0.019 0.12 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.048 0.037 0.24 5 -10000 0 5
RHOA 0.025 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.028 -10000 0 -0.4 1 1
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
VCL -0.002 0.037 0.17 13 -10000 0 13
EFNA1 0.027 0.004 -10000 0 -10000 0 0
LPP -0.003 0.031 0.18 8 -10000 0 8
Ephrin A1/EPHA2 0.039 0.045 -10000 0 -0.44 1 1
SEC6/SEC8 0.01 0.021 -10000 0 -10000 0 0
MGAT3 0.001 0.062 0.19 1 -10000 0 1
HGF/MET 0.029 0.067 -10000 0 -0.38 3 3
HGF 0.006 0.095 -10000 0 -0.44 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.02 0.032 -10000 0 -0.25 6 6
actin cable formation 0.058 0.095 0.22 85 -0.33 1 86
KIAA1543 -0.014 0.064 0.18 11 -0.38 4 15
KIFC3 0.014 0.032 0.19 1 -10000 0 1
NCK1 0.023 0.011 -10000 0 -10000 0 0
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ACTN1 0.016 0.036 0.2 3 -10000 0 3
NCK1/GIT1 0.034 0.016 -10000 0 -10000 0 0
mol:GDP 0.048 0.037 -10000 0 -0.24 5 5
EXOC4 0.026 0.007 -10000 0 -10000 0 0
STX4 0.017 0.037 0.2 3 -10000 0 3
PIP5K1C 0.017 0.038 0.2 3 -10000 0 3
LIMA1 0.028 0.003 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.025 0.078 0.25 13 -0.35 1 14
adherens junction assembly -0.01 0.096 0.28 6 -0.5 8 14
IGF-1R heterotetramer/IGF1 0.002 0.1 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
MET 0.022 0.048 -10000 0 -0.41 6 6
PLEKHA7 0.003 0.07 0.2 3 -0.4 4 7
mol:GTP 0.052 0.04 -10000 0 -0.26 4 4
establishment of epithelial cell apical/basal polarity 0.024 0.082 0.33 12 -10000 0 12
cortical actin cytoskeleton stabilization 0.02 0.032 -10000 0 -0.25 6 6
regulation of cell-cell adhesion -0.002 0.036 0.17 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.02 0.032 -10000 0 -0.25 6 6
Signaling events mediated by PRL

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
CCNE1 0.025 0.032 -10000 0 -0.39 3 3
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 -0.031 0.14 -10000 0 -0.39 71 71
CDKN1A 0.012 0.05 -10000 0 -0.3 10 10
PRL-3/alpha Tubulin 0.031 0.034 -10000 0 -0.27 5 5
mol:Ca2+ -0.062 0.12 0.17 3 -0.34 76 79
AGT -0.066 0.19 -10000 0 -0.46 98 98
CCNA2 -0.007 0.046 -10000 0 -0.41 1 1
TUBA1B 0.028 0.003 -10000 0 -10000 0 0
EGR1 0.002 0.068 -10000 0 -0.32 22 22
CDK2/Cyclin E1 0.04 0.08 0.28 1 -0.36 4 5
MAPK3 0.009 0.029 -10000 0 -0.27 5 5
PRL-2 /Rab GGTase beta 0.04 0.007 -10000 0 -10000 0 0
MAPK1 0.009 0.029 -10000 0 -0.27 5 5
PTP4A1 -0.004 0.048 -10000 0 -10000 0 0
PTP4A3 0.019 0.042 -10000 0 -0.39 5 5
PTP4A2 0.027 0.004 -10000 0 -10000 0 0
ITGB1 0.009 0.029 -10000 0 -0.27 5 5
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.012 0.03 -10000 0 -0.3 2 2
Rab GGTase beta/Rab GGTase alpha 0.038 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 0.02 0.072 -10000 0 -10000 0 0
RABGGTA 0.026 0.007 -10000 0 -10000 0 0
BCAR1 -0.013 0.02 0.17 5 -10000 0 5
RHOC 0.011 0.039 -10000 0 -0.3 5 5
RHOA -0.002 0.072 -10000 0 -0.3 25 25
cell motility 0.019 0.074 0.31 2 -0.31 3 5
PRL-1/alpha Tubulin 0.023 0.067 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.01 0.1 -10000 0 -0.27 69 69
ROCK1 0.024 0.063 0.35 1 -0.3 2 3
RABGGTB 0.027 0.004 -10000 0 -10000 0 0
CDK2 0.028 0.003 -10000 0 -10000 0 0
mitosis -0.004 0.048 -10000 0 -10000 0 0
ATF5 0.019 0.057 -10000 0 -0.39 10 10
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.02 0.015 -10000 0 -10000 0 0
TRAF2/ASK1 0.033 0.027 -10000 0 -0.22 5 5
ATM 0.025 0.008 -10000 0 -10000 0 0
MAP2K3 -0.021 0.11 0.42 2 -0.38 20 22
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.019 0.11 0.36 2 -0.37 19 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.021 0.053 -10000 0 -0.43 7 7
TXN 0.008 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
GADD45A 0.027 0.019 -10000 0 -0.39 1 1
GADD45B 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
MAP3K6 0.026 0.022 -10000 0 -0.46 1 1
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
MAP3K4 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.019 -10000 0 -0.33 1 1
TAK1/TAB family -0.005 0.017 -10000 0 -0.13 7 7
RAC1/OSM/MEKK3 0.047 0.03 -10000 0 -0.21 5 5
TRAF2 0.023 0.041 -10000 0 -0.39 5 5
RAC1/OSM/MEKK3/MKK3 -0.007 0.092 -10000 0 -0.34 10 10
TRAF6 0.008 0.002 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.11 0.22 -10000 0 -0.46 143 143
CCM2 0.022 0.045 -10000 0 -0.39 6 6
CaM/Ca2+/CAMKIIB -0.051 0.14 -10000 0 -0.28 138 138
MAPK11 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.034 0.13 -10000 0 -0.25 137 137
OSM/MEKK3 0.036 0.032 -10000 0 -0.27 5 5
TAOK1 0.006 0.052 -10000 0 -0.33 12 12
TAOK2 0.014 0.005 -10000 0 -10000 0 0
TAOK3 0.014 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAP3K10 0.027 0.005 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.01 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.057 0.039 -10000 0 -0.24 4 4
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.017 0.086 -10000 0 -0.33 29 29
ATM 0.025 0.008 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
ATR 0.023 0.011 -10000 0 -10000 0 0
UBE2L3 0.027 0.006 -10000 0 -10000 0 0
FANCD2 0.016 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.045 0.077 -10000 0 -0.25 26 26
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.024 -10000 0 -10000 0 0
MRE11A 0.025 0.008 -10000 0 -10000 0 0
DNA-PK 0.048 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.012 0.097 -10000 0 -0.51 10 10
FANCF 0.023 0.043 -10000 0 -0.46 4 4
BRCA1 0.028 0.003 -10000 0 -10000 0 0
CCNE1 0.025 0.032 -10000 0 -0.39 3 3
CDK2/Cyclin E1 0.038 0.025 -10000 0 -0.27 3 3
FANCG 0.024 0.01 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.018 0.088 -10000 0 -0.33 30 30
FANCE 0.027 0.006 -10000 0 -10000 0 0
FANCC 0.027 0.005 -10000 0 -10000 0 0
NBN 0.025 0.009 -10000 0 -10000 0 0
FANCA 0.025 0.026 -10000 0 -0.39 2 2
DNA repair 0.012 0.085 0.28 6 -0.38 4 10
BRCA1/BARD1/ubiquitin 0.018 0.088 -10000 0 -0.33 30 30
BARD1/DNA-PK 0.046 0.069 -10000 0 -0.26 21 21
FANCL 0.027 0.019 -10000 0 -0.39 1 1
mRNA polyadenylation -0.017 0.086 0.33 29 -10000 0 29
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.073 -10000 0 -0.28 5 5
BRCA1/BACH1/BARD1/TopBP1 0.029 0.075 -10000 0 -0.28 25 25
BRCA1/BARD1/P53 0.036 0.076 -10000 0 -0.26 27 27
BARD1/CSTF1/BRCA1 0.032 0.079 -10000 0 -0.28 29 29
BRCA1/BACH1 0.028 0.003 -10000 0 -10000 0 0
BARD1 -0.002 0.12 -10000 0 -0.46 30 30
PCNA 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.033 0.08 -10000 0 -0.28 30 30
BRCA1/BARD1/UbcH7 0.032 0.079 -10000 0 -0.28 29 29
BRCA1/BARD1/RAD51/PCNA 0.044 0.079 -10000 0 -0.26 30 30
BARD1/DNA-PK/P53 0.052 0.073 -10000 0 -0.24 21 21
BRCA1/BARD1/Ubiquitin 0.018 0.088 -10000 0 -0.33 30 30
BRCA1/BARD1/CTIP 0.022 0.071 -10000 0 -0.26 29 29
FA complex 0.036 0.039 -10000 0 -10000 0 0
BARD1/EWS 0.018 0.086 -10000 0 -0.33 29 29
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.023 0.043 -10000 0 -0.46 4 4
TOPBP1 0.024 0.01 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.034 0.075 0.25 27 -10000 0 27
BRCA1/BARD1 0.05 0.08 -10000 0 -0.25 26 26
CSTF1 0.027 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.001 0.082 -10000 0 -0.33 30 30
CDK2 0.028 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.026 -10000 0 -0.39 2 2
RAD50 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.018 0.088 -10000 0 -0.33 30 30
EWSR1 0.027 0.005 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.046 0.079 0.34 1 -10000 0 1
CRKL 0.021 0.082 0.31 6 -0.31 1 7
mol:DAG 0.021 0.062 -10000 0 -0.29 1 1
HRAS 0.026 0.084 0.3 14 -10000 0 14
MAPK8 0.022 0.098 0.2 44 -0.3 6 50
RAP1A 0.023 0.083 0.31 7 -0.31 1 8
GAB1 0.023 0.083 0.31 7 -0.31 1 8
MAPK14 0.024 0.093 0.2 43 -0.36 2 45
EPO -0.014 0.12 -10000 0 -0.38 51 51
PLCG1 0.021 0.063 -10000 0 -0.3 1 1
EPOR/TRPC2/IP3 Receptors 0.019 0.06 -10000 0 -0.38 10 10
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.024 0.089 -10000 0 -0.35 2 2
GAB1/SHC/GRB2/SOS1 0.05 0.08 0.27 6 -10000 0 6
EPO/EPOR (dimer) 0.007 0.1 -10000 0 -0.27 54 54
IRS2 0.022 0.084 0.31 7 -0.31 1 8
STAT1 0.021 0.069 -10000 0 -0.34 1 1
STAT5B 0.024 0.066 -10000 0 -0.34 1 1
cell proliferation 0.015 0.097 0.2 51 -0.28 5 56
GAB1/SHIP/PIK3R1/SHP2/SHC 0.031 0.073 -10000 0 -0.34 2 2
TEC 0.012 0.098 0.29 6 -0.37 8 14
SOCS3 0.027 0.022 -10000 0 -0.46 1 1
STAT1 (dimer) 0.021 0.068 -10000 0 -0.34 1 1
JAK2 0.022 0.02 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
EPO/EPOR (dimer)/JAK2 0.046 0.085 -10000 0 -0.33 1 1
EPO/EPOR 0.007 0.1 -10000 0 -0.27 54 54
LYN 0.025 0.021 -10000 0 -0.39 1 1
TEC/VAV2 0.016 0.1 0.28 2 -0.39 11 13
elevation of cytosolic calcium ion concentration 0.019 0.059 -10000 0 -0.38 10 10
SHC1 0.028 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.024 0.087 -10000 0 -0.22 47 47
mol:IP3 0.021 0.062 -10000 0 -0.29 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.089 0.31 6 -0.34 3 9
SH2B3 0.026 0.027 -10000 0 -0.39 1 1
NFKB1 0.024 0.094 0.2 44 -0.36 2 46
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.051 -10000 0 -0.25 8 8
PTPN6 0.02 0.081 0.3 4 -0.32 1 5
TEC/VAV2/GRB2 0.025 0.11 0.29 2 -0.39 10 12
EPOR 0.019 0.06 -10000 0 -0.38 10 10
INPP5D 0.025 0.031 -10000 0 -0.46 2 2
mol:GDP 0.049 0.081 0.27 6 -10000 0 6
SOS1 0.028 0.004 -10000 0 -10000 0 0
PLCG2 0.025 0.023 -10000 0 -0.46 1 1
CRKL/CBL/C3G 0.036 0.078 0.29 2 -0.3 1 3
VAV2 0.018 0.091 0.31 7 -0.33 4 11
CBL 0.021 0.081 0.31 7 -0.31 1 8
SHC/Grb2/SOS1 0.021 0.063 -10000 0 -0.3 1 1
STAT5A 0.024 0.066 -10000 0 -0.34 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.04 0.076 -10000 0 -0.38 1 1
LYN/PLCgamma2 0.034 0.026 -10000 0 -0.3 2 2
PTPN11 0.028 0.002 -10000 0 -10000 0 0
BTK 0.022 0.083 0.31 6 -0.31 1 7
BCL2 0.04 0.11 0.34 1 -0.71 5 6
ceramide signaling pathway

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.014 0.097 0.28 5 -0.46 9 14
BAG4 0.023 0.023 -10000 0 -0.46 1 1
BAD 0.016 0.049 0.18 17 -0.21 1 18
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.39 15 15
BAX 0.013 0.042 0.19 6 -0.21 1 7
EnzymeConsortium:3.1.4.12 0.007 0.026 0.069 13 -0.091 12 25
IKBKB 0.025 0.097 0.29 12 -0.46 7 19
MAP2K2 0.015 0.043 0.19 11 -10000 0 11
MAP2K1 0.015 0.044 0.19 10 -10000 0 10
SMPD1 0.008 0.035 0.13 5 -0.15 6 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.064 0.12 0.27 44 -0.45 6 50
MAP2K4 0.013 0.041 0.19 6 -10000 0 6
protein ubiquitination 0.022 0.1 0.28 9 -0.46 8 17
EnzymeConsortium:2.7.1.37 0.015 0.047 0.19 10 -10000 0 10
response to UV 0 0 0.002 11 -10000 0 11
RAF1 0.014 0.042 0.2 9 -0.19 1 10
CRADD 0.028 0.002 -10000 0 -10000 0 0
mol:ceramide 0.013 0.042 0.12 12 -0.16 7 19
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.012 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.013 0.04 0.16 6 -0.21 1 7
TRADD 0.027 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.017 0.048 0.19 9 -0.22 1 10
MAPK1 0.017 0.045 0.19 9 -10000 0 9
p50/RELA/I-kappa-B-alpha 0.037 0.013 -10000 0 -10000 0 0
FADD 0.055 0.12 0.23 71 -0.45 7 78
KSR1 0.014 0.045 0.19 8 -0.19 2 10
MAPK8 0.011 0.045 0.18 9 -0.22 2 11
TRAF2 0.023 0.041 -10000 0 -0.39 5 5
response to radiation 0 0 0.002 3 -10000 0 3
CHUK 0.016 0.094 0.28 5 -0.46 7 12
TNF R/SODD 0.033 0.023 -10000 0 -0.33 1 1
TNF 0.008 0.088 -10000 0 -0.4 23 23
CYCS 0.022 0.051 0.16 22 -10000 0 22
IKBKG 0.023 0.1 0.3 12 -0.46 7 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.016 0.095 -10000 0 -0.48 9 9
RELA 0.027 0.006 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AIFM1 0.02 0.048 0.16 18 -10000 0 18
TNF/TNF R/SODD 0.033 0.061 -10000 0 -0.24 21 21
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.021 0.089 -10000 0 -0.56 10 10
NSMAF 0.027 0.11 0.27 17 -0.44 9 26
response to hydrogen peroxide 0 0 0.002 11 -10000 0 11
BCL2 0.022 0.039 -10000 0 -0.41 4 4
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.006 -10000 0 -10000 0 0
VDR 0.026 0.031 -10000 0 -0.46 2 2
Cbp/p300/PCAF 0.035 0.069 -10000 0 -0.29 19 19
EP300 0.026 0.022 -10000 0 -0.46 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.086 -10000 0 -0.38 14 14
KAT2B 0.007 0.092 -10000 0 -0.46 19 19
MAPK14 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.013 0.092 0.19 4 -0.33 13 17
RAR alpha/9cRA/Cyclin H 0.035 0.061 0.22 1 -0.38 1 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.015 0.11 -10000 0 -0.36 28 28
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.013 0.059 -10000 0 -0.35 7 7
NCOR2 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 -10000 0 -0.33 2 2
RXRs/RARs/NRIP1/9cRA -0.018 0.12 0.28 1 -0.53 11 12
NCOA2 -0.009 0.12 -10000 0 -0.46 36 36
NCOA3 0.027 0.006 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.031 -10000 0 -0.46 2 2
RARG 0.027 0.022 -10000 0 -0.46 1 1
RAR gamma1/9cRA 0.037 0.015 -10000 0 -0.28 1 1
MAPK3 0.028 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.022 0.053 -10000 0 -0.46 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.011 0.088 -10000 0 -0.48 5 5
RARA 0.005 0.043 -10000 0 -0.22 6 6
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.03 0.13 -10000 0 -0.43 37 37
PRKCA 0.028 0.03 -10000 0 -0.43 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.028 0.13 -10000 0 -0.52 17 17
RXRG -0.034 0.12 -10000 0 -0.33 57 57
RXRA 0.008 0.048 -10000 0 -0.28 2 2
RXRB 0.002 0.061 -10000 0 -0.32 5 5
VDR/Vit D3/DNA 0.019 0.022 -10000 0 -0.33 2 2
RBP1 -0.048 0.16 -10000 0 -0.39 88 88
CRBP1/9-cic-RA -0.033 0.11 -10000 0 -0.27 88 88
RARB -0.008 0.12 -10000 0 -0.46 36 36
PRKCG -0.02 0.13 -10000 0 -0.38 58 58
MNAT1 0.026 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.11 0.31 1 -0.47 8 9
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.009 0.1 -10000 0 -0.44 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.12 0.22 1 -0.36 38 39
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.028 0.14 -10000 0 -0.52 17 17
positive regulation of DNA binding 0.026 0.054 -10000 0 -0.36 1 1
NRIP1 -0.033 0.16 -10000 0 -0.91 7 7
RXRs/RARs -0.034 0.14 -10000 0 -0.51 21 21
RXRs/RXRs/DNA/9cRA -0.004 0.077 -10000 0 -0.46 5 5
PRKACA 0.028 0.004 -10000 0 -10000 0 0
CDK7 0.027 0.006 -10000 0 -10000 0 0
TFIIH 0.051 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.042 0.052 -10000 0 -10000 0 0
CCNH 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.024 -10000 0 -10000 0 0
S1P3 pathway

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.042 0.15 -9999 0 -0.39 85 85
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.006 0.06 -9999 0 -0.25 14 14
GNAO1 0.024 0.04 -9999 0 -0.42 4 4
S1P/S1P3/G12/G13 0.045 0.039 -9999 0 -0.24 7 7
AKT1 -0.005 0.11 -9999 0 -0.48 19 19
AKT3 0.019 0.088 -9999 0 -0.66 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.042 0.15 -9999 0 -0.39 85 85
GNAI2 0.025 0.011 -9999 0 -10000 0 0
GNAI3 0.028 0.007 -9999 0 -10000 0 0
GNAI1 0.026 0.023 -9999 0 -0.46 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.022 0.052 -9999 0 -0.45 6 6
S1PR2 0.027 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.065 -9999 0 -0.32 10 10
MAPK3 0.016 0.059 -9999 0 -0.36 5 5
MAPK1 0.013 0.059 -9999 0 -0.36 5 5
JAK2 0.016 0.08 -9999 0 -0.42 8 8
CXCR4 0.009 0.076 -9999 0 -0.38 8 8
FLT1 0.027 0.021 -9999 0 -0.38 1 1
RhoA/GDP 0.018 0.007 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.005 -9999 0 -10000 0 0
SRC 0.015 0.059 -9999 0 -0.36 5 5
S1P/S1P3/Gi 0.021 0.065 -9999 0 -0.32 10 10
RAC1 0.026 0.007 -9999 0 -10000 0 0
RhoA/GTP 0.026 0.07 -9999 0 -0.34 5 5
VEGFA 0.023 0.045 -9999 0 -0.38 6 6
S1P/S1P2/Gi 0.024 0.048 -9999 0 -0.27 5 5
VEGFR1 homodimer/VEGFA homodimer 0.038 0.04 -9999 0 -0.27 7 7
RHOA 0.025 0.009 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.013 0.1 -9999 0 -0.24 77 77
GNAQ 0.027 0.005 -9999 0 -10000 0 0
GNAZ 0.013 0.08 -9999 0 -0.41 17 17
G12/G13 0.037 0.018 -9999 0 -0.27 1 1
GNA14 -0.041 0.17 -9999 0 -0.46 71 71
GNA15 0.025 0.031 -9999 0 -0.46 2 2
GNA12 0.025 0.02 -9999 0 -0.39 1 1
GNA13 0.028 0.003 -9999 0 -10000 0 0
GNA11 0.024 0.038 -9999 0 -0.46 3 3
Rac1/GTP 0.021 0.072 -9999 0 -0.34 6 6
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.011 0.089 -10000 0 -0.24 56 56
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.035 0.011 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.002 -10000 0 -10000 0 0
Gs family/GTP -0.014 0.086 -10000 0 -0.25 59 59
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 0.008 0.022 0.068 59 -10000 0 59
GNAL -0.03 0.16 -10000 0 -0.46 59 59
GNG2 0.026 0.007 -10000 0 -10000 0 0
CRH -0.014 0.012 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.034 -10000 0 -0.31 6 6
MAPK11 0.008 0.001 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.008 0.043 0.13 56 -0.12 1 57
BUB1B 0.01 0.03 0.12 5 -0.15 3 8
PLK1 0.01 0.025 0.093 14 -10000 0 14
PLK1S1 0.013 0.026 0.12 5 -0.18 4 9
KIF2A 0.008 0.022 0.19 1 -10000 0 1
regulation of mitotic centrosome separation 0.01 0.025 0.093 14 -10000 0 14
GOLGA2 0.027 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.033 0.043 -10000 0 -0.21 9 9
WEE1 0.009 0.065 0.17 1 -0.3 18 19
cytokinesis 0.009 0.051 -10000 0 -0.22 4 4
PP2A-alpha B56 0.06 0.049 -10000 0 -0.53 3 3
AURKA 0.011 0.029 0.11 2 -0.18 7 9
PICH/PLK1 0.016 0.04 0.17 4 -10000 0 4
CENPE 0.008 0.021 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.023 0.19 1 -10000 0 1
PPP2CA 0.027 0.006 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.016 0.025 0.12 9 -0.16 2 11
PAK1 0.025 0.009 -10000 0 -10000 0 0
SPC24 0.019 0.06 -10000 0 -0.39 11 11
FBXW11 0.027 0.006 -10000 0 -10000 0 0
CLSPN 0.01 0.032 -10000 0 -0.24 6 6
GORASP1 0.024 0.009 -10000 0 -10000 0 0
metaphase 0 0.002 0.015 8 -0.011 3 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.014 0.049 20 -10000 0 20
G2 phase of mitotic cell cycle -0.001 0.002 0.012 2 -10000 0 2
STAG2 0.028 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.042 0.18 -10000 0 -0.5 66 66
spindle elongation 0.01 0.025 0.093 14 -10000 0 14
ODF2 0.028 0.005 -10000 0 -10000 0 0
BUB1 0.028 0.048 -10000 0 -0.58 3 3
TPT1 0.001 0.049 -10000 0 -0.18 31 31
CDC25C 0.001 0.064 -10000 0 -0.27 24 24
CDC25B 0.014 0.072 -10000 0 -0.39 16 16
SGOL1 -0.008 0.044 0.12 1 -0.13 56 57
RHOA 0.025 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.031 0.045 -10000 0 -0.23 2 2
CDC14B 0.006 0.021 -10000 0 -0.34 2 2
CDC20 0.019 0.06 -10000 0 -0.39 11 11
PLK1/PBIP1 0.009 0.021 -10000 0 -0.15 2 2
mitosis -0.001 0.005 0.023 11 -10000 0 11
FBXO5 0.009 0.025 0.12 7 -0.12 1 8
CDC2 0.001 0.002 -10000 0 -0.014 2 2
NDC80 0.024 0.02 -10000 0 -0.39 1 1
metaphase plate congression 0.007 0.047 -10000 0 -0.24 17 17
ERCC6L 0.014 0.042 -10000 0 -0.22 2 2
NLP/gamma Tubulin 0.008 0.017 0.066 7 -0.11 2 9
microtubule cytoskeleton organization 0.001 0.049 -10000 0 -0.18 31 31
G2/M transition DNA damage checkpoint 0 0.003 0.013 13 -10000 0 13
PPP1R12A 0.028 0.003 -10000 0 -10000 0 0
interphase 0 0.003 0.013 13 -10000 0 13
PLK1/PRC1-2 0.04 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.044 0.03 -10000 0 -10000 0 0
RAB1A 0.028 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.009 0.022 0.085 20 -10000 0 20
mitotic prometaphase 0 0.003 0.017 17 -10000 0 17
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.058 0.17 1 -0.48 5 6
microtubule-based process 0.026 0.024 -10000 0 -10000 0 0
Golgi organization 0.01 0.025 0.093 14 -10000 0 14
Cohesin/SA2 0.023 0.021 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.041 0.007 -10000 0 -10000 0 0
KIF20A 0.027 0.006 -10000 0 -10000 0 0
APC/C/CDC20 0.022 0.039 -10000 0 -0.19 10 10
PPP2R1A 0.027 0.004 -10000 0 -10000 0 0
chromosome segregation 0.009 0.02 -10000 0 -0.15 2 2
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.067 0.098 0.22 146 -10000 0 146
C13orf34 0.009 0.022 0.078 20 -10000 0 20
NUDC 0.007 0.047 -10000 0 -0.24 17 17
regulation of attachment of spindle microtubules to kinetochore 0.01 0.03 0.12 5 -0.15 3 8
spindle assembly 0.009 0.021 0.077 15 -10000 0 15
spindle stabilization 0.013 0.026 0.12 5 -0.18 4 9
APC/C/HCDH1 0.023 0.02 -10000 0 -0.27 2 2
MKLP2/PLK1 0.026 0.024 -10000 0 -10000 0 0
CCNB1 0.027 0.007 -10000 0 -10000 0 0
PPP1CB 0.028 0.004 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.002 0.074 -10000 0 -0.35 14 14
TUBG1 0.012 0.022 -10000 0 -0.21 3 3
G2/M transition of mitotic cell cycle 0.005 0.034 -10000 0 -0.23 2 2
MLF1IP 0.006 0.018 -10000 0 -0.28 2 2
INCENP 0.028 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.042 0.15 -10000 0 -0.39 85 85
alphaV beta3 Integrin 0.024 0.07 -10000 0 -0.29 23 23
PTK2 0.008 0.088 -10000 0 -0.44 8 8
positive regulation of JNK cascade 0.01 0.092 -10000 0 -0.34 13 13
CDC42/GDP 0.043 0.12 0.32 3 -0.42 14 17
Rac1/GDP 0.039 0.12 0.3 2 -0.41 12 14
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.026 0.12 -10000 0 -0.42 13 13
nectin-3/I-afadin 0.023 0.066 -10000 0 -0.31 18 18
RAPGEF1 0.027 0.11 0.33 4 -0.45 9 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.11 -10000 0 -0.5 10 10
PDGFB-D/PDGFRB -0.042 0.15 -10000 0 -0.39 85 85
TLN1 0.001 0.034 0.17 2 -0.33 2 4
Rap1/GTP 0.014 0.074 -10000 0 -0.33 8 8
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.017 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.023 0.066 -10000 0 -0.31 18 18
PVR 0.027 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.03 0.14 0.35 3 -0.5 14 17
MLLT4 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.009 0.1 -10000 0 -0.28 11 11
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.034 0.031 -10000 0 -0.33 3 3
positive regulation of lamellipodium assembly 0.017 0.082 -10000 0 -0.34 7 7
PVRL1 0.022 0.038 -10000 0 -0.46 3 3
PVRL3 0.008 0.086 -10000 0 -0.44 18 18
PVRL2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
CDH1 0.021 0.053 -10000 0 -0.46 6 6
CLDN1 0.002 0.091 -10000 0 -0.44 20 20
JAM-A/CLDN1 0.029 0.081 -10000 0 -0.25 31 31
SRC 0.002 0.12 -10000 0 -0.52 13 13
ITGB3 0.01 0.087 -10000 0 -0.41 21 21
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.031 -10000 0 -0.33 3 3
FARP2 0.019 0.16 -10000 0 -0.6 15 15
RAC1 0.026 0.007 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.036 0.061 -10000 0 -0.26 18 18
nectin-1/I-afadin 0.034 0.031 -10000 0 -0.33 3 3
nectin-2/I-afadin 0.039 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.032 0.066 -10000 0 -0.27 21 21
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.027 0.022 -10000 0 -0.46 1 1
positive regulation of filopodium formation 0.01 0.092 -10000 0 -0.34 13 13
alphaV/beta3 Integrin/Talin 0.045 0.089 0.26 15 -0.32 7 22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
PIP5K1C 0.001 0.038 -10000 0 -0.36 3 3
VAV2 0.033 0.13 -10000 0 -0.55 7 7
RAP1/GDP 0.043 0.11 0.31 4 -0.41 6 10
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.036 0.061 -10000 0 -0.26 18 18
nectin-3(dimer)/I-afadin/I-afadin 0.023 0.066 -10000 0 -0.31 18 18
Rac1/GTP 0.03 0.1 -10000 0 -0.41 7 7
PTPRM 0.005 0.043 -10000 0 -0.23 13 13
E-cadherin/beta catenin/alpha catenin 0.062 0.054 -10000 0 -0.44 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.044 0.069 -10000 0 -10000 0 0
UGCG 0.001 0.12 -10000 0 -0.56 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT 0.036 0.12 0.28 7 -0.43 12 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.003 0.12 -10000 0 -0.55 22 22
mol:DAG 0.004 0.094 -10000 0 -0.76 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.049 0.098 -10000 0 -0.46 5 5
FRAP1 0.046 0.11 0.27 2 -0.49 7 9
FOXO3 0.048 0.094 0.32 3 -0.4 3 6
AKT1 0.05 0.093 0.26 3 -0.4 3 6
GAB2 0.023 0.038 -10000 0 -0.46 3 3
SMPD1 0.007 0.11 -10000 0 -0.58 17 17
SGMS1 0.02 0.069 -10000 0 -0.58 6 6
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 0.005 0.019 -10000 0 -0.28 2 2
CALM1 0.026 0.007 -10000 0 -10000 0 0
cell proliferation 0.046 0.089 0.26 3 -0.38 7 10
EIF3A 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.031 -10000 0 -0.34 2 2
RPS6KB1 0.011 0.083 -10000 0 -0.83 2 2
mol:sphingomyelin 0.004 0.094 -10000 0 -0.76 7 7
natural killer cell activation 0 0.001 -10000 0 -0.012 1 1
JAK3 0.012 0.084 -10000 0 -0.38 22 22
PIK3R1 0.027 0.032 -10000 0 -0.46 2 2
JAK1 0.03 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MYC 0.081 0.12 0.36 15 -10000 0 15
MYB -0.078 0.34 -10000 0 -1.2 45 45
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.044 0.081 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.083 -10000 0 -0.75 2 2
mol:PI-3-4-5-P3 0.043 0.081 -10000 0 -0.34 2 2
Rac1/GDP 0.017 0.022 -10000 0 -0.26 2 2
T cell proliferation 0.044 0.08 0.26 9 -10000 0 9
SHC1 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.02 -10000 0 -0.062 50 50
PRKCZ 0.042 0.078 0.24 5 -0.32 1 6
NF kappa B1 p50/RelA 0.06 0.1 -10000 0 -0.49 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.051 -10000 0 -0.37 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
IL2RA -0.01 0.12 -10000 0 -0.39 47 47
IL2RB 0.023 0.053 -10000 0 -0.4 8 8
TERT -0.056 0.16 -10000 0 -0.39 97 97
E2F1 -0.011 0.14 -10000 0 -0.42 46 46
SOS1 0.028 0.004 -10000 0 -10000 0 0
RPS6 0.025 0.009 -10000 0 -10000 0 0
mol:cAMP 0.001 0.01 0.03 50 -10000 0 50
PTPN11 0.028 0.003 -10000 0 -10000 0 0
IL2RG 0.016 0.076 -10000 0 -0.39 17 17
actin cytoskeleton organization 0.044 0.08 0.26 9 -10000 0 9
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.019 0.022 -10000 0 -0.38 1 1
PIK3CA 0.021 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.033 -10000 0 -0.24 2 2
LCK 0.02 0.063 -10000 0 -0.38 12 12
BCL2 0.042 0.12 -10000 0 -0.85 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.023 0.023 -10000 0 -0.46 1 1
Caspase 8 (4 units) 0.044 0.076 -10000 0 -0.4 1 1
NEF -0.006 0.035 -10000 0 -10000 0 0
NFKBIA 0.023 0.027 -10000 0 -10000 0 0
BIRC3 0.017 0.081 -10000 0 -0.38 14 14
CYCS 0.02 0.077 0.21 18 -0.44 1 19
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CD247 0.001 0.11 -10000 0 -0.35 34 34
MAP2K7 0.033 0.14 0.32 2 -0.77 10 12
protein ubiquitination 0.041 0.096 0.24 18 -0.39 9 27
CRADD 0.028 0.002 -10000 0 -10000 0 0
DAXX 0.027 0.006 -10000 0 -10000 0 0
FAS 0.026 0.022 -10000 0 -0.46 1 1
BID 0.018 0.072 0.19 3 -0.47 1 4
NF-kappa-B/RelA/I kappa B alpha 0.044 0.07 -10000 0 -0.33 10 10
TRADD 0.027 0.006 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.02 0.013 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.07 -10000 0 -0.32 11 11
MAPK8 0.03 0.13 0.29 3 -0.7 10 13
APAF1 0.028 0.002 -10000 0 -10000 0 0
TRAF1 0.017 0.065 -10000 0 -0.39 13 13
TRAF2 0.023 0.041 -10000 0 -0.39 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.025 0.076 0.2 3 -0.27 12 15
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.029 0.1 -10000 0 -0.47 12 12
CHUK 0.041 0.1 0.24 17 -0.42 9 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.052 0.043 -10000 0 -0.24 1 1
TCRz/NEF -0.004 0.1 -10000 0 -0.31 48 48
TNF 0.008 0.088 -10000 0 -0.4 23 23
FASLG -0.022 0.14 -10000 0 -0.5 40 40
NFKB1 0.024 0.028 -10000 0 -0.2 1 1
TNFR1A/BAG4/TNF-alpha 0.033 0.061 -10000 0 -0.24 21 21
CASP6 0.041 0.11 -10000 0 -0.54 9 9
CASP7 0.043 0.12 0.35 15 -0.42 7 22
RELA 0.023 0.029 -10000 0 -0.2 1 1
CASP2 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.039 0.12 0.3 27 -0.41 7 34
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.023 -10000 0 -0.33 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.006 -10000 0 -10000 0 0
MAP3K14 0.04 0.1 0.24 11 -0.44 11 22
APAF-1/Caspase 9 0.013 0.076 -10000 0 -0.34 2 2
BCL2 0.027 0.12 0.28 3 -0.65 10 13
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.001 0.15 -9999 0 -0.47 22 22
MAP3K8 0.023 0.038 -9999 0 -0.46 3 3
FOS 0.002 0.11 -9999 0 -0.5 11 11
PRKCA 0.021 0.032 -9999 0 -0.42 2 2
PTPN7 0.003 0.09 -9999 0 -0.4 24 24
HRAS 0.026 0.02 -9999 0 -0.4 1 1
PRKCB 0.016 0.057 -9999 0 -0.41 8 8
NRAS 0.027 0.005 -9999 0 -10000 0 0
RAS family/GTP 0.044 0.024 -9999 0 -0.21 1 1
MAPK3 0.01 0.096 -9999 0 -0.6 8 8
MAP2K1 0.011 0.079 -9999 0 -0.45 9 9
ELK1 0.021 0.02 -9999 0 -10000 0 0
BRAF 0.012 0.044 -9999 0 -0.31 6 6
mol:GTP -0.001 0.002 -9999 0 -0.005 66 66
MAPK1 0.013 0.081 -9999 0 -0.57 5 5
RAF1 0.009 0.056 -9999 0 -0.39 5 5
KRAS 0.026 0.007 -9999 0 -10000 0 0
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 0.014 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.037 0.021 -10000 0 -10000 0 0
CDKN1B 0.017 0.062 -10000 0 -0.29 1 1
CDKN1A 0.016 0.052 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -10000 0 0
AKT1 0.01 0.046 -10000 0 -0.29 8 8
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.012 0.024 -10000 0 -0.3 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.058 -10000 0 -0.28 9 9
AKT1/ASK1 0.039 0.066 -10000 0 -0.28 1 1
BAD/YWHAZ 0.047 0.022 -10000 0 -10000 0 0
RICTOR 0.025 0.009 -10000 0 -10000 0 0
RAF1 0.025 0.009 -10000 0 -10000 0 0
JNK cascade -0.036 0.063 0.27 9 -10000 0 9
TSC1 0.013 0.055 -10000 0 -0.29 1 1
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.072 0.28 3 -0.28 6 9
EP300 0.026 0.022 -10000 0 -0.46 1 1
mol:GDP 0.015 0.058 -10000 0 -0.29 13 13
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.054 -10000 0 -0.29 1 1
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.012 -10000 0 -0.26 1 1
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAPKAP1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.041 0.07 0.29 8 -0.21 11 19
YWHAH 0.027 0.004 -10000 0 -10000 0 0
AKT1S1 0.015 0.052 -10000 0 -0.28 7 7
CASP9 0.015 0.046 -10000 0 -0.28 5 5
YWHAB 0.026 0.007 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.047 0.072 0.3 10 -10000 0 10
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.049 0.024 -10000 0 -0.28 1 1
YWHAE 0.027 0.006 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.02 0.056 -10000 0 -0.3 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.002 0.081 -10000 0 -0.33 25 25
CHUK 0.014 0.053 -10000 0 -0.28 8 8
BAD/BCL-XL 0.044 0.064 0.26 1 -10000 0 1
mTORC2 0.031 0.013 -10000 0 -10000 0 0
AKT2 0.014 0.014 -10000 0 -0.3 1 1
FOXO1-3a-4/14-3-3 family 0.049 0.09 0.25 13 -0.39 8 21
PDPK1 0.027 0.022 -10000 0 -0.46 1 1
MDM2 0.017 0.062 -10000 0 -0.29 1 1
MAPKKK cascade -0.04 0.071 0.28 6 -0.28 3 9
MDM2/Cbp/p300 0.062 0.078 0.27 10 -10000 0 10
TSC1/TSC2 0.015 0.057 0.29 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.075 0.26 10 -10000 0 10
glucose import -0.094 0.12 0.21 6 -0.24 208 214
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.061 0.18 1 -0.34 7 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.096 0.12 0.21 4 -0.24 209 213
GSK3A 0.015 0.053 -10000 0 -0.28 7 7
FOXO1 0.014 0.05 -10000 0 -0.29 1 1
GSK3B 0.029 0.064 -10000 0 -0.28 5 5
SFN 0.024 0.04 -10000 0 -0.42 4 4
G1/S transition of mitotic cell cycle 0.041 0.067 0.25 8 -10000 0 8
p27Kip1/14-3-3 family 0.03 0.062 -10000 0 -0.43 3 3
PRKACA 0.028 0.004 -10000 0 -10000 0 0
KPNA1 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.018 0.031 -10000 0 -0.25 2 2
CRKL 0.026 0.019 -10000 0 -0.39 1 1
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DOCK1 0.027 0.022 -10000 0 -0.46 1 1
ITGA4 0.021 0.051 -10000 0 -0.39 8 8
alpha4/beta7 Integrin/MAdCAM1 0.045 0.064 -10000 0 -0.26 2 2
EPO -0.02 0.12 -10000 0 -0.39 51 51
alpha4/beta7 Integrin 0.034 0.046 -10000 0 -0.28 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.04 -10000 0 -0.27 8 8
EPO/EPOR (dimer) 0.001 0.1 -10000 0 -0.28 58 58
lamellipodium assembly 0.038 0.081 -10000 0 -0.34 10 10
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.33 2 2
ARF6 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.004 0.058 -10000 0 -0.29 7 7
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
MADCAM1 0.001 0.073 -10000 0 -0.39 16 16
cell adhesion 0.043 0.063 -10000 0 -0.26 2 2
CRKL/CBL 0.035 0.02 -10000 0 -0.27 1 1
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC -0.004 0.08 0.18 12 -0.28 10 22
ITGB7 0.026 0.031 -10000 0 -0.46 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.02 0.094 -10000 0 -0.24 56 56
p130Cas/Crk/Dock1 0.017 0.076 -10000 0 -0.35 2 2
VCAM1 -0.015 0.13 -10000 0 -0.4 51 51
RHOA 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.039 -10000 0 -10000 0 0
BCAR1 -0.021 0.069 0.18 16 -0.27 9 25
EPOR 0.019 0.057 -10000 0 -0.39 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.083 -10000 0 -0.35 10 10
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.004 0.11 -10000 0 -0.46 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.009 0.023 -10000 0 -0.19 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
MAP3K12 0.026 0.028 -10000 0 -0.42 2 2
FGR 0.027 0.019 -10000 0 -0.39 1 1
p38 alpha/TAB1 -0.024 0.069 -10000 0 -0.31 18 18
PRKG1 0.001 0.11 -10000 0 -0.44 28 28
DUSP8 0.027 0.006 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.018 0.1 0.17 5 -0.34 15 20
apoptosis -0.023 0.066 -10000 0 -0.3 18 18
RAL/GTP 0.035 0.01 -10000 0 -10000 0 0
LYN 0.024 0.02 -10000 0 -0.39 1 1
DUSP1 0.005 0.1 -10000 0 -0.46 23 23
PAK1 0.025 0.008 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.061 0.036 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.045 -10000 0 -0.39 6 6
RAC1-CDC42/GTP 0.034 0.011 -10000 0 -10000 0 0
MAPK11 0.029 0.11 0.23 30 -0.35 14 44
BLK -0.035 0.14 -10000 0 -0.4 70 70
HCK 0.024 0.029 -10000 0 -0.42 2 2
MAP2K3 0.027 0.006 -10000 0 -10000 0 0
DUSP16 0.026 0.007 -10000 0 -10000 0 0
DUSP10 0.027 0.019 -10000 0 -0.39 1 1
TRAF6/MEKK3 0.034 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.1 0.22 22 -0.37 13 35
positive regulation of innate immune response 0.033 0.12 0.25 30 -0.41 15 45
LCK 0.018 0.063 -10000 0 -0.39 12 12
p38alpha-beta/MKP7 0.04 0.12 0.28 20 -0.4 12 32
p38alpha-beta/MKP5 0.041 0.12 0.25 27 -0.4 13 40
PGK/cGMP 0.002 0.076 -10000 0 -0.31 28 28
PAK2 0.02 0.013 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.034 0.13 0.26 28 -0.4 15 43
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
PAK3 0.003 0.077 -10000 0 -0.39 18 18
Aurora B signaling

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
Condensin I complex 0.017 0.029 -10000 0 -10000 0 0
STMN1 0.01 0.049 -10000 0 -0.3 11 11
Aurora B/RasGAP/Survivin 0.042 0.077 -10000 0 -0.27 24 24
Chromosomal passenger complex/Cul3 protein complex 0.011 0.054 -10000 0 -0.27 7 7
BIRC5 0.012 0.084 -10000 0 -0.39 22 22
DES -0.31 0.3 -10000 0 -0.56 296 296
Aurora C/Aurora B/INCENP 0.049 0.049 -10000 0 -0.22 13 13
Aurora B/TACC1 0.031 0.04 -10000 0 -0.23 10 10
Aurora B/PP2A 0.038 0.043 -10000 0 -0.26 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.01 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0.003 -10000 0 -10000 0 0
NDC80 0.011 0.036 -10000 0 -0.27 8 8
Cul3 protein complex 0.044 0.035 -10000 0 -0.28 3 3
KIF2C 0.017 0.026 -10000 0 -0.19 1 1
PEBP1 0.028 0.003 -10000 0 -10000 0 0
KIF20A 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.037 0.047 -10000 0 -0.3 8 8
SEPT1 0.02 0.055 -10000 0 -0.39 9 9
SMC2 0.027 0.005 -10000 0 -10000 0 0
SMC4 0.021 0.012 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.006 0.12 -10000 0 -0.57 19 19
PSMA3 0.027 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.015 0.023 -10000 0 -10000 0 0
AURKB 0.027 0.056 -10000 0 -0.39 9 9
AURKC 0.021 0.051 -10000 0 -0.41 7 7
CDCA8 0.028 0.019 -10000 0 -0.39 1 1
cytokinesis -0.001 0.058 -10000 0 -0.36 5 5
Aurora B/Septin1 0.03 0.082 -10000 0 -0.34 6 6
AURKA 0.022 0.045 -10000 0 -0.39 6 6
INCENP 0.029 0.006 -10000 0 -10000 0 0
KLHL13 0.025 0.038 -10000 0 -0.46 3 3
BUB1 0.028 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.039 0.068 -10000 0 -0.24 23 23
EVI5 0.029 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.051 0.053 -10000 0 -10000 0 0
SGOL1 0.025 0.009 -10000 0 -10000 0 0
CENPA 0.017 0.05 -10000 0 -0.28 5 5
NCAPG 0.026 0.007 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.038 0.043 -10000 0 -0.26 9 9
NCAPD2 0.026 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.039 0.042 -10000 0 -0.26 9 9
RHOA 0.025 0.009 -10000 0 -10000 0 0
NCAPH 0.027 0.004 -10000 0 -10000 0 0
NPM1 -0.008 0.11 -10000 0 -0.48 18 18
RASA1 0.024 0.031 -10000 0 -0.46 2 2
KLHL9 0.024 0.01 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.043 -10000 0 -0.26 9 9
PPP1CC 0.028 0.002 -10000 0 -10000 0 0
Centraspindlin 0.048 0.054 -10000 0 -0.26 1 1
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
NSUN2 0.009 0.058 -10000 0 -0.27 16 16
MYLK 0.012 0.032 -10000 0 -0.32 2 2
KIF23 0.029 0.005 -10000 0 -10000 0 0
VIM 0.01 0.046 -10000 0 -0.29 11 11
RACGAP1 0.029 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.094 -10000 0 -0.39 20 20
Chromosomal passenger complex 0.018 0.044 0.17 2 -0.24 3 5
Chromosomal passenger complex/EVI5 0.088 0.086 -10000 0 -0.36 6 6
TACC1 0.023 0.032 -10000 0 -0.46 2 2
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
CUL3 0.027 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.042 0.03 -9999 0 -10000 0 0
CLOCK 0.024 0.053 -9999 0 -0.46 6 6
TIMELESS/CRY2 0.04 0.022 -9999 0 -10000 0 0
DEC1/BMAL1 -0.012 0.11 -9999 0 -0.27 83 83
ATR 0.023 0.011 -9999 0 -10000 0 0
NR1D1 0.024 0.014 -9999 0 -10000 0 0
ARNTL 0.029 0.006 -9999 0 -10000 0 0
TIMELESS 0.024 0.014 -9999 0 -10000 0 0
NPAS2 0.023 0.057 -9999 0 -0.46 7 7
CRY2 0.027 0.006 -9999 0 -10000 0 0
mol:CO -0.01 0 -9999 0 -10000 0 0
CHEK1 0.026 0.008 -9999 0 -10000 0 0
mol:HEME 0.01 0 -9999 0 -10000 0 0
PER1 0.026 0.022 -9999 0 -0.46 1 1
BMAL/CLOCK/NPAS2 0.056 0.057 -9999 0 -0.3 11 11
BMAL1/CLOCK 0.013 0.07 -9999 0 -0.42 1 1
S phase of mitotic cell cycle 0.042 0.03 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.031 -9999 0 -10000 0 0
mol:NADPH 0.01 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.04 0.024 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.054 0.15 -9999 0 -0.39 84 84
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.044 0.097 -10000 0 -0.4 17 17
MAP4K1 0.015 0.07 -10000 0 -0.4 14 14
MAP3K8 0.024 0.038 -10000 0 -0.46 3 3
PRKCB 0.021 0.054 -10000 0 -0.41 8 8
DBNL 0.027 0.006 -10000 0 -10000 0 0
CRKL 0.026 0.019 -10000 0 -0.39 1 1
MAP3K1 0.012 0.058 -10000 0 -0.38 4 4
JUN 0.01 0.12 -10000 0 -0.58 18 18
MAP3K7 0.01 0.062 -10000 0 -0.37 5 5
GRAP2 0.017 0.066 -10000 0 -0.43 11 11
CRK 0.027 0.006 -10000 0 -10000 0 0
MAP2K4 0.016 0.073 0.26 9 -0.38 5 14
LAT 0.017 0.065 -10000 0 -0.39 13 13
LCP2 0.024 0.032 -10000 0 -0.39 3 3
MAPK8 0.012 0.13 -10000 0 -0.6 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.018 0.065 -10000 0 -0.35 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.052 0.096 -10000 0 -0.44 12 12
Regulation of Telomerase

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
Telomerase catalytic core complex -0.049 0.18 -10000 0 -0.59 16 16
RAD9A 0.025 0.008 -10000 0 -10000 0 0
AP1 -0.009 0.12 -10000 0 -0.33 63 63
IFNAR2 0.02 0.018 -10000 0 -10000 0 0
AKT1 0.003 0.049 -10000 0 -0.34 5 5
ER alpha/Oestrogen 0.003 0.068 -10000 0 -0.3 24 24
NFX1/SIN3/HDAC complex 0.022 0.045 -10000 0 -0.3 4 4
EGF -0.068 0.19 -10000 0 -0.46 98 98
SMG5 0.028 0.004 -10000 0 -10000 0 0
SMG6 0.027 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.028 0.028 -10000 0 -10000 0 0
TERT/c-Abl -0.043 0.18 -10000 0 -0.56 16 16
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.044 0.024 -10000 0 -10000 0 0
WT1 -0.07 0.16 -10000 0 -0.39 107 107
WRN 0.025 0.008 -10000 0 -10000 0 0
SP1 0.018 0.023 -10000 0 -10000 0 0
SP3 0.026 0.007 -10000 0 -10000 0 0
TERF2IP 0.027 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.026 0.17 -10000 0 -0.55 11 11
Mad/Max 0.034 0.036 -10000 0 -0.34 4 4
TERT -0.051 0.19 -10000 0 -0.63 14 14
CCND1 -0.005 0.2 0.44 2 -0.76 9 11
MAX 0.026 0.007 -10000 0 -10000 0 0
RBBP7 0.027 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.022 -10000 0 -0.46 1 1
TERF2 0.026 0.013 -10000 0 -10000 0 0
PTGES3 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
Telomerase/911 0.035 0.05 -10000 0 -10000 0 0
CDKN1B -0.023 0.095 -10000 0 -10000 0 0
RAD1 0.025 0.009 -10000 0 -10000 0 0
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
SAP30 0.026 0.019 -10000 0 -0.39 1 1
TRF2/PARP2 0.038 0.015 -10000 0 -10000 0 0
UBE3A 0.027 0.005 -10000 0 -10000 0 0
JUN 0.027 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.014 0.015 -10000 0 -10000 0 0
FOS -0.034 0.16 -10000 0 -0.46 63 63
IFN-gamma/IRF1 -0.017 0.12 -10000 0 -0.26 96 96
PARP2 0.026 0.007 -10000 0 -10000 0 0
BLM 0.027 0.019 -10000 0 -0.39 1 1
Telomerase 0.007 0.1 -10000 0 -0.56 8 8
IRF1 0.029 0.008 -10000 0 -10000 0 0
ESR1 0.006 0.095 -10000 0 -0.42 24 24
KU/TER 0.039 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.024 0.06 -10000 0 -0.4 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.026 0.06 -10000 0 -0.41 5 5
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.018 0.022 -10000 0 -10000 0 0
ATM 0.011 0.008 -10000 0 -10000 0 0
SMAD3 0.014 0.022 -10000 0 -0.27 3 3
ABL1 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.022 0.049 -10000 0 -0.47 5 5
MRE11A 0.025 0.008 -10000 0 -10000 0 0
HUS1 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 0.028 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.023 0.19 -10000 0 -0.63 11 11
NR2F2 0.028 0.02 -10000 0 -0.37 1 1
MAPK3 -0.007 0.018 -10000 0 -0.27 1 1
MAPK1 -0.007 0.018 -10000 0 -0.27 1 1
TGFB1/TGF beta receptor Type II 0.025 0.032 -10000 0 -0.38 3 3
NFKB1 0.027 0.005 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.008 -10000 0 -10000 0 0
NBN 0.025 0.009 -10000 0 -10000 0 0
EGFR 0.02 0.044 -10000 0 -0.47 4 4
mol:Oestrogen -0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.032 0.14 -10000 0 -0.34 88 88
MYC 0.021 0.012 -10000 0 -10000 0 0
IL2 0.01 0.029 -10000 0 -0.38 1 1
KU 0.039 0.01 -10000 0 -10000 0 0
RAD50 0.026 0.007 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
TGFB1 0.025 0.032 -10000 0 -0.39 3 3
TRF2/BLM 0.039 0.019 -10000 0 -0.26 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.031 0.18 -10000 0 -0.58 13 13
SP1/HDAC2 0.028 0.033 -10000 0 -10000 0 0
PINX1 0.025 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.026 0.17 -10000 0 -0.58 9 9
Smad3/Myc 0.024 0.021 -10000 0 -0.22 2 2
911 complex 0.043 0.025 -10000 0 -10000 0 0
IFNG -0.05 0.16 -10000 0 -0.38 97 97
Telomerase/PinX1 -0.027 0.17 -10000 0 -0.58 9 9
Telomerase/AKT1/mTOR/p70S6K 0.001 0.096 0.26 1 -0.47 8 9
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.025 0.17 -10000 0 -0.57 10 10
response to DNA damage stimulus -0.002 0.028 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.06 0.036 -10000 0 -10000 0 0
TRF2/WRN 0.036 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.026 0.17 -10000 0 -0.57 9 9
E2F1 0.004 0.082 -10000 0 -0.4 20 20
ZNFX1 0.026 0.006 -10000 0 -10000 0 0
PIF1 0.003 0.099 -10000 0 -0.39 31 31
NCL 0.027 0.006 -10000 0 -10000 0 0
DKC1 0.027 0.006 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.09 0.24 -10000 0 -1.1 3 3
PLK1 0.054 0.099 -10000 0 -0.68 7 7
BIRC5 0.048 0.11 -10000 0 -0.91 3 3
HSPA1B 0.089 0.24 -10000 0 -1.1 3 3
MAP2K1 0.036 0.037 -10000 0 -10000 0 0
BRCA2 0.083 0.25 -10000 0 -1.1 6 6
FOXM1 0.087 0.27 -10000 0 -1.4 3 3
XRCC1 0.088 0.24 -10000 0 -1.1 3 3
FOXM1B/p19 -0.015 0.24 -10000 0 -1.1 6 6
Cyclin D1/CDK4 0.056 0.25 -10000 0 -1 5 5
CDC2 0.09 0.25 -10000 0 -1.1 3 3
TGFA 0.071 0.26 0.56 1 -1 7 8
SKP2 0.11 0.24 0.73 1 -1 3 4
CCNE1 0.028 0.033 -10000 0 -0.38 3 3
CKS1B 0.088 0.24 -10000 0 -1.1 3 3
RB1 0.031 0.18 -10000 0 -0.84 7 7
FOXM1C/SP1 0.095 0.25 -10000 0 -1.2 3 3
AURKB 0.032 0.16 -10000 0 -0.75 15 15
CENPF 0.089 0.24 0.63 1 -1.1 3 4
CDK4 0.032 0.019 -10000 0 -10000 0 0
MYC 0.062 0.21 0.49 1 -0.91 3 4
CHEK2 0.035 0.037 -10000 0 -10000 0 0
ONECUT1 0.074 0.26 -10000 0 -1 6 6
CDKN2A -0.13 0.19 -10000 0 -0.39 187 187
LAMA4 0.081 0.25 -10000 0 -1.1 3 3
FOXM1B/HNF6 0.072 0.28 -10000 0 -1.3 5 5
FOS -0.006 0.44 -10000 0 -1.1 67 67
SP1 0.029 0.003 -10000 0 -10000 0 0
CDC25B 0.09 0.24 -10000 0 -1.1 3 3
response to radiation 0.015 0.023 -10000 0 -10000 0 0
CENPB 0.095 0.24 -10000 0 -1.1 3 3
CENPA 0.086 0.24 -10000 0 -1.2 3 3
NEK2 0.089 0.24 0.63 1 -1.1 3 4
HIST1H2BA 0.084 0.24 -10000 0 -1.1 3 3
CCNA2 0.03 0.021 -10000 0 -0.4 1 1
EP300 0.026 0.022 -10000 0 -0.46 1 1
CCNB1/CDK1 0.085 0.25 -10000 0 -1.3 3 3
CCNB2 0.087 0.24 0.73 1 -1.2 3 4
CCNB1 0.09 0.25 -10000 0 -1.1 3 3
ETV5 0.14 0.26 0.67 2 -1.1 3 5
ESR1 0.064 0.3 -10000 0 -1.1 16 16
CCND1 0.025 0.23 -10000 0 -1 5 5
GSK3A 0.036 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.062 0.047 -10000 0 -0.24 2 2
CDK2 0.031 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.026 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.094 0.24 -10000 0 -1.2 3 3
GAS1 0.085 0.26 -10000 0 -1.1 6 6
MMP2 0.073 0.25 -10000 0 -1.1 3 3
RB1/FOXM1C 0.08 0.26 0.6 1 -1.1 5 6
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.027 0.004 -9999 0 -10000 0 0
SPHK1 0.016 0.068 -9999 0 -0.39 14 14
GNAI2 0.024 0.009 -9999 0 -10000 0 0
mol:S1P 0.012 0.024 -9999 0 -10000 0 0
GNAO1 0.023 0.039 -9999 0 -0.41 4 4
mol:Sphinganine-1-P 0.007 0.047 -9999 0 -0.27 14 14
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.042 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.037 0.018 -9999 0 -0.27 1 1
S1PR3 0.022 0.052 -9999 0 -0.45 6 6
S1PR2 0.027 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.005 0.029 -9999 0 -0.24 2 2
S1PR5 0.024 0.04 -9999 0 -0.42 4 4
S1PR4 0.004 0.096 -9999 0 -0.39 29 29
GNAI1 0.026 0.022 -9999 0 -0.46 1 1
S1P/S1P5/G12 0.036 0.043 -9999 0 -0.25 3 3
S1P/S1P3/Gq -0.013 0.11 -9999 0 -0.38 14 14
S1P/S1P4/Gi 0.015 0.07 -9999 0 -0.38 7 7
GNAQ 0.027 0.005 -9999 0 -10000 0 0
GNAZ 0.012 0.079 -9999 0 -0.41 17 17
GNA14 -0.041 0.17 -9999 0 -0.46 71 71
GNA15 0.025 0.031 -9999 0 -0.46 2 2
GNA12 0.025 0.02 -9999 0 -0.39 1 1
GNA13 0.028 0.003 -9999 0 -10000 0 0
GNA11 0.024 0.038 -9999 0 -0.46 3 3
ABCC1 0.025 0.032 -9999 0 -0.39 3 3
TCGA08_rtk_signaling

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
PDGFRA 0.018 0.065 -10000 0 -0.44 10 10
HRAS 0.026 0.02 -10000 0 -0.4 1 1
EGFR 0.021 0.044 -10000 0 -0.46 4 4
AKT 0.071 0.073 0.28 17 -0.26 1 18
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.022 0.048 -10000 0 -0.39 7 7
FOXO4 0.026 0.031 -10000 0 -0.46 2 2
MET 0.022 0.048 -10000 0 -0.41 6 6
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PIK3CB 0.023 0.011 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.008 0.088 -10000 0 -0.4 22 22
PIK3R3 0.027 0.022 -10000 0 -0.46 1 1
PIK3R2 0.028 0.004 -10000 0 -10000 0 0
NF1 0.027 0.004 -10000 0 -10000 0 0
RAS 0.026 0.041 0.16 1 -0.24 3 4
ERBB2 0.027 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.067 0.073 0.25 6 -0.21 50 56
PI3K 0.055 0.073 0.24 31 -0.24 2 33
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
KRAS 0.026 0.007 -10000 0 -10000 0 0
FOXO 0.088 0.063 0.25 27 -10000 0 27
AKT2 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.027 0.006 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0 0.11 -10000 0 -0.41 4 4
TC10/GTP 0.002 0.097 -10000 0 -0.39 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.06 0.039 -10000 0 -0.26 4 4
HRAS 0.026 0.02 -10000 0 -0.4 1 1
APS homodimer 0.025 0.02 -10000 0 -0.39 1 1
GRB14 -0.017 0.14 -10000 0 -0.45 46 46
FOXO3 0.021 0.091 -10000 0 -0.6 10 10
AKT1 0.019 0.11 0.25 12 -0.41 1 13
INSR 0.029 0.023 -10000 0 -0.46 1 1
Insulin Receptor/Insulin 0.052 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.007 -10000 0 -10000 0 0
SORBS1 -0.051 0.18 -10000 0 -0.46 82 82
CRK 0.027 0.006 -10000 0 -10000 0 0
PTPN1 0.009 0.025 -10000 0 -10000 0 0
CAV1 -0.004 0.062 0.18 2 -0.24 4 6
CBL/APS/CAP/Crk-II/C3G 0.019 0.11 -10000 0 -0.25 66 66
Insulin Receptor/Insulin/IRS1/NCK2 0.059 0.04 -10000 0 -0.26 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.034 0.037 -10000 0 -0.24 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.064 -10000 0 -0.34 10 10
RPS6KB1 0.015 0.099 0.24 12 -0.38 1 13
PARD6A 0.025 0.029 -10000 0 -0.42 2 2
CBL 0.025 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.021 0.011 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.036 0.085 -10000 0 -0.39 1 1
HRAS/GTP 0.016 0.027 -10000 0 -10000 0 0
Insulin Receptor 0.029 0.023 -10000 0 -0.46 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.068 0.043 -10000 0 -0.25 4 4
PRKCI 0.018 0.04 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.002 0.071 -10000 0 -0.35 2 2
SHC1 0.028 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.039 0.029 -10000 0 -10000 0 0
PI3K 0.042 0.043 -10000 0 -0.24 3 3
NCK2 0.028 0.003 -10000 0 -10000 0 0
RHOQ 0.028 0.004 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
AKT2 0.022 0.11 0.26 12 -0.41 1 13
PRKCZ 0.014 0.057 -10000 0 -0.43 2 2
SH2B2 0.025 0.02 -10000 0 -0.39 1 1
SHC/SHIP 0.027 0.035 -10000 0 -0.24 4 4
F2RL2 -0.084 0.18 -10000 0 -0.39 136 136
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.046 0.025 -10000 0 -0.21 3 3
TC10/GTP/CIP4/Exocyst 0.037 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.072 0.033 -10000 0 -0.23 1 1
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.024 0.031 -10000 0 -0.46 2 2
NCK1 0.023 0.011 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.008 0.12 -10000 0 -0.26 80 80
TC10/GDP 0.02 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.059 0.032 -10000 0 -0.25 1 1
INPP5D 0.011 0.034 0.19 1 -0.24 6 7
SOS1 0.028 0.004 -10000 0 -10000 0 0
SGK1 -0.004 0.098 -10000 0 -0.63 12 12
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.024 0.038 -10000 0 -0.46 3 3
p62DOK/RasGAP 0.039 0.03 -10000 0 -10000 0 0
INS 0.019 0.027 -10000 0 -0.39 2 2
mol:PI-3-4-P2 0.011 0.034 0.19 1 -0.24 6 7
GRB2 0.027 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.009 0.096 0.24 10 -0.37 2 12
PTPRA 0.028 0.009 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.037 0.008 -10000 0 -10000 0 0
PDPK1 0.027 0.022 -10000 0 -0.46 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.025 0.029 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS1 0.043 0.035 -10000 0 -0.24 6 6
Insulin Receptor/Insulin/IRS3 0.035 0.029 -10000 0 -0.29 3 3
Par3/Par6 -0.008 0.11 -10000 0 -0.3 3 3
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.03 0.023 -10000 0 -0.28 2 2
VEGFR1 homodimer/NRP1 0.013 0.019 -10000 0 -0.28 2 2
mol:DAG -0.018 0.084 -10000 0 -0.35 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.033 -10000 0 -0.26 2 2
CaM/Ca2+ -0.004 0.084 -10000 0 -0.41 1 1
HIF1A 0.031 0.025 -10000 0 -0.45 1 1
GAB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.021 0.098 0.35 5 -0.5 2 7
PLCG1 -0.018 0.084 -10000 0 -0.35 2 2
NOS3 0.012 0.095 0.38 8 -0.39 2 10
CBL 0.025 0.008 -10000 0 -10000 0 0
mol:NO 0.024 0.12 0.48 17 -0.38 3 20
FLT1 0.018 0.023 -10000 0 -0.34 2 2
PGF -0.041 0.15 -10000 0 -0.39 84 84
VEGFR1 homodimer/NRP2/VEGFR121 0.04 0.039 -10000 0 -0.27 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
eNOS/Hsp90 0.021 0.1 0.39 5 -0.38 2 7
endothelial cell proliferation -0.003 0.086 0.36 8 -0.42 1 9
mol:Ca2+ -0.018 0.083 -10000 0 -0.35 2 2
MAPK3 -0.023 0.087 0.34 11 -0.38 1 12
MAPK1 -0.024 0.088 0.34 11 -0.38 1 12
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
PLGF homodimer -0.041 0.15 -10000 0 -0.39 84 84
PRKACA 0.028 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.004 0.11 -10000 0 -0.39 38 38
VEGFA homodimer 0.022 0.045 -10000 0 -0.39 6 6
VEGFR1 homodimer/VEGFA homodimer 0.027 0.036 -10000 0 -0.28 2 2
platelet activating factor biosynthetic process -0.024 0.083 0.33 10 -0.38 1 11
PI3K 0.011 0.085 -10000 0 -0.41 2 2
PRKCA -0.021 0.082 0.32 5 -0.4 1 6
PRKCB -0.022 0.086 0.35 5 -0.4 1 6
VEGFR1 homodimer/PLGF homodimer -0.011 0.098 -10000 0 -0.38 2 2
VEGFA 0.022 0.045 -10000 0 -0.39 6 6
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.018 0.084 -10000 0 -0.35 2 2
RASA1 0.02 0.042 -10000 0 -0.48 1 1
NRP2 0.026 0.026 -10000 0 -0.39 2 2
VEGFR1 homodimer 0.018 0.023 -10000 0 -0.34 2 2
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.018 0.13 0.47 16 -0.39 3 19
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.01 0.084 -10000 0 -0.41 2 2
mol:L-citrulline 0.024 0.12 0.48 17 -0.38 3 20
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.04 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.035 0.037 -10000 0 -0.27 1 1
CD2AP 0.027 0.006 -10000 0 -10000 0 0
PI3K/GAB1 0.019 0.087 -10000 0 -0.4 2 2
PDPK1 0.029 0.12 0.38 11 -0.5 2 13
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.041 0.038 -10000 0 -0.27 1 1
mol:NADP 0.024 0.12 0.48 17 -0.38 3 20
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.039 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.03 0.027 -10000 0 -0.28 2 2
S1P4 pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
CDC42/GTP 0.013 0.073 -10000 0 -0.31 7 7
PLCG1 0.005 0.061 -10000 0 -0.3 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.018 -10000 0 -0.27 1 1
cell migration 0.012 0.071 -10000 0 -0.3 7 7
S1PR5 0.024 0.04 -10000 0 -0.42 4 4
S1PR4 0.004 0.096 -10000 0 -0.39 29 29
MAPK3 0.005 0.061 -10000 0 -0.3 9 9
MAPK1 0.003 0.058 -10000 0 -0.28 9 9
S1P/S1P5/Gi 0.019 0.051 -10000 0 -0.26 8 8
GNAI1 0.026 0.022 -10000 0 -0.46 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.03 -10000 0 -0.25 5 5
RHOA 0.012 0.063 0.18 27 -0.24 1 28
S1P/S1P4/Gi 0.013 0.062 -10000 0 -0.31 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.012 0.079 -10000 0 -0.41 17 17
S1P/S1P4/G12/G13 0.034 0.06 -10000 0 -0.21 28 28
GNA12 0.025 0.02 -10000 0 -0.39 1 1
GNA13 0.028 0.003 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.023 0.038 -10000 0 -0.46 3 3
ELF1 0.009 0.075 -10000 0 -0.45 3 3
CCNA2 0.026 0.019 -10000 0 -0.39 1 1
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
JAK3 0.01 0.084 -10000 0 -0.39 22 22
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
JAK1 0.028 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.04 0.081 0.23 1 -0.37 2 3
SHC1 0.028 0.004 -10000 0 -10000 0 0
SP1 0.029 0.047 -10000 0 -0.33 8 8
IL2RA -0.016 0.11 -10000 0 -0.35 50 50
IL2RB 0.021 0.053 -10000 0 -0.4 8 8
SOS1 0.028 0.004 -10000 0 -10000 0 0
IL2RG 0.014 0.076 -10000 0 -0.4 17 17
G1/S transition of mitotic cell cycle 0.031 0.1 0.3 6 -0.59 7 13
PTPN11 0.029 0.002 -10000 0 -10000 0 0
CCND2 0.014 0.061 -10000 0 -0.57 5 5
LCK 0.018 0.063 -10000 0 -0.39 12 12
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.005 0.027 -10000 0 -0.39 1 1
CDK6 0.024 0.029 -10000 0 -0.42 2 2
CCND3 0.043 0.079 -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 -0.18 0.24 -10000 0 -0.46 220 220
CLTC 0.024 0.063 -10000 0 -0.34 11 11
calcium ion-dependent exocytosis 0.013 0.03 -10000 0 -10000 0 0
Dynamin 2/GTP 0.026 0.013 -10000 0 -0.21 1 1
EXOC4 0.026 0.007 -10000 0 -10000 0 0
CD59 0.015 0.031 -10000 0 -0.32 2 2
CPE 0.012 0.026 -10000 0 -0.22 6 6
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
membrane fusion 0.014 0.025 -10000 0 -10000 0 0
CTNND1 0.019 0.035 0.18 20 -10000 0 20
DNM2 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.051 0.2 9 -0.4 2 11
TSHR 0.005 0.036 -10000 0 -0.23 11 11
INS 0.003 0.093 -10000 0 -0.45 19 19
BIN1 0.02 0.058 -10000 0 -0.41 9 9
mol:Choline 0.014 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.011 -10000 0 -0.23 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.013 -10000 0 -0.2 1 1
JUP 0.013 0.031 -10000 0 -0.29 3 3
ASAP2/amphiphysin II 0.045 0.039 -10000 0 -0.22 9 9
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.014 0.03 -10000 0 -0.28 2 2
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.028 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.026 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.022 0.031 -10000 0 -0.29 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.035 0.051 0.33 4 -10000 0 4
positive regulation of phagocytosis 0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.017 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.012 0.023 -10000 0 -0.32 1 1
clathrin heavy chain/ACAP1 0.029 0.057 0.19 1 -0.4 4 5
JIP4/KLC1 0.049 0.016 -10000 0 -10000 0 0
EXOC1 0.027 0.005 -10000 0 -10000 0 0
exocyst 0.022 0.031 -10000 0 -0.29 3 3
RALA/GTP 0.02 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.019 0.036 0.18 22 -10000 0 22
NME1 0.014 0.011 -10000 0 -0.23 1 1
clathrin coat assembly 0.026 0.064 -10000 0 -0.34 11 11
IL2RA 0.005 0.038 -10000 0 -0.32 2 2
VAMP3 0.014 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.059 0.12 -10000 0 -0.32 11 11
EXOC6 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.022 -10000 0 -0.26 3 3
PLD2 0.015 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.006 -10000 0 -10000 0 0
PIP5K1C 0.015 0.027 -10000 0 -10000 0 0
SDC1 0.014 0.029 -10000 0 -0.32 2 2
ARF6/GDP 0.024 0.013 -10000 0 -0.23 1 1
EXOC7 0.028 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.037 0.053 -10000 0 -0.34 4 4
mol:Phosphatidic acid 0.014 0.025 -10000 0 -10000 0 0
endocytosis -0.043 0.038 0.22 9 -10000 0 9
SCAMP2 0.027 0.005 -10000 0 -10000 0 0
ADRB2 0.007 0.082 0.27 1 -0.34 11 12
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ASAP2 0.028 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.014 -10000 0 -0.2 1 1
KLC1 0.026 0.007 -10000 0 -10000 0 0
AVPR2 0.02 0.09 0.23 22 -0.33 12 34
RALA 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.051 -10000 0 -0.37 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.035 0.073 0.22 3 -0.31 4 7
adherens junction organization 0.011 0.094 0.22 1 -0.36 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.057 0.083 0.27 3 -0.44 2 5
FMN1 0.005 0.1 -10000 0 -0.36 15 15
mol:IP3 0.011 0.044 -10000 0 -0.36 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.023 0.085 -10000 0 -0.32 16 16
CTNNB1 0.025 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.05 0.19 1 -0.4 2 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.001 0.16 -10000 0 -0.66 19 19
CTNND1 0.03 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.079 -10000 0 -0.33 11 11
VASP 0.019 0.079 -10000 0 -0.34 11 11
ZYX 0.021 0.075 -10000 0 -0.34 10 10
JUB 0.019 0.081 -10000 0 -0.31 16 16
EGFR(dimer) 0.026 0.09 -10000 0 -0.35 13 13
E-cadherin/beta catenin-gamma catenin 0.041 0.046 -10000 0 -0.35 5 5
mol:PI-3-4-5-P3 0.022 0.062 0.21 1 -0.42 2 3
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.022 0.063 0.22 1 -0.43 2 3
FYN 0.024 0.073 0.23 6 -0.38 2 8
mol:Ca2+ 0.011 0.044 -10000 0 -0.35 2 2
JUP 0.027 0.03 -10000 0 -0.46 2 2
PIK3R1 0.027 0.032 -10000 0 -0.46 2 2
mol:DAG 0.011 0.044 -10000 0 -0.36 2 2
CDH1 0.022 0.052 -10000 0 -0.46 6 6
RhoA/GDP 0.062 0.08 0.26 4 -0.43 2 6
establishment of polarity of embryonic epithelium 0.02 0.077 -10000 0 -0.33 11 11
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
EGFR 0.021 0.044 -10000 0 -0.46 4 4
CASR 0.024 0.064 0.22 4 -0.34 2 6
RhoA/GTP 0.048 0.066 -10000 0 -0.32 2 2
AKT2 0.01 0.051 0.19 1 -0.4 2 3
actin cable formation 0.004 0.099 0.21 5 -0.36 14 19
apoptosis -0.041 0.08 0.34 4 -0.23 9 13
CTNNA1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.037 0.077 -10000 0 -0.47 2 2
PIP5K1A 0.018 0.08 -10000 0 -0.34 11 11
PLCG1 0.011 0.045 -10000 0 -0.36 2 2
Rac1/GTP 0.033 0.085 -10000 0 -0.42 5 5
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.022 0.048 0.41 6 -10000 0 6
PI3K Class IB/PDE3B 0.022 0.048 -10000 0 -0.41 6 6
PDE3B 0.022 0.048 -10000 0 -0.41 6 6
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.031 -9999 0 -0.46 2 2
ITGA4 0.021 0.051 -9999 0 -0.39 8 8
alpha4/beta7 Integrin 0.034 0.046 -9999 0 -0.28 10 10
alpha4/beta1 Integrin 0.034 0.04 -9999 0 -0.27 8 8
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.012 0.13 -10000 0 -0.63 13 13
oxygen homeostasis -0.002 0.011 -10000 0 -10000 0 0
TCEB2 0.026 0.026 -10000 0 -0.39 2 2
TCEB1 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.029 0.084 -10000 0 -0.43 1 1
EPO -0.024 0.16 -10000 0 -0.62 4 4
FIH (dimer) 0.022 0.02 -10000 0 -10000 0 0
APEX1 0.021 0.023 -10000 0 -10000 0 0
SERPINE1 -0.098 0.2 -10000 0 -0.68 9 9
FLT1 -0.014 0.18 -10000 0 -0.62 38 38
ADORA2A -0.024 0.16 0.37 3 -0.68 4 7
germ cell development -0.032 0.17 -10000 0 -0.71 5 5
SLC11A2 -0.022 0.16 -10000 0 -0.69 4 4
BHLHE40 -0.024 0.16 -10000 0 -0.69 4 4
HIF1AN 0.022 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.014 0.12 0.3 1 -0.42 1 2
ETS1 0.033 0.035 -10000 0 -0.38 3 3
CITED2 0.017 0.11 -10000 0 -0.75 6 6
KDR -0.011 0.19 -10000 0 -0.7 25 25
PGK1 -0.022 0.16 -10000 0 -0.69 4 4
SIRT1 0.026 0.022 -10000 0 -0.46 1 1
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT -0.013 0.19 -10000 0 -0.77 5 5
EPAS1 -0.003 0.078 0.22 1 -0.34 4 5
SP1 0.032 0.012 -10000 0 -10000 0 0
ABCG2 -0.027 0.17 -10000 0 -0.68 7 7
EFNA1 -0.021 0.16 -10000 0 -0.64 5 5
FXN -0.024 0.16 0.37 3 -0.68 4 7
POU5F1 -0.034 0.17 -10000 0 -0.74 5 5
neuron apoptosis 0.013 0.18 0.74 5 -10000 0 5
EP300 0.026 0.022 -10000 0 -0.46 1 1
EGLN3 -0.001 0.099 -10000 0 -0.41 27 27
EGLN2 0.022 0.02 -10000 0 -10000 0 0
EGLN1 0.022 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.045 0.024 -10000 0 -10000 0 0
VHL 0.025 0.009 -10000 0 -10000 0 0
ARNT 0.021 0.024 -10000 0 -10000 0 0
SLC2A1 -0.027 0.17 0.37 3 -0.67 6 9
TWIST1 -0.025 0.16 0.37 3 -0.69 6 9
ELK1 0.033 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.032 0.12 0.31 1 -10000 0 1
VEGFA -0.025 0.16 -10000 0 -0.67 5 5
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.024 0.07 -10000 0 -0.29 23 23
AKT1 0.059 0.091 0.34 9 -0.48 2 11
PTK2B 0.017 0.074 0.53 1 -0.56 2 3
VEGFR2 homodimer/Frs2 0.033 0.044 -10000 0 -0.64 2 2
CAV1 -0.004 0.11 -10000 0 -0.39 38 38
CALM1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.046 0.049 -10000 0 -0.59 2 2
endothelial cell proliferation 0.058 0.11 0.34 22 -0.45 2 24
mol:Ca2+ 0.024 0.053 0.36 1 -0.47 3 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.056 0.053 -10000 0 -0.56 2 2
RP11-342D11.1 0.012 0.048 -10000 0 -0.47 3 3
CDH5 0.025 0.029 -10000 0 -0.42 2 2
VEGFA homodimer 0.055 0.043 -10000 0 -0.26 1 1
SHC1 0.028 0.004 -10000 0 -10000 0 0
SHC2 0.021 0.052 -10000 0 -0.42 7 7
HRAS/GDP 0.043 0.047 -10000 0 -0.48 2 2
SH2D2A -0.037 0.15 -10000 0 -0.39 80 80
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.051 0.1 0.36 2 -0.45 5 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.008 0.1 -10000 0 -0.53 4 4
VEGFR1 homodimer 0.026 0.019 -10000 0 -0.39 1 1
SHC/GRB2/SOS1 0.072 0.057 -10000 0 -0.46 3 3
GRB10 0.023 0.05 0.36 1 -0.54 2 3
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.025 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.063 0.061 -10000 0 -0.55 2 2
HRAS 0.026 0.02 -10000 0 -0.4 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.016 0.055 -10000 0 -0.33 5 5
HIF1A 0.025 0.023 -10000 0 -0.46 1 1
FRS2 0.027 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.054 0.052 -10000 0 -0.56 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.05 -10000 0 -0.4 7 7
Nck/Pak 0.032 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.046 0.052 -10000 0 -0.59 2 2
mol:GDP 0.056 0.051 -10000 0 -0.44 3 3
mol:NADP 0.037 0.1 0.32 6 -0.4 9 15
eNOS/Hsp90 0.044 0.096 0.3 3 -0.39 6 9
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
mol:IP3 0.024 0.053 0.37 1 -0.48 3 4
HIF1A/ARNT 0.038 0.02 -10000 0 -0.33 1 1
SHB 0.025 0.009 -10000 0 -10000 0 0
VEGFA 0.023 0.045 -10000 0 -0.38 6 6
VEGFC -0.033 0.15 -10000 0 -0.39 74 74
FAK1/Vinculin 0.044 0.09 0.44 2 -0.59 2 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.075 -10000 0 -0.58 2 2
PTPN6 0.026 0.007 -10000 0 -10000 0 0
EPAS1 0.034 0.024 -10000 0 -0.33 2 2
mol:L-citrulline 0.037 0.1 0.32 6 -0.4 9 15
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.051 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer 0.05 0.054 -10000 0 -0.51 3 3
VEGFR2/3 heterodimer 0.029 0.053 -10000 0 -0.64 2 2
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.012 0.057 0.25 8 -0.53 2 10
VEGFR2 homodimer 0.021 0.047 -10000 0 -0.72 2 2
FLT1 0.026 0.019 -10000 0 -0.39 1 1
NEDD4 0.029 0.007 -10000 0 -10000 0 0
MAPK3 0.011 0.063 0.32 3 -0.44 3 6
MAPK1 0.012 0.064 0.3 5 -0.5 2 7
VEGFA145/NRP2 0.035 0.037 -10000 0 -0.27 7 7
VEGFR1/2 heterodimer 0.032 0.045 -10000 0 -0.64 2 2
KDR 0.021 0.047 -10000 0 -0.72 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.05 0.052 -10000 0 -0.47 3 3
SRC 0.026 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.02 0.07 0.3 6 -0.51 2 8
PI3K 0.032 0.054 -10000 0 -0.51 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.051 -10000 0 -0.59 2 2
FES 0.025 0.054 0.37 1 -0.48 3 4
GAB1 0.033 0.058 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.052 -10000 0 -0.59 2 2
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
SOS1 0.028 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.035 0.11 0.32 3 -0.38 7 10
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.047 -10000 0 -0.5 2 2
PI3K/GAB1 0.057 0.083 0.28 4 -0.49 2 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.056 0.058 -10000 0 -0.55 2 2
PRKACA 0.028 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.006 0.1 -10000 0 -0.47 5 5
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.025 0.054 0.37 1 -0.48 3 4
actin cytoskeleton reorganization 0.008 0.1 -10000 0 -0.52 4 4
PTK2 0.021 0.064 0.3 1 -0.63 2 3
EDG1 0.012 0.048 -10000 0 -0.47 3 3
mol:DAG 0.024 0.053 0.37 1 -0.48 3 4
CaM/Ca2+ 0.037 0.053 -10000 0 -0.44 3 3
MAP2K3 0.009 0.048 -10000 0 -0.45 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.057 0.064 -10000 0 -0.56 2 2
PLCG1 0.024 0.054 0.37 1 -0.48 3 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.055 -10000 0 -0.55 2 2
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.051 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.045 0.05 -10000 0 -0.59 2 2
cell migration 0.051 0.092 0.34 9 -0.52 2 11
mol:PI-3-4-5-P3 0.031 0.052 -10000 0 -0.47 2 2
FYN 0.027 0.019 -10000 0 -0.39 1 1
VEGFB/NRP1 0.028 0.049 -10000 0 -0.45 3 3
mol:NO 0.037 0.1 0.32 6 -0.4 9 15
PXN 0.028 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.042 -10000 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.039 0.049 -10000 0 -0.56 2 2
VHL 0.025 0.009 -10000 0 -10000 0 0
ITGB3 0.01 0.087 -10000 0 -0.41 21 21
NOS3 0.037 0.11 0.33 6 -0.45 8 14
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.058 -10000 0 -0.52 3 3
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.017 0.057 0.36 1 -0.45 3 4
PRKCB 0.014 0.061 0.36 1 -0.45 3 4
VCL 0.027 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.051 -10000 0 -0.47 3 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.052 -10000 0 -0.59 2 2
VEGFA165/NRP2 0.035 0.037 -10000 0 -0.27 7 7
MAPKKK cascade 0.036 0.053 -10000 0 -0.48 2 2
NRP2 0.026 0.026 -10000 0 -0.39 2 2
VEGFC homodimer -0.033 0.15 -10000 0 -0.39 74 74
NCK1 0.023 0.011 -10000 0 -10000 0 0
ROCK1 0.026 0.007 -10000 0 -10000 0 0
FAK1/Paxillin 0.043 0.092 0.44 2 -0.59 2 4
MAP3K13 0.014 0.047 -10000 0 -0.47 2 2
PDPK1 0.022 0.048 -10000 0 -0.43 2 2
Class I PI3K signaling events

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
ARF5/GTP 0 0.048 -10000 0 -10000 0 0
DAPP1 0.023 0.1 0.24 18 -0.36 12 30
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.13 0.27 6 -0.49 9 15
mol:DAG 0.016 0.075 0.2 24 -0.22 1 25
HRAS 0.027 0.019 -10000 0 -0.38 1 1
RAP1A 0.028 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.027 0.067 -10000 0 -0.31 6 6
PLCG2 0.025 0.023 -10000 0 -0.46 1 1
PLCG1 0.027 0.006 -10000 0 -10000 0 0
ARF5 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.004 0.039 -10000 0 -10000 0 0
ARF1/GTP 0.007 0.04 0.24 2 -10000 0 2
RHOA 0.025 0.009 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.003 0.041 -10000 0 -10000 0 0
ADAP1 -0.005 0.038 -10000 0 -10000 0 0
ARAP3 -0.004 0.038 -10000 0 -10000 0 0
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PREX1 0.027 0.006 -10000 0 -10000 0 0
ARHGEF6 0.022 0.053 -10000 0 -0.46 6 6
ARHGEF7 0.027 0.006 -10000 0 -10000 0 0
ARF1 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.028 0.007 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
FGR 0.027 0.019 -10000 0 -0.39 1 1
mol:Ca2+ 0.011 0.047 0.18 8 -10000 0 8
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.021 0.053 -10000 0 -0.46 6 6
ZAP70 0.007 0.092 -10000 0 -0.4 25 25
mol:IP3 0.011 0.058 0.19 15 -10000 0 15
LYN 0.024 0.02 -10000 0 -0.39 1 1
ARF1/GDP 0.028 0.068 -10000 0 -0.32 5 5
RhoA/GDP 0.039 0.046 0.24 4 -10000 0 4
PDK1/Src/Hsp90 0.049 0.024 -10000 0 -0.28 1 1
BLNK -0.017 0.14 -10000 0 -0.46 47 47
actin cytoskeleton reorganization 0.023 0.072 0.24 9 -0.4 1 10
SRC 0.026 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.006 0.013 -10000 0 -0.28 1 1
RAC1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.024 0.013 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.007 0.036 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.039 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.004 0.1 -10000 0 -0.34 16 16
BLK -0.035 0.14 -10000 0 -0.4 70 70
PDPK1 0.027 0.022 -10000 0 -0.46 1 1
CYTH1 -0.005 0.038 -10000 0 -10000 0 0
HCK 0.024 0.029 -10000 0 -0.42 2 2
CYTH3 -0.005 0.036 -10000 0 -10000 0 0
CYTH2 -0.006 0.036 -10000 0 -10000 0 0
KRAS 0.027 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.018 0.044 -10000 0 -0.45 1 1
SGK1 0.019 0.054 -10000 0 -0.34 5 5
INPP5D 0.025 0.031 -10000 0 -0.46 2 2
mol:GDP 0.014 0.066 -10000 0 -0.32 6 6
SOS1 0.028 0.004 -10000 0 -10000 0 0
SYK 0.024 0.038 -10000 0 -0.46 3 3
ARF6/GDP 0.024 0.044 0.23 4 -10000 0 4
mol:PI-3-4-5-P3 -0.005 0.034 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.003 0.041 -10000 0 -10000 0 0
VAV1 0.02 0.06 -10000 0 -0.45 8 8
mol:PI-3-4-P2 0.012 0.016 -10000 0 -0.33 1 1
RAS family/GTP/PI3K Class I 0.043 0.034 -10000 0 -10000 0 0
PLEKHA1 -0.006 0.012 -10000 0 -0.28 1 1
Rac1/GDP 0.026 0.065 -10000 0 -0.32 5 5
LAT 0.017 0.065 -10000 0 -0.39 13 13
Rac1/GTP 0.019 0.064 -10000 0 -0.33 4 4
ITK -0.011 0.046 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.015 0.093 0.22 23 -0.3 2 25
LCK 0.018 0.063 -10000 0 -0.39 12 12
BTK -0.005 0.04 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.061 -10000 0 -0.28 16 16
forebrain development -0.022 0.14 -10000 0 -0.52 15 15
GNAO1 0.023 0.039 -10000 0 -0.4 4 4
SMO/beta Arrestin2 0.023 0.07 -10000 0 -0.33 18 18
SMO 0.008 0.092 -10000 0 -0.46 19 19
ARRB2 0.026 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.048 0.08 0.25 5 -0.38 2 7
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.009 -10000 0 -10000 0 0
GNAI2 0.024 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.065 0.025 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.46 1 1
XPO1 0.024 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.022 0.15 -10000 0 -0.55 16 16
SAP30 0.026 0.019 -10000 0 -0.39 1 1
mol:GDP 0.008 0.092 -10000 0 -0.46 19 19
MIM/GLI2A 0.017 0.029 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.017 0.07 0.19 8 -10000 0 8
GLI3 0.036 0.08 0.25 6 -0.34 5 11
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.026 0.007 -10000 0 -10000 0 0
Gi family/GTP 0.008 0.072 -10000 0 -0.29 15 15
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.083 -10000 0 -0.41 6 6
GLI2/Su(fu) 0.023 0.074 0.2 1 -0.31 4 5
FOXA2 -0.017 0.13 -10000 0 -0.87 3 3
neural tube patterning -0.022 0.14 -10000 0 -0.52 15 15
SPOP 0.028 0.002 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.055 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
CSNK1G3 0.026 0.007 -10000 0 -10000 0 0
MTSS1 0.017 0.029 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.022 0.14 -10000 0 -0.52 15 15
SUFU 0.015 0.039 -10000 0 -0.23 1 1
LGALS3 0.025 0.031 -10000 0 -0.46 2 2
catabolic process 0.049 0.097 0.27 3 -0.42 5 8
GLI3A/CBP 0.003 0.08 -10000 0 -0.34 4 4
KIF3A 0.026 0.007 -10000 0 -10000 0 0
GLI1 -0.023 0.14 -10000 0 -0.53 15 15
RAB23 0.025 0.026 -10000 0 -0.39 2 2
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
IFT172 0.028 0.003 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.02 0.058 -10000 0 -0.32 2 2
GNAZ 0.012 0.079 -10000 0 -0.42 17 17
RBBP4 0.026 0.022 -10000 0 -0.46 1 1
CSNK1G1 0.028 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.029 0.071 0.2 1 -10000 0 1
STK36 0.024 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.005 0.073 -10000 0 -0.39 10 10
PTCH1 -0.022 0.16 -10000 0 -0.77 10 10
MIM/GLI1 -0.017 0.14 -10000 0 -0.57 9 9
CREBBP 0.003 0.08 -10000 0 -0.34 4 4
Su(fu)/SIN3/HDAC complex 0.015 0.088 -10000 0 -0.45 11 11
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.027 0.028 -10000 0 -10000 0 0
BIRC5 0.01 0.084 -10000 0 -0.39 22 22
NFKBIA 0.013 0.041 0.25 13 -10000 0 13
CPEB1 -0.04 0.16 -10000 0 -0.45 69 69
AKT1 0.013 0.041 0.25 13 -10000 0 13
NDEL1 0.027 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 0.024 0.024 -10000 0 -10000 0 0
NDEL1/TACC3 0.047 0.034 -10000 0 -10000 0 0
GADD45A 0.027 0.019 -10000 0 -0.39 1 1
GSK3B 0.023 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.025 0.026 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.014 0.004 -10000 0 -10000 0 0
TP53 0.017 0.028 -10000 0 -0.29 3 3
DLG7 0.008 0.016 -10000 0 -10000 0 0
AURKAIP1 0.026 0.019 -10000 0 -0.39 1 1
ARHGEF7 0.027 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.05 0.035 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.023 0.024 -10000 0 -10000 0 0
AURKA 0.015 0.02 -10000 0 -10000 0 0
AURKB 0.012 0.017 -10000 0 -0.15 3 3
CDC25B 0.011 0.028 -10000 0 -0.23 1 1
G2/M transition checkpoint 0.007 0.017 -10000 0 -10000 0 0
mRNA polyadenylation -0.01 0.089 -10000 0 -0.25 56 56
Aurora A/CPEB -0.009 0.089 -10000 0 -0.25 56 56
Aurora A/TACC1/TRAP/chTOG 0.056 0.044 -10000 0 -10000 0 0
BRCA1 0.028 0.003 -10000 0 -10000 0 0
centrosome duplication 0.025 0.026 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.033 -10000 0 -10000 0 0
spindle assembly 0.055 0.043 -10000 0 -10000 0 0
TDRD7 0.027 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.05 0.062 -10000 0 -0.3 4 4
CENPA 0.014 0.021 -10000 0 -0.18 4 4
Aurora A/PP2A 0.026 0.026 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.013 0.027 -10000 0 -10000 0 0
negative regulation of DNA binding 0.017 0.03 -10000 0 -0.29 3 3
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.009 -10000 0 -10000 0 0
RASA1 0.024 0.031 -10000 0 -0.46 2 2
Ajuba/Aurora A 0.007 0.017 -10000 0 -10000 0 0
mitotic prometaphase 0 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.02 -10000 0 -10000 0 0
TACC1 0.023 0.032 -10000 0 -0.46 2 2
TACC3 0.025 0.02 -10000 0 -0.39 1 1
Aurora A/Antizyme1 0.051 0.033 -10000 0 -10000 0 0
Aurora A/RasGAP 0.025 0.031 -10000 0 -0.27 2 2
OAZ1 0.027 0.005 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.026 0.005 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.019 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.014 0.004 -10000 0 -10000 0 0
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.018 0.019 -10000 0 -10000 0 0
PAK1 0.025 0.008 -10000 0 -10000 0 0
CKAP5 0.027 0.006 -10000 0 -10000 0 0
Aurora C signaling

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.042 0.047 -9999 0 -0.23 13 13
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.012 0.013 -9999 0 -10000 0 0
AURKB 0.02 0.055 -9999 0 -0.39 9 9
AURKC 0.021 0.051 -9999 0 -0.41 7 7
TRAIL 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
TNFSF10 0.017 0.04 -10000 0 -0.41 4 4
positive regulation of NF-kappaB transcription factor activity 0.018 0.055 -10000 0 -0.28 15 15
MAP2K4 0.043 0.055 0.21 3 -0.41 1 4
IKBKB 0.026 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.025 0.023 -10000 0 -0.46 1 1
SMPD1 0.009 0.015 -10000 0 -10000 0 0
IKBKG 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.076 -10000 0 -0.4 17 17
TRAIL/TRAILR2 0.025 0.034 -10000 0 -0.29 4 4
TRAIL/TRAILR3 0.019 0.052 -10000 0 -0.28 13 13
TRAIL/TRAILR1 0.025 0.034 -10000 0 -0.29 4 4
TRAIL/TRAILR4 0.018 0.055 -10000 0 -0.28 15 15
TRAIL/TRAILR1/DAP3/GTP 0.033 0.034 -10000 0 -0.22 4 4
IKK complex 0.021 0.034 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.003 -10000 0 -10000 0 0
MAPK3 0.008 0.027 -10000 0 -0.29 4 4
MAP3K1 0.031 0.052 -10000 0 -0.43 1 1
TRAILR4 (trimer) 0.012 0.076 -10000 0 -0.4 17 17
TRADD 0.027 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.025 0.023 -10000 0 -0.46 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.021 0.04 -10000 0 -0.36 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.008 0.027 -10000 0 -0.29 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.036 0.047 -10000 0 -0.24 1 1
mol:ceramide 0.009 0.015 -10000 0 -10000 0 0
FADD 0.02 0.013 -10000 0 -10000 0 0
MAPK8 0.052 0.065 0.24 6 -0.39 1 7
TRAF2 0.023 0.041 -10000 0 -0.39 5 5
TRAILR3 (trimer) 0.013 0.072 -10000 0 -0.4 15 15
CHUK 0.027 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.026 0.037 -10000 0 -0.24 4 4
DAP3 0.028 0.004 -10000 0 -10000 0 0
CASP10 0.07 0.096 0.34 26 -0.3 1 27
JNK cascade 0.018 0.055 -10000 0 -0.28 15 15
TRAIL (trimer) 0.017 0.04 -10000 0 -0.4 4 4
TNFRSF10C 0.013 0.072 -10000 0 -0.4 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.039 -10000 0 -0.24 1 1
TRAIL/TRAILR2/FADD 0.026 0.037 -10000 0 -0.24 4 4
cell death 0.009 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.04 -10000 0 -0.36 1 1
TRAILR2 (trimer) 0.026 0.008 -10000 0 -10000 0 0
CASP8 0.003 0.074 -10000 0 -0.5 9 9
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.047 -10000 0 -0.24 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.026 0.008 -10000 0 -10000 0 0
NFATC1 0.024 0.094 0.25 6 -0.37 7 13
NFATC2 0.008 0.082 0.21 4 -0.31 16 20
NFATC3 0.02 0.018 -10000 0 -0.35 1 1
YWHAE 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.001 0.078 0.2 5 -0.29 14 19
Exportin 1/Ran/NUP214 0.054 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.015 0.088 -10000 0 -0.32 9 9
BCL2/BAX 0.034 0.032 -10000 0 -0.29 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.02 0.008 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.01 0.079 0.23 2 -0.3 10 12
Calcineurin A alpha-beta B1/BCL2 0.022 0.039 -10000 0 -0.4 4 4
FKBP8 0.028 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.01 0.078 0.3 10 -0.22 2 12
KPNB1 0.028 0.002 -10000 0 -10000 0 0
KPNA2 0.028 0.004 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SFN 0.024 0.04 -10000 0 -0.42 4 4
MAP3K8 0.024 0.038 -10000 0 -0.46 3 3
NFAT4/CK1 alpha 0.03 0.021 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.047 0.095 0.26 1 -0.39 7 8
CABIN1 -0.001 0.078 0.21 5 -0.3 14 19
CALM1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
CAMK4 0.005 0.092 -10000 0 -0.4 25 25
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.028 0.004 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.024 0.068 -10000 0 -0.27 25 25
YWHAB 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.022 0.053 -10000 0 -0.46 6 6
MAPK9 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.034 0.099 0.26 4 -0.4 4 8
PRKCH 0.026 0.007 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.038 0.021 -10000 0 -0.33 1 1
CASP3 0.027 0.007 -10000 0 -10000 0 0
PIM1 0.026 0.022 -10000 0 -0.46 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.006 -10000 0 -10000 0 0
apoptosis 0.018 0.012 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.04 -10000 0 -0.34 1 1
PRKCB 0.021 0.054 -10000 0 -0.41 8 8
PRKCE 0.027 0.022 -10000 0 -0.46 1 1
JNK2/NFAT4 0.029 0.041 -10000 0 -0.32 1 1
BAD/BCL-XL 0.037 0.013 -10000 0 -10000 0 0
PRKCD 0.024 0.009 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.46 1 1
PRKCA 0.026 0.029 -10000 0 -0.42 2 2
PRKCG -0.031 0.13 -10000 0 -0.39 58 58
PRKCQ 0.017 0.069 -10000 0 -0.45 11 11
FKBP38/BCL2 0.034 0.031 -10000 0 -0.28 4 4
EP300 0.026 0.023 -10000 0 -0.46 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.097 0.26 5 -0.37 5 10
CaM/Ca2+/FKBP38 0.035 0.013 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.014 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.021 0.058 -10000 0 -0.23 24 24
NFATc/ERK1 0.036 0.095 0.25 6 -0.38 4 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.014 0.088 -10000 0 -0.32 9 9
NR4A1 0.018 0.1 0.24 6 -0.46 13 19
GSK3B 0.025 0.009 -10000 0 -10000 0 0
positive T cell selection 0.02 0.018 -10000 0 -0.35 1 1
NFAT1/CK1 alpha 0.009 0.06 0.16 1 -0.31 6 7
RCH1/ KPNB1 0.041 0.006 -10000 0 -10000 0 0
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
AKAP5 0.006 0.089 -10000 0 -0.39 25 25
MEF2D 0.027 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.094 0.26 5 -0.37 4 9
CREBBP 0.027 0.008 -10000 0 -10000 0 0
BCL2 0.022 0.039 -10000 0 -0.41 4 4
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.003 0.084 -10000 0 -0.34 13 13
KLHL20 0.025 0.07 0.19 10 -0.29 3 13
CYFIP2 0.025 0.029 -10000 0 -0.42 2 2
Rac1/GDP 0.024 0.077 0.33 5 -0.3 1 6
ENAH -0.008 0.11 -10000 0 -0.36 21 21
AP1M1 0.028 0.004 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.02 0.035 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.03 -10000 0 -0.19 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.044 -10000 0 -0.25 6 6
RAPGEF1 0 0.096 0.29 2 -0.38 5 7
CTNND1 0.028 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.003 0.11 -10000 0 -0.35 26 26
CRK 0.005 0.095 -10000 0 -0.4 7 7
E-cadherin/gamma catenin/alpha catenin 0.047 0.049 -10000 0 -0.36 6 6
alphaE/beta7 Integrin 0.038 0.025 -10000 0 -0.33 2 2
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.017 -10000 0 -10000 0 0
DLG1 0 0.082 -10000 0 -0.35 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.002 0.019 -10000 0 -10000 0 0
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.045 0.036 -10000 0 -0.25 6 6
PI3K 0.006 0.025 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.034 0.052 -10000 0 -0.42 6 6
TIAM1 0.021 0.053 -10000 0 -0.46 6 6
E-cadherin(dimer)/Ca2+ 0.053 0.039 -10000 0 -0.24 5 5
AKT1 0.012 0.03 0.14 1 -10000 0 1
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
CDH1 0.021 0.053 -10000 0 -0.46 6 6
RhoA/GDP 0.031 0.073 0.33 6 -10000 0 6
actin cytoskeleton organization 0.021 0.054 0.15 17 -0.21 3 20
CDC42/GDP 0.027 0.08 0.33 6 -10000 0 6
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.017 0.036 -10000 0 -0.32 5 5
ITGB7 0.026 0.031 -10000 0 -0.46 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.057 0.041 -10000 0 -0.25 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin 0.039 0.035 -10000 0 -0.23 6 6
mol:GDP 0.013 0.085 0.34 6 -0.34 1 7
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.031 -10000 0 -0.46 2 2
p120 catenin/RhoA/GDP 0.034 0.075 0.34 4 -10000 0 4
RAC1/GTP/IQGAP1 0.035 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.008 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.037 0.12 4 -0.17 6 10
NME1 0.027 0.018 -10000 0 -0.39 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.1 -10000 0 -0.41 8 8
regulation of cell-cell adhesion 0.013 0.029 -10000 0 -10000 0 0
WASF2 0.013 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.032 0.055 0.3 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.068 0.052 -10000 0 -0.32 6 6
CCND1 0.012 0.044 0.14 4 -0.21 6 10
VAV2 0.013 0.12 -10000 0 -0.56 5 5
RAP1/GDP 0.035 0.066 0.33 5 -10000 0 5
adherens junction assembly -0.005 0.099 -10000 0 -0.34 20 20
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.027 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.05 0.048 -10000 0 -0.44 2 2
E-cadherin/beta catenin 0.008 0.038 -10000 0 -0.34 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.007 0.1 -10000 0 -0.35 21 21
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.021 0.072 -10000 0 -0.37 12 12
E-cadherin/beta catenin/alpha catenin 0.044 0.041 -10000 0 -0.27 6 6
ITGAE 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.11 -10000 0 -0.36 26 26
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.043 0.05 -9999 0 -0.36 6 6
E-cadherin/beta catenin 0.031 0.041 -9999 0 -0.32 6 6
CTNNB1 0.024 0.009 -9999 0 -10000 0 0
JUP 0.026 0.031 -9999 0 -0.46 2 2
CDH1 0.021 0.053 -9999 0 -0.46 6 6
Canonical NF-kappaB pathway

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
FBXW11 0.028 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.084 0.23 27 -0.35 4 31
ERC1 0.026 0.008 -10000 0 -10000 0 0
RIP2/NOD2 0.031 0.037 -10000 0 -0.31 5 5
NFKBIA 0.023 0.042 -10000 0 -10000 0 0
BIRC2 0.024 0.01 -10000 0 -10000 0 0
IKBKB 0.026 0.008 -10000 0 -10000 0 0
RIPK2 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.048 0.095 0.27 1 -0.4 9 10
NEMO/A20/RIP2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.042 0.088 0.26 1 -0.39 12 13
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.042 0.081 -10000 0 -0.39 9 9
BCL10/MALT1/TRAF6 0.049 0.02 -10000 0 -10000 0 0
NOD2 0.022 0.046 -10000 0 -0.43 5 5
NFKB1 0.029 0.009 -10000 0 -10000 0 0
RELA 0.028 0.01 -10000 0 -10000 0 0
MALT1 0.025 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.035 0.015 -10000 0 -10000 0 0
ATM 0.025 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.023 0.067 -10000 0 -0.28 23 23
TRAF6 0.027 0.006 -10000 0 -10000 0 0
PRKCA 0.026 0.029 -10000 0 -0.42 2 2
CHUK 0.027 0.005 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
TNF 0.008 0.088 -10000 0 -0.4 23 23
NF kappa B1 p50/RelA 0.057 0.029 -10000 0 -0.37 1 1
BCL10 0.027 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.042 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.01 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0.052 0.092 0.26 2 -0.41 10 12
CYLD 0.027 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.095 0.26 2 -0.4 11 13
Arf6 downstream 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
PLAUR 0.01 0.077 -10000 0 -10000 0 0
regulation of axonogenesis -0.005 0.026 0.23 1 -10000 0 1
myoblast fusion -0.017 0.06 0.3 3 -10000 0 3
mol:GTP 0.011 0.04 -10000 0 -0.16 4 4
regulation of calcium-dependent cell-cell adhesion -0.041 0.057 0.26 5 -10000 0 5
ARF1/GTP 0.028 0.038 -10000 0 -10000 0 0
mol:GM1 0.004 0.028 -10000 0 -10000 0 0
mol:Choline 0.002 0.03 -10000 0 -0.28 3 3
lamellipodium assembly 0 0.062 -10000 0 -0.35 6 6
MAPK3 0.013 0.046 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.042 0.058 -10000 0 -0.26 5 5
ARF1 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.061 -10000 0 -0.3 3 3
ARF1/GDP 0.02 0.066 -10000 0 -0.27 4 4
ARF6 0.026 0.031 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 0.021 0.054 -10000 0 -0.46 6 6
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.045 -10000 0 -10000 0 0
actin filament bundle formation -0.017 0.063 0.27 3 -10000 0 3
KALRN -0.008 0.072 -10000 0 -0.25 32 32
RAB11FIP3/RAB11A 0.04 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.063 -10000 0 -0.28 3 3
NME1 0.026 0.021 -10000 0 -0.39 1 1
Rac1/GDP 0.019 0.064 -10000 0 -0.26 5 5
substrate adhesion-dependent cell spreading 0.011 0.04 -10000 0 -0.16 4 4
cortical actin cytoskeleton organization 0 0.062 -10000 0 -0.36 6 6
RAC1 0.026 0.007 -10000 0 -10000 0 0
liver development 0.011 0.04 -10000 0 -0.16 4 4
ARF6/GTP 0.011 0.04 -10000 0 -0.16 4 4
RhoA/GTP 0.025 0.036 -10000 0 -10000 0 0
mol:GDP 0 0.052 -10000 0 -0.3 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.039 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
PLD1 0.006 0.037 -10000 0 -0.32 3 3
RAB11FIP3 0.028 0.004 -10000 0 -10000 0 0
tube morphogenesis 0 0.062 -10000 0 -0.35 6 6
ruffle organization 0.005 0.026 -10000 0 -0.23 1 1
regulation of epithelial cell migration 0.011 0.04 -10000 0 -0.16 4 4
PLD2 0.013 0.031 -10000 0 -10000 0 0
PIP5K1A 0.005 0.026 -10000 0 -0.23 1 1
mol:Phosphatidic acid 0.002 0.03 -10000 0 -0.28 3 3
Rac1/GTP 0 0.062 -10000 0 -0.36 6 6
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.051 0.14 0.26 3 -0.36 22 25
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
AKT2 0.027 0.005 -10000 0 -10000 0 0
STXBP4 0.028 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.063 0.14 0.29 5 -0.38 27 32
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
TBC1D4 0.013 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
YWHAB 0.026 0.007 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.014 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.056 -10000 0 -0.39 9 9
PRKCI 0.02 0.013 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.028 0.004 -10000 0 -10000 0 0
GYS1 0.012 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.022 -10000 0 -0.46 1 1
TRIP10 0.027 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.031 0.042 -10000 0 -0.3 1 1
VAMP2 0.027 0.006 -10000 0 -10000 0 0
SLC2A4 -0.07 0.15 0.32 4 -0.41 28 32
STX4 0.028 0.004 -10000 0 -10000 0 0
GSK3B 0.019 0.009 -10000 0 -10000 0 0
SFN 0.024 0.04 -10000 0 -0.42 4 4
LNPEP 0.024 0.031 -10000 0 -0.46 2 2
YWHAE 0.027 0.006 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.023 0.059 0.25 6 -10000 0 6
GNAI2 0.024 0.009 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.03 -10000 0 -0.25 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
RhoA/GTP 0.024 0.061 -10000 0 -0.25 6 6
negative regulation of cAMP metabolic process 0.019 0.05 -10000 0 -0.26 8 8
GNAZ 0.012 0.079 -10000 0 -0.41 17 17
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.02 -10000 0 -0.39 1 1
S1PR5 0.024 0.04 -10000 0 -0.42 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.019 0.051 -10000 0 -0.26 8 8
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.46 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.048 0.065 -10000 0 -0.29 2 2
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.068 -10000 0 -10000 0 0
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.027 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -10000 0 -10000 0 0
FKBP3 0.027 0.006 -10000 0 -10000 0 0
Histones 0.054 0.059 -10000 0 -10000 0 0
YY1/LSF 0.008 0.077 -10000 0 -0.32 6 6
SMG5 0.028 0.004 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.018 0.037 -10000 0 -0.23 3 3
I kappa B alpha/HDAC1 0.026 0.05 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA 0.022 0.043 0.28 1 -0.26 1 2
HDAC1/Smad7 0.048 0.021 -10000 0 -10000 0 0
RANGAP1 0.027 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.029 0.05 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.033 0.064 0.24 1 -0.34 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.023 0.03 -10000 0 -0.42 2 2
GATA1 0.018 0.026 -10000 0 -0.39 1 1
Mad/Max 0.036 0.034 -10000 0 -0.33 4 4
NuRD/MBD3 Complex/GATA1/Fog1 0.032 0.052 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
NPC 0.016 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.022 -10000 0 -0.46 1 1
MAX 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
NFKBIA 0.015 0.03 -10000 0 -10000 0 0
KAT2B 0.007 0.092 -10000 0 -0.46 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.028 0.014 -10000 0 -10000 0 0
SIN3 complex 0.064 0.025 -10000 0 -10000 0 0
SMURF1 0.026 0.008 -10000 0 -10000 0 0
CHD3 0.027 0.006 -10000 0 -10000 0 0
SAP30 0.026 0.019 -10000 0 -0.39 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.008 0.068 -10000 0 -0.35 4 4
YY1/HDAC2 0.009 0.077 -10000 0 -0.32 6 6
YY1/HDAC1 0.009 0.076 -10000 0 -0.24 22 22
NuRD/MBD2 Complex (MeCP1) 0.034 0.028 -10000 0 -10000 0 0
PPARG -0.074 0.15 -10000 0 -0.28 157 157
HDAC8/hEST1B 0.055 0.012 -10000 0 -10000 0 0
UBE2I 0.028 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.049 -10000 0 -10000 0 0
MBD3L2 -0.017 0.025 -10000 0 -0.39 2 2
ubiquitin-dependent protein catabolic process 0.047 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.031 0.05 -10000 0 -0.31 1 1
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.016 0.03 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
YY1 0.008 0.056 -10000 0 -0.27 18 18
HDAC8 0.028 0.002 -10000 0 -10000 0 0
SMAD7 0.026 0.008 -10000 0 -10000 0 0
NCOR2 0.028 0.004 -10000 0 -10000 0 0
MXD1 0.023 0.048 -10000 0 -0.46 5 5
STAT3 0.022 0.015 -10000 0 -0.3 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.023 0.077 -10000 0 -0.3 5 5
YY1/SAP30/HDAC1 0.023 0.077 -10000 0 -0.31 6 6
EP300 0.026 0.022 -10000 0 -0.46 1 1
STAT3 (dimer non-phopshorylated) 0.022 0.015 -10000 0 -0.3 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.03 -10000 0 -10000 0 0
histone deacetylation 0.03 0.035 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.025 0.034 -10000 0 -10000 0 0
nuclear export -0.054 0.012 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GATAD2B 0.028 0.004 -10000 0 -10000 0 0
GATAD2A 0.028 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.05 -10000 0 -0.26 2 2
GATA1/HDAC1 0.038 0.016 -10000 0 -0.27 1 1
GATA1/HDAC3 0.027 0.05 -10000 0 -10000 0 0
CHD4 0.026 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.023 0.067 -10000 0 -0.28 23 23
SIN3/HDAC complex/Mad/Max 0.031 0.035 -10000 0 -0.27 1 1
NuRD Complex 0.03 0.055 -10000 0 -0.33 2 2
positive regulation of chromatin silencing 0.051 0.057 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.041 0.029 -10000 0 -10000 0 0
HDAC complex 0.067 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.037 0.017 -10000 0 -0.27 1 1
FKBP25/HDAC1/HDAC2 0.051 0.017 -10000 0 -10000 0 0
TNF 0.008 0.088 -10000 0 -0.4 23 23
negative regulation of cell growth 0.028 0.039 -10000 0 -0.27 1 1
NuRD/MBD2/PRMT5 Complex 0.034 0.028 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.03 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.049 -10000 0 -0.29 3 3
SIN3/HDAC complex/NCoR1 0.026 0.04 -10000 0 -0.45 1 1
TFCP2 0.028 0.003 -10000 0 -10000 0 0
NR2C1 0.028 0.003 -10000 0 -10000 0 0
MBD3 0.027 0.005 -10000 0 -10000 0 0
MBD2 0.026 0.008 -10000 0 -10000 0 0
FoxO family signaling

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.008 0.043 -10000 0 -10000 0 0
PLK1 0.041 0.12 -10000 0 -0.82 2 2
CDKN1B 0.08 0.097 0.31 8 -0.39 2 10
FOXO3 0.057 0.11 -10000 0 -0.67 4 4
KAT2B 0.013 0.094 -10000 0 -0.46 19 19
FOXO1/SIRT1 0.03 0.042 -10000 0 -10000 0 0
CAT 0.046 0.13 -10000 0 -0.91 3 3
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
AKT1 0.034 0.017 -10000 0 -10000 0 0
FOXO1 0.016 0.044 0.23 2 -10000 0 2
MAPK10 0.025 0.069 0.2 30 -0.23 21 51
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.055 0.066 0.3 6 -0.4 1 7
response to oxidative stress 0.01 0.008 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.056 0.12 -10000 0 -0.77 3 3
XPO1 0.028 0.004 -10000 0 -10000 0 0
EP300 0.027 0.023 -10000 0 -0.46 1 1
BCL2L11 0.035 0.025 -10000 0 -10000 0 0
FOXO1/SKP2 0.025 0.041 -10000 0 -10000 0 0
mol:GDP 0.01 0.008 -10000 0 -10000 0 0
RAN 0.029 0.003 -10000 0 -10000 0 0
GADD45A 0.068 0.11 -10000 0 -0.58 7 7
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.039 0.098 -10000 0 -0.46 7 7
MST1 0.026 0.045 -10000 0 -0.4 5 5
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.035 0.078 -10000 0 -0.39 6 6
YWHAB 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.036 0.051 0.2 32 -0.23 5 37
MAPK9 0.036 0.043 0.2 30 -10000 0 30
YWHAG 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
SIRT1 0.026 0.024 -10000 0 -0.46 1 1
SOD2 0.07 0.093 -10000 0 -0.56 1 1
RBL2 0.04 0.17 -10000 0 -0.7 17 17
RAL/GDP 0.045 0.015 -10000 0 -10000 0 0
CHUK 0.034 0.015 -10000 0 -10000 0 0
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
RAL/GTP 0.048 0.015 -10000 0 -10000 0 0
CSNK1G1 0.028 0.004 -10000 0 -10000 0 0
FASLG -0.016 0.24 -10000 0 -1.3 15 15
SKP2 0.025 0.009 -10000 0 -10000 0 0
USP7 0.028 0.005 -10000 0 -10000 0 0
IKBKB 0.031 0.017 -10000 0 -10000 0 0
CCNB1 0.043 0.11 -10000 0 -0.76 2 2
FOXO1-3a-4/beta catenin 0.086 0.092 0.33 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.04 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
SGK1 0.032 0.026 -10000 0 -0.46 1 1
CSNK1G3 0.026 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.008 -10000 0 -10000 0 0
ZFAND5 0.052 0.066 0.37 3 -10000 0 3
SFN 0.024 0.04 -10000 0 -0.42 4 4
CDK2 0.028 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.037 0.083 -10000 0 -0.4 5 5
CREBBP 0.028 0.007 -10000 0 -10000 0 0
FBXO32 0.07 0.16 0.45 2 -1.1 3 5
BCL6 0.054 0.094 -10000 0 -10000 0 0
RALB 0.028 0.004 -10000 0 -10000 0 0
RALA 0.027 0.007 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.019 -9999 0 -0.39 1 1
Rac1/GDP 0.025 0.011 -9999 0 -10000 0 0
DOCK1 0.027 0.022 -9999 0 -0.46 1 1
ITGA4 0.021 0.051 -9999 0 -0.39 8 8
RAC1 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.034 0.046 -9999 0 -0.28 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.038 -9999 0 -0.23 8 8
alpha4/beta7 Integrin/Paxillin 0.04 0.038 -9999 0 -0.26 2 2
lamellipodium assembly 0.012 0.062 -9999 0 -0.34 8 8
PIK3CA 0.02 0.013 -9999 0 -10000 0 0
PI3K 0.027 0.03 -9999 0 -0.33 2 2
ARF6 0.026 0.007 -9999 0 -10000 0 0
TLN1 0.024 0.01 -9999 0 -10000 0 0
PXN 0.015 0.002 -9999 0 -10000 0 0
PIK3R1 0.025 0.031 -9999 0 -0.46 2 2
ARF6/GTP 0.05 0.036 -9999 0 -10000 0 0
cell adhesion 0.047 0.036 -9999 0 -10000 0 0
CRKL/CBL 0.035 0.02 -9999 0 -0.27 1 1
alpha4/beta1 Integrin/Paxillin 0.04 0.034 -9999 0 -10000 0 0
ITGB1 0.027 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.031 -9999 0 -0.46 2 2
ARF6/GDP 0.025 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.085 -9999 0 -0.27 10 10
p130Cas/Crk/Dock1 0.051 0.022 -9999 0 -0.28 1 1
VCAM1 -0.015 0.13 -9999 0 -0.4 51 51
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.037 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.037 -9999 0 -10000 0 0
BCAR1 0.027 0.006 -9999 0 -10000 0 0
mol:GDP -0.052 0.036 -9999 0 -10000 0 0
CBL 0.025 0.008 -9999 0 -10000 0 0
PRKACA 0.028 0.004 -9999 0 -10000 0 0
GIT1 0.028 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.037 -9999 0 -10000 0 0
Rac1/GTP 0.012 0.066 -9999 0 -0.37 8 8
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.025 0.009 -10000 0 -10000 0 0
SMAD2 0.003 0.05 0.25 2 -0.27 4 6
SMAD3 0.026 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.026 0.088 -10000 0 -0.44 15 15
SMAD4/Ubc9/PIASy 0.049 0.02 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.058 0.24 1 -10000 0 1
PPM1A 0.026 0.007 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.048 0.24 1 -0.25 4 5
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.025 0.067 -10000 0 -0.33 17 17
MAPK3 0.028 0.004 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
CTDSP1 0.027 0.006 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
CTDSPL 0.024 0.009 -10000 0 -10000 0 0
KPNB1 0.028 0.002 -10000 0 -10000 0 0
TGFBRAP1 0.012 0.088 -10000 0 -0.46 17 17
UBE2I 0.028 0.004 -10000 0 -10000 0 0
NUP153 0.027 0.006 -10000 0 -10000 0 0
KPNA2 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.027 0.005 -10000 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 0.037 0.02 -10000 0 -0.33 1 1
FBXW11 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.039 -10000 0 -0.27 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.048 0.22 3 -0.28 1 4
NFKBIA 0.016 0.034 -10000 0 -0.31 1 1
MAPK14 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.011 -10000 0 -10000 0 0
ARRB2 0.015 0.004 -10000 0 -10000 0 0
REL 0.019 0.064 -10000 0 -0.46 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.017 -10000 0 -0.28 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.012 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.02 0.007 -10000 0 -10000 0 0
PIK3R1 0.025 0.031 -10000 0 -0.46 2 2
NFKB1 0.013 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.032 -10000 0 -0.27 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.033 0.051 0.27 1 -0.28 1 2
SRC 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.33 2 2
NF kappa B1 p50/RelA 0.019 0.033 -10000 0 -0.28 1 1
IKBKB 0.026 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.024 0.038 -10000 0 -0.46 3 3
I kappa B alpha/PIK3R1 0.03 0.054 0.22 6 -0.26 3 9
cell death 0.032 0.049 0.26 1 -0.27 1 2
NF kappa B1 p105/c-Rel 0.024 0.039 -10000 0 -0.27 8 8
LCK 0.018 0.063 -10000 0 -0.39 12 12
BCL3 0.026 0.022 -10000 0 -0.46 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.027 -9999 0 -10000 0 0
HDAC3 0.027 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.037 0.017 -9999 0 -0.27 1 1
GATA1/HDAC5 0.038 0.016 -9999 0 -0.27 1 1
GATA2/HDAC5 0.035 0.026 -9999 0 -0.3 2 2
HDAC5/BCL6/BCoR 0.04 0.027 -9999 0 -10000 0 0
HDAC9 0.012 0.074 -9999 0 -0.39 17 17
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.019 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.012 -9999 0 -10000 0 0
HDAC5/YWHAB 0.039 0.011 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -9999 0 -10000 0 0
GATA2 0.023 0.03 -9999 0 -0.42 2 2
HDAC4/RFXANK 0.039 0.017 -9999 0 -0.27 1 1
BCOR 0.027 0.022 -9999 0 -0.46 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.027 0.005 -9999 0 -10000 0 0
HDAC5 0.028 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.038 0.012 -9999 0 -10000 0 0
Histones 0.026 0.037 -9999 0 -10000 0 0
ADRBK1 0.026 0.008 -9999 0 -10000 0 0
HDAC4 0.027 0.006 -9999 0 -10000 0 0
XPO1 0.028 0.004 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC4/Ubc9 0.039 0.01 -9999 0 -10000 0 0
HDAC7 0.028 0.003 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.009 -9999 0 -10000 0 0
TUBA1B 0.028 0.003 -9999 0 -10000 0 0
HDAC6 0.028 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.04 0.015 -9999 0 -0.27 1 1
CAMK4 0.005 0.092 -9999 0 -0.4 25 25
Tubulin/HDAC6 0.052 0.016 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.026 0.007 -9999 0 -10000 0 0
GATA1 0.018 0.026 -9999 0 -0.39 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.027 0.006 -9999 0 -10000 0 0
NR3C1 0.027 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.042 0.026 -9999 0 -10000 0 0
SRF 0.027 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.038 0.012 -9999 0 -10000 0 0
Tubulin 0.039 0.01 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.038 0.012 -9999 0 -10000 0 0
GNB1 0.027 0.006 -9999 0 -10000 0 0
RANGAP1 0.027 0.004 -9999 0 -10000 0 0
BCL6/BCoR 0.029 0.019 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.051 0.017 -9999 0 -10000 0 0
HDAC4/SRF 0.036 0.063 -9999 0 -0.24 24 24
HDAC4/ER alpha 0.023 0.072 -9999 0 -0.3 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.026 0.037 -9999 0 -10000 0 0
cell motility 0.052 0.015 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.028 0.004 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.01 -9999 0 -10000 0 0
BCL6 0.02 0.013 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.006 -9999 0 -10000 0 0
Hsp90/HDAC6 0.038 0.012 -9999 0 -10000 0 0
ESR1 0.006 0.095 -9999 0 -0.42 24 24
HDAC6/HDAC11 0.035 0.022 -9999 0 -0.33 1 1
Ran/GTP/Exportin 1 0.043 0.03 -9999 0 -10000 0 0
NPC 0.016 0.002 -9999 0 -10000 0 0
MEF2C 0.017 0.066 -9999 0 -0.43 11 11
RAN 0.028 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.067 0.05 -9999 0 -0.24 5 5
GNG2 0.026 0.007 -9999 0 -10000 0 0
NCOR2 0.028 0.004 -9999 0 -10000 0 0
TUBB2A 0.027 0.006 -9999 0 -10000 0 0
HDAC11 0.024 0.023 -9999 0 -0.46 1 1
HSP90AA1 0.026 0.007 -9999 0 -10000 0 0
RANBP2 0.028 0.003 -9999 0 -10000 0 0
ANKRA2 0.026 0.007 -9999 0 -10000 0 0
RFXANK 0.027 0.019 -9999 0 -0.39 1 1
nuclear import -0.033 0.013 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.031 -9999 0 -0.46 2 2
PLK4 0.027 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.013 0.022 -9999 0 -0.33 2 2
Alternative NF-kappaB pathway

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.04 0.007 -9999 0 -10000 0 0
FBXW11 0.027 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -10000 0 0
CHUK 0.027 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.074 0.034 -9999 0 -10000 0 0
NFKB1 0.027 0.005 -9999 0 -10000 0 0
MAP3K14 0.028 0.002 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.037 0.029 -9999 0 -0.27 4 4
RELB 0.024 0.037 -9999 0 -0.39 4 4
NFKB2 0.027 0.004 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.034 0.024 -9999 0 -0.22 4 4
regulation of B cell activation 0.034 0.024 -9999 0 -0.22 4 4
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.006 -10000 0 -9999 0 0
MDM2/SUMO1 0.039 0.031 -10000 0 -9999 0 0
HDAC4 0.027 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0.007 0.007 -10000 0 -9999 0 0
SUMO1 0.027 0.005 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.012 0.012 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.011 0.008 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.028 0.003 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.028 0.003 -10000 0 -9999 0 0
SUMO1/HDAC4 0.042 0.026 -10000 0 -9999 0 0
SUMO1/HDAC1 0.041 0.029 -10000 0 -9999 0 0
RANGAP1 0.027 0.004 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.061 0.027 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.005 -10000 0 -9999 0 0
Ran/GTP 0.03 0.027 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.027 0.006 -10000 0 -9999 0 0
UBE2I 0.028 0.004 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.031 0.037 0.22 10 -9999 0 10
NPC 0.016 0.002 -10000 0 -9999 0 0
PIAS2 0.026 0.008 -10000 0 -9999 0 0
PIAS1 0.027 0.004 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
Arf1 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
coatomer protein complex 0.012 0.029 0.21 3 -10000 0 3
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.017 0.023 0.14 4 -10000 0 4
AP2 0.029 0.019 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.009 -10000 0 -10000 0 0
CD4 0.025 0.029 -10000 0 -0.42 2 2
CLTA 0.025 0.009 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.007 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.033 0.012 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.006 -10000 0 -10000 0 0
mol:Choline 0.007 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.005 -10000 0 -10000 0 0
DDEF1 0.006 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.013 -10000 0 -10000 0 0
AP2M1 0.02 0.013 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.013 -10000 0 -10000 0 0
ARFIP2 0.024 0.012 -10000 0 -10000 0 0
COPA 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.044 -10000 0 -0.2 1 1
ARF1/GTP/ARHGAP10 0.019 0.006 -10000 0 -10000 0 0
GGA3 0.028 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.026 0.018 -10000 0 -0.22 2 2
AP2A1 0.027 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.04 -10000 0 -0.2 12 12
ARF1/GDP/Membrin 0.026 0.021 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.017 0.029 -10000 0 -0.24 1 1
PLD2 0.007 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.002 -10000 0 -10000 0 0
PIP5K1A 0.008 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.022 0.019 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.002 -10000 0 -10000 0 0
GOSR2 0.013 0.021 -10000 0 -0.31 2 2
USO1 0.011 0.029 -10000 0 -0.31 4 4
GBF1 0.01 0.036 -10000 0 -0.31 6 6
ARF1/GTP/Arfaptin 2 0.038 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.033 -10000 0 -0.26 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 514 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WA.A7H4 TCGA.WA.A7GZ TCGA.UP.A6WW TCGA.UF.A7JV
109_MAP3K5 0.034 0.034 0 0.034
47_PPARGC1A 0.028 0.028 0.028 -0.46
105_BMP4 0.028 0.028 0.028 0.028
105_BMP6 0.028 0.028 0 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 -0.39
131_RELN/VLDLR 0.072 0.072 0.072 0
30_TGFB1/TGF beta receptor Type II 0.028 0.028 0.03 0.028
84_STAT5B 0.031 0.03 -0.43 0.034
84_STAT5A 0.031 0.03 -0.43 0.034
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/HNSC-TP/14527301/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/HNSC-TP/15078965/Gistic2_Analysis_15080839/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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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